Publications

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2017
Richter D, Moraga I, Winkelmann H, Birkholz O, Wilmes S, Schulte M, Kraich M, Kenneweg H, Beutel O, Selenschik P, Paterok D, Gavutis M, Schmidt T, Garcia KC, Müller TD, Piehler J (2017) Ligand-induced type II interleukin-4 receptor dimers are sustained by rapid re-association within plasma membrane microcompartments., Nat Commun, 8, 15976.
[Abstract] [DOI] [pdf]
The spatiotemporal organization of cytokine receptors in the plasma membrane is still debated with models ranging from ligand-independent receptor pre-dimerization to ligand-induced receptor dimerization occurring only after receptor uptake into endosomes. Here, we explore the molecular and cellular determinants governing the assembly of the type II interleukin-4 receptor, taking advantage of various agonists binding the receptor subunits with different affinities and rate constants. Quantitative kinetic studies using artificial membranes confirm that receptor dimerization is governed by the two-dimensional ligand–receptor interactions and identify a critical role of the transmembrane domain in receptor dimerization. Single molecule localization microscopy at physiological cell surface expression levels, however, reveals efficient ligand-induced receptor dimerization by all ligands, largely independent of receptor binding affinities, in line with the similar STAT6 activation potencies observed for all IL-4 variants. Detailed spatiotemporal analyses suggest that kinetic trapping of receptor dimers in actin-dependent microcompartments sustains robust receptor dimerization and signalling.
Luuk A. Lubbers, Martin van Hecke, Corentin Coulais (2017) A nonlinear beam model to describe the postbuckling of wide neo-Hookean beams, Journal of the Mechanics and Physics of Solids, 106, 191-206.
[DOI] [pdf]
Indrani Chakraborty, Vera Meester, Casper van der Wel and Daniela J. Kraft (2017) Colloidal Joints with Designed Motion Range and Tunable Joint Flexibility, Nanoscale, 9, 7814-7821.
[DOI]
Hadi Arjmandi-Tash, Nikita Lebedev, Pauline M.G. van Deursen, Jan Aarts, Grégory F. Schneider, (2017) Hybrid cold and hot-wall reaction chamber for the rapid synthesis of uniform graphene, Carbon, 118, 438-442.
[DOI]
S. Blok, R.R. Agundez Mojarro, L.A. Maduro, M. Blaauboer, S.J. van der Molen (2017) Inelastic cotunneling with energy-dependent contact transmission, Journal of Chemical Physics, 146, 092325.
[DOI]
Becchetti A, Crescioli S, Zanieri F, Petroni G, Mercatelli R, Coppola S, Gasparoli L, D'Amico M, Pillozzi S, Crociani O, Stefanini M, Fiore A, Carraresi L, Morello V, Manoli S, Brizzi MF, Ricci D, Rinaldi M, Masi A, Schmidt T, Quercioli F, Defilippi P, Arcangeli A. (2017) The conformational state of hERG1 channels determines integrin association, downstream signaling, and cancer progression., Science Signaling, 10, eaaf3236.
[Abstract] [DOI] [pdf]
Ion channels regulate cell proliferation, differentiation, and migration in normal and neoplastic cells through cell-cell and cell-extracellular matrix (ECM) transmembrane receptors called integrins. K+ flux through the human ether-à-go-go-related gene 1 (hERG1) channel shapes action potential firing in excitable cells such as cardiomyocytes. Its abundance is often aberrantly high in tumors, where it modulates integrin-mediated signaling. We found that hERG1 interacted with the β1 integrin subunit at the plasma membrane of human cancer cells. This interaction was not detected in cardiomyocytes because of the presence of the hERG1 auxiliary subunit KCNE1 (potassium voltage-gated channel subfamily E regulatory subunit 1), which blocked the β1 integrin-hERG1 interaction. Although open hERG1 channels did not interact as strongly with β1 integrins as did closed channels, current flow through hERG1 channels was necessary to activate the integrin-dependent phosphorylation of Tyr397 in focal adhesion kinase (FAK) in both normal and cancer cells. In immunodeficient mice, proliferation was inhibited in breast cancer cells expressing forms of hERG1 with impaired K+ flow, whereas metastasis of breast cancer cells was reduced when the hERG1/β1 integrin interaction was disrupted. We conclude that the interaction of β1 integrins with hERG1 channels in cancer cells stimulated distinct signaling pathways that depended on the conformational state of hERG1 and affected different aspects of tumor progression.
Hande E. Cingil, Emre B. Boz, Giovanni Biondaro, Renko de Vries, Martien A. Cohen Stuart, Daniela J. Kraft, Paul van der Schoot, and Joris Sprakel (2017) Illuminating the Reaction Pathways of Viromimetic Assembly, J. Am. Chem. Soc, 139 (13), 4962-4968.
[DOI]
Askes SH, Leeuwenburgh VC, Pomp W, Arjmandi-Tash H, Tanase S, Schmidt T, Bonnet S (2017) Water-Dispersible Silica-Coated Upconverting Liposomes: Can a Thin Silica Layer Protect TTA-UC against Oxygen Quenching?, ACS Biomater Sci Eng, 3, 322-334.
[Abstract] [DOI] [pdf]
Light upconversion by triplet−triplet annihilation (TTA-UC) in nanoparticles has received considerable attention for bioimaging and light activation of prodrugs. However, the mechanism of TTA-UC is inherently sensitive for quenching by molecular oxygen. A potential oxygen protection strategy is the coating of TTA-UC nanoparticles with a layer of oxygen- impermeable material. In this work, we explore if (organo)silica can fulfill this protecting role. Three synthesis routes are described for preparing water-dispersible (organo)silica-coated red-to-blue upconverting liposomes. Their upconversion proper- ties are investigated in solution and in A549 lung carcinoma cells. Although it was found that the silica offered no protection from oxygen in solution and after uptake in A549 cancer cells, upon drying of the silica-coated liposome dispersion in an excess of (organo)silica precursor, interesting liposome−silica nanocomposite materials were obtained that were capable of generating blue light upon red light excitation in air.
C. Cirillo, S. Voltan, E.A. Ilyina, J.M. Hernández, A. García-Santiago, J. Aarts and C. Attanasio (2017) Long-range proximity effect in Nb-based heterostructures induced by a magnetically inhomogeneous permalloy layer, New J. Phys., 19, 023037.
[DOI]

2016
M.S. van Deen, B.P. Tighe, and M. van Hecke (2016) Contact changes of sheared systems: Scaling, correlations, and mechanisms, Physical Review E, 94.
[DOI] [pdf]
Corentin Coulais (2016) Periodic cellular materials with nonlinear elastic homogenized stress-strain response at small strains, Int. J. Solids Struct. , 97-98, 226-238.
[DOI] [pdf]
Geert Wortel, Olivier Dauchot, and Martin van Hecke (2016) Criticality in Vibrated Frictional Flows at a Finite Strain Rate, Physical Review Letters, 117, 198002.
[DOI] [pdf]
Bastiaan Florijn,Corentin Coulais, and Martin van Hecke (2016) Programmable mechanical metamaterials: the role of geometry, Soft Matter, 12, 8736-8743.
[DOI] [pdf]
G. Nienhuis (2016) Analogies between optical and quantum mechanical angular momentum, Philosophical Transactions of the Royal Society A, 375, 20150443.
[DOI]
P. Kumar, M. Bulk, A. Webb, L. van der Weerd, T.H. Oosterkamp, M.I. Huber, L. Bossoni (2016) A novel approach to quantify different iron forms in ex-vivo human brain tissue, Scientific Reports, 12, 6, 38916.
[DOI]
Chencheng Xu, Hongchu Du, Alexander J.H. van der Torren, Jan Aarts, Chun-Lin Jia & Regina Dittmann (2016) Formation mechanism of Ruddlesden-Popper-type antiphase boundaries during the kinetically limited growth of Sr rich SrTiO3 thin films, Scientific Reports, 6, 38296.
[DOI]
A.J.H. van der Torren, S.J. van der Molen, J. Aarts (2016) Imaging pulsed laser deposition growth of homo-epitaxial SrTiO3 by low-energy electron microscopy, Nanotechnology, 11, 27, 495702.
[DOI]
J. Jobst, A.J.H. van der Torren, E.E. Krasovskii, J. Balgley, C.R. Dean, R.M. Tromp, S.J. van der Molen (2016) Quantifying electronic band interactions in van der Waals materials using angle-resolved reflected-electron spectroscopy, Nature Communications, 11, 7, 13621.
[DOI]
F. M. Buters, M. J. Weaver, H. J. Eerkens, K. Heeck, S. de Man, and D. Bouwmeester (2016) Optomechanics with a polarization nondegenerate cavity, Phys. Rev. A, 12, 94, 063813.
[DOI]
Casper van der Wel and Daniela J Kraft (2016) Automated tracking of colloidal clusters with sub-pixel accuracy and precision, Journal of Physics: Condensed Matter, Nr. 4 Special Issue: Emerging Leaders, 29, 044001.
[DOI]
Vera Meester and Daniela J. Kraft (2016) Spherical, Dimpled, and Crumpled Hybrid Colloids with Tunable Surface Morphology, Langmuir, 32 (41), 10668-10677.
[DOI]
G. Mattoni, P. Zubko, F. Maccherozzi, A.J.H. van der Torren, D.B. Boltje, M. Hadjimichael, N. Manca, S. Catalano, M. Gibert, Y. Liu, J. Aarts, J.-M. Triscone, S.S. Dhesi & A.D. Caviglia (2016) Striped nanoscale phase separation at the metal–insulator transition of heteroepitaxial nickelates, Nature Communications, 7, 13141.
[DOI]
Askes SH, Pomp W, Hopkins SL, Kros A, Wu S, Schmidt T, Bonnet S (2016) Imaging Upconverting Polymersomes in Cancer Cells: Biocompatible Antioxidants Brighten Triplet-Triplet Annihilation Upconversion., Small, 12, 5579-5590.
[Abstract] [DOI] [pdf]
Light upconversion is a very powerful tool in bioimaging as it can eliminate autofluorescence, increase imaging contrast, reduce irradiation damage, and increase excitation penetration depth in vivo. In particular, triplet–triplet annihilation upconverting (TTA-UC) nanoparticles and liposomes offer high upconversion efficiency at low excitation power. However, TTA-UC is quenched in air by oxygen, which also leads to the formation of toxic singlet oxygen. In this work, polyisobutylene-monomethyl polyethylene glycol block copolymers are synthesized and used for preparing polymersomes that upconvert red light into blue light in absence of oxygen. In addition, it is demonstrated that biocompatible antioxidants such as l-ascorbate, glutathionate, l-histidine, sulfite, trolox, or even opti-MEM medium, can be used to protect the TTA-UC process in these polymersomes resulting in red-to-blue upconversion under aerobic conditions. Most importantly, this approach is also functional in living cells. When A549 lung carcinoma cells are treated with TTA-UC polymersomes in the presence of 5 × 10−3 M ascorbate and glutathionate, upconversion in the living cells is one order of magnitude brighter than that observed without antioxidants. These results propose a simple chemical solution to the issue of oxygen sensitivity of TTA-UC, which is of paramount importance for the technological advancement of this technique in biology.
A. Singh, C. Jansen, K. Lahabi, and J. Aarts (2016) High-Quality CrO2 Nanowires for Dissipation-less Spintronics, Phys. Rev. X, 6, 041012.
[DOI]
Moeton M, Stassen OM, Sluijs JA, van der Meer VW, Kluivers LJ, van Hoorn H, Schmidt T, Reits EA, van Strien ME, Hol EM (2016) GFAP isoforms control intermediate filament network dynamics, cell morphology, and focal adhesions., Cell. Mol. Life Sci., 73, 4101-20.
[Abstract] [DOI] [pdf]
Glial fibrillary acidic protein (GFAP) is the characteristic intermediate filament (IF) protein in astrocytes. Expression of its main isoforms, GFAPα and GFAPδ, varies in astrocytes and astrocytoma implying a potential regulatory role in astrocyte physiology and pathology. An IF-network is a dynamic structure and has been functionally linked to cell motility, proliferation, and morphology. There is a constant exchange of IF-proteins with the network. To study differences in the dynamic properties of GFAPα and GFAPδ, we performed fluorescence recovery after photobleaching experiments on astrocytoma cells with fluorescently tagged GFAPs. Here, we show for the first time that the exchange of GFP–GFAPδ was significantly slower than the exchange of GFP–GFAPα with the IF-network. Furthermore, a collapsed IF-network, induced by GFAPδ expression, led to a further decrease in fluorescence recovery of both GFP–GFAPα and GFP–GFAPδ. This altered IF-network also changed cell morphology and the focal adhesion size, but did not alter cell migration or proliferation. Our study provides further insight into the modulation of the dynamic properties and functional consequences of the IF-network composition.
Casper van der Wel, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich & Daniela J. Kraft (2016) Lipid membrane-mediated attraction between curvature inducing objects, Scientific Reports , 6, 32825.
[DOI]
S. Voltan, C. Cirillo, H.J. Snijders, K. Lahabi, A. García-Santiago, J.M. Hernández, C. Attanasio, and J. Aarts (2016) Emergence of the stripe-domain phase in patterned permalloy films, Physical Review B, 94, 094406.
[DOI]
R. Gaudio, J.J. Renema, Z. Zhou, V.B. Verma, A.E. Lita, J. Shainline, M.J. Stevens, R.P. Mirin, S. Woo Nam, M.P. van Exter, M.J.A. de Dood, A. Fiore (2016) Experimental investigation of the detection mechanism in WSi nanowire superconducting single photon detectors, Applied Physics Letters, 109, 3, 031101.
[DOI]
M.J. Weaver, B. Pepper, F. Luna, F.M. Buters, H.J. Eerkens, G. Welker, B. Perock, K. Heeck, S. de Man, D. Bouwmeester (2016) Nested trampoline resonators for optomechanics, Applied Physics Letters, 108, 3, 033501.
[DOI]
D. Ding, L.M.C. Pereira, J.F. Bauters, M.J.R. Heck, G. Welker, A. Vantomme, J.E. Bowers, M.J.A. de Dood, D. Bouwmeester (2016) Multidimensional Purcell effect in an ytterbium-doped ring resonator, Nature Photonics, 10, 6, 385-388.
[DOI]
V.T. Tenner, M.J.A. de Dood, M.P. van Exter (2016) Measurement of the Phase and Intensity Profile of Surface Plasmon Laser Emission, ACS Photonics, 3, 6, 942-946.
[DOI]
G. Nienhuis (2016) Conservation laws and symmetry transformations of the electromagnetic field with sources, Phys. Rev. A, 93, 023840.
[DOI]
Corentin Coulais, Eial Teomy, Koen de Reus, Yair Shokef & Martin van Hecke (2016) Combinatorial design of textured mechanical metamaterials, Nature, 535, 529-532.
[DOI] [pdf]
S. Voltan, A. Singh, J. Aarts (2016) Triplet generation and upper critical field in superconducting spin valves based on CrO 2, Physical Review B, 94, 054503.
[DOI]
H. Snijders, J. A. Frey, J. Norman, M. P. Bakker, E. C. Langman, A. Gossard, J. E. Bowers, M. P. van Exter, D. Bouwmeester, W. Löffler (2016) Purification of a single photon nonlinearity, Nature Communications, 08, 7, 12578.
[DOI]
L. van Haandel, G.M. Bremmer, E.J.M. Hensen, Th. Weber (2016) Influence of sulfiding agent and pressure on structure and performance of CoMo/Al2O3 hydrodesulfurization catalyst, Journal of Catalysis, 10, 342, 27-39.
[DOI]
G.M. Bremmer, L. van Haandel, E.J.M. Hensen, J.W.M. Frenken, P.J. Kooyman (2016) The instability of NiMoS2 and CoMoS2 HDS Catalyst at ambient conditions: A quasi-in-situ HRTEM and XPS Study, J. Phys. Chem. C.
[DOI] [pdf]
Melle T.J.J.M. Punter, Armando Hernandez-Garcia, Daniela J. Kraft, Renko de Vries, and Paul van der Schoot (2016) Self-Assembly Dynamics of Linear Virus-Like Particles: Theory and Experiment, J. Phys. Chem. B, 120, 6286-6297.
[DOI]
Scott Waitukaitis and Martin van Hecke (2016) Origami building blocks: Generic and special four-vertices, Physical Review E, 93, 023003.
[DOI] [pdf]
A. Vinante, M. Bahrami, A. Bassi, O. Usenko, G. Wijts, T.H. Oosterkamp (2016) Upper bounds on spontaneous wave-function collapse models using millikelvin-cooled nanocantilevers, Phys. Rev. Lett., 3, 116, 090402.
[DOI] [pdf]
Jan van Ruitenbeek (2016) Molecular machines and devices, Beilstein Journal, 7, 310-311.
[DOI] [pdf]
Waqqar Ahmed1,Jan M. van Ruitenbeek (2016) One-step Synthesis of Cetyltrimethylammonium Bromide Stabilized Spherical Gold Nanoparticles, Journal of Nanoscience with Advanced Technology, 1(3), 20-24.
[Abstract] [DOI] [pdf]
For the synthesis of spherical Au nanoparticles (NPs), Turkevich method is very popular. However, in this method the citrate reduction of gold is carried out at high temperature, which is often a draw back. Herein, we describe a near room-temperature synthesis of cetyltrimethylammonium bromide (CTAB) stabilized spherical Au NPs of various sizes in a novel one-step synthesis protocol. We show that, in a growth solution containing CTAB, HAuCl4 and ascorbic acid, nucleation can be induced by the addition of AgNO3. This allowed us to eliminate the necessity of the presence of seed particles for NP growth. We show that NP size is strongly influenced by the CTAB to Ag molar ratio in the reaction medium. By tuning the CTAB to Ag molar ratio the sizes of the NPs can be tuned from 8 to 64 nm. Owing to the ease of synthesis and superior properties, CTAB stabilized NPs can replace the conventional citrate capped NPs for many applications.
Jan van Ruitenbeek, Monica Morales Masis, Enrique Miranda (2016) Resistive switching from fundamentals of nanoionic redox processes to memristive device applications., , 197-224.
[DOI]
S. Tewari, P. Roulleau, C. Grenier, F. Portier, A. Cavanna, U. Gennser, D. Mailly, and P. Roche (2016) Robust quantum coherence above the Fermi sea, Physical review B, 93, 035420 .
[Abstract] [DOI] [pdf]
In this paper we present an experiment where we measured the quantum coherence of a quasiparticle injected at a well-defined energy above the Fermi sea into the edge states of the integer quantum Hall regime. Electrons are introduced in an electronic Mach-Zehnder interferometer after passing through a quantum dot that plays the role of an energy filter. Measurements show that above a threshold injection energy, the visibility of the quantum interferences is almost independent of the energy. This is true even for high energies, up to 130 μeV , well above the thermal energy of the measured sample. This result is in contradiction with our theoretical predictions, which instead predict a continuous decrease of the interference visibility with increasing energy.
T G A Verhagen, H N Tinkey, H C Overweg, M van Son, M Huber, J M van Ruitenbeek and J Aarts (2016) Temperature dependence of spin pumping and Gilbert damping in thin Co/Pt bilayers, Journal of Physics: Condensed Matter, 28,5.
[Abstract] [DOI] [pdf]
We report on the temperature dependence of the spin-pumping effect and the Gilbert damping in Co/Pt bilayers grown on Silicon oxide by measuring the change of the linewidth in a ferromagnetic resonance (FMR) experiment. By varying the Co thickness ${{d}_{\text{Co}}}$ between 1.5 nm and 50 nm we find that the damping increases inversely proportional to ${{d}_{\text{Co}}}$ at all temperatures between 300 K and 5 K, showing that the spin pumping effect does not depend on temperature. We also find that the linewidth increases with decreasing temperature for all thicknesses down to about 30 K, before leveling off to a constant, or even decreasing again. This behavior is similar to what is found in bulk ferromagnets, leading to the conclusion that in thin films a conductivity-like damping mechanism is present similar to what is known in crystals.
N.V. Khotkevych, Yu.A. Kolesnichenko, J.M. van Ruitenbeek (2016) Quantum interference patterns around magnetic impurities in a 2D electron gas with strong Rashba spin-orbit interaction, Physica E.
[Abstract] [DOI] [pdf]
Explicit dependencies of the local density of states and the magnetization local density of states have been obtained around magnetic point defects in a two-dimensional electron gas with Rashba spin-orbit interaction . The expressions are given in the Born approximation for arbitrary magnitude and orientation of the defect magnetic moment, and for arbitrary size of the constant of spin-orbit interaction alpha/. On the basis of our asymptotically exact formulas a procedure for the determination of the constant alpha/ in STM experiments is proposed. The novel analytical results are compared with the numerical and approximate results of previous work. At variance with earlier work we find that that magnetic scattering in the presence of spin-orbit interaction does not modify the local density of states and that the spin texture resulting from in-plain orientation of the defect magnetic moment, and elastic scattering, is not a purely in-plane spin texture.
Faezeh Nami, Peter Gast, Edgar J. J. Groenen (2016) Rapid Freeze-Quench EPR Spectroscopy: Improved Collection of Frozen Particles, Applied Magnetic Resonance.
[Abstract] [DOI] [pdf]
Rapid freeze-quench (RFQ) in combination with electron paramagnetic resonance (EPR) spectroscopy at X-band is a proven technique to trap and characterize paramagnetic intermediates of biochemical reactions. Preparation of suitable samples is still cumbersome, despite many attempts to remedy this problem, and limits the wide applicability of RFQ EPR. We present a method, which improves the collection of freeze-quench particles from isopentane and their packing in an EPR tube. The method is based on sucking the particle suspension into an EPR tube with a filter at the bottom. This procedure results in a significant reduction of the required volume of reactants, which allows the economical use of valuable reactants such as proteins. The approach also enables the successful collection of smaller frozen particles, which are generated at higher flow rates. The method provides for a reproducible, efficient and fast collection of the freeze-quench particles and can be easily adapted to RFQ EPR at higher microwave frequencies than X-band.
Apetri MM, Harkes R, Subramaniam V, Canters GW, Schmidt T, Aartsma TJ (2016) Direct Observation of α-Synuclein Amyloid Aggregates in Endocytic Vesicles of Neuroblastoma Cells., PLoS ONE, 11, e0153020.
[Abstract] [DOI] [pdf]
Aggregation of α-synuclein has been linked to both familial and sporadic Parkinson's disease. Recent studies suggest that α-synuclein aggregates may spread from cell to cell and raise questions about the propagation of neurodegeneration. While continuous progress has been made characterizing α-synuclein aggregates in vitro, there is a lack of information regarding the structure of these species inside the cells. Here, we use confocal fluorescence microscopy in combination with direct stochastic optical reconstruction microscopy, dSTORM, to investigate α-synuclein uptake when added exogenously to SH-SY5Y neuroblastoma cells, and to probe in situ morphological features of α-synuclein aggregates with near nanometer resolution. We demonstrate that using dSTORM, it is possible to follow noninvasively the uptake of extracellularly added α-synuclein aggregates by the cells. Once the aggregates are internalized, they move through the endosomal pathway and accumulate in lysosomes to be degraded. Our dSTORM data show that α-synuclein aggregates remain assembled after internalization and they are shortened as they move through the endosomal pathway. No further aggregation was observed inside the lysosomes as speculated in the literature, nor in the cytoplasm of the cells. Our study thus highlights the super-resolution capability of dSTORM to follow directly the endocytotic uptake of extracellularly added amyloid aggregates and to probe the morphology of in situ protein aggregates even when they accumulate in small vesicular compartments.
Vera Meester, Ruben W. Verweij, Casper van der Wel, and Daniela J. Kraft (2016) Colloidal Recycling: Reconfiguration of Random Aggregates into Patchy Particles, ACS Nano, 10 (4), 4322–4329.
[DOI]
Waqqar Ahmed, Jan M. van Ruitenbeek (2016) One-step Synthesis of Cetyltrimethylammonium Bromide Stabilized Spherical Gold Nanoparticles, J Nanosci Adv Tech, 1(3), 20-24.
[DOI] [pdf]
Marlous Kamp, Michiel Hermes, Carlos M. van Kats, Daniela J. Kraft, Willem K. Kegel, Marjolein Dijkstra, and Alfons van Blaaderen (2016) Selective Depletion Interactions in Mixtures of Rough and Smooth Silica Spheres, Langmuir, 32 (5), 1233-1240.
[DOI]
Margot Segers, Marjolein Sliepen, Daniela J. Kraft, Martin Möller, Pascal Buskens (2016) Synthesis of sub-micron sized hollow, and nanoporous phenylsiloxane spheres through use of phenyltrimethoxysilane as surfmer: Insights into the surfactant and factors influencing the particle architecture, Colloids and Surfaces A, 497, 378-384.
[DOI]
I.M. Dildar, D.B. Boltje, M.B.S. Hesselberth, J. Aarts (2016) Mesoscopic transport in thin films of La0.67Sr0.33MnO3, Thin Solid Films, 598, 305-310.
[DOI]
Beletkaia, E., S. F. Fenz, W. Pomp, B. E. Snaar-Jagalska, P. W. C. Hogendoorn, and T. Schmidt (2016) CXCR4 signaling is controlled by immobilization at the plasma membrane., BBA - Mol Cell Res, 1863, 607-616.
[Abstract] [DOI] [pdf]
Understanding of the regulation mechanisms of CXCR4 signaling is essential for revealing its role in physiological and pathological processes. Though biochemical pathways following CXCR4 activation by its ligand CXCL12 are well established, knowledge about the receptor dynamics on the plasma membrane remains limited. Here we used Ewing sarcoma-derived cells to unravel the processes that are involved in regulating CXCR4 dynamics on the plasma membrane during receptor signaling. Single-molecule epi-fluorescence microscopy showed that CXCR4 was present in monomeric state on the plasma membrane independent of receptor stimulation. However, upon activation freely diffusing receptors were immobilized in a ligand concentration-dependent manner. CXCR4 immobilization was strongly correlated with the ability for G-protein signaling and was a precursor of subsequent endocytotic events. Our data suggest that, a balanced regulation of G-protein dependent and independent pathways is required for controlling CXCR4 receptor mobility, and potentially subsequent controlled signal transduction.
B. C. Hiesmayr, M. J. A. de Dood, and W. Löffler (2016) Observation of Four-Photon Orbital Angular Momentum Entanglement, Phys. Rev. Lett. (Editor's Suggestion), 116, 073601.
[DOI]
Tulotta C, Stefanescu C, Beletkaia E, Bussmann J, Tarbashevich K, Schmidt T, Snaar-Jagalska BE (2016) Inhibition of cross-species CXCR4 signaling by the small molecule IT1t impairs triple negative breast cancer early metastases in zebrafish., Dis Model Mech, 9, 141-153.
[Abstract] [DOI] [pdf]
Triple-negative breast cancer (TNBC) is a highly aggressive and recurrent type of breast carcinoma that is associated with poor patient prognosis. Because of the limited efficacy of current treatments, new therapeutic strategies need to be developed. The CXCR4-CXCL12 chemokine signaling axis guides cell migration in physiological and pathological processes, including breast cancer metastasis. Although targeted therapies to inhibit the CXCR4-CXCL12 axis are under clinical experimentation, still no effective therapeutic approaches have been established to block CXCR4 in TNBC. To unravel the role of the CXCR4-CXCL12 axis in the formation of TNBC early metastases, we used the zebrafish xenograft model. Importantly, we demonstrate that cross-communication between the zebrafish and human ligands and receptors takes place and human tumor cells expressing CXCR4 initiate early metastatic events by sensing zebrafish cognate ligands at the metastatic site. Taking advantage of the conserved intercommunication between human tumor cells and the zebrafish host, we blocked TNBC early metastatic events by chemical and genetic inhibition of CXCR4 signaling. We used IT1t, a potent CXCR4 antagonist, and show for the first time its promising anti-tumor effects. In conclusion, we confirm the validity of the zebrafish as a xenotransplantation model and propose a pharmacological approach to target CXCR4 in TNBC.
T.G.A. Verhagen, H.N. Tinkey, H.C. Overweg, M. van Son, M. Huber,J.M. van Ruitenbeek and J. Aarts (2016) Temperature dependence of spin pumping and Gilbert damping in thin Co/Pt bilayers, J. Phys.: Condensed Matter, 28, 056004.
[DOI]

2015
Jan van Ruitenbeek (2015) The Netherlands’ Physical Society, NNV, a vibrant community of 4000 physicists, Europhysics News , Volume 46, Number 3, 22–25.
[Abstract] [DOI] [pdf]
It was a lively conference, the annual meeting of the Netherlands’ Physical Society (Nederlandse Natuurkundige Vereniging, NNV) on April 10 at Eindhoven University of Technology. In addition to the plenary morning sessions and six parallel sessions in the afternoon, there were award ceremonies for the Teacher of the year and for the best Bachelor thesis, a Young Speakers Contest and a Physics Market. And the 2015 winner of the prestigious Physica award, Marileen Dogterom, delivered the Physica lecture. But what precisely is the NNV?
Jan van Ruitenbeek en Rinke Wijngaarden (2015) Impressies van het NNV Klimaatsymposium, Nederlands Tijdschrift voor Natuurkunde.
[DOI]
Jan van Ruitenbeek (2015) Naar een Engelstalige en digitale uitgave., Nederlands Tijdschrift voor Natuurkunde.
[DOI]
Jan van Ruitenbeek (2015) Reactie op de wetenschapsvisie 2025, Nederlands Tijdschrift voor Natuurkunde.
[DOI]
Sumit Tewari, Jacob Bakermans, Christian Wagner, Federica Galli, Jan M. van Ruitenbeek (2015) Testing monoatomic gold chains using a 3D motion controlled scanning tunneling microscope, NEVAC blad, 53.
[DOI] [pdf]
Carlos Sabater, Carlos Untiedt and Jan M. van Ruitenbeek (2015) Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains, Beilstein Journal of Nanotechnology, 6, 2338–2344.
[Abstract] [DOI] [pdf]
This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.
Geelen D, Thete A, Schaff O, Kaiser A, van der Molen SJ, Tromp R (2015) eV-TEM: Transmission electron microscopy in a low energy cathode lens instrument., Ultramicroscopy, 159 Pt 3, 482-7.
[DOI]
Guinevere Mathies, Peter Gast, N. Dennis Chasteen, Ashley N. Luck, Anne B. Mason, Edgar J. J. Groenen (2015) Exploring the Fe(III) binding sites of human serum transferrin with EPR at 275 GHz, Journal of Biological Inorganic Chemistry, 20, 487-496.
[DOI] [pdf]
F. Hammerath, M. Moroni, L. Bossoni, S. Sanna, R. Kappenberger, S. Wurmehl, A.U.B. Wolter, M.A. Afrassa, Y. Kobayashi, M. Sato, B. Buchner, P. Carretta (2015) Enhancement of low-frequency fluctuations and superconductivity breakdown in Mn-doped La1-yYyFeAsO0.89F0.11 superconductors, Phys. Rev. B., 92, 020505.
[DOI] [pdf]
G.J. Verbiest, M.J. Rost (2015) Beating beats mixing in heterodyne detection schemes, Nature Communications, 3, 6, 6444.
[DOI] [pdf]
Jobst, Johannes Kautz, Jaap Geelen, Daniel Tromp, Rudolf M van der Molen, Sense Jan (2015) Nanoscale measurements of unoccupied band dispersion in few-layer graphene., Nature communications, 6, -.
[Abstract] [DOI]
The properties of any material are fundamentally determined by its electronic band structure. Each band represents a series of allowed states inside a material, relating electron energy and momentum. The occupied bands, that is, the filled electron states below the Fermi level, can be routinely measured. However, it is remarkably difficult to characterize the empty part of the band structure experimentally. Here, we present direct measurements of unoccupied bands of monolayer, bilayer and trilayer graphene. To obtain these, we introduce a technique based on low-energy electron microscopy. It relies on the dependence of the electron reflectivity on incidence angle and energy and has a spatial resolution 10nm. The method can be easily applied to other nanomaterials such as van der Waals structures that are available in small crystals only. C1 Huygens-Kamerlingh Onnes Laboratorium, Leiden Institute of Physics, Leiden University, P.O. Box 9504, Leiden N.L. 2300 R.A. Netherlands.
Sand LG, Scotlandi K, Berghuis D, Snaar-Jagalska BE, Picci P, Schmidt T, Szuhai K, Hogendoorn PC (2015) CXCL14, CXCR7 expression and CXCR4 splice variant ratio associate with survival and metastases in Ewing sarcoma patients., Eur. J. Cancer, 51, 2624-33.
[Abstract] [DOI] [pdf]
PURPOSE: Ewing sarcoma (EWS) is the second most common sarcoma of bone in children and young adults. Patients with disseminated disease at diagnosis or early relapse have a poor prognosis. Our goal was to identify novel predictive biomarkers for these patients, focusing on chemokines, specifically genes involved in the CXCR4-pathway because of their established role in metastasis and tumour growth. METHODS: Total RNA isolated from therapy-naïve tumour samples (n=18; panel I) and cell lines (n=21) was used to study expression of CXCR4-pathway related genes and CXCR4 splice variants (CXCR4-2: Small and CXCR4-1: Large) by RT-Q-PCR. Expression levels were correlated to overall survival (OS) and event free survival (EFS). Study results were validated in an independent series of 26 tumour samples (panel II) from therapy-naïve tumour samples. RESULTS: CXCL12, CXCR4, CXCR7 and CXCL14 were expressed and high CXCR7 and CXCL14 expression showed a positive correlation with EFS and OS and a negative correlation with metastasis development. Both splice variants CXCR4 were expressed in cell lines and tumour samples and CXCR4-1/CXCR4-2 ratio was significantly higher in tumour samples compared to cell lines and correlated with an improved EFS and OS. The results from the test panel were validated in an independent sample panel. CONCLUSIONS: We identified a set of genes involved in CXCR4 signalling that may be used as a marker to predict survival and metastasis development in Ewing sarcoma.
F. Scarpelli, A. L. Arrieta, P. Gast, E. J. J. Groenen, S. Milikisyants, M. E. P. Murphy, M. Huber (2015) A Single-Crystal EPR Study at 95 GHz of the Type-2 Copper Site of Nitrite Reductase From Alcaligenes faecalis, Applied Magnetic Resonance, 46, 411-420.
[DOI] [pdf]
Maryam Hashemi Shabestari, Pravin Kumar, Ine M. J. Segers-Nolten, Mireille M. A. E. Claessens, Bart D. van Rooijen, Vinod Subramaniam , Martina Huber (2015) Three Long-Range Distance Constraints and an Approach Towards a Model for the α-Synuclein-Fibril Fold, Applied Magnetic Resonance, 46, 369-388.
[DOI] [pdf]
Pravin Kumar, Ine M. J. Segers-Nolten, Nathalie Schilderink, Vinod Subramaniam, Martina Huber (2015) Parkinson’s Protein α-Synuclein Binds Efficiently and with a Novel Conformation to Two Natural Membrane Mimics, PLOS ONE .
[DOI] [pdf]
Martin van Son, Simon Lindhoud, Matthijs van der Wild, Carlo P. M. van Mierlo, and Martina Huber (2015) Double Electron−Electron Spin Resonance Tracks Flavodoxin Folding, Journal of Physical Chemistry B, 119, 13507–13514.
[DOI] [pdf]
Jesika Schilder, Wei-Min Liu, Pravin Kumar,b Mark Overhand,a Martina Huber and Marcellus Ubbink (2015) Protein docking using an ensemble of spin labels optimized by intra-molecular paramagnetic relaxation enhancement, Phys. Chem. Chem. Phys..
[DOI]
Deni Mance, Peter Gast, Martina Huber, Marc Baldus, and Konstantin L. Ivanov (2015) The magnetic field dependence of cross-effect dynamic nuclear polarization under magic angle spinning, THE JOURNAL OF CHEMICAL PHYSICS, 142, 234201.
[DOI] [pdf]
G.M. Bremmer, L. van Haandel, E.J.M. Hensen, J.W.M. Frenken, P.J. Kooyman (2015) A quasi in situ HRTEM study of the air stability of ((Ni/Co)MoS2 Hydrodesulfurization catalysts, Microsc. Microanal., 21, 801-802.
[DOI] [pdf]
L. van Haandel, G.M. Bremmer, P.J. Kooyman, J.A.R. van Veen, Th. Weber, E.J.M. Hensen (2015) Structure-activity correlations in hydrodesulfurization reactions over Ni-promoted MoxW(1-x)S2/Al2O3 catalysts., Catalysis, 5, 7276-7287.
[DOI]
V. Chikkadi, E. Woldhuis, M. van Hecke and P. Schall (2015) Correlations of strain and plasticity in a flowing foam, EPL, 112, 36004.
[DOI] [pdf]
Mykhailo Azarkh and Edgar J. J. Groenen (2015) Temperature Determination by EPR at 275 GHz and the Detection of Temperature Jumps in Aqueous Samples, J. Phys. Chem. B, 119, 13416–13421.
[DOI] [pdf]
Harkes R, Keizer VI, Schaaf MJ, Schmidt T (2015) Depth-of-Focus Correction in Single-Molecule Data Allows Analysis of 3D Diffusion of the Glucocorticoid Receptor in the Nucleus., PLoS ONE, 10, e0141080.
[Abstract] [DOI] [pdf]
Single-molecule imaging of proteins in a 2D environment like membranes has been frequently used to extract diffusive properties of multiple fractions of receptors. In a 3D environment the apparent fractions however change with observation time due to the movements of molecules out of the depth-of-field of the microscope. Here we developed a mathematical framework that allowed us to correct for the change in fraction size due to the limited detection volume in 3D single-molecule imaging. We applied our findings on the mobility of activated glucocorticoid receptors in the cell nucleus, and found a freely diffusing fraction of 0.49±0.02. Our analysis further showed that interchange between this mobile fraction and an immobile fraction does not occur on time scales shorter than 150 ms.
Geert H. Wortel and Martin van Hecke (2015) Anisotropy of weakly vibrated granular flows, Physical Review E , 92, 040201(R).
[DOI] [pdf]
Sand LG, Jochemsen AG, Beletkaia E, Schmidt T, Hogendoorn PC, Szuhai K (2015) Novel splice variants of CXCR4 identified by transcriptome sequencing., Biochem. Biophys. Res. Commun., 466, 89-94.
[Abstract] [DOI] [pdf]
Chemokine receptor CXCR4 is involved in tumor growth, angiogenesis and metastasis. Its function is regulated in many ways and one of them is alternative splicing. We identified two novel coding splice variants (CXCR4-3 and CXCR4-4) of CXCR4 in Ewing sarcoma (EWS) cell lines by whole transcriptome sequencing and validated these with reverse transcriptase- PCR and Sanger sequencing. The novel splice variants were expressed at RNA level in Ewing sarcoma samples and in other tumor cell lines and placenta, but not in lung. Due to inclusion of an additional exon the new isoforms have a 70 and 33 amino acid elongation of the N-terminal end of CXCR4. For validation at protein and functional level, the identified isoforms and normal CXCR4 were cloned into an EYFP tagged vector and ectopically expressed in HEK293T cell line and EWS cell line A673. Of the novel isoforms CXCR4-3 showed cell membrane localization and a functional response after addition of CXCR4 ligand CXCL12a. CXCR4-4 showed strong cytoplasmic accumulation and no response to ligand treatment. The role of the newly discovered isoforms in CXCR4 signaling is likely to be limited. Our data stresses the importance of functional validation of newly identified isoforms.
Pedro M. Reis, Heinrich M. Jaeger, Martin van Hecke (2015) Design Matter: A perspective, Extreme Mechanics Letters, 5, 25-29.
[DOI] [pdf]
Mykhailo Azarkh, , Edgar J.J. Groenen (2015) Simulation of multi-frequency EPR spectra for a distribution of the zero-field splitting, Journal of Magnetic Resonance, 255, 106-113.
[DOI] [pdf]
Q. Wang, J. J. Renema, A. Gaggero, F. Mattioli, R. Leoni, M. P. van Exter and M. J. A. de Dood (2015) How noise affects quantum detector tomography, J. Appl. Phys., 10, 118, 134501.
[DOI]
S.B. Roobol, M.E. Cañas Ventura, M. Bergman, M.A. van Spronsen, W.G. Onderwaater, P.C. van der Tuijn, R. Koehler, A. Ofitserov G.J.C. van Baarle, J.W.M. Frenken (2015) The ReactorAFM: Non-contact atomic force microscope operating under high-pressure and high-temperature catalytic conditions., Rev. Sci. Instrum. , 86, 033706.
[DOI]
M.A. van Spronsen, G.J.C. van Baarle, C.T. Herbschleb, J.W.M. Frenken, I.M.N. Groot (2015) Erratum to "High-pressure operando STM studies giving insight in CO oxidation and NO reduction over Pt(110)" [Catal. Today 244 (2015) 85-95]., Catal. Today, 256, 384.
[DOI]
Qiang Wang, Jelmer J. Renema, Andreas Engel, Martin P. van Exter, and Michiel J. A. de Dood (2015) Local detection efficiency of a NbN superconducting single photon detector explored by a scattering scanning near-field optical microscope, Opt. Express, 09, 23, 24873.
[DOI]
F. Mariani and M. P. van Exter (2015) Scattering of guided light by a single hole in a dielectric slab, Optics Express, 06, 23, 17539.
[DOI]
C. B. Smiet, S. Candelaresi, A. Thompson, J. Swearngin, J. W. Dalhuisen, and D. Bouwmeester (2015) Self-Organizing Knotted Magnetic Structures in Plasma, Phys. Rev. Lett., 08, 115, 095001.
[DOI]
E. Woldhuis, V. Chikkadi, M.S. van Deen, P. Schall and M. van Hecke (2015) Fluctuations in flows near jamming, Soft Matter, 11, 7024-7031.
[DOI] [pdf]
Corentin Coulais, Johannes T. B. Overvelde, Luuk A. Lubbers, Katia Bertoldi, and Martin van Hecke (2015) Discontinuous Buckling of Wide Beams and Metabeams, Physical Review Letters, 115, 044301.
[DOI] [pdf]
M.P. Bakker, T. Ruytenberg, W. Löffler, A. Barve, L. Coldren, M.P. van Exter, D. Bouwmeester (2015) Quantum dot nonlinearity through cavity-enhanced feedback with a charge memory, Phys. Rev. B. (rapid), 91, 24, 241305-5.
[DOI] [pdf]
J.J. Renema, Q. Wang, R. Gaudio, I. Komen, K. op ’t Hoog, D. Sahin, A. Schilling, M.P. van Exter, A. Fiore, A. Engel, M.J.A. de Dood (2015) Position-Dependent Local Detection Efficiency in a Nanowire Superconducting Single-Photon Detector, Nano Lett., 15, 7, 4541-4545.
[DOI] [pdf]
O.W.B. Benningshof, D.H. Nguyen, M.R. Dadema, A.F. Beker, T.H. Oosterkamp, R. Jochemsen (2015) Characterization of the channel walls roughness in photonic crystal fibers, Physica E, 2, 66, 33-39.
[DOI] [pdf]
I.M. Dildar, M. Neklyudova, Q. Xu, H.W. Zandbergen, S. Harkema, D. Boltje and J. Aarts, (2015) Growing LaAlO3/SrTiO3 interfaces by sputter deposition, AIP Advances , 5, 067156.
[DOI]
M. Kumar, K. Kumar Vidya Sethu, and J.M. van Ruitenbeek (2015) Molecule assisted ferromagnetic atomic chain formation, Phys. Rev. B, june, 91, 245404.
[Abstract] [DOI] [pdf]
One dimensional systems strongly enhance the quantum character of electron transport. Such systems can be realized in 5d transition metals Au, Pt, and Ir, in the form of suspended monatomic chains between bulk leads. Atomic chains between ferromagnetic leads would open up many perspectives in the context of spin-dependent transport and spintronics, but the evidence suggests that for pure metals only the mentioned three 5d metals are susceptible to chain formation. It has been argued that the stability of atomic chains made up from ferromagnetic metals is compromised by the same exchange interaction that produces the local moments. Here we demonstrate that magnetic atomic chains can be induced to form in break junctions under the influence of light molecules. Explicitly, we find deuterium assisted chain formation in the 3d ferromagnetic transition metals Fe and Ni. Chain lengths up to eight atoms are formed upon stretching the ferromagnetic atomic contact in deuterium atmosphere at cryogenic temperatures. From differential conductance spectra vibronic states of D2 can be identified, confirming the presence of deuterium in the atomic chains. Shot noise spectroscopy indicates the presence of weakly spin polarized transmission channels.
F. M. Buters, H. J. Eerkens, K. Heeck, M. J. Weaver, B. Pepper, S. de Man, and D. Bouwmeester (2015) Experimental exploration of the optomechanical attractor diagram and its dynamics, Phys. Rev. A, 07, 92, 013811.
[DOI]
M. P. Bakker, H. Snijders, W. Löffler, A. V. Barve, L. A. Coldren, D. Bouwmeester, M. P. van Exter (2015) Homodyne detection of coherence and phase shift of a quantum dot in a cavity, Opt. Lett., 06, 40, 3173.
[DOI] [pdf]
G.J. Verbiest, D.J. van der Zalm, T.H. Oosterkamp, M.J. Rost (2015) A subsurface add-on for standard atomic force microscopes, Rev. Sci. Instrum., 86, 033704.
[Abstract] [DOI] [pdf]
The application of ultrasound in an Atomic Force Microscope (AFM) gives access to subsurface information. However, no commercially AFM exists that is equipped with this technique. The main problems are the electronic crosstalk in the AFM setup and the insufficiently strong excitation of the cantilever at ultrasonic (MHz) frequencies. In this paper, we describe the development of an add-on that provides a solution to these problems by using a special piezo element with a lowest resonance frequency of 2.5 MHz and by separating the electronic connection for this high frequency piezo element from all other connections. In this sense, we support researches with the possibility to perform subsurface measurements with their existing AFMs and hopefully pave also the way for the development of a commercial AFM that is capable of imaging subsurface features with nanometer resolution.
Torren A.J.K, S.J. van der Molen, and J. Aarts (2015) Formation of a mixed ordered termination on the surface of LaAlO3(001), Physical Review B, 91, 245426.
[DOI]
A. Singh, S. Voltan, K. Lahabi, and J. Aarts (2015) Colossal Proximity Effect in a Superconducting Triplet Spin Valve Based on the Half-Metallic Ferromagnet CrO2, Physical Review X, 5, 021019.
[DOI]
J.J. Renema, R.J. Rengelink, I. Komen, Q. Wang, R. Gaudio, K.P.M. Op 't Hoog, Z. Zhou, D. Sahin, A. Fiore, P. Kes, J. Aarts, M.P. van Exter, M.J.A. de Dood, E.F.C. Driessen (2015) The effect of magnetic field on the intrinsic detection efficiency of superconducting single-photon detectors, Appl. Phys. Lett. , 106 (9), 092602.
[DOI] [pdf]
S.H.C. Askes,N.L. Mora, R. Harkes, R.I. Koning, B. Koster, T. Schmidt, A. Kros & S. Bonnet (2015) Imaging the lipid bilayer of giant unilamellar vesicles using red-to-blue light upconversion., Chem. Comm., 51, 9137.
[Abstract] [DOI] [pdf]
Red-to-blue triplet–triplet annihilation upconversion was obtained in giant unilamellar vesicles. The upconverted light was homo- geneously distributed across the membrane and could be utilized for the imaging of individual giant vesicles in three dimensions. These results show the great potential of TTA-UC for imaging applications under anoxic conditions.
T.G.A. Verhagen, I. Leermakers, J.M. van Ruitenbeek, and J. Aarts (2015) Detecting Rashba fields at the interface between Co and Si oxide by ferromagnetic resonance, Physical Review B, 91, 184402.
[DOI]
Morten P. Bakker, Ajit V. Barve, Thomas Ruytenberg, Wolfgang Löffler, Larry A. Coldren, Dirk Bouwmeester, and Martin P. van Exter (2015) Polarization degenerate solid-state cavity quantum electrodynamics, Phys. Rev. B, 03, 91, 115319.
[DOI]
H. J. Eerkens, F. M. Buters, M. J. Weaver, B. Pepper, G. Welker, K. Heeck, P. Sonin, S. de Man, and D. Bouwmeester (2015) Optical side-band cooling of a low frequency optomechanical system, Optics Express, 04, 23, 8014-8020.
[DOI]
A. Pezzarossa, F. Zosel & T. Schmidt. (2015) Visualization of HRas Domains in the Plasma Membrane of Fibroblasts., Biophys. J., 108, 1870.
[Abstract] [DOI] [pdf]
The plasma membrane is a highly complex, organized structure where the lateral organization of signaling proteins is tightly regulated. In the case of Ras proteins, it has been suggested that the differential activity of the various isoforms is due to protein localization in separate membrane compartments. To date, direct visualization of such compartmentalization has been achieved only by electron microscopy on membrane sheets. Here, we combine photoactivated light microscopy with quantitative statistical analysis to visualize protein distribution in intact cells. In particular, we focus on the localization of HRas and its minimal anchoring domain, CAAX. We demonstrate the existence of a complex partitioning behavior, where small domains coexist with larger ones. The protein content in these domains varied from two molecules to tens of molecules. We found that 40% of CAAX and 60% of HRas were localized in domains. Subsequently, we were able to manipulate protein distributions by inducing coalescence of supposedly cholesterol-enriched domains. Clustering resulted in an increase of the localized fraction by 15%.
M.A. van Spronsen, G.J.C. van Baarle, C.T. Herbschleb, J.W.M. Frenken, I.M.N. Groot (2015) High-pressure operando STM studies giving insight in CO oxidation and NO reduction over Pt(110), Catalysis Today, 244, 85-95.
[Abstract] [DOI] [pdf]
Two catalytic systems have been studied at high pressures on the Pt(1 1 0) surface on an atomic level. The first system was the oxidation of CO by O2 towards CO2. In the framework of the second reaction, namely NO reduction, the effect of room temperature exposure of the surface to NO and H2 was investigated. To study these reaction systems at relevant pressures, the ReactorSTM has been used. This is a unique system which consists of a compact STM in which a flow reactor is integrated. The combined reactor with STM is housed inside a conventional vacuum system to allow for traditional surface science preparation and analysis techniques. The STM images obtained with the ReactorSTM under reaction conditions show the lifting of the (1x2) missing row reconstruction by high-pressure CO exposure. The lifting is followed by the formation of the (1x1) metallic Pt(1 1 0) structure for high CO/O2 ratios and a (1x2) lifted-row type surface oxide structure for more O2-rich conditions. The room temperature exposure of Pt(1 1 0) to H2 results in the formation of a (1x4) missing-row structure and deeper, nested missing rows. The exposure to high-pressure NO removes these missing-row structures.
Wouter G. Ellenbroek, Varda F. Hagh, Avishek Kumar, M.F. Thorpe, and Martin van Hecke (2015) Rigidity Loss in Disordered Systems: Three Scenarios, Physical Review Letters (Cover), 114, 135501.
[pdf]
H.E. Balcioglu, H. van Hoorn, D.M. Donato, T. Schmidt and E.H.J. Danen. (2015) The integrin expression profile modulates orientation and dynamics of force transmission at cell–matrix adhesions., J Cell Science, 128, 1316.
[Abstract] [DOI] [pdf]
Integrin adhesion receptors connect the extracellular matrix (ECM) to the cytoskeleton and serve as bidirectional mechanotransducers. During development, angiogenesis, wound healing and cancer progression, the relative abundance of fibronectin receptors, including integrins a5b1 and avb3, changes, thus altering the integrin composition of cell–matrix adhesions. Here, we show that enhanced avb3 expression can fully compensate for loss of a5b1 and other b1 integrins to support outside-in and inside-out force transmission. a5b1 and avb3 each mediate actin cytoskeletal remodeling in response to stiffening or cyclic stretching of the ECM. Likewise, a5b1 and avb3 support cellular traction forces of comparable magnitudes and similarly increase these forces in response to ECM stiffening. However, cells using avb3 respond to lower stiffness ranges, reorganize their actin cytoskeleton more substantially in response to stretch, and show more randomly oriented traction forces. Centripetal traction force orientation requires long stress fibers that are formed through the action of Rho kinase (ROCK) and myosin II, and that are supported by a5b1. Thus, altering the relative abundance of fibronectin-binding integrins in cell–matrix adhesions affects the spatiotemporal organization of force transmission.
Geert Wortel, Tamás Börzsönyi, Ellák Somfai, Sandra Wegner, Balázs Szabó, Ralf Stannarius and Martin van Hecke (2015) Heaping, secondary flows and broken symmetry in flows of elongated granular particles, Soft Matter, Open Access.
[pdf]
Martin van Hecke (2015) Slow granular flows: The dominant role of tiny fluctuations, Comptes Rendus Physique, 16, 37-44.
[pdf]
Scott Waitukaitis, Rémi Menaut, Bryan Gin-ge Chen, and Martin van Hecke (2015) Origami Multistability: From Single Vertices to Metasheets, Physical Review Letters, 114, 055503.
[pdf]
Joost R. Wolters, Guido Avvisati, Fabian Hagemans, Teun Vissers, Daniela J. Kraft, Marjolein Dijkstra and Willem K. Kegel (2015) Self-assembly of "Mickey Mouse" shaped colloids into tube-like structures: experiments and simulations, Soft Matter , 11, 1067 - 1077.
[DOI]
Jianhui Liao, Sander Blok, Sense Jan van der Molen, Sandra Diefenbach, Alexander W. Holleitner, Christian Schoenenberger, Anton Vladyka, Michel Calame (2015) Ordered nanoparticle arrays interconnected by molecular linkers: electronic and optoelectronic properties, CHEMICAL SOCIETY REVIEWS, 44, 999-1014.
[DOI]
J. Kautz, V. A. E. C. Janssen, R. M. Tromp, S. J. van der Molen (2015) Differential reactivity of alkanethiols with Si(111)-Au 2D surface alloys, SURFACE SCIENCE, 632, 245426.
[DOI]
E.J. Devid, P.N. Martinho, M.V. Kamalakar, I. Šalitroš, Ú. Prendergast, J.F. Dayen, V. Meded, T. Lemma, R. González-Prieto, F. Evers, T.E. Keyes, M. Ruben, B. Doudin, S.J. van der Molen (2015) Spin transition in arrays of gold nanoparticles and spin crossover molecules., ACS NANO, 4496–4507.
[DOI]
Jansen KA, Donato DM, Balcioglu HE, Schmidt T, Danen EH, Koenderink GH (2015) A guide to mechanobiology: Where biology and physics meet., Biochim. Biophys. Acta, 1853, 3043-52.
[Abstract] [DOI] [pdf]
Cells actively sense and process mechanical information that is provided by the extracellular environment to make decisions about growth, motility and differentiation. It is important to understand the underlying mechanisms given that deregulation of the mechanical properties of the extracellular matrix (ECM) is implicated in various diseases, such as cancer and fibrosis. Moreover, matrix mechanics can be exploited to program stem cell differentiation for organ-on-chip and regenerative medicine applications. Mechanobiology is an emerging multidisciplinary field that encompasses cell and developmental biology, bioengineering and biophysics. Here we provide an introductory overview of the key players important to cellular mechanobiology, taking a biophysical perspective and focusing on a comparison between flat versus three dimensional substrates. This article is part of a Special Issue entitled: Mechanobiology.
Kamran M, Friebe VM, Delgado JD, Aartsma TJ, Frese RN, Jones MR (2015) Demonstration of asymmetric electron conduction in pseudosymmetrical photosynthetic reaction centre proteins in an electrical circuit., Nat Commun.
[DOI]
J. Kautz, J. Jobst, C. Sorger, R.M. Tromp, H.B. Weber, S.J. van der Molen (2015) Low-Energy Electron Potentiometry: Contactless Imaging of Charge Transport on the Nanoscale, SCIENTIFIC REPORTS, 5, L18–L21.
[DOI]

