LaserLaB - Molecular Biophysics

Research Output 1999 2019

2011

Phase-stabilized optical frequency domain imaging at 1-mu m for the measurement of blood flow in the human choroid

Braaf, B., Vermeer, K. A., Sicam, V. A. D. P., Zeeburg, E., van Meurs, J. C. & de Boer, J. F., 2011, In : Optics Express. 19, 21, p. 20886-20903 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
blood flow
artifacts
interference
transplantation
epithelium

Polarization-Sensitive Optical Coherence Tomography Imaging of Benign and Malignant Laryngeal Lesions: An In Vivo Study

Burns, J. A., Kim, K. H., de Boer, J. F., Anderson, R. R. & Zeitels, S. M., 2011, In : Otolaryngology and Head and Neck Surgery. 145, 1, p. 91-99

Research output: Contribution to JournalArticleAcademicpeer-review

Vocal Cords
Optical Coherence Tomography
Tongue
Birefringence
Pathology

Polarization-sensitive optical frequency domain imaging based on unpolarized light

Kim, K. H., Park, B. H., Tu, Y. P., Hasan, T., Lee, B., Li, J. & de Boer, J. F., 2011, In : Optics Express. 19, 2, p. 552-561 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
polarization
animal models
cancer
wavelengths
chickens

Prestress strengthens the shell of norwalk virus nanoparticles

Baclayon, M., Shoemaker, G. K., Uetrecht, C., Crawford, S. E., Estes, M. K., Prasad, B. V. V., Heck, A. J. R., Wuite, G. J. L. & Roos, W. H., 2011, In : Nano Letters. 11, 11, p. 4865 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

viruses
Viruses
Nanoparticles
nanoparticles
Mechanical stability

Probing ribosomal protein-RNA interactions with an external force

Mangeol, P. J. J., Bizebard, T., Chiaruttini, C., Dreyfus, M., Springer, M. & Bockelmann, U., 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 45, p. 18272-18276 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Process and apparatus for a wavelength tuning source

de Boer, J. F., Bouma, B. E., Yun, S-H., Oh, W. Y. & Tearney, G. J., 2011

Research output: PatentOther research output

File

Quantifying how DNA stretches, melts and changes twist under tension

Gross, P., Laurens, N., Oddershede, L. B., Bockelmann, U., Peterman, E. J. G. & Wuite, G. J. L., 2011, In : Nature Physics. 7, 9, p. 731-736 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

deoxyribonucleic acid
elastic properties
worms
genome
twisting

Reproducibility of Retinal Nerve Fiber Layer Thickness Measurements Using Spectral Domain Optical Coherence Tomography

Wu, H., de Boer, J. F. & Chen, T. C., 2011, In : Journal of Glaucoma. 20, 8, p. 470-476 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Optical Coherence Tomography
Nerve Fibers
Glaucoma
Nose
Nonparametric Statistics

Searching for simplicity in the analysis of neurons and behavior

Stephens, G. J., Osborne, L. C. & Bialek, W., 13 Sep 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, p. 15565-15571

Research output: Contribution to JournalArticleAcademicpeer-review

Sequence-specific stalling of DNA polymerase gamma and the effects of mutations causing progressive ophthalmoplegia

Atanassova, N., Fuste, J. M., Wanrooij, S., Macao, B., Goffart, S., Backstrom, S., Farge, G. A., Khvorostov, I., Larsson, N. G., Spelbrink, J. N. & Falkenberg, M., 2011, In : Human Molecular Genetics. 20, 6, p. 1212-1223 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Ophthalmoplegia
Mitochondrial DNA
Mutation
Enzymes
Chronic Progressive External Ophthalmoplegia

Single Molecule Analysis, Series Methods in Molecular Biology

Peterman, E. J. G. & Wuite, G. J. L., 2011, New York: Humana Press.

Research output: Book / ReportBookAcademicpeer-review

Single-protein motion on microtubules and in cell membranes

van den Wildenberg, S. M. J. L., 2011, 129 p.

