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Debasish Chaudhuri

Publications and source records attributed to Debasish Chaudhuri.

At least 55 records · Page 3Linked to original sources

Re-entrant phase separation in nematically aligning active polar particles

We present a numerical study of the phase behavior of repulsively interacting active polar particles that align their active velocities nematically. The amplitude of the active velocity, and the noise in its orientational alignment control the active nature of the system. At high values of orientational noise, the structural fluid undergoes a continuous nematic-isotropic transition in active orientation. This transition is well separated from an active phase separation, characterized by the formation of high density hexatic clusters, observed at lower noise strengths. With increasing activity, the system undergoes a re-entrant fluid-phase separation-fluid transition. The phase coexistence at low activity can be understood in terms of motility induced phase separation. In contrast, the re-melting of hexatic clusters, and the collective motion at low orientational noise are dominated by flocking behavior. At high activity, sliding and jamming of polar sub-clusters, formation of grain boundaries, lane formation, and subsequent fragmentation of the polar patches mediate remelting.

cond-mat.soft↗

Morphological and dynamical properties of semiflexible filaments driven by molecular motors

We consider an explicit model of a semiflexible filament moving in two dimensions on a gliding assay of motor proteins, which attach to and detach from filament segments stochastically, with a detachment rate that depends on the local load experienced. Attached motor proteins move along the filament to one of its ends with a velocity that varies non-linearly with the motor protein extension. The resultant force on the filament drives it out of equilibrium. The distance from equilibrium is reflected in the end-to-end distribution, modified bending stiffness, and a transition to spiral morphology of the polymer. The local stress dependence of activity results in correlated fluctuations in the speed and direction of the center of mass leading to a series of ballistic-diffusive crossovers in its dynamics.

cond-mat.soft↗

Cross-linker mediated compaction and local morphologies in a model chromosome

Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The binders cluster together via the polymer mediated attraction, in turn, folding the polymer. Using molecular dynamics simulations, and a mean field description, we explicitly demonstrate the continuous nature of the folding transition, characterized by unimodal distributions of the polymer size across the transition. At the transition point the chromatin size and cross-linker clusters display large fluctuations, and a maximum in their negative cross-correlation, apart from a critical slowing down. Along the transition, we distinguish the local chain morphologies in terms of topological loops, inter-loop gaps, and zippering. The topologies are dominated by simply connected loops at the criticality, and by zippering in the folded phase.

cond-mat.soft↗

Confinement and crowding control the morphology and dynamics of a model bacterial chromosome

Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such a model chromosome spontaneously adopts a helical shape, which is further compacted by molecular crowders to occupy a nucleoid-like subvolume of the cell. With increasing cell length, the longitudinal size of the chromosome increases in a non-linear fashion to finally saturate, its morphology gradually opening up while displaying a changing number of helical turns. For shorter cells, the chromosome extension varies non-monotonically with cell size, which we show is associated with a radial to longitudinal spatial reordering of the crowders. Confinement and crowders constrain chain dynamics leading to anomalous diffusion. While the scaling exponent for the mean squared displacement of center of mass grows and saturates with cell length, that of individual loci displays broad distribution with a sharp maximum.

physics.bio-ph↗

Bidirectional motion of filaments: Role of motor proteins and passive cross linkers

In eukaryotic cells, motor proteins (MP) bind to cytoskeletal filaments and move along them in a directed manner generating active stresses. During cell division a spindle structure of overlapping antiparallel microtubules (MT) form whose stability and dynamics under the influence of MPs has been studied extensively. Although passive cross linkers (PCL) were known to provide structural stability to filamentous network, consequences of the interplay between ATP dependent active forces of MPs and passive entropic forces of PCLs on MT overlap remains largely unexplored. Here, we formulate and characterize a model to study this, using linear stability analysis and numerical integration. In presence of PCLs, we find dynamic phase transitions with changing activity exhibiting regimes of stable partial overlap with or without oscillations, instability towards complete overlap, and stable limit cycle oscillations that emerge via a supercritical Hopf bifurcation characterized by an oscillation frequency determined by the MP and PCL parameters. We show that the overlap dynamics and stability depend crucially on whether both the MTs of overlapping pair are movable or one is immobilized, having potential implications for in vivo and in vitro studies.

physics.bio-ph↗

Entropy production by active particles: Coupling of odd and even functions of velocity

