LaserLaB - Molecular Biophysics

Research Output 1999 2019

2014

Scale-Dependent Nonaffine Elasticity of Semiflexible Polymer Networks

Atakhorrami, M., Koenderink, G. H., Palierne, J. F., MacKintosh, F. C. & Schmidt, C. F., 2014, In : Physical Review Letters. 112, 8, 088101.

Research output: Contribution to JournalArticleAcademicpeer-review

elastic properties
polymers
filaments
rigidity
organelles

Self-assembly and characterization of small and monodisperse dye nanospheres in a protein cage

Luque, D., Snijder, J., Brasch, M., Burnley, R. J., Koay, M. S. T., Carrascosa, J. L., Wuite, G. J. L., Roos, W. H., Heck, A. J. R., Cornelissen, J. L. M., Torres, C. & Caston, J. R., 2014, In : Chemical Science. 5, p. 575-581

Research output: Contribution to JournalArticleAcademicpeer-review

Nanospheres
Self assembly
Coloring Agents
Viruses
Proteins

smAP: Manipulating DNA by Ultrasound - Single-Molecules Go Acoustic

Sitters, G., Kamsma, D., Peterman, E. J. G. & Wuite, G. J. L., 2014, In : Biophysical Journal. 106, 2, p. 387A-387A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Temporal Focusing, Line and Point-Scanning Two-Photon Fluorescence Microscopy for In Vivo Imaging: A Comparative Study of Signal Levels and Bleaching Rates

Girard, J. J. & Peterman, E. J. G., 2014, In : Biophysical Journal. 106, 2, p. 603A-604A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

The cost of being right: DNA replication in optical tweezers

Hoekstra, T. P., 2014

Research output: PhD ThesisPhD Thesis - Research external, graduation VUAcademic

Open Access
File

The role of the cytoskeleton in sensing changes in gravity by nonspecialized cells

Vorselen, D., Roos, W. H., MacKintosh, F. C., Wuite, G. J. L. & van Loon, J. J. W. A., 2014, In : FASEB Journal. 28, 2, p. 536-547

Research output: Contribution to JournalArticleAcademicpeer-review

Gravitation
Cytoskeleton
Space Flight
Altered Gravity
Biophysics

Ultra-responsive soft matter from strain-stiffening hydrogels

Jaspers, M., Dennison, M., Mabesoone, M. F. J., MacKintosh, F. C., Rowan, A. E. & Kouwer, P. H. J., 2014, In : Nature Communications. 5, 5808.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
stiffening
Hydrogels
Gels
gels
Stiffness

Visualization and quantification of nascent RAD51 filament formation at single-monomer resolution

Candelli, A., Holpthausen, J. T., Depken, M., Brouwer, I., Franker, M. A. M. L., Marchetti, M., Heller, I., Bernard, S., Garcin, E. B., Modesti, M., Wyman, C., Wuite, G. J. L. & Peterman, E. J. G., 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 2014, 111, p. 15090-15095

Research output: Contribution to JournalArticleAcademicpeer-review

Single-Stranded DNA
Visualization
Monomers
Optical tweezers
Accessories
2013

A computational study of robust formation of spatial protein patterns

Sokolowski, T. R., 2013

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Analytical approximation for chemical potential in organic materials with Gaussian density of states

Sharma, A. & Sheinman, M., 2013, In : Journal of Physics D: Applied Physics. 46, 12, p. 125106 125106.

Research output: Contribution to JournalArticleAcademicpeer-review

Chemical potential
organic materials
approximation
Carrier mobility
carrier mobility

A place for time: the spatiotemporal structure of neural dynamics during natural audition

Stephens, G. J., Honey, C. J. & Hasson, U., 2013, In : Journal of Neurophysiology. 110, 9, p. 2019-2026

Research output: Contribution to JournalArticleAcademicpeer-review

Hearing
Magnetic Resonance Imaging
Auditory Cortex
Brain
Automatic Data Processing