2014
W Dednam1,C Sabater, M A Fernandez, C Untiedt, J J Palacios and M J Caturla1 (2014) Modeling contact formation between atomic-sized gold tips via molecular dynamics, Journal of Physics: Conference Series, Volume 574, conference 1 .
[Abstract] [DOI] [pdf]
The formation and rupture of atomic-sized contacts is modelled by means of molecular dynamics simulations. Such nano-contacts are realized in scanning tunnelling microscope and mechanically controlled break junction experiments. These instruments routinely measure the conductance across the nano-sized electrodes as they are brought into contact and separated, permitting conductance traces to be recorded that are plots of conductance versus the distance between the electrodes. One interesting feature of the conductance traces is that for some metals and geometric configurations a jump in the value of the conductance is observed right before contact between the electrodes, a phenomenon known as jump-to-contact. This paper considers, from a computational point of view, the dynamics of contact between two gold nano-electrodes. Repeated indentation of the two surfaces on each other is performed in two crystallographic orientations of face-centred cubic gold, namely (001) and (111). Ultimately, the intention is to identify the structures at the atomic level at the moment of first contact between the surfaces, since the value of the conductance is related to the minimum cross-section in the contact region. Conductance values obtained in this way are determined using first principles electronic transport calculations, with atomic configurations taken from the molecular dynamics simulations serving as input structures.
J.M. Ruitenbeek (2014) De Natuurkunde tot 2025., Nederlands Tijdschrift voor Natuurkunde .
[DOI]
Yuan H, Orrit M (2014) Temperature cycles unravel the dynamics of single biomolecules., Biophys. J., 106, 3-4.
[DOI]
M.H. van Es, J. Tank, J. Preiner, P. Hinterdorfer, T.H. Oosterkamp (2014) Single molecule binding dynamics measured with atomic force microscopy., Ultramicroscopy, 140, 32-36.
[DOI] [pdf]
V.T. Tenner, A.N. van Delft, M.J.A. de Dood, M.P. van Exter (2014) Loss and scattering of surface plasmon polaritons on optically-pumped hole arrays, Journal of Optics, 16, 11, 114019.
[DOI] [pdf]
D. Ding, M.J.A. de Dood, J.F. Bauters, M.J.R. Heck, J.E. Bowers, D. Bouwmeester (2014) Fano resonances in a multimode waveguide coupled to a high-Q silicon nitride ring resonator, Optics Express, 22 (6), 6778-6790.
[pdf]
J.J. Renema, R. Gaudio, Q. Wang, Z. Zhou, A. Gaggero, F. Mattioli, R. Leoni, D. Sahin, M.J.A. de Dood, A. Fiore, M.P. van Exter (2014) Experimental test of theories of the detection mechanism in a nanowire superconducting single photon detector, Physical Review Letters , 112 (11), 117604.
[pdf]
M.P. Bakker, A.V. Barve, A. Zhan, L.A. Coldren, M.P. van Exter, D. Bouwmeester (2014) Polarization degenerate micropillars fabricated by designing elliptical oxide apertures, Applied Physics Letters, 104 (15), 151109.
[pdf]
Bastiaan Florijn, Corentin Coulais and Martin van Hecke (2014) Programmable Mechanical Metamaterials, Physical Review Letters, 113, 175503.
[pdf]
Eli Wandersman and Martin van Hecke (2014) Nonlocal granular rheology: Role of pressure and anisotropy, EPL, 105, 24002.
[pdf]
D. Hetharia, M. P. van Exter, W. Löffler (2014) The Role of Spatial Coherence and Orbital Angular Momentum of Light in Astronomy, Phys. Rev. A, 90, 063801.
[Abstract] [DOI]
With the help of a laboratory-scale experiment we studied how objects in outer space which "twist" light, such as rotating black holes, could be investigated from earth by observing light's orbital angular momentum in an astronomical telescope. The light is considered to come from a star behind the light-twisting object, and we address here the problem that stars emit spatially incoherent light in contrast to an ideal point source. In this case, the situation is much more complex as there are no simple formulas to calculate how the light propagates, in particular if we are interested how the spatial correlations are modified by our light-twisting astronomical object. But we were able to find a simple intuitive model that agrees well with our experimental data and numerical simulations; this allows us to give guidelines for future astronomical observations. We find that this will be a tough but very interesting challenge.
S. Faez, P. Türschmann, H.R. Haakh, S. Götzinger, and V. Sandoghdar (2014) Coherent Interaction of Light and Single Molecules in a Dielectric Nanoguide, Phys. Rev. Lett., 113, 213601.
[pdf]
S. Kelly, F. Galli, J. Aarts, Shameek Bose, M. Sharma, and C. Leighton (2014) Direct real space observation of magneto-electronic inhomogeneity in ultra-thin film La0.5Sr0.5CoO3−δ on SrTiO3(001), Applied Physics Letters, 105, 112909.
[DOI]
S.J. Kelly, Y. Kim, E. Eliseev, A. Morozovska, S. Jesse, M.D. Biegalski, J.F. Mitchell, H. Zheng, J. Aarts, I. Hwang, S. Oh, J. Sik Choi, T. Choi, B. Ho Park, S.V. Kalinin, P. Maksymovych (2014) Controlled mechnical modification of manganite surface with nanoscale resolution, Nanotechnology, 25 (47), 475302.
[DOI]
Y. Gloaguen, C. Rebreyend, M. Lutz, P. Kumar, M. Huber, J.I. van der Vlugt, S. Schneider, B. de Bruin (2014) An isolated Nitridyl radical-bridged {Rh(N∙)Rh} complex, Angew. Chem. Int. Ed., 53, 6814-6818.
[DOI] [pdf]
M. Hashemi Shabestari, M. van Son, A. Moretto, M. Crisma, C. Toniolo, M. Huber (2014) Conformation and EPR characterization of rigid, 3^10-helical peptides with TOAC spin labels: models for short distances, Peptide Science, 102, 244-251.
[DOI]
M. Hashemi Shabestari, C.J.A.M. Wolfs, R.B. Spruijt, H. van Amerongen, M. Huber (2014) Exploring the structure of the 100 Amino-Acid residue long N-terminus of the plant antenna protein CP29, Biophysical Journal, 106, 1349-1358.
[pdf]
W. Löffler, J. F. Nye, J. Hannay (2014) An experiment on the shifts of reflected C-lines, J. Opt., 16, 085703.
[DOI]
J. B. Götte, W. Löffler, M. R. Dennis (2014) Eigenpolarizations for Giant Transverse Optical Beam Shifts, Phys. Rev. Lett. , 112, 233901.
[DOI]
S Coppola, G Caracciolo and T Schmidt. (2014) Exact occupation probabilities for intermittent transport and application to image correlation spectroscopy., New J. Phys., 16, 113057.
[Abstract] [DOI] [pdf]
Intermittent transport is frequently observed in nature and has been proven to accelerate search processes at both the macroscopic (e.g., animals looking for food) and microscopic scale (e.g., protein-DNA interactions). In living cells, active transport of membrane proteins (e.g., membrane receptors) or intracellular vesicles (organelles) has been extensively studied as an example of intermittent behavior. The intermittent stochastic process is commonly analyzed in terms of first-passage probabilities. Here we derive exact occupation probabilities of intermittent active transport, making such analysis available for image correlation spectroscopy techniques. The power of this new theoretical framework is demonstrated on intracellular trafficking of lipid/DNA nanoparticles in living cells for which we were allowed to quantify switching time scales.
M. Kumar, K. Kumar, and J.M. van Ruitenbeek (2014) Molecule assisted ferromagnetic atomic chain formation, preprint.
[pdf]
J.M. van Ruitenbeek (2014) Introducing the Netherlands’ Physical Society, Il Nuovo Saggiatore, 30, 72-77.
[pdf]
M. Morales, E.A. Miranda, J.M. van Ruitenbeek (2014) Quantum point contact conduction, In : Resistive switching – from fundamentals of nanoionic redox processes to memristive device applications, D. Ielmini and R. Waser, eds, Wiley-VCH, in print.
W. Ahmed, C. Glass, J.M. van Ruitenbeek (2014) Facile synthesis of gold nanoworms with tunable length and aspect ratio through oriental attachment of nanoparticles., Nanoscale, 8, 6, 13222-13227.
[Abstract] [DOI] [pdf]
We report a seedless protocol based on the oriented attachment of nanoparticles for the synthesis of Au nanoworms (NWs). NWs are grown by reducing HAuCl4 with ascorbic acid (AA) in high pH reaction medium and in the presence of growth directional agents, cetyltrimethylammonium bromide (CTAB) and AgNO3. Although we have used the same reducing and growth directional agents as typically used for the synthesis of Au nanorods, the growth mechanism of NWs is markedly different from that of nanorods. Instead of the anisotropic growth of seed particles, the NWs grow through oriented attachment of nanoparticles. By varying different reaction parameters we have seen that the length of NWs can be controlled from tens of nanometers to a micrometer. Furthermore, the aspect ratio (AR) can be tuned from 2 to 30. This is almost the whole range of AR and length for Au nanorods so far achieved with seed-mediated multiple step synthesis protocols.
C. Glass, W. Ahmed, J.M. van Ruitenbeek (2014) Tuning the Morphology of lead zirconate titanate (PZT) Nanostructures., Materials Lett., 6, 125, 71-74.
[Abstract] [DOI] [pdf]
We describe the synthesis of PZT nanoparticles using a hydrothermal method. We demonstrate that the morphology of the PZT nanoparticles can be controlled by tuning the concentration of the mineraliser, KOH. The experimental results show that for low concentrations of KOH (2 M) the reaction kinetics favor a high yield of spherical particles with an average diameter of 5.3 mm. However, higher concentrations of KOH lead to the formation of branched nanostructures containing up to 8 mm long nanorods. TEM and XRD investigations provide evidence that the branches are single crystalline. The influence of KOH concentration on polymer induced particle formation is discussed.
B. C. Hiesmayr and W. Löffler (2014) Mutually Unbiased Bases and Bound Entanglement, Physica Scripta, 04, 2014, 014017.
[DOI]
Sachse R, Dondapati SK, Fenz SF, Schmidt T & Kubick S. (2014) Membrane protein synthesis in cell-free systems: From bio-mimetic systems to bio-membranes., FEBS Lett., 588, 2774-81.
[Abstract] [DOI] [pdf]
When taking up the gauntlet of studying membrane protein functionality, scientists are provided with a plethora of advantages, which can be exploited for the synthesis of these difficult-to-express proteins by utilizing cell-free protein synthesis systems. Due to their hydrophobicity, membrane proteins have exceptional demands regarding their environment to ensure correct functionality. Thus, the challenge is to find the appropriate hydrophobic support that facilitates proper membrane protein folding. So far, various modes of membrane protein synthesis have been presented. Here, we summarize current state-of-the-art methodologies of membrane protein synthesis in biomimetic-supported systems. The correct folding and functionality of membrane proteins depend in many cases on their integration into a lipid bilayer and subsequent posttranslational modification. We highlight cell-free systems utilizing the advantages of biological membranes.
Armando Hernandez-Garcia, Daniela J. Kraft, Anne F.J. Janssen, Paul H. H. Bomans, Nico A.J.M. Sommerdijk, Dominique M.E. Thies-Weesie, Marco E. Favretto, Roland Brock, Frits A. de Wolf, Marc W. T. Werten, Paul van der Schoot, Martien Cohen Stuart & Renko de Vries (2014) Design and self-assembly of simple coat proteins for artificial viruses, Nature Nanotechnology, 8, 9, 698–702.
[DOI]
Carl P. Goodrich, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke, Andrea J. Liu and Sidney R. Nagel (2014) Jamming in finite systems: Stability, anisotropy, fluctuations and scaling, Physical Review E, 90, 022138 Editor.
[pdf]
Merlijn S. van Deen, Johannes Simon, Zorana Zeravcic, Simon Dagois-Bohy, Brian P. Tighe, and Martin van Hecke (2014) Contact changes near jamming, Physical Review E, 90, 020202(R).
[pdf]
S. Mittal, J. Fan, S. Faez, A. Migdall, J. M. Taylor, and M. Hafezi (2014) Topologically Robust Transport of Photons in a Synthetic Gauge Field., Phys.Rev.Lett., 113, 087403.
[Abstract] [DOI] [pdf]
Electronic transport is localized in low-dimensional disordered media. The addition of gauge fields to disordered media leads to fundamental changes in the transport properties. We implement a synthetic gauge field for photons using silicon-on-insulator technology. By determining the distribution of transport properties, we confirm that waves are localized in the bulk and localization is suppressed in edge states. Our system provides a new platform for investigating the transport properties of photons in the presence of synthetic gauge fields.
Hedde van Hoorn, Rolf Harkes, Ewa M. Spiesz, Cornelis Storm, Danny van Noort, Benoit Ladoux, and Thomas Schmidt (2014) The Nanoscale Architecture of Force-Bearing Focal Adhesions., Nano Lett., 14, 4257–4262.
[Abstract] [DOI] [pdf]
The combination of micropillar array technology to measure cellular traction forces with super-resolution imaging allowed us to obtain cellular traction force maps and simultaneously zoom in on individual focal adhesions with single-molecule accuracy. We achieved a force detection precision of 500 pN simultaneously with a mean single-molecule localization precision of 30 nm. Key to the achievement was a two-step etching process that provided an integrated spacer next to the micropillar array that permitted stable and reproducible observation of cells on micropillars within the short working distance of a high-magnification, high numerical aperture objective. In turn, we used the technology to characterize the super-resolved structure of focal adhesions during force exertion. Live-cell imaging on MCF-7 cells demonstrated the applicability of the inverted configuration of the micropillar arrays to dynamics measurements. Forces emanated from a molecular base that was localized on top of the micropillars. What appeared as a single adhesion in conventional microscopy were in fact multiple elongated adhesions emanating from only a small fraction of the adhesion on the micropillar surface. Focal adhesions were elongated in the direction of local cellular force exertion with structural features of 100–280 nm in 3T3 Fibroblasts and MCF-7 cells. The combined measure of nanoscale architecture and force exerted shows a high level of stress accumulation at a single site of adhesion.
A.A. Marten, M. Bux, P.C. Thune, T.H. Oosterkamp, L.C.P.M. de Smet (2014) Detailed AFM force spectroscopy of the interaction between CD44-IgG fusion protein and hayluronan, BioNanoSci, 7, 4, 232-239.
[Abstract] [DOI]
Abstract Atomic force microscopy (AFM) force spectroscopy was used to study the single-molecule rupture events of the interaction between hyaluronan (HA) and the binding domain of its cell surface receptor CD44. AFM probes were amino terminated with 3-aminopropyl triethoxy silane (APTES) followed by covalent coupling of protein A, enabling the binding of the CD44–HA-binding domain, as part of a CD44–Fc fusion protein. HA was covalently bound to APTES-coated silicon surfaces. Single-rupture events were recorded at various loading rates revealing an energy barrier: Eb=24±1 kT and characteristic distance: xβ=1.3±0.1 nm for this interaction. This quantification will be of interest in applications and research involving the use of the CD44–Fc fusion protein since we observe a weaker interaction between HA and CD44–Fc than what has been reported for the entire native CD44 molecule
P. Gast, F.G.J. Broeren, S. Sottini, R. Aoki, A. Takashina, T. Yamaguchi, T. Kohzuma, E.J.J. Groenen (2014) The type 1 copper site of pseudoazurin: Axial and rhombic, J. Inorg. Biochem., 04, 137, 57–63.
[pdf]
M.E. van Royen, W.A. van Cappellen, B. Geverts, T. Schmidt, A.B. Houtsmuller and M.J. Schaaf. (2014) Androgen receptor complexes probe DNA for recognition sequences by short random interactions., J. Cell Sci., 127, 1406-16.
[Abstract] [DOI] [pdf]
Owing to the tremendous progress in microscopic imaging of fluorescently labeled proteins in living cells, the insight into the highly dynamic behavior of transcription factors has rapidly increased over the past decade. However, a consistent quantitative scheme of their action is still lacking. Using the androgen receptor (AR) as a model system, we combined three different fluorescence microscopy assays: single-molecule microscopy, photobleaching and correlation spectroscopy, to provide a quantitative model of the action of this transcription factor. This approach enabled us to distinguish two types of AR-DNA binding: very brief interactions, in the order of a few hundred milliseconds, and hormone-induced longer-lasting interactions, with a characteristic binding time of several seconds. In addition, freely mobile ARs were slowed down in the presence of hormone, suggesting the formation of large AR-co-regulator complexes in the nucleoplasm upon hormone activation. Our data suggest a model in which mobile hormone-induced complexes of transcription factors and co-regulators probe DNA by briefly binding at random sites, only forming relatively stable transcription initiation complexes when bound to specific recognition sequences.
A.M.J. den Haan, G.H.C.J. Wijts, F. Galli, O. Usenko, G.J.C. van Baarle, D.J. van der Zalm, T.H. Oosterkamp (2014) Atomic resolution STM in a cryogen free dilution refrigerator at 15 mK, Rev. Sci. Instrum. , 85, 035112.
F.L. Groeneweg, M.E. van Royen, S. Fenz, V. Keizer, B. Geverts, J. Prins, E.R. de Kloet, A.B. Houtsmuller, T. Schmidt & M.J. Schaaf. (2014) Quantitation of Glucocorticoid Receptor DNA-Binding Dynamics by Single-Molecule Microscopy and FRAP., PLoS One, 9, e90532.
[Abstract] [DOI] [pdf]
Recent advances in live cell imaging have provided a wealth of data on the dynamics of transcription factors. However, a consistent quantitative description of these dynamics, explaining how transcription factors find their target sequences in the vast amount of DNA inside the nucleus, is still lacking. In the present study, we have combined two quantitative imaging methods, single-molecule microscopy and fluorescence recovery after photobleaching, to determine the mobility pattern of the glucocorticoid receptor (GR) and the mineralocorticoid receptor (MR), two ligand-activated transcription factors. For dexamethasone-activated GR, both techniques showed that approximately half of the population is freely diffusing, while the remaining population is bound to DNA. Of this DNA-bound population about half the GRs appeared to be bound for short periods of time (∼0.7 s) and the other half for longer time periods (∼2.3 s). A similar pattern of mobility was seen for the MR activated by aldosterone. Inactive receptors (mutant or antagonist-bound receptors) show a decreased DNA binding frequency and duration, but also a higher mobility for the diffusing population. Likely, very brief (≤1 ms) interactions with DNA induced by the agonists underlie this difference in diffusion behavior. Surprisingly, different agonists also induce different mobilities of both receptors, presumably due to differences in ligand-induced conformational changes and receptor complex formation. In summary, our data provide a consistent quantitative model of the dynamics of GR and MR, indicating three types of interactions with DNA, which fit into a model in which frequent low-affinity DNA binding facilitates the search for high-affinity target sequences.
M. Azarkh, L.V. Penkova, S.V. Kats, O.A. Varzatskii, Y.Z. Voloshin, and E.J.J. Groenen (2014) A Mononuclear Mn(II) Pseudoclathrochelate Complex Studied by Multi-Frequency Electron-Paramagnetic-Resonance Spectroscopy, J. Phys. Chem. Lett., 02, 5, 886-889.
[pdf]
M. B. S. Hesselberth, S. J. van der Molen, and J. Aarts (2014) The surface structure of SrTiO3 at high temperatures under influence of oxygen, APPLIED PHYSICS LETTERS, 104, 051609.
[DOI]
Geert H. Wortel, Joshua A. Dijksman, and Martin van Hecke (2014) Rheology of weakly vibrated granular media, Physical Review E, 89, 012202.
[pdf]
S.F. Fenz, R. Sachse, T. Schmidt & S. Kubick (2014) Cell-free synthesis of membrane proteins: Tailored cell models out of microsomes., Biochim Biophys Acta., 1838, 1382-8.
[Abstract] [DOI] [pdf]
Incorporation of proteins in biomimetic giant unilamellar vesicles (GUVs) is one of the hallmarks towards cell models in which we strive to obtain a better mechanistic understanding of the manifold cellular processes. The reconstruction of transmembrane proteins, like receptors or channels, into GUVs is a special challenge. This procedure is essential to make these proteins accessible to further functional investigation. Here we describe a strategy combining two approaches: cell-free eukaryotic protein expression for protein integration and GUV formation to prepare biomimetic cell models. The cell-free protein expression system in this study is based on insect lysates, which provide endoplasmic reticulum derived vesicles named microsomes. It enables signal-induced translocation and posttranslational modification of de novo synthesized membrane proteins. Combining these microsomes with synthetic lipids within the electroswelling process allowed for the rapid generation of giant proteo-liposomes of up to 50μm in diameter. We incorporated various fluorescent protein-labeled membrane proteins into GUVs (the prenylated membrane anchor CAAX, the heparin-binding epithelial growth factor like factor Hb-EGF, the endothelin receptor ETB, the chemokine receptor CXCR4) and thus presented insect microsomes as functional modules for proteo-GUV formation. Single-molecule fluorescence microscopy was applied to detect and further characterize the proteins in the GUV membrane. To extend the options in the tailoring cell models toolbox, we synthesized two different membrane proteins sequentially in the same microsome. Additionally, we introduced biotinylated lipids to specifically immobilize proteo-GUVs on streptavidin-coated surfaces. We envision this achievement as an important first step toward systematic protein studies on technical surfaces.
Edwin J. Devid, Paulo N. Martinho, Venkata M. Kamalakar, Una Prendergast, Christian Kuebel, Tibebe Lemma, Jean-Francois Dayen, Tia. E. Keyes, Bernard Doudin, Mario Ruben, Sense Jan van der Molen, (2014) The influence of molecular mobility on the properties of networks of gold nanoparticles and organic ligands, BEILSTEIN JOURNAL, 5, 1664–1674.
[DOI]
Sandy Klemm, Stefan Semrau, Kay Wiebrands, Dylan Mooijman, Dina A. Faddah, Rudolf Jaenisch, Alexander van Oudenaarden (2014) Transcriptional profiling of cells sorted by RNA abundance, NATURE METHODS, 11.
[Abstract] [DOI]
e have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of mouse induced pluripotent stem cells (iPSCs) isolated from a heterogeneous reprogramming culture. This method is broadly applicable to profiling transcriptionally distinct cellular states without requiring antibodies or transgenic fluorescent proteins.
Heinrich D, Ecke M, Jasnin M, Engel U, Gerisch G (2014) Reversible membrane pearling in live cells upon destruction of the actin cortex., Biophys. J..
[DOI]
Aquino G, Tweedy L, Heinrich D, Endres RG (2014) Memory improves precision of cell sensing in fluctuating environments., Sci Rep.
[DOI]
T.G.A. Verhagen, D.B. Boltje, J.M. van Ruitenbeek, and J. Aarts (2014) Magnetic properties of Sm-Co thin films grown on MgO(100) from a single alloy target., J. Appl. Phys., 116, 053903.
[Abstract] [DOI] [pdf]
We have grown epitaxial Sm-Co thin films by sputter deposition from a single alloy target with a nominal SmCo5 composition on Cr(100)-buffered MgO(100) single-crystal substrates. By varying the Ar gas pressure, we can change the composition of the film from a SmCo5-like to a Sm2Co7-like phase. The composition, crystal structure, morphology, and magnetic properties of these films have been determined using Rutherford Backscattering, X-ray diffraction, and magnetization measurements. We find that we can grow films with, at room temperature, coercive fields as high as 3.3 T, but with a remanent magnetization which is lower than can be expected from the texturing. This appears to be due to the Sm content of the films, which is higher than expected from the content of the target, even at the lowest possible sputtering pressures. Moreover, we find relatively large variations of film properties using targets of nominally the same composition. At low temperatures, the coercive fields increase, as expected for these hard magnets, but in the magnetization, we observe a strong background signal from the paramagnetic impurities in the MgO substrates.
M.G. Flokstra, S.J. Ray, S.J. Lister, J. Aarts, H. Luetkens, T. Prokscha, A. Suter, E. Morenzoni, and S. L. Lee (2014) Measurement of the spatial extent of inverse proximity in a Py/Nb/Py superconducting trilayer using low-energy muon-spin rotation, Physical Review B , 89, 054510.
[DOI]
Elie Wandersman and Martin van Hecke (2014) Nonlocal Granular Rheology: Role of Pressure and Anisotropy, EPL, 105, 24002.
[pdf]
F. van Beijnum, P.J. van Veldhoven, E.J. Geluk, G.W. ‘t Hooft, and M.P. van Exter (2014) Loss compensation of extraordinary optical transmission, Appl. Phys. Lett., 104, 061112.
[pdf]
S.C. Yorulmaz, M.P. van Exter, M.J.A. de Dood (2014) The role of spatial and temporal modes in pulsed parametric down-conversion, Optics Express, 22, Issue 5, 5913-5926.
[pdf]
F. van Beijnum. A.S. Meeussen, C. Retif, and M.P. van Exter (2014) Rayleigh scattering of surface plasmons by sub-wavelength holes, Optics Express.
O. Beutel, J. Nikolaus, O. Birkholz, C. You, T. Schmidt, A. Herrmann and J. Piehler. (2014) High-fidelity protein targeting into membrane lipid microdomains in living cells., Angew Chem Int Ed Engl., 53, 1311-1315.
[Abstract] [DOI] [pdf]
Lipid analogues carrying three nitrilotriacetic acid (tris-NTA) head groups were developed for the selective targeting of His-tagged proteins into liquid ordered (lo ) or liquid disordered (ld ) lipid phases. Strong partitioning into the lo phase of His-tagged proteins bound to tris-NTA conjugated to saturated alkyl chains (tris-NTA DODA) was achieved, while tris-NTA conjugated to an unsaturated alkyl chain (tris-NTA SOA) predominantly resided in the ld phase. Interestingly, His-tag-mediated lipid crosslinking turned out to be required for efficient targeting into the lo phase by tris-NTA DODA. Robust partitioning into lo phases was confirmed by using viral lipid mixtures and giant plasma membrane vesicles. Moreover, efficient protein targeting into lo and ld domains within the plasma membrane of living cells was demonstrated by single-molecule tracking, thus establishing a highly generic approach for exploring lipid microdomains in situ.
P. Gast, F.G.J. Broerena, S. Sottinia, R. Aokib, A. Takashinab, T. Yamaguchib, T. Kohzumab, E. J.J. Groenena (2014) The type 1 copper site of pseudoazurin: Axial and rhombic, J. Inorg. Biochem., 137, 57–63.
[pdf]
P. Gast, R. T. L. Herbonnet, J. Klare, A. Nalepa, C. Rickert, D. Stellinga, L. Urban, K. Möbius, A. Savitsky, H.-J. Steinhoff and E. J. J. Groenen (2014) Hydrogen bonding of nitroxide spin labels in membrane proteins, Phys. Chem. Chem. Phys., 06, 16, 15910.
[Abstract] [DOI] [pdf]
On the basis of experiments at 275 GHz, we reconsider the dependence of the continuous-wave EPR spectra of nitroxide spin-labeled protein sites in sensory- and bacteriorhodopsin on the micro-environment. The high magnetic field provides the resolution necessary to disentangle the effects of hydrogen bonding and polarity. In the gxx region of the 275 GHz EPR spectrum, bands are resolved that derive from spin-label populations carrying no, one or two hydrogen bonds. The gxx value of each population varies hardly from site to site, significantly less than deduced previously from studies at lower microwave frequencies. The fractions of the populations vary strongly, which provides a consistent description of the variation of the average gxx and the average nitrogen-hyperfine interaction Azz from site to site. These variations reflect the difference in the proticity of the micro-environment, and differences in polarity contribute marginally. Concomitant W-band ELDOR-detected NMR experiments on the corresponding nitroxide in perdeuterated water resolve population-specific nitrogen-hyperfine bands, which underlies the interpretation for the proteins.
Liu, Z., Galli, F., Janssen, K., Jiang, ., Linhua,, van der Linden, H.J., de Geus, D., Voskamp, P., Kuil, M., Olsthoorn, R., Oosterkamp, T., Hankemeier, T., Abrahams, J.P. (2014) Stable Single Walled Carbon Nanotube•Streptavidin Complex for Bio–Recognition, The Journal of Physical Chemistry ..
Zunfeng Liu ,Federica Galli, Willem-Jan Waterreus, Elisabeth Meulenbroek, Roman I. Koning, Gerda E. M. Lamers, René C. L. Olsthoorn, Navraj Pannu, Tjerk. H. Oosterkamp, Abraham J. Koster, Remus Th. Dame, Jan Pieter Abrahams (2014) Single Walled Carbon Nanotubes as a Scaffold to Concentrate  DNA for Studying DNA-Protein Interactions, .
B.A. Ashcroft, J. de Sonneville, Y. Yuana, S. Osanto, R. Bertina, M.E. Kuil, T.H. Oosterkamp (2014) Determination of the size distribution of blood microparticles directly in plasma using atomic force microscopy and microfluidics, Biomed. Microdevices.
O. Balmes, A. Resta, D. Wermeille, R. Felici, M.E. Messing, K. Deppert, Z. Liu, M.E. Grass, H. Bluhm, R. van Rijn, J.W.M. Frenken, R. Westerström, S. Blomberg, J. Gustafson, J.N. Andersen, E. Lundgren (2014) Reversible formation of a PdCx phase in Pd nanoparticles upon CO and O2 exposure, PCCP .
Jelmer J.T. Wagenaar, Monica Morales-Masis, and Jan M. van Ruitenbeek (2014) Observing 'quantized' conductance steps in silver sulfide: two parallel resistive switching mechanisms., .
N. Markesevic, S.S.R. Oemrawsingh, D. Schultz, E.G. Gwinn, D. Bouwmeester (2014) Polarization resolved measurements of individual DNA-stabilized silver clusters, Adv. Optical Mater.
[pdf]
Tabares LC, Gupta A, Aartsma TJ, Canters GW (2014) Tracking electrons in biological macromolecules: from ensemble to single molecule., Molecules.
[DOI]
Jendrny M, Aartsma TJ, Köhler J (2014) Insights into the excitonic states of individual chlorosomes from Chlorobaculum tepidum., Biophys. J..
[DOI]
Kamran M, Delgado JD, Friebe V, Aartsma TJ, Frese RN (2014) Photosynthetic protein complexes as bio-photovoltaic building blocks retaining a high internal quantum efficiency., Biomacromolecules.
[DOI]
Gupta A, Aartsma TJ, Canters GW (2014) One at a time: intramolecular electron-transfer kinetics in small laccase observed during turnover., J. Am. Chem. Soc..
[DOI]
Sanli Faez, Sense Jan van der Molen, Michel Orrit (2014) Optical tracing of multiple charges in single-electron devices, PHYSICAL REVIEW B, 90, 205405.
[DOI]
J. Kautz, M.W. Copel, M.S. Gordon, R.M. Tromp, S.J. van der Molen (2014) Titration of submonolayer Au growth on Si(111), PHYSICAL REVIEW B, 89, 035416 .
[DOI]
Hennie Valkenier, Constant Guedon, Troels M. Markussen, Kristian S. Thygesen, Sense Jan van der Molen, Jan C. Hummelen (2014) Cross-conjugation and quantum interference: a general correlation?, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16, 653-662.
[DOI]

2013
Shabestari, T. Plug, M. M. Motazacker, N. J. Meeuwenoord, D. V. Filippov, J. C. M. Meijers, M. Huber (2013) The Aggregation Potential of the 1–15- and 1–16-Fragments of the Amyloid β Peptide and Their Influence on the Aggregation of Aβ40, Applied Magnetic Resonance, 44, 1345-1345.
[DOI] [pdf]
Martina Huber (2013) EPR approaches to disorder in proteins, Electron Paramagnetic Resonance, 23, 79–102 .
[DOI] [pdf]
Orrit M (2013) Towards a molecular view of glass heterogeneity., Angew. Chem. Int. Ed. Engl., 52, 163–166.
[DOI]
Khatua S, Orrit M (2013) Toward single-molecule microscopy on a smart phone., ACS Nano, 7, 8340–8343.
[DOI]
Yu K, Zijlstra P, Sader JE, Xu QH, Orrit M (2013) Damping of acoustic vibrations of immobilized single gold nanorods in different environments., Nano Lett., 13, 2710–2716.
[DOI]
B. van den Broek, B.A. Ashcroft, T.H. Oosterkamp, J. van Noort (2013) Parallel nanometric 3D tracking of intracellular gold nanorods using multifocal two-photon microscopy, Nano Lett., 13, 980-986.
[DOI] [pdf]
G.J. Verbiest, T.H. Oosterkamp, M.J. Rost (2013) Subsurface-AFM: sensitivity to the heterodyne signal, Nanotechnology, 24, 365701.
[DOI] [pdf]
G.J. Verbiest, T.H. Oosterkamp, M.J. Rost (2013) Cantilever dynamics in heterodyne force microscopy., Ultramicroscopy, 135, 113-120.
[DOI]
Wang Q, de Dood MJ. (2013) An absorption-based superconducting nano-detector as a near-field optical probe, Opt. Express, 21, 3682.
[DOI]
de Man, S and Gonzalez-Silveira, M and Visser, D and Bakker, R and Schreuders, H and Baldi, A and Dam, B and Griessen, R (2013) Combinatorial method for direct measurements of the intrinsic hydrogen permeability of separation membrane materials, Journal of Membrane Science, 444, 70.
[DOI]
G. Nienhuis (2013) Ray optics, wave optics and quantum mechanics, in: The Angular Momentum of Light, D.L. Andrews and M. Babiker, eds. (Cambridge University Press, Cambridge, 2013) , 98-134.
[DOI]
A.M. Nugrowati, J.P. Woerdman (2013) Non-integer OAM beam shifts of Hermite–Laguerre–Gaussian beams, Opt. Commun., 308, 253.
[DOI]
M G Blamire, C B Smiet, N Banerjee and J W A Robinson (2013) Field modulation of the critical current in magnetic Josephson junctions, Supercond. Sci. Technol., 26, 055017.
[DOI]
M.P. van Exter, E.R. Eliel, J.P. Woerdman (2013) Quantum entanglement of orbital angular momentum, “The Angular Momentum of Light”, D.L. Andrews and M. Babiker, eds. (Cambridge University Press, Cambridge, 2013), 385-406.
Daniela J. Kraft, Raphael Wittkowski, Borge ten Hagen, Kazem V. Edmond, David J. Pine, and Hartmut Löwen (2013) Brownian motion and the hydrodynamic friction tensor for colloidal particles of complex shape, Physical Review E, 11, 88, 050301(R).
[DOI]
Manohar Kumar, Oren Tal, Roel H. M. Smit, Alexander Smogunov, Erio Tosatti, and Jan M. van Ruitenbeek (2013) Shot noise and magnetism of Pt atomic chains: Accumulation of points at the boundary, Phys. Rev. B, 12, 88, 245431.
[Abstract] [DOI] [pdf]
Pt is known to show spontaneous formation of monatomic chains upon breaking a metallic contact. From model calculations, these chains are expected to be spin polarized. However, direct experimental evidence for or against magnetism is lacking. Here, we investigate shot noise as a potential source of information on the magnetic state of Pt atomic chains. We observe a remarkable structure in the distribution of measured shot-noise levels, where the data appear to be confined to the region of nonmagnetic states. While this suggests a nonmagnetic ground state for the Pt atomic chains, from calculations we find that the magnetism in Pt chains is due to “actor” electron channels, which contribute very little to ballistic conductance and noise. On the other hand, there are weakly polarized “spectator” channels, which carry most of the current and are only slightly modified by the magnetic state.
Waqqar Ahmed, Christian Glass, E. Stefan Kooij and Jan M. van Ruitenbeek (2013) Tuning the deposition of gold nanorods on patterned substrates, Nanotechnology, 12, 25, 035301.
[Abstract] [DOI] [pdf]
The controlled patterning of anisotropic gold nanoparticles is of crucial importance for many applications related to their optical properties. In this paper, we report that gold nanorods prepared by a seed-mediated synthesis protocol (without any further functionalization) can be selectively deposited on hydrophilic parts of hydrophobic–hydrophilic contrast patterned substrates. We have seen that, when nanorods with lengths much smaller than the width of the hydrophilic stripe are used, they disperse on these stripes with random orientation and tunable uniform particle separation. However, for nanorods having lengths comparable to the width of the hydrophilic stripes, confinement-induced alignment occurs. We observe that different interactions governing the assembly forces can be modulated by controlling the concentration of assembling nanorods and the width of the hydrophilic stripes, leading to markedly different degrees of alignment. Our strategy can be replicated for other anisotropic nanoparticles to produce well-controlled patterning of these nanoentities on surfaces.
N.V. Khotkevych, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek (2013) Fermi surface contours obtained from scanning tunnelling microscope images around surface point defects, New J. Phys., 12, 15, 123013.
[Abstract] [DOI] [pdf]
We present a theoretical analysis of the standing wave patterns in scanning tunneling microscope (STM) images, which occur around surface point defects. We consider arbitrary dispersion relations for the surface states and calculate the conductance for a system containing a small-size tunnel contact and a surface impurity. We find rigorous theoretical relations between the interference patterns in the real-space STM images, their Fourier transforms and the Fermi contours of two-dimensional electrons. We propose a new method for reconstructing Fermi contours of surface electron states, directly from the realspace STM images around isolated surface defects.
Siet van den Wildenberg, Rogier van Loo, and Martin van Hecke (2013) Shock Waves in Weakly Compressed Granular Media, Physical Review Letters, 111, 218003.
[pdf]
P.G. van Rhee, P. Zijlstra, T.G.A. Verhagen, J. Aarts, M.I. Katsnelson, J.C. Maan, M. Orrit and P.C.M. Christianen (2013) Giant Magnetic Susceptibility of Gold Nanorods Detected by Magnetic Alignment, Physical Review Letters, 9, 111, 127202.
[DOI]
Gijs Katgert, Brian P. Tighe and Martin van Hecke (2013) The jamming perspective on wet foams, Soft Matter, C3sm, 51543e.
[pdf]
G.J. Verbiest, T.H. Oosterkamp, M.J. Rost (2013) Cantilever dynamics in heterodyne force microscopy., Ultramicroscopy, 7, 135, 113-120.
N.V. Khotkevych, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek (2013) Electron tunneling into surface states through an inhomogeneous barrier: asymptotically exact solution of the problem and STM theory, Low Temp. Phys., 3, 39, 384-389.
[Abstract] [DOI] [pdf]
We have found an asymptotically exact solution of the Schrödinger equation for electrons tunneling into surface states through an inhomogeneous barrier of large amplitude. Assuming an elliptic dispersion law for the charge carriers the “standing wave” pattern in the conductance of the system resulting from the electron scattering by a single defect in the vicinity of the surface is analyzed.
E. Tartaglini, T.G.A. Verhagen, F. Galli, M.L. Trouwborst, R. Müller, T. Shiota, J. Aarts, and J. M. van Ruitenbeek (2013) New Directions in Point Contact Spectroscopy based on Scanning Tunneling Microscopy techniques, Low Temp. Phys., 3, 39, 249-260.
[Abstract] [DOI] [pdf]
Igor Yanson showed 38 years ago for the first time a point-contact measurement where he probed the energy resolved spectroscopy of the electronic scattering inside the metal. Since this first measurement, the pointcontact spectroscopy (PCS) technique improved enormously. The application of the scanning probe microscopy (SPM) techniques in the late 1980s allowed achieving contacts with a diameter of a single atom. With the introduction of the mechanically controlled break junction technique, even spectroscopy on freely suspended chains of atoms could be performed. In this paper, we briefly review the current developments of PCS and show recent experiments in advanced scanning PCS based on SPM techniques. We describe some results obtained with both needle-anvil type of point contacts and scanning tunneling microscopy (STM). We also show our first attempt to lift up with a STM a chain of single gold atoms from a Au(110) surface.
I.M. Dildar, D.B. Boltje, M.H.S. Hesselberth, J. Aarts, Q. Xu, H.W. Zandbergen,and S. Harkema (2013) Non-conducting interfaces of LaAlO3/SrTiO3 produced in sputter deposition: The role of stoichiometry, Applied Physics Letters, 102, 121601.
[DOI]
Mickael L. Perrin, Christopher.J.O. Verzijl, Christian A. Martin, Ahson J. Shaikh, Rienk Eelkema, Jan H. van Esch, Jan M. van Ruitenbeek, Jos M. Thijssen, Herre S. J. van der Zant, Diana Dulić (2013) Large tunable image charge effects in single-molecule junctions, Nature Nanotechnology, 3, 8, 282-287.
[Abstract] [DOI] [pdf]
Metal/organic interfaces critically determine the characteristics of molecular electronic devices, because they influence the arrangement of the orbital levels that participate in charge transport. Studies on self-assembled monolayers show molecule-dependent energy-level shifts as well as transport-gap renormalization, two effects that suggest that electricfield polarization in the metal substrate induced by the formation of image charges plays a key role in the alignment of the molecular energy levels with respect to the metal’s Fermi energy. Here, we provide direct experimental evidence for an electrode-induced gap renormalization in single-molecule junctions. We study charge transport through single porphyrintype molecules using electrically gateable break junctions. In this set-up, the position of the occupied and unoccupied molecular energy levels can be followed in situ under simultaneous mechanical control. When increasing the electrode separation by just a few a˚ngstro¨ms, we observe a substantial increase in the transport gap and level shifts as high as several hundreds of meV. Analysis of this large and tunable gap renormalization based on atomic charges obtained from density functional theory confirms and clarifies the dominant role of image-charge effects in single-molecule junctions.
S. van den Wildenberg, M. van Hecke and X. Jia (2013) Evolution of Granular Packings by Nonlinear Acoustic Waves, EPL, 101, 14004.
[pdf]
W. Löffler, N. Hermosa, A. Aiello, and J.P. Woerdman (2013) Total internal reflection of orbital angular momentum beams, J. Opt., 15, 014012.
[pdf]
J. Götte, M. Hentschel, and W. Löffler (2013) Beyond catoptrics, J. Opt., 15, 010301.
[pdf]
G. Hartland, H.Okamoto, M.Orrit, P. Zijlstra (2013) Optical studies of single metal nanoparticles, Phys. Chem. Chem. Phys., 15, 4090-4092.
[pdf]
A.A.L. Nicolet, M.A. Kol'chenko, C. Hofmann, B. Kozankiewicz, M. Orrit (2013) Nanoscale probing of charge transport in an organic field-effect transistor at cryogenic temperatures, Phys. Chem. Chem. Phys., 15, 4415-4421.
[pdf]
H.Yuan, S.Khatua, P. Zijlstra,M. Yorulmaz, M. Orrit (2013) Thousand-fold enhancement of single-molecule fluorescence near a single gold nanorod, Angew. Chem. Int. Ed., 52, 1217-1221.
[pdf]
M. Orrit (2013) Towards a molecular view of glass heterogeneity, Angew. Chem. Int. Ed., 52, 163-166.
[pdf]
C. Bonato, J. Hagemeier, D. Gerace, S.M. Thon, H. Kim, L.C. Andreani, P.M. Petroff, M.P. van Exter, D. Bouwmeester (2013) far-field emission profiles from L3 photonic crystal cavity modes, Photonics and Nanostructures-Fundamentals and Applications, 11, Issue 1, 37-47.
[pdf]
Fall, A., de Cagny, H., Bonn, D., Ovarlez, G., Wandersman, E., Dijksman, J.A., van Hecke, M. (2013) Rheology of sedimenting particle pastes, Journal of Rheology, 57, 1237.
[pdf]
K.A. Yates, M.S. Anwar, J. Aarts, O. Conde, M. Eschrig, T. Löfwander and L.F. Cohen (2013) Andreev spectroscopy of CrO2 thin films on TiO2 and Al2O3, EPL, 9, 103, 67005.
K.A. Yates, M.S. Anwar, J. Aarts, O. Conde, M. Eschrig, T. Löfwander and L.F. Cohen (2013) Andreev spectroscopy of CrO2 thin films on TiO2 and Al2O3, EPL, 103, 67005.
[DOI]
M.P. van Exter, V.T. Tenner, F. van Beijnum, M.J.A. de Dood, P.J. van Veldhoven, E.J. Geluk, G.W. 't Hooft (2013) Surface plasmon dispersion in metal hole array lasers, Optics Express, 21 Issue 22, 27422-27437.
[pdf]
D. Schultz, S.M. Copp, N. Markesevic, K. Gardner, S.S.R. Oemrawsingh, D. Bouwmeester, E. Gwinn (2013) Dual-color nanoscale assemblies of structurally stable, few-atom silver clusters, as reported by fluorescence resonance energy transfer, ACS Nano, 7 Issue 11, 9798-9807.
[pdf]
D. Geelen, W. Löffler (2013) Walsh modes and radial quantum correlations of spatially entangled photons, Optics Letters, 38, Issue 20, 4108-4111.
[pdf]
P.F. Chimento, P.F.A. Alkemade, G.W. 't Hooft, E.R. Eliel (2013) Optical angular momentum conversion in a nanoslit: reply, Optics Letters, 38, Issue 19, 3891-3891.
[pdf]
M.P. Bakker, D.J. Suntrup, H. Snijders, T.A. Truong, P.M. Petroff, D. Bouwmeester, M.P. van Exter (2013) Fine tuning of micropillar cavity modes through repetitive oxidations, Optics Letters, 38, Issue 17, 3308-3311.
[pdf]
B.C. Hiesmayr, W. Löffler (2013) Complementarity reveals bound entanglement of two twisted phonons, New Journal of Physics, 15, 083036.
[pdf]
J.J. Renema, G. Frucci, Z. Zhou, F. Mattioli, A. Gaggero, R. Leoni, M.J.A. de Dood, A. Fiore, M.P. van Exter (2013) Universal response curve for nanowire superconducting single-photon detectors, Physical Review B, 87, Issue 17, 174526.
[pdf]
S.J. van der Molen (2013) Single-atom switches: Toggled with electrical current., NAT NANOTECHNOL, 8, 622–623.
[DOI]
D. Schultz, K. Gardner, S.S.R. Oemrawsingh, N. Markesevic, K. Olsson, M. Debord, D. Bouwmeester, E. Gwinn (2013) Evidence for rod-shaped DNA-stabilized silver nanocluster emitters, Advanced Materials, 25, Issue 20, 2797-2803.
[pdf]
F. van Beijnum, P.J. van Veldhoven, E.J. Geluk, M.J.A. de Dood, G.W. 't Hooft, M.P. van Exter (2013) Surface plasmon lasing observed in metal hole arrays, Physical Review Letters, 110, Issue 20, 206802.
[pdf]
M.P. Bakker, D.J. Suntrup, H. Snijders, T.A. Truong, P.M. Petroff, M.P. van Exter, D. Bouwmeester (2013) Monitoring the formation of oxide apertures in micropillar cavities, Applied Physics Letters, 102, Issue 10, 101109.
[pdf]
Q. Wang, M.J.A. de Dood (2013) An absorption-based superconducting nano-detector as a near-field optical probe, Optics Express, 21, Issue 3, 3682-3692.
[pdf]
M. van Wijk, M. Dienwiebel, J.W.M. Frenken, A. Fasolino (2013) Superlubric to stick-slip sliding of incommensurate graphene flakes on graphite, Phys. Rev. B, 88, 235423.
E. Tartaglini, T. G. A. Verhagen, F. Galli, M. L. Trouwborst, R. Müller, T. Shiota, J. Aarts and J. M. van Ruitenbeek (2013) New directions in point-contact spectroscopy based on scanning tunneling microscopy techniques (Review Article), Fizika Nizkikh Temperatur , 39, 249-260 .
M.S. Anwar and J. Aarts (2013) Anomalous transport in half-metallic ferromagnetic CrO2, Phys. Rev. B. , 88, 085123 .
[DOI]
J. M. Giesbers, K. Uhlirova, M. Konecny, E. C. Peters, M. Burghard, J. Aarts, C. F. J. Flipse (2013) Interface-Induced Room-Temperature Ferromagnetism in Hydrogenated Epitaxial Graphene, Phys. Rev. Lett. , 111, 166101.
[DOI]
Yunseok Kim, Simon J. Kelly, Anna Morozovska, Ehsan Kabiri Rahani, Evgheni Strelcov, Eugene Eliseev, Stephen Jesse, Michael D. Biegalski, Nina Balke, Nicole Benedek, Dmitri Strukov, J. Aarts, Inrok Hwang, Sungtaek Oh, Jin Sik Choi, Taekjib Choi, Bae Ho Park, Vivek B. Shenoy, Peter Maksymovych, and Sergei V. Kalinin (2013) Mechanical Control of Electroresistive Switching, Nanoletters , 13, 4068-4074.
[DOI]
B.E. Snaar-Jagalska, A. Cambi, T. Schmidt & S. de Keijzer. (2013) Single-molecule imaging technique to study the dynamic regulation of GPCR function at the plasma membrane., Methods Enzymol., 521, 47-67.
[Abstract] [DOI] [pdf]
The lateral diffusion of a G-protein-coupled receptor (GPCR) in the plasma membrane determines its interaction capabilities with downstream signaling molecules and critically modulates its function. Mechanisms that control GPCR mobility, like compartmentalization, enable a cell to fine-tune its response through local changes in the rate, duration, and extent of signaling. These processes are known to be highly dynamic and tightly regulated in time and space, usually not completely synchronized in time. Therefore, bulk studies such as protein biochemistry or conventional confocal microscopy will only yield information on the average properties of the interactions and are compromised by poor time resolution. Single-particle tracking (SPT) in living cells is a key approach to directly monitor the function of a GPCR within its natural environment and to obtain unprecedented detailed information about receptor mobility, binding kinetics, aggregation states, and domain formation. This review provides a detailed description on how to perform single GPCR tracking experiments.
Dupont, A. Gorelashvili, M. Schueller, V. Wehnekamp, F. Arcizet, D. Katayama, Y. Lamb, D. C. Heinrich, D. (2013) Three-dimensional single-particle tracking in live cells: news from the third dimension, NEW JOURNAL, 15.
[Abstract] [DOI]
Single-particle tracking (SPT) is of growing importance in the biophysical community. It is used to investigate processes such as drug and gene delivery, viral uptake, intracellular trafficking or membrane-bound protein mobility. Traditionally, SPT is performed in two dimensions (2D) because of its technical simplicity. However, life occurs in three dimensions (3D) and many methods have been recently developed to track particles in 3D. Now, is the third dimension worth the effort? Here we investigate the differences between the 2D and 3D analyses of intracellular transport with the 3D development of a time-resolved mean square displacement (MSD) analysis introduced previously. The 3D trajectories, and the 2D projections, of fluorescent nanoparticles were obtained with an orbital tracking microscope in two different cell types: in Dictyostelium discoideum ameba and in adherent, more flattened HuH-7 human cells. As expected from the different 3D organization of both cells' cytoskeletons, a third of the active transport was lost upon projection in the ameba whereas the identification of the active phases was barely affected in the HuH-7 cells. In both cell types, we found intracellular diffusion to be anisotropic and the diffusion coefficient values derived from the 2D analysis were therefore biased.
Tweedy, L Meier, B Stephan, J Heinrich, D Endres, RG (2013) Distinct cell shapes determine accurate chemotaxis, SCIENTIFIC REPORTS, 3.
[Abstract] [DOI]
The behaviour of an organism often reflects a strategy for coping with its environment. Such behaviour in higher organisms can often be reduced to a few stereotyped modes of movement due to physiological limitations, but finding such modes in amoeboid cells is more difficult as they lack these constraints. Here, we examine cell shape and movement in starved Dictyostelium amoebae during migration toward a chemoattractant in a microfluidic chamber. We show that the incredible variety in amoeboid shape across a population can be reduced to a few modes of variation. Interestingly, cells use distinct modes depending on the applied chemical gradient, with specific cell shapes associated with shallow, difficult-to-sense gradients. Modelling and drug treatment reveals that these behaviours are intrinsically linked with accurate sensing at the physical limit. Since similar behaviours are observed in a diverse range of cell types, we propose that cell shape and behaviour are conserved traits. C1 [Tweedy, Luke; Endres, Robert G.] Univ London Imperial Coll Sci Technol & Med, Dept Life Sci, London, England. [Tweedy, Luke; Endres, Robert G.] Univ London Imperial Coll Sci Technol & Med, Ctr Integrat Syst Biol & Bioinformat, London, England. [Meier, Boern; Stephan, Juergen; Heinrich, Doris] Univ Munich, Fac Phys, Munich, Germany. [Meier, Boern; Stephan, Juergen; Heinrich, Doris] Univ Munich, Ctr Nanosci CeNS, Munich, Germany. [Heinrich, Doris] Leiden Univ, Leiden Inst Phys, Leiden, Netherlands.
Sense Jan van der Molen, Ron Naaman, Elke Scheer, Jeffrey B. Neaton , Abraham Nitzan, Douglas Natelson, N. J. Tao, Herre van der Zant, Marcel Mayor, Mario Ruben, Mark Reed, Michel Calame, (2013) Visions for a molecular future, NATURE NANOTECHNOLOGY, 8, 385–389.
[DOI]
Jean-Francois Dayen, Edwin Devid, Mutta Venkata Kamalakar, Dmitry Golubev, Constant Guedon, Vina Faramarzi, Bernard Doudin, Sense Jan van der Molen (2013) Enhancing the Molecular Signature in Molecule-Nanoparticle Networks Via Inelastic Cotunneling, ADVANCED MATERIALS, 25, 400–404 .
[DOI]

