Publications

2024

82. How bacteria actively use passive physics to make biofilms

L. Chai, V. Zaburdaev, R. Kolter; PNAS. doi: 10.1073/pnas.240384212 (2024)

81. Estimation of the mass density of biological matter from refractive index measurements

C. Möckel, T. Beck, S. Kaliman, S. Abuhattum, K. Kim, J. Kolb, D. Wehner, V. Zaburdaev, J. Guck; Biophysical Reports. doi: 10.1016/j.bpr.2024.100156 (2024)

80. A deep-learning workflow to predict upper tract urothelial carcinoma protein-based subtypes from H&E slides supporting the prioritisation of patients for molecular testing

M. Angeloni, T. van Doeveren, S. Lindner, P. Volland, J. Schmelmer, S. Foersch, C. Matek, R. Stoehr, C. I. Geppert, H. Heers, S. Wach, H. Taubert, D. Sikic, B. Wullich, G. JLH van Leenders, V. Zaburdaev, M. Eckstein, A. Hartmann, J.L. Boormans, F. Ferrazzi, V. Bahlinger; The Journal of Pathology: Clinical Research. doi: 10.1002/2056-4538.12369 (2024)

79. Where bacteria and eukaryotes meet;

L. Chai, E. A. Shank, V. Zaburdaev; Journal of Bacteriology. doi: 10.1128/jb.00049-23 (2024)

78. Mean zero artificial diffusion for stable finite element approximation of convection in cellular aggregate formation;

S. Firooz, B.D. Reddy, V. Zaburdaev, P. Steinmann; Computer Methods in Applied Mechanics and Engineering. doi: 10.1016/j.cma.2023.116649 (2024)

77. Residual cells and nutrient availability guide wound healing in bacterial biofilms;

Y.Ye, M. Ghrayeb, S. Miercke, S. Arif, S. Müller, T. Mascher, L. Chai, V. Zaburdaev; Royal Society of Chemistry. doi: 10.1039/D3SM01032E (2024)

2023

76. Periodic ethanol supply as a path toward unlimited lifespan of Caenorhabditis elegans dauer larvae;

X. Zhang, S. Penkov, T. V. Kurzchalia, V. Zaburdaev; Frontiers in Aging. doi: 10.3389/fragi.2023.1031161 (2023)

75. Amphiphiles formed from synthetic DNA-nanomotifs mimic the step-wise dispersal of transcriptional clusters in the cell nucleus;

X. Tschurikow, A. Gadzekpo, M. P.Tran, R. Chatterjee, M. Sobucki, V. Zaburdaev, K. Göpfrich, L. Hilbert; Nano Lett. doi: https://doi.org/10.1021/acs.nanolett.3c01301 (2023)

74. A DNA Segregation Module for Synthetic Cells;

2022

73. On continuum modeling of cell aggregation phenomena;

S. Firooz, S. Kaessmair, V. Zaburdaev, A. Javili and P. Steinmann, Journal of the Mechanics and Physics of Solids doi: https://doi.org/10.1016/j.jmps.2022.105004 (2022)

72. A Pili-Driven Bacterial Turbine;

W. Pönisch and V. Zaburdaev, Frontiers in Physics doi: https://doi.org/10.3389/fphy.2022.875687 (2022)

71. Unbiased retrieval of frequency-dependent mechanical properties from noisy time-dependent signals;

S. Abuhattum, H.S. Kuan, P. Müller, J. Guck and V. Zaburdaev, Biophysical Reports doi: https://doi.org/10.1016/j.bpr.2022.100054 (2022)

2021

70. Thermal fluctuations assist mechanical signal propagation in coiled-coil proteins;

J. Clopés, J. Shin, M. Jahnel, S. W. Grill and V. Zaburdaev, Physical Review E doi: https://doi.org/10.1103/PhysRevE.104.054403 (2021)

69. RNA polymerase II clusters form in line with surface condensation on regulatory chromatin;

68. The Potential of OMICs Technologies for the Treatment of Immune‐Mediated Inflammatory Diseases;

C. G. Anhang, C. Xu, M. G. Raimondo, R. Atreya, A. Maier, G. Schett, V. Zaburdaev, S. Rauber and A. Ramming, International Journal of Molecular Sciences doi.org/ 10.3390/ijms22147506 (2021)

67. The hierarchical packing of euchromatin domains can be described as multiplicative cascades;

A. Noa, H.S. Kuan, V. Aschmann, V. Zaburdaev and L. Hilbert, PLoS Comp. Biol. doi: 10.1371/journal.pcbi.1008974 (2021)

66. Transcription organizes euchromatin via microphase separation;

L. Hilbert, Y. Sato, K. Kuznetsova, T. Bianucci, H. Kimura, F. Jülicher, A. Honigmann, V. Zaburdaev and N. L. Vastenhouw, Nature Communications doi: 10.1038/s41467-021-21589-3 (2021)

