LaserLaB - Molecular Biophysics

Research Output 1999 2019

2012

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

Laurens, N., Rusling, D. A., Pernstich, C., Brouwer, I., Halford, S. E. & Wuite, G. J. L., 2012, In : Nucleic Acids Research. 40, 11, p. 4988-4997 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
DNA
Proteins
Torque
Genetic Phenomena
DNA Restriction Enzymes

Filament-Length-Controlled Elasticity in 3D Fiber Networks

Broedersz, C. P., Sheinman, M. & MacKintosh, F. C., 2012, In : Physical Review Letters. 108, 6, 078102.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
filaments
elastic properties
fibers
elastic bending
crossovers

Frustration of the Isotropic-Columnar Phase Transition of Colloidal Hard Platelets by a Transient Cubatic Phase

Marechal, M., Patti, A. & Dennison, M., 2012, In : Physical Review Letters. 108, 20, p. 206101 206101.

Research output: Contribution to JournalArticleAcademicpeer-review

frustration
platelets
vitrification
crystallization
life (durability)

How does the DNA sequence affect the Hill curve of transcriptional response?

Sheinman, M. & Kafri, Y., 2012, In : Physical Biology. 9, 5, 056006.

Research output: Contribution to JournalArticleAcademicpeer-review

Transcription Factors
DNA

Mechanics of bacteriophage maturation

Roos, W. H., Gertsman, I., May, E. R., Brooks, C. L., Johnson, J. E. & Wuite, G. J. L., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 7, p. 2342-2347 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

bacteriophage
mechanics
maturation
Young modulus
fatigue

Mechanistic Insights into the Twin-Arginine Translocation Cycle of Escherichia Coli by an In Vivo Single-Molecule Approach

Oswald, F., Wildenberg, S. M. J. L., Yau, K. W., van Ulsen, J. P., Wuite, G. J. L., Bollen, Y. J. M. & Peterman, E. J. G., 2012, In : Biophysical Journal. 102, 3, p. 664A-664A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Molecular dynamics simulation studies of platelets with square cross-sectional area: formation of a stable cubatic phase

Wilson, M. R., Duncan, P. D. & Dennison, M., 2012, In : Soft Matter. 8, 12, p. 3348-3356

Research output: Contribution to JournalArticleAcademicpeer-review

Platelets
platelets
Molecular dynamics
molecular dynamics
Relaxation time

Multiple actin binding domains of Ena/VASP proteins determine actin network stiffening

Gentry, B. S., van der Meulen, S., Noguera, P., Alonso-Latorre, B., Plastino, J. & Koenderink, G. H., 2012, In : European Biophysics Journal. 41, 11, p. 979-990 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Actins
Binding Sites
Elasticity
ENA-VASP proteins
Cluster Analysis

Multiplexing Biochemical Signals

de Ronde, W. H., 2012

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

Open Access
File

Nanocolloidal albumin-IRDye 800CW: a near-infrared fluorescent tracer with optimal retention in the sentinel lymph node

Heuveling, D. A., Visser, G. W. M., de Groot, M., de Boer, J. F., Salumbides - Baclayon, M., Roos, W. H., Wuite, G. J. L., Leemans, C. R., de Bree, R. & van Dongen, G. A. M. S., 2012, In : European Journal of Nuclear Medicine and Molecular Imaging. 39, 7, p. 1161-1168 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Indocyanine Green
Albumins
Serum Albumin
Fluorescence
Injections

New Tool for Single Molecule Manipulation: Optical Pushing

Sitters, G., Laurens, N., de Rijk, E. J., Peterman, E. J. G. & Wuite, G. J. L., 2012, In : Biophysical Journal. 102, 3, p. 385A-386A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Nonequilibrium fluctuations of a remodeling in vitro cytoskeleton

Stuhrmann, B., Soares e Silva, M., Depken, S. M., MacKintosh, F. C. & Koenderink, G. H., 2012, In : Physical Review E. 86, 2, 020901.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Cytoskeleton
Remodeling
Non-equilibrium
Fluctuations
Actin

Nonlinear effective-medium theory of disordered spring networks

Sheinman, M., Broedersz, C. P. & MacKintosh, F. C., 2012, In : Physical Review E. 85, 2, 021801.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Bulk Modulus
bulk modulus
Calculate
Numerical Results
Network Connectivity

