Related papers: Coarse Grain Molecular Dynamics Simulation of Fibr…
Molecular Dynamics simulations of a coarse-grained bead-spring model of flexible macromolecules tethered with one end to the surface of a cylindrical pore are presented. Chain length $N$ and grafting density $\sigma$ are varied over a wide…
A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach groups of monomers are mapped onto a single pseudoatom (a blob) and the…
The Single Chain Mean Field theory is used to simulate the equilibrium structure of phospholipid membranes at the molecular level. Three levels of coarse-graining of DMPC phospholipid surfactants are present: the detailed 44-beads double…
Stochastic dynamics, such as molecular dynamics, are important in many scientific applications. However, summarizing and analyzing the results of such simulations is often challenging, due to the high dimension in which simulations are…
Conjugated organic molecules play a central role in a wide range of optoelectronic devices, including organic light-emitting diodes, organic field-effect transistors, and organic solar cells. A major bottleneck in the computational design…
Subclinical leaflet thrombosis (SLT) is a potentially serious complication of aortic valve replacement with a bioprosthetic valve in which blood clots form on the replacement valve. SLT is associated with increased risk of transient…
The mechanical behavior of closed-cell foams in compression is analyzed by means of the finite element simulation of a representative volume element of the microstructure. The digital model of the foam includes the most relevant details of…
Stiff and dense fibrin networks in chronic blood clots impede drug penetration and distribution into the clot core, limiting the efficacy of thrombolytic therapies. Acoustic cavitation of microbubbles is a promising strategy to enhance drug…
Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…
We present high resolution ($1024^3$) simulations of super-/hyper-sonic isothermal hydrodynamic turbulence inside an interstellar molecular cloud (resolving scales of typically 20 -- 100 AU), including a multi-disperse population of dust…
Background and Objective: Hemodynamic analysis of blood flow through arteries and veins is critical for diagnosing cardiovascular diseases, such as aneurysms and stenoses, and for investigating cardiovascular parameters, such as turbulence…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
In this work, we review previously developed coarse-grained (CG) particle models for biological membrane and red blood cells (RBCs) and discuss the advantages of the CG particle method over the continuum and atomic simulations on modeling…
A persistent challenge in predictive molecular modeling of thermoset polymers is to capture the effects of chemical composition and degree of crosslinking (DC) on dynamical and mechanical properties with high computational efficiency. We…
Cardiac disease and clinical intervention may both lead to an increased risk for thrombosis events due to modified blood flow in the heart, and thereby a change in the mechanical stimuli of blood cells passing through the chambers of the…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
We perform kinetic Monte Carlo simulations of flow-induced nucleation in polymer melts with an algorithm that is tractable even at low undercooling. The configuration of the non-crystallized chains under flow is computed with a recent…
We present a systematic coarse-graining (CG) strategy for many particle molecular systems based on cluster expansion techniques. We construct a hierarchy of coarse-grained Hamiltonians with interaction potentials consisting of two, three…
In this paper, the grinding of powder inside a ball mill is studied using the Bonded Cell Method (BCM) implemented in the framework of Contact Dynamics. In BCM the parent particles are divided into cells that are glued to one another until,…