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Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Using thermodynamic and variational principles we examine a basic phase field model for a mixture of two incompressible fluids in strongly perforated domains. With the help of the multiple scale method with drift and our recently introduced…
This work deals with numerical simulation of water freezing and thawing in a complex three-dimensional geometry of a porous medium. The porous structure is represented by a virtual container filled with glass beads. Phase transition…
The athermal quasistatic deformation method provides an elegant solution to overcome the limitation of short time spans in molecular simulations. It provides overdamped conditions, allowing for the extraction of purely structural responses…
We apply the immersed boundary (or IB) method to simulate deformation and detachment of a periodic array of wall-bounded biofilm colonies in response to a linear shear flow. The biofilm material is represented as a network of Hookean…
Reductions of the self-consistent mean field theory model of amphiphilic molecules in solvent can lead to a singular family of functionalized Cahn-Hilliard energies. We modify these energies, mollifying the singularities to stabilize the…
In this paper we show and discuss the use of a versatile interaction potential approach coupled with an immersed boundary method to simulate a variety of flows involving deformable bodies. In particular, we focus on two kinds of problems,…
In this paper we discuss a family of viscous Cahn-Hilliard equations with a non-smooth viscosity term. This system may be viewed as an approximation of a "forward-backward" parabolic equation. The resulting problem is highly nonlinear,…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
Multiphase flow in porous media occurs in several disciplines including petroleum reservoir engineering, petroleum systems' analysis, and CO$_2$ sequestration. While simulations often use a fully implicit discretization to increase the time…
We investigate two-phase flow in porous media and derive a two-scale model, which incorporates pore-scale phase distribution and surface tension into the effective behavior at the larger Darcy scale. The free-boundary problem at the pore…
The microscopic structure of a plant cell wall is given by cellulose microfibrils embedded in a cell wall matrix. In this paper we consider a microscopic model for interactions between viscoelastic deformations of a plant cell wall and…
The advective Cahn-Hilliard equation describes the competing processes of stirring and separation in a two-phase fluid. Intuition suggests that bubbles will form on a certain scale, and previous studies of Cahn-Hilliard dynamics seem to…
We use numerical simulations to examine two-dimensional particle mixtures that strongly phase separate in equilibrium. When the system is externally driven in the presence of quenched disorder, plastic flow occurs in the form of meandering…
This paper introduces a new discrete fracture model accounting for non-isothermal compositional multiphase Darcy flows and complex networks of fractures with intersecting, immersed and non immersed fractures. The so called…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
We propose a novel decoupled unconditionally stable numerical scheme for the simulation of two-phase flow in a Hele-Shaw cell which is governed by the Cahn-Hilliard-Hele-Shaw system (CHHS) with variable viscosity. The temporal…
The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…
Incorporating the inherent heterogeneity of living systems into models of active nematics is essential to provide a more realistic description of biological processes such as bacterial growth, cell dynamics and tissue development.…
We propose a model of antibiotic diffusion through a bacterial biofilm when diffusion and/or absorption barriers develop in the biofilm. The idea of this model is: We deduce details of the diffusion process in a medium in which direct…