Operational Stability of Organic Field‐Effect Transistors

Bobbert, P. A., Sharma, A., Matthijssen, S. J. G., Kemerink, M. & de Leeuw, D. M., 2012, In : Advanced Materials. 24, p. 1146-1158

Research output: Contribution to JournalArticleAcademicpeer-review

Organic field effect transistors
Gate dielectrics
Transistors
Protons
Redox reactions

Orientational Order of Carbon Nanotube Guests in a Nematic Host Suspension of Colloidal Viral Rods

Puech, N., Dennison, M., Blanc, C., van der Schoot, P., van Roij, R., Poulin, P. & Grelet, E., 2012, In : Physical Review Letters. 108, 24, p. 247801 247801.

Research output: Contribution to JournalArticleAcademicpeer-review

viruses
rods
carbon nanotubes
birefringence
flexibility

Phase diagram of hard snowman-shaped particles

Dennison, M. & Milinkovic, K., 2012, In : Journal of Chemical Physics. 137, 4, p. 044507 044507.

Research output: Contribution to JournalArticleAcademicpeer-review

Phase diagrams
phase diagrams
Crystals
crystals
Phase behavior

Probing the impact of loading rate on the mechanical properties of viral nanoparticles

Snijder, J., Ivanovska, I. L., Salumbides - Baclayon, M., Roos, W. H. & Wuite, G. J. L., 2012, In : Micron. 43, 12, p. 1343-1350 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

loading rate
Atomic Force Microscopy
Capsid
Viruses
Nanoparticles

Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A

Farge, G. A., Laurens, N., Broekmans, O. D., Wildenberg, S. M. J. L., Dekker, L. C. M., Gaspari, M., Gustafsson, C. M., Peterman, E. J. G., Falkenberg, M. & Wuite, G. J. L., 2012, In : Nature Communications. 3, 1013.

Research output: Contribution to JournalArticleAcademicpeer-review

Nucleic Acid Denaturation
Protein Denaturation
Denaturation
biopolymer denaturation
sliding

Real-time eye motion compensation for OCT imaging with tracking SLO

Vienola, K. V., Braaf, B., Sheehy, C. K., Yang, Q., Tiruveedhula, P., Arathorn, D. W., de Boer, J. F. & Roorda, A., 1 Nov 2012, In : Biomedical Optics Express. 3, 11, p. 2950-2963

Research output: Contribution to JournalArticleAcademicpeer-review

Substrate Specificity and Dynamic Instability of RAD51-Filament Assembly on Single- and Double-Stranded DNA

Candelli, A., Holthausen, T. J., Depken, S. M., Modesti, M., Wyman, C., Wuite, G. J. L. & Peterman, E. J. G., 2012, In : Biophysical Journal. 102, 3, p. 280A-280A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

The Cost of Being Right During Replication

Hoekstra, T. P., Depken, S. M., Gross, P., Peterman, E. J. G. & Wuite, G. J. L., 2012, In : Biophysical Journal. 102, 3, p. 15A-15A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

The Polyphenol EGCG Inhibits Amyloid Formation Less Efficiently at Phospholipid Interfaces than in Bulk Solution

Engel, M. F. M., van den Akker, C., Schleeger, M., Veliko, K. P., Koenderink, G. H. & Bonn, M., 2012, In : Journal of the American Chemical Society. 134, 36, p. 14781-14788 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Polyphenols
Amyloid
Phospholipids
Membranes
Medical problems

Twist, Stretch and Melt: Quantifying How DNA Complies to Tension

Gross, P., Laurens, N., Oddershede, L. B., Bockelmann, U., Wuite, G. J. L. & Peterman, E. J. G., 2012, In : Biophysical Journal. 102, 3, p. 420A-421A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access

Unlocking Internal Prestress from Protein Nanoshells

Klug, W. S., Roos, W. H. & Wuite, G. J. L., 2012, In : Physical Review Letters. 109, 16, 168104.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
viruses
apexes
elastic properties
proteins
incompatibility

Versatile Optical Tweezers with Single Base-Pair Resolution

Heller, I., Laurens, N., Vorselen, D., Kruijssen, D. L. H., Peterman, E. J. G. & Wuite, G. J. L., 2012, In : Biophysical Journal. 102, 3, p. 578A-578A