2012
J.W.M. Beenakker, B.A. Ashcroft, J.H.N. Lindeman, T.H. Ooosterkamp (2012) Mechanical properties of the extracellular matrix of the aorta studied by enzymatic treatments, Biophys. J., 102, 1731-1737.
[DOI] [pdf]
B.A. Ashcroft, J. de Sonneville, Y. Yuana, S. Osanto, R. Bertine, M.E. Kuijl, T.H. Oosterkamp (2012) Determination of the size distribution of blood microparticles directly in plasma using atomic force microscopy and microfluids, Biomedical Microdevices, 14, 641-649.
[DOI] [pdf]
M. Robotta, C. Hintze, S. Schildknecht, N. Zijlstra, C. Jüngst, C. Karreman, M. Huber, M. Leist, V. Subramaniam, M. Drescher (2012) Locally resolved membrane binding affinity of the N-terminus of α-synuclein, Biochemistry, 51, 3960-3962.
[DOI]
Daniela J. Kraft, Willem K. Kegel, Paul van der Schoot (2012) A Kinetic Zipper Model and the Assembly of Tobacco Mosaic Virus, Biophysical Journal , 6, 102 (12), 2845-2855.
[DOI]
Daniela J. Kraft, Ran Ni, Frank Smallenburg, Michiel Hermes, Kisun Yoon, David A. Weitz, Alfons van Blaaderen, Jan Groenewold, Marjolein Dijkstra, and Willem K. Kegel (2012) Surface roughness directed self-assembly of patchy particles into colloidal micelles, PNAS, Highlighted on the Cover, 109 (27), 10787-10792.
[DOI]
I. Mubeen Dildar, C. Beekman, Xin He, and J. Aarts (2012) Hall effect measurements on strained and unstrained thin films of La0.7Ca0.3MnO3 and La0.7Sr0.3MnO3, PHYSICAL REVIEW B, 85, 205103.
[DOI]
M.S. Anwar, M. Veldhorst, A. Brinkman and J. Aarts (2012) Long range supercurrents in ferromagnetic CrO2 using a multilayer contact structure, APPLIED PHYSICS LETTERS , 100, 052602.
[DOI]
I. M. Dildar, D. Boltje, M. Hesselberth, Q. Xu, H. Zandbergen, S. Harkema, J. Aarts (2012) Conductivity of LaAlO3/SrTiO3 Interfaces Made by Sputter Deposition, e-Journal of Surface Science and Nanotechnology, 10, 619-623.
[DOI]
S.F. Fenz, A. Pezzarossa and T. Schmidt (2012) The Basics and Potential of Single-Molecule Tracking in Cellular Biophysics., In: Edward H. Egelman, editor: Comprehensive Biophysics - Biophysical Techniques, 2, 260-272.
[pdf]
Gustiananda, M, Andreoni, A, Tabares, LC, Tepper, AWJW, Fortunato, L, Aartsma, TJ, Canters, GW (2012) Sensitive detection of histamine using fluorescently labeled, BIOSENSORS & BIOELECTRONICS, 31, 419-425.
[DOI]
Elmalk, AT, Salverda, JM, Tabares, LC, Canters, GW, Aartsma, TJ (2012) Probing redox proteins on a gold surface by single molecule fluorescence, JOURNAL OF CHEMICAL PHYSICS, 136, 3745-3750.
[DOI]
Jendrny, M, Aartsma, TJ, Kohler, J (2012) Fluorescence Excitation Spectra from Individual Chlorosomes of the Green, JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3, 3745-3750.
[DOI]
L.R. Gomez, A.M. Turner, M. van Hecke, and V. Vitelli (2012) Shocks near Jamming, Phys. Rev. Lett, 108, 058001.
[pdf]
J.A. Dijksman, F. Rietz, K. Lorincz, M. van Hecke and W. Losert (2012) Refractive Index Matched Scanning of Dense Granular Materials, Rev. Sci. Instr., 83, 011301 .
[pdf]
S. Slotterback, M. Mailman, K. Ronaszegi, M. van Hecke, M. Girvan, W. Losert (2012) Onset of Irreversibility in Cyclic Shear of Granular Packings, Phys. Rev. E , 85, 021309 .
[pdf]
M van Hecke (2012) Running on Cornflour, Nature, 487, 174 .
[pdf]
K. Nichol and M van Hecke (2012) Flow Induced Fluctuations Create a Granular Fluid-Effective Viscosity and Fluctuations, Phys. Rev. E, 85, 061309 .
[pdf]
S. Dagois-Bohy, B.P. Tighe, J. Simon, S. Henkes and M. van Hecke (2012) Soft Sphere Packings at Finite Pressure but Unstable to Shear, Phys. Rev. Lett., 109, 095703 .
[pdf]
E. Wandersman J. A. Dijksman and M. van Hecke (2012) Particle diffusion in slow granular bulk flows, EPL editors choice), 100, 38006.
[pdf]
(2012) Highly Conductive Molecular Junctions Based on Direct Binding of Benzene to Platinum Electrodes., Phys. Rev. Lett. , 109, 046801.
[DOI] [pdf]
N.V. Khotkevych and Yu.A. Kolesnichenko, and J.M. van Ruitenbeek (2012) Theory of scanning tunneling spectroscopy of thin films., Low Temperature Physics (Kharkiv) , 38.
Jelmer J.T. Wagenaar, Monica Morales-Masis, and Jan M. van Ruitenbeek (2012) Observing quantized conductance steps in silver sulfide: two parallel resistive switching mechanisms., J. Appl. Phys., 111, 014302 .
[pdf]
Manohar Kumar, Rémi Avriller, Alfredo Levy Yeyati, and Jan M. van Ruitenbeek (2012) Detection of vibration mode scattering in electronic shot noise., Phys. Rev. Lett. , 108.
[DOI] [pdf]
J.M. van Ruitenbeek (2012) Viewpoint: High Currents, When Hot, Physics , 5, 85 .
[pdf]
Jan van Ruitenbeek (2012) Dispersion forces unveiled, Nature Materials , 11, 834-835 .
[pdf]
S.C. Yorulmaz and M.J.A. de Dood, (2012) Characterization of parametric down-conversion in periodically-poled KTP crystals with a picosecond pump, SPIE proc., Vol. 8440, 84400G.
[pdf]
B. Wang, X.J. Wang, M.J.A. de Dood, R.M. Guo, L. Wang, M. Vanhoutte, J. Michel, L.C. Kimerling, and Z Zhou (2012) Photoluminescence quantum efficiency and energy transfer of ErRE silicate (RE = Y, Yb) thin films, J. Phys. D: Appl. Phys., 45, 165101.
[pdf]
A. Vinante, A. Kirste, A. den Haan, O, Usenko, G. Wijts, E. Jeffrey, P. Sonin, D. Bouwmeester, and T.H. Oosterkamp (2012) High sensitivity SQUID-detection and feedback-cooling of an ultrasoft microcantilever, Appl. Phys. Lett., 101, 123101.
[pdf]
A.J.H. van der Torren, S.C. Yorulmaz, J.J. Renema, M.P. van Exter, and M.J.A. de Dood, (2012) Spatially entangled four-photon states from a periodically poled potassium-titanyl-phosphate crystal, Phys. Rev. A, 85, 043837.
[pdf]
T. van der Sar, J. Hagemeier, W. Pfaff, E.C. Heeres, S.M. Thon, H. Kim, P.M. Petroff, T.H. Oosterkamp, D. Bouwmeester, and R. Hanson, (2012) Effect of a nanoparticle on the optical properties of a photonic crystal cavity: theory and experiment, J. Opt. Soc. Am. B, 29, pp. 698-703.
[pdf]
V. D. Salakhutdinov, E. R. Eliel, and W. Löffler, (2012) Full-Field Quantum Correlations of Spatially Entangled Photons, Phys. Rev. Lett., 108, 173604.
[pdf]
F. Ricci, W. Löffler, M. P. van Exter (2012) Instability of higher-order optical vortices analyzed with a multi-pinhole interferometer, Opt. Express, 20, 22961.
[pdf]
J. J. Renema, G. Frucci, M. J. A. de Dood, R. Gill, A. Fiore, and M. P. van Exter (2012) Tomography and state reconstruction with superconducting single-photon detectors, Phys. Rev. A , 86, 062113.
[pdf]
J. J. Renema, G. Frucci, Z. Zhou, F. Mattioli, A. Gaggero, R. Leoni, M. J. A. de Dood, A. Fiore, and M. P. van Exter, (2012) Modified detector tomography technique applied to a superconducting multiphoton nanodetector, Opt. Express, 20, 2806-2813.
[pdf]
B. Pepper, E. Jeffrey, R. Ghobadi, C. Simon, and D. Bouwmeester (2012) Macroscopic superpositions via nested interferometry: finite temperature and decoherence considerations, New J. Phys., 14, 115025.
[pdf]
B. Pepper, R. Ghobadi, E. Jeffrey, C. Simon, and D. Bouwmeester (2012) Optomechanical superpositions via nested interferometry, Phys. Rev. Lett., 109, 023601.
[pdf]
H.D. Pires, J. Woudenberg, and M.P. van Exter, (2012) Statistical properties of two-photon speckles, Phys. Rev. A, 85, 033807.
[pdf]
S.S.R. Oemrawsingh, N. Markesevic, E.G. Gwinn, E.R. Eliel, and D. Bouwmeester (2012) Spectral Properties of Individual DNA-Hosted Silver Nanoclusters at Low Temperatures, J. Phys. Chem., 116, 25568.
[pdf]
A.M. Nugrowati, W.G. Stam, and J.P. Woerdman (2012) Position measurement of non-integer OAM beams with structurally invariant propagation, Opt. Expr., 20, 27429.
[pdf]
W. Löffler, A. Aiello, and J.P. Woerdman (2012) Observation of OAM sidebands due to optical reflection, Phys. Rev. Lett., 109, 113602.
[pdf]
W. Löffler, A. Aiello, and J.P. Woerdman (2012) Spatial Coherence and Optical Beam Shifts, Phys. Rev. Lett., 109, 213901.
[pdf]
N. Hermosa, A. Aiello, and J.P. Woerdman (2012) Radial mode dependence of optical beam shifts, Opt. Lett., 37, pp. 1044-1046.
[pdf]
J. Hagemeier, C. Bonato, T.-A. Truong, H. Kim, G.J. Beirne, M. Bakker, M.P. van Exter, Y. Luo, P. Petroff, and D. Bouwmeester (2012) H1 photonic crystal cavities for hybrid quantum information protocols, Opt. Express, 20, 24714.
[pdf]
D. Giovanni, F.M. Miatto, J. Romero, S.M. Barnett, J.P. Woerdman, and M.J. Padgett (2012) Determining the dimensionality of bipartite orbital-angular-momentum entanglement using multi-sector phase masks, New J. Phys., 14, 073046.
[pdf]
J.W. Dalhuisen and D. Bouwmeester (2012) Twistors and electromagnetic knots, J. Phys. A: Math. Theor., 45, 135201.
[pdf]
M. P. van Exter, J. Woudenberg, H. Di Lorenzo Pires, and W. H. Peeters, (2012) Bosonic, fermionic, and anyonic symmetry in two-photon random scattering, Phys. Rev. A, 85, 033823.
[pdf]
P.F. Chimento, P.F.A. Alkemade, G.W. t Hooft, and E.R. Eliel (2012) Optical angular momentum conversion in a nanoslit, Opt. Lett., 37, 4946-4948.
[pdf]
C. Bonato, J. Gudat, K. de Vries, S.M. Thon, H. Kim, P.M. Petroff, M.P. van Exter, and D. Bouwmeester (2012) Optical modes in oxide-apertured micropillar cavities, Opt. Lett., 37, 4678.
[pdf]
F. van Beijnum, C. Retif, C.B. Smiet, H. Liu, P. Lalanne, and M.P. van Exter, (2012) Quasi-cylindrical wave contribution in experiments on extraordinary optical transmission, Nature, 492, 411.
[pdf]
F. van Beijnum, J. Sirre, C. Retif, and M.P. van Exter, (2012) Speckle correlation functions applied to surface plasmons, Phys. Rev. B, 85, 035437.
[pdf]
Lj. Babic, L.T. van Dellen, and M.J.A. de Dood (2012) Fano interpretation of second harmonic generation in a photonic crystal on a gel, Appl. Phys. Lett., 101, 261120.
[pdf]
A. Aiello and J.P. Woerdman, (2012) Role of spatial coherence in Goos-Hanchen and Imbert-Fedorov shifts: reply to comment, Opt. Lett., 37, 1057.
[pdf]
A. Gupta , I. Nederlof, S. Sottini, A. W. J. Tepper, E. J. J. Groenen, E. A.J. Thomassen, and G. W. Canters (2012) Role of Tyr108 in the enzyme mechanism of the small laccase from Streptomyces coelicolor, J. Am. Chem. Soc., 134, 18213–18216.
[pdf]
G. Mathies, S. Sottini, P. Kyritsis, E.J.J. Groenen (2012) High-frequency EPR study of the high-spin FeII complex Fe[(SPPh2)2N]2, J. Magn. Reson., 224, 94-100.
[pdf]
G. Mathies, R.M. Almeida, P. Gast, J.J.G. Moura, E.J.J. Groenen (2012) Multifrequency EPR Study of Fe+3 and Co+2 in the Active Site of Desulforedoxin, J. Phys. Chem. B, 116, 7122-7128.
[pdf]
S. Sottini, E. J.J. Groenen (2012) A Comment on the Pseudo-nuclear Zeeman Effect, J. Magn. Reson., 218, 11-15.
[pdf]
S. Scanu, J. F?rster, M.G. Finiguerra, M.H. Shabestari, M. Huber, M. Ubbink (2012) The Complex of Cytochrome f and Plastocyanin from Nostoc sp. PCC 7119 is Highly Dynamic, ChemBioChem, 13 (9), 1312-1318.
[pdf]
M. Drescher, M. Huber, V. Subramaniam (2012) Hunting the Chameleon: Structural Conformations of the Intrinsically Disordered Protein Alpha-Synuclein, ChemBioChem, 13 (6), 761-768.
[pdf]
Y. Tian, P. Navarro, B. Kozankiewicz, M. Orrit (2012) Spectral diffusion of single dibenzoterrylene molecules in 2,3-Dimethylanthracene, ChemPhysChem, 13, 3510-3515.
[pdf]
P. Zijlstra, P.M.R. Paulo, K. Yu, Q.H. Xu, M. Orrit (2012) Chemical interface damping in single gold nanorods and its near elimination by tip-specific functionalization, Angew. Chem. Int. Ed., 51, 8352-8355.
[pdf]
M. Yorulmaz, S. Khatua, P. Zijlstra, A. Gaiduk, M. Orrit (2012) Luminescence quantum yield of single gold nanorods, Nano. Lett., 12 (8), 4385-4391.
[pdf]
P.V. Ruijgrok (Ph.D. thesis) (2012) Optical manipulation and study of single gold nanoparticles in solution, .
[pdf]
P. Zijlstra, P.M.R. Paulo, M. Orrit (2012) Optical detection of single non-absorbing molecules using the surface plasmon resonance of a gold nanorod, Nature Nanotech., 7, 379-382.
[pdf]
P. Zijlstra, M. van Stee, N. Verhart, Z. Gu, M. Orrit (2012) Rotational diffusion and alignment of short gold nanorods in an external electric field, Phys. Chem. Chem. Phys., 14, 4584-4588.
[pdf]
P.V. Ruijgrok, P. Zijlstra, A.L. Tchebotareva, M. Orrit (2012) Damping of acoustic vibrations of single gold nanoparticles optically trapped in water, Nano Lett., 12, 1063-1069.
[pdf]
H. Yuan, T. Xia, M. Plazanet, B. Deme, M. Orrit (2012) Crystallite nucleation in supercooled glycerol near the glass transition, J. Chem. Phys., 136, 041102.
[pdf]
H. Yuan, M. Orrit (2012) Reaction pathways from single-molecule trajectories, ChemPhysChem, 13, 681-683.
[pdf]
A. Gaiduk, M. Yorulmaz, E. Ishow, M. Orrit (2012) Absorption, luminescence, and sizing of organic dye nanoparticles and of patterns formed upon dewetting, ChemPhysChem, 13, 946-951.
[pdf]
C. Beekman, I. Komissarov, J. Aarts (2012) Large electric-field effects on the resistance of La0.67Ca0.33MnO3 microstructures, Physical Review B , 85, issue 24, 245115.
F.M. Miatto, H. Di Lorenzo Pires, S.M. Barnett, M.P. van Exter (2012) Spatial Schmidt modes generated in parametric down-conversion, Eur. Phys. J. D, 66, 263:1-11.
[Abstract] [DOI]
This paper presents the general spatial Schmidt decomposition of two-photon fields generated in spontaneous parametric down-conversion (SPDC). It discusses in particular the separation of the radial and azimuthal degrees of freedom, the role of projection in modal analysis, and the benefits of phase mismatch. ...
Exter (2012) Spatial Schmidt modes generated ni parametric down-conversion, .
C.M. Guédon, H. Valkenier, T. Markussen, KS Thygesen, J.C. Hummelen , S.J. van der Molen (2012) Observation of quantum interference in molecular charge transport., NAT NANOTECHNOL, 7, 305–309.
[DOI]
N.V. Khotkevych, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek (2012) Aharonov-Bohm Type Oscillations in a System of Two Tunnel Point-Contacts in the Presence of a Single Scatterer: Determination of the Depth of the Buried Impurity, J. Phys.: Conf. Ser., 400, 042031.
[Abstract] [DOI] [pdf]
The conductance of a system containing two tunnel point-contacts and a single subsurface scatterer in the presence of a magnetic ¯eld is investigated theoretically. A general formula for the dependence of the conductance on the distance between contacts, the defect position, and the magnetic ¯eld is obtained. It is shown that in the presence of a magnetic ¯eld the conductance undergoes Aharonov-Bohm type oscillations. We ¯nd a simple relation between the period of the oscillations and the depth of the subsurface impurity. On the basis of this fact a new and easy method of determination the depth of the buried impurity is proposed.
Jelmer J.T. Wagenaar, Monica Morales-Masis, and Jan M. van Ruitenbeek (2012) Observing 'quantized' conductance steps in silver sulfide: two parallel resistive switching mechanisms., , J. Appl. Phys., 111,, 2012.
A. Hellman, A. Resta, N.M. Martin, J. Gustafson, A. Trinchero, P.-A. Carlsson, O. Balmes, R. Felici, R. van Rijn, J.W.M. Frenken, J.N. Andersen, E. Lundgren, H. Grönbeck (2012) The active phase of palladium during methane oxidation, J. Phys. Chem. Lett., 3, 678-682.
G.J. Verbiest, J.N. Simon, T.H. Oosterkamp, M.J. Rost (2012) Subsurface atomic force microscopy: towards a quantitative understanding., Nanotechnology, 23 , 145704.
T. van der Sar, J. Hagemeier, W. Pfaff, E.C. Heeres, S. Thon, H. Kim, P. Petroff, T.H. Oosterkamp, D. Bouwmeester, R. Hanson (2012) Effect of a nanoparticle on the optical properties of a photonic crystal cavity: theory and experiment, J. Opt. Soc. Am. B, 29, 698-703.
E.C. Heeres, T.H. Oosterkamp, N. de Jonge (2012) Size of the localized electron emission sites on a closed multiwalled carbon nanotube, Phys. Rev. Lett., 108, 036804.
N.V. Khotkevych and Yu.A. Kolesnichenko, and J.M. van Ruitenbeek (2012) Theory of scanning tunneling spectroscopy of thin films., Low Temperature Physics (Kharkiv), 38.
Manohar Kumar, Rémi Avriller, Alfredo Levy Yeyati, and Jan M. van Ruitenbeek (2012) Detection of vibration mode scattering in electronic shot noise., Rev. Lett., 108.
Mubeen Dildar, C. Beekman, Xin He, and J. Aarts (2012) Hall effect measurements on strained and unstrained thin ?lms of La0.7 Ca0.3 MnO3 and La0.7 Sr0.3 MnO3.I., PHYSICAL REVIEW B, 85, 205103.
M. S. Anwar, M. Veldhorst, A. Brinkman, and J. Aarts (2012) Long range supercurrents in ferromagnetic CrO2 using a multilayer contact structure, Appl. Phys. Lett., 100, 052602.
Arcizet, Delphine Capito, Sofia Gorelashvili, Mari Leonhardt, Carolin Vollmer, Marion Youssef, Simon Rappl, Susanne Heinrich, Doris (2012) Contact-controlled amoeboid motility induces dynamic cell trapping in 3D-microstructured surfaces, SOFT MATTER, 8.
[Abstract] [DOI]
On flat substrates, several cell types exhibit amoeboid migration, which is characterized by restless stochastic successions of pseudopod protrusions. The orientation and frequency of new membrane protrusions characterize efficient search modes, which can respond to external chemical stimuli as observed during chemotaxis in amoebae. To quantify the influence of mechanical stimuli induced by surface topography on the migration modes of the amoeboid model organism Dictyostelium discoideum, we apply high resolution motion analysis in microfabricated pillar arrays of defined density and geometry. Cell motion is analyzed by a two-state motility-model, distinguishing directed cellular runs from phases of isotropic migration that are characterized by randomly oriented cellular protrusions. Cells lacking myosin
Ueta, H Groot, IMN Juurlink, LBF Kleyn, (2012) Evidence of stable high-temperature D-x-, JOURNAL, 136.
[Abstract] [DOI]
We demonstrate the formation of complexes involving attractive interactions between D and
S. M. Schramm, S. J. van der Molen, R. M. Tromp, (2012) Intrinsic Instability of Aberration-Corrected Electron Microscopes, PHYSICAL REVIEW LETTERS, 109, 163901 .
[DOI]

2011
E. H. Huisman, M. L. Trouwborst, F. L. Bakker, B. J. van Wees and S. J. van der Molen (2011) The mechanical response of lithographically defined break junctions, J. Appl. Phys. , 109, 104305 .
[DOI]
J. van Wezel, T.H. Oosterkamp (2011) A nanoscale experiment measuring gravity's role in breaking the unitarity of quantum dynamics, Proc. R. Soc. A., 468, 35-56.
[DOI] [pdf]
Jos Zwanikken, Katerina Ioannidou, Daniela Kraft and René van Roij (2011) Reversible emulsification controlled by ionic surfactants and responsive nanoparticles, Soft Matter, Highlighted on the Cover , 7, 11093-11097.
[DOI]
V. N. Kushnir, S. L. Prischepa, C. Cirillo, A. Vecchione, C. Attanasio, M. Yu. Kupriyanov, and J. Aarts (2011) Multiple order parameter configurations in superconductor/ferromagnet multilayers, PHYSICAL REVIEW B , 84, 214512.
[DOI]
A. Vecchione, R. Fittipaldi, C. Cirillo, M. Hesselberth, J. Aarts, S.L. Prischepa, V.N. Kushnir, M.Yu. Kupriyanov, C. Attanasio (2011) X-ray scattering study of interfacial roughness in Nb/PdNi multilayers, Surface Science , 605, 1791–1796.
[DOI]
C. Beekman, J. Zaanen, and J. Aarts (2011) Nonlinear mesoscopic transport in a strongly cooperative electron system: The La0.67Ca0.33MnO3 microbridge, PHYSICAL REVIEW B , 83, 235128.
[DOI]
I. T. M. Usman, K. A. Yates, J. D. Moore, K. Morrison, V. K. Pecharsky, K. A. Gschneidner, T. Verhagen and J. Aarts, V. I. Zverev, J. W. A. Robinson, J. D. S. Witt, and M. G. Blamire, L. F. Cohen (2011) Evidence for spin mixing in holmium thin film and crystal samples, PHYSICAL REVIEW B , 83, 144518.
[DOI]
V.N. Kushnir, S.L. Prischepa, J. Aarts, C. Bell, C. Cirillo, and C. Attanasio (2011) Effect of the variation of the exchange energy on the superconducting critical temperature of S/F/S trilayers, Eur. Phys. J. B , 80, 445–449 .
[DOI]
M. S. Anwar and J. Aarts (2011) Inducing supercurrents in thin films of ferromagnetic CrO2, Supercond. Sci. Technol. , 24, 024016 (9pp).
[DOI]
E. J. Salumbides, V. Maslinskas, I. M. Dildar, A. L. Wolf, E.-J. van Duijn, K. S. E. Eikema, and W. Ubachs (2011) High-precision frequency measurement of the 423-nm Ca I line, PHYSICAL REVIEW A , 83, 012502.
[DOI]
Anna Pezzarossa, Susanne Fenz & Thomas Schmidt (2011) Probing Structure and Dynamics of the Cell Membrane with Single Fluorescent Prot, Springer Series on Fluorescence, Ed.: G. Jung, 113.
[pdf]
Tobias Meckel, Stefan Semrau, Marcel Schaaf & Thomas Schmidt (2011) Robust assessment of protein complex formation in vivo via single molecule inten, J. Biomed. Opt, 16, 076016.
[Abstract] [DOI] [pdf]
The formation of protein complexes or clusters in the plasma membrane is essential for many biological processes, such as signaling. We develop a tool, based on single-molecule microscopy, for following cluster formation in vivo. Detection and tracing of single autofluorescent proteins have become standard biophysical techniques. The determination of the number of proteins in a cluster, however, remains challenging. The reasons are (i) the poor photophysical stability and complex photophysics of fluorescent proteins and (ii) noise and autofluorescent background in live cell recordings. We show that, despite those obstacles, the accurate fraction of signals in which a certain (or set) number of labeled proteins reside, can be determined in an accurate an robust way in vivo. We define experimental conditions under which fluorescent proteins exhibit predictable distributions of intensity and quantify the influence of noise. Finally, we confirm our theoretical predictions by measurements of the intensities of individual enhanced yellow fluorescent protein (EYFP) molecules in living cells. Quantification of the average number of EYFP-C10HRAS chimeras in diffraction-limited spots finally confirm that the membrane anchor of human Harvey rat sarcoma (HRAS) heterogeneously distributes in the plasma membrane of living Chinese hamster ovary cells.
Arnauld Serge, Sandra de Keijzer, Freek Van Hemert, Mark R. Hickman, Dale Hereld, Thomas Schmidt and B. Ewa Snaar-Jagaska (2011) Quantification of GPCR internalization by single-molecule microscopy in living cells., Integrative Biology, 3, 675-683.
[Abstract] [DOI] [pdf]
Receptor internalization upon ligand stimulation is a key component of a cell's response and allows a cell to correctly sense its environment. Novel fluorescent methods have enabled the direct visualization of the agonist-stimulated G-protein-coupled receptors (GPCR) trafficking in living cells. However, it is difficult to observe internalization of GPCRs in vivo due to intrinsic autofluorescence and cytosolic signals of fluorescently labeled GPCRs. This study uses the superior positional accuracy of single-molecule fluorescence microscopy to visualize in real time the internalization of Dictyostelium discoideumcAMP receptors, cAR1, genetically encoded with eYFP. This technique made it possible to follow the number of receptors in time revealing that the fraction of cytosolic receptors increases after persistent agonist stimulation and that the majority of the receptors were degraded after internalization. The observed internalization process was phosphorylation dependent, as shown with the use of a phosphorylation deficient cAR1 mutant, cm1234-eYFP, or stimulation with an antagonist, Rp-cAMPS that does not induce receptor phosphorylation. Furthermore, experiments done in mound-stage cells suggest that intrinsic, phosphorylation-induced internalization of cAR1 is necessary for Dictyostelium wild type cells to progress properly through multicellular development. To our knowledge, this observation illustrates for the first time phosphorylation-dependent internalization of single cAR1 molecules in living cells and its involvement in multicellular development. This very sensitive imaging of receptor internalization can be a useful and universal approach for pharmacological characterization of GPCRs in other cell types.
Marcel J. M. Schaaf & Thomas Schmidt (2011) In Vivo Single-Molecule Microscopy Using the Zebrafish Model System., in Y. Sako & M. Ueda (eds.), Cell Signaling Reactions: Single-Molecular Kinetic.
[DOI] [pdf]
Stefan Semrau, Laurent Holtzer, Marcos Gonzalez-Gaitan & Thomas Schmidt (2011) Quantification of biological interactions with Particle Image Cross Correlation, Biophys. J, 100, 1810-8.
[Abstract] [DOI] [pdf]
A multitude of biological processes that involve multiple interaction partners are observed by two-color microscopy. Here we describe an analysis method for the robust quantification of correlation between signals in different color channels: particle image cross-correlation spectroscopy (PICCS). The method, which exploits the superior positional accuracy obtained in single-object and single-molecule microscopy, can extract the correlation fraction and length scale. We applied PICCS to correlation measurements in living tissues. The morphogen Decapentaplegic (Dpp) was imaged in wing imaginal disks of fruit fly larvae and we quantified what fraction of early endosomes contained Dpp.
Stefan Semrau, Anna Pezzarossa & Thomas Schmidt (2011) Microsecond Single-Molecule Tracking (usSMT)., Biophys. Lett, 100, L19-L21.
[Abstract] [DOI] [pdf]
Here we report on a method to track individual molecules on nanometer length and microsecond timescales using an optical microscope. Our method is based on double-labeling of a molecule with two spectrally distinct fluorophores and illuminating it with laser pulses of different wavelengths that partially overlap temporally. We demonstrate our method by using it to resolve the motion of short DNA oligomers in solution down to a timescale of 100 μs.
Tepper, AWJW, Aartsma, TJ, Canters, GW (2011) Channeling of electrons within SLAC, the small laccase from Streptomyces, FARADAY DISCUSSIONS, 148, 161-171.
[DOI]
den Hollander, MJ, Magis, JG, Fuchsenberger, P, Aartsma, TJ, Jones, MR, Frese, RN (2011) Enhanced Photocurrent Generation by Photosynthetic Bacterial Reaction, LANGMUIR, 27, 10282-10294.
[DOI]
Magis, GJ, Olsen, JD, Reynolds, NP, Leggett, GJ, Hunter, CN, Aartsma, TJ, Frese, RN (2011) Use of Engineered Unique Cysteine Residues to Facilitate Oriented, PHOTOCHEMISTRY AND PHOTOBIOLOGY, 87, 1050-1057.
[DOI]
Krzeminski, L, Ndamba, L, Canters, GW, Aartsma, TJ, Evans, SD, Jeuken, LJC (2011) Spectroelectrochemical Investigation of Intramolecular and Interfacial, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133, 15085-15093.
[DOI]
Tabares, LC, Kostrz, D, Elmalk, A, Andreoni, A, Dennison, C, Aartsma, TJ, Canters, GW (2011) Fluorescence Lifetime Analysis of Nitrite Reductase from Alcaligenes, CHEMISTRY-A EUROPEAN JOURNAL, 17, 12015-12019.
[DOI]
Goldsmith, RH, Tabares, LC, Kostrz, D, Dennison, C, Aartsma, TJ, Canters, GW, Moerner, WE (2011) Redox cycling and kinetic analysis of single molecules of solution-phase, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF, 108, 17269-17274.
[DOI]
Krzeminski, L, Cronin, S, Ndamba, L, Canters, GW, Aartsma, TJ, Evans, SD, Jeuken, LJC (2011) Orientational Control over Nitrite Reductase on Modified Gold Electrode, JOURNAL OF PHYSICAL CHEMISTRY B, 115, 12607-12614.
[DOI]
J.A. Dijksman, G.H. Wortel, L.T.H. van Dellen, O. Dauchot and M. van Hecke (2011) Jamming, Yielding and Rheology of Weakly Vibrated Granular Media, Phys. Rev. Lett., 107, 108303 .
[pdf]
V. Vitelli and M. van Hecke (2011) Marginal Matters, Nature, 480, 325 .
[pdf]
M. L. Trouwborst, C. A. Martin, R. H. M. Smit, C. M. Guédon, T. A. Baart, S. J. van der Molen, and J. M. van Ruitenbeek, (2011) Transition Voltage Spectroscopy and the Nature of Vacuum Tunneling., Nano Letters , 11, 614-617 .
[DOI] [pdf]
C.A. Martin, R.H.M. Smit, R. van Egmond, H.S.J. van der Zant, and J.M. van Ruitenbeek (2011) A versatile low-temperature setup for the electrical characterization of single-molecule junctions., Review of Scientific Instruments, 82.
[pdf]
C. M. Guédon, J. Zonneveld, E.H. Valkenier, J.C. Hummelen, and S. J. van der Molen (2011) Controlling the interparticle distance in a 2D molecule-nanoparticle network, Nanotechnology.
[DOI] [pdf]
N.V. Khotkevych and Yu.A. Kolesnichenko, J.M. van Ruitenbeek (2011) Quantum interference effects in a system of two tunnel point-contacts in the presence of a single scatterer: simulation of a double-tip STM experiment, Low Temperature Physics (Kharkiv) , 37, 64 .
[pdf]
Sense Jan van der Molen and Peter Liljeroth (2011) Conductance Properties of Switchable Molecules, Chapter 20 in the book Molecular Switches, Edited by Ben L. Feringa and Wesley R. Browne Wiley-VCH, Weinheim, Germany, 719-777.
M. Morales-Masis, S.J. van der Molen, T. Hasegawa, J. M. van Ruitenbeek, (2011) Bulk and Surface Nucleation Processes in Ag2S Conductance Switches., Physical Review B , 84, 115310 .
[pdf]
M.L. Perrin, F. Prins, C.A. Martin, A.J. Shaikh, R. Eelkema, J.H. van Esch, T. Briza, R. Kaplanek, V. Kral, J.M. van Ruitenbeek, H.S.J. van der Zant, D. Djulic, (2011) Influence of the Chemical Structure on the Stability and Conductance of Porphyrin Single-Molecule Junctions., Angewandte Chemie, 50, 11223-11226 .
[pdf]
M.L. Perrin, C.A. Martin, F. Prins, A.J. Shaikh, R. Eelkema, J.H. van Esch, J.M. van Ruitenbeek, H.S.J. van der Zant, D. Djulic, Beilstein J (2011) Charge transport in a zinc-porphyrin single-molecule junction., Nanotechnology, 2, 714-719 .
[pdf]
J.M. van Ruitenbeek, Beilstein J (2011) Transport through molecular junctions ,Editorial., Nanotechnology, 2, 691-692 .
[pdf]
S.M. Thon, H. Kim, C. Bonato, J. Gudat, J. Hagemeier, P.M. Petroff, and D. Bouwmeester, (2011) Independent electrical tuning of separated quantum dots in coupled photonic crystal cavities, Appl. Phys. Lett., 99, 161102.
[pdf]
T. van der Sar, J. Hagemeier, W. Pfaff, E.C. Heeres, S.M. Thon, H. Kim, P.M. Petroff, T.H. Oosterkamp, D. Bouwmeester, and R. Hanson, (2011) Deterministic nanoassembly of a coupled quantum emitter-photonic crystal cavity system, Appl. Phys. Lett., 98, 193103.
[pdf]
B.J. Pors, F. Miatto, G.W. t Hooft, E.R. Eliel, and J.P. Woerdman, (2011) High-dimensional entanglement with orbital-angular-momentum states of light, J. Opt., 13, 064008.
[pdf]
B.J. Pors, C.H. Monken, E.R. Eliel, and J.P. Woerdman, (2011) Transport of orbital-angular-momentum entanglement through a turbulent atmosphere, Opt. Express, 19, 6671-6683.
[pdf]
H.D. Pires, F.M.G.J. Coppens, and M.P. van Exter, (2011) Type-I spontaneous parametric down-conversion with a strongly focused pump, Phys. Rev. A, 83, 033837.
[pdf]
W. Löffler, D.J. Broer, and J.P. Woerdman, (2011) Circular dichroism of cholesteric polymers and the orbital angular momentum of light, Phys. Rev. A, 83, 065801.
[pdf]
W. Löffler, M. P. van Exter, G. W. t Hooft, G. Nienhuis, D.J. Broer, and J.P. Woerdman, (2011) Search for Hermite-Gauss mode rotation in cholesteric liquid crystals, Opt. Express, 19, 12978.
[pdf]
W. Löffler, T. G. Euser, E. R. Eliel, M. Scharrer, P. St. J. Russell, and J.P. Woerdman, (2011) Fiber Transport of Spatially Entangled Photons, Phys. Rev. Lett., 106, 240505.
[pdf]
D. Kleckner, B. Pepper, E. Jeffrey, P. Sonin, S.M. Thon, and D. Bouwmeester, (2011) Optomechanical trampoline resonators, Opt. Express, 19, 19708.
[pdf]
N. Hermosa, A. Aiello, and J.P. Woerdman, (2011) Quadrant detector calibration for vortex beams, Optics. Lett., 36, 409.
[pdf]
N. Hermosa, A. M. Nugrowati, Andrea Aiello, and J. P. Woerdman, (2011) Spin Hall effect of light in metallic reflection, Optics. Lett., 36, 3200.
[pdf]
J. Gudat, C. Bonato, E. van Nieuwenburg, S. Thon, H. Kim, P.M. Petroff, M.P. van Exter, and D. Bouwmeester, (2011) Permanent tuning of quantum dot transitions to degenerate microcavity resonances, Appl. Phys. Lett., 98, 121111.
[pdf]
P.F. Chimento, N.V. Kuzmin, J. Bosman, P.F.A. Alkemade, G.W. (2011) A subwavelength slit as a quarter-wave retarder, Opt. Express, 19, 24219.
[pdf]
C. Bonato, E. van Nieuwenburg, J. Gudat, S. Thon, H. Kim, M.P. van Exter, and D. Bouwmeester, (2011) Strain tuning of quantum dot optical transitions via laser-induced surface defects, Phys. Rev. B, 84, 075306.
[pdf]
F. van Beijnum, C. Retif, C.B. Smiet, and M.P. van Exter, (2011) Transmission processes in random patterns of subwavelength holes, Opt. Lett., 36, 3666.
[pdf]
L. Babic, R. Leijssen, D.F.C. Driessen, and M.J.A. de Dood, (2011) Transfer of photonic crystal membranes to a transparent gel substrate, Opt. Express, 19, 19532.
[pdf]
A Aiello, and J.P. Woerdman, (2011) Goos-Hänchen and Imbert-Fedorov shifts of a nondiffracting Bessel beam, Optics Letters, 36, 543-545.
[pdf]
A Aiello, and J.P. Woerdman, (2011) Role of spatial coherence in Goos-Hänchen and Imbert-Fedorov shifts, Optics Letters, 36, 3151.
[pdf]
S. Carlotto, M. Zerbetto, M.H. Shabestari, A. Moretto, F. Formaggio, M. Crisma, C. Toniolo, M. Huber, A. Polimeno (2011) In Silico interpretation of cw-ESR at 9 and 95 GHz of Mono- and bis- TOAC-labeled Aib-homopeptides in fluid and frozen acetonitrile, J. Phys. Chem. B, 115(44), 13026-36.
[pdf]
M. Robotta, P. Braun, B. van Rooijen, V. Subramaniam, M. Huber, M. Drescher (2011) Direct Evidence of Coexisting Horseshoe and Extended Helix Conformations of Membrane-Bound Alpha-Synuclein, ChemPhysChem, 12 (2), 267-269.
[pdf]
D. Maganas, S. Sottini, P. Kyritsis, Edgar J.J. Groenen, F. Neese (2011) Theoretical Analysis of the Spin Hamiltonian Parameters in Co(II)S4 Complexes, Using Density Functional Theory and Correlated ab initio Methods, Inorg. Chem., 50 (18), 8741-8754.
[pdf]
G. Mathies, M. C. van Hemert, P. Gast, K. B. Sai, S. Gupta, H. A. Frank, J. Lugtenburg, E. J.J. Groenen (2011) Configuration of Spheroidene in the Photosynthetic Reaction Center of Rhodobacter sphaeroides: A Comparison of Wild-Type and Reconstituted R26, J. Phys. Chem. A, 115 (34), 9552-9556.
[pdf]
A.C. Wirtz, C. Hofmann, E.J.J. Groenen (2011) Stretched Polyethylene Films Probed by Single Molecules, ChemPhysChem, 12, 1519-1528.
[pdf]
G. Mathies, H. Blok, J.A.J.M. Disselhorst, P. Gast, H. van der Meer, D.M. Miedema, R.M. Almeida, J.J.G. Moura, W.R. Hagen, E.J.J. Groenen (2011) Continuous-wave EPR at 275 GHz: Application to high-spin Fe3+ systems, J. Magn. Res., 210, 126-132.
[pdf]
P. Zijlstra, M. Orrit (2011) Single metal nanoparticles: optical detection, spectroscopy and applications, Rep. Prog. Phys., 74, 106401.
[pdf]
P.V. Ruijgrok, N.R. Verhart, P. Zijlstra, A.L. Tchebotareva, M. Orrit (2011) Brownian fluctuations and heating of an optically aligned gold nanorod, Phys. Rev. Lett., 107, 037401.
[pdf]
M.J. Winterhalder, A. Zumbusch, M. Lippitz, M. Orrit (2011) Toward far-field vibrational spectroscopy of single molecules at room temperature, J. Phys. Chem. B, 115, 5425-5430.
[pdf]
A. Gaiduk, M. Yorulmaz, M. Orrit (2011) Correlated absorption and photoluminescence of single gold nanoparticles, ChemPhysChem., 12, 1536-1541.
[pdf]
H. Yuan, T. Xia, B. Schuler, M. Orrit (2011) Temperature-cycle single-molecule FRET microscopy on polyprolines, Phys. Chem. Chem. Phys., 13, 1762-1769.
[pdf]
A. Gaiduk, P.V. Ruijgrok, M. Yorulmaz, M. Orrit (2011) Making gold nanoparticles fluorescent for simultaneous absorption and fluorescence detection on the single particle level, Phys. Chem. Chem. Phys., 13, 149 - 153.
[pdf]
 M. Morales-Masis, S.J. van der Molen, T. Hasegawa, J. M. van Ruitenbeek (2011)  Bulk and Surface Nucleation Processes in Ag2S Conductance Switches, Physical Review B, 84.
 F. Mirjani, J.M. Thijssen, and S.J. van der Molen (2011) Advantages and limitations of transition voltage spectroscopy: a theoretical analysis, Physical Review B, 84.
 E.H. Huisman, M.L. Trouwborst, F.L. Bakker, B.J. van Wees, and S.J. van der Molen (2011)  The mechanical response of lithographically defined break junctions, Journal of Applied Physics, 109.
 C.A. Martin, R.H.M. Smit, R. van Egmond, H.S.J. van der Zant, and J.M. van Ruitenbeek (2011)  A versatile low-temperature setup for the electrical characterization of single-molecule junctions, Review of Scientific Instruments, 82.
N.V. Khotkevych and Yu.A. Kolesnichenko, J.M. van Ruitenbeek (2011)  Quantum interference effects in a system of two tunnel point-contacts in the presence of a single scatterer: simulation of a double-tip STM experiment., Low Temperature Physics (Kharkiv), 37.
S.M. Schramm, J. Kautz, A. Berghaus, O. Schaff, R.M. Tromp, and S.J. van der Molen (2011)  Low Energy Electron Microscopy and Spectroscopy with ESCHER: Status and Prospects., IBM Journal of Research and Development, 55, 1:1-1:7.
 M. L. Trouwborst, C. A. Martin, R. H. M. Smit, C. M. Guédon, T. A. Baart, S. J. van der Molen, and J. M. van Ruitenbeek (2011)  Transition Voltage Spectroscopy and the Nature of Vacuum Tunneling, Nano Letters, 11, 614-617.
 I. Sikharulidze, R. van Gastel, S.Schramm, J.P. Abrahams, B. Poelsema, R.M. Tromp and S.J. van der Molen (2011)  Low energy electron microscopy imaging using Medipix2 detectors, Nucl. Instr. and Meth. in Phys. Res. A, 633, S239-S242.
  J. te Riet, A.J. Katan, C. Rankl, S.W. Stahl, A.M. van Buul, I.Y. Phang, A. Gomez-Casado, P. Schön, J.W. Gerritsen, A. Cambi, A.E. Rowan, G.J. Vancso, P. Jonkheijm, J. Huskens, T.H. Oosterkamp, H. Gaub, . Hinterdorfer, C.G. Figor, S. Speller (2011) Interlaboratory round robin on cantilever calibration for AFM force spectroscopy, Ultramicroscopy, 111 , 1659.
A. Vinante, G. Wijts, O. Usenko, L. Schinkelshoek, T.H. Oosterkamp (2011) Magnetic resonance force microscopy of paramagnetic electron spins at millikelvin temperatures, Nature Communications, 2 , 572.
K.B. Gavan, J.H. Rector, K. Heeck, D. Chavan, G. Gruca, T.H. Oosterkamp, D. Iannuzzi (2011) Top-down approach to fiber-top cantilevers., Appl. Phys. Lett., 98 , 193103.
R. van Rijn, O. Balmes, A. Resta, D. Wermeille, R. Westerström, J. Gustafson, R. Felici, E. Lundgren, J.W.M. Frenken (2011) Surface structure and reactivity of Pd(100) during CO oxidation near ambient pressures., PCCP, 13 , 13167-13171.
T. van der Sar, J. Hagemeier, W. Pfaff, E.C. Heeres, S.M. Thon, H. Kim, P.M. Petroff, T.H. Oosterkamp, D. Bouwmeester, R. Hanson (2011) Deterministic nanoassembly of a coupled quantum emitter-photonic crystal cavity system., Appl. Phys. Lett., 98, 193103.
E.C. Heeres, T.H. Oosterkamp, N. de Jonge (2011) Making carbon nanotube electron sources of defined lengths and with closed caps., Nanotechnology, 22 , 235308.
R. Westerström, M.E. Messing, S. Blomberg, A. Hellman, H. Grönbeck, J. Gustafson, N.M. Martin, O. Balmes, R. van Rijn, J.N. Andersen, K. Deppert, H. Bluhm, Z. Liu, M.E. Grass, M. Hävecker, E. Lundgren (2011) Oxidation and reduction of Pd(100) and aerosol-deposited Pd nanoparticles, Phys. Rev. B, 83, 115440.
O. Usenko, A. Vinante, G.H.J.C. Wijts, T.H. Oosterkamp (2011) A superconducting quantum interference device based read-out of a subattonewton force sensor operating at millikelvin temperatures, Appl. Phys. Lett., 98 , 133105.
M. S. Anwar, and J. Aarts.M. S. Anwar, and J. Aarts (2011) Inducing supercurrents in thin films of ferromagnetic CrO2., Supercond. Sci. Technol., 24,, 024016.
Meier, Born Zielinski, Alejandro Weber, Christoph Arcizet, Delphine Youssef, Simon Franosch, Thomas Raedler, Joachim O. Heinrich, Doris (2011) Chemotactic cell trapping in controlled alternating gradient fields, PROCEEDINGS, 108.
[Abstract] [DOI]
Directed cell migration toward spatio-temporally varying chemotactic stimuli requires rapid cytoskeletal reorganization. Numerous studies provide evidence that actin reorganization is controlled by intracellular redistribution of signaling molecules, such as the PI4,5P2/PI3,4,5P3 gradient. However, exploring underlying mechanisms is difficult and requires careful spatio-temporal control of external chemotactic stimuli. We designed a microfluidic setup to generate alternating chemotactic gradient fields for simultaneous multicell exposure, greatly facilitating statistical analysis. For a quantitative description of intracellular response dynamics, we apply alternating time sequences of spatially homogeneous concentration gradients across 300 mu m, reorienting on timescales down to a few seconds. Dictyostelium discoideum amoebae respond to gradient switching rates below 0.02 Hz by readapting their migration direction. For faster switching, cellular repolarization ceases and is completely stalled at 0.1 Hz. In this "chemotactically trapped" cell state, external stimuli alternate faster than intracellular feedback is capable to respond by onset of directed migration. To investigate intracellular actin cortex rearrangement during gradient switching, we correlate migratory cell response with actin repolymerization dynamics, quantified by a fluorescence distribution moment of the GFP fusion protein LimE Delta cc. We find two fundamentally different cell polarization types and we could reveal the role of PI3-Kinase for cellular repolarization. In the early aggregation phase, PI3-Kinase enhances the capability of D. discoideum cells to readjust their polarity in response to spatially alternating gradient fields, whereas in aggregation competent cells the effect of PI3-Kinase perturbation becomes less relevant.
M. Morales-Masis, S. J. van der Molen, T. Hasegawa, J. M. van Ruitenbeek, (2011) Bulk and surface nucleation processes in Ag2S conductance switches, PHYSICAL REVIEW B, 84, 115310 .
[DOI]
F. Mirjani, J. M. Thijssen, S. J. van der Molen (2011) Advantages and limitations of transition voltage spectroscopy: A theoretical analysis, PHYSICAL REVIEW B, 84, 115402 .
[DOI]
S. M. Schramm, J. Kautz, A. Berghaus, O. Schaff, R. M. Tromp, S. J. van der Molen (2011) Low-energy electron microscopy and spectroscopy with ESCHER: Status and prospects, IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 55.
[DOI]
I. Sikharulidze, R. van Gastel, S. Schramm, J. P. Abrahams, B. Poelsema, R. M. Tromp, S. J. van der Molen, (2011) Low energy electron microscopy imaging using Medipix2 detector, NUCLEAR INSTRUMENTS & METHODS, 633, S239–S242.
[DOI]