A toolbox for generating single-stranded DNA in optical tweezers experiments

Candelli, A., Hoekstra, T. P., Farge, G. A., Gross, P., Peterman, E. J. G. & Wuite, G. J. L., 2013, In : Biopolymers. 99, 9, p. 611-620 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Optical Tweezers
Optical tweezers
Single-Stranded DNA
DNA
Molecules

Biological Polymers: Confined, Bent, and Driven

Alvarado, J., 2013

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Design and implementation of a bacterial signaling circuit

Lazova, M. D., 2013

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Dynamical behavior of disordered spring networks

Yucht, M. G. & Sheinman, M., 2013, In : Soft Matter. 9, 29, p. 7000-7006

Research output: Contribution to JournalArticleAcademicpeer-review

Rheology
rheology
display devices
Dilution
dilution

Dynamics and Structural Transitions in Rad51-Single-Stranded DNA Complexes

Brouwer, I., Candelli, A., Bernard, S., Modesti, M., Peterman, E. J. G. & Wuite, G. J. L., 2013, In : Biophysical Journal. 104, 2, p. 75A-75A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Elastic response of filamentous networks with compliant crosslinks

Sharma, A., Sheinman, M., Heidemann, M. & Mac Kintosh, F. C., 2013, In : Physical Review E. 88, 5, 052705.

Research output: Contribution to JournalArticleAcademicpeer-review

Elastic Modulus
Filament
modulus of elasticity
filaments
Finite Strain

Fluctuation-Stabilized Marginal Networks and Anomalous Entropic Elasticity

Dennison, M., Sheinman, M., Storm, C. & Mac Kintosh, F. C., 2013, In : Physical Review Letters. 111, 9, p. 095503 095503.

Research output: Contribution to JournalArticleAcademicpeer-review

elastic properties
rigidity
shear
temperature

Integrin and defensin modulate the mechanical properties of adenovirus

Snijder, J., Reddy, V. S., May, E. R., Roos, W. H., Nemerow, G. R. & Wuite, G. J. L., 2013, In : Journal of Virology. 87, 5, p. 2756-2766

Research output: Contribution to JournalArticleAcademicpeer-review

Defensins
Capsid
integrins
Adenoviridae
alpha-Defensins

Kinesins in Caenorhabditis Elegans Chemosensory Cilia Relay to Drive Intracellular Transport

Prevo, B., Mangeol, P. J. J., Oswald, F., Scholey, J. M. & Peterman, E. J. G., 2013, In : Biophysical Journal. 104, 2, p. 652A-652A 1 p.

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Molecular motors robustly drive active gels to a critically connected state

Alvarado, J., Sheinman, M., Sharma, A. & Mac Kintosh, F. C., 2013, In : Nature Physics. 9, 9, p. 591-597

Research output: Contribution to JournalArticleAcademicpeer-review

gels
contraction
myosins
polymers
metabolism

Myosin Activity Drives Cytoskeletal Networks to a Critically Connected State

Alvarado, J., Sheinman, M., Sharma, A. & Mac Kintosh, F. C., 2013, In : Biophysical Journal. 104, 2, p. 550A-550A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Nonlinear Elasticity: From Single Chain to Networks and Gels

Carillo, J. M. Y., MacKintosh, F. C. & Dobrynin, A. V., 2013, In : Macromolecules. 46, 9, p. 3679-3692

Research output: Contribution to JournalArticleAcademicpeer-review

Elasticity
Gels
Molecular dynamics
Elongation
Elastic moduli

Optical apparatus for multiple points of view three-dimensional microscopy and method

Mangeol, P. J. J. & Peterman, E. J. G., 2013

Research output: PatentOther research output

Open Access
File

Phase diagram of hard asymmetric dumbbell particles

Milinkovic, K. & Dennison, M., 2013, In : Physical Review E. 87, 3, p. 032128 032128.

