arXiv subjects

Suman Majumder

Publications and source records attributed to Suman Majumder.

At least 37 records · Page 2Linked to original sources

arXiv2023

Activity Induced Enhanced Diffusion of a Polymer in Poor Solvent

By means of Brownian dynamics simulations we study the steady-state dynamic properties of a flexible active polymer in a poor solvent condition. Our results show that the effective diffusion constant of the polymer $D_{\rm eff}$ gets significantly enhanced as activity increases, much like in active particles. The simulation data are in agreement with a theoretically constructed Rouse model of active polymer, demonstrating that irrespective of the strength of activity, the long-time dynamics of the polymer chain is characterized by a universal Rouse-like scaling $D_{\rm eff} \sim N^{-1}$, where $N$ is the chain length.

cond-mat.soft↗

arXiv2023

Segregation disrupts the Arrhenius behavior of an isomerization reaction

Co-existence of phase segregation and \emph{interconversion} or \emph{isomerization} reaction among molecular species leads to fascinating structure formation in biological and chemical world. Using Monte Carlo simulations of the prototype Ising model, we explore the chemical kinetics of such a system consisting of a binary mixture of \emph{isomers}. Our results reveal that even though the two concerned processes are individually Arrhenius in nature, the Arrhenius behavior of the \emph{isomerization} reaction gets significantly disrupted due to an interplay of the nonconserved dynamics of the reaction and the conserved diffusive dynamics of phase segregation. The approach used here can be potentially adapted to understand reaction kinetics of more complex reactions.

cond-mat.stat-mech↗

arXiv2022

Disentangling Growth and Decay of Domains During Phase Ordering

Using Monte Carlo simulations we study the phase ordering dynamics of a \textit{multi}-species system modeled via the prototype $q$-state Potts model. In such a \textit{multi}-species system, we identify a spin states or species as the \textit{winner} if it has survived as the majority in the final state, otherwise we mark them as \textit{loser}. We disentangle the time ($t$) dependence of the domain length of the \textit{winner} from \textit{losers}, rather than monitoring the average domain length obtained by treating all spin states or species alike. The kinetics of domain growth of the \textit{winner} at a finite temperature in space dimension $d=2$ reveal that the expected Lifshitz-Cahn-Allen scaling law $\sim t^{1/2}$ can be observed with no early-time corrections, even for system sizes much smaller than what is traditionally used. Up to a certain period, all the others species, i.e., the \textit{losers}, also show a growth that, however, is dependent on the total number of species, and slower than the expected $\sim t^{1/2}$ growth. Afterwards, the domains of the \textit{losers} start decaying with time, for which our data strongly suggest the behavior $\sim t^{-z}$, where $z=2$ is the dynamical exponent for nonconserved dynamics. We also demonstrate that this new approach of looking into the kinetics also provides new insights for the special case of phase ordering at zero temperature, both in $d=2$ and $d=3$.

cond-mat.stat-mech↗

arXiv2022

Activity Mediated Globule to Coil Transition of a Flexible Polymer in Poor Solvent

Understanding the role of self-propulsion on the conformational properties of active filamentous objects has relevance in biology. In this context, we consider a flexible bead-spring model polymer for which along with both attractive and repulsive interactions among the non-bonded monomers, activity for each bead works along its intrinsic direction of self-propulsion. We study its kinetics in the overdamped limit, following a quench from good to poor solvent condition. We observe that with low activities, though the kinetic pathways remain similar, the scaling exponent for the relaxation time of globule formation becomes smaller than that for the passive case. Interestingly, for higher activities when self-propulsion dominates over interaction energy, the polymer becomes more extended. In its steady state, the variation of the spatial extension of the polymer, measured via its gyration radius, shows two completely different scaling regimes: The corresponding Flory exponent changes from $1/3$ to $3/5$ similar to a transition of the polymer from a globular state to a self-avoiding walk. This can be explained by an interplay among three energy scales present in the system, viz., the "ballistic", thermal, and interaction energy.

cond-mat.soft↗

arXiv2022

Role of temperature and alignment activity on kinetics of coil-globule transition of a flexible polymer

We study the nonequilibrium kinetics during the coil-globule transition of a flexible polymer chain with active beads after a quench from good to poor solvent condition using molecular dynamics simulation. Activity for each bead is introduced via the well-known Vicsek-like alignment rule due to which the velocity of a bead tries to align towards the average direction of its neighbors. We investigate the role of quenching temperature with varying activity during collapse of this polymer. We find that although for lower activities the kinetics remains qualitatively similar for different temperatures, for higher activity noticeable differences can be identified.

cond-mat.soft↗

arXiv2021

Kryging: Geostatistical analysis of large-scale datasets using Krylov subspace methods