2010
Daniela J. Kraft, Julius W.J. de Folter, Bob Luigjes, Sonja I.R. Castillo, Stefano Sacanna, Albert P. Philipse and Willem K. Kegel (2010) Conditions for Equilibrium Solid-Stabilized Emulsions, The Journal of Physical Chemistry B, 114(32), 10347-10356.
[DOI]
Daniela J. Kraft, Bob Luigjes, Julius W.J. de Folter, Albert P. Philipse, and Willem K. Kegel (2010) Evolution of Equilibrium Pickering Emulsions—A Matter of Time Scales, Journal of Physical Chemistry B , 114 (38), 12257-12263.
[DOI]
Daniela J. Kraft, Jan Hilhorst, Maria A.P. Heinen, Mathijs J. Hoogenraad, Bob Luigjes, and Willem K. Kegel (2010) Patchy Polymer Colloids with Tunable Anisotropy Dimensions, Part of the Special Section “Clusters in Complex Fluids”, The Journal of Physical Chemistry B, Highlighted on the Cover of the Special Issue, 115 (22), 7175-7181.
[DOI]
M. Morales-Masís, H.D. Wiemhöfer, and J.M. van Ruitenbeek (2010) Towards a Quantitative Description of Solid Electrolyte Conductance Switches, Nanoscale, 08, 2, 2275-2280.
[Abstract] [DOI] [pdf]
We present a quantitative analysis of the steady-state electronic transport in a resistive switching device. The device is composed of a thin film of Ag2S (solid electrolyte) contacted by a Pt nano-contact acting as ion-blocking electrode, and a large-area Ag reference electrode. When applying a bias voltage both ionic and electronic transport occurs, and depending on the polarity it causes an accumulation of ions around the nano-contact. At small applied voltages (pre-switching) we observed this as a strongly nonlinear current–voltage curve, which is modeled using the Hebb–Wagner treatment for polarization of a mixed conductor. This model correctly describes the transport of the electrons within the polarized solid electrolyte in the steady-state up until the resistance switching, covering the entire range of non-stoichiometries, and including the supersaturation range just before the deposition of elemental silver. In this way, it is a step towards a quantitative understanding of the processes that lead to resistance switching.
S. Kelly, F. Galli, I. Komissarov, J. Aarts (2010) Loss of spin glass behavior in ultrathin AuFe films, Phys. Rev. B , 81, 132402.
Anna Kicheva, Laurent Holtzer, Ortrud Wartlick, Thomas Schmidt & Marcos Gonzále (2010) Quantitative Imaging of Morphogen Gradients in Drosophila Imaginal Discs., in Imaging in Developmental Biology: A Laboratory Manual. Chap.37, CSHL Press.
[pdf]
Paige Shaklee, Timon Idema, Marileen Dogterom, Cees Storm & Thomas Schmidt (2010) Kinesin recycling in stationary membrane tubes., Biophys. J, 99, 1835-1841.
[Abstract] [DOI] [pdf]
Collections of motors dynamically organize to extract membrane tubes. These tubes grow but often pause or change direction as they traverse an underlying microtubule (MT) network. In vitro, membrane tubes also stall: they stop growing in length despite a large group of motors available at the tip to pull them forward. In these stationary membrane tubes in vitro, we find that clusters of processive kinesin motors form and reach the tip of the tube at regular time intervals. The average times between cluster arrivals depends on the time over which motors depart from the tip, suggesting that motors are recycled toward the tip. Numerical simulations of the motor dynamics in the membrane tube and on the MTs show that the presence of cooperative binding between motors quantitatively accounts for the clustering observed experimentally. Cooperative binding along the length of the MT and a nucleation point at a distance behind the tip define the recycling period. Based on comparison of the numerical results and experimental data, we estimate a cooperative binding probability and concentration regime where the recycling phenomenon occurs.
Stefan Semrau, Marilyn Monster, Matthijs van der Knaap, Bobby Florea, Thomas Schmidt and Mark Overhand (2010) Membrane lysis by gramicidin S visualized in red blood cells and giant vesicles., BBA Biomembranes, 1798, 2033-2039.
[Abstract] [DOI] [pdf]
The cationic amphiphilic antimicrobial peptide gramicidin S (GS) is an effective antibiotic. Its applicability is however restricted to topical infections due to its hemolytic activity. In this study, the process of GS induced hemolysis was investigated in detail for the first time. The morphological changes of red blood cells (RBCs) inflicted by GS were visualized and explained in terms of a physical model. The observed fast rupture events were further investigated with giant unilamellar vesicles (GUVs) as model systems for RBCs. Measurements of membrane fluctuations in GUVs revealed that the membrane surface tension was increased after incubation with GS. These findings are in agreement with the hypothesis that amphiphilic peptides induce membrane rupture by an increase in membrane tension.
Freek van Hemert, Milena Lazova, B.Ewa Snaar-Jagalska & Thomas Schmidt (2010) Mobility of G proteins is heterogeneous and polarized during chemotaxis., J. Cell Sci, 123, 2922-30.
[Abstract] [DOI] [pdf]
The interaction of G-protein-coupled receptors with G proteins is a key event in transmembrane signal transduction that leads to vital decision-making by the cell. Here, we applied single-molecule epifluorescence microscopy to study the mobility of both the Gβγ and the Gα2 subunits of the G protein heterotrimer in comparison with the cAMP receptor responsible for chemotactic signaling in Dictyostelium discoideum. Our experimental results suggest that ~30% of the G protein heterotrimers exist in receptor-precoupled complexes. Upon stimulation in a chemotactic gradient, this complex dissociates, subsequently leading to a linear diffusion and collision amplification of the external signal. We further found that Gβγ was partially immobilized and confined in an agonist-, F-actin- and Gα2-dependent fashion. This led to the hypothesis that functional nanometric domains exist in the plasma membrane, which locally restrict the activation signal, and in turn, lead to faithful and efficient chemotactic signaling.
Timon Idema, Stefan Semrau, Cornelis Storm & Thomas Schmidt (2010) Membrane mediated sorting., Phys. Rev. Lett, 104, 198102-1:4.
[Abstract] [DOI] [pdf]
Inclusions in biological membranes may interact via deformations they induce on the shape of that very membrane. Such deformations are a purely physical effect, resulting in nonspecific forces between the inclusions. In this Letter we show that this type of interaction can organize membrane domains and hence may play an important biological role. Using a simple analytical model we predict that membrane inclusions sort according to the curvature they impose. We verify this prediction by both numerical simulations and experimental observations of membrane domains in phase separated vesicles.
Paige M. Shaklee, Stefan Semrau, Stefan Kubick, Marileen Dogterom & Thomas Schmidt (2010) Protein incorporation in giant vesicles under physiological conditions., Chem. Bio. Chem, 11, 175:179.
[Abstract] [DOI] [pdf]
Proteins were incorporated into giant vesicles (GVs) under physiological conditions by using electroformation. The figure shows these fluorescently labeled GVs in which proteins are encapsulated. Our method opens doors to investigating the membrane properties of native, intracellular membranes.
Paige M. Shaklee, Line Bourel-Bonnet, Marileen Dogterom & Thomas Schmidt (2010) Nonprocessive motor dynamics at the microtubule membrane tube interface., Biophys. J, 98, 93-100.
[Abstract] [DOI] [pdf]
Key cellular processes such as cell division, membrane compartmentalization, and intracellular transport rely on motor proteins. Motors have been studied in detail on the single motor level such that information on their step size, stall force, average run length, and processivity are well known. However, in vivo, motors often work together, so that the question of their collective coordination has raised great interest. Here, we specifically attach motors to giant vesicles and examine collective motor dynamics during membrane tube formation. Image correlation spectroscopy reveals directed motion as processive motors walk at typical speeds (≤500 nm/s) along an underlying microtubule and accumulate at the tip of the growing membrane tube. In contrast, nonprocessive motors exhibit purely diffusive behavior, decorating the entire length of a microtubule lattice with diffusion constants at least 1000 times smaller than a freely-diffusing lipid-motor complex in a lipid bilayer (1 μm2/s); fluorescence recovery after photobleaching experiments confirm the presence of the slower-moving motor population at the microtubule-membrane tube interface. We suggest that nonprocessive motors dynamically bind and unbind to maintain a continuous interaction with the microtubule. This dynamic and continuous interaction is likely necessary for nonprocessive motors to mediate bidirectional membrane tube dynamics reported previously.
Salverda, JM, Patil, AV, Mizzon, G, Kuznetsova, S, Zauner, G, Akkilic, N, Canters, GW, Davis, JJ, Heering, HA, Aartsma, TJ (2010) Fluorescent Cyclic Voltammetry of Immobilized Azurin: Direct Observation, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 49, 5776-5779.
[DOI]
Magis, GJ, den Hollander, MJ, Onderwaater, WG, Olsen, JD, Hunter, CN, Aartsma, TJ, Frese, RN (2010) Light harvesting, energy transfer and electron cycling of a native, BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798, 637-645.
[DOI]
Davis, JJ, Peters, B, Xi, W, Appel, J, Kros, A, Aartsma, TJ, Stan, R, Canters, GW (2010) Large Amplitude Conductance Gating in a Wired Redox Molecule, JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1, 1541-1546.
[DOI]
M. van Hecke (2010) Jamming of Soft Particles - Geometry, Mechanics, Scaling and Isostaticity, J. Phys. Cond. Matt., 22, 033101 .
[pdf]
P. Schall and M. van Hecke (2010) Shear Bands in Matter with Granularity, Annual Rev. Fluid Mech., 42, 67 .
[pdf]
A.O.N. Siemens and M. van Hecke (2010) Jamming - A Simple Introduction, Physica A, 389, 4255 .
[pdf]
K. Nichol, A. Zanin, R. Bastien, E. Wandersman and M. van Hecke (2010) Flow-induced Agitations Create a Granular Fluid, Phys. Rev. Lett., 104, 078302 .
[pdf]
S. Henkes, M. van Hecke and W. van Saarloos (2010) Critical jamming of frictional grains in the generalized isostaticity picture, EPL , 90, 14003 .
[pdf]
M. E. Möbius, G. Katgert and M. van Hecke (2010) Relaxation and Flow in Linearly Sheared Two-Dimensional Foams, EPL, 90, 44003 .
[pdf]
M. E. Möbius, T. Xia, W. van Saarloos, M. Orrit, and M. van Hecke (2010) Aging and solidification of supercooled glycerol, J. Phys. Chem. B , 114, 7439 .
[pdf]
S. Henkes, K. Shundyak, W. van Saarloos and M. van Hecke (2010) Local contact numbers in two dimensional packings of frictional disks, Soft Matter, 6, 2935 .
[pdf]
J.A. Dijksman and M. van Hecke (2010) Granular Flows in Split-Bottom Geometries, Soft Matter, 6, 2901 .
[pdf]
B.P. Tighe, J.H. Snoeijer, Th. J.H. Vlugt and M. van Hecke (2010) The force network ensemble for granular packings, Soft Matter, 6, 2908 .
[pdf]
G. Katgert, B.P. Tighe, M. E. Möbius and M. van Hecke (2010) Couette Flow of Two-Dimensional Foams, EPL, 90, 54002 .
[pdf]
B. P. Tighe, E. Woldhuis, J. J.C. Remmers, W. van Saarloos, and M. van Hecke (2010) Model for the Scaling of Stresses and Fluctuations in Flows near Jamming, Phys. Rev. Lett., 105, 088303 .
[pdf]
G. Katgert and M. van Hecke (2010) Jamming and Geometry of Two-Dimensional Foams, EPL, 92, 34002 .
[pdf]
J.A. Dijksman, E. Wandersman and M. van Hecke (2010) Follow the bouncing balls! -- 3-D imaging of flowing granular suspensions, Chaos, 20, 041105 .
[pdf]
O. Dauchot, D. J. Durian and M. van Hecke (2010) Dynamical Heterogeneities in Grains and Foams, Accepted for Chapter of Dynamical heterogeneities in glasses, colloids, and granular media .
[pdf]
J.A. Dijksman, E. Wandersman, S. Slotterback, C.R. Berardi, W.D. Updegraff, M. van Hecke and W. Losert (2010) From Frictional to Viscous Flows - Three Dimensional Imaging and Rheology of Gravitational Suspensions., Phys. Rev. E, 060301 .
[pdf]
Review Article. (2010) Theory of oscillations in the STM resulting from subsurface defects, Ye.S. Avotina, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek,, submitted.
[pdf]
C.A. Martin, J.M. van Ruitenbeek, and H.S.J. van der Zant, (2010) Sandwich-type gated mechanical break junctions, Nanotechnology , 21.
[DOI] [pdf]
R.H.M. Smit and J.M. van Ruitenbeek (2010) Atomic chains, Handbook of Nanophysics, Nanotubes and Nanowires, Klaus Sattler, , Ch. 35, pp. 1-14..
[pdf]
J.M. van Ruitenbeek (2010) Quasi-ballistic electron transport in atomic wires., The Oxford Handbook of Nanoscience and Nanotechnology Vol I: Basic Aspects, A. Narlikar and Y. Fu, eds., Oxford University Press, I.
[pdf]
M. van Zalk, A. Brinkman, J. Aarts, and H. Hilgenkamp (2010) Interface resistance of YBa2Cu3O7−δ/La0.67Sr0.33MnO3 ramp-type contacts, Physical Review B , 82, 134513.
S.R. Zandbergen and M.J.A. de Dood, (2010) Experimental observation of strong edge effects on the pseudodiffusive transport of light in photonic graphene, Phys. Rev. Lett., 104, o43903.
[pdf]
S.M. Thon, W.T.M. Irvine, D. Kleckner, and D. Bouwmeester, (2010) Polychromatic photonic quasicrystal cavities, Phys. Rev. Lett., 104, 243901.
[pdf]
W.H. Peeters, J.J.D. Moerman, and M.P. van Exter, (2010) Observation of Two-Photon Speckle Patterns, Phys. Rev. Lett., 104, 173601.
[pdf]
M. Merano, N. Hermosa, A. Aiello, and J.P. Woerdman (2010) Demonstration of a quasi-scalar angular Goos-Hänchen effect, Opt. Lett., 35, 3562-3564.
[pdf]
M. Merano, N. Hermosa, J.P. Woerdman, and A. Aiello (2010) How orbital angular momentum affects beam shifts in optical reflection, Phys. Rev. A, 82, 023817.
[pdf]
H. Di Lorenzo Pires, J. Woudenberg, and M.P. van Exter, (2010) Measurement of spatial coherence of partially coherent light with and without orbital angular momentum, J. Opt. Soc. Am. A, 27, 2630.
[pdf]
H. Di Lorenzo Pires, J. Woudenberg, and M.P. van Exter, (2010) Measurement of the orbital angular momentum spectrum of partially coherent beams, Opt. Lett., 35, 889.
[pdf]
H. Di Lorenzo Pires, H.C.B. Florijn, and M.P. van Exter, (2010) Measurement of the spiral spectrum of entangled two-photon states, Phys. Rev. Lett., 104, 020505.
[pdf]
W. Löffler, M.P. van Exter, G.W. t Hooft, E.R. Eliel, K. Hermans, D.J. Broer, and J.P. Woerdman, (2010) Polarization-dependent Goos-Hänchen shift at a graded dielectric interface, Opt. Comm., 283, 3367.
[pdf]
D. Kleckner, W.T.M. Irvine, S.S.R. Oemrawsingh, and D. Bouwmeester, (2010) Diffraction-limited high-finesse optical cavities, Phys. Rev. Lett., 104, 043814.
[pdf]
F. Haupt, S.S.R. Oemrausing, S.M. Thon, H. Kim, D. Kleckner, D. Ding, D.J. Suntrup, P.M. Petroff, and D. Bouwmeester (2010) Fiber-connectorized micropillar cavities, Appl. Opt. Lett., 97, 131113.
[pdf]
S.J.M. Habraken and G. Nienhuis, (2010) Universal description of geometric phases in higher-order optical modes bearing orbital angular momentum, Opt. Lett., 35, 3535.
[pdf]
S.J.M. Habraken and G. Nienhuis, (2010) Geometric phases in astigmatic optical modes of arbitrary order, J. Math. Phys., 51, 082702.
[pdf]
P.F. Chimento, G.W. t Hooft, and E.R. Eliel, (2010) Plasmonic tomography of optical vortices, Opt. Lett., 35, 3775.
[pdf]
C. Bonato, F. Haupt, S.S.R. Oemrawsingh, J. Gudat, D.P. Ding, M.P. van Exter, and D. Bouwmeester, (2010) CNOT and Bell-state analysis in the weak-coupling cavity QED regime, Phys. Rev. Lett., 104, 160503.
[pdf]
G.C.G. Berkhout, and M.W. Beijersbergen, (2010) Measuring optical vortices in a speckle pattern using a multi-pinhole interferometer, Opt. Express, 18, 13836.
[pdf]
G.C.G. Berkhout, M.P.J. Lavery, J. Courtial, M.W. Beijersbergen, and M.J. Padgett, (2010) Efficient Sorting of Orbital Angular Momentum States of Light, Phys. Rev. Lett., 105, 153601.
[pdf]
Lj. Babić, and M. de Dood, (2010) Interpretation of Fano lineshape reversal in the reflectivity spectra of photonic crystal slabs, Optics Express, 18, 26569-26582.
[pdf]
Malte Drescher, Bart D. van Rooijen, Gertjan Veldhuis, Vinod Subramaniam, Martina Huber (2010) A Stable Lipid-Induced Aggregate of α-Synuclein, J. Am. Chem. Soc., 132 (12), 4080-4082.
[pdf]
Stefania Tanase, Silvia Sottini, Valerie Marvaud, Edgar J.J. Groenen, Lise-Marie Chamoreau (2010) Anion-Induced Assembly of Hexacoordinate Rare-Earth(III) Complexes, Eur. J. Inorg. Chem., 3478-3483.
[pdf]
Eugenio Daviso, Anna Diller, Peter Gast, A. Alia, Johan Lugtenburg, Marc G. M?ller, J?rg Matysik (2010) Action Spectroscopy on Dense Samples of Photosynthetic Reaction Centers of Rhodobacter sphaeroides WT Based on Nanosecond Laser-Flash C-13 Photo-CIDNP MAS NMR, Appl. Magn. Res., 38, 105-116.
[pdf]
Dimitrios Maganas, Sergey Milikisyants, Jorrit M. A. Rijnbeek, Silvia Sottini, Nikolaos Levesanos, Panayotis Kyritsis, Edgar J. J. Groenen (2010) A Multifrequency High-Field Electron Paramagnetic Resonance Study of Co(II)S4 Coordination, Inorg. Chem., 49 (2), 595-605.
[pdf]
Eugenio Daviso, Shipra Prakash, A. Alia, Peter Gast, Gunnar Jeschke, J?rg Matysik (2010) Nanosecond-Flash N-15 Photo-CIDNP MAS NMR on Reaction Centers of Rhodobacter sphaeroides R26, Appl. Magn. Res., 37, 63-49.
[pdf]
E. Bordignon, H. Brutlach, L. Urban, A. Hideg, A. Savitsky, A. Schnegg, P. Gast, M. Engelhard, E.J.J. Groenen, K. M?bius, H.-J. Steinhoff (2010) Heterogeneity in the nitroxide micro-environment: polarity and proticity effects in spinlabeled proteins studied by multi frequency EPR, Appl. Magn. Res., 37, 391-403.
[pdf]
Silvia Sottini, Peter Gast, Anneloes Blok, Gerard W. Canters, Davide Cavazzini, Gian Luigi Rossi, Edgar J.J. Groenen (2010) A proton ENDOR study of Azurin, Appl. Magn. Res., 37, 219-227.
[pdf]
A. Gaiduk, M. Yorulmaz, P.V. Ruijgrok, M. Orrit (2010) Room-temperature detection of a single molecule's absorption by photothermal contrast, Science, 330, 353-356.
[pdf]
A. Gaiduk, P.V. Ruijgrok, M. Yorulmaz, M. Orrit (2010) Detection limits in photothermal microscopy, Chemical Science, 1, 343-350.
[pdf]
Ted Xia (Ph.D. thesis) (2010) Probing spatial heterogeneity in supercooled glycerol and temporal heterogeneity with single-molecule FRET in polyprolines, .
[pdf]
M. E. Möbius,T. Xia, W. van Saarloos, M. Orrit, M. van Hecke (2010) Aging and solidification of supercooled glycerol, J. Phys. Chem. B, 114, 7439-7444.
[pdf]
M.Orrit (2010) Chemical and physical aspects of charge transfer in the fluorescence intermittency of single molecules and quantum dots, Photochem. Photobiol. Sci., 9, 637-642.
[pdf]
F.Kulzer, T.Xia, M.Orrit (2010) Single molecules as optical nanoprobes for soft and complex matter, Angew. Chem. Int. Ed., 49, 854-866.
[pdf]
A.L. Tchebotareva, P.V. Ruijgrok, P. Zijlstra, M. Orrit (2010) Probing the acoustic vibrations of single metal nanoparticles by ultrashort laser pulses, Laser & Photon. Rev., 4, 581-597.
[pdf]
M. Flokstra, J.M. van der Knaap, J. Aarts (2010) Magnetic coupling in superconducting spin valves with strong ferromagnets, Physical Review B , 82, 184523.
M.S. Anwar, F. Czeschka, M. Hesselberth, M. Porcu, J. Aarts (2010) Long-range supercurrents through half-metallic ferromagnetic CrO2, Physical Review B Editor's choice , 82, 100501.
J. Aarts, C. Attanasio, C. Bell, C. Cirillo, M. Flokstra, J.M. v.d. Knaap (2010) Superconductor/Ferromagnet Hybrids: Bilayers and Spin Switching, Chapter 13 in: Nanoscience and Engineering in Superconductivity. Editors: V. Moschalkov, R. Wördenweber, W. Lang. ISBN 978-3-642-15136-1 (2010) .
 Raoul van Gastel, Sense Jan van der Molen en Ruud Tromp (2010) Oppervlakken filmen met trage elektronen, Nederlands Tijdschrift voor Natuurkunde, 332-336.
J.M. van Ruitenbeek (2010)  Quasi-ballistic electron transport in atomic wires., The Oxford Handbook of Nanoscience and Nanotechnology, A. Narlikar and Y. Fu, eds., Oxford University Press. ISBN 9780199533046, Vol. I: Basic Aspects..
R.H.M. Smit and J.M. van Ruitenbeek (2010)  Atomic chains, Handbook of Nanophysics, Nanotubes and Nanowires, Klaus Sattler, ed., CRC Press, Print ISBN 978-1-4200-7542-7.
 M. Morales-Masís, H.D. Wiemhöfer, and J.M. van Ruitenbeek (2010)  Towards a quantitative description of solid electrolyte conductance switches, arXiv:1004.3078v1, Nanoscale.
Ye.S. Avotina, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek (2010) Theory of oscillations in the STM conductance resulting from subsurface defects (Review Article)., Low Temp. Phys., 36, 1066-1084.
[Abstract] [DOI] [pdf]
In this review we present recent theoretical results concerning investigations of single subsurface defects by means of a scanning tunneling microscope (STM). These investigations are based on the effect of quantum interference between the electron partial waves that are directly transmitted through the contact and the partial waves scattered by the defect. In particular, we have shown the possibility imaging the defect position below a metal surface by means of STM. Different types of subsurface defects have been discussed: point-like magnetic and nonmagnetic defects, magnetic clusters in a nonmagnetic host metal, and nonmagnetic defects in a s-wave superconductor. The effect of Fermi surface anisotropy has been analyzed. Also, results of investigations of the effect of a strong magnetic field to the STM conductance of a tunnel point contact in the presence of a single defect has been presented.
C.A. Martin, J.M. van Ruitenbeek, and H.S.J. van der Zant (2010)  Sandwich-type gated mechanical break junctions, Nanotechnology, 21.
Liu, Z.F., Jiang, L.H., Galli, F., Nederlof, I, Olsthoorn, R.C.L., Lamers, G.E.M., Oosterkamp, T.H., Abrahams, J.P. (2010) A Graphene Oxide center dot Streptavidin Complex for Biorecognition - Towards Affinity Purification, Advanced Functional Materials, vol. 20, 2857-2865..
E.C.M. Disseldorp, F.C. Tabak, A.J. Katan, M.B.S. Hesselberth, T.H. Oosterkamp, J.W.M. Frenken, W.M. van Spengen (2010) Response to Comment on MEMS-based high speed scanning probe microscopy, Rev. Sci. Instrum., 81 , 117102.
J.W.M. Beenakker, J.H.N. Lindeman, B. Ashcroft, M.H. van Es, N.B.R. Koekkoek, F.A. Prins, J.F. Tielemans, H. Abdul-Hussien, R.A. Bank, T.H. Oosterkamp (2010) Distinct defects in collagen micro-architecture underlie vessel wall failure in growing aortic abdominal aneurysms and aneurysms in Marfan syndrome, Atherosclerosis Suppl., 11 , 101.
B.A. Ashcroft, T.H. Oosterkamp (2010) AutoMicromanager: A microscopy scripting toolkit for LABVIEW and other programming environments. , Rev. Sci. Instrum., 81 , 113708.
E.C.M. Disseldorp, F.C. Tabak, A.J. Katan, M.B.S. Hesselberth, T.H. Oosterkamp, J.W.M. Frenken, W.M. van Spengen (2010) MEMS-based high speed scanning probe microscopy, Rev. Sci. Instrum., 81 , 043702.
 W.M. van Spengen, G.H.J.C. Wijts, V.A.I. Turq, J.W.M. Frenken (2010) Microscale friction reduction by normal force modulation in MEMS, Adhesion Aspects in MEMS-NEMS , 339-350.
W.M. van Spengen, V.A.I. Turq, J.W.M. Frenken.Beilstein J. (2010) The description of friction of silicon MEMS with surface roughness: virtues and limitations of a stochastic Prandtl-Tomlinson model and the simulation of vibration-induced friction reduction, Nanotechnol., 1 , 163-171.
J. Gustafson, R. Westerström, O. Balmes, A. Resta, R. van Rijn, X. Torrelles, C.T. Herbschleb, J.W.M. Frenken, E. Lundgren (2010) Reply to Comment on Catalytic activity of the Rh surface oxide: CO oxidation over Rh(111) under realistic conditions, J. Phys. Chem. C, 114, 22372-22373.
W.M. van Spengen, S.B. Roobol, W.P. Klaassen, T.H. Oosterkamp. (2010) The MEMSamp: using (RF-)MEMS switches for the micromechanical amplification of electronic signals, J. Micromech. Microeng., 20.
 B.L.M. Hendriksen, M.D. Ackermann, R. van Rijn, D. Stoltz, I. Popa, O. Balmes, A. Resta, D. Wermeille, R. Felici, S. Ferrer, J.W.M. Frenken (2010) The role of steps in surface catalysis and reaction oscillations, Nature Chemistry, 2, 730-734.
C.T. Herbschleb, S.C. Bobaru, J.W.M. Frenken (2010) High-pressure STM study of NO reduction by CO on Pt(100), Catalysis Today, 154 , 61-67 .
M. S. Anwar, F. Czeschka, M. Hesselberth, M. Porcu, J. Aarts (2010) Long range supercurrents through half-metallic ferromagnetic CrO2., Phys. Rev. B., 82, 100501.
R. van Rijn, O. Balmes, R. Felici, J. Gustafson, D. Wermeille, R. Westerström, E. Lundgren, J.W.M. Frenken (2010) Comment on CO oxidation on Pt-group metals from ultrahigh vacuum to near atmospheric pressures. 2. Palladium and Platinum, J. Phys. Chem. C, 114, 6875-6876.
F.C. Tabak, E.C.M. Disseldorp, G.H. Wortel, A.J. Katan, M.B.S. Hesselberth, T.H. Oosterkamp, J.W.M. Frenken, W.M. van Spengen (2010) MEMS-based fast scanning probe microscopes, Ultramicroscopy, 110 , 599-604.
A.V. Patil, A.F. Beker, F.G.M. Wiertz, H.A. Heering, G. Coslovich, R. Vlijm, T.H. Oosterkamp (2010) Fabrication and characterization of polymer insulated carbon nanotube modified electrochemical nanoprobes, Nanoscale, 2, 734-738.
J.W.M. Frenken, T.H. Oosterkamp (2010) When mica and water meet, Nature, 464, 38-39.
G. Dong, E.B. Fourré, F.C. Tabak et al (2010) How boron nitride forms a regular nanomesh on Rh(111). How boron nitride forms a regular nanomesh on Rh(111), Phys. Rev. Lett., 104, 096102.
T.H. Oosterkamp, M. Poggio, C.L. Degen, H.J. Mamin, D. Rugar (2010) Frequency domain multiplexing of force signals with application to magnetic resonance force microscopy., Appl. Phys. Lett., 96, 083107.
R. van Rijn, M.D. Ackermann, O. Balmes, T. Dufrane, A. Geluk, H. Gonzalez, H. Isem, E. de Kuyper, L. Petit, V.A. Sole, D. Wermeille, R. Felici, J.W.M. Frenken (2010) Ultrahigh vacuum/high-pressure flow reactor for surface x-ray diffraction and grazing incidence small angle x-ray scattering studies close to conditions for industrial catalysis, Rev. Sci. Instrum., 81, 014101.
J. Gustafson, R. Westerström, O. Balmes, A. Resta, R. van Rijn, X. Torrelles, C.T. Herbschleb, J.W.M. Frenken, E. Lundgren. (2010) Catalytic activity of the Rh Surface Oxide: CO oxidation over rh(111) under realistic conditions, J. Phys. Chem. C, 114, 4580-4583.
Y. Yuana, T.H. Oosterkamp, S. Bahatyrova, B. Ashcroft, P. Garcia Rodriguez, R.M. Bertina, S. Osanto. (2010) Atomic force microscopy: a novel approach to the detection of nanosized blood microparticles, J. Thrombosis and Haemostasis, 8, 315-323.
E.C. Heeres, A.J. Katan, M.H. van Es, A.F. Beker, M. Hesselberth, D.J. van der Zalm, T.H. Oosterkamp (2010) A compact multipurpose nanomanipulator for use inside a scanning electron microscope, Rev. Sci. Instrum., 81, 23704 .
J.H.N. Lindeman, B.A. Ashcroft, J.W.M. Beenakker, M.H. van Es, N.B.R. Koekkoek, F.A. Prins, J.F. Tielemans, H. Abdul-Hussien, R.A. Bank, T.H. Oosterkamp (2010) Distinct defects in collagen micro-architecture cause vessel wall failure in the aortic abdominal aneurysm and Marfan syndrome., PNAS, 107, 862-865.
Sackmann, Erich Keber, Felix Heinrich, Doris (2010) Physics of Cellular Movements, ANNUAL REVIEW, 1.
[Abstract] [DOI]
The survival of cells depends on perpetual active motions, including (a) bending excitations of the soft cell envelopes, (b) the bidirectional transport of materials and organelles between the cell center and the periphery, and (c) the ongoing restructuring of the intracellular macromolecular scaffolds mediating global cell changes associated with cell adhesion locomotion and phagocytosis. Central questions addressed are the following: How can this bustling motion of extremely complex soft structures be characterized and measured? What are the major driving forces? Further topics include (a) the active dynamic control of global shape changes by the interactive coupling of the aster-like soft scaffold of microtubules and the network of actin filaments associated with the cell envelope (the actin cortex) and (b) the generation of propulsion forces by solitary actin gelation waves propagating within the actin cortex.
A. J. Kronemeijer, E. H. Huisman, H. B. Akkerman, A. M. Goossens, I. Katsouras, P. A. van Hal, T. C. T. Geuns, S. J. van der Molen, P. W. M. Blom, D. M. de Leeuw (2010) Electrical characteristics of conjugated self-assembled monolayers in large-area molecular junctions, APPLIED PHYSICS LETTERS, 97, 173302 .
[DOI]
A. J. Kronemeijer, E. H. Huisman, I. Katsouras, P. A. van Hal, T. C. T. Geuns, P. W. M. Blom, S. J. van der Molen, D. M. de Leeuw, (2010) Universal Scaling in Highly Doped Conducting Polymer Films, PHYSICAL REVIEW LETTERS, 105, 156604 .
[DOI]
Sense Jan van der Molen, Peter Liljeroth (2010) Charge transport through molecular switches, JOURNAL OF PHYSICS: CONDENSED MATTER, 22.
[DOI]

2009
Daniela J. Kraft, Wessel S. Vlug, Carlos M. van Kats, Alfons van Blaaderen, Arnout Imhof and Willem K. Kegel (2009) Self-Assembly of Colloids with Liquid Protrusions, Journal of the American Chemical Society, 131(3), 1182-1186.
[DOI]
Daniela J. Kraft, Jan Groenewold and Willem K. Kegel (2009) Colloidal molecules with well-controlled bond angles, Soft Matter, 5(20), 3823-3826.
[DOI]
Fan-Tso Chien and John van Noort (2009) 10 years of tension on chromatin: results from single molecule force spectroscop, Curr Pharm Biotechnol, 10, 474--485.
[Abstract] [pdf]
The compact, yet dynamic organization of chromatin plays an essential role in regulating gene expression. Although the static structure of chromatin fibers has been studied extensively, the controversy about the higher order folding remains. In the past ten years a number of studies have addressed chromatin folding with single molecule force spectroscopy. By manipulating chromatin fibers individually, the mechanical properties of the fibers were quantified with piconewton and nanometer accuracy. Here, we review the results of force induced chromatin unfolding and compare the differences between experimental conditions and single molecule manipulation techniques like force and position clamps. From these studies, five major features appeared upon forced extension of chromatin fibers: the elastic stretching of chromatin's higher order structure, the breaking of internucleosomal contacts, unwrapping of the first turn of DNA, unwrapping of the second turn of DNA, and the dissociation of histone octamers. These events occur sequentially at the increasing force. Resolving force induced structural changes of chromatin fibers at the single molecule level will help to provide a physical understanding of processes involving chromatin that occur in vivo and will reveal the mechanical constraints that are relevant for processing and maintenance of DNA in eukaryotes.
Maik Engeholm and Martijn de Jager and Andrew Flaus and Ruth Brenk and John van Noort and Tom Owen-Hughes (2009) Nucleosomes can invade DNA territories occupied by their neighbors., Nat Struct Mol Biol, Feb, 16, 151--158.
[Abstract] [DOI] [pdf]
Nucleosomes are the fundamental subunits of eukaryotic chromatin. They are not static entities, but can undergo a number of dynamic transitions, including spontaneous repositioning along DNA. As nucleosomes are spaced close together within genomes, it is likely that on occasion they approach each other and may even collide. Here we have used a dinucleosomal model system to show that the 147-base-pair (bp) DNA territories of two nucleosomes can overlap extensively. In the situation of an overlap by 44 bp or 54 bp, one histone dimer is lost and the resulting complex can condense to form a compact single particle. We propose a pathway in which adjacent nucleosomes promote DNA unraveling as they approach each other and that this permits their 147-bp territories to overlap, and we suggest that these events may represent early steps in a pathway for nucleosome removal via collision.
Wiepke J A Koopmans and Ruth Buning and Thomas Schmidt and John van Noort (2009) spFRET using Alternating Excitation and FCS reveals Progressive DNA Unwrapping i, Biophys J, July, In print, x-x.
[Abstract] [DOI] [pdf]
Accessibility to DNA wrapped in nucleosomes is essential for nuclear processes such as DNA transcription. Large conformational changes in nucleosome structure are required to facilitate protein binding to target sites within nucleosomal DNA. Transient unwrapping of DNA from nucleosome ends can provide an intrinsicexposure of wrapped DNA, allowing proteins to bind DNA that would otherwise be occluded in the nucleosome. The molecular details underlying these mechanisms remain to be resolved. Here we show how DNA unwrapping occurs progressively from both nucleosome ends. We performed singlepair fluorescence resonance energy transfer (spFRET) spectroscopy with alternating laser excitation (ALEX) on nucleosomes either in free solution or confined in a gel after PAGE separation. We combined ALEX-spFRET with a correlation analysis onselected bursts of fluorescence, to resolve a variety of unwrapped nucleosome conformations. The experiments reveal thatnucleosomes are unwrapped with an equilibrium constant of ~0.2–0.6 at nucleosome ends and ~0.1 at a location 27 basepairsinside the nucleosome, but still remain stably associated. Our findings, obtained using a powerful combination of single-molecule fluorescence techniques and gel electrophoresis, emphasize the delicate interplay between DNA accessibility and condensation in chromatin.
Maarten Kruithof and Fan-Tso Chien and Andrew Routh and Colin Logie and Daniela Rhodes and John van Noort (2009) Single-molecule force spectroscopy reveals a highly compliant helical folding fo, Nat Struct Mol Biol, May, 16, 534--540.
[Abstract] [DOI] [pdf]
The compaction of eukaryotic DNA into chromatin has been implicated in the regulation of all DNA processes. To unravel the higher-order folding of chromatin, we used magnetic tweezers and probed the mechanical properties of single 197-bp repeat length arrays of 25 nucleosomes. At forces up to 4 pN, the 30-nm fiber stretches like a Hookian spring, resulting in a three-fold extension. Together with a high nucleosome-nucleosome stacking energy, this points to a solenoid as the underlying topology of the 30-nm fiber. Unexpectedly, linker histones do not affect the length or stiffness of the fiber but stabilize its folding. Fibers with a nucleosome repeat length of 167 bp are stiffer, consistent with a two-start helical arrangement. The observed high compliance causes extensive thermal breathing, which forms a physical basis for the balance between DNA condensation and accessibility.
M. Kruithof and J. van Noort (2009) Hidden Markov analysis of nucleosome unwrapping under force., Biophys J, May, 96, 3708--3715.
[Abstract] [DOI] [pdf]
Transient conformational changes of DNA-protein complexes play an important role in the DNA metabolism but are generally difficult to resolve. Single molecule force spectroscopy has the unique capability to follow such reactions but Brownian fluctuations in the end-to-end distance of a DNA tether can obscure these events. Here we measured the force-induced unwrapping of DNA from a single nucleosome and show that hidden Markov analysis, adopted for the nonlinear force-extension of DNA, can readily resolve unwrapping events that are significantly smaller than the Brownian fluctuations. The resulting probability distributions of the tether length are used to accurately resolve small changes in contour length and persistence length. The latter is shown to be directly related to the DNA bending angle of the complex. The wormlike chain-adapted hidden Markov analysis can be used for any transient DNA-protein complex and provides a robust method for the investigation of these transient events.
Heinz Neumann and Susan Hancock and Ruth Buning and Andrew Routh and Lynda Chapman and Joanna Somers and Tom Owen-Hughes and John van Noort and Daniela Rhodes and Jason Chin (2009) Site-specifically acetylated histones define the structural and functional role, Submitted for publication, x-x.
[Abstract] [pdf]
H3K56 acetylation defines the epigenetic status of human embryonic stem cells, and orchestrates DNA replication, chromosome condensation, transcription, telomeric silencing, and DNA repair. The mechanistic bases of these phenomena are poorly understood and their investigation requires homogeneously acetylated H3K56, which has previously been impossible to synthesize. Here we report a method for the production of homogenously, site-specifically acetylated recombinant histones. Nucleosomes and chromatin arrays bearing H3K56Ac demonstrate that acetylation does not directly antagonize the compaction of chromatin or nucleosome stability. The observed twofold increase in DNA breathing supports the proposal that deacetylation of H3K56Ac mediates silencing by restricting partial unwrapping of the DNA at the entry-exit point of the nucleosome. We observe a small effect of the modification on SWI/SNF mediated remodelling and dimer exchange that may contribute to the effect of the acetylation on histone gene transcription and these effects may be coupled to the effect on DNA breathing.
John van Noort (2009) Genen in chromatine: de verpakking bepaalt de boodschap, NTvN, 336-341.
[Abstract] [pdf]
DNA vormt in onze cellen complexen met eiwitten. De structuur van dit complex, chromatine genaamd, is al 30 jaar het onderwerp van discussie. Wij hebben een magnetisch pincet gebruikt om een enkel DNA-molecuul, opgevouwen in chromatine, letterlijk te ontrafelen. Niet alleen de vouwing van het DNA is opgehelderd, maar ook de soort en sterkte van de interacties die hier voor zorgen.
Marcel J M Schaaf, Wiepke J A Koopmans, Tobias Meckel, John van Noort, B. Ewa Snaar-Jagalska, Thomas Schmidt and Herman P Spaink (2009) Single-molecule microscopy reveals membrane microdomain organization of cells in, Biophys J, Aug, 97, 1206--1214.
[Abstract] [DOI] [pdf]
It has been possible for several years to study the dynamics of fluorescently labeled proteins by single-molecule microscopy, but until now this technology has been applied only to individual cells in culture. In this study, it was extended to stem cells and living vertebrate organisms. As a molecule of interest we used yellow fluorescent protein fused to the human H-Ras membrane anchor, which has been shown to serve as a model for proteins anchored in the plasma membrane. We used a wide-field fluorescence microscopy setup to visualize individual molecules in a zebrafish cell line (ZF4) and in primary embryonic stem cells. A total-internal-reflection microscopy setup was used for imaging in living organisms, in particular in epidermal cells in the skin of 2-day-old zebrafish embryos. Our results demonstrate the occurrence of membrane microdomains in which the diffusion of membrane proteins in a living organism is confined. This membrane organization differed significantly from that observed in cultured cells, illustrating the relevance of performing single-molecule microscopy in living organisms.
Joke J F A van Vugt and Martijn de Jager and Magdalena Murawska and Alexander Brehm and John van Noort and Colin Logie (2009) Multiple aspects of ATP-dependent nucleosome translocation by RSC and Mi-2 are d, PLoS One, 4, e6345.
[Abstract] [DOI] [pdf]
BACKGROUND: Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50\% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. METHODOLOGY/PRINCIPAL FINDINGS: We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. CONCLUSIONS/SIGNIFICANCE: Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.
Koen Wagner and Geri Moolenaar and John van Noort and Nora Goosen (2009) Single-molecule analysis reveals two separate DNA-binding domains in the Escheri, Nucleic Acids Res, Feb.
[Abstract] [DOI] [pdf]
The UvrA protein is the initial damage-recognizing factor in bacterial nucleotide excision repair. Each monomer of the UvrA dimer contains two ATPase sites. Using single-molecule analysis we show that dimerization of UvrA in the presence of ATP is significantly higher than with ADP or nonhydrolyzable ATPgammaS, suggesting that the active UvrA dimer contains a mixture of ADP and ATP. We also show that the UvrA dimer has a high preference of binding the end of a linear DNA fragment, independent on the presence or type of cofactor. Apparently ATP binding or hydrolysis is not needed to discriminate between DNA ends and internal sites. A significant number of complexes could be detected where one UvrA dimer bridges two DNA ends implying the presence of two separate DNA-binding domains, most likely present in each monomer. On DNA containing a site-specific lesion the damage-specific binding is much higher than DNA-end binding, but only in the absence of cofactor or with ATP. With ATPgammaS no discrimination between a DNA end and a DNA damage could be observed. We present a model where damage recognition of UvrA depends on the ability of both UvrA monomers to interact with the DNA flanking the lesion.
Stefan Semrau & Thomas Schmidt (2009) Membrane heterogeneity – from lipid domains to curvature effects., Soft Matter, 5, 3174:3186.
[Abstract] [DOI] [pdf]
The interest in membrane heterogeneity started with two biological questions: how is the plasma membrane organized on a microscopic scale and what is the influence of this structure on biological processes? The earliest model that set out to answer these questions was the homogeneous fluid mosaic (S. J. Singer and G. L. Nicolson, Science, 1972, 175, 720–731). This model was refined by including heterogeneity (Fig. 1), where either the lipid composition or the proteins were given the leading role. Both concepts are in the process of being reconciled in the light of new experiments on lipid–protein interactions. Those interactions range from specific chemical to unspecific and purely physical. The latter comprise membrane curvature mediated interactions which have recently been shown to influence a large number of biological processes. In parallel to the conception of refined models, new experimental techniques to determine membrane microstructure were developed. Single-molecule fluorescence has emerged as one of the leading technologies since it delivers the required spatial resolution and can be employed in living cells. In a complementary approach artificial model systems are used to study specific biophysical aspects of membranes in isolation and in a controllable way. Nowadays, artificial membranes have outgrown their initial status as simplistic mock cells: a rich spectrum of different phases and phase transitions and the unique possibility to study membrane material properties make them an exciting subject of research in their own right (U. Seifert, Adv. Phys., 1997, 46(1), 13–137, S. L. Veatch and S. L. Keller, Biochim. Biophys. Acta, 2005, 1746(3), 172–185). In this review we discuss state-of-the-art models for membrane microstructure on the basis of key experiments. We show how phase separated artificial membranes can be used to gain fundamental insight into lipid composition based heterogeneity and membrane mediated interactions. Finally, we review the basics of single-molecule tracking experiments in live cells and a new unbiased analysis method for single-molecule position data.
Henriette Jensenius, Dionne C.G. Klein, Martin van Hecke, Tjerk H. Oosterkamp, Thomas Schmidt and Jens C. Jensenius. (2009) Mannan-Binding Lectin: Structure, Oligomerization and Flexibility Studied by Ato, J. Mol. Biol, 391, 246:259.
[Abstract] [DOI] [pdf]
Mannan-binding lectin (MBL) is the archetypical pathogen recognition molecule of the innate immune defense. Upon binding to microorganisms, reactions leading to the destruction of the offender ensue. MBL is an oligomer of structural subunits each composed of three identical polypeptides. We used atomic force microscopy to reveal tertiary and quaternary structures of MBL. The images in both air and buffer show a quaternary structure best described as “sertiform”, that is, a hub from which the subunits fan out. The dimensions conform to those calculated from primary and secondary structures. The subunits associate with a preferred angle of 40° between them. This angle is stable with respect to the degree of oligomerization for MBL of four subunits or more. Due to an interruption in the collagenous sequence, the arms of the subunits are expected to form a kink. We find that ∼ 30% of the subunits are kinked and the kink angle distributed, quite broadly, around 145°. The conformation and flexibility of the MBL molecule that we observe differ distinctly from the popular view of a “bouquet-like” configuration as that found for related members of the complement system such as C1q. This structural information will further the understanding of the specific functioning of the MBL pathway of complement activation.
Laurent Holtzer & Thomas Schmidt (2009) Tracking of Individual Molecules in Cells and Tissue., Single Particle Tracking and Single Molecule Energy Transfer, C. Bräuchle, D.C., -.
[pdf]
Stefan Semrau, Timon Idema, Thomas Schmidt & Cornelis Strom (2009) Membrane mediated interactions measured using membrane domains, Biophys. J, 96, 4906:4915.
[DOI] [pdf]
Thomas Schmidt & Gerhard Schütz (2009) Single Molecule Analysis of Biomembranes., Handbook of Single-Molecule Biophysics, A. van Oijen & P. Hinterdorfer (eds.), , 19-42.
[pdf]
Pedro Miguel Ribeiro Paulo, Alexander Gaiduk, Florian Kulzer, Gabby Krens, Herman P. Spaink, Thomas Schmidt and Michel Orrit. (2009) Photothermal Correlation Spectroscopy of Gold Nanoparticles in Solution., J. Phys. Chem. C, 113, 11451:11457.
[Abstract] [DOI] [pdf]
We demonstrate correlation analysis of the photothermal signal from gold nanoparticles diffusing in solution. Our experimental setup is primarily optimized for large detection volumes and therefore has a relatively low numerical aperture (0.25). This requirement limits light collection and detection efficiency, but we can nevertheless detect particles as small as 20 nm in diameter in 100 μs. Photothermal correlation spectroscopy (PCS) in water and in water:glycerol mixtures gives access to characteristic diffusion times of some tens of milliseconds. Diffusion is enhanced for high pump intensities, due to the increased temperature around the particle. The photothermal signal at the detector arises from the interference of the scattered probe beam and a reference field. In the forward configuration, the reference is the transmitted probe beam itself. In the backward configuration, the reference wave is a reflection by a nearby interface. It has an optical phase difference depending on the distance of the particle to the reflecting interface. The backward signal also includes the directly modulated scattering signal. Potential applications of photothermal correlation in biological labeling are demonstrated on bacteriophage virus particles carrying 20 nm gold labels.
Strianese, M, Zauner, G, Tepper, AWJW, Bubacco, L, Breukink, E, Aartsma, TJ, Canters, GW, Tabares, LC (2009) A protein-based oxygen biosensor for high-throughput monitoring of cell, ANALYTICAL BIOCHEMISTRY, 385, 242-248.
[DOI]
Liu, LN, Aartsma, TJ, Thomas, JC, Zhou, BC, Zhang, YZ (2009) FRAP Analysis on Red Alga Reveals the Fluorescence Recovery Is Ascribed, PLOS ONE, 4, 5776-5779.
[DOI]
G. Katgert, A. Latka, M. E. Möbius and M. van Hecke (2009) Flow in linearly sheared two dimensional foams from bubble to bulk scale, Phys. Rev. E, 79, 066318 .
[pdf]
P. H. Hovenkamp, R. W. J. M. van der Ham, G. A. van Uffelen, M. van Hecke, J. A. Dijksman and W. Star (2009) Spore movement driven by the spore wall in an eusporangiate fern, Grana, 48, 122 .
[pdf]
H. Jensenius, D. C. G. Klein, M. van Hecke, T. H. Oosterkamp, T. Schmidt and J. C. Jensenius (2009) Mannan-Binding Lectin - Structure, Oligomerization, and Flexibility Studied by Atomic Force Microscopy, J. Mol. Biol, 391, 246 .
[pdf]
W. G. Ellenbroek, Z. Zeravcic, W. van Saarloos and M. van Hecke (2009) Non-affine respons - Jammed packings vs. spring networks, EPL, 87, 34004 .
[pdf]
W. G. Ellenbroek, M. van Hecke and W. van Saarloos (2009) Jammed frictionless disks - Connecting local and global response, Phys. Rev .E, 80, 061307 .
[pdf]
J. A. Dijksman and M. van Hecke (2009) The role of tap duration for the steady state density of vibrated granular media, EPL, 88, 44001 .
[pdf]
Ye.S. Avotina, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek, (2009) The signature of a single subsurface defect in the conductance of a tunnel point-contact., J. Physics: Conf. Ser. , 150.
[pdf]
J.M. van Ruitenbeek (2009) Atomic wires of carbon, Physics , 2, 42 .
[pdf]
M. Morales-Masis, S.J. van der Molen, W.T. Fu, M.B. Hesselberth, and J.M. van Ruitenbeek, (2009) Conductance switching in Ag2S devices fabricated by in-situ sulphurization, Nanotechnology, , 20, 095710.
[pdf]
C.A. Martin, R.H.M. Smit, H.S.J. van der Zant, and J.M. van Ruitenbeek (2009) A nanoelectromechanical single-atom switch, Nano Lett., 9, 2940-2945 .
[pdf]
R.H.M. Smit, A.I. Mares, M. Häfner, P. Pou, J.C. Cuevas Rodriguez, and J.M. van Ruitenbeek, (2009) Metallic properties of magnesium point contacts., New J. of Phys. , 11, 073043 .
[pdf]
O. Tal, M. Kiguchi, W.H.A. Thijssen, D. Djukic, C. Untiedt, R.H.M. Smit, and J.M. van Ruitenbeek, (2009) Molecular signature of highly conductive metal-molecule-metal junctions, Phys. Rev. B , 80, 085427 .
[pdf]
A.F. Otte, M. Ternes, S. Loth, C.P. Lutz, C.F. Hirjibehedin, and A.J. Heinrich (2009) Spin excitations of a Kondo-screened atom coupled to a second magnetic atom., Phys. Rev. Lett. , 103.
[DOI] [pdf]
Ye.S. Avotina, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek, (2009) Magneto-Orientation and quantum size effects in spin-polarized STM conductance In the presence of a subsurface magnetic cluster., Phys. Rev. B , 80, 115333.
[pdf]
Raoul van Gastel, Sense Jan van der Molen, Irakli Sikharulidze, Georg Gademann, Julia Jungmann, Ron M.A. Heeren en Marc Vrakking, (2009) Ruisloos deeltjes detecteren, Nederlands Tijdschrift voor Natuurkunde , 75-11, 374-377 .
[pdf]
S.M. Thon, M.T. Rakher, H. Kim, J. Gudat, W.T.M. Irvine, P.M. Petroff, and D. Bouwmeester (2009) Strong coupling through optical positioning of a quantum dot in a photonic crystal cavity, Appl. Phys. Lett., 94, 111115.
[pdf]
M.T. Rakher, N.G. Stoltz, L.A. Coldren, P.M. Petroff, and D. Bouwmeester (2009) Externally mode-matched cavity quantum electrodynamics with charge-tunable quantum dots, Phys. Rev. Lett., 102, 097403.
[pdf]
W.H. Peeters, J.J. Renema, and M.P. van Exter, (2009) Engineering of two-photon quantum correlation behind a double slit, Phys. Rev. A, 79, 043817.
[pdf]
M. Merano, J. B. Götte, A. Aiello, M. P. van Exter, and J. P. Woerdman, (2009) Goos-Hänchen shift for a rough metallic mirror, Opt. Exp., 17, 10864-10870.
[pdf]
M. Merano, A. Aiello, M. P. van Exter, and J. P. Woerdman, (2009) Observing angular deviations in the specular reflection of a light beam, Nature Photonics, 3, 337.
[pdf]
H. Di Lorenzo Pires and M.P. van Exter, (2009) Near-field correlations in the two-photon field, Phys. Rev. A, 80, 053820.
[pdf]
H. Di Lorenzo Pires, C.H. Monken, and M.P. van Exter, (2009) Direct measurement of transverse-mode entanglement in two-photon states, Phys. Rev. A, 80, 022307.
[pdf]
H. Di Lorenzo Pires and M.P. van Exter, (2009) Observation of near-field correlations in spontaneous parametric down-conversion, Phys. Rev. A, 79, 041801.
[pdf]
S.J.M. Habraken and G. Nienhuis (2009) Rotationally induced vortices in optical cavity modes, J. Opt. A, 11, 094006.
[pdf]
S.J.M. Habraken and G. Nienhuis (2009) Rotational stabilization and destabilization of an optical cavity, Phys. Rev. A, 79, 011805.
[pdf]
M.P. van Exter, J. Gudat, G. Nienhuis, and D. Bouwmeester (2009) Spin quantum jumps in a singly charged quantum dot, Phys. Rev. A, 80, 023812.
[pdf]
E.F.C. Driessen, F.R. Braakman, E.M. Reiger, S.N. Dorenbos, V. Zwiller, and M.J.A. de Dood (2009) Impedance model for the polarization-dependent optical absorption of superconducting single-photon detectors,, Eur. Phys. J.: Appl. Phys., 47, 10701.
[pdf]
E.F.C. Driessen and M.J.A. de Dood (2009) The Perfect Absorber, Appl. Phys. Lett., 94, 171109.
[pdf]
C. Bonato, D. Ding, J. Gudat, S. Thon, H. Kim, P.M. Petroff, M.P. van Exter, and D. Bouwmeester (2009) Tuning micropillar cavity birefringence by laser induces surface defects, Appl. Phys. Lett., 95, 251104.
[pdf]
C.W.J. Beenakker, J.W.F. Venderbos, and M.P. van Exter, (2009) Two-Photon Speckle as a Probe of Multi-Dimensional Entanglement, Phys. Rev. Lett., 102, 193601.
[pdf]
G.C.G. Berkhout and M.W. Beijersbergen, (2009) Using a multipoint interferometer to measure the orbital angular momentum of light in astrophysics, J. Opt. A, 11, 094021.
[pdf]
A. Aiello, M. Merano, and J. P. Woerdman, (2009) Duality between spatial and angular shift in optical reflection, Phys. Rev. A, 80, 061801.
[pdf]
A. Aiello, M. Merano, and J. P. Woerdman, (2009) Brewster cross polarization, Opt. Lett., 34, 1207.
[pdf]
Eugenio Daviso, Shipra Prakash, A. Alia, Peter Gast, Johannes Neugebauer, Gunnar Jeschke, J?rg Matysik (2009) The electronic structure of the primary electron donor of reaction centers of purple bacteria at atomic resolution as observed by photo-CIDNP 13C NMR, Proc. Natl. Acad. Sci., 106, 52, 22281-22286.
[pdf]
Sergey Milikisyants, Francesco Scarpelli, Michelina G. Finiguerra, Marcellus Ubbink, Martina Huber (2009) A pulsed EPR method to determine distances between paramagnetic centers with strong spectral anisotropy and radicals: The dead-time free RIDME sequence, J. Magn. Res., 201, 48-56.
[pdf]
Francesco Scarpelli, Malte Drescher, Tania Rutters-Meijneke, Andrea Holt, Dirk T.S. Rijkers, J. Antoinette Killian, Martina Huber (2009) Aggregation of Transmembrane Peptides Studied by Spin-Label EPR, J. Phys. Chem. B, 113 (36), 12257-12264.
[pdf]
H. Blok, I. Akimoto, S. Milikisyants, P. Gast, E.J.J. Groenen, J. Schmidt (2009) FID detection of EPR and ENDOR Spectra at High Microwave Frequencies, J. Magn. Res., 201, 57-60.
[pdf]
Armand W.J.W.Tepper, Sergey Milikisyants, Silvia Sottini, Erik Vijgenboom, Edgar J.J. Groenen, Gerard W.Canters (2009) Identification of a Radical Intermediate in the Enzymatic Reduction of Oxygen by a Small Laccase, J. Am. Chem. Soc., 131, 11680-11682.
[pdf]
Silvia Sottini, Guinevere Mathies, Peter Gast, Dimitrios Maganas, Panayotis Kyritsis, Edgar J.J. Groenen (2009) A W-band pulsed EPR/ENDOR study of Co(II)S4 coordination in the Co[(SPPh2)(SPiPr2)N]2 complex, Phys. Chem. Chem. Phys., 11, 6727-6732.
[pdf]
T.Xia, L.Xiao, M. Orrit (2009) Micron-sized structure in a thin glycerol film revealed by fluorescent probes, J. Phys. Chem. B 113, 15724-15729 .
[pdf]
M. Orrit (2009) From Langmuir-Blodgett films to single molecules, Colloids and Surfaces B: Biointerfaces, 74, 396-400.
[pdf]
M. Orrit, T.Basché (2009) Steady light from quantum dots, at last. But how?, ChemPhysChem, 10, 2383-2385.
[pdf]
M. Orrit (2009) Photons pushed together, Nature, 460, 42-44.
[pdf]
M.A. Kol'chenko, A.A.L. Nicolet, M.D. Galouzis, C. Hofman, B. Kozankiewicz, M. Orrit (2009) Single molecules detect ultra-slow oscillators in a molecular crystal excited by ac voltages, New J. Phys., 11, 023037.
[pdf]
A.L. Tchebotareva, M.A. van Dijk, P.V. Ruijgrok, V. Fokkema, M.H.S. Hesselberth, M. Lippitz, M. Orrit (2009) Acoustic and Optical Modes of Single Dumbbells of Gold Nanoparticles, ChemPhysChem, 10, 111-114.
[pdf]
M. Flokstra, J. Aarts (2009) Domain-wall enhancement of superconductivity in superconductor/ferromagnet hybrids: Case of weak ferromagnets, Physical Review B 80, Issue 14, 144513 (2009) , 80, Issue 14, 144513.
D.G. Gheorghe, R.J. Wijngaarden, C. Bell, J. Aarts (2009) Magnetization rotation in a superconductor/ferromagnet bilayer ring structure, Physical Review B , 80, Issue 14, 144518.
C. Cirillo, C. Bell, G. Iannone, S.L. Prischepa, J. Aarts, C. Attanasio (2009) Nonmonotonic behavior of the anisotropy coefficient in superconductor-ferromagnet-superconductor trilayers, Physical Review B , 80, Issue 9, 094510 .
Y.Q. Zhang, Z.D. Zhang, J. Aarts (2009) Charge-order melting and magnetic phase separation in thin films of Pr0.7Ca0.3MnO3, Physical Review B , 79, Issue 22, 224422.
A.S. Prokhorov, E.S. Zhukova, B.P. Gorshunov, M.B.S. Hesselberth, J. Aarts, G.J. Nieuwenhuys, S. Kaiser, M. Dressel (2009) Localization of conduction electrons in the ferromagnetic clusters AuFe, JETP Letters, 89, Issue 9, 466-470 .
M. van Zalk, M. Veldhorst, A. Brinkman, J. Aarts, H. Hilgenkamp (2009) Magnetization-induced resistance-switching effects in La0.67Sr0.33MnO3/YBa2Cu3O7− bi- and trilayers, Physical Review B, 79, Issue 13, 134509.
B. Gorshunov, S. Kaiser, E.S. Zhukova, A.S. Prokhorov, M.B.S. Hesselberth, J. Aarts, G. J. Nieuwenhuys, M. Dressel (2009) Charge carrier localization due to ferromagnetic clusters in concentrated AuFe alloys, Physical Review B , 79, Issue 5, 054203.
S.L. Prischepa, V.N. Kushnir, E.A. Ilyina, C.A. Attanasio, C. Cirillo, J. Aarts (2009) Microscopic proximity effect parameters in S/N and S/F heterostructures, Proceedings of the NATO Advanced Research Workshop on Electron Transport in Nanosystems Yalta, Ukraine 17-21 Series: NATO Science for Peace and Security Series B: Physics and Biophysics Bonca, Janez; Kruchinin, Sergei (Eds.), 2009, XXII, 398 p., Hardco.
C. Beekman (2009) Elektrische veldeffecten in mangaten een alternatief voor silicium, Eureka , 24, 14-17.
M. Morales-Masis S.J. van der Molen, W.T. Fu, M.B. Hesselberth, J.M. van Ruitenbeek (2009) Conductance switching in Ag(2)S devices fabricated by in situ sulfurization., NANOTECHNOLOGY , 20.
[DOI]
R. van Gastel, I. Sikharulidze, S. Schramm, J. P. Abrahams, B. Poelsema, R. M. Tromp, S. J. van der Molen (2009) Medipix 2 detector applied to low energy electron microscopy, ULTRAMICROSCOPY, 110, 33–35.
[DOI]
Everardus H. Huisman, Constant M. Guedon, Bart J. van Wees, Sense Jan van der Molen, (2009) Interpretation of Transition Voltage Spectroscopy, NANO LETTERS, 9, 3909–3913.
[DOI]
Edzard M. Geertsema, Sense Jan van der Molen, Marco Martens, Ben L. Feringa (2009) Optimizing rotary processes in synthetic molecular motors, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE USA, 106, 16919–16924.
[DOI]
M. L. Trouwborst, E. H. Huisman, S. J. van der Molen, B. J. van Wees, (2009) Bistable hysteresis and resistance switching in hydrogen-gold junctions, PHYSICAL REVIEW B, 80, 081407.
[DOI]
Sense Jan van der Molen, Jianhui Liao, Tibor Kudernac, Jon S. Agustsson, Laetitia Bernard, Michel Calame, Bart J.van Wees, Ben L. Feringa, Christian Schoenenberger (2009) Light-Controlled Conductance Switching of Ordered Metal-Molecule-Metal Devices, NANO LETTERS, 9, 76–80.
[DOI]