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

Open Access
File

Structure and dynamics of active actin-myosin networks: An in vitro perspective

Soares e Silva, M., 2011, 197 p.

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

Open Access
File

Studying kinesin's enzymatic cycle using a single-motor confocal motility assay, employing Forster resonance energy transfer

Lansky, Z. & Peterman, E. J. G., 2011, In : Methods in Molecular Biology. 778, p. 19-32 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

The DNA double helix challenged by force

Gross, P., 2011

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

Open Access
File

The mitochondrial DNA helicase TWINKLE can assemble on a closed circular template and support initiation of DNA synthesis

Jemt, E., Farge, G. A., Backstrom, S., Holmlund, T., Gustafsson, C. M. & Falkenberg, M., 2011, In : Nucleic Acids Research.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
DNA Helicases
Mitochondrial DNA
DNA
DNA Replication
Circular DNA

Voelen en Vervormen van Virussen

Snijder, J., Wuite, G. J. L. & Roos, W. H., 2011, In : Nederlands Tijdschrift voor Natuurkunde. 77, p. 70-74 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Wide-Range Calibration of Corneal Backscatter Analysis by In Vivo Confocal Microscopy

Hillenaar, T., Sicam, V. A. D. P., Vermeer, K. A., Braaf, B., Remeijer, L., Cals, R. H. H. & de Boer, J. F., 2011, In : Investigative Ophthalmology and Visual Science. 52, 5, p. 2136-2146 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Confocal Microscopy
Calibration
Polymethyl Methacrylate
Light
Cornea
2010

Actieve materialeigenschappen van de levende cel.

Koenderink, G. H. & MacKintosh, F. C., 2010, In : Nederlands Tijdschrift voor Natuurkunde. 76, 5, p. 146

Research output: Contribution to JournalArticleAcademicpeer-review

Actin Filament Length Tunes Elasticity of Flexibly Cross-Linked Actin Networks

Kasza, K. E., Broedersz, C. P., Koenderink, G. H., Lin, Y. C., Messner, W., Nakamura, F., Stossel, T. P., Mac Kintosh, F. C. & Weitz, D. A., 2010, In : Biophysical Journal. 99, 4, p. 1091-1100

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Elasticity
Actin Cytoskeleton
Actins
Filamins
Biopolymers

Active cellular materials

MacKintosh, F. C. & Schmidt, C. F., 2010, In : Current Opinion in Cell Biology. 22, 1, p. 29-35 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Polymerization
Proteins
Theoretical Models
Research

Brownian Motion of Stiff Filaments in a Crowded Environment

Fakhri, N., MacKintosh, F. C., Lounis, B., Cognet, L. & Pasquali, M., 2010, In : Science. 330, 6012, p. 1804-1807

Research output: Contribution to JournalArticleAcademicpeer-review

filaments
carbon nanotubes
stiffness
crowding
thermal diffusion

Combining optical tweezers, single-molecule fluorescence microscopy, and microfluidics for studies of DNA-protein interactions

Gross, P., Farge, G. A., Peterman, E. J. G. & Wuite, G. J. L., 2010, In : Methods in Enzymology. 475, p. 427-453 27 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Optical Tweezers
Optical tweezers
Microfluidics
Fluorescence microscopy
Fluorescence Microscopy

Cross-link governed dynamics of biopolymer networks

Broedersz, C. P., Depken, S. M., Yao, N. Y., Pollak, M. R., Weitz, D. A. & Mac Kintosh, F. C., 2010, In : Physical Review Letters. 105, 23, p. 238101 4 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
biopolymers
stress relaxation
relaxation time
shear
proteins

Diffusive and directional intracellular dynamics measured by field-based dynamic light scattering

Joo, C., Evans, C. L., Stapanic, T., Hasan, T. & de Boer, J. F., 2010, In : Optics Express. 18, 3, p. 2858-2871 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
light scattering
colchicine
adenosine triphosphate
inhibitors
depletion

Divalent Cations Crosslink Vimentin Intermediate Filament Tail Domains to Regulate Network Mechanics