Research output: Contribution to JournalMeeting AbstractOther research output

Open Access
2011

(89)Zr-Nanocolloidal Albumin-Based PET/CT Lymphoscintigraphy for Sentinel Node Detection in Head and Neck Cancer: Preclinical Results

Heuveling, D. A., Visser, G. W. M., Salumbides - Baclayon, M., Roos, W. H., Wuite, G. J. L., Hoekstra, O. S., Leemans, C. R., de Bree, R. & van Dongen, G. A. M. S., 2011, In : Journal of Nuclear Medicine. 52, 10, p. 1580-1584 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Lymphoscintigraphy
Head and Neck Neoplasms
Albumins
Neoplasms
cyhalothrin

A brief introduction to single-molecule fluorescence methods

Wildenberg, S. M. J. L., Prevo, B. & Peterman, E. J. G., 2011, Single Molecule Analysis, Series Methods in Molecular Biology. Peterman, EJG. & Wuite, GJL. (eds.). New York: Humana Press, Vol. 783. p. 81-99

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

Fluorescence
Molecules
Fluorescence microscopy
Distance measurement
Fluorescent Dyes

ACTIVE GELS Motors keep dynamics steady

MacKintosh, F. C., 2011, In : Nature Materials. 10, 6, p. 414-415

Research output: Contribution to JournalArticleAcademicpeer-review

Actins
filaments
Molecular Motor Proteins
Drosophila
myosins

Active multistage coarsening of actin networks driven by myosin motors

e Silva, M. S., Depken, S. M., Stuhrmann, B., Korsten, M., MacKintosh, F. C. & Koenderink, G. H., 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 23, p. 9408-9413

Research output: Contribution to JournalArticleAcademicpeer-review

myosins
filaments
coalescing
buckling
locomotion

Active soft matter

MacKintosh, F. C. & Cates, M. E., 2011, In : Soft Matter. 7, 7, p. 3050-3051

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Automated segmentation by pixel classification of retinal layers in ophthalmic OCT images

Vermeer, K. A., van der Schoot, J. H., Lemij, H. G. & de Boer, J. F., 2011, In : Biomedical Optics Express. 2, 6, p. 1743-1756 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Biopolymers: from structural hierarchy to nonlinear rheology

Piechocka, I. K., 2011, 165 p.

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

Open Access
File

Carbon nanotubes as mechanical probes of equilibrium and non-equilibrium cytoskeletal networks

Fakhri, N., Enderlein, J., Pasquali, M., MacKintosh, F. C. & Schmidt, C. F., 2011, In : European Biophysics Journal. 40, 1, p. 159 1 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA-protein interactions

Candelli, A., Wuite, G. J. L. & Peterman, E. J. G., 2011, In : Physical Chemistry Chemical Physics - PCCP. 13, 16, p. 7263-7272 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Fluorescence microscopy
Fluidics
Molecules
DNA
Proteins

Control of non-linear elasticity in F-actin networks with microtubules

Lin, Y. C., Koenderink, G. H., MacKintosh, F. C. & Weitz, D. A., 2011, In : Soft Matter. 7, 3, p. 902-906

Research output: Contribution to JournalArticleAcademicpeer-review

Actins
Elasticity
filaments
elastic properties
stiffening

Criticality and isostaticity in fiber networks

Broedersz, C. P., Mao, X., Lubensky, D. & MacKintosh, F. C., 2011, In : Nature Physics. 7, 12, p. 983-988

Research output: Contribution to JournalArticleAcademicpeer-review

fibers
elastic properties
rigidity
thresholds
rubber

Discrete fracture patterns of virus shells reveal mechanical building blocks

Ivanovska, I. L., Miranda, R., Carrascosa, J. L., Wuite, G. J. L. & Schmidt, C. F., 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 31, p. 12611-12616 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Viruses
Bacteriophages
Reverse engineering
Capsid Proteins
Materials science

Editorial: Preface: Single molecule analysis methods and protocols

Peterman, E. J. G. & Wuite, G. J. L., 24 Oct 2011, Single Molecule Analysis: Methods and Protocols. Peterman, E. J. G. & Wuite, G. J. L. (eds.). Vol. 783. p. v-vi (Methods in Molecular Biology; vol. 783).

