Related papers: Coarse Grain Molecular Dynamics Simulation of Fibr…
Computational fluid dynamics and discrete element method (CFD-DEM) coupling is an efficient and powerful tool to simulate particle-fluid systems. However, current volume-averaged CFD-DEM relying on direct grid-based mapping between the…
Herein, epoxy resin is cured by coupling quantum chemical (QC) calculations with molecular dynamics (MD) simulations that enable parameter-free prediction of material characteristics. A polymer network is formed by the reaction between base…
Fracture resistance of blood clots plays a crucial role in physiological hemostasis and pathological thromboembolism. Although recent experimental and computational studies uncovered the poro-viscoelastic property of blood clots and its…
Brownian dynamics of colloidal particles on complex surfaces has found important applications in diverse physical, chemical and biological processes. However, current Brownian dynamics simulation algorithms mostly work for relatively simple…
We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the…
We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov et al. J. Chem. Phys. \textbf{132}, 11876, 2010). Starting from the…
An ordinary state-based peridynamic material model is proposed for single sheet graphene. The model is calibrated using coarse grained molecular dynamics simulations. The coarse graining method allows the dependence of bond force on bond…
Melts of 3-dimensional dendritic beads-springs, namely coarse-grained soft-clusters, are studied by molecular dynamics simulations. The goal is to elucidate the unique dynamics of giant molecules, or generally speaking, 3-dimensional…
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel,…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
Partitioned cellular automata are known to be an useful tool to simulate linear and nonlinear problems in physics, specially because they allow for a straightforward way to define conserved quantities and reversible dynamics. Here we show…
Changes in cardiovascular hemodynamics are closely related to the development of aortic regurgitation, a type of valvular heart disease. Metrics derived from blood flows are used to indicate aortic regurgitation onset and evaluate its…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
This paper worked towards modeling blood platelets. Blood platelets, also known as thrombocytes, play a key role in blood clotting which is a vital human function. Furthermore, the role of these entities in strokes, myocardial infarctions,…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
Microfluidic technology has emerged as a powerful tool for studying complex biological processes with enhanced precision and control. A microfluidic chip was designed to emulate human-like microvascular networks with precise control over…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
We study with molecular dynamics simulations of a generic bead-spring model the cyclic crazing behaviour of glassy polymers. The aim is to elucidate the mechanical response of sole fibrillated craze matter as well as its interaction with…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…