arXiv subjects

Subhajit Paul

Publications and source records attributed to Subhajit Paul.

26 records · Page 2Linked to original sources

arXiv2021

Effects of Alignment Activity on the Collapse Kinetics of a Flexible Polymer

Dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an alignment rule adapted from the Vicsek model. Following a quench from the high-temperature coil phase to a low-temperature state point, we study the coarsening kinetics via molecular dynamics (MD) simulations using the Langevin thermostat. For the passive polymer case the low-temperature equilibrium state is a compact globule. Results from our MD simulations reveal that though the globular state is also the typical final state in the active case, the nonequilibrium pathways to arrive at such a state differ from the passive picture due to the alignment interaction among the beads. We notice that deviations from the intermediate "pearl-necklace"-like arrangement, that is observed in the passive case, and the formation of more elongated dumbbell-like structures increase with increasing activity. Furthermore, it appears that while a small active force on the beads certainly makes the coarsening process much faster, there exists nonmonotonic dependence of the collapse time on the strength of active interaction. We quantify these observations by comparing the scaling laws for the collapse time and growth of pearls with the passive case.

cond-mat.soft↗

arXiv2021

Motion of a Polymer Globule with Vicsek-like Activity: From Super-diffusive to Ballistic Behavior

Via molecular dynamics simulation with Langevin thermostat we study the structure and dynamics of a flexible bead-spring active polymer model after a quench from good to poor solvent conditions. The self propulsion is introduced via a Vicsek-like alignment activity rule which works on each individual monomer in addition to the standard attractive and repulsive interactions among the monomeric beads. We observe that the final conformations are in the globular phase for the passive as well as for all the active cases. By calculating the bond length distribution, radial distribution function, etc., we show that the kinetics and also the microscopic details of these \textit{pseudo equilibrium} globular conformations are not the same in all the cases. Moreover, the center-of-mass of the polymer shows a more directed trajectory during its motion and the behavior of the mean-squared-displacement gradually changes from a super-diffusive to ballistic under the influence of the active force in contrast to the diffusive behavior in the passive case.

cond-mat.soft↗

arXiv2021

Knots are Generic Stable Phases in Semiflexible Polymers

Semiflexible polymer models are widely used as a paradigm to understand structural phases in biomolecules including folding of proteins. Since stable knots are not so common in real proteins, the existence of stable knots in semiflexible polymers has not been explored much. Here, via extensive replica exchange Monte Carlo simulation we investigate the same for a bead-stick and a bead-spring homopolymer model that covers the whole range from flexible to stiff. We establish the fact that the presence of stable knotted phases in the phase diagram is dependent on the ratio $r_b/r_{\rm{min}}$ where $r_b$ is the equilibrium bond length and $r_{\rm{min}}$ is the distance for the strongest nonbonded contacts. Our results provide evidence for both models that if the ratio $r_b/r_{\rm{min}}$ is outside a small window around unity then depending on the bending stiffness one always encounters stable knotted phases along with the usual frozen and bent-like structures at low temperatures. These findings prompt us to conclude that knots are generic stable phases in semiflexible polymers.

cond-mat.soft↗

arXiv2020

How Do Clusters in Phase-Separating Active Matter Systems Grow? A study for Vicsek activity in systems undergoing vapor-solid transition

Via molecular dynamics simulations we have studied kinetics of vapor-"solid" phase transition in an active matter model in which self-propulsion is introduced via the well-known Vicsek rule. The overall density of the particles is chosen in such a way that the evolution morphology consists of disconnected clusters that are defined as regions of high density of particles. Our focus has been on understanding the influence of the above mentioned self-propulsion on structure and growth of these clusters by comparing the results with those for the passive limit of the model that also exhibits vapor-"solid" transition. While in the passive case the growth occurs due to standard diffusive mechanism, the Vicsek activity leads to a very rapid growth, via a process that is practically equivalent to the ballistic aggregation mechanism. The emerging growth law in the latter case has been accurately estimated and explained by invoking information on velocity and structural aspects of the clusters into a relevant theory. Some of these results are also discussed with reference to a model for the active Brownian particles.

