arXiv subjects

Gil Ariel

Publications and source records attributed to Gil Ariel.

25 records · Page 2Linked to original sources

arXiv2019

A phase diagram for bacterial swarming

Bacterial swarming is a rapid mass-migration, in which thousands of cells spread collectively to colonize a surface. Physically, swarming is a natural example of active particles that use energy to generate motion. Accordingly, understanding the constraints physics imposes on the dynamics is essential to understand the mechanisms underlying the swarming phenomenon. We present new experiments of swarming Bacillus subtilis mutants with different aspect ratios and densities. Analyzing the dynamics reveals a rich phase diagram of qualitatively distinct swarming regimes, describing how the shape and density of cells govern the global dynamical characteristics of the entire swarm. Moreover, we show that under standard conditions bacteria inhabit a region of phase space that is associated with rapid mixing and robust dynamics, with homogeneous density and no preferred direction of motion. This contrasts characteristic clustering behavior of self-propelled rods that is recovered only for very elongated mutant species. Thus, bacteria have adapted their physics to optimize the principle functions assumed for swarming.

cond-mat.soft↗

arXiv2019

Conservative, Dissipative and Super-diffusive Behavior of a Particle Propelled in a Regular Flow

A recent model of Ariel et al. [1] for explaining the observation of Lévy walks in swarming bacteria suggests that self-propelled, elongated particles in a periodic array of regular vortices perform a super-diffusion that is consistent with Lévy walks. The equations of motion, which are reversible in time but not volume preserving, demonstrate a new route to L'evy walking in chaotic systems. Here, the dynamics of the model is studied both analytically and numerically. It is shown that the apparent super-diffusion is due to "sticking" of trajectories to elliptic islands, regions of quasi-periodic orbits reminiscent of those seen in conservative systems. However, for certain parameter values, these islands coexist with asymptotically stable periodic trajectories, causing dissipative behavior on very long time scales.

nlin.CD↗

arXiv2018

θ-parareal schemes

A weighted version of the parareal method for parallel-in-time computation of time dependent problems is presented. Linear stability analysis for a scalar weighing strategy shows that the new scheme may enjoy favorable stability properties with marginal reduction in accuracy at worse. More complicated matrix-valued weights are applied in numerical examples. The weights are optimized using information from past iterations, providing a systematic framework for using the parareal iterations as an approach to multiscale coupling. The advantage of the method is demonstrated using numerical examples, including some well-studied nonlinear Hamiltonian systems.

math.NA↗

arXiv2015

Parareal methods for highly oscillatory dynamical systems

We introduce a new strategy for coupling the parallel in time (parareal) iterative methodology with multiscale integrators. Following the parareal framework, the algorithm computes a low-cost approximation of all slow variables in the system using an appropriate multiscale integrator, which is refined using parallel fine scale integrations. Convergence is obtained using an alignment algorithm for fast phase-like variables. The method may be used either to enhance the accuracy and range of applicability of the multiscale method in approximating only the slow variables, or to resolve all the state variables. The numerical scheme does not require that the system is split into slow and fast coordinates. Moreover, the dynamics may involve hidden slow variables, for example, due to resonances. We propose an alignment algorithm for almost-periodic solution, in which case convergence of the parareal iterations is proved. The applicability of the method is demonstrated in numerical examples.

math.NA↗

arXiv2004

Competition between condensation of monovalent and multivalent ions in DNA aggregation

We discuss the distribution of ions around highly charged PEs when there is competition between monovalent and multivalent ions, pointing out that in this case the number of condensed ions is sensitive to short-range interactions, salt, and model-dependent approximations. This sensitivity is discussed in the context of recent experiments on DNA aggregation, induced by multivalent counterions such as spermine and spermidine.

cond-mat.soft↗

arXiv2002

The Persistence Length of a Strongly Charged, Rod-like, Polyelectrolyte in the Presence of Salt

The persistence length of a single, intrinsically rigid polyelectrolyte chain, above the Manning condensation threshold is investigated theoretically in presence of added salt. Using a loop expansion method, the partition function is consistently calculated, taking into account corrections to mean-field theory. Within a mean-field approximation, the well-known results of Odijk, Skolnick and Fixman are reproduced. Beyond mean-field, it is found that density correlations between counterions and thermal fluctuations reduce the stiffness of the chain, indicating an effective attraction between monomers for highly charged chains and multivalent counterions. This attraction results in a possible mechanical instability (collapse), alluding to the phenomenon of DNA condensation. In addition, we find that more counterions condense on slightly bent conformations of the chain than predicted by the Manning model for the case of an infinite cylinder. Finally, our results are compared with previous models and experiments.

cond-mat.stat-mech↗

arXiv2002

Polyelectrolyte Persistence Length: Attractive Effect of Counterion Correlations and Fluctuations

The persistence length of a single, strongly charged, stiff polyelectrolyte chain is investigated theoretically. Path integral formulation is used to obtain the effective electrostatic interaction between the monomers. We find significant deviations from the classical Odijk, Skolnick and Fixman (OSF) result. An induced attraction between monomers is due to thermal fluctuations and correlations between bound counterions. The electrostatic persistence length is found to be smaller than the OSF value and indicates a possible mechanical instability (collapse) for highly charged polyelectrolytes with multivalent counterions. In addition, we calculate the amount of condensed counterions on a slightly bent polyelectrolyte. More counterions are found to be adsorbed as compared to the Manning condensation on a cylinder.

cond-mat.soft↗