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Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small…
A model for ionization and recombination collisions in a multifluid plasma is formulated using the framework introduced in previous work [{Phys. Plasmas} \textbf{22}, 093512 (2015)]. The exchange source terms for density, momentum and…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
Accurate identification of interactions between protein residues and ligand functional groups is essential to understand molecular recognition and guide rational drug design. Existing deep learning approaches for protein-ligand…
In tissues, cells in direct physical contact with each other can exchange ions or molecules via protein clusters called gap junctions that form channels across the membranes of adjacent cells. Here, we use a simplified biomimetic approach,…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…
Plasmoid-mediated reconnection is investigated for nonlinear Peeling-Ballooning Edge-Localized Modes (P-B ELMs). The formation of current sheets and the transition to 3-D current sheet instability is demonstrated through fully nonlinear…
The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…
This paper considers membranes of globular structure in the framework of the cell model technique. Coupled micropolar and Brinkman-type equations are used to model the flow of micropolar fluid through a spherical cell, consisting of solid…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
We report the observation of a premelting transition at chemically sharp solid-liquid interfaces using molecular-dynamics simulations. The transition is observed in the solid-Al/liquid-Pb system and involves the formation of a liquid…
A molecular-dynamics type simulation method, which is suitable for investigating the dewetting dynamics of thin and viscous liquid layers, is discussed. The efficiency of the method is exemplified by studying a two-parameter depinning-like…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Shapes of biological membranes are dynamically regulated in living cells. Although membrane shape deformation by proteins at thermal equilibrium has been extensively studied, nonequilibrium dynamics have been much less explored. Recently,…
Cells modify their volume in response to changes in osmotic pressure but it is usually assumed that other active shape variations do not involve significant volume fluctuations. Here we report experiments demonstrating that water transport…
We propose a diffuse interface model to describe tumor as a multicomponent deformable porous medium. We include mechanical effects in the model by coupling the mass balance equations for the tumor species and the nutrient dynamics to a…
The paper presents an approach for overcoming modeling problems of typical life science applications with partly unknown mechanisms and lacking quantitative data: A model family of reaction diffusion equations is built up on a mesoscopic…