arXiv subjects

Sakuntala Chatterjee

Publications and source records attributed to Sakuntala Chatterjee.

At least 19 recordsLinked to original sources

arXiv2026

Jamming transition in an active exclusion process

Multiple studies on active matter have shown that activity can induce or suppress a phase transition, or modify the critical behavior of a passive system. Here we investigate how activity affects the jamming transition which is a paradigmatic example of nonequilibrium phase transitions in passive systems. We consider a one-dimensional system of active particles with hardcore interactions and a direction of self-propulsion which can be reversed at a given switching rate. For a class of particle hop rates and infinite switching rate, our model reduces to a passive system which is known to exhibit a transition between a high-density fluid phase and a low-density jammed phase in the stationary state. Using Monte Carlo simulations and a mean field theory, we study how the mean mobility of the particle and the hole cluster distribution vary with density and finite switching rate. Our main result is that activity hinders the formation of jam and can even inhibit it; more precisely, we find that the jamming transition occurs at a critical density that decreases with decreasing switching rate, and at sufficiently small switching rate, the system exists only in the fluid phase.

cond-mat.stat-mech↗

arXiv2026

A Novel Mechanism of Ordering in a Coupled Driven System: Vacancy Induced Phase Separation

We study a coupled driven system where two different species of particles, along with some vacancies or holes, move on a landscape whose shape fluctuates with time. The movement of the particles is guided by the local shape of the landscape, and this shape is also affected by the presence of different particle species. When a particle species push the landscape in the same (opposite) direction of its own motion, it is called an aligned (a reverse) bias. Aligned bias promotes ordering while reverse bias destroys it. In absence of vacancies, the system reduces to previously studied LH model with different kinds of ordered and disordered phases which could be explained as a competition or cooperation between aligned bias and reverse bias. This interplay is expected to remain unaffected even when vacancies are present since vacancies do not impart any kind of bias on the landscape. However, we find presence of vacancies effectively weakens the reverse bias and this significantly changes the outcome of the competition between the two bias types. As a result novel ordered phases emerge which were not seen before. We analytically calculate the new phase boundaries within mean field approximation. We show even when aligned bias is weaker than reverse bias, it is possible to find long range order in the system. We discover two new phases where particle species showing weak aligned bias phase separate and the other species with strong reverse bias stays mixed with the vacancies. We call these phases finite current with partial phase separation (FPPS) and vacancy induced phase separation (VIPS). The landscape beneath the phase separated species takes the form of a macroscopic hill or valley in FPPS phase. But in VIPS phase it has the shape like a plateau whose height scales as square root of system size. The landscape in the remaining part of the system is disordered in both these phases.

cond-mat.stat-mech↗

arXiv2025

Dynamics of chemo-receptor activity with time-periodic attractant field

When exposed to a time-periodic chemical signal, an \textit{E.~coli} cell responds by modulating its receptor activity in a similar time-periodic manner. However, there exists a phase lag between the applied signal and the activity response. We study the variation of the activity amplitude and phase lag as a function of the applied frequency~$\omega$, using numerical simulations. The amplitude increases with~$\omega$, reaches a plateau, and then decreases again for large~$\omega$. The phase lag increases monotonically with~$\omega$ and finally saturates to $3\pi/2$ when~$\omega$ is large. The activity is no longer a single-valued function of the attractant signal, and plotting activity versus attractant concentration over one complete time period generates a loop. We monitor the loop area as a function of~$\omega$ and find two peaks for small and large~$\omega$, and a sharp minimum at intermediate~$\omega$ values. We explain these results as an interplay between the time scales associated with adaptation, activity switching, and applied signal variation. In particular, for very large~$\omega$, the quasi-equilibrium approximation for activity dynamics breaks down, a regime that has not been explored in earlier studies. We perform analytical calculations in this limit and find good agreement with our simulation results.

