Related papers: A 2D model for hydrodynamics and biology coupling …
Viscoelastic surface rheology plays an important role in multiphase systems. A typical example is the actin cortex which surrounds most animal cells. It shows elastic properties for short time scales and behaves viscous for longer time…
The sessile microbial communities known as biofilms exhibit varying architectures as environmental factors are varied, which for immersed biofilms includes the shear rate of the surrounding flow. Here we modify an established agent-based…
We use state-of-the-art molecular dynamics simulations to study hydrodynamic effects on aging during kinetics of phase separation in a fluid mixture. The domain growth law shows a crossover from a diffusive regime to a viscous hydrodynamic…
Numerical hydrodynamical simulations have proven a successful means of reproducing many of the statistical properties of the Lyman-Alpha forest as measured in high redshift quasar spectra. Pseudo-hydrodynamical methods based only on…
We propose two closely--related Lagrangian numerical methods for the simulation of physical processes involving advection, reaction and diffusion. The methods are intended to be used in settings where the flow is nearly incompressible and…
This paper introduces a one-dimensional NPZD-model developed to simulate biological activity in a turbulent ocean water column. The model consists of a system of coupled semilinear parabolic equations. An initial-boundary value problem is…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
Nutrient gradients and limitations play a pivotal role in the life of all microbes, both in their natural habitat as well as in artificial, microfluidic systems. Spatial concentration gradients of nutrients in densely packed cell…
Modelling interfacial dynamics with soluble surfactants in a multiphase system is a challenging task. Here, we consider the numerical approximation of a phase-field surfactant model with fluid flow. The nonlinearly coupled model consists of…
We investigate the effective coupling between heat and fluid dynamics within a thin fluid layer in contact with a solid structure via a rough surface. Moreover, the opposing vertical surfaces of the thin layer are in relative motion. This…
We formally extend the energy landscape approach for the thermodynamics of liquids to account for saddle points. By considering the extensive nature of macroscopic potential energies, we derive the scaling behavior of saddles with system…
The work analyzes a one-dimensional viscoelastic model of blood vessel growth under nonlinear friction with surroundings, and provides numerical simulations for various growing cases. For the nonlinear differential equations, two sufficient…
Active matter has been widely studied in recent years because of its rich phenomenology, whose mathematical understanding is still partial. We present some results, based on [8, 17] linking microscopic lattice gases to their macroscopic…
In this paper, we aim to synthesize cell microscopy images under different molecular interventions, motivated by practical applications to drug development. Building on the recent success of graph neural networks for learning molecular…
A stochastic model is used to assess the effect of external parameters on the development of submerged biofilms on smooth and rough surfaces. The model includes basic cellular mechanisms, such as division and spreading, together with an…
We study the application of a recently introduced hierarchical description of traffic flow control by driver-assist vehicles to include lane changing dynamics. Lane-dependent feedback control strategies are implemented at the level of…
Near-field hydrodynamic interactions between bacteria and no-slip solid surfaces are the main mechanism underlying surface entrapment of bacteria. In this study, we employ a chiral two-body model to simulate bacterial dynamics near the…
We study dynamics of clustering in systems containing active particles that are immersed in an explicit solvent. For this purpose we have adopted a hybrid simulation method, consisting of molecular dynamics and multi-particle collision…
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…
Moving micron scale objects are strongly coupled to each other by hydrodynamic interactions. The strength of this coupling decays as the inverse particle separation when the two objects are sufficiently far apart. It has been recently…