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Understanding the mechanism of nucleation of the stable phase inside the metastable parent phase during a first order phase transition has been a subject of outstanding interest in natural science. The problem becomes even more challenging…
Directed growth, anisotropic cell shapes, and confinement drive self-organization in multicellular systems. We investigate the influence of particle shape on the distribution and dynamics of nematic microdomains in a minimal in-silico model…
There are rich emergent phase behaviors in non-equilibrium active systems. Flocking and clustering are two representative dynamic phases. The relationship between these two phases is still unclear. In the paper, we numerically investigate…
We study the dynamical formation of disoriented chiral condensates in very high energy nucleus-nucleus collisions using Bjorken hydrodynamics and relativistic nucleation theory. It is the dynamics of the first order confinement phase…
This work explores the influence of domain size of a non-compact two dimensional annular domain on the evolution of pattern formation that is modelled by an \textit{activator-depleted} reaction-diffusion system. A closed form expression is…
The spontaneous formation and subsequent growth, dissolution, merger and competition of social groups bears similarities to physical phase transitions in metastable finite systems. We examine three different scenarios, percolation, spinodal…
Recent advances in diffusion models have shown remarkable potential in the conditional generation of novel molecules. These models can be guided in two ways: (i) explicitly, through additional features representing the condition, or (ii)…
We investigate the oscillatory dynamics and bifurcation structure of a reaction-diffusion system with bistable nonlinearity and mass conservation, which was proposed by [Otsuji et al, PLoS Comp. Biol. 3 (2007), e108]. The system is a useful…
We present a dynamical description and analysis of non-equilibrium transitions in the noisy one-dimensional Ginzburg-Landau equation for an extensive system based on a weak noise canonical phase space formulation of the Freidlin-Wentzel or…
The central task in the study of self-organization is to explore the general mechanism of emergences. However, this is inhibited by the missing of a full knowledge of the microscopic dynamics of emergence. Here, in this study, the…
Structure formation and constant reorganization of the actin cytoskeleton are key requirements for the function of living cells. Here we show that a minimal reconstituted system consisting of actin filaments, crosslinking molecules and…
This paper is concerned with stochastic reaction-diffusion kinetics governed by the reaction-diffusion master equation. Specifically, the primary goal of this paper is to provide a mechanistic basis of Turing pattern formation that is…
We report new chemoconvective pattern formation phenomena observed in a two-layer system of miscible fluids filling a vertical Hele-Shaw cell. We show both experimentally and theoretically that the concentration-dependent diffusion coupled…
Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the…
We examine a spatially discrete reaction diffusion model based on the interactions that create a periodic pattern in the Drosophila eye imaginal disc. This model is capable of generating a regular hexagonal pattern of gene expression behind…
We identify a new type of pattern formation in spatially distributed active systems. We simulate one-dimensional two-component systems with predator-prey local interaction and pursuit-evasion taxis between the components. In a sufficiently…
Systems with long-range interactions quenched into a metastable state near the pseudospinodal exhibit nucleation that is qualitatively different than the classical nucleation observed near the coexistence curve. We have observed nucleation…
We analyzed conditions for Hopf and Turing instabilities to occur in two-component fractional reaction-diffusion systems. We showed that the eigenvalue spectrum and fractional derivative order mainly determine the type of instability and…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
Shapes of biological membranes are dynamically regulated in living cells. Although membrane shape deformation by proteins at thermal equilibrium has been extensively studied, nonequilibrium dynamics have been much less explored. Recently,…