65. Continuum Theory of Active Phase Separation in Cellular Aggregates;

H.S. Kuan, W. Pönisch, F. Jülicher, and V. Zaburdaev, Physical Review Letters doi: 10.1103/PhysRevLett.126.018102 (2021)

2020

64. Maturation of Monocyte-Derived DCs Leads to Increased Cellular Stiffness, Higher Membrane Fluidity, and Changed Lipid Composition;

63. High-Precision Protein-Tracking With Interferometric Scattering Microscopy;

R. W. Taylor, C. Holler, R. G. Mahmoodabadi, M. Küppers, H. M. Dastjerdi, V. Zaburdaev, A. Schambony, and V. Sandoghdar, Frontiers in Cell and Developmental Biology doi: 10.3389/fcell.2020.590158 (2020)

62. Liquid Phase Separation Controlled by pH;

O. Adame-Arana, C. A.Weber, V. Zaburdaev, J. Prost, and F. Jülicher, Biophysical Journal doi: 10.1016/k.bpj.2020.07.044 (2020)

61. Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation;

D. Kaptan, S. Penkov, X. Zhang, V. R. Gade, B. K. Raghuraman, R. Galli, J. L. Sampaio, R. Haase, E. Koch, A. Shevchenko, V. Zaburdaev, and T. V. Kurzchalia, Aging Cell doi: 10.1111/acel.13214 (2020)

60. Ultrahigh-speed imaging of rotational diffusion on a lipid bilayer;

2019

59. Rectification of Bacterial Diffusion in Microfluidic Labyrinths;
A. Weber, M. Bahrs, Z. Alirezaeizanjani, X. Zhang, C. Beta, and V. Zaburdaev, Frontiers in Physics doi: 10.3389/fphy.2019.00148 (2019)

58. Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis;
Y. Sato, L. Hilbert, H. Oda, Y. Wan, J. M. Heddleston, T-L.Chew, V. Zaburdaev, P. Keller, T. Lionnet, N. Vastenhouw, and H. Kimura, Development, 146 (19), dev179127  (2019)

57. How bacterial cells and colonies move on solid substrates;
W. Pönisch, C.A. Weber, V. Zaburdaev, Physical Review E 99 (4), 042419 (2019)

56. Identifying the mechanism for superdiffusivity in mouse fibroblast motility;
G. Passucci, M. E. Brasch, J. H. Henderson, V. Zaburdaev,  and M. L. Manning, PLoS Comp. Biol. 15 (2), e1006732 (2019)

55. The shape of pinned forced polymer loops;
W. Huang and V. Zaburdaev, Soft Matter, 15 (8), 1785-1792 (2019)

2018

54. Intracellular mass density increase is accompanying but not sufficient for stiffening and growth arrest of yeast cells;
S. Abuhattum, K. Kim, T. Franzmann, A. Eßlinger, D. Midtvedt, R. Schlüßler, S. Möllmert, H.S. Kuan, S. Alberti, V. Zaburdaev and J. Guck,  Frontiers in Physics, 6:131 (2018)

53. Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation;
W. Pönisch, K.B. Eckenrode, K. Alzurqa, H. Nasrollahi, C. Weber, V. Zaburdaev and N. Biais, Scientific reports 8 (1), 16567 (2018)

52. Exactly solvable dynamics of forced polymer loops; W. Huang, Y.T. Lin, D. Froemberg, J. Shin, F. Jülicher, and V. Zaburdaev
New Journal of Physics, 20 113005 (2018)

51. Genetic noise mechanism for power-law switching in bacterial flagellar motors;
M.I. Krivonosov, V. Zaburdaev, S.V Denisov, M.V. Ivanchenko, Journal of Physics A: Mathematical and Theoretical 51 (26), 265601 (2018)

50. Relative distance between tracers as a measure of diffusivity within moving aggregates;
W. Pönisch, V Zaburdaev, The European Physical Journal B 91 (2), 27 (2018)

49. Chemotactic drift speed for bacterial motility pattern with two alternating turning events;
E.V. Pankratova, A.I. Kalyakulina, M.I. Krivonosov, S.V. Denisov, K.M. Taute, and V. Zaburdaev, PloS one 13 (1), e0190434 (2018)

2017

48. Live cell X-ray imaging of autophagic vacuoles formation and chromatin dynamics in fission yeast;
N. Strelnikova, N. Sauter, M. Guizar-Sicairos, M. Göllner, A. Diaz, P. Delivani, M. Chacón, I. M. Tolić, V. Zaburdaev, and T. Pfohl,
Scientific Reports 7,13775 (2017)

47. Elasticity-based polymer sorting in active fluids: A Brownian dynamics study; J. Shin, A. G. Cherstvy, W. K. Kim, and V. Zaburdaev,  Phys. Chem. Chem. Phys. 19, 18338-18347 (2017)

46. A tunable refractive index matching medium for live imaging cells, tissues and model organisms; T. Boothe, L. Hilbert, M. Heide, L. Berninger, W. B. Huttner, V. Zaburdaev, N. L. Vastenhouw, E. W. Myers, D. N. Drechsel, and J. C. Rink, eLife 2017; 6: e27240 (2017)

45. Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos; S. R. Joseph, M. Pálfy, L. Hilbert, M. Kumar, J. Karschau, V. Zaburdaev, A. Shevchenko, N. L. Vastenhouw, eLife 2017;6:e23326 (2017).

