arXiv subjects

Sakuntala Chatterjee

Publications and source records attributed to Sakuntala Chatterjee.

36 records · Page 2Linked to original sources

arXiv2018

Current reversal in interacting colloids under time-periodic drive

Using molecular dynamics simulations, we study particle-transport in a system of interacting colloidal particles on a ring, where the system is driven by a time-dependent external potential, moving along the ring. We consider two driving protocols: (i) the external potential barrier moves with a uniform velocity $v$ along the ring, and (ii) it moves in discrete jumps with jump-length $l$ and waiting time $τ$ with an effective velocity $v=l/τ$. The time-averaged (dc) particle current, which always remains positive in case (i), interestingly reverses its direction in case (ii) upon tuning the particle-number density $ρ_0$ and the effective barrier velocity $v$. We also find a scaling form for the current in terms of number density, barrier velocity, barrier height and temperature of the system.

cond-mat.stat-mech↗

arXiv2018

Optimal methylation noise for best chemotactic performance of {\sl E. coli}

In response to a concentration gradient of nutrient, E. coli bacterium modulates the rotational bias of flagellar motors which control its run-and-tumble motion, to migrate towards regions of high nutrient concentration. Presence of stochastic noise in the biochemical pathway of the cell has important consequence on the switching mechanism of motor bias, which in turn affects the runs and tumbles of the cell. We model the intra-cellular reaction network in terms of coupled time-evolution of three stochastic variables, kinase activity, methylation level and CheY-P protein level, and study the effect of methylation noise on the chemotactic performance of the cell. In presence of a spatially varying nutrient concentration profile, a good chemotactic performance allows the cell to climb up the concentration gradient fast and localize in the nutrient-rich regions in the long time limit. Our simulations show that the best performance is obtained at an optimal noise strength. While it is expected that chemotaxis will be weaker for very large noise, it is counter-intuitive that the performance worsens even when noise level falls below a certain value. We explain this striking result by detailed analysis of CheY-P protein level statistics for different noise strengths. We show that when the CheY-P level falls below a certain (noise-dependent) threshold, the cell tends to move down the concentration gradient of the nutrient, which has a detrimental effect on its chemotactic response. This threshold value decreases as noise is increased, and this effect is responsible for noise-induced enhancement of chemotactic performance. In a harsh chemical environment, when the nutrient degrades with time, the amount of nutrient intercepted by the cell trajectory, is an effective performance criterion. In this case also, we find an optimum noise strength, depending on the nutrient lifetime.

q-bio.CB↗

arXiv2018

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. In one case, the energy cost is assumed to be proportional to the absolute magnitude of the height gradient (gradient model) and in the other case it is proportional to the square of the height gradient (Gaussian model). For the gradient model we find that the membrane velocity is a non-monotonic function of the elastic constant $μ$, and reaches a peak at $μ=μ^\ast$. For $μ< μ^\ast$ the system fails to reach a steady state and the membrane energy keeps increasing with time. For the Gaussian model, the system always reaches a steady state and the membrane velocity decreases monotonically with the elastic constant $ν$ for all nonzero values of $ν$. Multiple filaments give rise to protrusions at different regions of the membrane and the elasticity of the membrane induces an effective attraction between the two protrusions in the Gaussian model which causes the protrusions to merge and a single wide protrusion is present in the system. In both the models, the relative time-scale between the membrane and filament dynamics plays an important role in deciding whether the shape of elasticity-velocity curve is concave or convex. Our numerical simulations agree reasonably well with our analytical calculations.

physics.bio-ph↗

arXiv2017

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. In all these ordered phases the two particle species phase separate completely from each other, but the underlying landscape may either show complete ordering, with macroscopic regions with distinct average slopes, or may show coexistence of ordered and disordered regions, depending on the differential nature of effect produced by the particle species on the landscape. We discuss several aspects of static properties of these phases in this paper, and we discuss the dynamics of these phases in the sequel.

cond-mat.stat-mech↗

arXiv2017

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. In this paper we discuss the dynamics. We show that in the ordered phases macroscopic particle clusters move over an ergodic time-scale growing exponentially with system size but the ordered landscape shows dynamics over a faster time-scale growing as a power of system size. We present a scaling ansatz that describes several dynamical correlation functions of the landscape measured in steady state.