Lin, Y. C., Broedersz, C. P., Rowat, A. C., Wedig, T., Herrmann, H., MacKintosh, F. C. & Weitz, D. A., 2010, In : Journal of Molecular Biology. 399, 4, p. 637-644 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Intermediate Filaments
Divalent Cations
Vimentin
Mechanics
Intermediate Filament Proteins

DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme

Zaremba, M., Lyubchenko, Y. L., Laurens, N., van den Broek, B., Wuite, G. J. L. & Siksnys, V., 2010, In : Nucleic Acids Research. 38, 20, p. 7142-7154 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Chromosome Pairing
DNA
Enzymes
Atomic Force Microscopy

Elasticity in Ionically Cross-Linked Neurofilament Networks

Yao, N. Y., Broedersz, C. P., Lin, Y. C., Kasza, K. E., MacKintosh, F. C. & Weitz, D. A., 2010, In : Biophysical Journal. 98, 10, p. 2147-2153 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Intermediate Filaments
Elasticity
Neurons
Cytoskeleton
Ions

Experimental demonstration of an intensity minimum at the focus of a laser beam created by spatial coherence: application to the optical trapping of dielectric particles

Raghunathan, S. B., van Dijk, T., Peterman, E. J. G. & Visser, T. D., 2010, In : Optics Letters. 35, 24, p. 4166-4168 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
trapping
laser beams
refraction
masks

From Modes to Movement in the Behavior of Caenorhabditis elegans

Stephens, G. J., Johnson-Kerner, B., Bialek, W. & Ryu, W. S., 16 Nov 2010, In : PLoS ONE. 5, 11

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

In vivo 3D human vocal fold imaging with polarization sensitive optical coherence tomography and a MEMS scanning catheter

Kim, K. H., Burns, J. A., Bernstein, J. J., Maguluri, G. N., Park, B. H. & de Boer, J. F., 2010, In : Optics Express. 18, 14, p. 14644-14653 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Measurement of nonlinear rheology of cross-linked biopolymer gels

Broedersz, C. P., Kasza, K. E., Jawerth, L. M., Munster, S., Weitz, D. A. & MacKintosh, F. C., 2010, In : Soft Matter. 6, 17, p. 4120-4127 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Biopolymers
biopolymers
Rheology
rheology
Gels

Mechanical properties of viruses

Roos, W. H. & Wuite, G. J. L., 2010, Emerging Topics in Physical Virology. Stockley, P. & Twarock, R. (eds.). London: Imperial College Press

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

method for rangings and noise reduction of low coherence interferometry LCI and optical coherence tomography OCT signals by parallel detection of spectral bands

Boer, JF. D., Tearney, G. J. & Bouma, BE., 2010, US Patent 7,797,119. (US Patent 7,797,119).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

spectral bands
noise reduction
interferometry
tomography
shot noise

Microtubule Elasticity: Connecting All-Atom Simulations with Continuum Mechanics

Sept, D. & MacKintosh, F. C., 2010, In : Physical Review Letters. 104, 1, p. 018101

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
continuum mechanics
elastic properties
systems simulation
atoms
stiffness

Mixed Microtubules Steer Dynein-Driven Cargo Transport into Dendrites

Kapitein, L. C., Schlager, M. A., Kuijpers, M., Wulf, P. S., van Spronsen, M., MacKintosh, F. C. & Hoogenraad, C. C., 2010, In : Current Biology. 20, 4, p. 290-299 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Dyneins
dendrites
Dendrites
Microtubules
microtubules

Norwalk Virus Assembly and Stability Monitored by Mass Spectrometry

Shoemaker, G. K., van Duijn, E. J., Crawford, S. E., Uetrecht, C., Baclayon, M., Roos, W. H., Wuite, G. J. L., Estes, M. K., Prasad, B. V. V. & Heck, A. J. R., 2010, In : Molecular and Cellular Proteomics. 9, 8, p. 1742-1751 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Optical coherence tomography in multiple sclerosis: a systematic review and meta-analysis

