Prof. Dr. Vasily Zaburdaev
Chair of Mathematics in Life Sciences
Friedrich-Alexander-Universität Erlangen-Nürnberg
vasily.zaburdaev@fau.de
See my profile at FAU
Theoretical biophysics, Statistical Physics, Active Systems, Anomalous diffusion and random walks
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Publications
2024
A deep-learning workflow to predict upper tract urothelial carcinoma protein-based subtypes from H&E slides supporting the prioritization of patients for molecular testing
In: Journal of Pathology: Clinical Research 10 (2024), Article No.: e12369
ISSN: 2056-4538
DOI: 10.1002/2056-4538.12369 , , , , , , , , , , , , , , , , , , , , :
Mean zero artificial diffusion for stable finite element approximation of convection in cellular aggregate formation
In: Computer Methods in Applied Mechanics and Engineering 419 (2024), p. 116649
ISSN: 0045-7825
DOI: 10.1016/j.cma.2023.116649 , , , :
Estimation of the mass density of biological matter from refractive index measurements
In: Biophysical Reports (2024), p. 100156
ISSN: 2667-0747
DOI: 10.1016/j.bpr.2024.100156 , , , , , , , , :
2022
Unbiased retrieval of frequency-dependent mechanical properties from noisy time-dependent signals
In: Biophysical Reports 2 (2022), Article No.: 100054
ISSN: 2667-0747
DOI: 10.1016/j.bpr.2022.100054 , , , , :
On continuum modeling of cell aggregation phenomena
In: Journal of the Mechanics and Physics of Solids 167 (2022), Article No.: 105004
ISSN: 0022-5096
DOI: 10.1016/j.jmps.2022.105004 , , , , :
A Pili-Driven Bacterial Turbine
In: Frontiers in Physics 10 (2022)
ISSN: 2296-424X
DOI: 10.3389/fphy.2022.875687 , :
A DNA Segregation Module for Synthetic Cells
In: Small (2022)
ISSN: 1613-6829
DOI: 10.1002/smll.202202711 , , , , , , , :
Spatial, structural and density determinants of DC:T cell interaction under immunostimulatory conditions
In: EUROPEAN JOURNAL OF IMMUNOLOGY, HOBOKEN: 2022 , , , , , :
2021
The potential of omics technologies for the treatment of immune‐mediated inflammatory diseases
In: International Journal of Molecular Sciences 22 (2021), Article No.: 7506
ISSN: 1422-0067
DOI: 10.3390/ijms22147506 , , , , , , , , :
Thermal fluctuations assist mechanical signal propagation in coiled-coil proteins
In: Physical Review E 104 (2021)
ISSN: 2470-0045
DOI: 10.1103/PhysRevE.104.054403 , , , , :
Transcription organizes euchromatin via microphase separation
In: Nature Communications 12 (2021), Article No.: 1360
ISSN: 2041-1723
DOI: 10.1038/s41467-021-21589-3 , , , , , , , , :
Continuum Theory of Active Phase Separation in Cellular Aggregates
In: Physical Review Letters 126 (2021)
ISSN: 0031-9007
DOI: 10.1103/PhysRevLett.126.018102 , , , :
The hierarchical packing of euchromatin domains can be described as multiplicative cascades
In: PLoS Computational Biology 17 (2021), Article No.: e1008974
ISSN: 1553-734X
DOI: 10.1371/journal.pcbi.1008974 , , , , :
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
In: Molecular Systems Biology 17 (2021), Article No.: e10272
ISSN: 1744-4292
DOI: 10.15252/msb.202110272 , , , , , , , , , , :
2020
Liquid Phase Separation Controlled by pH
In: Biophysical Journal (2020)
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2020.07.044 , , , , :
Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation
In: Aging Cell (2020)
ISSN: 1474-9718
DOI: 10.1111/acel.13214 , , , , , , , , , , , :
Maturation of Monocyte-Derived DCs Leads to Increased Cellular Stiffness, Higher Membrane Fluidity, and Changed Lipid Composition