Research output: Chapter in Book / Report / Conference proceedingForeword/postscriptAcademic

Effect of Coulomb scattering from trapped charges on the mobility in an organic field-effect transistor

Sharma, A., Janssen, N. M. A., Matthijssen, S. J. G., de Leeuw, D. M., Kemerink, M. & Bobbert, P. A., 2011, In : Physical Review B (Condensed Matter and Materials Physics). 83, 12, p. 125310

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Organic field effect transistors
field effect transistors
Scattering
scattering
Gate dielectrics

Effects of Salts on Internal DNA Pressure and Mechanical Properties of Phage Capsids

Evilevitch, A., Roos, W. H., Ivanovska, I. L., Jeembaeva, M., Jonsson, B. & Wuite, G. J. L., 2011, In : Journal of Molecular Biology. 405, 1, p. 18-23 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Capsid
Bacteriophages
Salts
Pressure
Atomic Force Microscopy

Engineering alginate for intervertebral disc repair

Bron, J. L., Vonk, L. A., Smit, T. H. & Koenderink, G. H., 2011, In : Journal of the Mechanical Behavior of Biomedical Materials. 4, 7, p. 1196-1205

Research output: Contribution to JournalArticleAcademicpeer-review

Alginate
Repair
Stiffness
Scaffolds
Gelation

How to perform a nanoindentation experiment on a virus

Roos, W. H., 2011, Single Molecule Analysis, Series Methods in Molecular Biology. Peterman, EJG. & Wuite, GJL. (eds.). New York: Humama press, 2011 p.

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

How to Quantify Protein Diffusion in the Bacterial Membrane

Wildenberg, S. M. J. L., Bollen, Y. J. M. & Peterman, E. J. G., 2011, In : Biopolymers. 95, 5, p. 312-321 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Proteins
Membranes
Bacteria
Probability distributions
Membrane Proteins

Influence of the semiconductor oxidation potential on the operational stability of organic field-effect transistors

Sharma, A., Matthijssen, S. J. G., Bobbert, P. A. & de Leeuw, D. M., 2011, In : Applied Physics Letters. 99, 10, p. 103302-103302-3

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
field effect transistors
relaxation time
oxidation
shift
threshold voltage

Introduction to optical tweezers: background, system designs, and commercial solutions

van Mameren, J., Wuite, G. J. L. & Heller, I., 2011, Single Molecule Analysis: Methods and Protocols. Peterman, EJG. & Wuite, GJL. (eds.). New York: Humana Press, p. 1-20 20 p. (Methods in Molecular Biology; vol. 783).

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

systems engineering
molecules
spatial resolution
trapping
methodology

JUMPING MODE ATOMIC FORCE MICROSCOPY ON GRANA MEMBRANES FROM SPINACH

Sznee, K., Dekker, J. P., Dame, R. T., Van Roon, H., Wuite, G. J. L. & Frese, R. N., 2011, In : Journal of Biological Chemistry. 286, 45, p. 39164-39171

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Thylakoids
Spinacia oleracea
Atomic Force Microscopy
Atomic force microscopy
Photosystem II Protein Complex

Mechanics of soft composites of rods in elastic gels

Das, M. & MacKintosh, F. C., 2011, In : Physical Review E. 84, 6, p. 061906 9 p., 061906.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Mechanics
Compressibility
rods
Composite
gels

Molecular motors stiffen non-affine semiflexible polymer networks

Broedersz, C. P. & MacKintosh, F. C., 2011, In : Soft Matter. 7, 7, p. 3186-3191

Research output: Contribution to JournalArticleAcademicpeer-review

Polymers
polymers
filaments
stiffening
Mechanics

Nonlinear Viscoelasticity of Actin Transiently Cross-linked with Mutant alpha-Actinin-4

Yao, N. Y., Becker, D. J., MacKintosh, F. C., Pollak, M. R. & Weitz, D. A., 2011, In : Journal of Molecular Biology. 411, 5, p. 1062-1071

Research output: Contribution to JournalArticleAcademicpeer-review

Actinin
Actins
Mutation
Focal Segmental Glomerulosclerosis
Microfilament Proteins

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