LaserLaB - Molecular Biophysics

Research Output 1999 2019

2015

DNA-Induced Viral Assembly Studied in Real-Time by Optical Tweezers, Acoustic Force Spectroscopy and Atomic Force Microscopy

van Rosmalen, M. G. M., Biebricher, A. S., Kamsma, D., Zlotnick, A., Wuite, G. J. L. & Roos, W. H., 2015, In : Biophysical Journal. 108, 2, p. 170A-170A

Research output: Contribution to JournalMeeting AbstractOther research output

DNA Translocations in Real-Time: Insights into Non-Homologous End Joining Pathway

Candelli, A., Brouwer, I., Sitters, G., Heerema, S., Modesti, M., Peterman, E. J. G. & Wuite, G. J. L., 2015, In : Biophysical Journal. 108, 2, p. 507A-507A

Research output: Contribution to JournalMeeting AbstractOther research output

Driven diffusive systems with mutually interactive Langmuir kinetics

Vuijk, H. D., Rens, R., Vahabi, M., MacKintosh, F. C. & Sharma, A., 2015, In : Physical Review E. 91, 3, p. 032143 032143.

Research output: Contribution to JournalArticleAcademicpeer-review

Driven Diffusive Systems
Kinetics
kinetics
Asymmetric Exclusion Process
Mean Field Equation

Effect of levosimendan on the contractility of muscle fibers from nemaline myopathy patients with mutations in the nebulin gene

de Winter, J. M., Joureau, B., Sequeira Oliveira, V., Clarke, N. F., van der Velden, J., Stienen, G. J. M., Granzier, H., Beggs, A. H. & Ottenheijm, C. A. C., 2015, In : Skeletal Muscle. 5, 12.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Nemaline Myopathies
Muscles
Mutation
Slow-Twitch Muscle Fibers
Troponin C

Functional differentiation of cooperating kinesin-2 motors orchestrates cargo import and transport in C. elegans cilia

Prevo, B., Mangeol, P., Oswald, F., Scholey, J. M. & Peterman, E. J. G., 2015, In : Nature Cell Biology. 17, 12, p. 1536-1545

Research output: Contribution to JournalArticleAcademicpeer-review

Kinesin
Cilia
Axoneme
Caenorhabditis elegans
Recycling

Grab & Watch: Correlative Optical Tweezers-Fluorescence Microscopy (CTFM) as a Versatile Tool for Biological Studies

Wuite, G. J. L. & Peterman, E. J. G., 2015, In : Biophysical Journal. 108, 2, p. 166A-166A

Research output: Contribution to JournalMeeting AbstractOther research output

Implications of ADP-Stimulated Cross-Bridge Cycling for Diastolic and Systolic Heart Failure

Sequeira Oliveira, V., dos Remedios, C., Stienen, G. J. M. & van der Velden, J., 2015, In : Biophysical Journal. 108, 2, p. 199A-200A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Inherently unstable networks collapse to a critical point

Sheinman, M., Sharma, A., Alvarado, J., Koenderink, G. H. & MacKintosh, F. C., 2015, In : Physical Review E. 92, 1, p. 012710 012710.

Research output: Contribution to JournalArticleAcademicpeer-review

Critical point
critical point
Collapsing
Unstable
Nonequilibrium Systems

Kinesin Illuminated

Prevo, B., 2015

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

Open Access
File
Kinesin

Material properties of viral nanocages explored by atomic force microscopy

van Rosmalen, M. G. M., Roos, W. H. & Wuite, G. J. L., 2015, In : Methods in Molecular Biology. 1252, p. 115-137

Research output: Contribution to JournalArticleAcademicpeer-review

Atomic Force Microscopy
Capsid
Product Packaging
Diagnostic Imaging
Life Cycle Stages

Mechanics of Extracellular Vesicles from Red Blood Cells

Vorselen, D., Dommelen, S. M., van Loon, J. J. W. A., Schiffelers, R. M., Roos, W. H. & Wuite, G. J. L., 2015, In : Biophysical Journal. 108, 2, p. 242A-242A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Membrane-Protein Diffusion in E. coli: A Random Walk in a Heterogeneous Landscape

Varadarajan, A., Oswald, F., Bollen, Y. J. M. & Peterman, E. J. G., 2015, In : Biophysical Journal. 108, 2, p. 323A-323A

