LaserLaB - Molecular Biophysics

Research Output 1999 2019

2016

Direct Quantitative Detection of Doc2b-Induced Hemifusion in Optically Trapped Membranes

Brouwer, I., Giniatullina, A., Laurens, N., van Weering, J. R. T., Bald, D., Groffen, A. J. A. & Wuite, G. J. L., 2016, In : Biophysical Journal. 110, 3, p. 520A-520A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization

Driessen, R. P. C., Lin, S., Waterreus, W. J., van der Meulen, A. L. H., van der Valk, R. A., Laurens, N., Moolenaar, G. F., Pannu, N. S., Wuite, G. J. L., Goosen, N. & Dame, R. T., 2016, In : Scientific Reports. 6, 29422.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chromatin
DNA
Proteins
Helix-Turn-Helix Motifs
Sulfolobus solfataricus

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

Brouwer, I., Sitters, G., Candelli, A., Modesti, M., Peterman, E. J. G. & Wuite, G. J. L., 2016, In : Biophysical Journal. 110, 3, p. 63A-63A

Research output: Contribution to JournalMeeting AbstractOther research output

DNA Twist Stability Changes with Magnesium(2+) Concentration

Broekmans, O. D., King, G. A., Stephens, G. J. & Wuite, G. J. L., 2016, In : Physical Review Letters. 116, 25, 258102.

Research output: Contribution to JournalArticleAcademicpeer-review

magnesium
deoxyribonucleic acid
elastic properties
buffers
cations

Dynein Dynamics in Vivo: A Single-Molecule View on its Function in Intraflagellar Transport

Mijalkovic, J., Prevo, B., Oswald, F., Mangeol, P. J. J. & Peterman, E. J. G., 2016, In : Biophysical Journal. 110, 3, p. 458A-458A

Research output: Contribution to JournalMeeting AbstractOther research output

Elasticity of fibrous networks under uniaxial prestress

Vahabi, M., Sharma, A., Licup, A. J., van Oosten, A. S. G., Galie, P. A., Janmey, P. A. & MacKintosh, F. C., 2016, In : Soft Matter. 12, 22

Research output: Contribution to JournalArticleAcademicpeer-review

Elasticity
elastic properties
axial strain
stiffening
Hydrogels

Elastic regimes of subisostatic athermal fiber networks

Licup, A. J., Sharma, A. & MacKintosh, F. C., 2016, In : Physical Review E. 93, 1, 012407.

Research output: Contribution to JournalArticleAcademicpeer-review

Fiber
Mechanics
fibers
Network Architecture
stiffening

Extracellular Matrix Mechanics and Implications for Cellular Mechanosensing

Jansen, K. A., 2016

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

Open Access
File
Mechanics
Extracellular Matrix

Fibrin Networks Support Recurring Mechanical Loads by Adapting their Structure across Multiple Scales

Kurniawan, N. A., Vos, B. E., Biebricher, A. S., Wuite, G. J. L., Peterman, E. J. G. & Koenderink, G. H., 2016, In : Biophysical Journal. 111, 5, p. 1026-1034

Research output: Contribution to JournalArticleAcademicpeer-review

Fibrin
Scleroproteins
Optical Tweezers
Biopolymers
Biocompatible Materials

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles

Kononova, O., Snijder, J., Kholodov, Y., Marx, K. A., Wuite, G. J. L., Roos, W. H. & Barsegov, V., 2016, In : PLoS Computational Biology. 12, 1, e1004729.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Nonlinear Dynamics
Nanoparticles
Capsid
nanoparticles
capsid

From single-molecule to organism-level biophysics

Broekmans, O. D., 2016

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

Open Access
File
biophysics
organisms

Hierarchical compression of Caenorhabditis elegans locomotion reveals phenotypic differences in the organization of behaviour

Gomez-Marin, A., Stephens, G. J. & Brown, A. E. X., 2016, In : Journal of the Royal Society Interface. 13, 121, 20160466.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Caenorhabditis elegans
Locomotion
Compressibility
Animals
Neurology

High-resolution real-time dual-view imaging with multiple point of view microscopy

Mangeol, P. J. J. & Peterman, E. J. G., 2016, In : Biomedical Optics Express. 7, 9, p. 3631-3642

