Related papers: Effective potentials and electrostatic interaction…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Modeling and direct numerical simulation of particle-laden flows have a tremendous variety of applications in science and engineering across a vast spectrum of scales from pollution dispersion in the atmosphere, to fluidization in the…
We study a phenomenological electropermeabilization model in a periodic medium representing biological tissue. Starting from a cell-level model describing the electric potential and the degree of porosity, we perform dimension analysis to…
Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous…
With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Microswimmers typically operate in complex environments. In biological systems, often diverse species are simultaneously present and interact with each other. Here, we derive a (time-dependent) particle-scale statistical description, namely…
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…
In this thesis, the electrostatic interaction between two chemically identical colloids, both carrying constant surface potential is studied in the limit of short inter-particle separation at the interface of two immiscible fluids. Using an…
For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…
The liquid crystalline model biomembrane system consisting of a stack of interacting membranes is studied by the newly developed Fourier Monte Carlo simulation technique. In comparison to perturbation theory, substantial quantitative…
Active motions of a biological membrane can be induced by non-thermal fluctuations that occur in the outer environment of the membrane. We discuss the dynamics of a membrane interacting hydrodynamically with an active wall that exerts…
The fast Ewald methods are widely used to compute the point-charge electrostatic interactions in molecular simulations. The key step that introduces errors in the computation is the particle-mesh interpolation. In this work, the optimal…
Nonlocal coordinate space optical potentials for the scattering of 65 MeV protons from nuclei ranging in mass from 6Li to 238U have been defined by folding a complex, medium dependent effective interaction with the density matrix elements…
In this work we describe a set of Coarse-grained (CG) tools that allow to simulate the uptake of the nanoparticles (NPs) coated with proteins by a lipid bilayer. We describe a CG model to calculate the adsorption energies and the most…
In biological settings membranes typically interact locally with other membranes or the extracellular matrix in the exterior, as well as with internal cellular structures such as the cytoskeleton. Characterization of the dynamic properties…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
Classical molecular dynamics simulations have recently become a standard tool for the study of electrochemical systems. State-of-the-art approaches represent the electrodes as perfect conductors, modelling their responses to the charge…
A self-consistent theory is proposed for the general problem of interacting undulating fluid membranes subject to the constraint that they do not interpenetrate. We implement the steric constraint via an exact functional integral…
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…