cond-mat.stat-mech↗

arXiv2016

Actin filaments growing against a barrier with fluctuating shape

We study force generation by a set of parallel actin filaments growing against a non-rigid obstacle, in 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 non-rigid 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. We find the shape fluctuations of the barrier strongly affects the force generation mechanism. The qualitative nature of the force-velocity curve is crucially determined by the relative time-scale of filament and barrier dynamics. The height profile of the barrier also shows interesting variation with the external load. Our analytical calculation within mean-field theory shows reasonable agreement with our simulation results.

q-bio.SC↗

arXiv2016

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 proposed earlier [Phys. Rev. E 89, 022138 (2014)]. The defects move with uniform velocity and change the particle hopping rates locally. We explore the collective effects of the defects on the spatial structure and transport properties of the system. We also introduce an SSEP with ordered sequential (sitewise) update and elucidate the close connection with our model.

cond-mat.stat-mech↗

arXiv2016

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 density 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.

cond-mat.stat-mech↗

arXiv2015

Optimal search in E.coli chemotaxis

We study chemotaxis of a single {\sl 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. In the limit of very slow nutrient diffusion, the bacterium effectively experiences a Gaussian concentration profile with a fixed width. In this case we find that there exists an optimum width of the Gaussian when the average first passage time is minimum, {\sl i.e.}, the search process is most efficient. We verify the existence of the optimum width for the deterministic initial position of the bacterium and also for the stochastic initial position, drawn from uniform and steady state distributions. Our numerical simulation in a model of a non-Markovian random walker agrees well with our analytical calculations in a related coarse-grained model. We also present our simulation results for the case when the nutrient diffusion and bacterial motion occur over comparable time-scales and the bacterium senses a time-varying concentration field.

q-bio.CB↗

arXiv2014

Boundary induced phase transition with stochastic entrance and exit

We study an open-chain totally asymmetric exclusion process (TASEP) with stochastic gates present at the two boundaries. The gating dynamics has been modeled keeping the physical system of ion-channel gating in mind. These gates can randomly switch between an open state and a closed state. In the open state, the gates are highly permeable such that any particle arriving at the gate immediately passes through. In the closed state, a particle gets trapped at the gate and cannot pass through until the gate switches open again. We calculate the phase-diagram of the system and find important and non-trivial differences with the phase-diagram of a regular open-chain TASEP. In particular, depending on switching rates of the two gates, the system may or may not admit a maximal current phase. Our analytic calculation within mean-field theory captures the main qualitative features of our Monte Carlo simulation results. We also perform a refined mean-field calculation where the correlations at the boundaries are taken into account. This theory shows significantly better quantitative agreement with our simulation results.

cond-mat.stat-mech↗

arXiv2014

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. By tuning these variables, the most efficient transport can be achieved in either direction along the ring. These features can be understood in terms of a traveling density wave propagating in the system. Our results could be experimentally tested, e.g., in a system of colloidal particles driven by a moving optical tweezer.

cond-mat.stat-mech↗

arXiv2011

Chemotaxis When Bacteria Remember: Drift versus Diffusion

{\sl Escherichia coli} ({\sl 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. Recent work has viewed chemotaxis as a compromise between drift toward favorable regions and accumulation in favorable regions. A number of earlier studies assume that a bacterium resets its memory at tumbles -- a fact not borne out by experiment -- and make use of approximate coarse-grained descriptions. Here, we revisit the problem of chemotaxis without resorting to any memory resets. We find that when bacteria respond to the environment in a non-adaptive manner, chemotaxis is generally dominated by diffusion, whereas when bacteria respond in an adaptive manner, chemotaxis is dominated by a bias in the motion. In the adaptive case, favorable drift occurs together with favorable accumulation. We derive our results from detailed simulations and a variety of analytical arguments. In particular, we introduce a new coarse-grained description of chemotaxis as biased diffusion, and we discuss the way it departs from older coarse-grained descriptions.

cond-mat.stat-mech↗

arXiv2010

Determinant representation for some transition probabilities in the TASEP with second class particles