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microscopy
microscopy
Biological Phenomena
high resolution
Fluorescence

How Kinesin Motor Proteins Deal with Traffic Jams

Kushwaha, V. S., Miedema, D. M., Denisov, D. V., Acar, S., Nienhuis, B., Schall, P. & Peterman, E. J. G., 2016, In : Biophysical Journal. 110, 3, p. 462A-462A

Research output: Contribution to JournalMeeting AbstractAcademic

KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs

Mangeol, P. J. J., Prevo, B. & Peterman, E. J. G., 2016, In : Molecular Biology of the Cell. 27, 12, p. 1948-1957

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Molecular Dynamics Simulation
Software
Color

Local dynamic mechanical analysis for heterogeneous soft matter using ferrule-top indentation

van Hoorn, H., Kurniawan, N. A., Koenderink, G. H. & Iannuzzi, D., 2016, In : Soft Matter. 12, 12, p. 3066-3073

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Dynamic mechanical analysis
indentation
Indentation
Tissue
probes

Mechanical Unfolding of an Autotransporter Passenger Protein Reveals the Secretion Starting Point and Processive Transport Intermediates

Baclayon, M., van Ulsen, P., Mouhib, H., Hashemi Shabestari, M., Verzijden, T., Abeln, S., Roos, W. H. & Wuite, G. J. L., 2016, In : ACS Nano. 10, 6, p. 5710-5719

Research output: Contribution to JournalArticleAcademicpeer-review

protease
secretions
passengers
Hemoglobin
hemoglobin

Modeling semiflexible polymer networks (vol 86, 995, 2014)

Broedersz, C. P. & MacKintosh, F. C., 2016, In : Reviews of Modern Physics. 88, 3, 039903.

Research output: Contribution to JournalArticleAcademicpeer-review

MOTOR PROTEINS Kinesin's gait captured

Peterman, E. J. G., 2016, In : Nature Chemical Biology. 12, 4, p. 206-207

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Kinesin
Gait
Hand
Microtubules
Microscopy

MreB-Dependent Organization of the E-coli Cytoplasmic Membrane Controls Membrane Protein Diffusion

Oswald, F., Varadarajan, A., Lill, H., Peterman, E. J. G. & Bollen, Y. J. M., 2016, In : Biophysical Journal. 110, 5, p. 1139-1149

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Prokaryotic Cells
Thymidine Monophosphate
Membrane Proteins
Cell Membrane
Escherichia coli

Multi-scale strain-stiffening of semiflexible bundle networks

Piechocka, I. K., Jansen, K. A., Broedersz, C. P., Kurniawan, N. A., MacKintosh, F. C. & Koenderink, G. H., 2016, In : Soft Matter. 12, 7, p. 2145-2156

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
stiffening
fibrin
Fibrin
bundles
Fibers

Multispectral Scanning Light Ophthalmoscope (MSLO) using optimized illumination schemes

Damodaran, M., Vienola, K. V., Braaf, B. & de Boer, J. F., 9 Dec 2016, The Association for Research in Vision and Ophthalmology. 12 ed. Vol. 57. p. 1697 1697 p.

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademic

parameter
health

Nonlinear Mechanics of Athermal Branched Biopolymer Networks

Rens, R., Vahabi, M., Licup, A. J., MacKintosh, F. C. & Sharma, A., 2016, In : Journal of Physical Chemistry B. 120, 26, p. 5831-5841

Research output: Contribution to JournalArticleAcademicpeer-review

Biopolymers
biopolymers
Mechanics
Collagen
Actins

On-site residence time in a driven diffusive system: Violation and recovery of a mean-field description

Messelink, J., Rens, R., Vahabi, M., Mac Kintosh, F. C. & Sharma, A., 2016, In : Physical Review E. 93, 1, 012119.