2008
Ye.S. Avotina, Yu.A. Kolesnichenko, S.B. Roobol, and J.M. van Ruitenbeek (2008) Conductance of a tunnel point-contact of noble metals in the presence of a single defect, Low Temperature Physics [Fiz. Nizk. Temp. 34, 268–272], 03, 34, 207-210.
[Abstract] [DOI] [pdf]
In a previous paper Ye. S. Avotina et al., Phys. Rev. B 74, 085411 2006, the effect of Fermi surface anisotropy on the conductance of a tunnel point contact with a single point-like defect situated in its vicinity was investigated theoretically. The oscillatory dependence of the conductance on the distance between the contact and the defect was found for a general Fermi surface geometry. In the present paper the method developed in the cited work is applied to the calculation of the conductance of noble metal contacts. An original algorithm, which enables the computation of the conductance for any parametrically specified Fermi surface, is proposed. On this basis a pattern of the conductance oscillations, which can be observed by the method of scanning tunneling microscopy, is obtained for different orientations of the surface for the noble metals.
Wiepke J A Koopmans and Thomas Schmidt and John van Noort (2008) Nucleosome immobilization strategies for single-pair FRET microscopy., Chemphyschem, Oct, 9, 2002--2009.
[Abstract] [DOI] [pdf]
All genomic transactions in eukaryotes take place in the context of the nucleosome, the basic unit of chromatin, which is responsible for DNA compaction. Overcoming the steric hindrance that nucleosomes present for DNA-processing enzymes requires significant conformational changes. The dynamics of these have been hard to resolve. Single-pair Fluorescence Resonance Energy Transfer (spFRET) microscopy is a powerful technique for observing conformational dynamics of the nucleosome. Nucleosome immobilization allows the extension of observation times to a limit set only by photobleaching, and thus opens the possibility of studying processes occurring on timescales ranging from milliseconds to minutes. It is crucial however, that immobilization itself does not introduce artifacts in the dynamics. Here we report on various nucleosome immobilization strategies, such as single-point attachment to polyethylene glycol (PEG) or surfaces coated with bovine serum albumin (BSA), and confinement in porous agarose or polyacrylamide gels. We compare the immobilization specificity and structural integrity of immobilized nucleosomes. A crosslinked star polyethylene glycol coating performs best with respect to tethering specificity and nucleosome integrity, and enables us to reproduce for the first time bulk nucleosome unwrapping kinetics in single nucleosomes without immobilization artifacts.
M. Kruithof and F. Chien and M. de Jager and J. van Noort (2008) Subpiconewton dynamic force spectroscopy using magnetic tweezers., Biophys J, Mar, 94, 2343--2348.
[Abstract] [DOI] [pdf]
We introduce a simple method for dynamic force spectroscopy with magnetic tweezers. This method allows application of subpiconewton force and twist control by calibration of the applied force from the height of the magnets. Initial dynamic force spectroscopy experiments on DNA molecules revealed a large hysteresis that is caused by viscous drag on the magnetic bead and will conceal weak interactions. When smaller beads are used, this hysteresis is sufficiently reduced to reveal intramolecular interactions at subpiconewton forces. Compared with typical quasistatic force spectroscopy, a significant reduction of measurement time is achieved, allowing the real-time study of transient structures and reaction intermediates. As a proof of principle, nucleosome-nucleosome interactions on a subsaturated chromatin fiber were analyzed.
Florian Kulzer, Thomas Schmidt, Michel Orrit & Herman P. Spaink (2008) Photothermal Detection of Individual Gold Nanoparticles: Perspectives for High-T, Chem. Phys. Chem, 9, 1761-6.
[Abstract] [DOI] [pdf]
We use photothermal microscopy to detect and image individual gold nanoparticles that are either embedded in a polymer film or immobilized in an aqueous environment. Reducing the numerical aperture of the detection optics allows us to achieve a 200-fold-enlarged detection volume while still retaining sufficient detectivity. We characterize the capabilities of this approach for the detection of gold colloids with a diameter of 20 nm, with emphasis on practical aspects that are important for high-throughput-screening applications. The extended detection volume in combination with the stability of the photothermal signal are major advantages compared to fluorescence-based approaches, which are limited by photoblinking and photobleaching. Careful consideration is given to the trade-off between the maximum increase in local temperature that can be tolerated by a biological specimen and the minimum integration time needed to reliably determine whether a given volume contains a target species. We find that our approach has the potential to increase the detection-limited flow rate (i.e. the limit given by the detection volume divided by the minimum detection time) by two to three orders of magnitude.
S.F.Gabby Krens, Shuning He, Gerda E.M. Lamers, Annemarie H. Meijer, Jeroen Bakkers, Thomas Schmidt, Herman P. Spaink and B. Ewa Snaar-Jagalskaa. (2008) Distinct functions for ERK1 and ERK2 in cell migration processes during zebrafish, Dev. Biol, 319, 370-83.
[Abstract] [DOI] [pdf]
The MAPKs are key regulatory signaling molecules in many cellular processes. Here we define differential functions for ERK1 and ERK2 MAPKs in zebrafish embryogenesis. Morpholino knockdown of ERK1 and ERK2 resulted in cell migration defects during gastrulation, which could be rescued by co-injection of the corresponding mRNA. Strikingly, Erk2 mRNA cross-rescued ERK1 knockdown, but erk1 mRNA was unable to compensate for ERK2 knockdown. Cell-tracing experiments revealed a convergence defect for ERK1 morphants without a severe posterior-extension defect, whereas ERK2 morphants showed a more severe reduction in anterior–posterior extension. These defects were primary changes in gastrulation cell movements and not caused by altered cell fate specification. Saturating knockdown conditions showed that the absence of FGF-mediated dual-phosphorylated ERK2 from the blastula margin blocked initiation of epiboly, actin and tubulin cytoskeleton reorganization processes and further arrested embryogenesis, whereas ERK1 knockdown had only a mild effect on epiboly progression. Together, our data define distinct roles for ERK1 and ERK2 in developmental cell migration processes during zebrafish embryogenesis.
Sandra de Keijzer, Arnauld Serge, Freek van Hemert, Piet Lommerse, Gerda Lamers, Herman P. Spaink, Thomas Schmidt and B. Ewa Snaar-Jagalska. (2008) A Spatially Restricted Increase in Receptor Mobility is Involved in Directional Sensing., J. Cell Sci, 121, 1750-7.
[Abstract] [DOI] [pdf]
The directed cell migration towards a chemotactic source, chemotaxis, involves three complex and interrelated processes: directional sensing, cell polarization and motility. Directional sensing allows migrating eukaryotic cells to chemotax in extremely shallow gradients (<2% across the cell body) of the chemoattractant. Although directional sensing has been observed as spatially restricted responses along the plasma membrane, our understanding of the `compass' of the cell that controls the gradient-induced translocation of proteins during chemotactic movements is still largely lacking. Until now, the dynamical behaviour and mobility of the chemoattractant-receptor molecule has been neglected in models describing the directional sensing mechanisms. Here, we show by single-molecule microscopy an agonist-induced increase in the mobile fraction of cAMP-receptor at the leading edge of chemotacting Dictyostelium discoideum cells. The onset of receptor mobility was correlated to the uncoupling and activation of the Gα2-protein. A finite-element simulation showed that the increase in mobile fraction of the activated receptor enabled the amplified generation of activated Gβγ-dimers at the leading edge of the cell, faithfully representing a primary linear amplification step in directional sensing. We propose here that modulation of the receptor mobility is directly involved in directional sensing and provides a new mechanistic basis for the primary amplification step in current theoretical models that describe directional sensing.
Paige Shaklee, Timon Idema, Gerbrand Koster, Cees Storm, Thomas Schmidt and Marileen Dogterom. (2008) Bidirectional membrane tube dynamics driven by nonprocessive motors., Proc. Natl. Acad. Sci, 105, 7993-7997.
[Abstract] [DOI] [pdf]
In cells, membrane tubes are extracted by molecular motors. Although individual motors cannot provide enough force to pull a tube, clusters of such motors can. Here,weinvestigate, using a minimal in vitro model system, how the tube pulling process depends on fundamental properties of the motor species involved. Previously, it has been shown that processive motors can pull tubes by dynamic association at the tube tip. We demonstrate that, remarkably, nonprocessive motors can also cooperatively extract tubes. Moreover, the tubes pulled by nonprocessive motors exhibit rich dynamics as compared to those pulled by their processive counterparts. We report distinct phases of persistent growth, retraction, and an intermediate regime characterized by highly dynamic switching between the two. We interpret the different phases in the context of a single-species model. The model assumes only a simple motor clustering mechanism along the length of the entire tube and the presence of a length-dependent tube tension. The resulting dynamic distribution of motor clusters acts as both a velocity and distance regulator for the tube. We show the switching phase to be an attractor of the dynamics of this model, suggesting that the switching observed experimentally is a robust characteristic of nonprocessive motors. A similar system could regulate in vivo biological membrane networks.
Stefan Semrau, Timon Idema, Laurent Holtzer, Thomas Schmidt and Cees Storm (2008) Accurate determination of elastic parameters for multi-component membranes., Phys. Rev. Lett, 100, 088101-4.
[DOI] [pdf]
Sandra de Keijzer and Thomas Schmidt (2008) Single-molecule imaging of cellular signaling in vivo., in Single Molecules and Nanotechnology, Springer Series in Biophysics, R. Rigle, 12, 107-129.
[pdf]
Frese, RN, Pamies, JC, Olsen, JD, Bahatyrova, S, van der Weij-de Wit,CD, Aartsma, TJ, Otto, C, Hunter, CN, Frenkel, D, van Grondelle, R (2008) Protein shape and crowding drive domain formation and curvature in, BIOPHYSICAL JOURNAL, 94, 640-647.
[DOI]
Arteni, AA, Liu, LN, Aartsma, TJ, Zhang, YZ, Zhou, BC, Boekema, EJ (2008) Structure and organization of phycobilisomes on membranes of the red, PHOTOSYNTHESIS RESEARCH, 95, 169-174.
[DOI]
Zauner, G, Strianese, M, Bubacco, L, Aartsma, TJ, Tepper, AWJW, Canters, GW (2008) Type-3 copper proteins as biocompatible and reusable oxygen sensors, INORGANICA CHIMICA ACTA, 361, 1116-1121.
[DOI]
Kuznetsova, S, Zauner, G, Aartsma, TJ, Engelkamp, H, Hatzakis, N, Rowan, AE, Nolte, RJM, Christianen, PCM, Canters, GW (2008) The enzyme mechanism of nitrite reductase studied at single-molecule, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF, 105, 3250-3255.
[DOI]
Liu, LN, Aartsma, TJ, Frese, RN (2008) Dimers of light-harvesting complex 2 from Rhodobacter sphaeroides, FEBS JOURNAL, 275, 3157-3166.
[DOI]
Liu, LN, Elmalk, AT, Aartsma, TJ, Thomas, JC, Lamers, GEM, Zhou, BC, Zhang, YZ (2008) Light-Induced Energetic Decoupling as a Mechanism for, PLOS ONE, 3, 34946-34953.
[DOI]
Liu, LN, Aartsma, TJ, Thomas, JC, Lamers, GEM, Zhou, BC, Zhang, YZ (2008) Watching the Native Supramolecular Architecture of Photosynthetic, JOURNAL OF BIOLOGICAL CHEMISTRY, 283, 34946-34953.
[DOI]
F. J. Verbaan, S. M. Bal, D. J. van den Berg, J. A. Dijksman, M. van Hecke, H. Verpoorten, (2008) A. van den Berg, R. Luttge, J. A. Bouwstra - Improved piercing of microneedle arrays in dermatomed human skin by an impact insertion method, J. Contr. Release, 128, 80-88 .
[pdf]
K. Sakaie, D. Fenistein, T. J. Carroll, M. van Hecke, and P. Umbanhowar (2008) MR Imaging of Reynolds Dilatancy in the Bulk of Smooth Granular Flows, Eur. Phys. Lett, 84, 38001 .
[pdf]
G. Katgert, M. E. Möbius, M. van Hecke (2008) Rate Dependence and Role of Disorder in Linearly Sheared Two-Dimensional Foams, Phys. Rev. Lett., 101, 058301 .
[pdf]
Ye.S. Avotina, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek, (2008) Influence of a single defect on the conductance of a tunnel point contact between a normal metal and a superconductor., Low Temp. Phys. [Fiz. Nizk. Temperatur] , 34, 1184-1191.
[pdf]
C.A. Martin, D. Ding, J.K. Sørensen, T Bjørnholm, J.M. van Ruitenbeek, and H.S.J. van der Zant, (2008) Fullerene-based anchoring groups for molecular electronics., JACS , 130, 13198-13199.
[pdf]
A.F. Otte (2008) Can data be stored in a single magnetic atom?, Europhysics News , 39, 31-34.
[pdf]
A.F. Otte, M. Ternes, K. von Bergmann, S. Loth, H. Brune, C.P. Lutz, C.F. Hirjibehedin, and A.J. Heinrich, (2008) The role of magnetic anisotropy in the Kondo effect., Nature Physics , 4, 847-850.
[pdf]
M. Kiguchi, O. Tal, S. Wohlthat, F. Pauli, M. Krieger, D. Djukic, J.C. Cuevas, and J.M. van Ruitenbeek, (2008) Highly conductive molecular junctions based on direct binding of benzene to platinum electrodes., Phys. Rev. Lett. , 101.
[DOI] [pdf]
Ye.S. Avotina, Yu.A. Kolesnichenko, and J.M. van Ruitenbeek, (2008) The signature of subsurface Kondo impurities in the local tunnel current., J. Phys: Condens. Matter , 20.
[pdf]
C.A. Martin, D. Ding, H.S.J. van der Zant, and J.M. van Ruitenbeek, (2008) Lithographic mechanical break junctions for single-molecule measurements in vacuum: possibilities and limitations., New J. Phys. , 10.
[pdf]
W.H.A. Thijssen, M. Strange, J.M.J. aan de Brugh, and J.M. van Ruitenbeek, (2008) Formation and properties of metal-oxygen atomic chains., New J. Phys. , 10.
[pdf]
O. Tal, M. Krieger, B. Leerink, and J.M. van Ruitenbeek, (2008) Electron-vibration interaction in single-molecule junctions: from contact to tunneling regime., Phys. Rev. Lett. , 100.
[DOI] [pdf]
T. Shiota, A.I. Mares, A.M.C. Valkering, T.H. Oosterkamp, and J.M. van Ruitenbeek, (2008) Mechanical properties of Pt monatomic chains, Phys. Rev. B , 77.
[pdf]
I.K. Yanson, O.I. Shklyarevskii, J.M. van Ruitenbeek, and S. Speller, (2008) Aluminium nanowires: influence of work hardening on conductance histograms., Phys. Rev. B, 77.
[pdf]
D. Stolwijk, E.F.C. Driessen, M.A. Verschuuren, G.W. tHooft, M.P. van Exter, and M.J.A. deDood (2008) Enhanced coupling of plasmons in hole arrays with periodic dielectric antennas, Opt. Lett., 33, 363.
[pdf]
V.A. Sautenkov, Y.V. Rostovtsev, and E.R. Eliel (2008) Observation of narrow Autler-Townes components in the resonant response of a dense atomic gas, Phys. Rev. A, 78, 013802.
[pdf]
M.T. Rakher, N.G. Stoltz, L.A. Coldren, P.M. Petroff, and D. Bouwmeester (2008) Polarization-switchable single photon source using the Stark effect, Appl. Phys. Lett., 93, 091118.
[pdf]
J.B. Pors, S.S.R. Oemrawsingh, A. Aiello, M.P. van Exter, E.R. Eliel, G.W. t Hooft, and J.R. Woerdman, (2008) Shannon dimensionality of quantum channels and its application to photon entanglement, Phys. Rev. Lett., 101, 120502.
[pdf]
J.B. Pors, A. Aiello, S.S.R. Oemrawsingh, M.P. van Exter, E.R. Eliel, and J.R. Woerdman, (2008) Angular phase-plate analyzers for measuring the dimensionality of multimode fields, Phys. Rev. A, 77, 033845.
[pdf]
W.H. Peeters and M.P. van Exter, (2008) Optical characterization of periodically-poled KTP, Proc. SPIE, 6988, 6988-13.
[pdf]
W.H. Peeters, and M.P. van Exter (2008) Optical characterization of periodically-poled KTiOPO4, Opt. Express., 16, 7344-7360.
[pdf]
G. Nienhuis and S. Habraken (2008) The structure of twisted cavity modes,, Quantum Optics IX (OSA; eds. N.P. Bigelow, J.H. Eberly and C.R. Stroud Jr.), 19-62.
[pdf]
G. Nienhuis (2008) Angular momentum and vortices in optics,, Structured light and its applications (Academic Press, Burlington, MA; ed. D.L. Andrews), 19-62.
[pdf]
H. Di Lorenzo Pires and C.H. Monken, (2008) On the statistics of the entropy-depolarization relation in random light scattering, Opt. Express, 16, 21059-21068.
[pdf]
D. Kleckner, I. Pikovski, E. Jeffrey, L. Ament, E.R. Eliel, J. van den Brink, and D. Bouwmeester (2008) Creating and verifying a quantum superposition in a micro-optomechanical system, New J. of Physics, 10, 095020.
[pdf]
W.T.M. Irvine and D. Bouwmeester (2008) Linked and knotted beams of light, Nature Physics, 4, 716-720.
[pdf]
S.J.M. Habraken and G. Nienhuis (2008) Orbital angular momentum in twisted and rotating cavity modes,, Proc. SPIE, 6483, 6905-04.
[pdf]
S.J.M. Habraken and G. Nienhuis (2008) Modes of a rotating astigmatic optical cavity, Phys. Rev. A, 77, 053803.
[pdf]
J.B. Götte, A. Aiello, and J.P. Woerdman (2008) Loss-induced transition of the Goos-Hänchen effect for metals and dielectrics, Opt. Express., 16, 3961-3969.
[pdf]
S.J. van Enk and G. Nienhuis (2008) Rotating photons,, Proc. SPIE, 6483, 6905-.
[pdf]
M.J.A. deDood, E.F.C. Driessen, D. Stolwijk, and M.P. van Exter (2008) Observation of coupling between surface plasmons in index-matched hole arrays, Phys. Rev. B, 77, 115437.
[pdf]
M.J.A. de Dood, E.F.C. Driessen, D. Stolwijk, M.P. van Exter, M.A. Verschuuren, en G.W. t Hooft (2008) Solid-state index matching of surface plasmons, Proc. SPIE, 6987, 6987-38.
[pdf]
E.F.C. Driessen, P.O.M. Heemskerk, D. Stolwijk, E.W.J.M. van der Drift, and M.J.A. de Dood (2008) Asymmetry reversal and waveguide modes in photonic crystal slabs,, Proc. SPIE, 6989, 6989-15.
[pdf]
G.C.G. Berkhout, and M.W. Beijersbergen (2008) Method for probing the orbital angular momentum of optical vortices in electromagnetic waves from astronomical objects, Phys. Rev. Lett., 101, 100801.
[pdf]
A. Aiello and J.P. Woerdman (2008) Role of beam propagation in Goos-Hanchen and Imbert-Fedorov shifts, Opt. Lett., 33, 1437-1439.
[pdf]
Esha Roy, Thierry Rohmer, Peter Gast, Gunnar Jeschke, A. Alia, J?rg Matysik (2008) Characterization of the primary electron pair in reaction centers of Heliobacillus mobilis by 13C photo-CIDNP MAS NMR, Biochemistry, 47, 4629-4635.
[pdf]
A. Aguirre, P. Gast, S. Orlinskii, I. Akimoto, E.J.J. Groenen, H. El Mkami, E. Goovaerts, S. van Doorslaer (2008) Multifrequency EPR analysis of the positive polaron in I-2-doped poly(3-hexylthiophene) and in poly[2-methoxy-5-(3,7-dimethyloctyloxy)]-1,4-phenylenevinylene, Phys. Chem. Chem. Phys., 10, 7129-7138.
[pdf]
T.N. Kropacheva, R.N.S. van der Haas, R. van der Steen, P. Gast, H.J. Schuitmaker, J. Lugtenburg (2008) Binding and acid-base properties of novel photosensitizing drugs in micellar and liposome solutions, J. Porph. Phthaloc., 12, 75-84.
[pdf]
M. Drescher, G. Veldhuis, B.D. van Rooijen, S. Milikisyants, V. Subramaniam, M. Huber (2008) Antiparallel arrangement of the helices of vesicle-bound alpha-synuclein, J. Am. Chem. Soc., 130 (25), 7796-7797.
[pdf]
S. Milikisyants, E.J.J. Groenen, M. Huber (2008) Observer-selective double electron-electron-spin resonance, a pulse sequence to improve orientation selection, J. Magn. Reson., 192, 275-279.
[pdf]
J.E. Banham, C.M. Baker, S. Ceola, I.J. Day, G.H. Grant, E.J.J. Groenen, C.T. Rodgers, G. Jeschke, C.R. Timmel (2008) Distance measurements in the borderline region of applicability of CW EPR and DEER: A model study on a homologous series of spin-labelled peptides, J. Magn. Reson., 191, 202-21.
[pdf]
S. Milikisyants, S. Sottini, J.A.J.M. Disselhorst, H. van der Meer, E.J.J. Groenen (2008) A modification of the commercial ESR900 cryostat to enable three-dimensional Electron Paramagnetic Resonance studies of crystals, Rev. Sci. Instrum., 79 046107.
[pdf]
S.B. Orlinskii, J. Schmidt, P.G. Baranov, M. Bickermann, B.M. Epelbaum, A. Winnacker (2008) Observation of the triplet meta-stable state of shallow donor pairs in AIN crystals with a negative-U behavior: A high-frequency EPR and ENDOR study, Phys. Rev. Lett., 100, 256404.
[pdf]
S.B. Orlinskii, J. Schmidt, P.G. Baranov, V. Lorrmann, I. Riedel, D. Rauh, V. Dyakonov (2008) Identification of shallow Al donors in Al-doped ZnO nanocrystals: EPR and ENDOR spectroscopy, Phys. Rev. B, 77, 115334.
[pdf]
C. Bell, S. Milikisyants, M. Huber, J. Aarts (2008) Spin dynamics in a superconductor-ferromagnet proximity system, Phys. Rev. Lett., 100 047002.
[pdf]
T. Xia, M. Orrit, Kees Storm en Wim van Saarloos (2008) Verrassend gedrag van onderkoeld glycerol boven de glasovergang, Nederlands Tijdschrift voor Natuurkunde, 74-10, 340.
A. Nicolet, C. Hofmann, M.A. Kol'chenko, M. Orrit (2008) Anthracene-based Organic Field-Effect Transistor: Temperature Dependence of the Current-Voltage Characteristics, Mol. Cryst. Liq. Cryst., 497, 218-227.
[pdf]
P. Zijlstra, A. L. Tchebotareva, J. W. M. Chon, M. Gu, M. Orrit (2008) Acoustic Oscillations and Elastic Moduli of Single Gold Nanorods, Nano Lett., 8, 3493-3497.
[pdf]
R. Zondervan, T. Xia, H. van der Meer, C. Storm, F. Kulzer, W. van Saarloos, M. Orrit (2008) Soft glassy rheology of Supercooled molecular liquids, Proc. Natl. Acad. Sci. USA, 13, 4993-4998.
[pdf]
A. Sigl, Chr. Scharnagl, J. Friedrich, A. Gourdon, M. Orrit (2008) 2-methylterrylene in hexadecane: Do we see single rotational quantum jumps of methyl groups?, J. Chem. Phys., 128, 044508-044516.
[pdf]
C. Bell, S. Milikisyants, M. Huber and J. Aarts (2008) Spin Dynamics in a Superconductor-Ferromagnet Proximity System, Physical Review Letters, 100, 047002.
I. Komissarov, Y. Zhang, G. J. Nieuwenhuys, E. Morenzoni, T. Prokscha, A. Suter and J. Aarts (2008) Investigating the occurrence of magnetic order in strained thin films of Pr0.5Ca0.5MnO3 by muon spin relaxation, EPL , 83, 47013.
E. Morenzoni, H. Luetkens, T. Prokscha, A. Suter, S. Vongtragool, F. Galli, M.B. Hesselberth, N. Garifianov, R. Khasanov (2008) Depth-dependent spin dynamics of canonical spin-glass films: a low-energy muon-spin-rotation study, PRL 100, 100, 147205 .
M. Saoudi, H. Fritzsche, G.J. Nieuwenhuys, M.B.S. Hesselberth (2008) Size Effect in the Spin Glass Magnetization of Thin AuFe Films as Studied by Polarized Neutron Reflectometry, Physical Review Letters, 100, 057204.
A.S. Prokhorov, E.S. Zhukova, I.E. Spector, B.P. Gorshunov, M.SB.S. Hesselberth, J. Aarts, G.J. Nieuwenhuys, S. Kaiser, M. Dressel (2008) RKKY interaction and a pseudo-gap in terahertz conductivity spectra of the AuFe spin glass, Physics of metals and metallography, 106, 247-252.
S.L. Prischepa, C. Cirillo, C. Bell, V.N. Kusnir, J. Aarts, C. Attanasio, M.Y. Kupriyanov (2008) Resistive transitions in Nb/Cu0.41Ni0.59/Nb trilayers, JETP Letters , 88, 375 - 379.
Panayotis Spathis, Sylvain Colson, Feng Yang, Cornelis J. van der Beek, Piotr Gierowski, Takasada Shibauchi, Yuji Matsuda, Marat Gaifullin, Ming Li and Peter H. Kes (2008) c-axis coupling in underdoped Bi2Sr2CaCu2O8+ with varying degrees of disorder, Physical Review B, 77, 104503.
Arcizet, Delphine Meier, Boern Sackmann, Erich Raedler, Joachim O. Heinrich, Doris (2008) Temporal Analysis of Active and Passive Transport in Living Cells, PHYSICAL REVIEW LETTERS, 101.
[Abstract] [DOI]
The cellular cytoskeleton is a fascinating active network, in which Brownian motion is intercepted by distinct phases of active transport. We present a time-resolved statistical analysis dissecting phases of directed motion out of otherwise diffusive motion of tracer particles in living cells. The distribution of active lifetimes is found to decay exponentially with a characteristic time tau(A)=0.65 s. The velocity distribution of active events exhibits several peaks, in agreement with a discrete number of motor proteins acting collectively.
Everardus H. Huisman, Marius L. Trouwborst, Frank L. Bakker, Bert de Boer, Bart J. van Wees, Sense Jan van der Molen, (2008) Stabilizing Single Atom Contacts by Molecular Bridge Formation, NANO LETTERS, 8, 3381–3385.
[DOI]
Nikolaos Tombros, Luuk Buit, Imad Arfaoui, Theodoros Tsoufis, Dimitrios Gournis, Pantelis N. Trikalitis, Sense Jan van der Molen, Petra Rudolf, Bart J. van Wees (2008) Charge transport in a single superconducting tin nanowire encapsulated in a multiwalled carbon nanotube, NANO LETTERS, 8, 3060–3064.
[DOI]
M. L. Trouwborst, E. H. Huisman, F. L. Bakker, S. J. van der Molen, B. J. van Wees (2008) Single atom adhesion in optimized gold nanojunctions, PHYSICAL REVIEW LETTERS, 100, 175502 .
[DOI]
Avotina YS, Kolesnichenko YA, Ruitenbeek JM (2008) The signature of subsurface Kondo impurities in the local tunnel current., J Phys Condens Matter.
[DOI]

2007
W. J A Koopmans and A. Brehm and C. Logie and T. Schmidt and J. van Noort (2007) Single-pair FRET microscopy reveals mononucleosome dynamics., J Fluoresc, Nov, 17, 785--795.
[Abstract] [DOI] [pdf]
We applied spFRET microscopy for direct observation of intranucleosomal DNA dynamics. Mononucleosomes, reconstituted with DNA containing a FRET pair at the dyad axis and exit of the nucleosome core particle, were immobilized through a 30 bp DNA tether on a polyethyleneglycol functionalized slide and visualized using Total Internal Reflection Fluorescence microscopy. FRET efficiency time-traces revealed two types of dynamics: acceptor blinking and intramolecular rearrangements. Both Cy5 and ATTO647N acceptor dyes showed severe blinking in a deoxygenated buffer in the presence of 2\% betaME. Replacing the triplet quencher betaME with 1 mM Trolox eliminated most blinking effects. After suppression of blinking three subpopulations were observed: 90\% appeared as dissociated complexes; the remaining 10\% featured an average FRET efficiency in agreement with intact nucleosomes. In 97\% of these intact nucleosomes no significant changes in FRET efficiency were observed in the experimentally accessible time window ranging from 10 ms to 10's of seconds. However, 3\% of the intact nucleosomes showed intervals with reduced FRET efficiency, clearly distinct from blinking, with a lifetime of 120 ms. These fluctuations can unambiguously be attributed to DNA breathing. Our findings illustrate not only the merits but also typical caveats encountered in single-molecule FRET studies on complex biological systems.
Belinda Haupt, Matthew Osbourn, Rudolf Spanhoff, Sandra de Keijzer, Annette Müller-Taubenberger, B. Ewa Snaar-Jagalska and Thomas Schmidt (2007) Asymmetric Elastic Properties of Dictyostelium Discoideum Relates to Chemotaxis., Langmuir, 23, 9352-7.
[Abstract] [DOI] [pdf]
In this study we used an AFM to investigate the cytoskeletal properties of live Dictyostelium discoideum cells by measuring the local stiffness across individual living cells. We have examined differences in elastic properties of polarized and unpolarized AX3 wild type and the mutant DAip1- cells, as well as the differences in the front and rear of the cells in relation to organization of the actin cytoskeleton. We found that the average Young's modulus increases upon polarization for the thin regions of the cell and that in polarized cells, the cell front was stiffer than the cell back. We also found that AX3 cells were stiffer than DAip1- cells. This finding suggests that actin polymerization is one of the major determinants of cell motility in Dictyostelium. In addition, a thin agarose film was studied as a model system to examine the influence of the substrate of thin materials probed with the AFM.
Laurent Holtzer, Tobias Meckel, and Thomas Schmidt (2007) Nanometric three-dimensional tracking of individual quantum dots in cells., Appl. Phys. Lett., 90, 053902..
[DOI] [pdf]
Stefan Semrau and Thomas Schmidt (2007) Particle image correlation spectroscopy (PICS). Retrieving nanometer-scale corre, Biophys J., 92, 613..
[DOI] [pdf]
Zauner, G, Lonardi, E, Bubacco, L, Aartsma, TJ, Canters, GW, Tepper, AWJW (2007) Tryptophan-to-dye fluorescence energy transfer applied to oxygen sensing, CHEMISTRY-A EUROPEAN JOURNAL, 13, 7085-7090.
[DOI]
Magis, JG, Frese, RN, Olsen, JD, Hunter, CN, Aartsma, TJ (2007) Enhanced stability of photosynthetic energy transfer proteins on gold, BIOPHYSICAL JOURNAL, 341, 507A-507A.
Frese, RN, Pamies, JC, Aartsma, TJ, Frenkel, D, van Grondelle, R (2007) Depletion interaction between proteins drives the formation of protein, BIOPHYSICAL JOURNAL, 341, 221A-221A.
de Ruijter, WPF, Segura, JM, Cogdell, RJ, Gardiner, AT, Oellerich, S, Aartsma, TJ (2007) Fluorescence-emission spectroscopy of individual LH2 and LH3 complexes, CHEMICAL PHYSICS, 341, 320-325.
[DOI]
M. Depken, J. B. Lechman, M. van Hecke, W van Saarloos and G. S. Grest (2007) Stresses in Smooth Flows of Dense Granular Media, Eur. Phys. Lett., 78, 58001 .
[pdf]
E. Somfai, M. van Hecke, W. G. Ellenbroek, K. Shundyak and W. van Saarloos (2007) Critical and non-critical jamming of frictional grains, Phys. Rev. E. R., 75, 020301 .
[pdf]
K. Shundyak, M. van Hecke and W. van Saarloos (2007) Force mobilization and generalized isostaticity in jammed packings of frictional grains, Phys. Rev. E. R., 75, 010301 .
[pdf]
A.R.T. van Eerd, W. G. Ellenbroek, M. van Hecke, J. H. Snoeijer, and T. J. H. Vlugt (2007) Tail of the Contact Force Distribution in Static Granular Materials, Phys. Rev. E R, 75, 060302 .
[pdf]
M. van Hecke (2007) Materials Science - Shape Matters, Science, 317, 49-50 .
[pdf]
C.F. Hirjibehedin, C.-Y. Lin, A.F. Otte, M. Ternes, C.P. Lutz, B.A. Jones, and A.J. Heinrich, (2007) Large Magnetic Anisotropy of a Single Atomic Spin Embedded in a Surface Molecular Network, Science , 317, 1199-1203.
[pdf]
M.R. Calvo, A.I. Mares, V. Climent, J.M. van Ruitenbeek, and C. Untiedt, (2007) Formation of atomic-sized contacts by electrochemical methods., proceedings of the TNT2006 Conference on "Trends in Nanotechnology", Phys. Stat. Sol. , 204, 1677 .
[pdf]
Ye.S. Avotina, Yu.A. Kolesnichenko, A.F. Otte, and J.M. van Ruitenbeek, (2007) Magneto-quantum oscillations of the conductance of a tunnel point-contact in the presence of a single defect., Phys. Rev. B , 75.
[pdf]
A.I. Mares, D.F. Urban, J. Bürki, H. Grabert, C.A. Stafford, and J.M. van Ruitenbeek, (2007) Electronic and atomic shell structure in aluminum nanowires., Nanotechnology, 18.
[pdf]
O. Gurlu, A. van Houselt, W.H.A. Thijssen, J.M. van Ruitenbeek, B. Poelsema, and H.J.W. Zandvliet, (2007) Controlled damaging and repair of self-organised nanostructures by atom manipulation at room temperature., Nanotechnology , 18.
[pdf]
M. Kiguchi, D. Djukic, and J.M. van Ruitenbeek, (2007) Effect of bonding of a CO molecule on the conductance of atomic metal wires., Nanotechnology , 18, 035205 .
[pdf]
D. Djukic en J.M. van Ruitenbeek, (2007) Stemmen van een molecuul., Nederlands Tijdschrift voor Natuurkunde , 73, 10-11.
[pdf]
M. Kiguchi, R. Stadler, I.S. Kristensen, D. Djukic, and J.M. van Ruitenbeek, (2007) Evidence for a single hydrogen molecule connected by an atomic chain, Phys. Rev. Lett, , 98.
[pdf]
C. Untiedt, M.J. Caturla, R. Calvo, J.J. Palacios, R.C. Segers, and J.M. van Ruitenbeek, (2007) Formation of a metallic contact: jump to contact revisited, Phys. Rev. Lett. , 98 .
[pdf]
G. Puentes, A. Aiello, D. Voigt, and J.P. Woerdman, (2007) Entangled mixed-state generation by twin-photon scattering, Phys. Rev.  A , 75, 032319.
[pdf]
W.H. Peeters, E.J.K. Verstegen, and M.P. van Exter, (2007) Orbital angular momentum analysis of high-dimensional entanglement, Phys. Rev.  A , 76, 042302.
[pdf]
M. Merano, A. Aiello, G.W. t Hooft, M.P. van Exter, E.R. Eliel, and J.P. Woerdman, (2007) Observation of Goos-Hanchen shifts in metallic reflection, Optics Express , 15, 15928-15934.
[pdf]
N. Kuzmin, P.F.A. Alkemade, G.W. t Hooft, and E.R. Eliel (2007) Bouncing surface plasmons, Opt. Express, 15, 13757-13767.
[pdf]
N. Kuzmin, G.W. t Hooft, E.R. Eliel, G. Gbur, H.F. Schoutern, and T.D. Visser (2007) Enhancement of spatial coherence by surface plasmons, Opt. Lett., 32, 445-447.
[pdf]
T. Klaassen, M.P. van Exter, and J.P. Woerdman, (2007) Characterization of scattering in an optical Fabry-Perot resonator, Appl. Opt., 46, 5210-5215.
[pdf]
T. Klaassen, M.P. van Exter, and J.P. Woerdman, (2007) Characterization of a Fabry-Perot resonator with diamond-machined mirrors, Opt. Commun., 275, 385-388.
[pdf]
S.J.M. Habraken and G. Nienhuis, (2007) Modes of a twisted optical cavity, Phys. Rev. A , 75, 033819.
[pdf]
S.J. van Enk and G. Nienhuis, (2007) Photons in polychromatic rotating modes, Phys. Rev. A , 76, 053825.
[pdf]
M.P. van Exter, P.S.K. Lee, S. Doesburg S, and J.P. Woerdman, (2007) Mode counting in high-dimensional orbital angular momentum entanglement, Optics Express, 15, 6431-6438.
[pdf]
A. Aiello, G. Puentes, and J.P. Woerdman, (2007) Linear optics and quantum maps, Phys. Rev. A, 76, 032323.
[pdf]
E.F.C. Driessen, D. Stolwijk, and M.J.A. de Dood, (2007) Asymmetry reversal in the reflection from a two-dimensional photonic cyrstal, Opt. Lett., 32, 3137-3139.
[pdf]
A. Aiello, G. Puentes, D. Voigt, and J.P. Woerdman, (2007) Maximally entangled mixed-state generation via local operations, Phys. Rev. A, 75, 062118.
[pdf]
I.B. Klenina, W.O. Feikema, P. Gast, M.G. Zvereva, I.I. Proskuryakov (2007) Mechanism of photoinduced electron transfer in photosystem II reaction centers, BIOFIZIKA, 52, 57-62.
B.J. van Rossum, W.B.S. van Liemt, P. Gast, J. Lugtenburg, H.J.M. de Groot (2007) 13C1H heteronuclear dipolar correlation studies of the hydrogen bonding of the quinines in Rhodobacter sphaeroides R26 reaction centers, Appl. Magn. Res., 31, 145-158.
A. Diller, E. Roy, P. Gast, H.J. van Gorkom, H.J.M. de Groot, C. Glaubitz, G. Jeschke, J. Matysik, Alia (2007) 15N photochemically induced dynamic nuclear polarization magic-angle spinning NMR analysis of the electron donor of photosystem II, Proc. Natl. Acad. Sci., 104, 31, 12767-12771.
A. Diller, S. Prakash, Alia, P. Gast, J. Matysik, G. Jeschke (2007) Signals in solid-state photochemically induced dynamic nuclear polarization recover faster than signals obtained with the longitudinal relaxation time, J. Phys. Chem. B, 111, 10606-10614.
S. Prakash, Alia, P. Gast, H.J.M. de Groot, G. Jeschke, J. Matysik (2007) 13C chemical shift map of the active cofactors in photosynthetic reaction centers of Rhodobacter sphaeroides revealed by photo-CIDNP MAS NMR, Biochemistry, 46, 8953-8960.
D.O. Tolmachev, N.G. Romanov, P.G. Baranov, C. de Mello Doneg?, A. Meijerink, S.B. Orlinskii, J. Schmidt (2007) ODMR investigation of tunnelling recombination processes in ZnO nanocrystals, 15th Int. Symp. "Nanostructures: Physics and Technology", Novosibirsk, Russia, June 25-29, 2007.
S. Fujiyoshi, M. Fujiwara, C. Kim, M. Matsushita, A.M. van Oijen, J. Schmidt (2007) A single-component reflecting objective for low-temperature spectroscopy in the entire visible region, Appl. Phys. Lett., 91, 5 051125.
A.C. Wirtz, M.C. van Hemert, J. Lugtenburg, H.A. Frank, E.J.J. Groenen (2007) Two stereoisomers of spheroidene in the Rhodobacter sphaeroides R26 reaction center. A DFT analysis of resonance Raman spectra., Biophys. J., 93, 981-991.
[pdf]
P. Gajula, S. Milikisyants, H.-J. Steinhoff, M. Huber (2007) A Short Note on Orientation selection in the DEER experiments on a native cofactor and a spin label in the reaction centre of Rhodobacter sphaeroides, Appl. Magn. Reson, 31, 91-104.
L. Benisvy, R. Kannappan, Y.-F. Song, S. Milikisyants, M. Huber, I. Mutikainen, U. Turpeinen, P. Gamez, L. Bernasconi, E.J. Baerends, F. Hartl, J. Reedijk (2007) A Square Planar Nickel(II) Mono Radical Complex with a Bis(salicylidine)diamine Ligand, EURJIC, 5, 637-642.
I.V. Borovykh, P. Gast, S.A. Dzuba (2007) The dynamical transition in proteins of bacterial photosynthetic reaction centers observed with echo-detected EPR of specific spin labels, Appl. Magn. Res., 31, 159-166.
P. Gajula, I.V. Borovykh, C. Beier, T. Shkuropatova, P. Gast, H.-J. Steinhoff (2007) Spin-labeled photosynthetic reaction centers from Rhodobacter sphaeroides studied by electron paramagnetic resonance spectroscopy and molecular dynamics simulations, Appl. Magn. Res., 31, 167-178.
E. Roy, Alia, P. Gast, H. van Gorkom, H.J.M. de Groot, G. Jeschke, J. Matysik (2007) Photochemically induced dynamic nuclear polarisation in the reaction center of the green sulphur bacteria Chlorobium tepidum observed by 13C MAS NMR, Biochem. Biophys. Acta, 1767, 610-615.
E. Roy, A. Diller, Alia, P. Gast, H.J. van Gorkom, H.J.M. de Groot, G. Jeschke, J. Matysik (2007) Magnetic field dependence of 13C photo-CIDNP MAS NMR in plant photosystems I and II, Appl. Magn. Res., 31, 193-204.
M. A. van Dijk (2007) Nonlinear-Optical Studies of Single Gold Nanoparicles, .
[pdf]
A. Nicolet (2007) Single-Molecule Probes in Organic Field-Effect Transistors, .
[pdf]
M. Orrit (2007) Quantum light switch, Nature. Phys, 3, 755-756.
[pdf]
F. Cichos, C. von Borczyskowski, M. Orrit (2007) Power-law intermittency of single emitters, Curr. Opin. Colloid. Interface. Sci, 12, 272-284.
[pdf]
A. Sigl, M. Orrit, R. Jankowiak, J. Friedrich (2007) Terrylene in hexadecane revisited: A hole burning study, J. Chem. Phys., 127, 084510-084517.
[pdf]
A. Nicolet, P. Bordat, C. Hofmann, M. A. Kol'chenko, B. Kozankiewicz, R. Brown, M. Orrit (2007) Single Dibenzoterrylene Molecules in an Anthracene Crystal: Main Insertion Sites, ChemPhysChem, 8, 1926-1936.
[pdf]
C. von Borczyskowski, J. K?hler, W. E. Moerner, M. Orrit, J. Wrachtrup (2007) Single-Molecule Electron Spin Resonance, Appl. Magn. Reson., 31, 665-676.
[pdf]
R. Zondervan, F. Kulzer, G. C. G. Berkhout, M. Orrit (2007) Local viscosity of Supercooled glycerol near Tg Probed by rotational diffusion of ensembles and single dye molecules, Proc. Natl. Acad. Sci. USA, 31, 12628-12633.
[pdf]
A. Nicolet, C. Hofmann, M. A. Kol'chenko, B. Kozankiewicz, M. Orrit (2007) Single Dibenzoterrylene Molecules in an Anthracene Crystal: Spectroscopy and Photophysics, ChemPhysChem, 8, 1215-1220.
[pdf]
M.A. van Dijk, M. Lippitz, D. Stolwijk, M. Orrit (2007) A Common-Path Interferometer for Time-Resolved and Shot-Noise-Limited Detection of Single Nanoparticles, Opt. Express, 15, 2273-2287.
[pdf]
C. Beekman, I. Komissarov, M. Hesselberth, J. Aarts (2007) Transport properties of microstructured ultrathin films of La0.67Ca0.33MnO3 on SrTiO3, Appl. Phys. Lett. , 91, 062101 .
A.A. Armenio, C. Bell, J. Aarts, C. Attanasio (2007) High-velocity instabilities in the vortex lattice of Nb/permalloy bilayers, .
A.A. Armenio, C. Bell, J. Aarts, C. Attanasio (2007) High-velocity instabilities in the vortex lattice of Nb/permalloy bilayers, Phys. Rev. B , 76, 054502.
C. Cirillo, A. Rusanov, C. Bell, J. Aarts (2007) Depairing current behavior in superconducting Nb/Pd81Ni19 bilayers, Phys. Rev. B, 75, 174510.
Y.Q. Zhang, Y.L. Zhu, Z.D. Zhang, J. Aarts (2007) Defect-induced charge-order melting in thin films of Pr0.5Ca0.5MnO3, Jn. Appl. Phys, 101, 063919.
Meckel T, Gall L, Semrau S, Homann U, Thiel G (2007) Guard cells elongate: relationship of volume and surface area during stomatal movement., Biophys. J..
[DOI]
Laetitia Bernard, Yavor Kamdzhilov, Michel Calame, Sense Jan van der Molen, Jianhui Liao, Christian Schoenenberger, (2007) Spectroscopy of molecular junction networks obtained by place exchange in 2D nanoparticle arrays, THE JOURNAL OF PHYSICAL CHEMISTRY, 111, 18445–18450.
[DOI]
Zheng Ming Wu, M. Steinacher, R. Huber, M. Calame, S. J. van der Molen, C. Schoenenberger (2007) Feedback controlled electromigration in four-terminal nanojunctions, APPLIED PHYSICS LETTERS, 91, 053118 .
[DOI]
L.Bernard, M. Calame, S. J. van der Molen, J. Liao, C. Schoenenberger (2007) Controlled formation of metallic nanowires via Au nanoparticle ac trapping, NANOTECHNOLOGY, 18.
[DOI]

2006
D.J. Kraft, Roger D. Bengtson, B.N. Breizman, D.G. Chavers, C.C. Dobson, J.E. Jones and V.T. Jacobson (2006) Analysis of multifrequency interferometry in a cylindrical plasma, Rev. Sci. Instrum., 77, 10E910.
[DOI]
Lommerse PH, Vastenhoud K, Pirinen NJ, Magee AI, Spaink HP, Schmidt T (2006) Single-molecule diffusion reveals similar mobility for the Lck, H-ras, and K-ras, Biophys J, 91, 1090-7.
[DOI] [pdf]
Kuznetsova, S, Zauner, G, Schmauder, R, Mayboroda, OA, Deelder, AM, Aartsma, TJ, Canters, GW (2006) A Forster-resonance-energy transfer-based method for fluorescence, ANALYTICAL BIOCHEMISTRY, 350, 52-60.
[DOI]
Ketelaars, M, Segura, JM, Oellerich, S, de Ruijter, WPF, Magis, G, Aartsma, TJ, Matsushita, M, Schmidt, J, Cogdell, RJ, Kohler, J (2006) Probing the electronic structure and conformational flexibility of, JOURNAL OF PHYSICAL CHEMISTRY B, 110, 18710-18717.
[DOI]
P. Umbanhowar and M. van Hecke (2006) Force dynamics in weakly vibrated granular packings, Phys. Rev. E R, 72, 30301.
[pdf]
M. Depken, W. van Saarloos, and M. van Hecke (2006) Continuum approach to wide shear zones in quasistatic granular matter, Phys. Rev. E, 73, 031302 .
[pdf]
W. G. Ellenbroek, E. Somfai, M. van Hecke and W. van Saarloos (2006) Critical Scaling in Linear Response of Frictionless Granular Packings near Jamming, Phys. Rev. Lett., 97, 258001 .
[pdf]
J. H. Snoeijer, W. G. Ellenbroek, T. J. H. Vlugt, and M. van Hecke (2006) Sheared Force Networks - Anisotropies, Yielding, and Geometry, Phys. Rev. Lett, 96, 098001.
[pdf]
D. Fenistein, J. W. van de Meent, and M. van Hecke (2006) Core Precession and Global Modes in Granular Bulk Flow, Phys. Rev. Lett., 96, 118001 .
[pdf]
Ye.S. Avotina, Yu.A. Kolesnichenko, A.F. Otte, and J.M. van Ruitenbeek, (2006) Signature of Fermi-surface anisotropy in point contact conductance in the presence of defects., Physical Review B , 74, 085411 .
[pdf]
D. Djukic and J.M. van Ruitenbeek, (2006) Shot noise measurement on a single molecule., Nano Letters, , 6, 789.
[pdf]
W.H.A. Thijssen, D. Marjenburgh, R.H. Bremmer, and J.M. van Ruitenbeek, (2006) Oxygen enhanced atomic chain formation., Phys. Rev. Lett. , 96.
[pdf]
W.H.A. Thijssen, D. Djukic, A.F. Otte, R.H. Bremmer, J.M. van Ruitenbeek, (2006) Vibrationally Induced Two-Level Systems in Single-Molecule Junctions, Phys. Rev. Lett. , 97.
[pdf]
Jan van Ruitenbeek, (2006) Live-action alloy nanowires, Nature Nanotechnology , 1, 164-165.
[pdf]
B. Zambon and G. Nienhuis. (2006) Increased trapping efficiency with force-assisted velocity-selective coherent population trapping., J. of Phys. B, 39, 1065.
[pdf]
L.T. Vuong, T.D. Grow, A. Ishaaya, A.L. Gaeta, G.W. t Hooft, E.R. Eliel, and G. Fibich. (2006) Collapse of optical vortices., Phys. Rev. Lett., 96, 133901.
[pdf]
F. Schuller, G. Nienhuis and M. Ducloy. (2006) Fluctuation-dissipation approach to van der Waals potentials between atoms and dielectric bodies., Mol. Phys., 104, 229-231.
[pdf]
G. Puentes, D. Voigt, A. Aiello, and J.P. Woerdman. (2006) Tunable spatial decoherers for polarization-entangled photons., Opt. Lett., 31, 2057.
[pdf]
S.S.R. Oemrawsingh, J.A. de Jong, X. Ma, A. Aiello, E.R. Eliel, G.W. t Hooft, and J.P. Woerdman. (2006) High-dimensional analyzers for spatial quantum entanglement., Phys. Rev. A, 73, 032339.
[pdf]
G. Nienhuis. (2006) Polychromatic and rotating beams of light., J. of Phys. B, 39, S529.
[pdf]
P.S.K. Lee and M.P. van Exter. (2006) Spatial labeling in a two-photon interferometer., Phys. Rev. A, 73, 063827.
[pdf]
P.S.K. Lee, M.P. van Exter, J.P. Woerdman. (2006) Time-resolved polarization decoherence in metal hole arrays with correlated photons., J. Opt. Soc. Am. B, 23, 134-138.
[pdf]
T. Klaassen, A. Hoogeboom, M.P. van Exter, J.P. Woerdman. (2006) Resonant trapping of scattered light in a degenerate resonator., Opt. Commun., 260, 365-371.
[pdf]
M.P. van Exter, A. Aiello, S.S.R. Oemrawsingh, G. Nienhuis, and J.P. Woerdman. (2006) Effect of spatial filtering on Schmidt decomposition of entangled photons., Phys. Rev. A, 74, 012309.
[pdf]
E. Altewischer, X. Ma, M.P. van Exter, J.P. Woerdman. (2006) Resonant Bragg scatter of surface plasmons on nanohole arrays., New. J. Phys., 8, 57.
[pdf]
A. Aiello, G. Puentes, D. Voigt and J.P. Woerdman. (2006) Maximum-likelihood estimation of Mueller matrices., Opt. Lett., 31, 817-819.
[pdf]
A. Aiello, J. Visser, G. Nienhuis and J.P. Woerdman. (2006) Angular spectrum of quantized light beams., Opt. Lett., 31, 525-257.
[pdf]
M. Fittipaldi, H.J. Wijma, M.P. Verbeet, G.W. Canters, M. Huber (2006) The Electronic Structure of the two Copper Sites in Nitrite Reductase by 9 and 95 GHz EPR on Cavity Mutants, Appl. Magn. Reson., 30, 3-4.
P. Gajula, I.V. Borovykh, C. Beier, P. Gast, M. Huber, H.-J. Steinhoff (2006) A study on the structure and dynamics of spin labeled proteins by MD simulations and EPR spectroscopy, Proceedings of the NIC workshop on "From Computational Biophysics to Systems Biology 2006" (Ed. U.H.E. Hansmann, J. Meinke, S. Mohanty, O. Zimmermann), 34, 145-148.
S. Prakash, Alia, P. Gast, H.J.M. de Groot, J. Matysik, G. Jeschke (2006) Photo-CIDNP MAS NMR in intact cells of Rhodobacter sphaeroides R26: Molecular and atomic resolution at nanomolar concentration, J. Am. Chem. Soc., 128, 12794-12799.
P.G. Baranov, N.G. Romanov, D.O. Tolmachev, C. de Mello Doneg?, A. Meijerink, S.B. Orlinskii, J. Schmidt (2006) Giant Change in the Intensity of Tunneling Afterglow in Excited ZnO Quantum Dots induced by the Spin Reorientation of Electron-Hole Pairs in Static and Microwave Magnetic Fields, JETP Lett., 84, 7, 400-403.
M. Ketelaars, J.-M. Segura, S. Oellerich, W.P.F. de Ruijter, G. Magis, T.J. Aartsma, M. Matsushita, J. Schmidt, R.J. Cogdell, J. K?hler (2006) Probing the Electronic Structure and Conformational Flexibility of Individual Light-Harvesting 3 Complexes by Optical Single-Molecule Spectroscopy, J. Phys. Chem. B, 110, 37, 18710-18717.
M.G. Finiguerra, H. Blok, M. Ubbink, M. Huber (2006) High-field (275 GHz) spin-label EPR for high-resolution polarity determination in proteins, J. Magn. Reson., 180, 197-202.
A.C. Wirtz, C. Hofmann, E.J.J. Groenen (2006) Spincoated polyethylene films probed by single molecules, J. Phys Chem. B, 110, 43, 21623-21629.
I.V. Borovykh, S. Ceola, P. Gajula, P. Gast, H-J. Steinhoff, M. Huber (2006) Distance between a native cofactor and a spin label in the reaction centre of Rhodobacter sphaeroides by a two-frequency pulsed electron paramagnetic resonance method and molecular dynamics simulations, J. Magn. Reson., 180, 178-185.
S.B. Orlinskii, H. Blok, J. Schmidt, P.G. Baranov, C. de Mello Doneg?, A. Meijerink (2006) Donor-acceptor pairs in the confined structure of ZnO nanocrystals, Phys. Rev., B 74 045204.
M. Fittipaldi, M. Huber, G.C.M. Warmerdam, E.C. de Waal, G.W. Canters, D. Cavazzini, G.L. Rossi, E.J.J. Groenen (2006) Spin-density distribution in the copper site of azurin, Chem Phys Chem, 7, 6, 1286-1293.
A.C. Wirtz, M. Dokter, C. Hofmann, E.J.J. Groenen (2006) Spincoated polyethylene films for single-molecule optics, Chem. Phys. Letters, 417, 383-388.
A.C. Wirtz, M. Dokter, C. Hofmann, E.J.J. Groenen (2006) Spincoated polyethylene films for single-molecule optics, Chem. Phys. Lett., 417, 383-388.
[pdf]
R. Zondervan (2006) Single-molecule dynamics at variable temperatures., .
[pdf]
R. Zondervan, F. Kulzer, H. van der Meer, J.A.J.M. Disselhorst, M. Orrit (2006) Laser-driven microsecond temperature cycles analyzed by fluorescence polarization microscopy, Biophys. J., 90, 2958-2969.
[pdf]
A. Nicolet, M.A. Kol´chenko, B. Kozankiewicz, M. Orrit (2006) Intermolecular intersystem crossing in single-molecule spectroscopy: Terrylene in anthracene crystal, J. Chem. Phys., 124, 164711.
[pdf]
M.A. van Dijk, A.L. Tchebotareva, M. Orrit, M. Lippitz, S. Berciaud, D. Lasne, L. Cognet, B. Lounis (2006) Absorption and scattering microscopy of single metal nanoparticles, Phys. Chem. Chem. Phys., 8, 3486-3495.
[pdf]
C. Hofmann, M. Orrit (2006) Four-Level Optical Lineshape of a Single Molecule Coupled to a Single Tunneling Two-Level System, J. Phys. Chem. B, 110, 18925-18932.
[pdf]
A.C. Wirtz, C. Hofmann, E.J.J. Groenen (2006) Spin-Coated Polyethylene Films Probed by Single Molecules, J. Phys. Chem. B, 110, 21623-21629.
[pdf]
A.C. Wirtz (2006) Optically Probing Structure and Organization, .
[pdf]
A. S. Prokhorov, V. B. Anzin, D. A. Vitukhnovskii, E. S. Zhukova, I. E. Spektor, B. P. Gorshunov, S. Vongtragool, M. B. S. Hesselberth, J. Aarts, G. J. Nieuwenhuys, M. Dumm, D. Faltermeier, S. Kaiser, S. Yasin, M. Dressel, N. Drichko (2006) Terahertz spectroscopy of AuFe spin glasses, Journal of experimental and theoretical physics , 103, 887.
C. Bell, S. Tursucu and J. Aarts (2006) Flux-flow-induced giant magnetoresistance in all-amorphous superconductor-ferromagnet hybrids, Phys. Rev. B , 74, 214520.
B. Gorshunov, A. S. Prokhorov, S. Kaiser, D. Faltermeier, S. Yasin, M. Dumm, N. Drichko, E. S. Zhukova, I. E. Spektor, S. Vongtragool, M. B. S. Hesselberth, J. Aarts, G. J. Nieuwenhuys and M. Dresse (2006) Charge localization due to RKKY interaction in the spin-glass AuFe, Europhys. Lett , 76, 938.
R. S. Keizer, M. G. Flokstra, J. Aarts and T. M. Klapwijk (2006) Critical voltage of a mesoscopic superconductor, Phys. Rev. Lett. , 147002 , 96.
J. Aarts and A. Y. Rusanov (2006) The effects of magnetization switching on the superconducting properties of S/F bilayers and F/S/F trilayers, Comptes Rendus Physique , 7, 99.
A. Yu. Rusanov, S. Habraken, and J. Aarts (2006) Inverse spin switch effects in ferromagnet-superconductor-ferromagnet trilayers with strong ferromagnets, Phys. Rev. B, 73, 060505.
Z. Q. Yang, Y. Q. Zhang, J. Aarts and H. W. Zandbergen (2006) Enhancing the charge ordering temperature in thin films of Pr0.5Ca0.5MnO3 by strain, Phys. Lett. 88, , 88, 072507 .
C. Cirillo, J. Aarts, C. Attanasio (2006) Critical temperatures in proximity coupled Nb/Pd0.86Ni0.14 bilayers, Phys. stat. sol. (c), 3, No. 9, 3015-3018 .
A. Yu. Rusanov, J. Aarts, M. Aprili (2006) Depairing Currents in Bilayers of Nb/Pd89Ni11, A. Yu. Rusanov, J. Aarts, M. Aprili: Nanoscale Devices - Fundamentals and Applications Proceedings of the NATO Advanced Research Workshop on Nanoscale Devices - Fundamentals and Applications, Kishinev, Moldova, 18-22 September 2004. Series: NATO Science S, 233.
Heinrich, Doris Sackmann, Erich (2006) Active mechanical stabilization of the viscoplastic intracellular space of Dictyostelia cells by microtubule-actin crosstalk, ACTA BIOMATERIALIA, 2.
[Abstract] [DOI]
The micro-viscoelasticity, of the intracellular space of Dictyostelium discoideum cells is studied by evaluating the intracellular transport of magnetic force probes and their viscoelastic responses to force pulses of 20-700 pN. The role of the actin cortex, the microtubule (
M. Teresa Gonzalez, Songmei Wu, Roman Huber, Sense J. van der Molen, Christian Schoenenberger, Michel Calame (2006) Electrical conductance of molecular junctions by a robust statistical analysis, NANO LETTERS, 6, 2238–2242.
[DOI]
Nathalie Katsonis, Tibor Kudernac, Martin Walko, Sense Jan van der Molen, Bart J. van Wees, Ben L. Feringa (2006) Reversible conductance switching of single diarylethenes on a gold surface, ADVANCED MATERIALS, 18, 1397–1400 .
[DOI]
M. L. Trouwborst, S. J. van der Molen, B. J. van Wees (2006) The role of Joule heating in the formation of nanogaps by electromigration, JOURNAL OF APPLIED PHYSICS, 99, 114316 .
[DOI]
N. Tombros, S.J. van der Molen (2006) Separating spin and charge transport in single-wall carbon nanotubes, PHYSICAL REVIEW B, 73, 233403 .
[DOI]
S.J. van der Molen (2006) Magneto-Coulomb effect in spin-valve devices, PHYSICAL REVIEW B, 73, 220406.
[DOI]
S.J van der Molen, (2006) Stochastic and photochromic switching of diarylethenes studied by scanning tunnelling microscopy, NANOTECHNOLOGY, 17.
[DOI]

