Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
A dynamic load-balancing algorithm for molecular dynamics simulation on multi-processor systems
1991
Abstract A new algorithm for dynamic load-balancing on multi-processor systems and its application to the molecular dynamics simulation of the spinodal phase separation are presented. The load-balancer is distributed among the processors and embedded in the application itself. Tests performed on a transputer network show that the load-balancer behaves almost ideally in this application. The same approach can be easily extended to different multi-processor topologies or applications.
Electrophoretic properties of charged colloidal suspensions: Application of a hybrid MD/LB method
2006
Abstract Electrophoretic properties of charged colloidal suspensions are investigated using a hybrid simulation method. In this method, the colloidal particles are propagated via Newton’s equations of motion using molecular dynamics (MD), while they are coupled to a structureless solvent that is modelled by the Lattice-Boltzmann (LB) method.
Micelles of the chiral biocompatible surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl)dimethylammonium bromide (DMEB): molecular dynamics …
2017
RATIONALE: The study of self-assembly processes of surfactant molecules in the gas phase is of great interest for several theoretical and technological reasons related to their possible exploitation as drug carriers, protein shields and cleaning agents in the gas phase. METHODS: The stability and fragmentation patterns of singly and multiply charged (either positively or negatively) aggregates of the surfactant (1R,2S)-dodecyl(2-hydroxy-1-methyl-2-phenylethyl)dimethyl ammonium bromide (DMEB) in the gas phase have been studied by ion mobility mass spectrometry and tandem mass spectrometry. Molecular dynamics (MD) simulations of positively and negatively singly and multiply charged DMEB aggre…
The structure and dynamics of Cl-substituted tetraphenyl- and tetrabenzyl-tin(IV)
1999
Abstract The crystal and molecular structure of (o-ClC6H4CH2)4Sn has been determined by X-ray crystallography. Tin is in a slightly distorted environment. The molecular dynamics of (p-ClC6H4)4Sn, (o-ClC6H4)4Sn and (o-ClC6H4CH2)4Sn have been investigated by variable temperature 119Sn Mossbauer spectroscopy (VTMS). A Debye-solid behaviour has been detected for (p-ClC6H4)4Sn, where, on the other hand, no influence by hydrogen–chlorine interaction on the magnitude of the dynamics data and functions seems to occur. For the o-Cl-substituted derivatives, a non-Debye-solid character could be advanced.
Statistical characterization of self-assembled charged nanoparticle structures
2013
We propose a novel approach for description of dynamics of nanostructure formation for a system consisting of oppositely charged particles. The combination of numerical solution of analytical Bogolyubov–Born–Green–Kirkwood–Yvon (BBGKY) type equation set with reverse Monte Carlo (RMC) method allows us to overcome difficulties of standard approaches, such as kinetic Monte Carlo or Molecular Dynamics, to describe effects of long-range Coulomb interactions. Moreover, this allows one to study the system dynamics on realistic time and length scales. We applied this method to a simple short-range Lenard–Jones (LJ)-like three- (3D) and two-dimensional (2D) system combining the long-range Coulomb an…
Molecular dynamics simulations of the nano-scale room-temperature oxidation of aluminum single crystals
2005
The oxidation of aluminum single crystals is studied using molecular dynamics (MD) simulations with dynamic charge transfer between atoms. The simulations are performed on three aluminum low-index surfaces ((1 0 0), (1 1 0) and (1 1 1)) at room temperature. The results show that the oxide film growth kinetics is independent of the crystallographic orientation under the present conditions. Beyond a transition regime (100 ps) the growth kinetics follow a direct logarithmic law and present a limiting thickness of 3 nm. The obtained amorphous structure of the oxide film has initially Al excess (compared to the composition of Al2O3) and evolves, during the oxidation process, to an Al percentage …
Fick Diffusion Coefficients in Ternary Liquid Systems from Equilibrium Molecular Dynamics Simulations
2012
An approach for computing Fick diffusivities directly from equilibrium molecular dynamics (MD) simulations is presented and demonstrated for a ternary chloroform–acetone–methanol liquid mixture. In our approach, Fick diffusivities are calculated from the Maxwell–Stefan (MS) diffusivities and the so-called matrix of thermodynamic factors. MS diffusivities describe the friction between different molecular species and can be directly computed from MD simulations. The thermodynamic factor describes the deviation from ideal mixing behavior and is difficult to extract from both experiments and simulations. Here, we show that the thermodynamic factor in ternary systems can be obtained from density…
Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators.
2021
Abstract Recent theoretical studies have demonstrated that the behaviour of molecular knots is a sensitive indicator of polymer structure. Here, we use knots to verify the ability of two state-of-the-art algorithms—configuration assembly and hierarchical backmapping—to equilibrate high-molecular-weight (MW) polymer melts. Specifically, we consider melts with MWs equivalent to several tens of entanglement lengths and various chain flexibilities, generated with both strategies. We compare their unknotting probability, unknotting length, knot spectra, and knot length distributions. The excellent agreement between the two independent methods with respect to knotting properties provides an addit…
Effects of mutations of wild-type alpha-synuclein on its structure and dimerization and consequences for the Parkinson's disease : answers from coars…
2022
Alpha-synuclein is a protein of 140 amino acids, intrinsically disordered and found abundantly in the brain and whose toxic aggregation there is the hallmark of the Parkinson's disease.The aim of the thesis is to understand the effects of certain mutations on the dimerization of alpha-synuclein and to contribute to understand its involvement in Parkinson's disease by using coarse-grained molecular dynamics. Coarse-grained molecular dynamics trajectories were computed using the UNited-RESidue (UNRES) program and provided unprecedented sampling (over an effective time of the order of milliseconds) of the alpha-synuclein structures in monomeric and dimeric forms. These data were generated both…
Computer simulations of critical phenomena and phase behaviour of fluids
2010
Computer simulation techniques such as Monte Carlo (MC) and Molecular Dynamics (MD) methods yield numerically exact information (apart from statistical errors) on model systems of classical statistical mechanics. However, a systematic limitation is the restriction to a finite (and often rather small) particle number N (or box linear dimension L, respectively). This limitation is particularly restrictive near critical points (due to the divergence of the correlation length of the order parameter) and for the study of phase equilibria (possibly involving interfaces, droplets, etc.). Starting out with simple lattice gas (Ising) models, finite size scaling analyses have been developed to overco…