Non-equilibrium stochastic dynamics of several active Brownian systems are modeled in terms of non-linear velocity dependent force. In general, this force may consist of both even and odd functions of velocity. We derive the expression for total entropy production in such systems using the Fokker-Planck equation. The result is consistent with the expression for stochastic entropy production in the reservoir, that we obtain from probabilities of time-forward and time-reversed trajectories, leading to fluctuation theorems. Numerical simulation is used to find probability distribution of entropy production, which shows good agreement with the detailed fluctuation theorem.

cond-mat.stat-mech↗

Rotational diffusion under torque: Microscopic reversibility and excess entropy

We consider rotational diffusion for two systems - a macrospin under external magnetic field, and a particle diffusing on the surface of a sphere under external torque. Microstates in the two cases transform differently under time-reversal. This results in Clausius like dependence of stochastic entropy production (EP) for macrospins, and an excess EP for diffusion of particles on sphere. The total EP in both the cases obey fluctuation theorems. For macrospins, we derive analytical expression for probability distribution of total EP in the adiabatic limit. Numerical simulations show that the distribution functions of EP agree well with theoretical predictions.

cond-mat.stat-mech↗

Forced desorption of semiflexible polymers, adsorbed and driven by molecular motors

We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the filament. The stochastic binding-unbinding of the motor proteins and their ability to move along the polymer, generates active forces. As the pulling force reaches a threshold value, the polymer eventually desorbs from the substrate. Performing molecular dynamics simulations of the polymer in presence of a Langevin heat bath, and stochastic motor activity, we obtain desorption phase diagrams. The correlation time for fluctuations in desorbed fraction increases as one approaches complete desorption, captured quantitatively by a power law spectral density. We present theoretical analysis of the phase diagram using mean field approximations in the weakly bending limit of the polymer and performing linear stability analysis. This predicts increase in the desorption force with the polymer bending rigidity, active velocity and processivity of the motor proteins to capture the main features of the simulation results.

physics.bio-ph↗

Macrospin in external magnetic field: Entropy production and fluctuation theorems

We consider stochastic rotational dynamics of a macrospin at a constant temperature, in presence of an external magnetic field. Starting from the appropriate Langevin equation which contains multiplicative noise, we calculate entropy production (EP) along stochastic trajectories, and obtain fluctuation theorems. The system remains inherently out of equilibrium due to a spin torque supporting azimuthal current, leading to an excess EP apart from the EP due to heat dissipation. The anomaly may be removed using a redefinition of dissipated heat and stochastic work done. Using numerical simulations, we obtain distribution functions for entropy production along stochastic trajectories to find good agreement with the detailed fluctuation theorem.

cond-mat.stat-mech↗

Stochastic thermodynamics of macrospins with fluctuating amplitude and direction

We consider stochastic energy balance and entropy production (EP) in a generalized Langevin dynamics of macrospins, allowing for both amplitude and direction fluctuations, under external magnetic field. EP is calculated using Fokker-Planck equation, distinguishing between reversible and irreversible parts of probability currents. The system entropy increases due to irreversible non-equilibrium processes, and reduces as heat dissipates to surrounding environment. Using path probability distributions of time-forward trajectories and conjugate trajectories under time reversal, we obtain fluctuation theorems (FT) for total stochastic EP. We show that the choice of conjugate trajectories is crucial in obtaining entropy like quantities that obey FTs.

cond-mat.stat-mech↗

Stochastic models of classical particle pumps : Density dependence of directed current

We present and compare different versions of a simple particle pump-model that describes average directed current of repulsively interacting particles in a narrow channel, due to time-varying local potentials. We analyze the model on discrete lattice with particle exclusion, using three choices of potential-dependent hopping rates that obey microscopic reversibility. Treating the strength of the external potential as a small parameter with respect to thermal energy, we present a perturbative calculation to obtain the expression for average directed current. This depends on driving frequency, phase, and particle density. The directed current vanishes as density goes to zero or close packing. For two choices of hopping rates, it reaches maximum at intermediate densities, while for a third choice, it shows a curious current reversal with increasing density. This can be interpreted in terms of a particle-hole symmetry. Stochastic simulations of the model show good agreement with our analytic predictions.