Research output: Contribution to JournalMeeting AbstractOther research output

Nonthermal fluctuations of the mitotic spindle

Smith, K., Griffin, B., Byrd, H., MacKintosh, F. C. & Kilfoil, M. L., 2015, In : Soft Matter. 11, 22, p. 4396-4401

Research output: Contribution to JournalArticleAcademicpeer-review

spindles
Yeast
Cells
nuclei
DNA

Pathomechanisms in heart failure: the contractile connection

Stienen, G. J. M., 2015, In : Journal of Muscle Research and Cell Motility. 36, 1, p. 47-60

Research output: Contribution to JournalArticleAcademicpeer-review

Heart Failure
Diastolic Heart Failure
Connectin
Systolic Heart Failure
Calcium

Probing the blueprint of life: The development and application of novel single molecule methods

Sitters, G., 2015

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

Open Access
File

Quadriceps muscle fibre dysfunction in patients with pulmonary arterial hypertension

Manders, E., Ruiter, G., Bogaard, H. J., Stienen, G. J. M., Vonk Noordegraaf, A., de Man, F. S. & Ottenheijm, C. A. C., 2015, In : European Respiratory Journal. 45, 6, p. 1737-1740

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Quantification of IFT-Dynein Dynamics in C. elegans

Mijalkovic, J., Prevo, B., Oswald, F., Mangeol, P. J. J. & Peterman, E. J. G., 2015, In : Biophysical Journal. 108, 2, p. 134A-134A

Research output: Contribution to JournalArticleAcademic

Rapid changes in NADH and flavin autofluorescence in rat cardiac trabeculae reveal large mitochondrial complex II reserve capacity

Wüst, R. C. I., Helmes, M. H. B. & Stienen, G. J. M., 2015, In : Journal of Physiology - London. 593, 8, p. 1829-1840

Research output: Contribution to JournalArticleAcademicpeer-review

NAD
Flavin-Adenine Dinucleotide
Saponins
4,6-dinitro-o-cresol
Mitochondria

Resolving the Kinetic States of a Proofreading DNA Polymerase

Lin, S., Cabanas Danes, J., Hoekstra, T. P., Kamsma, D., Sitters, G., Depken, S. M., Dame, R. T. & Wuite, G. J. L., 2015, In : Biophysical Journal. 108, 2, p. 70A-70A

Research output: Contribution to JournalMeeting AbstractOther research output

Small steps and giant leaps

Prevo, B. & Peterman, E. J. G., 2015, In : eLife. 4, p. e08366 e08366.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Kinesin
Microtubules
Proteins

Stability and anomalous entropic elasticity of subisostatic random-bond networks

Wigbers, M. C., Mac Kintosh, F. C. & Dennison, M., 2015, In : Physical Review E. 92, p. 042145

Research output: Contribution to JournalArticleAcademicpeer-review

Anomalous
Elasticity
elastic properties
Modulus
rigidity

Stress controls the mechanics of collagen networks

Licup, A. J., Munster, S., Sharma, A., Sheinman, M., Jawerth, L. M., Fabry, B., Weitz, D. A. & MacKintosh, F. C., 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 31, p. 9573-9578

Research output: Contribution to JournalArticleAcademicpeer-review

collagens
synthetic fibers
stress-strain relationships
connective tissue
stiffening

Synergistic role of ADP and Ca2+ in diastolic myocardial stiffness

Sequeira Oliveira, V., Najafi, A., McConnell, M., Fowler, E. D., Bollen, A. E., Wüst, R. C. I., dos Remedios, C., Helmes, M. H. B., White, E., Stienen, G. J. M., Tardiff, J., Kuster, D. W. D. & van der Velden, J., 2015, In : Journal of Physiology - London. 593, 17, p. 3899-3916

Research output: Contribution to JournalArticleAcademicpeer-review

Adenosine Diphosphate
Cardiac Myocytes
Creatine Kinase
Membranes
Diastolic Heart Failure

Tension-Dependent Stability of Torsionally Constrained DNA: Melting Precedes Overwinding

King, G. A., Peterman, E. J. G. & Wuite, G. J. L., 2015, In : Biophysical Journal. 108, 2, p. 233A-233A