We study the transition probabilities for the totally asymmetric simple exclusion process (TASEP) on the infinite integer lattice with a finite, but arbitrary number of first and second class particles. Using the Bethe ansatz we present an explicit expression of these quantities in terms of the Bethe wave function. In a next step it is proved rigorously that this expression can be written in a compact determinantal form for the case where the order of the first and second class particles does not change in time. An independent geometrical approach provides insight into these results and enables us to generalize the determinantal solution to the multi-class TASEP.

cond-mat.stat-mech↗

arXiv2010

Importance of boundary effects in diffusion of hydrocarbon molecules in a one-dimensional zeolite channel

Single-file diffusion of propane and toluene molecules inside a narrow, effectively one-dimensional zeolite pore was experimentally studied by Czaplewski {\sl et al.} Using a stochastic lattice gas approach, we obtain an analytical description of this process for the case of single-component loading. We show that a good quantitative agreement with the experimental data for the desorption temperature of the hydrocarbon molecules can be obtained if the desorption process from the boundary is associated with a higher activation energy than the diffusion process in the bulk. We also present Dynamical Monte Carlo simulation results for two-component loading which demonstrate in agreement with the experimental findings the effects of mutual blockage of the molecules due to single-file diffusion.

cond-mat.stat-mech↗

arXiv2009

Diffusion of a hydrocarbon mixture in a one-dimensional zeolite channel: an exclusion model approach

Zeolite channels can be used as effective hydrocarbon traps. Earlier experiments (Czaplewski {\sl et al.}, 2002) show that the presence of large aromatic molecules (toluene) block the diffusion of light hydrocarbon molecules (propane) inside the narrow pore of a zeolite sample. As a result, the desorption temperature of propane is significantly higher in the binary mixture than in the single component case. In order to obtain further insight into these results, we use a simple lattice gas model of diffusion of hard-core particles to describe the diffusive transport of two species of molecules in a one-dimensional zeolite channel. Our dynamical Monte Carlo simulations show that taking into account an Arrhenius dependence of the single molecule diffusion coefficient on temperature, one can explain many significant features of the temperature programmed desorption profile observed in experiments. However, on a closer comparison of the experimental curve and our simulation data, we find that it is not possible to reproduce the higher propane current than toluene current near the desorption peak seen in experiment. We argue that this is caused by a violation of strict single-file behavior.

cond-mat.stat-mech↗

arXiv2008

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 characterising 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). We demonstrate this by numerical studies of several dynamical correlation functions for two probes and also for a macroscopic number of probes. Our results are consistent with the expectation that the short-ranged correlations induced by the Ising interaction should not affect the large time and large distance properties of the system, implying that scaling forms remain the same as in the medium with no interactions present.

cond-mat.stat-mech↗

arXiv2007

Dynamics of Shock Probes in Driven Diffusive Systems

We study the dynamics of shock-tracking probe particles in driven diffusive systems and also in equilibrium systems. In a driven system, they induce a diverging timescale that marks the crossover between a passive scalar regime at early times and a diffusive regime at late times; a scaling form characterises this crossover. Introduction of probes into an equilibrium system gives rise to a system-wide density gradient, and the presence of even a single probe can be felt across the entire system.

cond-mat.stat-mech↗

arXiv2005

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 auto-correlation function in steady state and in the aging regime, and space-time correlation functions in steady state. We have also calculated these quantities analytically in a related surface model. The steady state auto-correlation is a scaling function of t/L^z, where L is the system size and z the dynamic exponent. Starting from a finite intercept, the scaling function decays with a cusp, in the small argument limit. The finite value of the intercept indicates the existence of long range order in the system. The space-time correlation, which is a function of r/L and t/L^z, is non-monotonic in t for fixed r. The aging auto-correlation is a scaling function of t_1 and t_2 where t_1 is the waiting time and t_2 the time difference. This scaling function decays as a power law for t_2 \gg t_1; for t_1 \gg t_2, it decays with a cusp as in steady state. To reconcile the occurrence of strong fluctuations in the steady state with the fact of an ordered state, we measured the distribution function of the length of the largest cluster. This shows that fluctuations never destroy ordering, but rather the system meanders from one ordered configuration to another on a relatively rapid time scale.

cond-mat.stat-mech↗