cond-mat.stat-mech↗

Pumping single-file colloids: Absence of current reversal

We consider the single-file motion of colloidal particles interacting via short-ranged repulsion and placed in a traveling wave potential, that varies periodically in time and space. Under suitable driving conditions, a directed time-averaged flow of colloids is generated. We obtain analytic results for the model using a perturbative approach to solve the Fokker-Planck equations. The predictions show good agreement with numerical simulations. We find peaks in the time-averaged directed current as a function of driving frequency, wavelength and particle density and discuss possible experimental realizations. Surprisingly, unlike a closely related exclusion dynamics on a lattice, the directed current in the present model does not show current reversal with density. A linear response formula relating current response to equilibrium correlations is also proposed.

cond-mat.stat-mech↗

Stochastic ratcheting of two dimensional colloids : Directed current and dynamical transitions

We present results of molecular dynamics simulations for two-dimensional repulsively interacting colloids driven by a one dimensional asymmetric and commensurate ratchet potential, switching on and off stochastically. This drives a time-averaged directed current of colloids, exhibiting resonance with change in ratcheting frequency, where the resonance frequency itself depends non-monotonically on density. Using scaling arguments, we obtain analytic results that show good agreement with numerical simulations. With increasing ratcheting frequency, we find non-equilibrium re-entrant transitions between solid and modulated liquid phases.

cond-mat.soft↗

Absence of jamming in ant trails: Feedback control of self propulsion and noise

We present a model of ant traffic considering individual ants as self-propelled particles undergoing single file motion on a one-dimensional trail. Recent experiments on unidirectional ant traffic in well-formed natural trails showed that the collective velocity of ants remains approximately unchanged, leading to absence of jamming even at very high densities [ John et. al., Phys. Rev. Lett. 102, 108001 (2009) ]. Assuming a feedback control mechanism of self-propulsion force generated by each ant using information about the distance from the ant in front, our model captures all the main features observed in the experiment. The distance headway distribution shows a maximum corresponding to separations within clusters. The position of this maximum remains independent of average number density. We find a non-equilibrium first order transition, with the formation of an infinite cluster at a threshold density where all the ants in the system suddenly become part of a single cluster.

physics.bio-ph↗

Active Brownian particles: Entropy production and fluctuation-response

Within the Rayleigh-Helmholtz model of active Brownian particles activity is due to a non-linear velocity dependent force. In the presence of an external trapping potential or a constant force, the steady state of the system breaks detailed balance producing a net entropy. Using molecular dynamics simulations, we obtain the probability distributions of entropy production in these steady states. The distribution functions obey detailed fluctuation theorem for entropy production. Using simulation results, we further show that the steady state response function obeys a modified fluctuation-dissipation relation.

cond-mat.stat-mech↗

Stochastic thermodynamics of active Brownian particles

Examples of self propulsion in strongly fluctuating environment is abound in nature, e.g., molecular motors and pumps operating in living cells. Starting from Langevin equation of motion, we develop a fluctuating thermodynamic description of self propelled particles using simple models of velocity dependent forces. We derive fluctuation theorems for entropy production and a modified fluctuation dissipation relation, characterizing the linear response at non-equilibrium steady states. We study these notions in a simple model of molecular motors, and in the Rayleigh-Helmholtz and energy-depot model of self propelled particles.

cond-mat.stat-mech↗

Modified fluctuation-dissipation and Einstein relation at non-equilibrium steady states

Starting from the pioneering work of G. S. Agarwal [Zeitschrift für Physik 252, 25 (1972)], we present a unified derivation of a number of modified fluctuation-dissipation relations (MFDR) that relate response to small perturbations around non-equilibrium steady states to steady-state correlations. Using this formalism we show the equivalence of velocity forms of MFDR derived using continuum Langevin and discrete master equation dynamics. The resulting additive correction to the Einstein relation is exemplified using a flashing ratchet model of molecular motors.

cond-mat.stat-mech↗

Spontaneous helicity of a polymer with side-loops confined to a cylinder

Inspired by recent experiments on the spatial organization of bacterial chromosomes, we consider a type of "bottle brush" polymer consisting of a flexible backbone chain, to which flexible side loops are connected. We show that such a model with an open linear backbone spontaneously adopts a helical structure with a well-defined pitch when confined to small cylindrical volume. This helicity persists over a range of sizes and aspect-ratios of the cylinder, provided the packing fraction of the chain is suitably large. We analyze this results in terms of the interplay between the effective stiffness and actual intra-chain packing effects caused by the side-loops in response to the confinement. For the case of a circular backbone, mimicking e.g. the E. coli chromosome, the polymer adopts a linearized configuration of two parallel helices connected at the cylinder poles.

physics.bio-ph↗