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Immunophysics

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Publications Immunophysics Division

2015

Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes

Yen Ting Lin, Daniela Froemberg, Wenwen Huang, Petrina Delivani, Mariola Chacon, Iva M. Tolic, Frank Jülicher, Vasily Zaburdaev

Physical Review Letters 115 (20) 208102 (2015) | Journal

Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes

Yen Ting Lin, Daniela Froemberg, Wenwen Huang, Petrina Delivani, Mariola Chacon, Iva M. Tolic, Frank Juelicher, Vasily Zaburdaev

Physical Review Letters 115 (20) 208102 (2015) | Journal

During recombination, the DNA of parents exchange their genetic information to give rise to a genetically unique offspring. For recombination to occur, homologous chromosomes need to find each other and align with high precision. Fission yeast solves this problem by folding chromosomes in loops and pulling them through the viscous nucleoplasm. We propose a theory of pulled polymer loops to quantify the effect of drag forces on the alignment of chromosomes. We introduce an external force field to the concept of a Brownian bridge and thus solve for the statistics of loop configurations in space.

Pili-Induced Clustering of N-gonorrhoeae Bacteria

Johannes Taktikos, Yen Ting Lin, Holger Stark, Nicolas Biais, Vasily Zaburdaev

PLoS One 10 (9) e0137661 (2015) | Journal

Pili-Induced Clustering of N-gonorrhoeae Bacteria

Johannes Taktikos, Yen Ting Lin, Holger Stark, Nicolas Biais, Vasily Zaburdaev

PLOS ONE 10 (9) e0137661 (2015) | Journal | PDF

Type IV pili (Tfp) are prokaryotic retractable appendages known to mediate surface attachment, motility, and subsequent clustering of cells. Tfp are the main means of motility for Neisseria gonorrhoeae, the causative agent of gonorrhea. Tfp are also involved in formation of the microcolonies, which play a crucial role in the progression of the disease. While motility of individual cells is relatively well understood, little is known about the dynamics of N. gonorrhoeae aggregation. We investigate how individual N. gonorrhoeae cells, initially uniformly dispersed on flat plastic or glass surfaces, agglomerate into spherical microcolonies within hours. We quantify the clustering process by measuring the area fraction covered by the cells, number of cell aggregates, and their average size as a function of time. We observe that the microcolonies are also able to move but their mobility rapidly vanishes as the size of the colony increases. After a certain critical size they become immobile. We propose a simple theoretical model which assumes a pili-pili interaction of cells as the main clustering mechanism. Numerical simulations of the model quantitatively reproduce the experimental data on clustering and thus suggest that the agglomeration process can be entirely explained by the Tfp-mediated interactions. In agreement with this hypothesis mutants lacking pili are not able to form colonies. Moreover, cells with deficient quorum sensing mechanism show similar aggregation as the wild-type bacteria. Therefore, our results demonstrate that pili provide an essential mechanism for colony formation, while additional chemical cues, for example quorum sensing, might be of secondary importance.

Formation and dissolution of bacterial colonies

Christoph A. Weber, Yen Ting Lin, Nicolas Biais, Vasily Zaburdaev

Physical Review E 92 (3) 032704 (2015) | Journal

Many organisms form colonies for a transient period of time to withstand environmental pressure. Bacterial biofilms are a prototypical example of such behavior. Despite significant interest across disciplines, physical mechanisms governing the formation and dissolution of bacterial colonies are still poorly understood. Starting from a kinetic description of motile and interacting cells we derive a hydrodynamic equation for their density on a surface, where most of the kinetic coefficients are estimated from experimental data for N. gonorrhoeae bacteria. We use it to describe the formation of multiple colonies with sizes consistent with experimental observations. Finally, we show how the changes in the cell-to-cell interactions lead to the dissolution of the bacterial colonies. The successful application of kinetic theory to a complex far from equilibrium system such as formation and dissolution of living bacterial colonies potentially paves the way for the physical quantification of the initial stages of biofilm formation.

