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Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
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…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the…
We present a general and systematic theory of non-equilibrium dynamics of multi-component fluid membranes, in general, and membranes containing transmembrane proteins, in particular. Developed based on a minimal number of principles of…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
In this paper we introduce 1-$D$ and 2-$D$ discrete models for the dynamic granular matter formation process in the form of a system of difference equations. This approach allows us to differentiate between the influx of the rolling layer…
We discuss a class of models for particulate gels in which the particle contacts are described by an effective interaction combining a two-body attraction and a three-body angular repulsion. Using molecular dynamics, we show how varying the…
We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective…
The impact of nanomaterials on lung fluids or on the plasma membrane of living cells has prompted researchers to examine the interactions between nanoparticles and lipid vesicles. Recent studies have shown that nanoparticle-lipid…
For the model of periodic chronic myelogenous leukemia considered by Pujo-Menjouet, Mackey et al., model consisting of two delay differential equations, the equation for the density of so-called "resting cells" was studied from numerical…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
The behavior of lipid bilayer is important to understand the functionality of cells like the trafficking of ions between cells. Standard procedures to explore the properties of lipid bilayer and hemifused states typically use either…
We study a physical model for the interaction between general inclusions bound to fluid membranes that possess finite tension, as well as the usual bending rigidity. We are motivated by an interest in proteins bound to cell membranes that…
The prevalent scheme of a diffusion-mediated bimolecular reaction $A+B\rightarrow P$ is an adaptation of that proposed by Briggs and Haldane for enzyme action [{\em Biochem J.\/}, 19:338--339, 1925]. The purpose of this Note is to explain,…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
We propose and investigate a model for lipid raft formation and dynamics in biological membranes. The model describes the lipid composition of the membrane and an interaction with cholesterol. To account for cholesterol exchange between…