Research output: Contribution to JournalArticleAcademicpeer-review

Phase Diagram
phase diagrams
free energy
fluids
Range of data

Physical Mechanisms of DNA repair: A single molecule perspective

Candelli, A., 2013

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

PICH: A DNA Translocase Essential for Resolving Anaphase Bridged DNA

Biebricher, A. S., Hirano, S., Enzlin, J., Peterman, E. J. G., Hickson, I. & Wuite, G. J. L., 2013, In : Biophysical Journal. 104, 2, p. 540A-540A 1 p.

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

PICH: a DNA translocase specially adapted for processing anaphase bridge DNA

Biebricher, A. S., Hirano, S., Enzlin, J., Wiechens, N., Streicher, W. W., Huttner, D., Wang, L. H. C., Nigg, E. A., Owen-Hughes, T., Liu, Y., Peterman, E. J. G., Wuite, G. J. L. & Hickson, I. D., 2013, In : Molecular Cell. 51, 5, p. 691-701

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
DNA Helicases
Anaphase
DNA
Optical Tweezers
Nucleic Acid Denaturation

Probing the biophysical interplay between a viral genome and its capsid

Snijder, J., Uetrecht, C., Rose, R. J., Sanchez-Eugenia, R., Marti, G. A., Agirre, J., Guérin, D. M. A., Wuite, G. J. L., Heck, A. J. R. & Roos, W. H., 2013, In : Nature Chemistry. 5, 6, p. 502-509 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Genes
Viruses
Proteins
Mass spectrometry
Life cycle

RAD51-Nucleoprotein Filament Assembly Quantified at the Single-Molecule Level

Candelli, A., Holhausen, J. T., Depken, S. M., Franker, M. M., Maman, J., Pellegrini, E., Modesti, M., Wyman, C., Wuite, G. J. L. & Peterman, E. J. G., 2013, In : Biophysical Journal. 104, 2, p. 369A-369A 1 p.

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access
Fluorescence Microscopy
Freezing
DNA
Mechanics
Base Pairing

Revealing the Competition between Peeled-Ssdna, Melting Bubbles and S-DNA during DNA Overstretching using Fluorescence Microscopy

King, G. A., Gross, P., Bockelmann, U., Modesti, M., Wuite, G. J. L. & Peterman, E. J. G., 29 Jan 2013, In : Biophysical Journal. 104, 2, p. 262A - 262A 1 p.

Research output: Contribution to JournalMeeting AbstractAcademic

Open Access
Fluorescence Microscopy
Freezing
DNA
Base Pairing
AT Rich Sequence

Role of Mechanical Properties of Cell Mediated Vesicles in Membrane Fusion

Vorselen, D., Roos, W. H., van Loon, J. J. W. A. & Wuite, G. J. L., 2013, In : Biophysical Journal. 104, 2, p. 620A-620A 1 p.

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Single-molecule views on homologous recombination.

Candelli, A., Modesti, M., Peterman, E. J. G. & Wuite, G. J. L., 2013, In : Quarterly Reviews of Biophysics. 46, 4, p. 323-348

Research output: Contribution to JournalArticleAcademicpeer-review

Homologous Recombination
Recombinational DNA Repair
Recombinases
Nucleoproteins
Single-Stranded DNA

Statistical Thermodynamics of Natural Images

Stephens, G. J., Mora, T., Tkacik, G. & Bialek, W., 2013, In : Physical Review Letters. 110, 1, 018701.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
thermodynamics
statistical mechanics
invariance
critical point
pixels

STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA

Heller, I., Sitters, G., Broekmans, O. D., Farge, G. A., Menges, C., Wende, W., Hell, S. W., Peterman, E. J. G. & Wuite, G. J. L., 2013, In : Nature Methods. 10, 9, p. 910-U132

Research output: Contribution to JournalArticleAcademicpeer-review

Optical Tweezers
Optical tweezers
Stimulated emission
DNA
Proteins

STED Nanoscopy Combined with Optical Tweezers Reveals Spatial Dynamics of Proteins on Densely Covered DNA

Sitters, G., Heller, I., Broekmans, O. D., Farge, G. A., Menges, C., Wende, W., Hell, S. W., Peterman, E. J. G. & Wuite, G. J. L., 2013, In : Biophysical Journal. 104, 2, p. 210A-211

Research output: Contribution to JournalArticleAcademic

Open Access

Stress-Enhanced Gelation: A Dynamic Nonlinearity of Elasticity

Yao, N. Y., Broedersz, C. P., Depken, S. M., Becker, D. J., Pollak, M. R., MacKintosh, F. C. & Weitz, D. A., 2013, In : Physical Review Letters. 110, 1, 018103.