Analyzing massive spatial datasets using Gaussian process model poses computational challenges. This is a problem prevailing heavily in applications such as environmental modeling, ecology, forestry and environmental heath. We present a novel approximate inference methodology that uses profile likelihood and Krylov subspace methods to estimate the spatial covariance parameters and makes spatial predictions with uncertainty quantification. The proposed method, Kryging, applies for both observations on regular grid and irregularly-spaced observations, and for any Gaussian process with a stationary covariance function, including the popular $\Matern$ covariance family. We make use of the block Toeplitz structure with Toeplitz blocks of the covariance matrix and use fast Fourier transform methods to alleviate the computational and memory bottlenecks. We perform extensive simulation studies to show the effectiveness of our model by varying sample sizes, spatial parameter values and sampling designs. A real data application is also performed on a dataset consisting of land surface temperature readings taken by the MODIS satellite. Compared to existing methods, the proposed method performs satisfactorily with much less computation time and better scalability.

stat.ME↗

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

Zero-Temperature Coarsening in the Two-Dimensional Long-Range Ising Model

We investigate the nonequilibrium dynamics following a quench to zero temperature of the non-conserved Ising model with power-law decaying long-range interactions $\propto 1/r^{d+σ}$ in $d=2$ spatial dimensions. The zero-temperature coarsening is always of special interest among nonequilibrium processes, because often peculiar behavior is observed. We provide estimates of the nonequilibrium exponents, viz., the growth exponent $α$, the persistence exponent $θ$, and the fractal dimension $d_f$. It is found that the growth exponent $α\approx 3/4$ is independent of $σ$ and different from $α=1/2$ as expected for nearest-neighbor models. In the large $σ$ regime of the tunable interactions only the fractal dimension $d_f$ of the nearest-neighbor Ising model is recovered, while the other exponents differ significantly. For the persistence exponent $θ$ this is a direct consequence of the different growth exponents $α$ as can be understood from the relation $d-d_f=θ/α$; they just differ by the ratio of the growth exponents $\approx 3/2$. This relation has been proposed for annihilation processes and later numerically tested for the $d=2$ nearest-neighbor Ising model. We confirm this relation for all $σ$ studied, reinforcing its general validity.

cond-mat.stat-mech↗

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

Estimating intervention effects on infectious disease control: the effect of community mobility reduction on Coronavirus spread

Understanding the effects of interventions, such as restrictions on community and large group gatherings, is critical to controlling the spread of COVID-19. Susceptible-Infectious-Recovered (SIR) models are traditionally used to forecast the infection rates but do not provide insights into the causal effects of interventions. We propose a spatiotemporal model that estimates the causal effect of changes in community mobility (intervention) on infection rates. Using an approximation to the SIR model and incorporating spatiotemporal dependence, the proposed model estimates a direct and indirect (spillover) effect of intervention. Under an interference and treatment ignorability assumption, this model is able to estimate causal intervention effects, and additionally allows for spatial interference between locations. Reductions in community mobility were measured by cell phone movement data. The results suggest that the reductions in mobility decrease Coronavirus cases 4 to 7 weeks after the intervention.

stat.ME↗

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

Aging in the long-range Ising model

The current understanding of aging phenomena is mainly confined to the study of systems with short-ranged interactions. Little is known about the aging of long-ranged systems. Here, the aging in the phase-ordering kinetics of the two-dimensional Ising model with power-law long-range interactions is studied via Monte Carlo simulations. The dynamical scaling of the two-time spin-spin autocorrelator is well described by simple aging for all interaction ranges studied. The autocorrelation exponents are consistent with $λ=1.25$ in the effectively short-range regime, while for stronger long-range interactions the data are consistent with $λ=d/2=1$. For very long-ranged interactions, strong finite-size effects are observed. We discuss whether such finite-size effects could be misinterpreted phenomenologically as sub-aging.

cond-mat.stat-mech↗

arXiv2019

Understanding nonequilibrium scaling laws governing collapse of a polymer

Recent emerging interest in experiments of single-polymer dynamics urge computational physicists to revive their understandings, particularly in the nonequilibrium context. Here we briefly discuss the currently evolving approaches of investigating the evolution dynamics of homopolymer collapse in computer simulations. Primary focus of these approaches is to understand various dynamic scaling laws related to coarsening and aging during the collapse in space dimension $d=3$, using tools popular in nonequilibrium coarsening dynamics of particle or spin systems. In addition to providing an overview of those results, we also present new preliminary data for $d=2$.

cond-mat.stat-mech↗

arXiv2019

Statistical downscaling with spatial misalignment: Application to wildland fire PM$_{2.5}$ concentration forecasting