2005
Thijn van der Heijden and John van Noort and Hendrikje van Leest and Roland Kanaar and Claire Wyman and Nynke H Dekker and Nynke Dekker and Cees Dekker (2005) Torque-limited RecA polymerization on dsDNA., Nucleic Acids Res, 33, 2099--2105.
[Abstract] [DOI] [pdf]
The assembly of RecA onto a torsionally constrained double-stranded DNA molecule was followed in real time using magnetic tweezers. Formation of a RecA-DNA filament on the DNA tether was stalled owing to different physical processes depending on the applied stretching force. For forces up to 3.6 pN, the reaction stalled owing to the formation of positive plectonemes in the remaining DNA molecule. Release of these plectonemes by rotation of the magnets led to full coverage of the DNA molecule by RecA. At stretching forces larger than 3.6 pN, the twist induced during filament formation caused the reaction to stall before positive supercoils were generated. We deduce a maximum built-up torsion of 10.1 +/- 0.7 k(b)T. In vivo this built-up torsion may be used to favor regression of a stalled replication fork or to free the chromosomal DNA in E.coli from its condensing proteins.
John van Noort (2005) Unraveling bacteriorhodopsin., Biophys J, Feb, 88, 763--764.
[DOI] [pdf]
Dejan Ristic and Mauro Modesti and Thijn van der Heijden and John van Noort and Cees Dekker and Roland Kanaar and Claire Wyman (2005) Human Rad51 filaments on double- and single-stranded DNA: correlating regular an, Nucleic Acids Res, 33, 3292--3302.
[Abstract] [DOI] [pdf]
Recombinase proteins assembled into helical filaments on DNA are believed to be the catalytic core of homologous recombination. The assembly, disassembly and dynamic rearrangements of this structure must drive the DNA strand exchange reactions of homologous recombination. The sensitivity of eukaryotic recombinase activity to reaction conditions in vitro suggests that the status of bound nucleotide cofactors is important for function and possibly for filament structure. We analyzed nucleoprotein filaments formed by the human recombinase Rad51 in a variety of conditions on double-stranded and single-stranded DNA by scanning force microscopy. Regular filaments with extended double-stranded DNA correlated with active in vitro recombination, possibly due to stabilizing the DNA products of these assays. Though filaments formed readily on single-stranded DNA, they were very rarely regular structures. The irregular structure of filaments on single-stranded DNA suggests that Rad51 monomers are dynamic in filaments and that regular filaments are transient. Indeed, single molecule force spectroscopy of Rad51 filament assembly and disassembly in magnetic tweezers revealed protein association and disassociation from many points along the DNA, with kinetics different from those of RecA. The dynamic rearrangements of proteins and DNA within Rad51 nucleoprotein filaments could be key events driving strand exchange in homologous recombination.
Ralf Seidel and Joost G P Bloom and John van Noort and Christina F Dutta and Nynke H Dekker and Keith Firman and Mark D Szczelkun and Cees Dekker (2005) Dynamics of initiation, termination and reinitiation of DNA translocation by the, EMBO J, Dec, 24, 4188--4197.
[Abstract] [DOI] [pdf]
Type I restriction enzymes use two motors to translocate DNA before carrying out DNA cleavage. The motor function is accomplished by amino-acid motifs typical for superfamily 2 helicases, although DNA unwinding is not observed. Using a combination of extensive single-molecule magnetic tweezers and stopped-flow bulk measurements, we fully characterized the (re)initiation of DNA translocation by EcoR124I. We found that the methyltransferase core unit of the enzyme loads the motor subunits onto adjacent DNA by allowing them to bind and initiate translocation. Termination of translocation occurs owing to dissociation of the motors from the core unit. Reinitiation of translocation requires binding of new motors from solution. The identification and quantification of further initiation steps--ATP binding and extrusion of an initial DNA loop--allowed us to deduce a complete kinetic reinitiation scheme. The dissociation/reassociation of motors during translocation allows dynamic control of the restriction process by the availability of motors. Direct evidence that this control mechanism is relevant in vivo is provided.
Piet H.M. Lommerse, B. Ewa Snaar-Jagalska, Herman P. Spaink and Thomas Schmidt (2005) Single-Molecule Diffusion Measurements of H_Ras at the Plasma Membrane of Live C, J.Cell Sci, 118, 1799.
[DOI] [pdf]
Magis, JG, Stamouli, A, Martinsson, P, Oosterkamp, TH, Aartsma, TJ (2005) Unraveling the structure of the photosynthetic membrane: High-resolution, BIOPHYSICAL JOURNAL, 88, 421A-421A.
Schmauder, R, Librizzi, F, Canters, GW, Schmidt, T, Aartsma, TJ (2005) The oxidation state of a protein observed molecule-by-molecule, ChemPhysChem, 6, 1381-1386.
[DOI]
Schmauder, R, Alagaratnam, S, Chan, C, Schmidt, T, Canters, GW, Aartsma, TJ (2005) Sensitive detection of the redox state of copper proteins using, JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 10, 683-687.
[Abstract] [DOI] [pdf]
The blue copper protein azurin from Pseudo- monas aeruginosa has been covalently labelled with the fluorescing dye Cy5. The optical spectrum of the azurin changes markedly with its redox state. These changes are reflected in the fluorescence intensity of the dye through fluorescence resonance energy transfer (FRET). This provides a sensitive way to monitor biological redox events. The method shown to work in the nanomolar range of protein concentrations, can be easily extended into the sub-nanomolar regime and holds promise for single-molecule detection.
Frigaard, NU, Li, H, Martinsson, P, Das, SK, Frank, HA, Aartsma, TJ, Bryant, DA (2005) Isolation and characterization of carotenosomes from a, PHOTOSYNTHESIS RESEARCH, 86, 101-111.
[DOI]
M. van Hecke (2005) Granular matter - A tale of tails, Nature, 435, 1042 .
[pdf]
R. Mikkelsen, K. van der Weele, D. van der Meer, M. van Hecke, and D. Lohse (2005) Small-number statistics near the clustering transition in a compartmentalized granular gas, Phys. Rev. E, 71, 041302 .
[pdf]
E. Somfai, J.-N. Roux, J. H. Snoeijer, M. van Hecke, and W. van Saarloos (2005) Elastic wave propagation in confined granular systems, Phys. Rev. E, 72, 021301 .
[pdf]
I.K. Yanson, O.I. Shklyarevskii, Sz. Csonka, H. van Kempen, S. Speller, A.I. Yanson and J.M. van Ruitenbeek (2005) Atomic size oscillations in conductance histograms of gold nanowires and the influence of work hardening., Phys. Rev. Lett., 95.
[pdf]
A.M.C. Valkering, A.I. Mares, C. Untiedt, K. Babaei Gavan, T.H. Oosterkamp and J.M. van Ruitenbeek (2005) A force sensor for atomic point contacts., Rev. Sci. Instrum. , 76 .
[pdf]
A. Levy Yeyati and J.M. van Ruitenbeek, (2005) Transport at the atomic scale: atomic and molecular contacts., Les Houches Session LXXXI "Nanophysics: Coherence and Transport", H. Bouchiat et al., eds. Elsevier Amsterdam, 495-535.
[pdf]
J.M. van Ruitenbeek, (2005) Silver nanoswitch., Nature , 433.
[pdf]
A.I. Mares and J.M. van Ruitenbeek, (2005) Observation of shell effects in nanowires for the noble metals Cu, Ag, and Au., Phys. Rev. B , 72.
[pdf]
Jan van Ruitenbeek, (2005) Contacting individual molecules using mechanically controllable break junctions., Elke Scheer and Heiko Weber, in: "Introducing Molecular Electronics", G. Cuniberti, G. Fagas, and K. Richter, eds., Springer Lecture Notes in Physics Heidelberg,, 253-274.
[DOI] [pdf]
Ye.S. Avotina, YU.A. Kolesnichenko, A.N. Omelyanchouk, A.F. Otte, and J.M. van Ruitenbeek, (2005) Method to determine defect positions below a metal surface by STM., Phys. Rev. B , 71.
[pdf]
J.M. van Ruitenbeek (2005) Het atoom als gereedschap; de zin en onzin van nanotechnologie., De Academische boekengids, 49, 13-15.
[pdf]
D. Djukic, K.S. Thygesen, C. Untiedt, R.H.M. Smit, K.W. Jacobsen, and J.M. van Ruitenbeek, (2005) Stretching dependence of the vibration modes of a single-molecule Pt-H2-Pt junction., Phys. Rev. B, Rapid. Commun. , 71.
[pdf]
J. Visser and G. Nienhuis. (2005) The spectrum of a resonator with spherical aberrations., J. Opt. Soc. Am. A, 22, 2490.
[pdf]
J. Visser and G. Nienhuis. (2005) Vortices and angular momentum in general astigmatic modes., Proc. SPIE, Bellingham, WA, 5736, 126.
[pdf]
J. Visser, N.J. Zelders, G. Nienhuis. (2005) Wave description of geometric modes of a resonator., J. Opt. Soc. Am. A, 22, 1559-1566.
[pdf]
H.F. Schouten, N. Kuzmin, G. Dubois, T.D. Visser, G. Gbur, P.F.A. Alkemade, H. Blok, G.W. Hooft, D. Lenstra, E.R. Eliel. (2005) Plasmon-assisted two-slit transmission: Youngs experiment revisited., Phys. Rev. Lett., 94, 53901.
[pdf]
G. Puentes, D. Voigt, A. Aiello, and J.P. Woerdman. (2005) Experimental observation of universality in depolarised light scattering., Opt. Lett., 30, 3216.
[pdf]
S.S.R. Oemrawsingh, X. Ma, D. Voigt, A. Aiello, E.R. Eliel, G.W. t Hooft, and J.P. Woerdman. (2005) Experimental demonstration of fractional orbital angular momentum entanglement of two photons., Phys. Rev. Lett., 95, 240501.
[pdf]
P.S.K. Lee, M.P. van Exter, and J.P. Woerdman. (2005) How focused pumping affects type-II spontaneous parametric down-conversion., Phys. Rev. A, 72, 033803.
[pdf]
P.S.K. Lee, J.B. Pors, M.P. van Exter, J.P. Woerdman. (2005) Simple method for accurate characterization of birefringent crystals., Appl. Opt., 44, 866-870.
[pdf]
T. Klaassen, J. de Jong, M.P. van Exter, J.P. Woerdman. (2005) Transverse mode coupling in an optical resonator., Opt. Lett., 30, 1959-1961.
[pdf]
C. Genet, M.P. van Exter, J.P. Woerdman. (2005) Huygens description of resonance phenomena in subwavelength hole arrays., J. Opt. Soc. Am. A, 22, 998-1002.
[pdf]
C. Genet, E. Altewischer, M.P. van Exter, J.P. Woerdman. (2005) Optical depolarization induced by arrays of subwavelength metal holes., Phys. Rev. B, 71, 33409-1-4.
[pdf]
M.W. Beijersbergen and J.P. Woerdman. (2005) Measuring orbital angular momentum of light with a torsion pendulum., Proc. SPIE , 5736: 111 (SPIE, Bellingham.
[pdf]
E. Altewischer, X. Ma, M.P. van Exter, and J.P. Woerdman. (2005) Fano-type interference in the point-spread function of nanohole arrays., Opt. Lett., 30, 2436-2438.
[pdf]
E. Altewischer, M.P. van Exter, and J.P. Woerdman. (2005) Analytic model of optical depolarization in square and hexagonal nanohole arrays., J. Opt. Soc. Am. B, 22, 1731-1736.
[pdf]
E. Altewischer, Y.C. Oei, M.P. van Exter, J.P. Woerdman. (2005) Quantum decoherence versus classical depolarization in nanohole arrays., Phys. Rev. A, 72, 013817.
[pdf]
E. Altewischer, C. Genet, M.P. van Exter, and J.P. Woerdman. (2005) Polarization tomography of metallic nanohole arrays., Opt. Lett., 30, 90-92.
[pdf]
A. Aiello and J.P. Woerdman. (2005) Exact quantization of a paraxial electromagnetic field., Phys. Rev. A, 72, 060101.
[pdf]
A. Aiello, S.S.R. Oemrawsingh, E.R. Eliel, and J.P. Woerdman. (2005) Non-locality of high-dimensional two-photon orbital angular momentum., Phys. Rev. A, 72, 052114.
[pdf]
A. Aiello and J.P. Woerdman. (2005) Role of spatial coherence in polarization tomography., Opt. Lett., 30, 1599-1601.
[pdf]
A. Aiello, J.P. Woerdman. (2005) Physical bounds to the entropy-depolarization relation in random light scattering., Phys. Rev. Lett., 94, 090406.
[pdf]
M. Fittipaldi, H.J. Wijma, M.P. Verbeet, G.W. Canters, E.J.J. Groenen, M. Huber (2005) The Substrate-Bound Type 2 Copper Site of Nitrite Reductase: The Nitrogen Hyperfine Coupling of Nitrite Revealed by Pulsed EPR, Biochemistry, 44, 15193-15202.
S. Steigmiller, M. B?rsch, P. Gr?ber, M. Huber (2005) Distances between the b-subunits in the tether domain of F0F1-ATP synthase from E. coli, Biochim. Biophys. Acta, 1708, 143-153.
S.B. Orlinskii, H. Blok, E.J.J. Groenen, J. Schmidt, P.G. Baranov, C. de Mello Doneg?, A. Meijerink (2005) High-frequency EPR and ENDOR spectroscopy on semiconductor nanocrystals, Magn. Reson. Chem., 43, S140-S144.
S.B. Orlinskii, J. Schmidt, E.J.J. Groenen, P.G. Baranov, C. de Mello Doneg?, A. Meijerink (2005) Shallow donors in semiconductor nanoparticles: Limit of the effective mass approximation, Phys. Rev. Letters, 94, 9 097602.
H. Blok, J.A.J.M. Disselhorst, H.J. van der Meer, S.B. Orlinski, J. Schmidt (2005) CW and Pulsed EPR and ENDOR Spectroscopy at 275 GHz, Bruker Spin Report, 156, 3-8.
H. Blok, J.A.J.M. Disselhorst, H.J. van der Meer, S.B. Orlinskii, J. Schmidt (2005) ENDOR Spectroscopy at 275 GHz, J. Magn. Res., 173, 49-53.
R.A.L. Vallée, M. van der Auweraer, F.C. De Schryver, D. Beljonne, M. Orrit (2005) A Microscopic Model for the Fluctuations of Local Field and Spontaneous Emission of Single Molecules in Disordered Media, ChemPhysChem, 6, 81-91.
[pdf]
R. Verberk, J.W.M. Chon, M. Gu, M. Orrit (2005) Environment-dependent blinking of single semiconductor nanocrystals and statistical aging of ensembles, Physica E, 26, 19-23.
[pdf]
M. Lippitz, M.A. van Dijk, M. Orrit (2005) Third-Harmonic Generation from Single Gold Nanoparticles, Nano Lett., 5, 799-802.
[pdf]
R. Verberk (2005) Photon statistics and power-law blinking of single semiconductor nanocrystals, .
[pdf]
B. Lounis, M. Orrit (2005) Single-photon sources, Rep. Prog. Phys., 68, 1129-1179.
[pdf]
M. Lippitz, F. Kulzer, M. Orrit (2005) Statistical Evaluation of Single Nano-Object Fluorescence, ChemPhysChem, 6, 770-789.
[pdf]
M.A. Kol´chenko, B. Kozankiewicz, A. Nicolet, M. Orrit (2005) Intersystem crossing mechanisms and single-molecule fluorescence. Terrylene in anthracene crystals, Opt. Spectrosc., 98, 681-686.
[pdf]
M.A. van Dijk, M. Lippitz, M. Orrit (2005) Far-Field Optical Microscopy of Single Metal Nanoparticles, Acc. Chem. Res., 38, 594-601.
[pdf]
C. Hofmann, A. Nicolet, M.A. Kol´chenko, M. Orrit (2005) Towards nanoprobes for conduction in molecular crystals: dibenzoterrylene in anthracene crystals, Chem. Phys., 318, 1-6.
[pdf]
M.A. van Dijk, M. Lippitz, M. Orrit (2005) Detection of Acoustic Oscillations of Single Gold Nanospheres by Time-Resolved Interferometry, Phys. Rev. Lett., 95, 267406.
[pdf]
C. Cirillo, S.L. Prischepa, M. Salvato, C. Attanasio, M. Hesselberth & J. Aarts (2005) Superconducting proximity effect and interface transparency in Nb/PdNi bilayers, Physical Review B , 72, 144511 1-7.
Y.L. Qin, H.W. Zandbergen , Z.Q. Yang and J. Aarts (2005) Crystal structure of (La, Ca) MnO 3 ultrathin films deposited on SrTiO 3 substrates, J., Phil. Mag , 85, 4465.

2004
John van Noort and Thijn van der Heijden and Christina F Dutta and Keith Firman and Cees Dekker (2004) Initiation of translocation by Type I restriction-modification enzymes is associ, Nucleic Acids Res, 32, 6540--6547.
[Abstract] [DOI] [pdf]
Recognition of 'foreign' DNA by Type I restriction-modification (R-M) enzymes elicits an ATP-dependent switch from methylase to endonuclease activity, which involves DNA translocation by the restriction subunit HsdR. Type I R-M enzymes are composed of three (Hsd) subunits with a stoichiometry of HsdR2:HsdM2:HsdS1 (R2-complex). However, the EcoR124I R-M enzyme can also exist as a cleavage deficient, sub-assembly of HsdR1:HsdM2:HsdS1 (R1-complex). ATPS was used to trap initial translocation complexes, which were visualized by Atomic Force Microscopy (AFM). In the R1-complex, a small bulge, associated with a shortening in the contour-length of the DNA of 8 nm, was observed. This bulge was found to be sensitive to single-strand DNA nucleases, indicative of non-duplexed DNA. R2-complexes appeared larger in the AFM images and the DNA contour length showed a shortening of approximately 11 nm, suggesting that two bulges were formed. Disclosure of the structure of the first stage after the recognition-translocation switch of Type I restriction enzymes forms an important first step in resolving a detailed mechanistic picture of DNA translocation by SF-II DNA translocation motors.
John van Noort and Sander Verbrugge and Nora Goosen and Cees Dekker and Remus Thei Dame (2004) Dual architectural roles of HU: formation of flexible hinges and rigid filaments, Proc Natl Acad Sci U S A, May, 101, 6969--6974.
[Abstract] [DOI] [pdf]
The nucleoid-associated protein HU is one of the most abundant proteins in Escherichia coli and has been suggested to play an important role in bacterial nucleoid organization and regulation. Although the regulatory aspects of HU have been firmly established, much less is understood about the role of HU in shaping the bacterial nucleoid. In both functions (local) modulation of DNA architecture seems an essential feature, but information on the mechanical properties of this type of sequence-independent nucleoprotein complex is scarce. In this study we used magnetic tweezers and atomic force microscopy to quantify HU-induced DNA bending and condensation. Both techniques revealed that HU can have two opposing mechanical effects depending on the protein concentration. At concentrations <100 nM, individual HU dimers induce very flexible bends in DNA that are responsible for DNA compaction up to 50\%. At higher HU concentrations, a rigid nucleoprotein filament is formed in which HU appears to arrange helically around the DNA without inducing significant condensation.
Ralf Seidel and John van Noort and Carsten van der Scheer and Joost G P Bloom and Nynke H Dekker and Christina F Dutta and Alex Blundell and Terence Robinson and Keith Firman and Cees Dekker (2004) Real-time observation of DNA translocation by the type I restriction modificatio, Nat Struct Mol Biol, Sep, 11, 838--843.
[Abstract] [DOI] [pdf]
Type I restriction enzymes bind sequence-specifically to unmodified DNA and subsequently pull the adjacent DNA toward themselves. Cleavage then occurs remotely from the recognition site. The mechanism by which these members of the superfamily 2 (SF2) of helicases translocate DNA is largely unknown. We report the first single-molecule study of DNA translocation by the type I restriction enzyme EcoR124I. Mechanochemical parameters such as the translocation rate and processivity, and their dependence on force and ATP concentration, are presented. We show that the two motor subunits of EcoR124I work independently. By using torsionally constrained DNA molecules, we found that the enzyme tracks along the helical pitch of the DNA molecule. This assay may be directly applicable to investigating the tracking of other DNA-translocating motors along their DNA templates.
Martijn J. van Hemert, Maarten Niemantsverdriet, Thomas Schmidt, Claude Backend (2004) Isoform-specific differences in rapid nucleocytoplasmic shuttling cause distinct, J.Cell Sci, 117, 1411.
[DOI] [pdf]
Gerhard A. Blab, Thomas Schmidt, and Mats Nilsson (2004) Homogeneous detection of single rolling circle replication products, Anal.Chem, 76, 495.
[Abstract] [DOI] [pdf]
We describe a simple and straightforward approach for homogeneous and isothermal detection of individual rolling circle replication (RCR) products, which represent individual padlock probe circularization events. The RCR products constitute tens of kilobases long single-stranded tandem repeated copies of the probe sequence, and in solution, they fold into micrometer-sized random coils. The method is based on the local enrichment of fluorescence-labeled probes that hybridize to the coiled RCR products compared to the concentration of free probes in solution. We present a detailed characterization of the fluorescence-labeled products using a highly sensitive and fast microscopy setup. At a 104-fold excess of free label, we were able to detect and follow individual RCR products at a signal-to-background noise ratio of 27. This high signal-to-background noise ratio leaves room for analysis in a simple detection device at higher speeds or at lower labeling ratios.
P.H.M. Lommerse, H.P. Spaink and T. Schmidt (2004) In vivo plasma membrane organization: results of biophysical approaches, BBA, 1664, 119.
[DOI] [pdf]
Gerhard A. Blab, Silke Oellerich, Reinier Schumm, and Thomas Schmidt (2004) Wide-Field Imaging and Spectroscopy of Localized Fluorophores, Opt.Lett, 29, 727.
[Abstract] [DOI] [pdf]
A method that combines fluorescence imaging and spectroscopy of single molecules at room temperature is presented. This approach allows us to identify a number of imaged molecules unequivocally by simultaneously recording their fluorescence emission spectra. Furthermore, their spectral characteristics not only allow us to separate different fluorescent labels quantitatively and qualitatively but also provide information on the microenvironment of the molecules. This new method was successfully tested on a system of yellow-green and red fluorescent 20-nm latex beads, and its usefulness in studies of biological systems was illustrated for a preparation of combined binary ratio labeling–fluorescence in situ hybridization-stained mouse chromosomes.
Piet H.M. Lommerse, Gerhard A. Blab, Laurent Cognet, Gregory S. Harms, Ewa B. Snaar-Jagalska, Herman P. Spaink, Thomas Schmidt. (2004) Single-molecule imaging of lipid-anchored proteins reveals domains in the cytoplasmic leaflet of the cell membrane., Biophys.J, 86, 609.
[Abstract] [DOI] [pdf]
In the last decade evidence has accumulated that small domains of 50–700 nm in diameter are located in the exoplasmic leaflet of the plasma membrane. Most of these domains supposedly consist of specific sets of lipids and proteins, and are believed to coordinate signal transduction cascades. Whether similar domains are also present in the cytoplasmic leaflet of the plasma membrane is unclear so far. To investigate the presence of cytoplasmic leaflet domains, the H-Ras membrane-targeting sequence was fused to the C-terminus of the enhanced yellow fluorescent protein. Using single-molecule fluorescence microscopy, trajectories of individual molecules diffusing in the cytoplasmic leaflet of the plasma membrane were recorded. From these trajectories, the diffusion of individual membrane-anchored enhanced yellow fluorescent protein molecules was studied in live cells on timescales from 5 to 200 ms. The results show that the diffusion of 30–40% of the molecules is constrained in domains with a typical size of 200 nm. Neither breakdown of actin nor cholesterol extraction changed the domain characteristics significantly, indicating that the observed domains may not be related to the membrane domains identified so far.
Hofmann, C, Aartsma, TJ, Michel, H, Kohler, J (2004) Spectral dynamics in the B800 band of LH2 from Rhodospirillum, NEW JOURNAL OF PHYSICS, 6, 109-114.
[DOI]
Stamouli, A, Frenken, JWM, Oosterkamp, TH, Cogdell, RJ, Aartsma, TJ (2004) The electron conduction of photosynthetic protein complexes embedded in, FEBS LETTERS, 560, 109-114.
[DOI]
Gradinaru, CC, Martinsson, P, Aartsma, TJ, Schmidt, T (2004) Simultaneous atomic-force and two-photon fluorescence imaging of, ULTRAMICROSCOPY, 99, 235-245.
[DOI]
Hofmann, C, Aartsma, TJ, Kohler, J (2004) Energetic disorder and the B850-exciton states of individual, CHEMICAL PHYSICS LETTERS, 395, 373-378.
[DOI]
de Ruijter, WPF, Oellerich, S, Segura, JM, Lawless, AM, Papiz, M, Aartsma, TJ (2004) Observation of the energy-level structure of the low-light adapted B800, BIOPHYSICAL JOURNAL, 87, 3413-3420.
[DOI]
D. Fenistein, J. W. van de Meent and M. van Hecke (2004) Universal and wide shear zones in granular bulk flow, Phys. Rev. Lett., 92, 094301 .
[pdf]
J. H. Snoeijer, T. J. H. Vlugt, M. van Hecke and W. van Saarloos (2004) Force network ensemble, a new approach to static granular matter, 92, 054302 .
[pdf]
J. H. Snoeijer, M. van Hecke, E. Somfai, and W. van Saarloos (2004) Packing geometry and statistics of force networks in granular media, Phys. Rev. E, 70, 011301 .
[pdf]
J. H. Snoeijer, T. J. H. Vlugt, W. G. Ellenbroek, M. van Hecke, and J. M. J. van Leeuwen (2004) Ensemble theory for force networks in hyperstatic granular matter, Phys. Rev. E, 70, 061306 .
[pdf]
A.I. Yanson, I.K. Yanson and J.M. van Ruitenbeek (2004) Shell effects in heavy alkali-metal nanowires., in: "Molecular Nanowires and Other Quantum Objects", A.S. Alexandrov et al., eds. Kluwer Academic Publishers, Dordrecht,.
[pdf]
D.F. Urban, J. Bürki, A.I. Yanson, I.K. Yanson, C.A. Stafford, J.M. van Ruitenbeek, and Hermann Grabert (2004) Electronic shell effects and the stability of alkali nanowires., Solid State Commun, 1.
[pdf]
C. Untiedt, D.M.T. Dekker, D. Djukic and J.M. van Ruitenbeek (2004) Absence of magnetically-induced fractional quantization in atomic contacts., Phys. Rev. B , 69.
[pdf]
A.I. Mares, A.F. Otte, L.G. Soukiassian, R.H.M. Smit, and J.M. van Ruitenbeek (2004) Observation of electronic and atomic shell effects in gold nanowires., Phys. Rev B , 70.
[pdf]
R.H.M. Smit, C. Untiedt, and J.M. van Ruitenbeek (2004) High-bias stability of monatomic chains., Nanotechnology , 15.
J. Visser, G. Nienhuis. (2004) Interference between entangled photon states in space and time., Eur. Phys. J. D, 29, 301-308.
[pdf]
J. Visser, G. Nienhuis. (2004) Orbital angular momentum of general astigmatic modes., Phys. Rev. A, 70, 013809-1-12.
[pdf]
A.V. Taichenachev, A.M. Tuamikin, V.I. Yudin, G. Nienhuis. (2004) Steady state of atoms in a resonant field with elliptical polarization., Phys. Rev. A, 69, 33410-1-18.
[pdf]
G. Puentes, A. Aiello, J.P. Woerdman. (2004) Ray splitting in paraxial optical cavities., Phys. Rev., E, 69: 036209-1-6.
[pdf]
G. Puentes, A. Aiello, J.P. Woerdman. (2004) Chaotic ray dynamics in an optical cavity with a beam splitter., Opt. Lett., 29, 929-931.
[pdf]
O.N. Prudnikov, A.V. Taichenachev, A.M. Tumaikin, V.I. Yudin, G. Nienhuis. (2004) Basis of polarization-dressed states of an atom in an elliptically polarized resonant field, J. of Exp. and Theor. Physics., 99, 1137-1149.
[pdf]
S.S.R. Oemrawsing, J.A.W. van Houwelingen, E.R. Eliel, J.P. Woerdman, E.J.K. Verstegen, J.G. Kloosterboer, G.W. t Hooft. (2004) Production and characterization of spiral phase plates for optical wavelengths., Applied Optics., 43, 688-694.
[pdf]
S.S.R. Oemrawsingh, E.R. Eliel, J.P. Woerdman, E.J.K. Verstegen, J.G. Kloosterboer, G.W. t Hooft. (2004) Half-integral spiral phase plates for optical wavelengths., J. Opt. , A, 6: S288-S290.
[pdf]
S.S.R. Oemrawsingh, E.R. Eliel, G. Nienhuis, J.P. Woerdman. (2004) Intrinsic orbital angular momentum of paraxial beams with off-axis imprinted vortices., J. Opt. Soc. Am., A21, 2089-2096.
[pdf]
S.S.R. Oemrawsingh, A. Aeillo, E.R. Eliel, G. Nienhuis, J.P. Woerdman. (2004) How to observe high-dimensional two-photon entanglement with only two detectors., Phys. Rev. Lett., 92, 217901-1-4.
[pdf]
G. Nienhuis, J. Visser. (2004) Angular momentum and vortices in paraxial beams., J. of Opt. A - pure and appl. opt., 6, : S248-S250.
[pdf]
P.S.K. Lee, M.P. van Exter, J.P. Woerdman. (2004) Increased polarization-entangled photon flux via thinner crystals., Phys. Rev. A, 70, 043818.
[pdf]
T. Klaassen, A. Hoogeboom, M.P. van Exter, J.P. Woerdman. (2004) Gouy phase of nonparaxial eigenmodes in a folded resonator., J. Opt. Soc. Am., A21, : 1689-1693.
[pdf]
H.L. Haroutyunyan, G. Nienhuis. (2004) Resonances for coupled Bose-Einstein condensates., Phys. Rev. A, 70, 063603-1-9.
[pdf]
H.L. Haroutyunyan, G. Nienhuis. (2004) Diffraction by circular optical lattices., Phys. Rev. A, 70, 063408-1-8.
[pdf]
H.L. Haroutyunyan, G. Nienhuis. (2004) Phase dynamics of a multimode Bose-Einstein condensate controlled by decay., Phys. Rev. A, 69, 053621-1-12.
[pdf]
E. Altewischer, C. Genet, M.P. van Exter, J.P. Woerdman, P.F.A. Alkemade, A. van Zuuk, E.W.J.M. van der Drift. (2004) Polarization tomography of metallic nanohole arrays., Opt. Lett., 30, 90-92.
[pdf]
A. Aeillo, J.P. Woerdman. (2004) Intrinsic entanglement degradation by multimode detection., Phys. Rev. A, 70, 023808-1-12.
[pdf]
A. Szemik-Hojniak, G. Balkowski, G.W.H. Wurpel, J. Herbich, J.H. van der Waals, W.J. Buma (2004) The photophysics of 1,8-bis(dimethylamino)naphthalene in solution: internal charge transfer with a twist, J. Phys. Chem., A 108, 10623-10631.
J.H. van der Waals, C.H. Hilbers (2004) Moleculen doorgrond: kwantumchemie en spectroscopie, In: Geschiedenis van de Scheikunde in Nederland, III De ontwikkeling van de chemie in Nederland tussen 1945 en het begin van de jaren tachtig, Eds. E. Homburg and L.C. Palm, Delft University Press (2004).
D. M. Hofmann, H. Zhou, D. R. Pfisterer, H. Alves, B. K. Meyer, P. Baranov, N. Romanov, C. de Mello Donega, A. Meijering, S.B. Orlinskii, H. Blok, J. Schmidt (2004) Donors in ZnO nanocrystals, Phys. Stat. Sol., 1, 4, 908-911.
S.B. Orlinskii, J. Schmidt, P.G. Baranov, D.M. Hofmann, C. De Mello Doneg?, A. Meijerink (2004) Probing the wave function of shallow Li and Na donors in ZnO nanoparticles, Phys. Rev. Letters, 92, 4 047603.
H. Blok, J.A.J.M. Disselhorst, S.B. Orlinski, J. Schmidt (2004) A continuous-wave and pulsed electron spin resonance spectrometer operating at 275 GHz, J. Magn. Res., 166, 92-99.
[pdf]
H. Blok, S.B. Orlinski, J. Schmidt, P.G. Baranov (2004) Overhauser Effect of 67Zn Nuclear Spins in ZnO via Cross Relaxation Induced by the Zero-Point Fluctuations of the Phonon Field, Phys. Rev. Lett., 92, 4 047602.
E.J.J. Groenen, J. Schmidt (2004) High-frequency EPR, ESEEM and ENDOR studies of paramagnetic centres in single-crystalline materials, In: Very High Frequency (VHF) ESR/EPR, Biol.Magn.Reson. 22, eds. O. Grinberg, L.J. Berliner, Kluwer Academic Publishers, New York, 2004, 278-304.
R. Zondervan, F. Kulzer, M.A. Kol´chenko, M. Orrit (2004) Photobleaching of Rhodamine 6G in Poly(vinyl alcohol) at the Ensemble and Single-Molecule Levels, J. Phys. Chem. A, 108, 1657-1665.
[pdf]
F. Kulzer, M. Orrit (2004) Single-Molecule Optics, Annu. Rev. Phys. Chem., 55, 585-611.
[pdf]
Y.Q. Zhang, Z.D. Zhang and J. Aarts (2004) First-order nature of a metamagnetic transition and mechanism of giant magneto-resistance in Mn2Sb0.95Sn0.05, Phys. Rev. B, 70, 132407.
Z.-Q. Yang, R.W.A. Hendrikx, J. Aarts, Y.L. Qin and H.W. Zandbergen (2004) Physical properties and microstructures of ultra-thin (La,Ca)MnO3 films under different conditions of strain, Phys. Rev. B , 70, 174111.
A.Yu. Rusanov, M.B.S. Hesselberth, J. Aarts and A.I. Buzdin (2004) Enhancement of the superconducting transition temperature in Nb/Permalloy bilayers by controlling the domain state of the ferromagnet, Phys. Rev. Lett., 93, 057002.
A.Yu. Rusanov, M.B.S. Hesselberth and J. Aarts (2004) Depairing currents in superconducting films of Nb and amorphous MoGe, Phys. Rev. B, 70, 024510.
A.Yu. Rusanov, M.B.S. Hesselberth, S. Habraken and J. Aarts (2004) Depairing currents in superconductor ferromagnet Nb/CuNi trilayers close to Tc, Physica C 404, 404, 322-325.

2003
John van Noort and Thijn van Der Heijden and Martijn de Jager and Claire Wyman and Roland Kanaar and Cees Dekker (2003) The coiled-coil of the human Rad50 DNA repair protein contains specific segments, Proc Natl Acad Sci U S A, Jun, 100, 7581--7586.
[Abstract] [DOI] [pdf]
Protein structural features are usually determined by defining regularities in a large population of homogeneous molecules. However, irregular features such as structural variation and flexibility are likely to be missed, despite their vital role for their biological function. In this paper, we report the observation of striking irregularities in the flexibility of the coiled-coil region of the human Rad50 DNA repair protein. Existing methods to quantitatively analyze flexibility are applicable to homogeneous polymers only. Because protein coiled-coils cannot be assumed to be homogeneous, we develop a method to quantify the local flexibility from high-resolution atomic force microscopy images. Indeed, in Rad50 coiled-coils, two positions of increased flexibility are observed. We discuss how this dynamic structural feature is integral to Rad50 function.
Hofmann, C, Ketelaars, M, Matsushita, M, Michel, H, Aartsma, TJ, Kohler, J (2003) Single-molecule study of the electronic couplings in a circular array of, PHYSICAL REVIEW LETTERS, 90, 274A-274A.
[DOI]
de Ruijter, WPF, Oelledch, S, Segura, JM, Lawless, AM, Papiz, MZ, Aartsma, TJ (2003) Individual low-light LH2 (LL-LH2) complexes studied at low temperature, BIOPHYSICAL JOURNAL, 84, 274A-274A.
Stamouli, A, Klein, DCG, Oosterkamp, TH, Frenken, JWM, Cogdell, R, Aartsma, TJ (2003) Resolving the structure and organization of photosynthetic protein, BIOPHYSICAL JOURNAL, 84, 273A-273A.
Oellerich, S, Ketelaars, M, Segura, JM, de Ruijter, W, Kohler, J, Cogdell, R, Aartsma, TJ (2003) A single molecule study on bacterial light-harvesting complexes, BIOPHYSICAL JOURNAL, 84, 121A-121A.
Stamouli, A, Kafi, S, Klein, DCG, Oosterkamp, TH, Frenken, JWM, Cogdell, RJ, Aartsma, TJ (2003) The ring structure and organization of light harvesting 2 complexes in a, BIOPHYSICAL JOURNAL, 84, 2483-2491.
[DOI]
Hofmann, C, Aartsma, TJ, Michel, H, Kohler, J (2003) Direct observation of tiers in the energy landscape of a chromoprotein:, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF, 100, 15534-15538.
[DOI]
M. van Hecke (2003) Coherent and Incoherent structures in systems described by the 1D CGLE, Experiments and Identification, 174, 134 .
[pdf]
S. Horluck, M. van Hecke and P. Dimon (2003) Shock waves in two-dimensional granular flow - Effects of rough walls and polydispersity, Phys. Rev. E, 67, 021304 .
[pdf]
J. H. Snoeijer, M. van Hecke, E. Somfai and W. van Saarloos (2003) Force and weight distributions in granular media - Effects of contact geometry, Phys. Rev. E R., 67, 030302 .
[pdf]
L. Pastur, M. T. Westra, D. Snouck, W. van de Water, M van Hecke, C. Storm and W. van Saarloos (2003) Sources and holes in a one-dimensional traveling-wave convection experiment, Phys. Rev. E, 67, 036305 .
[pdf]
R. Mikkelsen, M. van Hecke and T. Bohr (2003) Influence of solitons on the transition to spatiotemporal chaos in coupled map lattices, Phys. Rev. E, 67, 046207 .
[pdf]
D. Fenistein and M. van Hecke (2003) Wide shear zones in granular bulk flow, Nature, 425, 256 .
[pdf]
M. Howard and M. van Hecke (2003) Hole-defect chaos in the one-dimensional complex Ginzburg-Landau equation, Phys. Rev. E, 68, 026213 .
[pdf]
R.H.M. Smit, C. Untiedt, G. Rubio-Bollinger, R.C. Segers, and J.M. van Ruitenbeek (2003) Observation of a parity oscillation in the conductance of atomic wires., Phys. Rev. Lett. , 91.
[pdf]
J.M. van Ruitenbeek (2003) Shot noise and channel composition of atomic-sized contacts., In: "Quantum Noise in Mesoscopic Physics", Y Nazarov, editor, Kluwer Academic Publishers, Dordrecht,, 33-50.
[pdf]
N. Agraït, A. Levy Yeyati and J.M. van Ruitenbeek (2003) Quantum properties of atomic-sized conductors., Physics Reports , 377.
[DOI] [pdf]
J.W.T. Heemskerk, Y. Noat, D.J. Bakker, J.M. van Ruitenbeek, B.J. Thijsse and P. Klaver (2003) A current induced transition in atomic-sized contacts of metallic alloys., Phys. Rev. B , 67.
[pdf]
S.K. Nielsen, Y. Noat, M. Brandbyge, R.H.M. Smit, K. Hansen, L.Y. Chen, F. Besenbacher and J.M. van Ruitenbeek (2003) Conductance of single-atom platinum contacts: Voltage dependence of the conductance histogram., Phys. Rev. B, , 67.
[pdf]
M.B. Willemsen, M.P. van Exter, J.P. Woerdman, F. Monti di Sopra, M. Moser, E. Kapon. (2003) Polarization supermodes of phase-coupled arrays of vertical-cavity semiconductor lasers., Laser Physics, 13, 324-327.
[pdf]
Y. Lien, E. van der Togt, M.P. van Exter, J.P. Woerdman. (2003) Resonant excess quantum noise in lasers with mixed guiding., Opt. Lett., 28, 1668-1670.
[pdf]
H.L. Haroutyunyan, G. Nienhuis. (2003) Analogy between a two-well Bose-Einstein condensate and atom diffraction., Phys. Rev., A67, 053611-1-7.
[pdf]
C. Genet, M.P. van Exter, J.P. Woerdman. (2003) Fano-type interpretation of red shifts and red tails in hole array transmission spectra., Opt. Commun., 225, 331-336.
[pdf]
P. Debernardi, G.P. Bava, F. Monti di Sopra, M.B. Willemsen. (2003) , IEEE J. Quantum Electron., 39, 109-119.
[pdf]
E. Altewischer, M.P. van Exter, J.P. Woerdman. (2003) Nonreciprocal reflection of a subwavelength hole array., Opt. Lett., 28, 1906-1908.
[pdf]
E. Altewischer, M.P. van Exter, J.P. Woerdman. (2003) Polarization analysis of propagating surface plasmons in a subwavelength hole array., J. Opt. Soc. Am., B20, 1927-1931.
[pdf]
A. Aiello, G. Nienhuis, J.P. Woerdman. (2003) Subthreshold optical parametric oscillator with nonorthogonal polarization eigenmodes., Phys. Rev., A67, 043803-1-15.
[pdf]
A. Aiello, M.P. van Exter, J.P. Woerdman. (2003) Ray chaos in optical cavities based upon standard laser mirrors., Phys. Rev., E68, 046208-1-4.
[pdf]
H. Blok, J.A.J.M. Disselhorst, S.B. Orlinskii, J. Schmidt, P.G. Baranov (2003) A new step in high-frequency EPR of defects in semiconductors, Physica B, 340-342, 1147-1150.
P.G. Baranov, S.I. Goloshchapov, G.A. Medvedkin, S.B. Orlinskii, V.G. Voevodin (2003) Magnetic resonance of Mn-related isolated centers and clusters in chalcopyrite crystal of (Zn,Mn)GeP2, Physica B, 340-342, 878-881.
I.V. Ilyin, M.V. Muzafarova, E.N. Mokhov, P.G. Baranov, S.B. Orlinskii, J. Schmidt (2003) Multivacancy clusters in silicon carbide, Physica B, 340-342, 128-131.
R. Zondervan, F. Kulzer, S.B. Orlinskii, M. Orrit (2003) Photoblinking of Rhodamine 6G in Poly(vinyl alcohol): Radical Dark State Formed through the Triplet, J. Phys. Chem. A, 107, 6770-6776.
M. Fittipaldi, R.A. Steiner, M. Matsushita, B.W. Dijkstra, E.J.J. Groenen, M. Huber (2003) Single-crystal EPR study at 95 GHz of the type 2 copper site of the inhibitor-bound quercetin 2,3-dioxygenase, Biophys. J., 85, 6, 4047-4054.
R.E.M. Diederix, M. Fittipaldi, J.A.R. Worrall, M. Huber, M. Ubbink, G.W. Canters (2003) Kinetic stability of the peroxidase activity of unfolded cytochrome c: Heme degradation and catalyst inactivation by hydrogen peroxide, Inorg. Chem., 42, 22, 7249-7257.
M.G. Finiguerra, I.M.C. van Amsterdam, S. Alagaratnam, M. Ubbink, M. Huber (2003) Anisotropic spin label mobilities in azurin from 95 GHz electron paramagnetic resonance spectroscopy, Chem. Phys. Lett., 382, 528-533.
L. Bubacco, M. van Gastel, E.J.J. Groenen, E. Vijgenboom, G.W. Canters (2003) Spectroscopic characterization of the electronic changes in the active site of Streptomyces antibioticus Tyrosinase upon binding of transition state analogue inhibitors, J. Biolog. Chem., 278, 9, 7381-7389.
I.M.C. van Amsterdam, M. Ubbink, G.W. Canters, M. Huber (2003) Measurement of a Cu-Cu distance of 26 ? by a pulsed EPR method, Angew. Chem. Int. Ed., 42, 1, 62-64.
M. Ubbink, J.A.R. Worrall, G.W. Canters, E.J.J. Groenen, M. Huber (2003) Paramagnetic resonance of biogical metal centers, Annu. Rev. Biophys. Biomol. Struct., 31, 393-422.
H.J. Wijma, M.J. Boulanger, A. Molon, M. Fittipaldi, M. Huber, M.E.P. Murphy, M.Ph. Verbeet, G.W. Canters (2003) Reconstitution of the type 1 active site of the H145G/A variants of Nitrite Reductase by ligand insertion, Biochemistry, 42, 4075-4083.
S.B. Orlinskii, J. Schmidt, E.N. Mokhov, P.G. Baranov (2003) Silicon and carbon vacancies in neutron irradiated SiC. A high-field Electron Paramagnetic Resonance study, Phys. Rev., B 67 125207.
D. Boyer, P. Tamarat, A. Maali, M. Orrit, B. Lounis (2003) Imaging single metal nanoparticles in scattering media by photothermal interference contrast, Physica E, 17, 537-540.
[pdf]
R. Verberk, M. Orrit (2003) Photon statistics in the fluorescence of single molecules and nanocrystals: Correlation functions versus distributions of on- and off-times, J. Chem. Phys., 119, 2214-2222.
[pdf]
R. Zondervan, F. Kulzer, S.B. Orlinskii, M. Orrit (2003) Photoblinking of Rhodamine 6G in Poly(vinyl alcohol): Radical Dark State Formed through the Triplet, J. Phys. Chem. A, 107, 6770-6776.
[pdf]
M. Orrit (2003) The Motions of an Enzyme Soloist, Science, 302, 239-240.
[pdf]
G. J. C. van Baarle, A. M. Troyanovski, T. Nishizaki, P. H. Kes and J. Aarts (2003) Imaging vortex configurations in thin films by STM, Appl. Phys. Lett. , 82, 1081.
A. Otop, G. R. Boogaard, R. W. A. Hendrikx, M. B. S. Hesselberth, C. Ciuhu, A. Lodder and J. Aarts (2003) Proximity effects in the superconductor/heavy-fermion bilayer system Nb/CeCu6, Europhys. Lett., 64, 91.
A. Otop, S. Sullow, M. B. S. Hesselberth and J. Aarts (2003) Proximity effects in CeCu6/Nb bilayers, Acta Phys. Pol., B34, 1169 .
T. Nishizaki, A. M. Troyanovski, G. J. C. v. Baarle, P. H. Kes and J. Aarts (2003) STM imaging of vortex structures in NbN thin films, Physica C , 388-389, 777.
I. M. Sutjahja, J. Aarts, A. A. Nugroho, M. Diantoro, M. O. Tjia, A. A. Menovsky and J. J. M. Franse (2003) Doping and field effects on the lowest Kramers doublet splitting in La1.6-xNd0.4SrxCuO4-delta single crystal, Physics C, 392, 207.
Z.Q. Yang, R. Hendrikx, Y. Qin, H.W. Zandbergen and J. Aarts (2003) Strain release of (La,Ca)MnO3 thin films by YBa2Cu3Oδ, Phys. Rev. B , 67, 024408.

2002
C.K. Riener, G. Kada, C. Borken, F. Kienberger, P. Hinterdorfer, H. Schindler, T. Schmidt and H. Gruber. (2002) Bioconjugation for biospecific detection of single molecules in atomic force microscopy and single-dye tracing., Recent Research Developments in Bioconjugate Chemistry, 1, 133.
[pdf]
Ralf Schmauder, Thomas Schmidt, Jan Pieter Abrahams and Maxim E. Kuil (2002) Screening crystallisation conditions using fluorescence correlation spectroscopy, Acta Cryst.D, 58, 1536.
[DOI] [pdf]
Thomas Schmidt, et al. (2002) Datasheet: Photostability Data for Fluorescent Dyes - an update., Single Molecules, 3, 327.
[pdf]
Wendling, M, Przyjalgowski, MA, Gulen, D, Vulto, SIE, Aartsma, TJ, van Grondelle, R, van Amerongen, H (2002) The quantitative relationship between structure and polarized, PHOTOSYNTHESIS RESEARCH, 71, 99-123.
[DOI]
Hoff, AJ, Aartsma, TJ (2002) Obituary: Jan Amesz (11 March 1934 29 January 2001), PHOTOSYNTHESIS RESEARCH, 71, 1-4.
[DOI]
Miller, M, Aartsma, TJ, Blankenship, RE (2002) Special issue in honour of Jan Amesz: Green and heliobacteria -, PHOTOSYNTHESIS RESEARCH, 71, VII-VII.
Oellerich, S, Ketelaars, M, Segura, JM, de Ruijter, W, Kohler, J, Schmidt, J, Aartsma, TJ (2002) The electronic structure of individual B800-820 (LH3) light-harvesting, BIOPHYSICAL JOURNAL, 82, 436A-436A.
Stamouli, A, Kafi, ST, Hoff, AJ, Frenken, JWM, Oosterkamp, TH, Aartsma, TJ (2002) Visualization of the molecular and electronic structure of, BIOPHYSICAL JOURNAL, 82, 56A-56A.
Ketelaars, M, de Rujiter, WPF, Hofmann, C, Kohler, J, Howard, TD, Cogdell, RJ, Schmidt, J, Aartsma, TJ (2002) Single molecule spectroscopy of LH1 at low temperature, BIOPHYSICAL JOURNAL, 82, 47A-47A.
Ketelaars, M, Hofmann, C, Kohler, J, Howard, TD, Cogdell, RJ, Schmidt, J, Aartsma, TJ (2002) Spectroscopy on individual light-harvesting 1 complexes of, BIOPHYSICAL JOURNAL, 83, 1701-1715.
Prokhorenko, VI, Holzwarth, AR, Nowak, FR, Aartsma, TJ (2002) Growing-in of optical coherence in the FMO antenna complexes, JOURNAL OF PHYSICAL CHEMISTRY B, 106, 9923-9933.
[DOI]
A.M. Troyanovski, M. van Hecke, N. Saha, J. Aarts and P. H. Kes (2002) STM imaging of flux line arrangements in the peak effect regime, Phys. Rev. Lett., 89, 147006 .
[pdf]
J.M. van Ruitenbeek en A.I. Yanson (2002) Quantumeigenschappen in nanodraden van metaalatomen., Nederlands Tijdschrift voor Natuurkunde, december, 10-14.
R.H.M. Smit, Y. Noat, C. Untiedt, N. D. Lang, M.C. van Hemert and J.M. van Ruitenbeek (2002) Measurement of the conductance of a hydrogen molecule., Nature , 419.
[pdf]
S.K. Nielsen, M. Brandbyge, K. Hansen, K. Stokbro, J.M. van Ruitenbeek, and F. Besenbacher (2002) Current-voltage curves of atomic-sized transition metal contacts: An explanation of why Au is Ohmic and Pt is not., Phys. Rev. Lett. , 89.
[pdf]
C. Untiedt, A.I. Yanson, R. Grande, G. Rubio-Bollinger, N. Agraït, S. Vieira and J.M. van Ruitenbeek (2002) Calibration of the length of a chain of single gold atoms., Phys. Rev. B , 66.
[pdf]
D.J. Bakker, Y. Noat, A.I. Yanson and J.M. van Ruitenbeek (2002) Effect of disorder on the conductance of a Cu atomic point contact., Phys. Rev. B , 65.
[pdf]
A.S. van de Nes, J.J.H.B. Schleipen, G.W. t Hooft; M.P. van Exter (2002) Feedback effects at stable and unstable resonant external cavity lengths, IEEE J. of Quantum Electron., 38, 1097-1101.
[pdf]
Y. Lien, S.M. de Vries, M.P. van Exter, J.P. Woerdman. (2002) Lasers as Toda oscillators., J. Opt. Soc. Am. B, 19, 1461-1466.
[pdf]
A.M. van der Lee, M.P. van Exter, H.A. Assadian, N.J. van Druten, J.P. Woerdman. (2002) Threshold behavior of a laser with nonorthogonal polarization modes., J. Opt. Soc. Am. B, 19, 1454-1460.
[pdf]
G.W. t Hooft (2002) Comment on Negative refraction makes a perfect lens, Phys. Rev. Lett., 87, 249701.
[pdf]
S.Y. Krylov, L.J.F. Hermans (2002) Unsual desorption dynamics of long molecules., Phys. Rev. B, 65, 092205 (1-4).
[pdf]
S.M. Dutra, J.P. Woerdman, J. Visser, G. Nienhuis. (2002) Route towards the ideal thresholdless laser., Phys. Rev. A, 65, 033824.
[pdf]
J. Dingjan, E. Altewischer, M.P. van Exter, J.P. Woerdman. (2002) Experimental observation of wave chaos in a conventional optical resonator., Phys. Rev. Lett., 88, 064101.
[pdf]
S.A. van den Berg, V.A. Sautenkov, G.W. t Hooft, E.R. Eliel. (2002) Polarization cross-coupling in a polymer microlaser upon double-pulse excitation., Phys. Rev. A, 65, 053821.
[pdf]
E. Altewischer, M.P. van Exter, J.P. Woerdman. (2002) Plasmon-assisted transmission of entangled photons., Nature, 418, 304-306.
[pdf]
A. Aiello, J.P. Woerdman. (2002) Dynamical vacuum fluctuations?, Opt. Commun., 213, 89-95.
[pdf]
A. Aiello, M.P. van Exter, G. Nienhuis, J.P. Woerdman. (2002) Does excess quantum noise exist in spontaneous processes?, Opt. Commun., 213, 81-87.
[pdf]
S.S.R. Oemrawsingh, W.J. van Drunen, E.R. Eliel, J.P. Woerdman. (2002) Two-dimensional wave-vector correlations in spontaneous parametric downconversion explored with an intensified CCD camera., J. Opt. Soc. Am. B, 19, 2391-2395.
[pdf]
J. Visser, E.R. Eliel, G. Nienhuis. (2002) Polarization entanglement in a crystal with threefold symmetry., Phys. Rev. A, 66, 033814.
[pdf]
J. Visser, G. Nienhuis, S.M. Dutra, M.P. van Exter, J.P. Woerdman. (2002) Quantum-trajectory description of laser noise with pump depletion., Phys. Rev. A, 65, 063809.
[pdf]
A.M. Dokter, M.C. van Hemert, C.M. In `t Velt, K. van der Hoef, J. Lugtenburg, H.A. Frank, E.J.J. Groenen (2002) Resonance Raman spectrum of all-trans spheroidene. DFT analysis and isotope labeling., J. Phys. Chem. A, 106, 41, 9463-9469.
[pdf]
M. Ketelaars, C. Hofmann, J. K?hler, T.D. Howard, R.J. Cogdell, J. Schmidt, T.J. Aartsma (2002) Spectroscopy on individual light-harvesting 1 complexes of Rhodopseudomonas acidophila, Biophys. J., 83, 3, 1701-1715.
I.M. Kooter, R.A. Steiner, B.W. Dijkstra, P.I. van Noort, M.R. Egmond, M. Huber (2002) EPR characterisation of the mononuclear Cu-containing Aspergillus japonicus quercetin 2,3-dioxygenase reveals dramatic changes upon anaerobic binding of substrates, Eur. J. Biochem., 269, 2971-2979.
J. Visser, E.J.J. Groenen (2002) The fine-structure in the lowest triplet state of C60 and C70, Chem. Phys. Lett., 356, 43-48.
D.M. Hoffmann, A. Hofstaetter, F. Leiter, H. Zhou, F. Henecker, B.K. Meyer, S.B. Orlinskii, J. Schmidt, P.G. Baranov (2002) Hydrogen a relevant shallow donor in Zinc Oxide, Phys. Rev. Lett., 88, 4 45504.
M.T. Bennebroek, A. van Duijn-Arnold, J. Schmidt, O.G. Poluektov, P.G. Baranov (2002) Self-trapped hole in silver-chloride crystals: A pulsed EPR/ENDOR study at 95 GHz, Phys. Rev., B 66 (2002) 054305.
M. van Gastel, Y. Nagano, R. Zondervan, G.W. Canters, L.J.C. Jeuken, G.C.M. Warmerdam, E.C. de Waal, E.J.J. Groenen (2002) Hydrogen bonding in the blue copper site. Resonance Raman study, J. Phys. Chem. B, 106, 15, 4018-4021.
X.L.R. Dauw, J. Visser, E.J.J. Groenen (2002) Wave function of C70 in the triplet state, J. Phys. Chem. A, 106, 15, 3754-3758.
A. Bloe?, Y. Durand, M. Matsushita, H. van der Meer, G.J. Brakenhoff, J. Schmidt (2002) Optical far-field microscopy of single molecules with 3.4 nm lateral resolution, J. of Microsc., 205, 76-85.
M. van Gastel, J.W.A. Coremans, H. Sommerdijk, M.C. van Hemert, E.J.J. Groenen (2002) An ab initio quantum-chemical study of the blue-copper site of azurin, J. Am. Chem. Soc., 124, 9, 2035-2041.
M. Matsushita, A. Bloe?, Y. Durand, J.Y.P. Butter, J. Schmidt, E.J.J. Groenen (2002) Single molecules as nanoprobes. A study of the Shpol'skii effect, J. Chem. Phys., 117, 7, 3383-3390.
A. Bloeß, Y. Durand, M. Matsushita, H. van der Meer, G.J. Brakenhoff, J. Schmidt (2002) Optical far-field microscopy of single molecules with 3.4 nm lateral resolution, J. Microsc.-Oxf., 205, 76-85.
[pdf]
M. Ketelaars, C. Hofmann, J. Köhler, T.D. Howard, R.J. Cogdell, J. Schmidt, T.J. Aartsma (2002) Spectroscopy on individual light-harvesting 1 complexes of 'Rhodopseudomonas acidophila', Biophys. J., 83, 1701-1715.
[pdf]
M. Matsushita, A. Bloeß, Y. Durand, J. Butter, J. Schmidt, E.J.J. Groenen (2002) Single molecules as nanoprobes. A study of the Shpol’skii effect, J. Chem. Phys., 117, 3383-3390.
[pdf]
D. Boyer, Ph. Tamarat, A. Maali, B. Lounis, M. Orrit (2002) Photothermal imaging of nano-meter-sized metal particles among scatterers, Science, 297, 1160-1163.
[pdf]
J.-M. Caruge, M. Orrit (2002) Investigations of local currents in a semiconductor by single-molecule spectroscopy, J. Lumin., 98, 1-5.
[pdf]
M. Orrit (2002) Molecular entanglements, Science, 298, 369-370.
[pdf]
R. Verberk, A.M. van Oijen, M. Orrit (2002) Simple model for the power-law blinking of single semiconductor nanocrystals, Phys. Rev. B, 66, 233202.
[pdf]
M. Orrit (2002) Photon Statistics in Single Molecule Experiments, Single Molecules, 3, 255-265.
[pdf]
M. Orrit (2002) Single-molecule spectroscopy: The road ahead, J. Chem. Phys., 117, 10938-10946.
[pdf]
Z. Q. Yang, R. W. A. Hendrikx, P. J. M. v. Bentum and J. Aarts (2002) Disorder-induced melting of the charge order in thin films of Pr0.5Ca0.5MnO3, Europhys. Lett., 58, 864.
A. M. Troyanovski, M. van Hecke, N. Saha, J. Aarts, and P. H. Kes (2002) STM Imaging of Flux Line Arrangements in the Peak Effect Regime, Phys. Rev. Lett., 89, 147006 .
A. Rusanov, R. Boogaard, M. Hesselberth, H. Sellier, J. Aarts (2002) Inhomogeneous superconductivity induced in a weak ferromagnet, Physica C 369, 300 , 369, 300.

