arXiv subjects

Yagyik Goswami

Publications and source records attributed to Yagyik Goswami.

5 recordsLinked to original sources

arXiv2026

Collective spatial reorganization from arrest to peeling and migration through density-dependent mobility in internal-state coordinates

Numerous problems in development, regeneration, and disease involve simultaneous evolution of both spatial organization and the internal state of the constituents in addition to local interactions and crowding. This motivates us to study a minimal model for interacting populations evolving in coupled spatial and internal-state coordinates. We focus on a specific transition of particular biological interest: the reorganization of dense collectives from compact or arrested states toward boundary-led peeling and migration. In our formulation, each particle carries a spatial position and a scalar internal state, and interacts through finite-range forces. Mobilities are defined on both spatial and internal-state coordinates with a density dependence, and are asymmetrically cross-coupled. We derive update equations for stochastic dynamics in the overdamped limit and perform numerical simulations. We find that mobility in internal-state coordinates alone provides an independent control axis for large-scale spatial reorganization. In particular, increasing the baseline internal-state diffusivity and tuning its density dependence drives a transition from arrested aggregates to a peeling-like regime with broad spatial excursions, strong outward radial bias, and edge-localized activity, while the baseline positional diffusivity is held fixed. The transition is accompanied by correlated broadening of spatial and internal-state displacements, systematic reorganization of radial density and density-curvature profiles, and a pronounced dependence on system size, consistent with the idea that growing aggregates can cross into a boundary-dominated migratory state. These results establish the utility of our approach and motivate a broader framework aimed at modeling state change, spatial redistribution, and neighborhood structure within a common formalism.

cond-mat.soft↗

arXiv2023

Yielding behaviour of active particles in bulk and in confinement

The investigation of collective behaviour in dense assemblies of self-propelled active particles has been motivated by a wide range of biological phenomena. Of particular interest are dynamical transitions of cellular and sub-cellular biological assemblies, including the cytoskeleton and the cell nucleus. Motivated by observations of mechanically induced changes in the dynamics of such systems, and the apparent role of confinement geometry, we study the transition between jammed and fluidized states of active particles assemblies, as a function of the strength and temporal persistence of active forces, and in different confinement geometries. Our results show that the fluidization transition broadly resembles yielding in amorphous solids, consistently with recent suggestions. More specifically, however, we find that a detailed analogy holds with the yielding transition under cyclic shear deformation, for finite persistence times. The fluidization transition is accompanied by driving induced annealing, strong dependence on the initial state of the system, a divergence of time scales to reach steady states, and a discontinuous onset of diffusive motion. We also observe a striking dependence of the transition on persistence times and on the nature of the confinement. Collectively, our results have implications in epigenetic cell state transitions induced by alterations in confinement geometry.

cond-mat.soft↗

arXiv2023

Kinetic reconstruction of free energies as a function of multiple order parameters

A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used, especially in the presence of large free energy barriers, to estimate free energies using biasing protocols and sampling of transition paths. Kinetic reconstructions of free energy barriers of intermediate height have been performed, with respect to a single order parameter, employing the steady state properties of unconstrained simulation trajectories when barrier crossing is achievable with reasonable computational effort. Considering such cases, we describe a method to estimate free energy surfaces with respect to multiple order parameters from a steady state ensemble of trajectories. The approach applies to cases where the transition rates between pairs of order parameter values considered is not affected by the presence of an absorbing boundary, whereas the macroscopic fluxes and sampling probabilities are. We demonstrate the applicability of our prescription on different test cases of random walkers executing Brownian motion in order parameter space with an underlying (free) energy landscape and discuss strategies to improve numerical estimates of the fluxes and sampling. We next use this approach to reconstruct the free energy surface for supercooled liquid silicon with respect to the degree of crystallinity and density, from unconstrained molecular dynamics simulations, and obtain results quantitatively consistent with earlier results from umbrella sampling.

cond-mat.stat-mech↗

arXiv2022

Liquid-liquid phase transition in deeply supercooled Stillinger-Weber silicon

The existence of a phase transition between two distinct liquid phases in single-component network-forming liquids (e.g., water, silica, silicon) has elicited considerable scientific interest. The challenge, both for experiments and simulations, is that the liquid-liquid phase transition occurs under deeply supercooled conditions, where crystallization occurs very rapidly. Thus, early evidence from numerical equation of state studies was challenged, with the argument that slow spontaneous crystallization had been misinterpreted as evidence of a second liquid state. Rigorous free energy calculations have subsequently confirmed the existence of a liquid-liquid phase transition in some models of water, and exciting new experimental evidence has since supported these computational results. Similar results have so far not been found for silicon. Here, we present results from free energy calculations performed for silicon modelled with the classical, empirical Stillinger-Weber potential. Through a careful study employing state-of-the-art constrained simulation protocols and numerous checks for thermodynamic consistency, we find that there are two distinct metastable liquid states and a phase transition. Our results resolve a long-standing debate concerning the existence of a liquid-liquid transition in supercooled liquid silicon and address key questions regarding the nature of the phase transition and the associated critical point.

cond-mat.soft↗

arXiv2021

Thermodynamics and kinetics of crystallisation in deeply supercooled Stillinger-Weber silicon

We study the kinetics of crystallization in deeply supercooled liquid silicon employing computer simulations and the Stillinger-Weber three body potential. The free energy barriers to crystallisation are computed using umbrella sampling Monte Carlo simulations, and for selected low temperature and zero pressure state points, using unconstrained molecular dynamics simulations to reconstruct the free energy from a mean first passage time formulation. We focus on state points that have been described in earlier work [Sastry and Angell, Nature Mater., 2, 739, 2003] as straddling a first order liquid-liquid phase transition (LLPT) between two metastable liquid states. It was argued subsequently [Ricci et al., Mol. Phys., 117, 3254, 2019] that the apparent phase transition is in fact due the loss of metastability of the liquid state with respect to the globally stable crystalline state. The presence or absence of a barrier to crystallization for these state points is therefore of importance to ascertain, with due attention to ambiguities that may arise from the choice of order parameters. We discuss our choice of order parameters and also our choice of methods to calculate the free energy at deep supercooling. We find a well-defined free energy barrier to crystallisation and demonstrate that both umbrella sampling and mean first passage time methods yield results that agree quantitatively. Our results thus provide strong evidence against the possibility that the liquids at state points close to the reported LLPT exhibit slow, spontaneous crystallisation, but they do not address the existence of a LLPT (or lack thereof). We also compute the free energy barriers to crystallisation at other state points over a broad range of temperatures and pressures, and discuss the effect of changes in the microscopic structure of the metastable liquid on the free energy barrier heights.

cond-mat.soft↗