Fine particulate matter, PM$_{2.5}$, has been documented to have adverse health effects and wildland fires are a major contributor to PM$_{2.5}$ air pollution in the US. Forecasters use numerical models to predict PM$_{2.5}$ concentrations to warn the public of impending health risk. Statistical methods are needed to calibrate the numerical model forecast using monitor data to reduce bias and quantify uncertainty. Typical model calibration techniques do not allow for errors due to misalignment of geographic locations. We propose a spatiotemporal downscaling methodology that uses image registration techniques to identify the spatial misalignment and accounts for and corrects the bias produced by such warping. Our model is fitted in a Bayesian framework to provide uncertainty quantification of the misalignment and other sources of error. We apply this method to different simulated data sets and show enhanced performance of the method in the presence of spatial misalignment. Finally, we apply the method to a large fire in Washington state and show that the proposed method provides more realistic uncertainty quantification than standard methods.

stat.AP↗

arXiv2019

Statistical Inference Based on a New Weighted Likelihood Approach

We discuss a new weighted likelihood method for parametric estimation. The method is motivated by the need for generating a simple estimation strategy which provides a robust solution that is simultaneously fully efficient when the model is correctly specified. This is achieved by appropriately weighting the score function at each observation in the maximum likelihood score equation. The weight function determines the compatibility of each observation with the model in relation to the remaining observations and applies a downweighting only if it is necessary, rather than automatically downweighting a proportion of the observations all the time. This allows the estimators to retain full asymptotic efficiency at the model. We establish all the theoretical properties of the proposed estimators and substantiate the theory developed through simulation and real data examples. Our approach provides an alternative to the weighted likelihood method of Markatou et al. (1997, 1998).

stat.ME↗

arXiv2019

Aging Phenomena during Phase Separation in Fluids: Decay of autocorrelation for vapor-liquid transitions

We performed molecular dynamics simulations to study relaxation phenomena during vapor-liquid transitions in a single component Lennard-Jones system. Results from two different overall densities are presented; one in the neighborhood of the vapor branch of the coexistence curve and the other being close to the critical density. The nonequilibrium morphologies, growth mechanisms and growth laws in the two cases are vastly different. In the low density case growth occurs via diffusive coalescence of droplets in a disconnected morphology. On the other hand, the elongated structure in the higher density case grows via advective transport of particles inside the tube-like liquid domains. The objective in this work has been to identify how the decay of the order-parameter autocorrelation, an important quantity to understand aging dynamics, differs in the two cases. In the case of the disconnected morphology, we observe a very robust power-law decay, as a function of the ratio of the characteristic lengths at the observation time and at the age of the system, whereas the results for the percolating structure appear rather complex. To quantify the decay in the latter case, unlike standard method followed in a previous study, here we have performed a finite-size scaling analysis. Outcome of this analysis shows the presence of a strong preasymptotic correction, while revealing that in this case also, albeit in the asymptotic limit, the decay follows a power-law. Even though the corresponding exponents in the two cases differ drastically, this study, combined with a few recent ones, suggests that power-law behavior of this correlation function is rather universal in coarsening dynamics.

cond-mat.stat-mech↗

arXiv2019

Pearl-Necklace-Like Local Ordering Drives Polypeptide Collapse

Collapse of the polypeptide backbone is an integral part of protein folding. Using polyglycine as a probe, we explore the nonequilibrium pathways of protein collapse in water. We find that the collapse depends on the competition between hydration effects and intra-peptide interactions. Once intra-peptide van der Waal interactions dominate, the chain collapses along a nonequilibrium pathway characterized by formation of pearl-necklace-like local clusters as intermediates that eventually coagulate into a single globule. By describing this coarsening through the contact probability as a function of distance along the chain, we extract a time-dependent length scale that grows in linear fashion. The collapse dynamics is characterized by a dynamical critical exponent $z=0.5$ that is much smaller than the values of $z=1-2$ reported for non-biological polymers. This difference in the exponents is explained by the instantaneous formation of intra-chain hydrogen bonds and local ordering that may be correlated with the observed fast folding times in proteins.

physics.bio-ph↗

arXiv2019

Phase ordering kinetics of the long-range Ising model

We use an efficient method that eases the daunting task of simulating dynamics in spin systems with long-range interaction. Our Monte Carlo simulations of the long-range Ising model for the nonequilibrium phase ordering dynamics in two spatial dimensions erform significantly faster than the standard Metropolis approach and considerably more efficiently than the kinetic Monte Carlo method. Importantly, this enables us to establish agreement with the theoretical prediction for the time dependence of domain growth, in contrast to previous numerical studies. This method can easily be generalized to applications in other systems.

cond-mat.stat-mech↗