Related papers: Continuum Electromechanical Modeling of Protein-Me…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion…
Different descriptions used to model a point-defect in an elastic continuum are reviewed. The emphasis is put on the elastic dipole approximation, which is shown to be equivalent to the infinitesimal Eshelby inclusion and to the…
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
For a wide range of applications, we need DEM simulations of granular matter in contact with flexible elastic boundaries. We present a novel method to describe the interaction between granular particles and a flexible elastic membrane.…
Electro-energy-reaction-diffusion systems are thermodynamically consistent continuum models for reaction-diffusion processes that account for temperature and electrostatic effects in a way that total charge and energy are conserved. The…
For many biotechnological applications it would be useful to better understand the effects produced by electric fields on lipid membranes. This review discusses several aspects of the electrostatic properties of a planar lipid membrane with…
Dislocations are the main carriers of the permanent deformation of crystals. For simulations of engineering applications, continuum models where material microstructures are represented by continuous density distributions of dislocations…
Eukaryotic cells intrinsically change their shape, by changing the composition of their membrane and by restructuring their underlying cytoskeleton. We present here further studies and extensions of a minimal physical model, describing a…
Polymeric materials that couple deformation and electrostatics have the potential for use in soft sensors and actuators with potential applications ranging from robotic, biomedical, energy, aerospace and automotive technologies. In contrast…
In this work, we propose and study the stability of nerve impulse propagation as electrical and mechanical signals through linear approximation. We present a potential energy stored in the biomembrane due to the deformation, bending, and…
A variety of models for the membrane-mediated interaction of particles in lipid membranes, mostly well-established in theoretical physics, is reviewed from a mathematical perspective. We provide mathematically consistent formulations in a…
We study the flow of an electrically charged fluid through an elastic and porous medium. A three continuum model consisting of an elastic solid, a viscous fluid, and a mobile charge continuum is used. The relevant laws of physics are…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
Cell membranes interact with a myriad of curvature-active proteins that control membrane morphology and are responsible for mechanosensation and mechanotransduction. Some of these proteins, such as those containing BAR domains, are curved…
We explore the pressure of active particles on curved surfaces and its relation to other interfacial properties. We use both direct simulations of the active systems as well as simulations of an equilibrium system with effective (pair)…