Related papers: Coarse Grain Molecular Dynamics Simulation of Fibr…
We use numerical simulations of turbulent cluster-forming regions to study the nature of dense filamentary structures in star formation. Using four hydrodynamic and magnetohydrodynamic simulations chosen to match observations, we identify…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
In melt-blowing processes mico- and nanofibers are produced by the extrusion of polymeric jets into a directed, turbulent high-speed airflow. Up to now the physical mechanism for the drastic jet thinning is not fully understood, since in…
Simulating large proteins using traditional molecular dynamics (MD) is computationally demanding. To address this challenge, we propose a novel tree-structured coarse-grained model that efficiently captures protein dynamics. By leveraging a…
The kinetics of dislocations is studied with computer simulation at loadings of different intensity. It is established that the dislocations have a few different structural states. The dislocations "with the micropore" play important role…
Pulmonary embolism (PE) is a highly mortal disease, currently assessed by pulmonary CT angiography. True-FISP MRI has emerged as an innocuous alternative that does not hold many of the limitations of x-ray imaging. However, True-FISP MRI is…
Reconstituted filamentous actin networks with myosin motor proteins form active gels, in which motor proteins generate forces that drive the network far from equilibrium. This motor activity can also strongly affect the network elasticity;…
In recent years, simulation methods based on the scaling of atomic potential functions, such as quasi-coarse-grained dynamics and coarse-grained dynamics, have shown promising results for modeling crystalline systems at multiple scales.…
We report a simulation study for bottle-brush polymers grafted on a rigid backbone. Using a standard coarse-grained bead-spring model extensive molecular dynamics simulations for such macromolecules under good solvent conditions are…
Human blood flow is a multi-scale problem: in first approximation, blood is a dense suspension of plasma and deformable red cells. Physiological vessel diameters range from about one to thousands of cell radii. Current computational models…
Numerical simulations to evaluate thoracic aortic hemodynamics include a computational fluid dynamic (CFD) approach or fluid-structure interaction (FSI) approach. While CFD neglects the arterial deformation along the cardiac cycle by…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Atherosclerosis, a chronic inflammatory cardiovascular disease, leads to arterial constriction caused by the accumulation of lipids, cholesterol, and various substances within artery walls. Such plaque can rupture, resulting in a blood clot…
Oriented block copolymers exhibit a buckling instability when submitted to a tensile test perpendicular to the lamellae direction. In this paper we study this behavior using a coarse grained molecular dynamics simulation approach. Coarse…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
We coarse-grain a model of closely-packed ellipses that can vary their aspect ratio to derive continuum equations for materials comprising confluent deformable particles such as epithelial cell layers. We show that contractile nearest…
We propose a coarse-grained theoretical model to capture the aging of microfluidic devices under different conditions including constant applied flow rate and constant applied pressure gradient. Microfluidic devices that sort cells by their…
A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…