cond-mat.soft↗

arXiv2020

Dependence of Cluster Growth on Coefficient of Restitution in a Cooling Granular Fluid

Starting from configurations having homogeneous spatial density, we study kinetics in a two-dimensional system of inelastically colliding hard particles, a popular model for cooling granular matter. Following an initial time period, the system exhibits a crossover to an inhomogeneous regime that is characterized by the formation and growth of particle-rich clusters. We present results on the time dependence of average mass of the clusters and that of average kinetic energy, obtained via event driven molecular dynamics simulations, for a wide range of values for the coefficient of restitution ($e$), by fixing the overall density of particles in the system to a constant number. The time of onset of crossover from homogeneous to the inhomogeneous regime, as is well known, strongly increases as one moves towards the elastic limit. Nevertheless, our presented results suggest that the asymptotic growth is independent of $e$, for uniform definition of cluster, onset of which has a different $e$-dependence than the onset of above mentioned crossover. In other words, not only the exponent but also the amplitude of the power-law growth, which is widely believed to be the form of the evolution, is at the most very weakly sensitive to the choice of $e$. While it is tempting to attribute this fact to the similar feature in the decay of energy, we caution that our current understanding is not matured enough to draw such a connection between cluster growth and energy decay in a meaningful manner.

cond-mat.soft↗

arXiv2019

Initial Correlation Dependence of Aging in Phase Separating Solid Binary Mixtures and Ordering Ferromagnets

Following quenches of initial configurations having long range spatial correlations, prepared at the demixing critical point, to points inside the miscibility gap, we study aging phenomena in solid binary mixtures. Results on the decay of the two-time order-parameter autocorrelation functions, obtained from Monte Carlo simulations of the two-dimensional Ising model, with Kawasaki exchange kinetics, are analyzed via state-of-the art methods. The outcome is compared with that obtained for the ordering in uniaxial ferromagnets. For the latter, we have performed Monte Carlo simulations of the same model using the Glauber mechanism. For both types of systems we provide comparative discussion of our results with reference to those concerning quenches with configurations having no spatial correlation. We also discuss the role of structure on the decay of these correlations.

cond-mat.stat-mech↗

arXiv2017

Dimension Dependence of Clustering Dynamics in Models of Ballistic Aggregation and Freely Cooling Granular Gas

Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling granular gas model (GGM), for each of which we quantify the time dependence of kinetic energy and average mass of clusters (that form due to inelastic collisions). These quantities, for both the models, exhibit power-law behavior, at least in the long time limit. For the BAM, corresponding exponents exhibit strong dimension dependence and follow a hyperscaling relation. In addition, in the high packing fraction limit the behavior of these quantities become consistent with a scaling theory that predicts an inverse relation between energy and mass. On the other hand, in the case of the GGM we do not find any evidence for such a picture. In this case, even though the energy decay, irrespective of packing fraction, matches quantitatively with that for the high packing fraction picture of the BAM, it is inversely proportional to the growth of mass only in one dimension, and the growth appears to be rather insensitive to the choice of the dimension, unlike the BAM.

cond-mat.stat-mech↗

arXiv2017

Ballistic Aggregation in Systems of Inelastic Particles: Cluster growth, structure and aging

We study far-from-equilibrium dynamics in models of freely cooling granular gas and ballistically aggregating compact clusters. For both the cases, from event driven molecular dynamics simulations we have presented detailed results on structure and dynamics in space dimensions $d=1$ and $2$. Via appropriate analyses it has been confirmed that the ballistic aggregation mechanism applies in $d=1$ granular gases as well. Aging phenomena for this mechanism, in both the dimensions, have been studied via the two-time density autocorrelation function. This quantity is demonstrated to exhibit scaling property similar to that in the standard phase transition kinetics. The corresponding functional forms have been quantified and discussed in connection with the structural properties. Our results on aging establish a more complete equivalence between the granular gas and the ballistic aggregation models in $d=1$.

cond-mat.stat-mech↗