44. Limit theorems for Lévy walks in d dimensions: rare and bulk fluctuations; I. Fouxon, S. Denisov, V. Zaburdaev, and E. Barkai, J. Phys. A: Math. Theor. 50, 154002 (2017).

43. Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates;  W. Poenisch, C. A. Weber, G. Juckeland, N. Biais, and V. Zaburdaev, New Journal of Physics 19, 015003 (2017).

2016

42. Superdiffusive dispersals impart the geometry of underlying random walks; V. Zaburdaev, I. Fouxon, S. Denisov, and E. Barkai, Phys. Rev. Lett. 117, 270601 (2016).

41. Nucleosomal arrangement affects single-molecule transcription dynamics; V. Fitz, J. Shin, C. Ehrlich, L. Farnung, P. Cramer, V. Zaburdaev, and S. W. Grill, PNAS, 113, 12733–12738  (2016).

40. Reaction front propagation of actin polymerization in a comb-reaction system; A. Iomin,  V. Zaburdaev,  T. Pfohl, Chaos, Solitons & Fractals 92, 115–122 (2016).

39. A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy; M.C. Munder, D.Midtvedt, T. Franzmann, E. Nüske, O. Otto, M. Herbig, E.Ulbricht, P. Müller, A. Taubenberger, S. Maharana, L. Malinovska, D. Richter, J. Guck, V. Zaburdaev, and  S. Alberti, eLife 2016;5:e09347 (2016).

2015

38. Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes; Y.T. Lin, D. Frömberg, W. Huang, P. Delivani, M. Chacón, I. M. Tolić, F. Jülicher, and V. Zaburdaev, Phys. Rev. Lett. 115, 208102 (2015).

37. Pili-Induced Clustering of N. gonorrhoeae Bacteria; J. Taktikos, Y.T. Lin, H. Stark, N. Biais, and V. Zaburdaev, PLoS ONE 10: e0137661 (2015).

36. Formation and dissolution of bacterial colonies; C.A. Weber, Y.T. Lin, N. Biais, and V. Zaburdaev, Phys. Rev. E 92, 032704 (2015).

35. Lévy walks; V. Zaburdaev, S. Denisov, J. Klafter, Rev. Mod. Phys. 87, 483 (2015).

34. Asymptotic densities of ballistic Lévy walks; D. Froemberg, M. Schmiedeberg, E. Barkai, and V. Zaburdaev, Phys. Rev. E 91, 022131 (2015).

33. Random walk patterns of a soil bacterium in open and confined environments; M. Theves, J. Taktikos, V. Zaburdaev, H. Stark, and C. Beta, Europhysics Letters 109, 28007 (2015).

2014

32. Uncovering the Mechanism of Trapping and Cell Orientation during Neisseria gonorrhoeae Twitching Motility; V. Zaburdaev, N. Biais, M. Schmiedeberg, J. Eriksson, A.-B. Jonsson, M. P. Sheetz, and D. A. Weitz, Biophys J 107, p1523–1531, (2014).

2013

31. How the Motility Pattern of Bacteria Affects Their Dispersal and Chemotaxis; J. Taktikos, H. Stark, and V. Zaburdaev, PLoS ONE 8, e81936 (2013).

30. A Bacterial Swimmer with Two Alternating Speeds of Propagation; M. Theves, J. Taktikos, V. Zaburdaev, H. Stark, and C. Beta, Biophysical journal 105, 1915–1924 (2013).

29. Space-Time Velocity Correlation Function for Random Walks; V. Zaburdaev, S. Denisov, and P. Hänggi, Phys. Rev. Lett. 110, 170604 (2013) [see also Supplementary Material].

28. Liquid transport facilitated by channels in Bacillus subtilis biofilms; J. N. Wilking, V. Zaburdaev, M. De Volder, R. Losick, M. P. Brenner, and D. A. Weitz, PNAS 110 (3), 848-852 (2013).