2001
M. de Jager and J. van Noort and D. C. van Gent and C. Dekker and R. Kanaar and C. Wyman (2001) Human Rad50/Mre11 is a flexible complex that can tether DNA ends., Mol Cell, Nov, 8, 1129--1135.
[Abstract] [DOI] [pdf]
The human Rad50 protein, classified as a structural maintenance of chromosomes (SMC) family member, is complexed with Mre11 (R/M) and has important functions in at least two distinct double-strand break repair pathways. To find out what the common function of R/M in these pathways might be, we investigated its architecture. Scanning force microscopy showed that the complex architecture is distinct from the described SMC family members. R/M consisted of two highly flexible intramolecular coiled coils emanating from a central globular DNA binding domain. DNA end-bound R/M oligomers could tether linear DNA molecules. These observations suggest that a unified role for R/M in multiple aspects of DNA repair and chromosome metabolism is to provide a flexible, possibly dynamic, link between DNA ends.
Storm, AJ and Van Noort, J. and De Vries, S. and Dekker, C. (2001) Insulating behavior for DNA molecules between nanoelectrodes at the 100 nm lengt, Applied Physics Letters, 79, 3881.
[Abstract] [DOI] [pdf]
Electrical transport measurements are reported for double-stranded DNA molecules located between nanofabricated electrodes. We observe the absence of any electrical conduction through these DNA-based devices, both at the single-molecule level as well as for small bundles of DNA. We obtain a lower bound of 10 TV for the resistance of a DNA molecule at length scales larger than 40 nm. It is concluded that DNA is insulating. This conclusion is based on an extensive set of experiments in which we varied key parameters such as the base-pair sequence, mixed sequence and homogeneous poly dG poly dC, length between contacts ~40–500 nm!, substrate ~SiO2 or mica!, electrode material ~gold or platinum!, and electrostatic doping fields. Discrepancies with other reports in the literature are discussed.
Gerhard A. Blab, Piet H.M. Lommerse, Laurent Cognet, Gregory S. Harms, and Thomas Schmidt. (2001) Two-Photon Excitation Action Cross-Sections of the Autofluorescent Proteins., Chem.Phys.Lett, 350, 71.
[Abstract] [DOI] [pdf]
We report on the values of the two-photon excitation action cross-sections of commercially available enhanced cyan, green, yellow, and red fluorescent proteins. The two-photon absorption spectra are very similar in shape to those measured for one-photon absorption. However, they exhibit a significant blueshift, which is attributed to the participation of a vibrational mode in the two-photon absorption process. The two-photon spectra are compared to that of flavine mononucleotide, which constitutes the main source of autofluorescence in mammalian cells. The definition of a relative detection yield between the autofluorescent proteins and flavine allows us to quantify the applicability of autofluorescent proteins in two-photon single-molecule studies in living cells.
Werner Trabesinger, Bert Hecht, Urs P. Wild, Gerhard J. Schütz, Hansgeorg Schindler and Thomas Schmidt. (2001) Statistical Analysis of Single Molecule Assays., Anal.Chem, 73, 1100.
[Abstract] [DOI] [pdf]
In chemical assays, specific molecular recognition events result in close physical proximity of two molecular species, e.g., ligands and receptors. Microscopy techniques that are able to image individual molecules allow for achieving a positional accuracy far beyond the resolution limit. Therefore, independent position determination, e.g., by dual-color microscopy, becomes possible, permitting determination of intermolecular distances beyond the resolution limit. Nonzero measured distances occur due to experimental inaccuracies in case of a recognition event or due to accidental close proximity between ligand−receptor pairs. Using general statistical considerations, finite measured distances between single ligand−receptor pairs are directly translated into probabilities for true molecular recognition or mere accidental proximity. This enables a quantitative statistical analysis of single recognition events. It is demonstrated that in a general assay, even in the presence of strong unspecific background, the probability for a certain diagnosis and a measure for its reliability can be extracted from the observation of a few binding events. The power of the method is demonstrated at the example of a single-molecule DNA hybridization assay. Our findings are of major importance for future assay miniaturization and assaying with minute amounts of analyte.
G.S. Harms, L. Cognet, G.A. Blab, P.H.M. Lommerse, H.P. Spaink and Th.Schmidt (2001) Autofluorescent Proteins in Single-Molecule Research, Biophys.J, 80, 2396.
[DOI] [pdf]
G.S. Harms, L. Cognet, G.A. Blab, P.H.M. Lommerse, H. Kahr, R. Gamsjäger, Herman P. Spaink, Nikolai M. Soldatov, Christoph Romanin and Thomas Schmidt. (2001) Single-Molecule Imaging of L-type Ca2+, Channels in Live Cells., Biophys.J, 81, 2639.
[Abstract] [DOI] [pdf]
L-type Ca2+ channels are an important means by which a cell regulates the Ca2+ influx into the cytosol on electrical stimulation. Their structure and dynamics in the plasma membrane, including their molecular mobility and aggregation, is of key interest for the in-depth understanding of their function. Construction of a fluorescent variant by fusion of the yellow-fluorescent protein to the ion channel and expression in a human cell line allowed us to address its dynamic embedding in the membrane at the level of individual channels in vivo. We report on the observation of individual fluorescence-labeled human cardiac L-type Ca2+ channels using wide-field fluorescence microscopy in living cells. Our fluorescence and electrophysiological data indicate that L-type Ca2+ channels tend to form larger aggregates which are mobile in the plasma membrane.
Thomas Schmidt (2001) Datasheet: Photostability Data for Fluorescent Dyes, Single Molecules, 2, 217.
[DOI] [pdf]
Aartsma, TJ, Matsushita, M, Ketelaars, M, Matushita, M, van Oijen, AM, Koehler, J, Schmidt, J (2001) Exciton states of an elliptically deformed LH2 ring., BIOPHYSICAL JOURNAL, 80, 152A-152A.
van Oijen, AM, Ketelaars, M, Matsushita, M, Kohler, J, Aartsma, TJ, Schmidt, J (2001) Unraveling the electronic structure of individual photosynthetic, BIOPHYSICAL JOURNAL, 80, 151A-151A.
Matsushita, M, Ketelaars, M, van Oijen, AM, Kohler, J, Aartsma, TJ, Schmidt, J (2001) Spectroscopy on the B850 band of individual light-harvesting 2 complexes, BIOPHYSICAL JOURNAL, 80, 1604-1614.
Ketelaars, M, van Oijen, AM, Matsushita, M, Kohler, J, Schmidt, J, Aartsma, TJ (2001) Spectroscopy on the B850 band of individual light-harvesting 2 complexes, BIOPHYSICAL JOURNAL, 80, 1591-1603.
Hoff, AJ, Aartsma, TJ (2001) Jan Amesz - 11.03.1934-29.01.2001, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1507, 3-4.
[DOI]
Kohler, J, van Oijen, AM, Ketelaars, M, Hofmann, C, Matsushita, M, Aartsma, TJ, Schmidt, J (2001) Optical spectroscopy of individual photosynthetic pigment protein, INTERNATIONAL JOURNAL OF MODERN PHYSICS B, 15, 3633-3636.
[DOI]
J. L. Hansen, M. van Hecke, A. Haaning, C. Ellegaard, K. H. Andersen, T. Bohr and T. Sams (2001) Instabilities in sand ripples, Nature, 410, 324 .
[pdf]
M. van Hecke and M. Howard (2001) Ordered and self-disordered dynamics of holes and defects in the one-dimensional complex Ginzburg-Landau equation, Phys. Rev. Lett. , 86, 2018 .
[pdf]
T. Bohr, M. van Hecke, R. Mikkelsen and M. Ipsen (2001) Breakdown of universality in transitions to spatiotemporal chaos, Phys. Rev. Lett., 86, 5482 .
[pdf]
K. H. Andersen, M. L. Chabanol and M. van Hecke (2001) Dynamical models for sand ripples beneath surface waves, Phys. Rev. E., 63, 066308 .
[pdf]
J. L. Hansen, M. van Hecke, C. Ellegaard, K. H. Andersen, T. Bohr T, A. Haaning and T. Sams (2001) Stability balloon for two-dimensional vortex ripple patterns, Phys. Rev. Lett , 87, 204301 .
[pdf]
M. Ipsen and M. van Hecke (2001) Composite zigzag structures in the 1D complex Ginzburg-Landau equation, Physica D, 160, 103 .
[pdf]
L. Brusch, A. Torcini, M. van Hecke, M. G. Zimmermann and M. Bär (2001) Modulated amplitude waves and defect formation in the one-dimensional complex Ginzburg-Landau equation, Physica D, 160, 127 .
[pdf]
A.I.Yanson, I.K. Yanson and J.M. van Ruitenbeek (2001) Shell structure in nanowires of simple metals., in: Electronic Correlations: from Meso- to Nano-Physics, T. Martin, G. Montambaux and J. Trân Thanh Vân, eds. EDP Sciences, , 3-9.
H.E. van de Brom (2001) Hagelruis in atomaire puntcontacten., Nederlands Tijdschrift voor Natuurkunde , 67, 59-66.
A.I. Yanson, I.K. Yanson and J.M. van Ruitenbeek (2001) Shell effects in alkali metal nanowires., Fiz. Nizk. Temp. Low Temperature Physics, Ukraine, , 27, 1092-1109.
H.E. van den Brom, Y. Noat and J.M. van Ruitenbeek (2001) Two-level systems in atomic-size point contacts., in:"Kondo Effect and Dephasing in Low-Dimensional Metallic Systems", V. Chandrasekhar, C. van Haesendonck and A. Zawadowski editors, NATO Science Series II: Math., Phys. and Chem., Kluwer Academic Publishers, Dordrecht, 50.
I.K. Yanson, V.V. Fisun, J.A. Mydosh and J.M. van Ruitenbeek (2001) Enhancement of Kondo temperature in nanometer-size point contacts., in:"Kondo Effect and Dephasing in Low-Dimensional Metallic Systems", V. Chandrasekhar, C. van Haesendonck and A. Zawadowski editors, NATO Science Series II: Math., Phys. and Chem.,Kluwer Academic Publishers, Dordrecht , 50.
A.I. Yanson, I.K. Yanson and J.M. van Ruitenbeek (2001) Crossover from electronic to atomic shell structure in alkali metal nanowires., Phys. Rev. Lett. , 87.
[pdf]
R.H.M. Smit, C. Untiedt, A.I. Yanson and J.M. van Ruitenbeek (2001) Common origin for surface reconstruction and the formation of chains of metal atoms, Phys. Rev. Lett. , 87.
[pdf]
J.M. van Ruitenbeek (2001) Noisy times ahead., Nature , 410, 424-425.
[pdf]
J.M. van Ruitenbeek (2001) Atomic-size metallic conductors., Naturwissenschaften , 88, 59-66.
[pdf]
E.C. Mos; G.W. t Hooft; J.J.H.B. Schleipen, H. de Waardt (2001) Chaotic self-pulsation and cross-modulation in a wavelength-selective external-cavity laser diode., IEEE J. of Quantum Electron., 37, 911-918.
[pdf]
S.A. van den Berg, G.W. t Hooft, E.R. Eliel. (2001) Orientational relaxation in polymer and dye solutions and its consequence for the laser threshold., Chem. Phys. Lett., 347, 167-172.
[pdf]
S.A. van den Berg, G.W. t Hooft, E.R. Eliel. (2001) Pulse-train formation in a gain-switched polymer laser resulting from spatial gain inhomogeneity., Phys. Rev., A63, 063809-1-7.
[pdf]
J. Dingjan, M.P. van Exter, J.P. Woerdman. (2001) Geometric modes in a single-frequency Nd:YVO4 laser., Opt. Commun., 188, 345-351.
[pdf]
N.J. van Druten, M.P. van Exter, J.P. Woerdman. (2001) Resonant excess quantum noise in focused-gain lasers., Opt. Lett., 26, 1176-1178.
[pdf]
N.J. van Druten, M.P. van Exter, and J.P. Woerdman. (2001) Equivalence of transverse modes in Raman amplifiers and microchip lasers., Opt. Commun., 200, 217-221.
[pdf]
N.J. van Druten, S.S.R. Oemrawsingh, Y. Lien, C. Serrat, M.P. van Exter, and J.P. Woerdman. (2001) Observation of transverse modes in a microchip laser with combined gain- and index-guiding., J. Opt. Soc. Am., B18 , 1793-1804.
[pdf]
S.M. Dutra and G. Nienhuis. (2001) What is a quantized mode in a leaky cavity?,, in Modern challenges in quantum optics eds. M. Orszag and J.C. Retamal (Springer, Berlin, 338-354.
[pdf]
E.R. Eliel, S.M. Dutra, S. Nienhuis, J.P. Woerdman. (2001) Comment on Orbital and intrinsic angular momentum of single photons and entangled pairs of photons generated by parametric down-conversion., Phys. Rev. Lett., 86, 5208-5208.
[pdf]
M.P. van Exter, N.J. van Druten, A.M. van der Lee, S.M. Dutra, G. Nienhuis, J.P. Woerdman. (2001) Semiclassical dynamics of excess quantum noise., Phys. Rev., A63, 043801-1-13.
[pdf]
H. Haroutyunyan, G. Nienhuis. (2001) Coherent control of atom dynamics in an optical lattice., Phys. Rev. A, 64, 3424-+.
[pdf]
A.M. van der Lee, M.P. van Exter, N.J. van Druten, J.P. Woerdman. (2001) A physical explanation of excess quantum noise due to non-orthogonal modes., New Journal of Physics, 3, 2.1-2.15.
[pdf]
Y. Lien, S.M. de Vries, N.J. van Druten, M.P. van Exter, J.P. Woerdman. (2001) Photon statistics of a laser with slow inversion., Phys. Rev. Lett., 86, 2786-2789.
[pdf]
F. Monti di Sopra, M. Moser, M. Brunner, M.B. Willemsen, M.P. van Exter, and E. Kapon. (2001) Polarization stability of phase-locked arrays of vertical-cavity surface-emitting lasers., IEEE Photon Technol. Lett., 13 , 1149-1151.
[pdf]
G.H.C. New, M.A. Yates, J.P. Woerdman. (2001) Diffractive origin of fractal resonator modes., Opt. Commun., 193, 261-266.
[pdf]
G. Nienhuis. (2001) Dynamics of atoms in optical lattices., Phys. Scripta., T95, 43-49.
[pdf]
G. Nienhuis. (2001) Entanglement and relative phase created by decay., J. Phys. A - Math. Gen., 34, 7867-7879.
[pdf]
G. Nienhuis. (2001) Macroscopic entanglement and relative phase. in Modern challenges in quantum optics, eds. M. Orszag and J.C. Retamal, (Springer, Berlin, 338-354.
[pdf]
M.B. Willemsen, M.P. van Exter, J.P. Woerdman. (2001) Polarization loxodrome of a vertical-cavity semiconductor laser., Opt. Commun., 199, 167-173.
[pdf]
M.B. Willemsen, A.S. van de Nes, M.P. van Exter, J.P. Woerdman, M. Kicherer, R. King, R. Jager, K.J. Ebeling. (2001) Polarization-resolved linewidth-power product of a vertical-cavity semiconductor laser., J. Appl. Phys., 89, 4183-4185.
[pdf]
J.P. Woerdman, M.P. van Exter, and N.J. van Druten. (2001) Quantum noise in small lasers, in Advances in Atomic, Molecular and Optical Physics. eds. B. Bederson and H. Walther, Vol. 47, Chapt. 5 (Academic Press, NY, 205-248 .
[pdf]
J.P. Woerdman, J. Dingjan, and M.P. van Exter. (2001) Cavity approach towards a coherent random laser., in Crystals and Light localization in the 21th century. Eds. C.M. Soukoulis Kluwer, 435-446 .
[pdf]
A. Labahn, M. Huber (2001) The G-tensor anisotropy of the triplet state of the primary electron donor in the photosynthetic bacterium Rhodobacter sphaeroides by high-field (95 GHz) EPR, Appl. Magn. Reson., 21, 383-389.
M. Huber, M. Lindgren, P. Hammarstr?m, L G. M?rtensson, U. Carlsson, G.R. Eaton, S.S. Eaton (2001) Phase memory relaxation times of spin labels in human carbonic anhydrase II: pulsed EPR to determine spin label location, Biophys. Chem., 94, 245-256.
R. Owenius, M. Engstr?m, M. Lindgren, M. Huber (2001) Influence of solvent polarity and hydrogen bonding on the EPR parameters of a nitroxide spin label studied by 9 GHz and 95 GHz EPR spectroscopy, and DFT calculations, J. Phys. Chem. A, 105, 10967-10977.
M. Huber (2001) The role of the electronic structure of the porphyrin in the efficiency of biomimetic model compounds for photosynthesis, Eur. J. Org. Chem., 4379-4389.
P.G. Baranov, E.N. Mokhov, S.B. Orlinskii, J. Schmidt (2001) Neutral and negatively charged silicon vacancies in neutron irradiated SiC: a high-field electron paramagnetic resonance study, Physica B, 308-310, 680-683.
J.H. van der Waals (2001) EPR of photo-excited triplet states: a personal account, Appl. Magn. Reson., 20, 545-561.
J. K?hler, A.M. van Oijen, M. Ketelaars, C. Hofmann, M. Matsushita, T.J. Aartsma, J. Schmidt (2001) Optical spectroscopy of individual photosynthetic pigment protein complexes, Int. J. of Mod. Phys. B, 15, 28, 29 & 30, 3633-3636.
A. Bloe?, Y. Durand, M. Matsushita, J. Schmidt, E.J.J. Groenen (2001) A single-molecule study of the relation between the resonance frequency and the orientation of a guest molecule in a Shpol'skii system, Chem. Phys. Lett., 344, 55-60.
A.M. van Oijen, M. Ketelaars, J. K?hler, T.J. Aartsma, J. Schmidt (2001) The electronic structure of single photosynthetic pigment-protein complexes, In: "Single molecule spectroscopy, Nobel Conference lectures", R. Rigler, M. Orrit, T. Basch? (eds.) Springer, 62-81.
A. v. Duijn-Arnold, R. Zondervan, P.G. Baranov, E.N. Mokhov, J. Schmidt (2001) The electronic structure of the N donor center in 4H-SiC and 6H-SiC, Mat. Sci. Forum, Trans Tech Publications Inc. ed. G. Pensl, D. Stephani, M. Hundhausen, vol's. 353-356, 525.
A.M. van Oijen, R. Verberk , Y. Durand, J. Schmidt, J.N.J. van Lingen, A.A. Bol, A. Meijerink (2001) Continuous-wave two-photon excitation of individual CdS nanocrystallites, Appl. Phys. Lett., 79, 6, 830-832.
Y. Durand, A. Bloe?, J. K?hler, E.J.J. Groenen, J. Schmidt (2001) Spectral diffusion of individual pentacene, terrylene and dibenzanthanthrene molecules in n-tetradecane, J. Chem. Phys., 114, 15, 6843-6850.
A. Bloe?, Y. Durand, M. Matsushita, R. Verberk, E.J.J. Groenen, J. Schmidt (2001) Microscopic structure in a Shpol'skii system. A single-molecule study of dibenzanthanthrene in n-tetradecane, J. Phys. Chem., 105, 13, 3016-3021.
M. Ketelaars, A.M. van Oijen, M. Matsushita, J. Köhler, J. Schmidt, T.J. Aartsma (2001) Spectroscopy on the B850 band of individual light-harvesting 2 complexes of 'Rhodopseudomonas acidophila': I. Experiments and Monte-Carlo simulations, Biophys. J., 80, 1591-1603.
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M. Matsushita, M. Ketelaars, A.M. van Oijen, J. Köhler, T.J. Aartsma, J. Schmidt (2001) Spectroscopy on the B850 band of individual light-harvesting 2 complexes of 'Rhodopseudomonas acidophila': II. Exciton states of an elliptically deformed ring aggregate, Biophys. J., 80, 1604-1614.
[pdf]
A. Bloeß, Y. Durand, M. Matsushita, R. Verberk, E.J.J. Groenen, J. Schmidt (2001) Microscopic structure in a Shpol’skii system. A single-molecule study of dibenzanthanthrene in 'n'-tetradecane, J. Phys. Chem. A, 105, 3016-3021.
[pdf]
Y. Durand, A. Bloeß, J. Köhler, E.J.J. Groenen, J. Schmidt (2001) Spectral diffusion of individual pentacene, terrylene and dibenzanthanthrene molecules in 'n'-tetradecane, J. Chem. Phys., 114, 6843-6850.
[pdf]
A.M. van Oijen, Y. Durand, R. Verberk, J. Schmidt, A. Meijerink (2001) Continuous-wave two-photon excitation of individual CdS nanocrystallites, Appl. Phys. Lett., 79, 830-832.
[pdf]
A. Bloe? Y. Durand, M. Matsushita, J. Schmidt, E.J.J. Groenen (2001) A single-molecule study of the relation between the resonance frequency and the orientation of a guest molecule in a Shpol’skii system, Chem. Phys. Lett., 344, 55-60.
[pdf]
A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt (2001) The electronic structure of single photosynthetic pigment-protein complexes, Single Molecule Spectroscopy - Nobel Conference Lectures, 62-81.
[pdf]
J. Köhler, A.M. van Oijen, M. Ketelaars, C. Hofmann, M. Matsushita, T.J. Aartsma, J. Schmidt (2001) Optical spectroscopy of individual photosynthetic pigment protein complexes, Int. J. Mod. Phys. B, 15, 3633-3636.
[pdf]
V. V. Ryazanov, V. A. Oboznov, A. Yu. Rusanov, A. V. Veretenikov, A. A. Golubov and J. Aarts (2001) Coupling of two superconductors through a ferromagnet : evidence for a -junction, Phys. Rev. Lett., 86, 2427 .
J. M. E. Geers, C. Attanasio, M. B. S. Hesselberth, J. Aarts and P.H. Kes (2001) Dynamic vortex ordering in thin a-NbGe films, Phys. Rev. B 63, 094511, 63, 094511.

2000
Klaus J. F. Kepplinger, Heike Kahr, Günter Förstner, Max Sonnleitner, Hansgeorg Schindler, Thomas Schmidt, Klaus Groschner, Nikolai M Soldatov, Christoph Romanin. (2000) A sequence in the carboxy-terminus of the α1C subunit important for targeting, conductance and open probability of L-type Ca2+ channels, FEBS Lett, 477, 161.
[Abstract] [DOI] [pdf]
The role of the 80-amino acid motif 1572–1651 in the C-terminal tail of α1C Ca2+ channel subunits was studied by comparing properties of the conventional α1C,77 channel expressed in HEK-tsA201 cells to three isoforms carrying alterations in this motif. Replacement of amino acids 1572–1651 in α1C,77 with 81 non-identical residues leading to α1C,86 impaired membrane targeting and cluster formation of the channel. Similar to α1C,86, substitution of its 1572–1598 (α1C,77L) or 1595–1652 (α1C,77K) segments into the α1C,77 channel yielded single-channel Ba2+ currents with increased inactivation, reduced open probability and unitary conductance, when compared to the α1C,77 channel. Thus, the C-terminal sequence 1572–1651 of the α1C subunit is important for membrane targeting, permeation and open probability of L-type Ca2+ channels.
L. Cognet, G.S. Harms, G.A. Blab, P.H.M. Lommerse and Th.Schmidt (2000) Simultaneous 'dual-color and dual- polarization' imaging of single molecules, Appl.Phys.Lett, 77, 4052.
[Abstract] [DOI] [pdf]
We report the observation of single-molecule colocalization and quantitative fluorescence resonant energy transfer by simultaneously imaging the emission and polarization characteristics of two colocalized fluorophores using a simple optical design. The methodology was tested using the ligand-receptor system streptavidin, fluorescence labeled with the dye Cy5, and biotin labeled with tetramethylrhodamine. Discrimination of the two dyes permitted the observation of single-pair fluorescence resonant energy transfer with an efficiency of 89%. The multidimensional character of our fluorescence microscopy combined with the robustness of our design provides a simple method suitable to study biomolecular interactions on the single molecule level.
Th. Schmidt and H. Schindler (2000) Analytical Chemistry and Biophysics at the Single-Molecule Level, in Organic Mesoscopic Chemistry, H. Masuhara & F.C. DeSchrijver eds., Blackwell.
[pdf]
Neerken, S, Ma, YZ, Aschenbrucker, J, Schmidt, KA, Nowak, FR, Permentier, HP, Aartsma, TJ, Gillbro, T, Amesz, J (2000) Kinetics of absorbance and anisotropy upon excited state relaxation in, PHOTOSYNTHESIS RESEARCH, 65, 261-268.
[DOI]
Steensgaard, DB, van Walree, CA, Permentier, H, Baneras, L, Borrego, CM, Garcia-Gil, J, Aartsma, TJ, Amesz, J, Holzwarth, AR (2000) Fast energy transfer between BChl d and BChl c in chlorosomes of the, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1457, 71-80.
[DOI]
van Oijen, AM, Ketelaars, M, Kohler, J, Aartsma, TJ, Schmidt, J (2000) Spectroscopy of individual light-harvesting 2 complexes of, BIOPHYSICAL JOURNAL, 78, 1570-1577.
Neerken, S, Aartsma, TJ, Amesz, J (2000) Pathways of energy transformation in antenna reaction center complexes, BIOCHEMISTRY, 39, 3297-3303.
[DOI]
Wendling, M, Pullerits, T, Przyjalgowski, MA, Vulto, SIE, Aartsma, TJ, van Grondelle, R, van Amerongen, H (2000) Electron-vibrational coupling in the Fenna-Matthews-Olson complex of, JOURNAL OF PHYSICAL CHEMISTRY B, 104, 5825-5831.
[DOI]
L. Brusch L, M. G. Zimmermann, M. van Hecke, M. Bär and A. Torcini (2000) Modulated amplitude waves and the transition from phase to defect chaos, Phys. Rev. Lett., 85, 86 .
[pdf]
J.M. van Ruitenbeek (2000) Oratie:"Bouwen in Schrödingers wereld", Leiden.
[pdf]
V.V. Fisun, I.K. Yanson, J.A. Mydosh and J.M. van Ruitenbeek (2000) Point-contact spectroscopy investigation of the Kondo size effect in CuCr and AuFe alloys., Low Temp. Phys. (Ukraine) , 26, 681-686.
A.I. Yanson, I.K. Yanson and J.M. van Ruitenbeek (2000) Supershell structure in alkali metal nanowires., Phys. Rev Lett. , 84.
[pdf]
J.M. van Ruitenbeek (2000) Experiments on conductance at the atomic scale., in: "Quantum Mesoscopic Phenomena and Mesoscopic Devices in Microelectronics", I.O. Kulik and R. Ellialtioglu, eds., NATO-ASI Series C: Math. Phys. Sci., Kluwer Academic Publishers, 599, 35-50.
J.M. van Ruitenbeek (2000) Conductance quantisation in metallic point contacts., in: "Metal Clusters on Surfaces: Structure, QuantumProperties, Physical Chemistry", K.H. Meiwes-Broer, ed. Springer-Verlag,Heidelberg, 175-210.
H.E. van den Brom and J.M. van Ruitenbeek (2000) Shot noise in metallic quantum point contacts., in: "Quantum physics at mesoscopic scale", C. Glattli, M. Sanquer and J. Trân Thanh Vân, eds. EDP Sciences, 145-150.
B. Ludoph and J.M. van Ruitenbeek (2000) Conductance fluctuations as a tool for investigating the quantum modes in atomic size metallic contacts., Phys. Rev. B. , 61.
[pdf]
H.E. van den Brom and J.M. van Ruitenbeek (2000) Shot noise suppression in metallic quantum point contacts., in: "Statistical and Dynamical Aspects of Mesoscopic Systems" , D. Reguera, G. Platero, L.L. Bonilla and J.M. Rubí, eds. Springer-Verlag Berlin Heidelberg, 114-122.
B. Ludoph, N. van der Post, E.N. Bratus, E.V. Bezuglyi, V.S. Shumeiko, G. Wendin and J.M. van Ruitenbeek (2000) Multiple Andreev reflection in single atom niobium junctions., Phys. Rev. B. , 61.
[pdf]
H. M??ler, M. Wittenberg, D. Niethammer, R.K. Mudrassagam, H. Kurreck, M. Huber (2000) EPR and ENDOR on radicals of chlorin- and bacteriochlorin-quinone model compounds for electron transfer in photosynthesis, Magn. Reson. in Chem., 38, 67-84.
X.L.R. Dauw, G.J.B. van den Berg, D.J. van den Heuvel, O.G. Poluektov, E.J.J. Groenen (2000) The triplet wavefunction of C60 from W-band ENDOR spectroscopy, J. Chem. Phys., 112, 16, 7102-7110.
M. van Gastel, L. Bubacco, E.J.J. Groenen, E. Vijgenboom, G.W. Canters (2000) EPR study of the dinuclear active copper site of tyrosinase from Streptomyces antibioticus, FEBS Lett., 474, 228-232.
Y. Durand, A. Bloess, A.M. van Oijen, J. K?hler, E.J.J. Groenen, J. Schmidt (2000) An optical study of single pentacene molecules in n-tetradecane, Chem. Phys. Lett., 317, 232-237.
M. van Gastel, G.W. Canters, H. Krupka, A. Messerschmidt, E.C. de Waal, G.C.M. Warmerdam, E.J.J. Groenen (2000) Axial ligation in blue-copper proteins. A W-band ESE detected EPR study of the azurin mutant M121H, J. Am. Chem. Soc., 122, 10, 2322-2328.
A.M. van Oijen, M. Ketelaars, J. K?hler, T.J. Aartsma, J. Schmidt (2000) Spectroscopy of individual light-harvesting 2 complexes of Rhodopseudomonas acidophila: diagonal disorder, intercomplex heterogeneity, spectral diffusion and energy transfer in the B800 band, Biophys. J., 78, 1570-1577.
Y. Durand, A. Bloeß, A.M. van Oijen, J. Köhler, E.J.J. Groenen, J. Schmidt (2000) An optical study of single pentacene molecules in 'n'-tetradecane, Chem. Phys. Letters, 317, 232-237.
[pdf]
A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt (2000) Spectroscopy of individual LH2 complexes of 'Rhodopseudomonas acidophila': Diagonal disorder, intercomplex heterogeneity, spectral diffusion and energy transfer in the B800 band, Biophys. J., 78, 1570-1577.
[pdf]
H.W. Zandbergen, J. Jansen, S. Freisem, T. Nojima and J. Aarts (2000) Atomic Structure and microstructure of very thin films of La0.73Ca0.27MnO3 on SrTiO3, Phil. Mag. A , 80, 337 – 350 .
A. M. Troianovsky, J. Aarts, P. H. Kes (2000) Collective and plastic vortex motion probed by STM, Physica B, 280, 225-226 .
V. V. Ryazanov, A. V. Veretennikov, V. A. Oboznov, A. Yu. Rusanov, V. A. Larkin, A. Golubov, J. Aarts (2000) Reentrant superconducting behavior of the Josephson SFS junction. Evidence for the pi-phase state, Physica C, 341, 1613.
A. V. Veretennikov, V. V. Ryazanov, V. A. Oboznov, A. Yu. Rusanov, V. A. Larkin, J. Aarts (2000) Supercurrents through the superconductor-ferromagnet-superconductor (SFS) junctions, Physica B 284, 495, 284, 495.
D. Groten, J. Aarts, G. J. C. van-Baarle, R. W. A. Hendrikx, G. J. Nieuwenhuys, J. A. Mydosh (2000) Ground-state properties of thin films of the heavy-fermion system CeCu6 with varying thickness, Physica B, 281, 53.
A. Schenck, F. N. Gygax, D. Andreica, M. Pinkpank, G. J. Nieuwenhuys, J. Aarts, S. Freisem; M. Hesselberth, J. A. Mydosh, E. Morenzoni, H. Gluckler, T. Prokscha, A. Amato (2000) Low-energy muon study of CMR and spin-glass films, Physica B 289, 331 , 289, 331.

1999
J. van Noort and F. Orsini and A. Eker and C. Wyman and B. de Grooth and J. Greve (1999) DNA bending by photolyase in specific and non-specific complexes studied by atom, Nucleic Acids Res, 27, 3875--3880.
[Abstract] [pdf]
Specific and non-specific complexes of DNA and photolyase are visualised by atomic force microscopy. As a substrate for photolyase a 1150 bp DNA restriction fragment was UV-irradiated to produce damaged sites at random positions. Comparison with a 735 bp undamaged DNA fragment made it possible to separate populations of specific and non-specific photolyase complexes on the 1150 bp fragment, relieving the need for highly defined substrates. Thus it was possible to compare DNA bending for specific and non-specific interactions. Non-specific complexes show no significant bending but increased rigidity compared to naked DNA, whereas specific complexes show DNA bending of on average 36 degrees and higher flexibility. A model obtained by docking shows that photolyase can accommodate a 36 degrees bent DNA in the vicinity of the active site.
van Noort, S.J.T. and Willemsen, O.H. and van der Werf, K.O. and de Grooth, B.G. and Greve, J. (1999) Mapping electrostatic forces using higher harmonics tapping mode atomic force mi, Langmuir, 27, 354.
[Abstract] [DOI] [pdf]
A simple model of a damped, harmonic oscillator is used to describe the motion of an atomic force microscope cantilever tapping in fluid. By use of experimentally obtained parameters, excellent agreement is found between theory and experimental results. From the model we estimate that the force applied on the sample can range up to 100 nN, depending on the surface charge density. Detailed analysis of the cantilever deflection reveals subtle differences in the oscillatory motion, as a result of differences in the tip?sample interaction, which can conveniently be visualized by spectral analysis. The amplitudes of the higher harmonic frequencies are shown to be sensitive for electrostatic interactions. Mapping of higher harmonic amplitudes is applied to qualitatively map the surface charge density of DNA molecules on poly-l-lysine coated mica.
S. J. van Noort and K. O. van Der Werf and B. G. de Grooth and J. Greve (1999) High speed atomic force microscopy of biomolecules by image tracking., Biophys J, Oct, 77, 2295--2303.
[Abstract] [DOI] [pdf]
An image-tracking procedure for atomic force microscopy is proposed and tested, which allows repeated imaging of the same area without suffering from lateral drift. The drift correction procedure is based on on-line cross-correlation of succeeding images. Using the image-tracking procedure allows zooming in on a small scan area over a long period and thus increases the frame rate inversely proportional to the scan area. Application of the procedure is demonstrated for diffusion of 5.4-kb DNA plasmids. With a scan area of 500 * 500 nm(2), a single plasmid can be imaged for more than 30 min at 4 s per frame, with a drift less than 10 nm. The high temporal resolution allows detailed analysis of the diffusion of DNA molecules. A diffusion coefficient of 30 nm(2)/s is found for most DNA molecules, though many molecules are temporally pinned to the mica surface, restricting diffusion.
O. H. Willemsen and M. M. Snel and S. J. van Noort and K. O. van der Werf and B. G. de Grooth and C. G. Figdor and J. Greve (1999) Optimization of adhesion mode atomic force microscopy resolves individual molecu, Ultramicroscopy, Oct, 80, 133--144.
[Abstract] [DOI] [pdf]
The force sensor of an atomic force microscope (AFM) is sensitive enough to measure single molecular binding strengths by means of a force-distance curve. In order to combine high-force sensitivity with the spatial resolution of an AFM in topography mode, adhesion mode has been developed. Since this mode generates a force-distance curve for every pixel of an image, the measurement speed in liquid is limited by the viscous drag of the cantilever. We have equipped our adhesion mode AFM with a cantilever that has a low viscous drag in order to reach pixel frequencies of 65 Hz. Optimized filtering techniques combined with an auto-zero circuitry that reduces the drift in the deflection signal, limited high- and low-frequency fluctuations in the height signal to 0.3 nm. This reduction of the height noise, in combination with a thermally stabilized AFM, allowed the visualization of individual molecules on mica with an image quality comparable to tapping mode. The lateral resolution in both the topography and the simultaneously recorded adhesion image are only limited by the size of the tip. Hardware and software position feedback systems allows individual molecules to be followed in time during more than 30 min with scan sizes down to 60 x 60 nm2.
Th. Schmidt, P. Hinterdorfer and H. Schindler (1999) Microscopy for Recognition of Individual Biomolecules, Microscopy Research and Technique, 44, 339.
[pdf]
G.S. Harms, M. Sonnleitner, G.J.Schütz, H.J. Gruber and T.Schmidt (1999) Single-Molecule Anisotropy Imaging, Biophys.J, 77, 2864.
[Abstract] [DOI] [pdf]
A novel method, single-molecule anisotropy imaging, has been employed to simultaneously study lateral and rotational diffusion of fluorescence-labeled lipids on supported phospholipid membranes. In a fluid membrane composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, in which the rotational diffusion time is on the order of the excited-state lifetime of the fluorophore rhodamine, a rotational diffusion constant, Drot = 7 × 107 rad2/s, was determined. The lateral diffusion constant, measured by direct analysis of single-molecule trajectories, was Dlat = 3.5 × 10−8 cm2/s. As predicted from the free-volume model for diffusion, the results exhibit a significantly enhanced mobility on the nanosecond time scale. For membranes of DPPC lipids in the Lβ gel phase, the slow rotational mobility permitted the direct observation of the rotation of individual molecules characterized by Drot = 1.2 rad2/s. The latter data were evaluated by a mean square angular displacement analysis. The technique developed here should prove itself profitable for imaging of conformational motions of individual proteins on the time scale of milliseconds to seconds.
M. Sonnleitner, G.J.Schütz and T.Schmidt (1999) Imaging Individual Fluorophores by 2-Photon Microscopy, Chem.Phys.Lett, 300, 221.
[Abstract] [pdf]
Wide-field epi-illumination of supported lipid membranes by a femtosecond near-infrared laser allowed us to identify and follow individual fluorescence labeled lipids in their motion within the membrane. The fluorophores were excited by two-photon absorption of the near-infrared beam as seen from a quadratic dependence of the fluorescence signal on the illumination intensity. The largely decreased background signal on two-photon excitation compared to that using one-photon excitation suggests that single-molecule imaging on native cell membranes will come into reach.
A. Sonnleitner, G.J.Schütz and T.Schmidt (1999) Free Brownian Motion of Individual Lipid Molecules in Biomembranes, Biophys.J, 77, 2638.
[Abstract] [DOI] [pdf]
The mobility of phospolipids in free-standing and supported membranes was investigated on the level of individual molecules. For the analysis of trajectories a new statistical treatment was developed that permitted us to clearly distinguish different types of diffusional motion. A freely diffusing subfraction of lipids within supported membranes was identified. Its mobility was characterized by a mean lateral diffusion constant of Dsupp = 4.6 μm2/s. In comparison, the mobility of lipids embedded in “free-standing” planar membranes yielded an increase in the mean diffusion constant by a factor of 4.5, Dfree = 20.6 μm2/s. This increase is attributed to the ultrathin (≤1 nm) lubricating water layer between membranes and glass support.
W. Trabesinger, G.J.Schütz, H.J.Gruber, H. Schindler and T.Schmidt (1999) Detection of Individual Oligonucleotide Pairing by Single Molecule Microscopy, Anal.Chem, 72, 270.
[Abstract] [DOI] [pdf]
Hybridization of 20mer probe oligonucleotides to complementary, surface-immobilized target oligonucleotides was visualized on a single-molecule basis by fluorescence microscopy. Coincident determination of the positions of both the target and the probe oligonucleotides using dual-wavelength fluorescence labeling allowed for highly reliable discrimination of specifically bound probe molecules from those being physisorbed. The figures of merit of the assay are characterized by the low probability for false positive (10-4) events and the high speed for detection of up to hundreds of different DNA fragments per second. The probability for false negative events is limited by the biochemical binding probability of short oligonucleotides. The potentials and limitations of this methodology for single-cell single-DNA analysis are discussed.
Vulto, SIE, Kennis, JTM, Streltsov, AM, Amesz, J, Aartsma, TJ (1999) Energy relaxation within the B850 absorption band of the isolated, JOURNAL OF PHYSICAL CHEMISTRY B, 103, 878-883.
[DOI]
Louwe, RJW, Vrieze, J, van der Vos, R, Aartsma, TJ, Hoff, AJ (1999) Linear dichroism in triplet-singlet difference spectra of photosynthetic, CHEMICAL PHYSICS LETTERS, 306, 25-32.
[DOI]
van Oijen, AM, Ketelaars, M, Kohler, J, Aartsma, TJ, Schmidt, J (1999) Unraveling the electronic structure of individual photosynthetic, SCIENCE, 285, 400-402.
[DOI]
van Oijen, AM, Ketelaars, M, Kohler, J, Aartsma, TJ, Schmidt, J (1999) Spectroscopy of individual LH2 complexes of Rhodopseudomonas acidophila:, CHEMICAL PHYSICS, 247, 53-60.
[DOI]
Vulto, SIE, de Baat, MA, Neerken, S, Nowak, FR, van Amerongen, H, Amesz, J, Aartsma, TJ (1999) Excited state dynamics in FMO antenna complexes from photosynthetic, JOURNAL OF PHYSICAL CHEMISTRY B, 103, 8153-8161.
[DOI]
Neerken, S, Schmidt, KA, Aartsma, TJ, Amesz, J (1999) Dynamics of energy conversion in reaction center core complexes of the, BIOCHEMISTRY, 38, 13216-13222.
[DOI]
M. van Hecke, C. Storm and W. van Saarloos (1999) Sources, sinks and wavenumber selection in coupled CGL equations and experimental implications for counter-propagating wave systems, Physica D, 134, 1 .
[pdf]
A.I. Yanson, I.K. Yanson and J.M. van Ruitenbeek (1999) Observation of shell structure in sodium nanowires., Nature , 400.
[pdf]
H.E. van den Brom and J.M. van Ruitenbeek (1999) Quantum suppression of shot noise in metallic atomic size contacts., Phys. Rev. Lett., , 82.
[pdf]
B. Ludoph, M.H. Devoret, D. Esteve, C. Urbina and J.M. van Ruitenbeek (1999) Evidence for saturation of channel transmission from conductance fluctuations in atomic-size point contacts., Phys. Rev. Lett., , 82.
[pdf]
B. Ludoph and J.M. van Ruitenbeek (1999) Thermopower of atomic size metallic contacts., Phys. Rev. B , 59.
[pdf]
A. van Duijn-Arnold, J. Schmidt, O.G. Poluektov, P.G. Baranov, E.N. Mokhov (1999) The electronic structure of the Be acceptor centers in 6H-SiC, Phys. Rev. B, 60, 23, 15799-15809.
A. van Duijn-Arnold, J. Mol, R. Verberg, P.G. Baranov, E.N. Mokhov, J. Schmidt (1999) The spatial distribution of the electronic wavefunction of the shallow boron acceptor in 4H- and 6H-SiC, Phys. Rev. B, 60, 15829-15847.
A.C.J. Brouwer, E.J.J. Groenen, M.C. van Hemert, J. Schmidt (1999) Isotope shifts and intersystem crossing for pentacene in p-terphenyl. The model system of single-molecule spectroscopy, J. Phys. Chem. A, 103, 45, 8959-8965.
A.M. van Oijen, M. Ketelaars, J. K?hler, T.J. Aartsma, J. Schmidt (1999) Unraveling the electronic structure of individual photosynthetic pigment-protein complexes, Science, 285, 400-402.
A.M. van Oijen, M. Ketelaars, J. K?hler, T.J. Aartsma, J. Schmidt (1999) Spectroscopy of individual LH2 complexes of Rhodopseudomonas acidophila localized excitations in the B800 band, Chem. Phys., 247, 53-60.
A.C.J. Brouwer, J. K?hler, A.M. van Oijen, E.J.J. Groenen, J. Schmidt (1999) Single-molecule fluorescence autocorrelation experiments on pentacene. The dependence of intersystem crossing on isotopic composition, J. Chem. Phys., 110, 18, 9151-9159.
R.S. Eachus, R.C. Baetzold, Th.D. Pawlik, O.G. Poluektov, J. Schmidt (1999) Spectroscopic and computational studies of [OsCl5(NO)]3- and [RuCl5(NO)]3- donors in AgCl, Phys. Rev. B, 59, 13, 8560-8571.
A.M. van Oijen, J. K?hler, J. Schmidt, M. M?ller, G.J. Brakenhoff (1999) Far-field fluorescence microscopy beyond the diffraction limit, J. Opt. Soc. Am., 16, 4, 909-915.
A.M. van Oijen, J. Köhler, J. Schmidt, M. Müller, G.J. Brakenhoff (1999) Far-field fluorescence microscopy beyond the diffraction limit, J. Opt. Soc. Am. A, 16, 909-915.
[pdf]
A.C.J. Brouwer, J. Köhler, A.M. van Oijen, E.J.J. Groenen, J. Schmidt (1999) Single-molecule fluorescence autocorrelation experiments on pentacene. The dependence of intersystem crossing on isotopic composition, J. Chem. Phys., 110, 9151-9159.
[pdf]
A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt (1999) Spectroscopy of individual LH2 complexes of 'Rhodopseudomonas acidophila': localized excitations in the B800 band, Chem. Phys., 247, 53-60.
[pdf]
A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt (1999) Unraveling the electronic structure of individual photosynthetic pigment-protein complexes, Science, 285, 400-402.
[pdf]
A.C.J. Brouwer, E.J.J. Groenen, M.C. van Hemert, J. Schmidt (1999) Isotope shifts and intersystem crossing for pentacene in p-terphenyl. A model system of single-molecule spectroscopy, J. Phys. Chem. A, 103, 8959-8965.
[pdf]
J. Aarts, I. Abu Shiekah and P. J. v.d. Zaag (1999) Domain structure in polycrystalline MnZn ferrite imaged by magnetic force microscopy, Jn. Appl. Physics, 85, 7302.
A. M. Troyanovsky, J. Aarts, P. H. Kes (1999) Collective and plastic vortex motion in superconductors at high flux densities, Nature, 399, 665.
M. Fäth, S. Freisem, A. A. Menovsky, Y. Tomioka, J. Aarts, J. A. Mydosh (1999) Spatially inhomogeneous metal-insulator transition in doped manganites, Science, 285, 1540.
H. W. Zandbergen, S. Freisem, T. Nojima, J. Aarts (1999) Magnetoresistance and atomic structure of ultrathin films of La0.73Ca0.27MnO3 on SrTiO3, Phys. Rev. B, 60, 10259.
M. Marchevsky, J. Aarts, P. H. Kes (1999) Depinning and anisotropic order in flowing and static vortex lattices in NbSe2 studied with magnetic decoration, Phys. Rev B, 60, 14601.
D. Groten, G. J. C. van Baarle, R. W. A. Hendrikx, J. Aarts, G. J. Nieuwenhuys, J. A. Mydosh (1999) Preparation and transport properties of high-quality thin films of the heavy-fermion system CeCu6, Physica B, 261, 30.
M. Fäth. J. Aarts, A. A. Menovsky, G. J. Nieuwenhuys, J. A. Mydosh (1999) Tunneling spectroscopy on the correlation effects in FeSi, Physica B , 261, 860.
H. W. Zandbergen, J. Aarts, S. Freisem, I. E. Graboy, O. Yu. Gorbenko and A. R. Kaul (1999) HREM study of domains in thin films of La0.73Ca0.27MnO3 and (La1-xPrx)0.7Ca0.3MnO3, In: Kluwer Academic Publishers, Dordrecht, The Netherlands. G. Van Tenderloo et al. (eds.), High-Temperature Superconductors and Novel Inorganic Materials, p. 239-243, ISBN:0792353463.