Research output: Contribution to JournalMeeting AbstractOther research output

The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics

Biebricher, A. S., Heller, I., Roijmans, R. F. H., Hoekstra, T. P., Peterman, E. J. G. & Wuite, G. J. L., 2015, In : Nature Communications. 6, p. 7304 7304.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Intercalating Agents
enzymes
deoxyribonucleic acid
Kinetics
DNA

The phenomenon of simplified scattering from rough surfaces to reflection in fractional space

Safdari, H., Vahabi, M. & Jafari, G., 2015, In : European Physical Journal B. Condensed Matter and Complex Systems. 88, 311, p. 1-6

Research output: Contribution to JournalArticleAcademicpeer-review

Scattering
scattering
wave scattering
Wave functions
integers

The striated muscles in pulmonary arterial hypertension: adaptations beyond the right ventricle

Manders, E., Rain, S., Bogaard, H. J., Handoko, M. L., Stienen, G. J. M., Vonk Noordegraaf, A., Ottenheijm, C. A. C. & de Man, F. S., 2015, In : European Respiratory Journal. 46, 3, p. 832-842

Research output: Contribution to JournalArticleAcademicpeer-review

Striated Muscle
Pulmonary Hypertension
Heart Ventricles
Muscles
Pulmonary Circulation

Unraveling the Interplay between Single-Stranded DNA-Binding Protein, DNA Polymerase and Single-Stranded DNA

Cabanas Danes, J., Hoekstra, T. P., Heller, I., Peterman, E. J. G. & Wuite, G. J. L., 2015, In : Biophysical Journal. 108, 2, p. 67A-67A

Research output: Contribution to JournalMeeting AbstractOther research output

2014

Amyloids: from molecular structure to mechanical properties

Gelderloos, C. C., 2014

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

Open Access
File

Biophysical chemistry: Strength in numbers

King, G. A. & Wuite, G. J. L., 2014, In : Nature Chemistry. 6, 1, p. 13-14

Research output: Contribution to JournalArticleAcademicpeer-review

Cytoplasmic Transport: Bacteria Turn to Glass Unless Kicked

Janmey, P. A. & MacKintosh, F. C., 2014, In : Current Biology. 24, 6, p. R226-R228

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Glass
glass
Bacteria
Cytoplasm
cytoplasm

Cytoskeletal organization in biomimetic liposomes

Tsai, F-C., 2014

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

Open Access
File

Direct Three-Dimensional Imaging with Multiple Point of View Microscopy

Mangeol, P. J. J. & Peterman, E. J. G., 2014, In : Biophysical Journal. 106, 2, p. 203A-203A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Direct Visualization and Quantification of Doc2B-Mediated Membrane Fusion

Brouwer, I., Giniatullina, A., Laurens, N., Groffen, A. J. A. & Wuite, G. J. L., 2014, In : Biophysical Journal. 106, 2, p. 517A-517A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

DNA-Intercalation Kinetics Elucidated by Single-Dye Fluorescence Microscopy and Force Spectroscopy

Biebricher, A. S., Heller, I., Peterman, E. J. G. & Wuite, G. J. L., 2014, In : Biophysical Journal. 106, 2, p. 277A-277A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Effect of Temperature on the Intrinsic Flexibility of DNA and Its Interaction with Architectural Proteins

Driessen, R. P. C., Sitter, G., Moolenaar, G. F., Wuite, G. J. L., Goosen, N. & Dame, R. T., 2014, In : Biochemistry. 2014, 53, p. 6430-6438

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Temperature
DNA
Proteins
Micromanipulation
Chromatin

Efficient fold-change detection based on protein-protein interactions

Buijsman, W. & Sheinman, M., 2014, In : Physical Review E. 89, 2, 022712.

Research output: Contribution to JournalArticleAcademicpeer-review

change detection
Change Detection
Protein-protein Interaction
Fold
proteins

Elasticity of Biomolecules: probing, pushing and pulling using atomic force microscopy

Baclayon, M., 2014, 180 p.