2012

27.  Langevin description of superdiffusive Levy processes;  S. Eule, V. Zaburdaev, R. Friedrich, and T. Geisel, Phys. Rev. E  86, 041134 (2012)

26. Collective dynamics of model microorganisms with chemotactic signaling; J. Taktikos, V. Zaburdaev, and H. Stark, Phys. Rev. E 85, 051901 (2012)

25. Levy walks with velocity fluctuations; S. Denisov, V. Zaburdaev, and P. Hanggi, Phys. Rev. E 85, 031148 (2012)

2010-2011

24. Modeling a self-propelled autochemotactic walker; J. Taktikos, V. Zaburdaev, and H. Stark, Phys. Rev. E 84, 041924 (2011)

23. Langevin dynamics deciphers the motility pattern of swimming parasites; V. Zaburdaev, S. Uppaluri, T. Pfohl, M. Engstler, R. Friedrich, and H. Stark, Phys. Rev. Lett. 106, 208103 (2011)

22. Perturbation spreading in many particle systems: a random walk approach; V. Zaburdaev, S. Denisov and P. Hanggi, Phys. Rev. Lett. 106, 180601 (2011)

2007-2009

21. On moments and scaling regimes in anomalous random walks; M. Schmiedeberg, V. Zaburdaev and H. Stark, J. Stat. Mech. P12020 (2009)

20. Fractional diffusion equation for ageing and equilibrated random walks; V. Zaburdaev and I. M. Sokolov, Appl. Nonlin. Dyn. 4,  79-97  (2009)

19. Random walks with random velocities; V. Zaburdaev, M. Schmiedeberg, and H. Stark, Phys. Rev. E. 78, 011119 (2008) [Virtual Journal of Biological Physics Research, 16(3) (2008)]

18. Microscopic approach to random walks; V. Yu. Zaburdaev, J. Stat. Phys. 133, 159-167 (2008)

17. Stochastic transport through complex comb structures; V. Yu. Zaburdaev, P. V. Popov, A. S. Romanov, and K. V. Chukbar , JETP 106, 999-1005 (2008)

16. Chaoticity of the wet granular gas; A. Fingerle, S. Herminghaus, and V. Yu. Zaburdaev, Phys. Rev. E 75, 061301 (2007)

15. Dry and wet granular shock waves; V. Yu. Zaburdaev and S. Herminghaus, Phys. Rev. E 75, 031304 (2007)

2005-2006

14. Free cooling of one-dimensional wet granular gas;  V. Yu. Zaburdaev, M. Brinkmann, and S. Herminghaus,  Phys. Rev. Lett. 97, 018001 (2006)

13. Random walk model with waiting times depending on the preceding jump length; V. Yu. Zaburdaev, J. Stat. Phys. 123, pp. 871-881 (2006)

12. Theory of Heat transport in Magnetized High-temperature Plasma; V. Yu. Zaburdaev, Plasma Phys. Rep. 31, pp. 1071-1077 (2005)

11. Kolmogorov-Sinai entropy of the wet granular gas; A. Fingerle, S. Herminghaus, and V. Yu. Zaburdaev, Phys. Rev. Lett. 95, 198001 (2005)

10. “Hermitian” states in the vortex quantum interaction; V.Yu. Zaburdaev, S.A. Romanov, and K.V. Chukbar, Physics-Uspekhi 48, pp.841-846 (2005)

9. Subdiffusion in random compressible flows; K. V. Chukrbar and V. Yu. Zaburdaev, Phys. Rev. E 71, 061105 (2005)

2003-2004

8. Enhanced Superdiffusion and Finite Velocity of Levy Flights; K.V. Chukbar and V.Yu. Zaburdaev, in Simplicity behind Complexity, ed. W. Klonowski, Pabst Science Publishers, 2004

7. Nonlinear Dynamics of Electron Vortex Lattices; V. Yu. Zaburdaev, V. V. Smirnov, and K. V. Chukbar, Plasma Phys. Rep. 30,  pp. 214-217 (2004)

6. Memory Effects in Stochastic Transport; V. Yu. Zaburdaev and K. V. Chukbar, JETP Lett. 77, pp. 551-555 (2003)

5. Comment on “Towards deterministic equations for Levy walks: The fractional material derivative”; K. V. Chukbar and V. Yu. Zaburdaev, Phys. Rev. E 68, 033101 (2003)

2000-2002

4. Enhanced Superdiffusion and Finite Velocity of Levy Flights; V. Yu. Zaburdaev and K.V. Chukbar, JETP 94, pp. 252-259 (2002)

3. Analogue of a Wave Equation of the First Order for Particles with an Acoustic-like Law of a Dispersion; V. Yu. Zaburdaev, Preprint IAE-6204/1 (2001)

2. Skin Effects in Dusty Plasmas; V. Yu. Zaburdaev, Plasma Phys. Rep. 27, pp. 407–411 (2001)

1. Theory of the Non-diffusive Penetration of a Magnetic Field into Conducting Medium; V. Yu. Zaburdaev, Plasma Phys. Rep. 26, pp. 462–464 (2000)