Research output: Contribution to JournalArticleAcademicpeer-review

gelation
elastic properties
biopolymers
nonlinearity
stiffening

Structural Transitions and Energy Landscape for Cowpea Chlorotic Mottle Virus Capsid Mechanics from Nanomanipulation in Vitro and in Silico

Kononova, O., Snijder, S., Brasch, M., Cornelissen, J., Dima, R. I., Marx, K. A., Wuite, G. J. L., Roos, W. H. & Barsegov, V., 2013, In : Biophysical Journal. 105, 8, p. 1893-1903

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Bromovirus
Capsid
Mechanics
Computer Simulation
Virus Assembly
2012

. Cognitive alterations in patients with non-affective psychotic disorder and their unaffected siblings and parents

Meijer, J. H., Simons, C. J. P., Quee, P. J. & Verweij, K., 2012, In : Acta psychiatrica scandinavica. 125, 1, p. 66-76

Research output: Contribution to JournalArticleAcademicpeer-review

Psychotic Disorders
Siblings
Parents
Verbal Learning
Short-Term Memory

A biophysical exploration of proteins and their substrates

Laurens, N., 2012

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Active diffusion: The erratic dance of chromosomal loci

MacKintosh, F. C., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 19, p. 7138-7139

Research output: Contribution to JournalArticleAcademicpeer-review

Actively Stressed Marginal Networks

Sheinman, M., Broedersz, C. P. & MacKintosh, F. C., 2012, In : Physical Review Letters. 109, 23, 238101.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
scaling
stiffness
elastic properties
magnetic permeability
fibers

Alba shapes the archaeal genome using a delicate balance of bridging and stiffening the DNA

Laurens, N., Driessen, R. P. C., Heller, I., Vorselen, D., Noom, M. C., Hol, F. J. H., White, M. F., Dame, R. T. & Wuite, G. J. L., 2012, In : Nature Communications. 3, 1328.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Archaeal Genome
stiffening
genome
deoxyribonucleic acid
Genes

Automated Tracking of Animal Posture and Movement during Exploration and Sensory Orientation Behaviors

Gomez-Marin, A., Partoune, N., Stephens, G. J. & Louis, M., 2012, In : PLoS ONE. 7, 8, e41642.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
posture
Posture
Animals
Software
animals

C. elegans Tracking and Behavioral Measurement

Likitlersuang, J., Stephens, G. J., Palanski, K. & Ryu, W. S. C., 2012, In : Journal of Visualized Experiments. 69, e4094.

Research output: Contribution to JournalArticleAcademicpeer-review

Classes of fast and specific search mechanisms for proteins on DNA

Sheinman, M., Benichou, O., Kafri, Y. & Voituriez, R., 2012, In : Reports on Progress in Physics. 75, 2, p. 026601

Research output: Contribution to JournalArticleAcademicpeer-review

deoxyribonucleic acid
proteins
thrust
discrimination
interactions

Dimensionality of charge transport in organic field-effect transistors

Sharma, A., van Oost, F. W. A., Kemerink, M. & Robbert, P. A., 2012, In : Physical Review B (Condensed Matter and Materials Physics). 85, 23, p. 235302

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Organic field effect transistors
Charge transfer
Semiconducting organic compounds
field effect transistors
Coulomb interactions

DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

Rusling, D. A., Laurens, N., Pernstich, C., Brouwer, I., Wuite, G. J. L. & Halford, S. E., 2012, In : Nucleic Acids Research. 40, 11, p. 4977-4987 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Synapses
DNA
DNA Restriction Enzymes
Enzymes