@article{ShinCherstvyKimetal.2017, author = {Shin, Jaeoh and Cherstvy, Andrey G. and Kim, Won Kyu and Zaburdaev, Vasily}, title = {Elasticity-based polymer sorting in active fluids: a Brownian dynamics study}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {19}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c7cp02947k}, pages = {18338 -- 18347}, year = {2017}, abstract = {While the dynamics of polymer chains in equilibrium media is well understood by now, the polymer dynamics in active non-equilibrium environments can be very different. Here we study the dynamics of polymers in a viscous medium containing self-propelled particles in two dimensions by using Brownian dynamics simulations. We find that the polymer center of mass exhibits a superdiffusive motion at short to intermediate times and the motion turns normal at long times, but with a greatly enhanced diffusivity. Interestingly, the long time diffusivity shows a non-monotonic behavior as a function of chain length and stiffness. We analyze how the polymer conformation and the accumulation of self-propelled particles, and therefore the directed motion of the polymer, are correlated. At the point of maximal polymer diffusivity, the polymer has preferentially bent conformations maintained by the balance between the chain elasticity and the propelling force generated by the active particles. We also consider the barrier crossing dynamics of actively-driven polymers in a double-well potential. The barrier crossing times are demonstrated to have a peculiar non-monotonic dependence, related to that of the diffusivity. This effect can be potentially utilized for sorting polymers from solutions in in vitro experiments.}, language = {en} } @misc{WeberBahrsAlirezaeizanjanietal.2019, author = {Weber, Ariane and Bahrs, Marco and Alirezaeizanjani, Zahra and Zhang, Xingyu and Beta, Carsten and Zaburdaev, Vasily}, title = {Rectification of Bacterial Diffusion in Microfluidic Labyrinths}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {801}, issn = {1866-8372}, doi = {10.25932/publishup-44122}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441222}, pages = {11}, year = {2019}, abstract = {In nature as well as in the context of infection and medical applications, bacteria often have to move in highly complex environments such as soil or tissues. Previous studies have shown that bacteria strongly interact with their surroundings and are often guided by confinements. Here, we investigate theoretically how the dispersal of swimming bacteria can be augmented by microfluidic environments and validate our theoretical predictions experimentally. We consider a system of bacteria performing the prototypical run-and-tumble motion inside a labyrinth with square lattice geometry. Narrow channels between the square obstacles limit the possibility of bacteria to reorient during tumbling events to an area where channels cross. Thus, by varying the geometry of the lattice it might be possible to control the dispersal of cells. We present a theoretical model quantifying diffusive spreading of a run-and-tumble random walker in a square lattice. Numerical simulations validate our theoretical predictions for the dependence of the diffusion coefficient on the lattice geometry. We show that bacteria moving in square labyrinths exhibit enhanced dispersal as compared to unconfined cells. Importantly, confinement significantly extends the duration of the phase with strongly non-Gaussian diffusion, when the geometry of channels is imprinted in the density profiles of spreading cells. Finally, in good agreement with our theoretical findings, we observe the predicted behaviors in experiments with E. coli bacteria swimming in a square lattice labyrinth created in amicrofluidic device. Altogether, our comprehensive understanding of bacterial dispersal in a simple two-dimensional labyrinth makes the first step toward the analysis of more complex geometries relevant for real world applications.}, language = {en} } @article{WeberBahrsAlirezaeizanjanietal.2019, author = {Weber, Ariane and Bahrs, Marco and Alirezaeizanjani, Zahra and Zhang, Xingyu and Beta, Carsten and Zaburdaev, Vasily}, title = {Rectification of Bacterial Diffusion in Microfluidic Labyrinths}, series = {Frontiers in Physics}, volume = {7}, journal = {Frontiers in Physics}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-424X}, doi = {10.3389/fphy.2019.00148}, pages = {11}, year = {2019}, abstract = {In nature as well as in the context of infection and medical applications, bacteria often have to move in highly complex environments such as soil or tissues. Previous studies have shown that bacteria strongly interact with their surroundings and are often guided by confinements. Here, we investigate theoretically how the dispersal of swimming bacteria can be augmented by microfluidic environments and validate our theoretical predictions experimentally. We consider a system of bacteria performing the prototypical run-and-tumble motion inside a labyrinth with square lattice geometry. Narrow channels between the square obstacles limit the possibility of bacteria to reorient during tumbling events to an area where channels cross. Thus, by varying the geometry of the lattice it might be possible to control the dispersal of cells. We present a theoretical model quantifying diffusive spreading of a run-and-tumble random walker in a square lattice. Numerical simulations validate our theoretical predictions for the dependence of the diffusion coefficient on the lattice geometry. We show that bacteria moving in square labyrinths exhibit enhanced dispersal as compared to unconfined cells. Importantly, confinement significantly extends the duration of the phase with strongly non-Gaussian diffusion, when the geometry of channels is imprinted in the density profiles of spreading cells. Finally, in good agreement with our theoretical findings, we observe the predicted behaviors in experiments with E. coli bacteria swimming in a square lattice labyrinth created in amicrofluidic device. Altogether, our comprehensive understanding of bacterial dispersal in a simple two-dimensional labyrinth makes the first step toward the analysis of more complex geometries relevant for real world applications.}, language = {en} } @article{ThevesTaktikosZaburdaevetal.2013, author = {Theves, Matthias and Taktikos, Johannes and Zaburdaev, Vasily and Stark, Holger and Beta, Carsten}, title = {A bacterial swimmer with two alternating speeds of propagation}, series = {Biophysical journal}, volume = {105}, journal = {Biophysical journal}, number = {8}, publisher = {Cell Press}, address = {Cambridge}, issn = {0006-3495}, doi = {10.1016/j.bpj.2013.08.047}, pages = {1915 -- 1924}, year = {2013}, abstract = {We recorded large data sets of swimming trajectories of the soil bacterium Pseudomonas putida. Like other prokaryotic swimmers, P. putida exhibits a motion pattern dominated by persistent runs that are interrupted by turning events. An in-depth analysis of their swimming trajectories revealed that the majority of the turning events is characterized by an angle of phi(1) = 180 degrees (reversals). To a lesser extent, turning angles of phi(2 Sigma Sigma Sigma Sigma) = 00 are also found. Remarkably, we observed that, upon a reversal, the swimming speed changes by a factor of two on average a prominent feature of the motion pattern that, to our knowledge, has not been reported before. A theoretical model, based on the experimental values for the average run time and the rotational diffusion, recovers the mean-square displacement of P. putida if the two distinct swimming speeds are taken into account. Compared to a swimmer that moves with a constant intermediate speed, the mean-square displacement is strongly enhanced. We furthermore observed a negative dip in the directional autocorrelation at intermediate times, a feature that is only recovered in an extended model, where the nonexponential shape of the run-time distribution is taken into account.}, language = {en} }