Related papers: Molecular dynamics simulation of reversibly self-a…
Structural organization and correlations are studied in very large packings of equally sized acrylic spheres, reconstructed in three-dimensions by means of X-ray computed tomography. A novel technique, devised to analyze correlations among…
A simple three-dimensional model of a fluid whose constituent particles interact via a short range attractive and long range repulsive potential is used to model the aggregation into large spherical-like clusters made up of hundreds of…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
Coagulation-fragmentation processes describe the stochastic association and dissociation of particles in clusters. Cluster dynamics with cluster-cluster interactions for a finite number of particles has recently attracted attention…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
We present a numerical simulation of a granular material using hydrodynamic equations. We show that, in the absence of external forces, such a system phase-separates into high density and low density regions. We show that this separation is…
The polymer dynamics of homogeneous C$_{60}$-polystyrene mixtures in the molten state are studied via molecular simulations using two interconnected levels of representation for polystyrene nanocomposites: (a) A coarse-grained…
Tight binding molecular dynamics simulations, with a non orthogonal basis set, are performed to study the fragmentation of carbon fullerenes doped with up to six silicon atoms. Both substitutional and adsorbed cases are considered. The…
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
We present a series of simulations of the fragmentation of a molecular cloud, leading to the formation of a cluster of protostellar cores. The purpose of these simulations is to address a specific numerical problem called artificial…
Confinement can have a considerable effect on the behavior of particle systems, and is therefore an effective way to discover new phenomena. A notable example is a system of identical bosons at low temperature under an external field…
Ellipsoidal particles confined at liquid interfaces exhibit complex self-assembly behaviour due to quadrupolar capillary interactions induced by meniscus deformation. These interactions cause particles to attract each other in either…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
In large scale structure formation, massive systems assemble through the hierarchical merging of less massive ones. Galaxy clusters, being the most massive and thus the most recent collapsed structures, still grow by accreting smaller…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
Colloidal particles can spontaneously self-assemble into ordered structures, which not only can manipulate the propagation of light, but also vibration or phonons. Using Monte Carlo simulation, we study the self-assembly of perfectly…
A particle-based model for mesoscopic fluid dynamics is used to simulate steady and unsteady flows around a circular and a square cylinder in a two-dimensional channel for a range of Reynolds number between 10 and 130. Numerical results for…
Molecular dynamics simulations of nanometer-sized lead clusters have been performed using the Lim, Ong and Ercolessi glue potential (Surf. Sci. {\bf 269/270}, 1109 (1992)). The binding energies of clusters forming crystalline (fcc),…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…