Effect of relative timescale on a system of particles sliding on a fluctuating energy landscape: Exact derivation of product measure condition.

We consider a system of hardcore particles advected by a fluctuating potential energy landscape, whose dynamics is in turn affected by the particles. Earlier studies have shown that as a result of two-way coupling between the landscape and the particles, the system shows an interesting phase diagram as the coupling parameters are varied. The phase diagram consists of various different kinds of ordered phases and a disordered phase.

Optimum transport in systems with time-dependent drive and short-ranged interactions.

We consider a one-dimensional lattice gas model of hardcore particles with nearest-neighbor interaction in presence of a time-periodic external potential. We investigate how attractive or repulsive interaction affects particle transport and determine the conditions for optimum transport, i.e.

Effect of receptor cooperativity on methylation dynamics in bacterial chemotaxis with weak and strong gradient.

We study methylation dynamics of the chemoreceptors as an Escherichia coli cell moves around in a spatially varying chemoattractant environment. We consider attractant concentration with strong and weak spatial gradient. During the uphill and downhill motion of the cell along the gradient, we measure the temporal variation of average methylation level of the receptor clusters.

Effect of receptor clustering on chemotactic performance of E. coli: Sensing versus adaptation.

We show how the competition between sensing and adaptation can result in a performance peak in Escherichia coli chemotaxis using extensive numerical simulations in a detailed theoretical model. Receptor clustering amplifies the input signal coming from ligand binding which enhances chemotactic efficiency. But large clusters also induce large fluctuations in total activity since the number of clusters goes down.

Dynamics of coupled modes for sliding particles on a fluctuating landscape.

The recently developed formalism of nonlinear fluctuating hydrodynamics (NLFH) has been instrumental in unraveling many new dynamical universality classes in coupled driven systems with multiple conserved quantities. In principle, this formalism requires knowledge of the exact expression of locally conserved current in terms of local density of the conserved components. However, for most nonequilibrium systems an exact expression is not available and it is important to know what happens to the predictions of NLFH in these cases.

Interplay between surface and bending energy helps membrane protrusion formation.

We consider a one-dimensional elastic membrane, which is pushed by growing filaments. The filaments tend to grow by creating local protrusions in the membrane and this process has surface energy and bending energy costs. Although it is expected that with increasing surface tension and bending rigidity, it should become more difficult to create a protrusion, we find that for a fixed bending rigidity, as the surface tension increases, protrusions are more easily formed.

Run-and-tumble motion with steplike responses to a stochastic input.

We study a simple run-and-tumble random walk whose switching frequencies between run mode and tumble mode depend on a stochastic signal. We consider a particularly sharp, steplike dependence, where the run-to-tumble switching probability jumps from zero to one as the signal crosses a particular value (say y_{1}) from below. Similarly, tumble-to-run switching probability also shows a jump like this as the signal crosses another value (y_{2} View Article and Find Full Text PDF

Actin filaments pushing against a barrier: Comparison between two force generation mechanisms.

To theoretically understand force generation properties of actin filaments, many models consider growing filaments pushing against a movable obstacle or barrier. In order to grow, the filaments need space and hence it is necessary to move the barrier. Two different mechanisms for this growth are widely considered in the literature.

Optimal methylation noise for best chemotactic performance of E. coli.

In response to a concentration gradient of chemoattractant, E. coli bacterium modulates the rotational bias of flagellar motors which control its run-and-tumble motion, to migrate towards regions of high chemoattractant concentration. Presence of stochastic noise in the biochemical pathway of the cell has important consequences on the switching mechanism of motor bias, which in turn affects the runs and tumbles of the cell in a significant way.

Actin filaments growing against an elastic membrane: Effect of membrane tension.

We study the force generation by a set of parallel actin filaments growing against an elastic membrane. The elastic membrane tries to stay flat and any deformation from this flat state, either caused by thermal fluctuations or due to protrusive polymerization force exerted by the filaments, costs energy. We study two lattice models to describe the membrane dynamics.

Publisher's Note: Ordered phases in coupled nonequilibrium systems: Dynamic properties [Phys. Rev. E 96, 022128 (2017)].

This corrects the article DOI: 10.1103/PhysRevE.96.

Ordered phases in coupled nonequilibrium systems: Static properties.

We study a coupled driven system in which two species of particles are advected by a fluctuating potential energy landscape. While the particles follow the potential gradient, each species affects the local shape of the landscape in different ways. As a result of this two-way coupling between the landscape and the particles, the system shows interesting new phases, characterized by different sorts of long-ranged order in the particles and in the landscape.