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

Open Access
File

Fiber-based polarization-sensitive OCT of the human retina with correction of system polarization distortions

Braaf, B., Vermeer, K. A., de Groot, M., Vienola, K. V. & de Boer, J. F., 2014, In : Biomedical Optics Express. 5, 8, p. 2736-2758

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
retina
Retina
Nerve Fibers
fibers
Noise

Forster resonance energy transfer and kinesin motor proteins

Prevo, B. & Peterman, E. J. G., 2014, In : Chemical Society Reviews. 43, p. 1144-1155

Research output: Contribution to JournalArticleAcademicpeer-review

Kinesin
Energy transfer
Proteins
Fluorophores
Biomolecules

Friction and Interactions between Bare DNA Molecules: The Role of DNA Handedness

King, G. A., Cortini, R., Lee, D. J., Kornyshev, A. & Wuite, G. J. L., 2014, In : Biophysical Journal. 106, 2, p. 439A-440A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

High-resolution mapping of intracellular fluctuations using carbon nanotubes

Fakhri, N., Wessel, A. D., Willms, C., Pasquali, M., Klopfenstein, D. R., MacKintosh, F. C. & Schmidt, C. F., 2014, In : Science. 344, 6187, p. 1031-1035

Research output: Contribution to JournalArticleAcademicpeer-review

carbon nanotubes
high resolution
cells
myosins
thermal diffusion

Illuminating the Cooperative Action of Kinesin-II and OSM-3-Kinesin in the Chemosensory Cilia of Caenorhabditis Elegans

Prevo, B., Oswald, F., Mangeol, P. J. J., Scholey, J. M. & Peterman, E. J. G., 2014, In : Biophysical Journal. 106, 2, p. 353A-353A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Imaging and quantification of trans-membrane protein diffusion in living bacteria.

Oswald, F., Bank, E., Bollen, Y. J. M. & Peterman, E. J. G., 2014, In : Physical Chemistry Chemical Physics - PCCP. 16, 25, p. 12625-12634

Research output: Contribution to JournalArticleAcademicpeer-review

Membrane Proteins
Bacteria
Fluorescence Microscopy
Thermal Diffusion
Cell Membrane

In Vitro-Reconstituted Nucleoids Can Block Mitochondrial DNA Replication and Transcription

Farge, G. A., Mehmedovic, M., Baclayon, M., Wildenberg, S. M. J. L., Roos, W. H., Gustafsson, C. M., Wuite, G. J. L. & Falkenberg, M., 2014, In : Cell Reports. 2014, 8, p. 66-74

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Transcription
DNA Replication
Mitochondrial DNA
DNA
Nucleic Acid Denaturation

Mobility Analysis of Super-Resolved Proteins on Optically Stretched DNA: Comparing Imaging Techniques and Parameters

Heller, I., Sitters, G., Broekmans, O. D., Biebricher, A. S., Wuite, G. J. L. & Peterman, E. J. G., 2014, In : ChemPhysChem. 15, p. 727-733

Research output: Contribution to JournalArticleAcademicpeer-review

imaging techniques
deoxyribonucleic acid
proteins
Imaging techniques
DNA

Modeling semiflexible polymer networks

Broedersz, C. P. & MacKintosh, F. C., 2014, In : Reviews of Modern Physics. 86, 3, p. 995-1036

Research output: Contribution to JournalArticleAcademicpeer-review

polymers
biopolymers
biology
rigidity
assemblies

Modulated growth, stability and interactions of liquid-like coacervate assemblies of elastin

Muiznieks, L. D., Cirulis, J. T., Reinhardt, D. P., Wuite, G. J. L., Pomes, R. & Keeley, F. W., 2014, In : Matrix Biology. 2014, 36, p. 39-50

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Tropoelastin
Elastin
Peptides
Surface Properties
Elasticity

Optical Tweezers Analysis of DNA-Protein Complexes

Heller, I., Hoekstra, T. P., King, G. A., Peterman, E. J. G. & Wuite, G. J. L., 2014, In : Chemical Reviews. 114, 6, p. 3087-3119

Research output: Contribution to JournalArticleAcademicpeer-review

Optical tweezers
DNA
Proteins
Assays
Molecules

Probing the Stochastic, Motor-Driven Properties of the Cytoplasm Using Force Spectrum Microscopy

Guo, M., Ehrlicher, A. J., Jensen, M. H., Renz, M., Moore, J. R., Goldman, R. D., Lippincott-Schwartz, J., MacKintosh, F. C. & Weitz, D. A., 2014, In : Cell. 158, 4, p. 822-832

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Atomic Force Microscopy
Microscopic examination
Cytoplasm
Physiology
Vimentin