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We extend a previously studied lattice model of particles with infinite repulsions to the case of finite energy interactions. The phase diagram is studied using grand canonical Monte Carlo simulation. Simulations of dynamical phenomena are…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
We perform an analytical investigation of the cell interface dynamics in the framework of a minimal phase field model of cell motility suggested in [1], which consists of two coupled evolution equations for the order parameter and a…
Linear kinetic Monte Carlo particle transport models are frequently employed in fusion plasma simulations to quantify atomic and surface effects on the main plasma flow dynamics. Separate codes are used for transport of neutral particles…
Ion exchange processes between an ion reservoir and a solid matrix are modeled under the assumption that near interface volumes reach equilibrium in a much faster time than the overall ion exchange process time while, in the bulk of the…
A discrete-to-continuum analysis for free-boundary problems related to crystalline films deposited on substrates is performed by $\Gamma$-convergence. The discrete model here introduced is characterized by an energy with two contributions,…
The behaviour of a system of ion channels formed across the cell membrane is presented. The infinite number of channels with an infinite coupling is introduced first as a reference point for the detailed derivation of the…
We present two modifications of the standard cell list algorithm for nonequilibrium molecular dynamics simulations of homogeneous, linear flows. When such a flow is modeled with periodic boundary conditions, the simulation box deforms with…
Fluid-particle systems are very common in many natural processes and engineering applications. However, accurately and efficiently modelling fluid-particle systems with complex particle shapes is still a challenging task. Here, we present a…
An implicit Euler finite-volume scheme for a parabolic reaction-diffusion system modeling biofilm growth is analyzed and implemented. The system consists of a degenerate-singular diffusion equation for the biomass fraction, which is coupled…
It is known that curvature relation plays a key role in the propagation of two-dimensional waves in an excitable model. Such a relation is believed to obey the eikonal equation for typical excitable models (e.g., the FitzHugh-Nagumo (FHN)…
In this study, we present a finite element solver for a thermodynamically consistent electrolyte model that accurately captures multicomponent ionic transport by incorporating key physical phenomena such as steric effects, solvation, and…
We introduce a system of equations that models a non-isothermal magnetoviscoelastic fluid. We show that the model is thermodynamically consistent, and that the critical points of the entropy functional with prescribed energy correspond…
We present the implementation of a solution scheme for fluid-structure interaction problems via the finite element software library deal.II. The solution scheme is an immersed finite element method in which two independent discretizations…
Under many physiological and pathological conditions such as division and migration, cells undergo dramatic deformations, under which their mechanical integrity is supported by cytoskeletal networks (i.e. intermediate filaments, F-actin,…
Distinguishing active from passive dynamics is a fundamental challenge in understanding the motion of living cells and other active matter systems. Here, we introduce a framework that combines physical modeling, analytical theory, and…
This paper studies the relations among system parameters, uniqueness, and stability of equilibria, for kinetic systems given in the form of polynomial ODEs. Such models are commonly used to describe the dynamics of nonnegative systems, with…
An interface description and numerical simulations of model A kinetics are used for the first time to investigate the intra-surface kinetics of phase ordering on corrugated surfaces. Geometrical dynamical equations are derived for the…
There is now growing evidence of the emergence and biological functionality of liquid crystal features, including nematic order and topological defects, in cellular tissues. However, how such features that intrinsically rely on particle…
This paper presents a new method to approximate the time-dependent convection-diffusion equations using conforming finite element methods, ensuring that the discrete solution respects the physical bounds imposed by the differential…