Ordered phases in coupled nonequilibrium systems: Dynamic properties.

We study the dynamical properties of the ordered phases obtained in a coupled nonequilibrium system describing advection of two species of particles by a stochastically evolving landscape. The local dynamics of the landscape also gets affected by the particles. In a companion paper we have presented static properties of different phases that arise as the two-way coupling parameters are varied.

Actin filaments growing against a barrier with fluctuating shape.

We study force generation by a set of parallel actin filaments growing against a nonrigid obstacle, in the presence of an external load. The filaments polymerize by either moving the whole obstacle, with a large energy cost, or by causing local distortion in its shape which costs much less energy. The nonrigid obstacle also has local thermal fluctuations due to which its shape can change with time and we describe this using fluctuations in the height profile of a one-dimensional interface with Kardar-Parisi-Zhang dynamics.

Symmetric exclusion processes on a ring with moving defects.

We study symmetric simple exclusion processes (SSEP) on a ring in the presence of uniformly moving multiple defects or disorders-a generalization of the model we proposed earlier [Phys. Rev. E 89, 022138 (2014)PLEEE81539-375510.

Large compact clusters and fast dynamics in coupled nonequilibrium systems.

We demonstrate particle clustering on macroscopic scales in a coupled nonequilibrium system where two species of particles are advected by a fluctuating landscape and modify the landscape in the process. The phase diagram generated by varying the particle-landscape coupling, valid for all particle densities and in both one and two dimensions, shows novel nonequilibrium phases. While particle species are completely phase separated, the landscape develops macroscopically ordered regions coexisting with a disordered region, resulting in coarsening and steady state dynamics on time scales which grow algebraically with size, not seen earlier in systems with pure domains.

Optimal search in E. coli chemotaxis.

We study chemotaxis of a single E. coli bacterium in a medium where the nutrient chemical is also undergoing diffusion and its concentration has the form of a Gaussian whose width increases with time. We measure the average first passage time of the bacterium at a region of high nutrient concentration.

Interacting particles in a periodically moving potential: traveling wave and transport.

We study a system of interacting particles in a periodically moving external potential, within the simplest possible description of paradigmatic symmetric exclusion process on a ring. The model describes diffusion of hardcore particles where the diffusion dynamics is locally modified at a uniformly moving defect site, mimicking the effect of the periodically moving external potential. The model, though simple, exhibits remarkably rich features in particle transport, such as polarity reversal and double peaks in particle current upon variation of defect velocity and particle density.

Chemotaxis when bacteria remember: drift versus diffusion.

Escherichia coli (E. coli) bacteria govern their trajectories by switching between running and tumbling modes as a function of the nutrient concentration they experienced in the past. At short time one observes a drift of the bacterial population, while at long time one observes accumulation in high-nutrient regions.

Strong molecular traffic control effect in TNU-9 zeolite channel topology.

Reactivity enhancement in a catalytic zeolite grain through molecular traffic control (MTC) rests on the basic notion that the reactant and product molecules prefer to diffuse along different channels inside the grain and therefore do not mutually hinder their transport in and out of the grain. We investigate the conditions of reactivity enhancement in the presence of MTC for a realistic channel topology that describes the pore structure of a TNU-9 zeolite. We compare the output current of an MTC system with a reference system, which does not show any channel selectivity.

Shock probes in a one-dimensional Katz-Lebowitz-Spohn model.

We consider shock probes in a one-dimensional driven diffusive medium with nearest-neighbor Ising interaction (KLS model). Earlier studies based on an approximate mapping of the present system to an effective zero-range process concluded that the exponents characterizing the decays of several static and dynamical correlation functions of the probes depend continuously on the strength of the Ising interaction. On the contrary, our numerical simulations indicate that over a substantial range of the interaction strength, these exponents remain constant and their values are the same as in the case of no interaction (when the medium executes an ASEP).

Dynamics of fluctuation-dominated phase ordering: hard-core passive sliders on a fluctuating surface.

We study the dynamics of a system of hard-core particles sliding downwards on a one-dimensional fluctuating interface, which in a special case can be mapped to the problem of a passive scalar advected by a Burgers fluid. Driven by the surface fluctuations, the particles show a tendency to cluster, but the hard-core interaction prevents collapse. We use numerical simulations to measure the autocorrelation function in steady state and in the aging regime, and space-time correlation functions in steady state.