In: Frontiers in Immunology 11 (2020), Article No.: 590121
ISSN: 1664-3224
DOI: 10.3389/fimmu.2020.590121 , , , , , , , , , , , , , , , , :
Ultrahigh-Speed Imaging of Rotational Diffusion on a Lipid Bilayer
In: Nano Letters 20 (2020), p. 7213-7219
ISSN: 1530-6984
DOI: 10.1021/acs.nanolett.0c02516 , , , , :
High-Precision Protein-Tracking With Interferometric Scattering Microscopy
In: Frontiers in Cell and Developmental Biology 8 (2020), Article No.: 590158
ISSN: 2296-634X
DOI: 10.3389/fcell.2020.590158 , , , , , , , :
2019
The shape of pinned forced polymer loops
In: Soft Matter 15 (2019), p. 1785-1792
ISSN: 1744-683X
DOI: 10.1039/c8sm02357c , :
Bacterial colonies as active droplets - from single cells to continuum theory
Joint 12th EBSA European Biophysics Congress / 10th IUPAP International Conference on Biological Physics (ICBP) (Madrid, July 20, 2019 - July 24, 2019)
In: EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, NEW YORK: 2019 , , :
Identifying the mechanism for superdiffusivity in mouse fibroblast motility
In: PLoS Computational Biology 15 (2019)
ISSN: 1553-734X
DOI: 10.1371/journal.pcbi.1006732 , , , , :
How bacterial cells and colonies move on solid substrates
In: Physical Review E 99 (2019), Article No.: 042419
ISSN: 2470-0045
DOI: 10.1103/PhysRevE.99.042419 , , :
Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis
In: Development 146 (2019)
ISSN: 1477-9129
DOI: 10.1242/dev.179127 , , , , , , , , , , :
Rectification of Bacterial Diffusion in Microfluidic Labyrinths
In: Frontiers in Physics 7 (2019), Article No.: 148
ISSN: 2296-424X
DOI: 10.3389/fphy.2019.00148 , , , , , :
2018
Intracellular Mass Density Increase Is Accompanying but Not Sufficient for Stiffening and Growth Arrest of Yeast Cells
In: Frontiers in Bioscience 6 (2018)
ISSN: 1093-9946
DOI: 10.3389/fphy.2018.00131 , , , , , , , , , , :
Exactly solvable dynamics of forced polymer loops
In: New Journal of Physics 20 (2018)
ISSN: 1367-2630
DOI: 10.1088/1367-2630/aae8f0 , , , , , :
Genetic noise mechanism for power-law switching in bacterial flagellar motors
In: Journal of Physics A: Mathematical and Theoretical 51 (2018)
ISSN: 1751-8113
DOI: 10.1088/1751-8121/aac543 , , , :
Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation
In: Scientific Reports 8 (2018)
ISSN: 2045-2322
DOI: 10.1038/s41598-018-34754-4 , , , , , , :
Relative distance between tracers as a measure of diffusivity within moving aggregates
In: European Physical Journal B 91 (2018)
ISSN: 1434-6028
DOI: 10.1140/epjb/e2017-80347-5 , :
Biophysical Techniques for the Study of Phase Transitions in Protein Droplets and Cells
In: Biophysical Journal 114 (2018), p. 204A-204A
ISSN: 0006-3495 , , , , , , , , , , , , :
2017
A tunable refractive index matching medium for live imaging cells, tissues and model organisms
In: eLife 6 (2017)
ISSN: 2050-084X
DOI: 10.7554/eLife.27240 , , , , , , , , , :
Limit theorems for Levy walks in d dimensions: rare and bulk fluctuations
In: Journal of Physics A: Mathematical and Theoretical 50 (2017)
ISSN: 1751-8113
DOI: 10.1088/1751-8121/aa5f6d , , , :
Transcription Locally Disperses Chromatin and Thereby Organizes the Global Architecture of Interphase Nuclei
In: Biophysical Journal 112 (2017), p. 211A-211A
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2016.11.1164 , , , , , :
Interphase chromatin is adaptively folded by ongoing transcription and RNA accumulation.