physics.bio-ph↗

arXiv2025

Bacterial Chemotaxis in a Traveling Wave Attractant Environment

We study single cell E.coli chemotaxis in a spatio-temporally varying attractant environment. Modeling the attractant concentration in the form of a traveling sine wave, we measure in our simulations, the chemotactic drift velocity of the cell for different propagation speed of the attractant wave. We find a highly non-trivial dependence where the chemotactic drift velocity changes sign, and also shows multiple peaks. For slowly moving attractant wave, drift velocity is negative, i.e. the drift motion is directed opposite to wave propagation. As the wave speed increases, drift velocity shows a negative peak, then changes sign, reaches a positive peak and finally becomes zero when the wave moves too fast for the cell to respond. We explain this rich behavior from the difference in attractant gradient perceived by the cell during its run along the propagation direction and opposite to it. In particular, when the cell moves in the same direction as the wave, the relative velocity of the cell with respect to the wave becomes zero when the wave speed matches the run speed. In this limit, the cell is able to ride the wave and experiences no concentration gradient during these runs. On the contrary, for runs in the opposite direction, no such effect is present and the effective gradient increases monotonically with the wave speed. We show, using detailed quantitative measurements, how this difference gives rise to the counter-intuitive behavior of chemotactic drift velocity described above.

q-bio.CB↗

arXiv2025

Persistent exclusion process with time-periodic drive

We study a persistent exclusion process with time-periodic external potential on a 1d periodic lattice through numerical simulations. A set of run-and-tumble particles move on a lattice of length $L$ and tumbling probability $\gamma \ll 1$ and interact among each other via hardcore exclusion. The effect of the external potential has been modeled as a special site where the tumbling probability is $1$. We call it a "defect" site and move its location along the ring lattice with speed $u$. In the case of $\gamma=0$ the system goes to a jammed state when there is no defect. But introduction of the moving defect creates a strongly phase-separated state where almost all active particles are present in a single large cluster, for small and moderate $u$. This striking effect is caused by the long-range velocity correlation of the active particles, induced by the moving defect. For large $u$, a single large cluster is no longer stable and breaks into multiple smaller clusters. For nonzero $\gamma$ a competition develops between the timescales associated with tumbling and defect motion. While the moving defect attempts to create long-range velocity order, bulk tumbling tends to randomize the velocity alignment. If $\gamma$ is comparable to $u/L$, then a relatively small number of tumbles take place during the time the moving defect travels through the entire system. In this case, the defect has enough time to restore the order in the system and our simulations show that the long-range order in velocity and density survive for $\gamma$ values in this range. As $\gamma$ increases further, long range order is destroyed and the system develops multiple regions of high and low density. We characterize the density inhomogeneity in this case by measuring subsystem density fluctuations and present a heatmap in the $\gamma$-$u$ plane showing the regions with most pronounced density inhomogeneities.

cond-mat.stat-mech↗

arXiv2025

Run-and-tumble chemotaxis using reinforcement learning

Bacterial cells use run-and-tumble motion to climb up attractant concentration gradient in their environment. By extending the uphill runs and shortening the downhill runs the cells migrate towards the higher attractant zones. Motivated by this, we formulate a reinforcement learning (RL) algorithm where an agent moves in one dimension in the presence of an attractant gradient. The agent can perform two actions: either persistent motion in the same direction or reversal of direction. We assign costs for these actions based on the recent history of the agent's trajectory. We ask the question: which RL strategy works best in different types of attractant environment. We quantify efficiency of the RL strategy by the ability of the agent (a) to localize in the favorable zones after large times, and (b) to learn about its complete environment. Depending on the attractant profile and the initial condition, we find an optimum balance is needed between exploration and exploitation to ensure the most efficient performance.

q-bio.CB↗

arXiv2024

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. We introduce a relative timescale $ω$ between the particle and landscape dynamics, and study its effect on the steady state properties. We find there exists a critical value $ω= ω_{c}$ when all configurations of the system are equally likely in the steady state. We prove this result exactly in a discrete lattice system and obtain an exact expression for $ω_c$ in terms of the coupling parameters of the system. We show that $ω_c$ is finite in the disordered phase, diverges at the boundary between the ordered and disordered phase, and is undefined in the ordered phase. We also derive $ω_c$ from a coarse-grained level description of the system using linear hydrodynamics. We start with the assumption that there is a specific value $ω^\ast$ of the relative timescale when correlations in the system vanish, and mean-field theory gives exact expressions for the current Jacobian matrix $A$ and compressibility matrix $K$. Our exact calculations show that Onsager-type current symmetry relation $AK = KA^{T}$ can be satisfied if and only if $ω^\ast = ω_c$ . Our coarse-grained model calculations can be easily generalized to other coupled systems.