Research output: Contribution to JournalArticleAcademicpeer-review

Driven Diffusive Systems
Asymmetric Exclusion Process
Residence Time
Mean Field
Recovery

Optical Pushing: A Tool for Parallelized Biomolecule Manipulation

Sitters, G., Laurens, N., de Rijk, E. J., Kress, H., Peterman, E. J. G. & Wuite, G. J. L., 2016, In : Biophysical Journal. 110, 1, p. 44-50

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microspheres
Lasers
Biophysics
Aptitude
Reaction Time

Optical Pushing: A Tool for Parallelized Biomolecule Manipulation (vol 110, pg 44, 2016)

Sitters, G., Laurens, N., de Rijk, E., Kress, H., Peterman, E. J. G. & Wuite, G. J. L., 2016, In : Biophysical Journal. 111, 2, p. 463-463

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Parallel line scanning ophthalmoscope for retinal imaging

Vienola, K. V., Damodaran, M., Braaf, B., Vermeer, K. A. & de Boer, J. F., 2 May 2016, p. 1696. 1 p.

Research output: Contribution to ConferencePosterOther research output

File
scanning
fovea
nerves
field of view
blood vessels

Porosity Governs Normal Stresses in Polymer Gels

de Cagny, H. C. G., Vos, B. E., Vahabi, M., Kurniawan, N. A., Doi, M., Koenderink, G. H., Mac Kintosh, F. & Bonn, D., 18 Nov 2016, In : Physical Review Letters. 117, 21, 217802.

Research output: Contribution to JournalArticleAcademicpeer-review

Probing biological interactions one molecule at a time: An optical tweezers analysis of protein-mediated membrane fusion and DNA repair

Brouwer, I., 2016

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

Open Access
File
Optical tweezers
Repair
Fusion reactions
Membranes
Molecules

Protein Nanocontainers from Nonviral Origin: Testing the Mechanics of Artificial and Natural Protein Cages by AFM

Heinze, K., Sasaki, E., King, N. P., Baker, D., Hilvert, D., Wuite, G. J. L. & Roos, W. H., 2016, In : Journal of Physical Chemistry B. 120, 26, p. 5945-5952

Research output: Contribution to JournalArticleAcademicpeer-review

Nanoindentation
Mechanics
atomic force microscopy
proteins
Proteins

Resolving coiled shapes reveals new reorientation behaviors in C-elegans

Broekmans, O. D., Rodgers, J. B., Ryu, W. S. & Stephens, G. J., 2016, In : eLife. 5, e17227.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Posture
Labels
Head
Food

Sliding sleeves of XRCC4-XLF bridge DNA and connect fragments of broken DNA

Brouwer, I., Sitters, G., Candelli, A., Heerema, S. J., Heller, I., de Melo, A. J., Zhang, H. S., Normanno, D., Modesti, M., Peterman, E. J. G. & Wuite, G. J. L., 2016, In : Nature. 535, 7613, p. 566

Research output: Contribution to JournalArticleAcademicpeer-review

DNA
Optical tweezers
Immune system
Fluorescence microscopy
Joining

Strain-controlled criticality governs the nonlinear mechanics of fibre networks

Sharma, A., Licup, A. J., Jansen, K. A., Rens, R., Sheinman, M., Koenderink, G. H. & MacKintosh, F. C., 2016, In : Nature Physics. 12, 6, p. 584

Research output: Contribution to JournalArticleAcademicpeer-review

fibers
collagens
rigidity
integrity
signatures

Strain-driven criticality underlies nonlinear mechanics of fibrous networks

Sharma, A., Licup, A. J., Rens, R., Vahabi, M., Jansen, K. A., Koenderink, G. H. & MacKintosh, F. C., 2016, In : Physical Review E. 94, 4, 042407.

Research output: Contribution to JournalArticleAcademicpeer-review

Criticality
Mechanics
Collagen
collagens
Critical Exponents
Open Access

Tuning the Music: Acoustic Force Spectroscopy (AFS) 2.0

Kamsma, D., Creyghton, R., Sitters, G., Peterman, E. J. G. & Wuite, G. J. L., 16 Feb 2016, In : Biophysical Journal. 110, 3, p. 501A-501A

Research output: Contribution to JournalMeeting AbstractAcademic

Tuning the Music: Acoustic Force Spectroscopy (AFS) 2.0

Kamsma, D., Creyghton, R., Sitters, G., Wuite, G. J. L. & Peterman, E. J. G., 2016, In : Methods. 105, p. 26-33

