Publications

Publications

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;

A. Pancholi* , T. Klingberg*, W. Zhang, R. Prizak, I. Mamontova, A. Noa, M. Sobucki, A. Y. Kobitsk, G. U. Nienhaus**, V. Zaburdaev** and L. Hilbert** (*equal contribution, **co-corresponding authors), Molecular Systems Biology doi: 10.15252/msb.202110272 (2021)

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;

J. Lühr, N. Alex, L. Amon, M. Kräter, M. Kubánková, E. Sezgin, C. H. K. Lehmann, L. Heger, G. F. Heidkamp, A-S. Smith, V. Zaburdaev, R. A. Böckmann, I. Levental, M. L. Dustin, C. Eggeling, J. Guck and D. Dudziak, Frontiers in Immunology doi: 10.3389/fimmu.2020.590121 (2020)

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.WeberV. 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;

M. MazaheriJ. EhrigA. ShkarinV. Zaburdaev, and V. Sandoghdar, Nano Letters doi: 10.1021/acs.nanolett.0c02516 (2020)


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 studyJ. 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)