cond-mat.stat-mech↗

arXiv2024

Run-and-tumble particle with saturating rates

We consider a run-and-tumble particle whose speed and tumbling rate are space-dependent on an infinite line. Unlike most of the previous work on such models, here we make the physical assumption that at large distances, these rates saturate to a constant. For our choice of rate functions, we show that a stationary state exists, and the exact steady state distribution decays exponentially or faster and can be unimodal or bimodal. The effect of boundedness of rates is seen in the mean-squared displacement of the particle that displays qualitative features different from those observed in the previous studies where it approaches the stationary state value monotonically in time; in contrast, here we find that if the initial position of the particle is sufficiently far from the origin, the variance in its position either varies nonmonotonically or plateaus before reaching the stationary state. These results are captured quantitatively by the exact solution of the Green's function when the particle has uniform speed but the tumbling rates change as a step-function in space; the insights provided by this limiting case are found to be consistent with the numerical results for the general model.

cond-mat.stat-mech↗

arXiv2023

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

We study one-dimensional hardcore lattice gases, with nearest-neighbor interactions, in the presence of an external potential barrier, that moves on the periodic lattice with a constant speed. We investigate how the nature of the interaction (attractive or repulsive) affects particle transport and determine, using numerical simulations and mean-field calculations, the conditions for an optimum transport in the system. Physically, the particle current induced by the time-dependent potential is opposed by a diffusive current generated by the density inhomogeneity (a traveling wave) built up in the system, resulting in a current reversal, that crucially depends on the speed of the barrier and particle-number density. Indeed the presence of nearest-neighbor interaction has a significant impact on the current: Repulsive interaction enhances the current, whereas attractive interaction suppresses it considerably. Quite remarkably, when the number density is low, the current increases with the strength of the repulsive interaction and the maximum current is obtained for the strongest possible repulsion strength, i.e., for the nearest-neighbor exclusion. However, at high density, very strong repulsion makes particle movement difficult in an overcrowded environment and, in that case, the maximal current is achieved for weaker repulsive interaction strength.

cond-mat.stat-mech↗

arXiv2022

Short time extremal response to step stimulus for a single cell {\sl E. coli}

After application of a step stimulus, in the form of a sudden change in attractant environment, the receptor activity and tumbling bias of an {\sl E. coli} cell change sharply to reach their extremal values before they gradually relax to their post-stimulus adapted levels in the long time limit. We perform numerical simulations and exact calculations to investigate the short time response of the cell. For both activity and tumbling bias, we exactly derive the condition for extremal response and find good agreement with simulations. We also make experimentally verifiable prediction that there is an optimum size of the step stimulus at which the extremal response is reached in the shortest possible time.

q-bio.CB↗

arXiv2022

Effect of switching time scale of receptor activity on chemotactic performance of Escherichia coli

In the chemotactic motion of Escherichia coli, the switching of transmembrane chemoreceptors between active and inactive states is one of the most important steps of the signaling pathway. We study the effect of this switching time-scale on the chemotactic performance of the cell. We quantify performance by the chemotactic drift velocity of the cell. Our extensive numerical simulations on a detailed theoretical model show that as the activity switching rate increases, the drift velocity increases and then saturates. Our data also show the mean duration of a downhill run decreases strongly with the switching rate, while that of an uphill run decreases relatively slowly. We explain this effect from temporal variation of activity along uphill and downhill trajectories. We show that for large and small switching rates the nature of activity variation show qualitatively different behaviors along a downhill run but similar behavior along an uphill run. This results in a stronger dependence of downhill run duration on the switching rate and relatively milder dependence for uphill run duration.