Petzold, A. F. S., de Boer, J. F., Schippling, S., Vermersch, P., Kardon, R., Green, A., Calabresi, P. A. & Polman, C. H., 2010, In : Lancet Neurology. 9, 9, p. 921-932 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Optical Coherence Tomography
Multiple Sclerosis
Meta-Analysis
Nerve Fibers
Optic Neuritis

Origins of Elasticity in Intermediate Filament Networks

Lin, Y. C., Yao, N. Y., Broedersz, C. P., Herrmann, H., MacKintosh, F. C. & Weitz, D. A., 2010, In : Physical Review Letters. 104, 5, p. 058101

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
filaments
elastic properties
stiffening
viscoelasticity
polymers

Physical virology

Roos, W. H., Bruinsma, R. F. & Wuite, G. J. L., 2010, In : Nature Physics. 6, p. 733-743 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

self assembly
genome
atomic force microscopy
viruses
fatigue (materials)

Poisson's Ratio in Composite Elastic Media with Rigid Rods

Das, M. & MacKintosh, F. C., 2010, In : Physical Review Letters. 105, 13, 4 p., 138102.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
elastic media
Poisson ratio
rods
composite materials
elastic properties

Role of DNA conformation in gene regulation

Metzler, R., van den Broek, B., Wuite, G. J. L. & Lomholt, M. A., 2010, Biophysics of DNA-protein interactions: From single molecules to biological systems. Williams, M. & Maher, J. (eds.). Springer

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Sampling Protein Form and Function with the Atomic Force Microscope

Baclayon, M., Roos, W. H. & Wuite, G. J. L., 2010, In : Molecular and Cellular Proteomics. 9, 8, p. 1678-1688 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Squeezing Protein Shells: How Continuum Elastic Models, Molecular Dynamics Simulations, and Experiments Coalesce at the Nanoscale

Roos, W. H., Gibbons, M. M., Arkhipov, A., Uetrecht, C., Watts, N. R., Wingfield, P. T., Steven, A. C., Heck, A. J. R., Schulten, K., Klug, W. S. & Wuite, G. J. L., 2010, In : Biophysical Journal. 99, 4, p. 1175-1181 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Capsid
Molecular Dynamics Simulation
Proteins
Molecular Models
Atomic Force Microscopy

Structural Hierarchy Governs Fibrin Gel Mechanics

Piechocka, I. K., Bacabac, R. G., Potters, M., MacKintosh, F. C. & Koenderink, G. H., 2010, In : Biophysical Journal. 98, 10, p. 2281-2289 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Structure and Dynamics of the Kinesin-Microtubule Interaction Revealed by Fluorescence Polarization Microscopy

Sosa, H. A., Asenjo, B. & Peterman, E. J. G., 2010, Methods in Cell Biology, Vol 95.. p. 505-519

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

The effect of ethylene oxide, glow discharge and electron beam on the surface characteristics of poly(L-lactide-co-caprolactone) and the corresponding cellular response of adipose stem cells

Kroeze, R. J., Helder, M. N., Roos, W. H., Wuite, G. J. L., Bank, R. A. & Smit, T. H., 2010, In : Acta Biomaterialia. 6, 6, p. 2060-2065

Research output: Contribution to JournalArticleAcademicpeer-review

Ethylene Oxide
Glow discharges
Stem cells
Argon
Electron beams

The Effect of Monastrol on the Processive Motility of a Dimeric Kinesin-5 Head/Kinesin-1 Stalk Chimera

Peterman, E. J. G., Lakamper, S., Thiede, C., Duselder, A., Reiter, S., Korneev, M. J., Kapitein, L. C. & Schmidt, C. F., 2010, In : Journal of Molecular Biology. 399, p. 1-8

Research output: Contribution to JournalArticleAcademicpeer-review

Kinesin
Head
Neck
Spindle Apparatus
Xenopus laevis

Ultrastructure and organization of bacterial chromosomes

Dame, R. T. & Dorman, C. J., 2010, Dordrecht: Springer. 9 p.

Research output: Book / ReportBookAcademicpeer-review

Bacterial Chromosomes
DNA Replication
Confined Spaces
Bacteria
Bacterial Genomes