Research output: Contribution to JournalArticleAcademicpeer-review

Music
Acoustics
Spectrum Analysis
Tuning
Spectroscopy

Uncoupling shear and uniaxial elastic moduli of semiflexible biopolymer networks: compression-softening and stretch-stiffening

van Oosten, A. S. G., Vahabi, M., Licup, A. J., Sharma, A., Galie, P. A., MacKintosh, F. C. & Janmey, P. A., 2016, In : Scientific Reports. 6, 19270.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
stiffening
biopolymers
softening
modulus of elasticity
shear

Unravelling the structural plasticity of stretched DNA under torsional constraint

King, G. A., Peterman, E. J. G. & Wuite, G. J. L., 2016, In : Nature Communications. 7, 11810.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
plastic properties
Plasticity
deoxyribonucleic acid
DNA
genome

Vesicle Mechanics: A Push into the Nanoscale

Vorselen, D., 2016, 176 p.

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

Open Access
File

Why motor proteins team up - Intraflagellar transport in C. elegans cilia

Mijalkovic, J., Prevo, B. & Peterman, E. J. G., 8 Jul 2016, In : Worm. 5, 2, p. e1170275

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Kinesin
Cilia
Dyneins
Proteins
Molecular Motor Proteins
2015

Acoustic force spectroscopy

Sitters, G., Kamsma, D., Thalhammer, G., Ritsch-Marte, M., Peterman, E. J. G. & Wuite, G. J. L., 2015, In : Nature Methods. 12, 1, p. 47-50

Research output: Contribution to JournalArticleAcademicpeer-review

Biomolecules
Acoustics
Spectrum Analysis
Spectroscopy
Equipment and Supplies

Acoustic Force Spectroscopy

Kamsma, D., Sitters, G., Thalhammer, G., Ritsch-Marte, M., Peterman, E. J. G. & Wuite, G. J. L., 2015, In : Biophysical Journal. 108, 2, p. 355A-355A

Research output: Contribution to JournalMeeting AbstractOther research output

Anomalous Discontinuity at the Percolation Critical Point of Active Gels

Sheinman, M., Sharma, A., Alvarado, J., Koenderink, G. H. & MacKintosh, F. C., 2015, In : Physical Review Letters. 114, 9, p. 098104 098104.

Research output: Contribution to JournalArticleAcademicpeer-review

critical point
discontinuity
gels
signatures

Building an artificial actin cortex on microscopic pillar arrays

Ayadi, R. & Roos, W. H., 2015, In : Methods in Cell Biology. 128, p. 105-124

Research output: Contribution to JournalArticleAcademicpeer-review

Actins
Artificial Cells
Biomimetics
Biopolymers
Eukaryotic Cells

Decreased creatine kinase is linked to diastolic dysfunction in rats with right heart failure induced by pulmonary artery hypertension

Fowler, E. D., Benoist, D., Drinkhill, M. J., Stones, R., Helmes, M. H. B., Wüst, R. C. I., Stienen, G. J. M., Steele, D. S. & White, E., 2015, In : Journal of Molecular and Cellular Cardiology. 86, p. 1-8

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Creatine Kinase
Pulmonary Hypertension
Pulmonary Artery
Muscle Cells
Heart Failure

Diaphragm Muscle Fiber Weakness and Ubiquitin-Proteasome Activation in Critically Ill Patients

Hooijman, P. E., Beishuizen, A., Witt, C. C., de Waard, M. C., Girbes, A. R. J., Spoelstra-de Man, A. M. E., Niessen, H. W., Manders, E., van Hees, H. W. H., van den Brom, C. E., Silderhuis, V., Lawlor, M. W., Labeit, S., Stienen, G. J. M., Hartemink, K. J., Paul, M. A., Heunks, L. M. A. & Ottenheijm, C. A. C., 2015, In : American Journal of Respiratory and Critical Care Medicine. 191, 10, p. 1126-1138

Research output: Contribution to JournalArticleAcademicpeer-review

Muscle Weakness
Proteasome Endopeptidase Complex
Ubiquitin
Diaphragm
Critical Illness

Direct quantitative detection of Doc2b-induced hemifusion in optically trapped membranes

Brouwer, I., Giniatullina, A., Laurens, N., van Weering, J. R. T., Bald, D., Wuite, G. J. L. & Groffen, A. J. A., 2015, In : Nature Communications. 6, p. 8387 8387.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
membranes
Membranes
SNARE Proteins
secretions
Phosphatidylserines

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