q-bio.CB↗

arXiv2022

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

We study methylation dynamics of the chemoreceptors as an {\sl E.coli} cell moves around in a spatially varying chemo-attractant 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. Our numerical simulations show that the methylation dynamics depends sensitively on the size of the receptor clusters and also on the strength of the gradient. At short times after the beginning of a run, the methylation dynamics is mainly controlled by short runs which are generally associated with high receptor activity. This results in demethylation at short times. But for intermediate or large times, long runs play an important role and depending on receptor cooperativity or gradient strength, the qualitative variation of methylation can be completely different in this time regime. For weak gradient, both for uphill and downhill runs, after the initial demethylation, we find methylation level increases steadily with time for all cluster sizes. Similar qualitative behavior is observed for strong gradient during uphill runs as well. However, the methylation dynamics for downhill runs in strong gradient show highly non-trivial dependence on the receptor cluster size. We explain this behavior as a result of interplay between the sensing and adaptation modules of the signaling network.

q-bio.CB↗

arXiv2021

Effect of receptor clustering on chemotactic performance of Escherichia coli: sensing versus adaptation

We show how the competition between sensing and adaptation can result in a performance peak in E.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 go down. The activity and hence the run-tumble motility now gets controlled by methylation levels which are part of adaptation module, rather than ligand binding. This reduces chemotactic efficiency.

q-bio.CB↗

arXiv2019

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. We address this question for the first time here in a system with coupled time evolution of sliding particles on a fluctuating energy landscape. In the disordered phase this system shows short-ranged correlations, this system shows short-ranged correlations, the exact form of which is not known, and so the exact expression for current cannot be obtained. We use approximate expressions based on mean-field theory and corrections to it, to test the prediction of NLFH using numerical simulations. In this process we also discover important finite size effects and show how they affect the predictions of NLFH. We find that our system is rich enough to show a large variety of universality classes. From our analytics and simulations we have been able to find parameter values which lead to diffusive, Kardar-Parisi-Zhang (KPZ), $5/3 $ Lévy and modified KPZ universality classes. Interestingly, the scaling function in the modified KPZ case turns out to be close to the Prähofer-Spohn function which is known to describe usual KPZ scaling. Our analytics also predict the golden mean and the $3/2$ Lévy universality classes within our model but our simulations could not verify this, perhaps due to strong finite size effects.

cond-mat.stat-mech↗

arXiv2019

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. This effect also gives rise to nontrivial dependence of membrane velocity on the surface tension, characterized by a dip and a peak. We explain this unusual phenomenon by studying in detail the interplay of the surface and the bending energy and show that this interplay is responsible for a qualitative shape change of the membrane, which gives rise to the above effect.

physics.bio-ph↗

arXiv2019

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 literature. In one class of models (type $A$), the filaments can directly push the barrier and move it, thereby performing some work in the process. In another type of models (type $B$), the filaments wait till thermal fluctuations of the barrier position create enough space between the filament tip and the barrier, and then they grow by inserting one monomer in that gap. The difference between these two types of growth seems microscopic and rather a matter of modelling details. However, we find that this difference has important effect on many qualitative features of the models. In particular, how the relative time-scale between the barrier dynamics and filament dynamics influences the force generation properties, are significantly different for type $A$ and $B$ models. We illustrate these differences for three types of barrier: a rigid wall-like barrier, an elastic barrier and a barrier with Kardar-Parisi-Zhang dynamics. Our numerical simulations match well with our analytical calculations. Our study highlights the importance of taking the details of filament-barrier interaction into account while modelling force generation properties of actin filaments.

physics.bio-ph↗

arXiv2019

Run-and-tumble motion with step-like responses to a stochastic input

We study a simple run-and-tumble random walk whose switching frequency from run mode to tumble mode and the reverse depend on a stochastic signal. We consider a particularly sharp, step-like 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 < y_1 ) from above. We are interested in characterizing the effect of signaling noise on the long time behavior of the random walker. We consider two different time-evolutions of the stochastic signal. In one case, the signal dynamics is an independent stochastic process and does not depend on the run-and-tumble motion. In this case we can analytically calculate the mean value and the complete distribution function of the run duration and tumble duration. In the second case, we assume that the signal dynamics is influenced by the spatial location of the random walker. For this system, we numerically measure the steady state position distribution of the random walker. We discuss some similarities and differences between our system and E.coli chemotaxis, which is another well-known run-and-tumble motion encountered in nature.

q-bio.CB↗

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↗