Formation and dissolution of bacterial colonies

Christoph A. Weber, Yen Ting Lin, Nicolas Biais, Vasily Zaburdaev

Physical Review E 92 (3) 032704 (2015) | Journal | PDF

Levy walks

Vasily Zaburdaev, S. Denisov, J. Klafter

Reviews of Modern Physics 87 (2) 483-530 (2015) | Journal

Random walk is a fundamental concept with applications ranging from quantum physics to econometrics. Remarkably, one specific model of random walks appears to be ubiquitous across many fields as a tool to analyze transport phenomena in which the dispersal process is faster than dictated by Brownian diffusion. The Levy-walk model combines two key features, the ability to generate anomalously fast diffusion and a finite velocity of a random walker. Recent results in optics, Hamiltonian chaos, cold atom dynamics, biophysics, and behavioral science demonstrate that this particular type of random walk provides significant insight into complex transport phenomena. This review gives a self-consistent introduction to Levy walks, surveys their existing applications, including latest advances, and outlines further perspectives.

Levy walks

V. Zaburdaev, S. Denisov, J. Klafter

Reviews of Modern Physics 87 (2) 483-530 (2015) | Journal

Asymptotic densities of ballistic Levy walks

D. Froemberg, M. Schmiedeberg, E. Barkai, Vasily Zaburdaev

Physical Review E 91 (2) 022131 (2015) | Journal

We propose an analytical method to determine the shape of density profiles in the asymptotic long-time limit for a broad class of coupled continuous-time random walks which operate in the ballistic regime. In particular, we show that different scenarios of performing a random-walk step, via making an instantaneous jump penalized by a proper waiting time or via moving with a constant speed, dramatically effect the corresponding propagators, despite the fact that the end points of the steps are identical. Furthermore, if the speed during each step of the random walk is itself a random variable, its distribution gets clearly reflected in the asymptotic density of random walkers. These features are in contrast with more standard nonballistic random walks.

Asymptotic densities of ballistic Lévy walks

D. Froemberg, M. Schmiedeberg, E. Barkai, V. Zaburdaev

Physical Review E 91 (2) 022131 (2015) | Journal | PDF

Random walk patterns of a soil bacterium in open and confined environments

M. Theves, J. Taktikos, V. Zaburdaev, H. Stark, C. Beta

EPL 109 (2) 28007 (2015) | Journal

Random walk patterns of a soil bacterium in open and confined environments

M. Theves, J. Taktikos, Vasily Zaburdaev, H. Stark, C. Beta

EPL 109 (2) 28007 (2015) | Journal

We used microfluidic tools and high-speed time-lapse microscopy to record trajectories of the soil bacterium Pseudomonas putida in a confined environment with cells swimming in close proximity to a glass-liquid interface. While the general swimming pattern is preserved, when compared to swimming in the bulk fluid, our results show that cells in the presence of two solid boundaries display more frequent reversals in swimming direction and swim faster. Additionally, we observe that run segments are no longer straight and that cells swim on circular trajectories, which can be attributed to the hydrodynamic wall effect. Using the experimentally observed parameters together with a recently presented analytic model for a run-reverse random walker, we obtained additional insight on how the spreading behavior of a cell population is affected under confinement. While on short time scales, the mean square displacement of confined swimmers grows faster as compared to the bulk fluid case, our model predicts that for large times the situation reverses due to the strong increase in effective rotational diffusion. Copyright (C) EPLA, 2015

Contact

Immunophysics Division
Prof. Vasily Zaburdaev
Principal Investigator

Max-Planck-Zentrum für Physik und Medizin
Kussmaulallee 2
Room 02.116
91054 Erlangen, Germany
+49 9131 8284 102

vasily.zaburdaev@mpzpm.mpg.de

Silke Besold

Secretary

Friedrich-Alexander-Universität Erlangen-Nürnberg
Chair of Mathematics in Life Sciences
Kussmaulallee 2
Room 02.122
91054 Erlangen, Germany
+49 9131 8284 104

silke.besold@fau.de

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