1998
Garcia-Parajo, MF and Veerman, JA and Van Noort, SJT and De Grooth, BG and Greve, J. and Van Hulst, NF (1998) Near-field optical microscopy for DNA studies at the single molecular level, Bioimaging, 6.
[Abstract] [DOI] [pdf]
An aperture-type near-field optical microscope (NSOM) with two polarization detection channels has been used to image fluorescently labelled DNA with high spatial resolution and single molecule fluorescence sensitivity. The sample has been engineered such that there is only one rhodamine dye per DNA strand. Lateral and vertical DNA dimensions in the shear-force image are 14 ± 2 nm and 1.4 ± 0.2 nm, respectively. No sample deformation was observed under our imaging conditions. Near-field fluorescence imaging of individual fluorophores shows an optical resolution of 70 nm at full-width at half-maximum. Large intensity differences between individual rhodamine molecules attached to DNA are observed from the NSOM images. Statistics on rhodamine dyes in different environments (attached to glass, embedded in a polymer layer and attached to DNA) show bleaching rates of 10-5. Total intensity line profiles together with in-plane angle orientation are used to characterize individual dyes. Rhodamine dyes show strong intensity fluctuations independent of the particular environment. These results are in contrast with the more stable photophysical behaviour as observed for carbocyanine molecules embedded in polymer matrices. The mobility of rhodamine - both lateral and rotational - is clearly influenced by its immediate surrounding and attachment to the surface.
S. J. van Noort and K. O. van der Werf and A. P. Eker and C. Wyman and B. G. de Grooth and N. F. van Hulst and J. Greve (1998) Direct visualization of dynamic protein-DNA interactions with a dedicated atomic, Biophys J, Jun, 74, 2840--2849.
[Abstract] [DOI] [pdf]
Photolyase DNA interactions and the annealing of restriction fragment ends are directly visualized with the atomic force microscope (AFM). To be able to interact with proteins, DNA must be loosely bound to the surface. When MgCl2 is used to immobilize DNA to mica, DNA is attached to the surface at distinct sites. The pieces of DNA in between are free to move over the surface and are available for protein interaction. After implementation of a number of instrumental improvements, the molecules can be visualized routinely, under physiological conditions and with molecular resolution. Images are acquired reproducibly without visible damage for at least 30 min, at a scan rate of 2 x 2 microm2/min and a root mean square noise of less than 0.2 nm. Nonspecific photolyase DNA complexes were visualized, showing association, dissociation, and movement of photolyase over the DNA. The latter result suggests a sliding mechanism by which photolyase can scan DNA for damaged sites. The experiments illustrate the potential that AFM presents for modern molecular biology.
G.J.Schütz, W. Trabesinger and T.Schmidt (1998) Direct Observation of Ligand Colocalization on Individual Receptor Molecules, Biophys.J, 74, 2223.
[Abstract] [DOI] [pdf]
We have exploited the novel methodology of far-field fluorescence microscopy at the single molecule level to study colocalization of two different ligand molecules on an individual receptor. The use of dual-wavelength single molecule imaging allows discrimination between isolated and colocalized ligands with an accuracy of 40 nm. In the case of very close proximity of the two ligands, below 7 nm, single pair Förster energy-transfer was observed. The latter finding unequivocally demonstrates colocalization of two ligands on an individual receptor.
Franken, EM, Neerken, S, Louwe, RJW, Amesz, J, Aartsma, TJ (1998) A permanent hole burning study of the FMO antenna complex of the green, BIOCHEMISTRY, 37, 5046-5051.
[DOI]
Lowe, RJW, Aartsma, TJ, Gast, P, Hulsebosch, RJ, Nan, HM, Vrieze, J, Hoff, AJ (1998) The triplet state of the FMO complex of the green sulfur bacterium Prosthecochloris aestuarii studied with single-crystal EPR, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1365, 373-384.
[DOI]
Neerken, S, Permentier, HP, Francke, C, Aartsma, TJ, Amesz, J (1998) Excited states and trapping in reaction center complexes of the green, BIOCHEMISTRY, 37, 10792-10797.
[DOI]
Streltsov, AM, Vulto, SIE, Shkuropatov, AY, Hoff, AJ, Aartsma, TJ, Shuvalov, VA (1998) B-A and B-B absorbance perturbations induced by coherent nuclear motions, JOURNAL OF PHYSICAL CHEMISTRY B, 102, 7293-7298.
[DOI]
Vulto, SIE, de Baat, MA, Louwe, RJW, Permentier, HP, Neef, T, Miller, M, van Amerongen, H, Aartsma, TJ (1998) Exciton simulations of optical spectra of the FMO complex from the green, JOURNAL OF PHYSICAL CHEMISTRY B, 102, 9577-9582.
[DOI]
van Oijen, AM, Ketelaars, M, Kohler, J, Aartsma, TJ, Schmidt, J (1998) Spectroscopy of single light-harvesting complexes from purple, JOURNAL OF PHYSICAL CHEMISTRY B, 102, 9363-9366.
[DOI]
Vulto, SIE, Neerken, S, Louwe, RJW, de Baat, MA, Amesz, J, Aartsma, TJ (1998) Excited-state structure and dynamics in FMO antenna complexes from, JOURNAL OF PHYSICAL CHEMISTRY B, 102, 10630-10635.
[DOI]
M. van Hecke (1998) Building blocks of spatiotemporal intermittency, Phys. Rev. Lett., 80, 1896 .
[pdf]
I.K. Yanson, V.V. Fisun, N.L. Bobrov, J.A. Mydosh and J.M. van Ruitenbeek (1998) Size-effect ofKondo scattering in point contacts revisited., Low Temperature Physics (Ukraine) , 24, 654-60.
A.I. Yanson, G. Rubio Bollinger, H.E. van den Brom, N. Agraït and J.M. van Ruitenbeek (1998) Formation and manipulation of a metallic wire of single gold atoms., Nature , 395.
[pdf]
H.E. van den Brom, A.I. Yanson and J.M. van Ruitenbeek (1998) Characterization of individual conductance steps in metallic quantum point contacts., Physica B , 252, 69-76.
Elke Scheer, Nicolás Agraït, Juan Carlos Cuevas, Alfredo Levy Yeyati, Bas Ludoph, Alvaro Martín-Rodero, Gabino Rubio Bollinger,Jan M. van Ruitenbeek and Cristian Urbina (1998) The signature of chemical valence in the electrical conduction through a single-atom contact., Nature , 394.
[DOI] [pdf]
A. Szemik-Hojniak, J.M. Zwier, W.J. Buma, R. Bursi, J.H. van der Waals (1998) Two ground state conformers of the proton sponge 1,8-bis (dimethylamino) naphthalene revealed by fluorescence spectroscopy and ab-initio calculations, J. Am. Chem. Soc., 120, 19, 4840-4844.
A.M. van Oijen, M. Ketelaars, J. K?hler, T.J. Aartsma, J. Schmidt (1998) Spectroscopy of single light-harvesting complexes from purple photosynthetic bacteria at 1.2 K, J. Phys. Chem. B, 102, 47, 9363-9366.
X.L.R. Dauw, M.V. Bronsveld, A. Kr?ger, J.B.M. Warntjes, M.R. Witjes, E.J.J. Groenen (1998) On the singlet excited states of C70 and C60, J. Chem. Phys., 109, 21, 9332-9339.
M.V. Bronsveld, X.L.R. Dauw, E.J.J. Groenen (1998) The triplet state of C70. A zero-field study, Chem. Phys. Lett., 293, 528-534.
X.L.R. Dauw, O.G. Poluektov, J.B.M. Warntjes, M.V. Bronsveld, E.J.J. Groenen (1998) Triplet-state dynamics of C70, J. Phys. Chem. A, 102, 18, 3078-3082.
A.M. van Oijen, J. K?hler, J. Schmidt, M. M?ller, G.J. Brakenhoff (1998) 3-Dimensional super-resolution by spectrally selective imaging, Chem. Phys. Lett., 292, 183-187.
A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1998) Detecting magnetic resonance through quantum jumps of single molecules, Phys. Rev. Lett., 80, 18, 3944-3947.
M. van Gastel, J.W.A. Coremans, L.J.C. Jeuken, G.W. Canters, E.J.J. Groenen (1998) Electron spin-echo envelope modulation spectrum of azurin at X-band, J. Phys. Chem. A, 102, 24, 4462-4470.
A. Arnold, T. Ikoma, O.G. Poluektov, P.G. Baranov, E.N. Mokhov, J. Schmidt (1998) Electronic structure of the deep boron acceptor in boron-doped 6H-SiC, Phys. Rev. B, 57, 3, 1607-1619.
G.J.B. van den Berg, D.J. van den Heuvel, O.G. Poluektov, I. Holleman, G. Meijer, E.J.J. Groenen (1998) Pulsed ENDOR studies at 95 GHz of the triplet state of 13C60, J. Magn. Res., 131, 39, 39-45.
J. K?hler, A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1998) Isotopomer selective spectroscopy on pentacene, J. Am. Chem. Soc., 120, 8, 1900-1905.
J. Köhler, A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1998) Isotopomer selective spectroscopy on pentacene, J. Am. Chem. Soc., 120, 1900-1905.
[pdf]
A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1998) Detecting magnetic resonance through quantum jumps of single molecules, Phys. Rev. Lett., 80, 3944-3947.
[pdf]
A.M. van Oijen, J. Köhler, J. Schmidt, M. Müller, G.J. Brakenhoff (1998) 3-Dimensional super-resolution by spectrally selective imaging, Chem. Phys. Lett., 292, 183-187.
[pdf]
A.M. van Oijen, M. Ketelaars, J. Köhler, T.J. Aartsma, J. Schmidt (1998) Spectroscopy of single light-harvesting complexes from purple photosynthetic bacteria at 1.2 K, J. Phys. Chem. B, 102, 9363-9366.
[pdf]
M. Marchevsky, A. Keurentjes, J. Aarts, and P. H. Kes (1998) Elastic deformations in field-cooled vortex lattices in NbSe2, Phys. Rev. B , 57, 6061.
J. Aarts, S. Freisem, R. Hendrikx, and H. W. Zandbergen (1998) Disorder effects in epitaxial thin films of (La,Ca)MnO3, Appl. Phys. Lett. , 72, 2975-2977 .
M. Faeth, J. Aarts, A. A. Menovsky, G. J. Nieuwenhuys and J. A. Mydosh (1998) Tunneling spectroscopy on the correlation effects in FeSi, Phys, Rev. B , 58, 15483.
D. Groten, A. C. Wallast, G. J. Nieuwenhuys, J. A. Mydosh and J. Aarts (1998) Superconducting properties of thin films of CeRu2, in ‘Superconducting superlattices II : native and artificial, Eds. I. Bozovic and D. Pavuna, proc. SPIE , 3480, 160.
S. Freisem, T. Nojima, R. W. A. Hendrikx, H. W. Zandbergen and J. Aarts (1998) Differences in properties of thin films of La0.73Ca0.27MnO3 grown on STO or LAO by sputter deposition, in ‘superconducting and related oxides Physics and nanoengineering III’, Eds I. Bozovic and D. Pavuna, proc. SPIE , 3481, 342.

1997
van Dusschoten, D. and van Noort, J. and Van As, H. (1997) Displacement imaging in porous media using the line scan NMR technique, Geoderma, 80, 405--416.
[Abstract] [DOI] [pdf]
Displacement imaging is a recent, powerful NMR method with which distributions of displacements can be acquired of e.g. fluids within a porous medium. Both motion parallel and perpendicular to the flow direction may be observed within a time window of a few milliseconds to several seconds. By combining displacement imaging with the line scan technique, one-dimensionally resolved measurements with a high temporal resolution ( < 1 min) of the spatial dependency of motion can be obtained. Here we present displacement images of flow through two simple model systems for soil: an unconsolidated glass bead water system and a sintered glass bead filter. It is demonstrated that the combination of displacement imaging and spatial resolution along a line is important to access both bulk displacement and local displacements in relation to the local porosity.
Van Noort, S.J.T. and Van der Werf, K.O. and De Grooth, B.G. and Van Hulst, NF and Greve, J. (1997) Height anomalies in tapping mode atomic force microscopy in air caused by adhesi, Ultramicroscopy, 69, 117--27.
[Abstract] [DOI] [pdf]
Height anomalies in tapping mode atomic force microscopy (AFM) in air are shown to be caused by adhesion. Depending on the damping of the oscillation the height of a sticking surface is reduced compared to less sticking surfaces. It is shown that the height artefacts result from a modulation of oscillatory movement of the cantilever. Damping and excitation of the cantilever by the driver continuously compete. As a consequence a severe modulation of the cantilever oscillation occurs, depending on the phase mismatch between the driver and the cantilever. Phase images of tapping mode AFM show contrast which correlates with adhesion. Examples of a partially removed gold layer on mica, a Langmuir-Blodgett film and DNA show height artefacts ranging up to 10 nm.
G.J.Schütz, H.Schindler and T.Schmidt (1997) Single Molecule Microscopy on Model Membranes Reveals Anomalous Diffusion, Biophys.J, 73, 1073.
[Abstract] [DOI] [pdf]
The lateral mobility of lipids in phospholipid membranes has attracted numerous experimental and theoretical studies, inspired by the model of Singer and Nicholson (1972. Science, 175:720–731) and the theoretical description by Saffman and Delbrück (1975. Proc. Natl. Acad. Sci. USA. 72:3111–3113). Fluorescence recovery after photobleaching (FRAP) is used as the standard experimental technique for the study of lateral mobility, yielding an ensemble-averaged diffusion constant. Single-particle tracking (SPT) and the recently developed single-molecule imaging techniques now give access to data on individual displacements of molecules, which can be used for characterization of the mobility in a membrane. Here we present a new type of analysis for tracking data by making use of the probability distribution of square displacements. The potential of this new type of analysis is shown for single-molecule imaging, which was employed to follow the motion of individual fluorescence-labeled lipids in two systems: a fluid-supported phospholipid membrane and a solid polymerstabilized phospholipid monolayer. In the fluid membrane, a high-mobility component characterized by a diffusion constant of 4.4 microns2/s and a low-mobility component characterized by a diffusion constant of 0.07 micron2/s were identified. It is proposed that the latter characterizes the so-called immobile fraction often found in FRAP experiments. In the polymer-stabilized system, diffusion restricted to corrals of 140 nm was directly visualized. Both examples show the potentials of such detailed analysis in combination with single-molecule techniques: with minimal interference with the native structure, inhomogeneities of membrane mobility can be resolved with a spatial resolution of 100 nm, well below the diffraction limit.
G.J.Schütz, H.Schindler and T.Schmidt (1997) Imaging Single Molecule Dichroism, Opt.Lett, 22, 651.
[Abstract] [DOI] [pdf]
Video-enhanced optical f luorescence microscopy has been used to determine the direction of the transition dipole moment of individual molecules. Fast electro-optical switching of the polarization of the excitation allowed us to detect the linear dichroism of single f luorophores in solid phospholipid membranes. Quantitative analysis of the f luorescence signal showed that rotational mobility is absent in solid biomembranes.
G.J.Schütz, H.J.Gruber, H.Schindler and T.Schmidt (1997) Fluorophores for Single Molecule Microscopy, J.Luminescence, 72-74, 18.
[Abstract] [pdf]
The fluorescence photoncount distributions, photobleaching characteristics, and saturation intensities of the commonly used fluorescence tags tetramethylrhodamine and phycoerythrin were measured on the level of individual molecules. Although, the fluorescence properties of phycoerythrin seem to be superior in view of single molecule detection, the increased photostability of tetramethylrhodamine coupled both, to a lipid or an antibody, makes it the molecule of choice for imaging applications.
T.Schmidt, P.Hinterdorfer and H.Schindler (1997) Mikroskopie zur Erkennung einzelner Biomoleküle (Microscopy for Recognition of Individual Biomolecules), Laser&Optolektronik, 29, 56.
[pdf]
Streltsov, AM, Aartsma, TJ, Hoff, AJ, Shuvalov, VA (1997) Oscillations within the B-L absorption band of Rhodobacter sphaeroides, CHEMICAL PHYSICS LETTERS, 266, 347-352.
[DOI]
Franken, EM, Shkuropatov, AY, Francke, C, Neerken, S, Gast, P, Shuvalov, VA, Hoff, AJ, Aartsma, TJ (1997) Reaction centers of Rhodobacter sphaeroides R-26 with selective, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1319, 242-250.
[DOI]
Vulto, SIE, Streltsov, AM, Aartsma, TJ (1997) Excited state energy relaxation in the FMO complexes of the green, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 4845-4850.
[DOI]
Franken, EM, Shkuropatov, AY, Francke, C, Neerken, S, Gast, P, Shuvalov, VA, Hoff, AJ, Aartsma, TJ (1997) Reaction centers of Rhodobacter sphaeroides R-26 with selective, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1321, 1-9.
[DOI]
Schellenberg, P, Louwe, RJW, Shochat, S, Gast, P, Aartsma, TJ (1997) Accumulated photon echo studies on bacterial photosynthetic reaction, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 6786-6790.
[DOI]
Vulto, SIE, Streltsov, AM, Shkuropatov, AY, Shuvalov, VA, Aartsma, TJ (1997) Subpicosecond excited-state relaxation of the accessory, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 7249-7255.
[DOI]
Louwe, RJW, Aartsma, TJ (1997) On the nature of energy transfer at low temperatures in the BChl a, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 7221-7226.
[DOI]
Kennis, JTM, Streltsov, AM, Vulto, SIE, Aartsma, TJ, Nozawa, T, Amesz, J (1997) Femtosecond dynamics in isolated LH2 complexes of various species of, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 7827-7834.
[DOI]
Kennis, JTM, Streltsov, AM, Permentier, H, Aartsma, TJ, Amesz, J (1997) Exciton coherence and energy transfer in the LH2 antenna complex of, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 8369-8374.
[DOI]
Louwe, RJW, Vrieze, J, Hoff, AJ, Aartsma, TJ (1997) Toward an integral interpretation of the optical steady-state spectra of, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 11280-11287.
[DOI]
Louwe, RJW, Vrieze, J, Aartsma, TJ, Hoff, AJ (1997) Toward an integral interpretation of the optical steady-state spectra of, JOURNAL OF PHYSICAL CHEMISTRY B, 101, 11273-11279.
[DOI]
Kennis, JTM, Shkuropatov, AY, van Stokkum, IHM, Gast, P, Hoff, AJ, Shuvalov, VA, Aartsma, TJ (1997) Formation of a long-lived P(+)B(A)(-)state in plant pheophytin-exchanged, BIOCHEMISTRY, 36, 16231-16238.
[DOI]
M. van Hecke and W. van Saarloos (1997) Convection in rotating annuli - Ginzburg-Landau equation with tunable coefficients, Phys. Rev. E, 55, R1259 .
[pdf]
M. van Hecke and B. A. Malomed (1997) A domain wall between single-mode and bimodal states and its transition to dynamical behavior in inhomogeneous systems, Physica D, 101, 131 .
[pdf]
R. Alvarez, M. van Hecke and W. van Saarloos (1997) Sources and sinks separating domains of left- and right-traveling waves - Experiment versus amplitude equations, Phys. Rev. E R, 56, R1306 .
[pdf]
A.I. Yanson and J.M. van Ruitenbeek (1997) Do histograms constitute a proof for conductance quantization?, Phys. Rev. Lett. , 79.
[pdf]
J.M. Krans and J.M. van Ruitenbeek (1997) Anomalous vacuum tunneling in antimony beak junctions., Surf. Sci. , 383.
J.M. van Ruitenbeek, J.M. Krans, H.E. van den Brom and L.J. de Jongh (1997) Conductance quantization in metals: some unsolved problems., in: "Nanowires", editors P.A. Serena and N. Garcia, NATO-ASI Series E: Appl.Sci. Kluwer Academic Publishers, 340.
J.M. van Ruitenbeek, M.H. Devoret, D. Esteve and C. Urbina (1997) Conductance quantization in metals: the influence of subband formation on the relatives tability of specific contact diameters., Phys. Rev. B , 56.
[pdf]
J.M. van Ruitenbeek (1997) Quantum point contacts between metals., in: "Mesoscopic electron transport", L.L. Sohn, L.P. Kouwenhoven and G. Schön, eds., NATO-ASI Series E: Appl. Sci., 345.
J. Köhler, J. Schmidt (1997) Perspectives of single-molecule magnetic-resonance spectroscopy, C R Acad. Sci. Ser. II Fasc. B-Mec., 324, 373-388.
[pdf]
M. Marchevsky, J. Aarts and P.H. Kes and M. V. Indenbom (1997) Observation of correlated vortex flow in NbSe2 with magnetic decoration, Phys.Rev.Lett. , 78, 531.
M. Marchevsky, J. Aarts and P.H. Kes and M. V. Indenbom (1997) Observation of correlated vortex flow in NbSe2 with magnetic decoration, Phys.Rev.Lett, 78, 531.
A.P. Volodin, A.A. Golubov and J. Aarts (1997) Vortex core shapes measured by STM, Z. Phys. B , 102, 317.
J. Aarts, J.M.E. Geers, E. Brück, A.A. Golubov and R. Coehoorn (1997) On the interface transparency of superconductor/ferromagnetic multilayers, Phys.Rev. B , 56, 2779.
J. Aarts (1997) Comment on magnetic-coherence-length scaling in metallic multilayers, Phys. Rev. B , 56, 8432.
L.A. Angurel, F. Amin, M. Polichetti, J. Aarts and P.H. Kes (1997) Dimensionality of collective pinning in 2H-NbSe2 single crystals, Phys. Rev. B , 56, 3425.
S. Freisem, A. Brockhoff, D.G. de Groot, B. Dam and J. Aarts (1997) Magnetic and transport properties of sputtered La0.67Ca0.33MnO3 thin films, Jn. Magn. Magn. Mat, 165, 380.
D. Groten, S. Ramakrishnan, B. Becker, G. J. Nieuwenhuys, J. A. Mydosh and J. Aarts (1997) Critical current measurements on thin films of CeRu2, Physica B, 230-232, 377.
M. Marchevsky, J. Aarts, and P. H. Kes (1997) Determination of the quenching temperature for the vortex lattice in field-cooling decoration experiments, Physica C, 282-287, 2083.
M. Marchevsky, A. Keurentjes, P. H. Kes and J. Aarts (1997) Double-sided decoration on NbSe2, Physica C, 282-287, 2085.

1996
Leermakers, F.A.M. and Noort, J. and Oversteegen, S.M. and Barneveld, P.A. and Lyklema, J. (1996) Bending moduli and spontaneous curvature in one-phase microemulsion systems. A m, Faraday Discussions, 104, 317--334.
[Abstract] [DOI] [pdf]
We use a lattice-based self-consistent field (SCF) theory to model one-phase microemulsion systems composed of solvents with limited miscibility and a non-ionic emulsifier. All relevant degrees of freedom are accounted for in a mean-field description; all molecules can distribute freely over the two bulk phases, accumulate at the interface and take all possible conformations, but cooperative fluctuations of the interface are ignored. The only constraint imposed on the system is a fixed geometry of the droplets. The constraint equilibrium is based on the thermodynamics of small systems. We consider systems with equal compositions of oil, water and surfactants in lamellar, cylindrical and spherical topology. We take the Gibbs energy of these three systems to evaluate the mechanical properties of the monolayers. We show that a Helfrich-type description of the microemulsion is possible in this SCF framework. However, the predicted mechanical properties of the system are not classical. Usually it is assumed that the mean bending modulus kc and the spontaneous curvature J0 are surfactant-dependent constants. We find that kc and J0 also depend strongly on the surfactant concentration. However, neither the product kcJ0 nor the saddle-splay modulus k depend on the composition as long as the interfaces do not interact. These results can be rationalised, as both kcJ0 and k can be found from the lateral pressure profile of the flat, relaxed interface. Another important observation is that the Gibbs energy of the microemulsion is not exactly a quadratic function of the imposed curvature, causing kc to depend weakly on the topology of the interface.
Van der Wel, NN and Putman, CAJ and Van Noort, SJT and De Grooth, BG and Emons, AMC (1996) Atomic force microscopy of pollen grains, cellulose microfibrils, and protoplast, Protoplasma, 194, 29--39.
[Abstract] [DOI] [pdf]
Atomic force microscopy (AFM) holds unique prospects for biological microscopy, such as nanometer resolution and the possibility of measuring samples in (physiological) solutions. This article reports the results of an examination of various types of plant material with the AFM. AFM images of the surface of pollen grains ofKalanchoe blossfeldiana andZea mays were compared with field emission scanning electron microscope (FESEM) images. AFM reached the same resolutions as FESEM but did not provide an overall view of the pollen grains. Using AFM in torsion mode, however, it was possible to reveal differences in friction forces of the surface of the pollen grains. Cellulose microfibrils in the cell wall of root hairs ofRaphanus sativus andZ. mays were imaged using AFM and transmission electron microscopy (TEM). Imaging was performed on specimens from which the wall matrix had been extracted. The cell wall texture of the root hairs was depicted clearly with AFM and was similar to the texture known from TEM. It was not possible to resolve substructures in a single microfibril. Because the scanning tip damaged the fragile cells, it was not possible to obtain images of living protoplasts ofZ. mays, but images of fixed and dried protoplasts are shown. We demonstrate that AFM of plant cells reaches resolutions as obtained with FESEM and TEM, but obstacles still have to be overcome before imaging of living protoplasts in physiological conditions can be realized.
T.Schmidt, G.J.Schütz, H.J.Gruber and H.Schindler (1996) Local Stoichiometries Determined by Counting Individual Molecules, Anal.Chem., 68, 4397.
[Abstract] [DOI] [pdf]
The capability of optical single-molecule microscopy for quantitative determination of local stoichiometries is demonstrated. Biotin−streptavidin embedded in a phospholipid membrane was chosen as a model system. At a local resolution of 30 nm and a time resolution of 35 ms, it was possible to determine local stoichiometries between one and four occurring in this system. The “stoichiometric resolution” of the method is analyzed by statistical means. From this a quantitative criterion is derived for the reliability in assigning a defined number of fluorophores to each individual fluorescence peak observed. It is shown that only a few (n ≈ 10) observations are sufficient for reliable assignments.
T.Schmidt, G.J.Schütz, W.Baumgartner, H.J.Gruber and H.Schindler (1996) Imaging of Single Molecule Diffusion., Proc.Natl.Acad.Sci. USA, 93, 2926.
[Abstract] [pdf]
In recent years observations at the level of individual atoms and molecules became possible by micros- copy and spectroscopy. Imaging of single f luorescence mole- cules has been achieved but has so far been restricted to molecules in the immobile state. Here we provide methodology for visualization of the motion of individual f luorescent mol- ecules. It is applied to imaging of the diffusional path of single molecules in a phospholipid membrane by using phospholip- ids carrying one rhodamine dye molecule. For this method- ology, f luorescence microscopy was carried to a sensitivity so that single f luorescent molecules illuminated for only 5 ms were resolvable at a signal y noise ratio of 28. Repeated illu- minations permitted direct observation of the diffusional motion of individual molecules with a positional accuracy of 30 nm. Such capability has fascinating potentials in bio- science—for example, to correlate biological functions of cell membranes with movements, spatial organization, and stoi- chiometries of individual components.
Kennis, JTM, Streltsov, AM, Aartsma, TJ, Nozawa, T, Amesz, J (1996) Energy transfer and exciton coupling in isolated B800-850 complexes of, JOURNAL OF PHYSICAL CHEMISTRY, 100, 2438-2442.
[DOI]
Aartsma, TJ, Amesz, J (1996) Reaction center and antenna processes in photosynthesis at low, PHOTOSYNTHESIS RESEARCH, 48, 99-106.
[DOI]
Kramer, H, Aartsma, TJ, Amesz, J (1996) Excited states and charge separation in membranes of the green sulfur, PHOTOCHEMISTRY AND PHOTOBIOLOGY, 64, 26-31.
[DOI]
L.J. de Jongh, D.A. van Leeuwen, J.M. van Ruitenbeek and J. Sinzig (1996) Magnetic properties of metal cluster compounds. Model systems for nano-sized metal particles., in:"Magnetism: a supramolecular function", O. Kahn editor, NATO-ASI SeriesC: Math. and Phys. Sci., Kluwer Academic Publishers, 484.
N. van der Post, J.A. Mydosh and J.M. van Ruitenbeek (1996) Size dependence study on the spin glass CuMn 1%., Phys. Rev. B, 53.
[pdf]
J.M. Krans, J.M. van Ruitenbeek and L.J. de Jongh (1996) Atomic structure and quantized conductance in metal point contacts., Physica B , 218.
N. van der Post and J.M. van ruitenbeek (1996) High stabilitySTM made of a break junction., Proc. of the 21st Int. Conf. on Low Temp. Phys., Chech. J. Phys. -suppl., 46.
I.K. Yanson, V.V. Fisun, R. Hesper, J.M. Krans, J.A. Mydosh N. van der Post and J.M. van Ruitenbeek (1996) Characterization of point-contacts showing size-effect in electron scattering by magnetic impurities., Physica B , 218.
J.M. van Ruitenbeek, A. Alvarez, I. Piñeyro, C. Grahmann, P. Joyez, M.H. Devoret, D. Esteve and C. Urbina (1996) Adjustable nanofabricated atomic size contacts., Rev. Sci. Instrum. , 67.
N. van der Post, F.L. Mettes, J.A. Mydosh, J.M. van Ruitenbeek and I.K. Yanson (1996) Size-effect of Kondo scattering by Fe impurities in Cu point contacts., Low Temp. Phys. (Kharkov) , 22.
N. van der Post, F.L. Mettes, J.A. Mydosh, J.M. van Ruitenbeek and I.K. Yanson (1996) Size dependence of Kondo scattering in point contacts: Fe impurities in Cu., Phys. Rev. B , 53.
[pdf]
J. Köhler, A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1996) On the intersystem crossing of pentacene in p-terphenyl, Chem. Phys. Lett., 250, 137-144.
[pdf]
A.C.J. Brouwer, J. Köhler, E.J.J. Groenen, J. Schmidt (1996) 13C isotope effects for pentacene in p-terphenyl. High resolution spectroscopy and single-spin detection, J. Chem. Phys., 105, 2212-2222.
[pdf]
J. Wrachtrup, C. von Borczyskowski, J. Köhler, J. Schmidt (1996) Magnetic resonance of single molecular spins, T. Basché, M. Orrit, W.E. Moerner, U.P. Wild (eds.), VCH, Weinheim, 159-189.
[pdf]
J.M.E. Geers, E. Brück, A.A. Golubov and J. Aarts (1996) Influence of the magnetic moment on the superconductivity in S/F systems, Czech. Jn. of Phys, 46 (suppl S2), 733.

1995
Rofe, CJ and Vannoort, J. and Back, PJ and Callaghan, PT (1995) NMR microscopy using large, pulsed magnetic-field gradients, Journal of Magnetic Resonance, Series B, 108, 125--136.
[Abstract] [DOI] [pdf]
The use of imaging schemes which employ large pulsed magnetic-field gradients to avoid susceptibility and diffusion artifacts in NMR microscopy is considered. The theory relating to these artifacts is briefly reviewed in the context of two specific pulse sequences, namely two-dimensional (i.e., slice-selective) phase-phase encoding and two-dimensional phase-frequency encoding in which the magnetization is recycled in a CPMG multi-pulse train. Experiments have been carried out using a specially constructed coil set which achieves gradient strengths of up to 6 T m-1 and a number of images are shown, both from a susceptibility phantom and from a geranium petiole. Some of the inherent advantages and disadvantages of the respective imaging schemes are demonstrated.
T.Schmidt, G.J.Schütz, W.Baumgartner H.J.Gruber and H.Schindler (1995) Characterization of Photophysics and Mobility of Single Molecules in a Fluid Lipid Membranes., J.Phys.Chem., 99, 17662.
[Abstract] [DOI] [pdf]
Properties of single fluorescence-labeled lipids in a fluid phospholipid membrane were analyzed using sensitive fluorescence microscopy. The high signal-to-noise ratio for detection of individual fluorescence-labeled molecules of 5-70 permitted detailed study of their photophysical parameters. From single fluorophores a signal of 49 counts/ms was detected when excited above their saturation intensity of 7.6 kW/cm2. These data, obtained at the level of individual fluorophores, are found to agree quantitatively with predictions from a conventional three-level model using known ensemble-averaged rate constants. Light-induced photochemistry of single fluorophores was found to occur as a sudden disappearance of their fluorescence characterized by a photobleaching efficiency of 9 x These photophysical properties of the fluorescence label permitted analysis of the motion of individual lipid molecules. Lipid motion was tracked at a rate of up to 66 images per second. The high fluorescence image-contrast allowed for determination of lipid positions with a precision of 30 nm. For short length-scales the observed trajectories were described by a random two-dimensional motion with a lateral diffusion constant of 1.42 x cm2/s. Free diffusion was found to be restricted to length-scales of 100 nm, attributed to membrane defects.
SCHELVIS, JPM, AARTSMA, TJ (1995) TRANSIENT ABSORPTION CHANGES OF A DEGENERATE DIMER INDUCED BY EXCITON, CHEMICAL PHYSICS, 194, 303-309.
[DOI]
KENNIS, JTM, AARTSMA, TJ, AMESZ, J (1995) ENERGY-TRANSFER BETWEEN ANTENNA COMPLEXES IN THE PURPLE SULFUR BACTERIA, CHEMICAL PHYSICS, 194, 285-289.
[DOI]
SCHELVIS, JPM, GERMANO, M, AARTSMA, TJ, VANGORKOM, HJ (1995) ENERGY-TRANSFER AND TRAPPING IN PHOTOSYSTEM-II CORE PARTICLES WITH, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1230, 165-169.
[DOI]
KRAMER, H, JONES, MR, FOWLER, GJS, FRANCKE, C, AARTSMA, TJ, HUNTER, CN, AMESZ, J (1995) ENERGY MIGRATION IN RHODOBACTER-SPHAEROIDES MUTANTS ALTERED BY, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1231, 89-97.
[DOI]
W. van Saarloos, M. van Hecke and R. Holyst (1995) Front propagation into unstable and metastable states in smectic-C* liquid crystals - Linear and nonlinear marginal-stability analysis, Phys. Rev. E, 52, 1773 .
[pdf]
M. van Hecke, E. de Wit and W. van Saarloos (1995) Coherent and incoherent drifting pulse dynamics in a complex Ginzburg-Landau equation, Phys. Rev. Lett., 75, 3830 .
[pdf]
N. van der Post, E.T. Peters, I.K. Yanson and J.M. van Ruitenbeek (1995) Transparency of atom-sized superconducting junctions., Proceedings of the 2nd Intern. Symposium on High Temperature Superconductivity and Tunneling Phenomena, 3-6 Sept. 1994, Slavyanogorsk, Ukraine, V.M. Svistunov,ed. .
J.M. Krans, I.K. Yanson and J.M. van Ruitenbeek (1995) Quantum- and subquantum conductance in Sb contacts., Proceedings of the 2ndIntern. Symposium on High Temperature Superconductivity and TunnelingPhenomena, 3-6 Sept. 1994, Slavyanogorsk, Ukraine, V.M. Svistunov, ed., 49-52.
J.M. Krans, J.M. van Ruitenbeek, V.V. Fisun, I.K. Yanson and L.J. de Jongh (1995) The signature of conductance quantization in metallic point contacts., Nature , 375.
J.M. Krans, C.J. Muller, N. van der Post, F.R. Postma, A.P. Sutton, T.N. Todorov and J.M. van Ruitenbeek (1995) Comment on "Quantized conductance in an atom-sized point contact"., Phys. Rev. Lett., , 74.
[pdf]
I.K. Yanson, V.V. Fisun, R. Hesper, A.V. Khotkevich, J.M. Krans, J.A. Mydosh and J.M. van Ruitenbeek (1995) Size dependence of Kondo scattering in point contacts., Phys. Rev. Lett. , 74.
[pdf]
J. Köhler, A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1995) Single molecule electron paramagnetic resonance spectroscopy: Hyperfine splitting owing to a single nucleus, Science, 268, 1457-1460.
[pdf]
H. van der Meer, J.A.J.M. Disselhorst, J. Köhler, A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1995) An insert for single-molecule magnetic-resonance spectroscopy in an external magnetic field, Rev. Sci. Instrum., 66, 4853-4856.
[pdf]
J. Aarts and A.P. Volodin (1995) Tunneling spectroscopy on correlated electron systems, Physica B, 206 & 207, 43.
P. Koorevaar, R. Coehoorn and J. Aarts (1995) Critical fields in Vanadium-based superconducting/ferromagnetic multilayers, Physica C, 248, 61.
M. Marchevski, L.A. Gurevitch, J. Aarts and P.H. Kes (1995) Flux droplet formation in NbSe2 single crystals, observed by decoration, Phys.Rev.Lett. , 75, 2400 .

1994
LOUWE, RJW, AARTSMA, TJ (1994) OPTICAL DEPHASING AND EXCITED-STATE DYNAMICS IN PHOTOSYNTHETIC, JOURNAL OF LUMINESCENCE, 58, 154-157.
[DOI]
VANNOORT, PI, AARTSMA, TJ, AMESZ, J (1994) ENERGY-TRANSFER AND TRAPPING OF EXCITATIONS IN MEMBRANES OF, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1184, 21-27.
[DOI]
SCHELVIS, JPM, VANNOORT, PI, AARTSMA, TJ, VANGORKOM, HJ (1994) ENERGY-TRANSFER, CHARGE SEPARATION AND PIGMENT ARRANGEMENT IN THE, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1184, 242-250.
[DOI]
KENNIS, JTM, AARTSMA, TJ, AMESZ, J (1994) ENERGY TRAPPING IN THE PURPLE SULFUR BACTERIA CHROMATIUM-VINOSUM AND, BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1188, 278-286.
[DOI]
M. van Hecke, P. C. Hohenberg and W. van Saarloos (1994) Amplitude equations for pattern forming systems, Fundamental problems in statistical mechanics VIII,edited by H. Van Beijeren and M. H. Ernst, Elsevier, p.245-278 .
[pdf]
D.A. van Leeuwen, J.M. van Ruitenbeek, L.J. de Jongh, A. Ceriotti, G. Pacchioni, G. Longoni, O.D. Häberlen and N. Rösch (1994) Quenching of magnetic moments by ligand-metal interactions in nano-sized magnetic metalclusters., Phys. Rev. Lett. , 73.
[pdf]
N. van der Post, E.T. Peters, I.K. Yanson and J.M. van Ruitenbeek (1994) Subgap structure as function of the barrier in superconducting tunnel junctions., Phys. Rev. Lett. , 73.
[pdf]
J.M. Krans and J.M. van Ruitenbeek (1994) Subquantum conductance steps in atom-sized contacts of the semimetal Sb., Phys. Rev. B , 50.
[pdf]
I.K. Yanson, V.V. Fisun, R. Hesper, A.V. Khotkevich, J.M. Krans, J.A. Mydoshand J.M. van Ruitenbeek (1994) Size effect in point-contact spectroscopy of magnetic impurities in metals., Low Temperature Physics (Ukraine) , 20.
J.M. Krans, C.J. Muller, I.K. Yanson, and J.M. van Ruitenbeek (1994) One atom point contacts., Physica B, , 194-196.
D.A. van Leeuwen, J.M. van Ruitenbeek, G. Schmid and L.J. de Jongh (1994) Size-dependent Stoner factor in Pd and Pt clusters., PhysicaB, , 194-196.
J. Köhler, A.C.J. Brouwer, E.J.J. Groenen, J. Schmidt (1994) Fluorescence detection of single molecule magnetic resonance for pentacene in p-terphenyl. The hyperfine interaction of a single triplet spin with a single 13C nuclear spin, Chem. Phys. Lett., 228, 47-52.
[pdf]
J.M. van Ruitenbeek, D.A. van Leeuwen and L.J. de Jongh (1994) Magnetic properties of metal cluster compounds, In: "Physics and chemistry of metal cluster compounds", L.J. de Jongh, ed. (Kluwer Academic Publ., 1994) , 277-306.
A.P. Volodin, J. Aarts, A.A. Menovsky, G.J. Nieuwenhuys and J.A. Mydosh (1994) Tunneling and point-contact spectroscopy on UPd2Al3 in the normal state, Physica B, 194-196, 2033.
P. Koorevaar, C. Zwart, R. Coehoorn and J. Aarts (1994) Interplay between superconductivity and magnetism in various superconducting/ferromagnetic multilayers, Physica B, 194-196, 2385 .
A.P. Volodin and J. Aarts (1994) Nanometer scale patterns etched into superconducting NbSe2 with an STM at 4.2 K, Physica C, 235-240, 1909.
J. Aarts, P. Koorevaar, T.A.C. Reydon and P. H. Kes (1994) Collective pinning behaviour of 2H_NbSe2 in tilted magnetic fields, proceedings 7th Int. Workshop on critical currents in superconductors, Ed. H. W. Weber, World Scientific .
P. Koorevaar, Y. Suzuki, R. Coehoorn and J. Aarts (1994) Decoupling of superconducting V by ultrathin Fe layers in V/Fe multilayers, Phys.Rev. B , 49, 441.
P. Koorevaar, P.H. Kes, A.E. Koshelev and J. Aarts (1994) Vortex lattice melting in multilayers with variable anisotropies, Phys. Rev. Lett. , 72, 3250.
J. Aarts, A.P. Volodin, A.A. Menovsky, G.J. Nieuwenhuys and J.A. Mydosh (1994) Tunneling spectroscopy on the heavy-fermion superconductors UPd2Al3 and UNi2Al3 in the normal state, Europhys. Lett. , 26, 203.

1993
M. van Hecke, W. van Saarloos and P.C. Hohenberg (1993) Comment on absolute and convective instabilities, Phys. Rev. Lett, 71, 2162 .
[pdf]
C.J. Muller, R. de Bruyn Ouboter, J.M. van Ruitenbeek and A.N. Omelyanchouk (1993) Classical limit of microwave detection in atomic-sized superconducting contacts., Phys. Rev. B: Rapid Commun. , 48.
[pdf]
C.J. Muller, J.M. van Ruitenbeek, C.W.J. Beenakker and R. de Bruyn Ouboter (1993) Conductance and supercurrent discontinuities in atomic size point contacts., Physica B, , 189.
J.M. Krans, C.J. Muller, I.K. Yanson, Th.C.M. Govaert, R. Hesper and J.M.van Ruitenbeek (1993) One atom point contacts., Phys. Rev. B: Rapid Commun. , 48.
[pdf]
J.M. van Ruitenbeek and D.A. van Leeuwen (1993) Size effects in orbital magnetism., Modern Physics Letters B Brief Reviews , 7.
Schmid, M. Harms, J.-O. Malm, J.-O. Bovin, J.M. van Ruitenbeek, H.W. Zandbergen and W.T. Fu (1993) Ligand-stabilized giant palladium clusters: promising candidates in heteroge-neous catalysis, J. Am. Chem. Soc., 115, 2046-2048.
[DOI] [pdf]
R.E. benfield, A.P. Maydwell, J.M. van Ruitenbeek and D.A. van Leeuwen (1993) Electronic spectra of metal cluster molecules, Z. Phys. D, 26, S 4-7.
[Abstract] [DOI] [pdf]
The electronic absorption spectra (UV- visible-NIR) of a range of molecular metal cluster com- pounds, including new spectra of Pts09(phen*)3602s in solution and Auss(PPhs)l~C16 in the solid state, are dis- cussed and compared with the spectra of colloidal par- ticles of the corresponding metals. We consider frontier orbital separations, the development of 'interband' ab- sorptions, the possible appearance of molecular plasma resonances, and charge-transfer in the solid state.
P. Koorevaar, W. Maj, P.H. Kes and J. Aarts (1993) Vortex-lattice transition in superconducting Nb/NbZr multilayers, Phys. Rev. B , 47, 934 .

1992
DEINUM, G, KLEINHERENBRINK, FAM, AARTSMA, TJ, AMESZ, J (1992) THE FLUORESCENCE YIELD OF RHODOPSEUDOMONAS-VIRIDIS IN RELATION TO THE, BIOCHIMICA ET BIOPHYSICA ACTA, 1099, 81-84.
[DOI]
SCHELVIS, JPM, LIU, BL, AARTSMA, TJ, HOFF, AJ (1992) THE ELECTRON-TRANSFER RATE FROM BPHA- TO QA IN REACTION CENTERS OF, BIOCHIMICA ET BIOPHYSICA ACTA, 1102, 229-236.
[DOI]
VANNOORT, PI, GORMIN, DA, AARTSMA, TJ, AMESZ, J (1992) ENERGY-TRANSFER AND PRIMARY CHARGE SEPARATION IN HELIOBACTERIUM-CHLORUM, BIOCHIMICA ET BIOPHYSICA ACTA, 1140, 15-21.
[DOI]
D.A. van Leeuwen, J.M. van Ruitenbeek, G. Schmid and L.J. de Jongh (1992) Size-dependent magnetisation of Pd clusters and colloids., Phys. Lett. A , 170.
C.J. Muller en J.M. van Ruitenbeek (1992) Instelbare puntcontacten en tunneljuncties over subatomaire afstanden., Ned. Tijdschrift v. Natuurkunde , 58.
C.J. Muller, J.M. van Ruitenbeek and L.J. de Jongh (1992) Conductance and supercurrent discontinuities in atomic scale metallic constrictions of variable width., Phys. Rev. Lett. , 69.
[pdf]
C.J. Muller, J.M. van Ruitenbeek and L.J. de Jongh (1992) Experimental observation of the transition from weak link to tunnel junction., Physica C , 191, 485-504.
[pdf]
A.P. Volodin, J. Aarts, I.V. Falkovsky and M.V. Fistul (1992) Sharp anomalies in the point-contact spectra of Bi2212 investigated with an adjustable point contact, Physica C, 201, 426.
W. Maj, K.-J. de Korver, P. Koorevaar and J. Aarts (1992) Critical currents as a probe for the phase diagram of Nb/NbZr multilayers, Superc. Sci. and Techn., 5, S483.
H. Douwes, T. Hatano and J. Aarts (1992) Critical temperatures and critical currents in sputtered thin films of Bi-Sr-Ca-Cu-O with varying O-concentration, Superc. Sci. and Techn., 5, S220.

1991
KLEINHERENBRINK, FAM, AARTSMA, TJ, AMESZ, J (1991) CHARGE SEPARATION AND FORMATION OF BACTERIOCHLOROPHYLL TRIPLETS IN, BIOCHIMICA ET BIOPHYSICA ACTA, 1057, 346-352.
[DOI]
DEINUM, G, KRAMER, H, AARTSMA, TJ, KLEINHERENBRINK, FAM, AMESZ, J (1991) FLUORESCENCE QUENCHING IN HELIOBACTERIUM-CHLORUM BY REACTION CENTERS IN, BIOCHIMICA ET BIOPHYSICA ACTA, 1058, 339-344.
[DOI]
DEINUM, G, OTTE, SCM, GARDINER, AT, AARTSMA, TJ, COGDELL, RJ, AMESZ, J (1991) ANTENNA ORGANIZATION OF RHODOPSEUDOMONAS-ACIDOPHILA - A STUDY OF THE, BIOCHIMICA ET BIOPHYSICA ACTA, 1060, 125-131.
[DOI]
J.M. van Ruitenbeek and D.A. van Leeuwen (1991) Model calculation of size effects in orbital magnetism., Phys. Rev. Lett. , 67.
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W. Maj and J. Aarts (1991) Outer layers determine the parallel critical field of a superconducting multilayer, Phys. Rev. B , 44, 7745.
J. Aarts, W. Maj, K.-J. de Korver, P. Koorevaar and P.H.Kes (1991) The crucial effect of the outer layers on the critical fields of Nb/NbZr-type superconducting superlattices, Physica C, 185-189, 2071.

1990
VANKAN, PJM, OTTE, SCM, KLEINHERENBRINK, FAM, NIEVEEN, MC, AARTSMA, TJ, VANGORKOM, HJ (1990) TIME-RESOLVED SPECTROSCOPY AT 10K OF THE PHOTOSYSTEM-II REACTION CENTER, BIOCHIMICA ET BIOPHYSICA ACTA, 1020, 146-152.
[DOI]
P.H. Kes, J. Aarts, V.M. Vinokur and C.J. v.d. Beek (1990) Dissipation in highly anisotropic superconductors, Phys. Rev. Lett. , 64, 1063.
J. Aarts, J. Meiresonne, H. Sprey and W. Maj (1990) Proximity effect in superconducting bilayers and multilayers, Phys. Rev. B , 41, 4739.
J. Aarts, K.-J. de Korver and P.H. Kes (1990) Dimensionality crossovers in the parallel critical fields of Nb/Nb0.6Zr0.4 multilayers, Europhys. Lett. , 12, 447 .
P. Koorevaar, J. Aarts, P. Berghuis, and P.H. Kes (1990) Tilt-modulus enhancement of the vortex lattice in thelayered superconductor 2H-NbSe2, Phys. Rev. B , 42, 1004.

1989
VANKAN, PJM, AARTSMA, TJ, AMESZ, J (1989) PRIMARY PHOTOSYNTHETIC PROCESSES IN HELIOBACTERIUM-CHLORUM AT 15-K, PHOTOSYNTHESIS RESEARCH, 22, 61-68.
DEINUM, G, AARTSMA, TJ, VANGRONDELLE, R, AMESZ, J (1989) SINGLET-SINGLET EXCITATION ANNIHILATION MEASUREMENTS ON THE ANTENNA OF, BIOCHIMICA ET BIOPHYSICA ACTA, 976, 63-69.
[DOI]
ROTOMSKIS, R, VANDEMEENT, EJ, AARTSMA, TJ, HOFF, AJ (1989) FLUORESCENCE-SPECTRA OF HEMATOPORPHYRIN AND HEMATOPORPHYRIN-DIACETATE, JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 3, 369-377.
[DOI]
A.-J. Hoeven, J. Aarts and P.K. Larsen (1989) Diffusion of Si into Ge studied by core level photoemission, J. Vac. Sci. Tech. A , 7, 5.
G.N.A. v.Veen, R.P. v.Ingen, T.S. Baller, J. Aarts, Guo Shu-Quan, C.F.J. Flipse, J.G. Lensink, C.W. Hagen and R. Griessen (1989) Properties of Bi-Sr-Ca-Cu oxide films produced by laser ablation deposition, Physica C, 157, 99.
P.H. Kes, J. Aarts, J. v.d.Berg, C.J. v.d.Beek, J.A. Mydosh (1989) Thermally assisted flux flow at small driving forces, Supercond. Sci. Tech., 1, 242.

1988
J. Aarts, A.-J. Hoeven and P.K. Larsen (1988) Crystal growth of Ge studied by reflection high-energy electron diffraction and photoemission, J. Vac. Sci. Technol. A , 6, 607.
J. Aarts, A.-J. Hoeven and P.K. Larsen (1988) Electronic structure of the Ge(111)-c(2x8) surface, Phys. Rev. B , 37, 8190.
J. Aarts, A.-J. Hoeven and P.K. Larsen (1988) Core-level study of the phase transition on the Ge(111)-c(2x8) surface, Phys. Rev. B , 38, 3925.
J. Aarts and P.K. Larsen (1988) RHEED studies of growing Ge and Si surfaces, NATO ASI Series volume B188, eds. P.K. Larsen and P.J. Dobson, Plenum Press.
A.-J. Hoeven, J.S.C. Kools, J. Aarts and P.C. Zalm (1988) Temperature dependence of the surface disorder on Ge(001) due to Ar-ion bombardment, in "Reflection High-Energy Electron Diffraction and reflection imaging of surfaces", NATO ASI Series volume B188, eds. P.K. Larsen and P.J. Dobson, Plenum Press.

1987
DZUGAN, TP, AARTSMA, TJ (1987) A CONTINUOUS, PUMPLESS FLOW CELL FOR INERT-GAS-PROTECTED SPECTROSCOPIC, APPLIED SPECTROSCOPY, 41, 1260-1261.
[DOI]
J. Aarts and P.K. Larsen (1987) Monolayer and bilayer growth on Ge(111) and Si(111), Su.Sci. , 188, 391.

1986
DZUGAN, TP, SCHMIDT, J, AARTSMA, TJ (1986) ON THE GROUND-STATE TAUTOMERIZATION OF 3-HYDROXYFLAVONE, CHEMICAL PHYSICS LETTERS, 127, 336-342.
[DOI]
MCMORROW, D, AARTSMA, TJ (1986) SOLVENT-MEDIATED PROTON-TRANSFER THE ROLES OF SOLVENT STRUCTURE AND, CHEMICAL PHYSICS LETTERS, 125, 581-585.
[DOI]
CHOU, P, AARTSMA, TJ (1986) THE PROTON-TRANSFER LASER - DUAL WAVELENGTH LASING ACTION IN BINARY DYE, JOURNAL OF PHYSICAL CHEMISTRY, 90, 721-723.
[DOI]
P.A. Veenhuizen, G. v. Kalkeren, J.C.P. Klaasse, A. Menovsky, A.C. Moleman, F.R. de Boer, J. Aarts (1986) On the intrinsic susceptibility of IV systems, Journ. Magn. Magn. Mat. , 54-57, 425.
J. Aarts, W. Gerits, P.K. Larsen (1986) Observations on intensity oscillations in reflection high energy electron diffraction during epitaxial growth of Si(100)and Ge(100), Appl. Phys. Lett. , 48, 931.

1985
J. Aarts, F.R. de Boer, P.F. de Chatel (1985) Consequences of an electron-phonon bound state for magnetization and susceptibility in CeAl2, Journ. Magn. Magn. Mat. , 49, 271.
J. Aarts, F.R. de Boer, P.F. de Chatel, A. Menovsky (1985) The magnetic behaviour of CePd3 at low temperatures, Sol. St. Comm. , 56, 623.

1984
MCMORROW, D, DZUGAN, TP, AARTSMA, TJ (1984) EXCITED-STATE DYNAMICS OF THE INTRAMOLECULAR PROTON-TRANSFER OF, CHEMICAL PHYSICS LETTERS, 103, 492-496.
[DOI]
CHOU, P, MCMORROW, D, AARTSMA, TJ, KASHA, M (1984) THE PROTON-TRANSFER LASER - GAIN SPECTRUM AND AMPLIFICATION OF, JOURNAL OF PHYSICAL CHEMISTRY, 88, 4596-4599.
[DOI]
D.E. Maclaughlin, Cheng Tien, L.C. Gupta, J. Aarts, F.R. de Boer, Z. Fisk (1984) Nuclear Quadrupole Resonance and heavy fermion superconductivity in CeCu2Si2, Phys. Rev. B , 30, 1577.

1983
J. Aarts, F.R. de Boer, D.E. MacLaughlin (1983) Nuclear magnetic resonance and relaxation in the paramagnetic state of CeCu2Si2, Physica B+C, 121, 162.

1982
AARTSMA, TJ, GOUTERMAN, M, JOCHUM, C, KWIRAM, AL, PEPICH, BV, WILLIAMS, LD (1982) PORPHYRINS .43. TRIPLET SUBLEVEL EMISSION OF PLATINUM, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 104, 6278-6283.
[DOI]
U. Rauchschwalbe, W. Lieke, C.D. Bredl, F. Steglich, J. Aarts, K.M. Martini, A.C. Mota (1982) Critical fields of the heavy fermion superconductor CeCu2Si2, Phys. Rev. Lett. , 49, 1448.

1981
J. Aarts, F.R. de Boer, S. Horn, F. Steglich (1981) High field magnetization of CeAl2 and (Ce,La)Al2, Physica B+C, 107, 381.

1980
AARTSMA, TJ, HESSELINK, WH, WIERSMA, DA (1980) RESONANT CARS SPECTROSCOPY OF S-TETRAZINE VAPOR, CHEMICAL PHYSICS LETTERS, 71, 424-428.
[DOI]
J. Aarts, W. Felsch, H. von Loehneisen, F. Steglich (1980) Frequency dependence of the freezing temperature in spin glasses : a comparative study of (La,Gd)B6, (Y,Gd)Al2 and (La,Gd)Al2, Z. Phys. B , 40, 127.

1979
F. Steglich, J. Aarts, C.D. Bredl, W. Lieke, D. Meschede, W. Franz, H. Schaefer (1979) Superconductivity in the presence of strong Pauli paramagnetism : CeCu2Si2, Phys. Rev. Lett., 43, 1892.

1978
AARTSMA, TJ, WIERSMA, DA (1978) PHOTON-ECHO DECAY OF NAPHTHALENE IN DURENE AND PERDEUTERO-NAPHTHALENE, CHEMICAL PHYSICS LETTERS, 54, 415-419.
[DOI]

1977
MORSINK, JBW, AARTSMA, TJ, WIERSMA, DA (1977) PHOTON-ECHO RELAXATION MEASUREMENTS WITH 2 DYE-LASERS - APPLICATION TO, CHEMICAL PHYSICS LETTERS, 49, 34-38.
[DOI]
AARTSMA, TJ, MORSINK, J, WIERSMA, DA (1977) OPTICAL-PHASE RELAXATION AT LOW-TEMPERATURE IN LOWEST 1B2U]-1A1G, CHEMICAL PHYSICS LETTERS, 47, 425-428.
[DOI]
P.F. de Chatel, J. Aarts, J.C.P. Klaasse (1977) Model calculation of the magnetic behaviour of mixed- valence systems, Comm. on Phys. , 2, 151.

1976
AARTSMA, TJ, WIERSMA, DA (1976) PHOTON-ECHO RELAXATION IN MOLECULAR MIXED CRYSTALS, CHEMICAL PHYSICS LETTERS, 42, 520-524.
[DOI]
AARTSMA, TJ, WIERSMA, DA (1976) COHERENT OPTICAL PHENOMENA IN ORGANIC MIXED CRYSTALS, OPTICS COMMUNICATIONS, 18, 201-202.
[DOI]
AARTSMA, TJ, WIERSMA, DA (1976) PHOTON-ECHO SPECTROSCOPY OF ORGANIC MIXED CRYSTALS, PHYSICAL REVIEW LETTERS, 36, 1360-1362.
[DOI]

1973
Aartsma, TJ, Wiersma, DA (1973) Stark and Zeeman effects on the lower electronic states of s-triazine, CHEMICAL PHYSICS, 1, 211-216.
[DOI]

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