In: Molecular Biology of the Cell 28 (2017)
ISSN: 1059-1524 , , , , , , :
Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos
In: eLife 6 (2017)
ISSN: 2050-084X
DOI: 10.7554/eLife.23326 , , , , , , , :
Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates
In: New Journal of Physics 19 (2017)
ISSN: 1367-2630
DOI: 10.1088/1367-2630/aa5483 , , , , :
Elasticity-based polymer sorting in active fluids: a Brownian dynamics study
In: Physical Chemistry Chemical Physics 19 (2017), p. 18338-18347
ISSN: 1463-9076
DOI: 10.1039/c7cp02947k , , , :
Live cell X-ray imaging of autophagic vacuoles formation and chromatin dynamics in fission yeast
In: Scientific Reports 7 (2017)
ISSN: 2045-2322
DOI: 10.1038/s41598-017-13175-9 , , , , , , , , , :
2016
Nucleosomal arrangement affects single-molecule transcription dynamics
In: Proceedings of the National Academy of Sciences of the United States of America 113 (2016), p. 12733-12738
ISSN: 0027-8424
DOI: 10.1073/pnas.1602764113 , , , , , , :
Subnuclear Spatial Structuring of Chromatin and Polymerase II during Transcription Activation of the Zebrafish Zygotic Genome
In: Biophysical Journal 110 (2016), p. 232A-233A
ISSN: 0006-3495 , , :
Reaction front propagation of actin polymerization in a comb-reaction system
In: Chaos Solitons & Fractals 92 (2016), p. 115-122
ISSN: 0960-0779
DOI: 10.1016/j.chaos.2016.09.011 , , :
A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy
In: eLife 5 (2016)
ISSN: 2050-084X
DOI: 10.7554/eLife.09347 , , , , , , , , , , , , , , :
Superdiffusive Dispersals Impart the Geometry of Underlying Random Walks
In: Physical Review Letters 117 (2016)
ISSN: 0031-9007
DOI: 10.1103/PhysRevLett.117.270601 , , , :
2015
Asymptotic densities of ballistic Levy walks
In: Physical Review E 91 (2015), Article No.: 022131
ISSN: 2470-0045
DOI: 10.1103/PhysRevE.91.022131 , , , :
Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes
In: Physical Review Letters 115 (2015)
ISSN: 0031-9007
DOI: 10.1103/PhysRevLett.115.208102 , , , , , , , :
A sol-gel transition of the cytoplasm driven by adaptive intracellular pH changes promotes entry into dormancy.
In: Molecular Biology of the Cell 26 (2015)
ISSN: 1059-1524 , , , , , , , , , :
Pili-Induced Clustering of N-gonorrhoeae Bacteria
In: PLoS ONE 10 (2015)
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0137661 , , , , :
Random walk patterns of a soil bacterium in open and confined environments
In: EPL - Europhysics Letters 109 (2015)
ISSN: 0295-5075
DOI: 10.1209/0295-5075/109/28007 , , , , :
Formation and dissolution of bacterial colonies
In: Physical Review E 92 (2015)
ISSN: 1539-3755
DOI: 10.1103/PhysRevE.92.032704 , , , :
Levy walks
In: Reviews of Modern Physics 87 (2015), p. 483-530
ISSN: 0034-6861
DOI: 10.1103/RevModPhys.87.483 , , :
2014
Uncovering the Mechanism of Trapping and Cell Orientation during Neisseria gonorrhoeae Twitching Motility
In: Biophysical Journal 107 (2014), p. 1523-1531
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2014.07.061 , , , , , , :
2013
How the Motility Pattern of Bacteria Affects Their Dispersal and Chemotaxis
In: PLoS ONE 8 (2013)
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0081936 , , :
A Bacterial Swimmer with Two Alternating Speeds of Propagation
In: Biophysical Journal 105 (2013), p. 1915-1924
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2013.08.047 , , , , :
Liquid transport facilitated by channels in Bacillus subtilis biofilms
In: Proceedings of the National Academy of Sciences of the United States of America 110 (2013), p. 848-852
ISSN: 0027-8424
DOI: 10.1073/pnas.1216376110 , , , , , :
Space-Time Velocity Correlation Function for Random Walks
In: Physical Review Letters 110 (2013)
ISSN: 0031-9007
DOI: 10.1103/PhysRevLett.110.170604 , , :
2012
Lévy walks with velocity fluctuations
In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85 (2012), Article No.: 031148
ISSN: 1550-2376
DOI: 10.1103/PhysRevE.85.031148 , , :
Langevin description of superdiffusive Lévy processes
In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 86 (2012), Article No.: 041134
ISSN: 1550-2376
DOI: 10.1103/PhysRevE.86.041134 , , , :
Collective dynamics of model microorganisms with chemotactic signaling
In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85 (2012), Article No.: 051901
ISSN: 1550-2376
DOI: 10.1103/PhysRevE.85.051901 , , :
2009
On moments and scaling regimes in anomalous random walks
In: Journal of Statistical Mechanics-Theory and Experiment (2009)
ISSN: 1742-5468
DOI: 10.1088/1742-5468/2009/12/P12020 , , :
2008
Random walks with random velocities
In: Physical Review E 78 (2008)
ISSN: 2470-0045
DOI: 10.1103/PhysRevE.78.011119 , , :
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