Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Crystallization in suspensions of hard spheres: a Monte Carlo and molecular dynamics simulation study
2011
The crystallization of a metastable melt is one of the most important non-equilibrium phenomena in condensed matter physics, and hard sphere colloidal model systems have been used for several decades to investigate this process by experimental observation and computer simulation. Nevertheless, there is still an unexplained discrepancy between the simulation data and experimental nucleation rate densities. In this paper we examine the nucleation process in hard spheres using molecular dynamics and Monte Carlo simulation. We show that the crystallization process is mediated by precursors of low orientational bond-order and that our simulation data fairly match the experimental data sets.
Protein corona composition of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles correlates strongly with the amino acid composition …
2017
Extensive molecular dynamics simulations reveal that the interactions between proteins and poly(ethylene glycol) (PEG) can be described in terms of the surface composition of the proteins. PEG molecules accumulate around non-polar residues while avoiding the polar ones. A solvent-accessible-surface-area model of protein adsorption accurately fits a large set of data on the composition of the protein corona of poly(ethylene glycol)- and poly(phosphoester)-coated nanoparticles recently obtained by label-free proteomic mass spectrometry.
Nanoscale oxide growth on Al single crystals at low temperatures: Variable charge molecular dynamics simulations
2006
We investigate the oxidation of aluminum low-index surfaces [(100), (110), and (111)] at low temperatures (300-600 K) and three different gas pressure values. We use molecular dynamics (MD) simulations with dynamic charge transfer between atoms where the interaction between atoms is described by the Es+ potential composed of the embedded atom method (EAM) potential and an electrostatic contribution. In the considered temperature range and under different gas pressure conditions, the growth kinetics follow a direct logarithmic law where the oxide thickness is limited to a value of ∼3 nm. The fitted curves allow us to determine the temperature and the pressure dependencies of the parameters i…
ReaxFF molecular dynamics simulation study of nanoelectrode lithography oxidation process on silicon (100) surface
2019
Abstract The nanoelectrode lithography has been strengthened in recent years as one of the most promising methods due to its high reproducibility, low cost and ability to manufacture nano-sized structures. In this work, the mechanism and the parametric influence in nanoelectrode lithography have been studied qualitatively in atomic scale using ReaxFF MD simulation. This approach was originally developed by van Duin and co-workers to investigate hydrocarbon chemistry. We have investigated the water adsorption and dissociation processes on Si (100) surface as well as the characteristics (structure, chemical composition, morphology, charge distribution, etc.) of the oxide growth. The simulatio…
Molecular Dynamics Simulations
2003
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T, pressure p) in runs carried out in the microcanonical (NVE) ensemble (N= particle number, V = volume, E = energy) is discussed, as well as the realization of other ensembles (e.g. the NVT ensemble). For a typical application example, molten SiO2, the estimation of various transport coefficients (self-diffusion constants, viscosity, thermal conductivity) is d…
From Gold Nanoseeds to Nanorods: The Microscopic Origin of the Anisotropic Growth
2016
Directly manipulating and controlling the size and shape of metal nanoparticles is a key step for their tailored applications. In this work, molecular dynamics simulations were applied to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. Different factors influencing the growth were selectively included in the models to unravel the role of the surfactants and ions. In the early stage of the growth, when the seed is only a few nanometers large, a dramatic symmetry breaking occurs as the surfactant layer preferentially covers the (100) and (110) facets, leaving the (111) facets unprotected. This anisotropic surfactant layer in turn promotes anisotropic gro…
Capillary Nematization of Semiflexible Polymers
2016
emiflexible polymers under good solvent conditions confined by two planar parallel repulsive walls are investigated for a wide range of monomer concentrations and distances between the walls, for a case where persistence length and contour length of the macromolecules are almost equal. Chain conformations and local nematic ordering near the walls are studied by both molecular dynamics methods and density functional theory, putting it in perspective with the recent work where the isotropic phase of semiflexible polymer solutions in the vicinity of a single repulsive wall in semi-infinite geometry is considered. Profiles of the total density of monomers as well as densities of end- and middle…
Temperature dependence of the local structure and lattice dynamics of wurtzite-type ZnO
2014
Temperature-dependent (10–300 K) Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra of polycrystalline wurtzitetype ZnO were analyzed using ab initio multiple-scattering theory and taking into account anisotropy of the crystallographic structure and thermal disorder. We employed two different simulation approaches: classical molecular dynamics (MD) and reverse Monte Carlo coupled with an evolutionary algorithm (RMC/EA method). The accuracy of several force-field models, which are commonly used in the MD simulations of bulk and nanostructured ZnO, was tested based on a comparison between the experimental and simulated Zn K-edge EXAFS spectra. It was found that available force…
Semiflexible Polymers in the Bulk and Confined by Planar Walls
2016
Semiflexible polymers in solution under good solvent conditions can undergo an isotropic-nematic transition. This transition is reminiscent of the well-known entropically-driven transition of hard rods described by Onsager’s theory, but the flexibility of the macromolecules causes specific differences in behavior, such as anomalous long wavelength fluctuations in the ordered phase, which can be understood by the concept of the deflection length. A brief review of the recent progress in the understanding of these problems is given, summarizing results obtained by large-scale molecular dynamics simulations and density functional theory. These results include also the interaction of semiflexib…
Monitoring molecular dynamics of bacterial cellulose composites reinforced with graphene oxide by carboxymethyl cellulose addition
2017
[EN] Broadband Dielectric Relaxation Spectroscopy was performed to study the molecular dynamics of dried Bacterial Cellulose/Carboxymethyl Cellulose-Graphene Oxide (BC/CMC-GO) composites as a function of the concentration of CMC in the culture media. At low temperature the dielectric spectra are dominated by a dipolar process labelled as a beta -relaxation, whereas electrode polarization and the contribution of dc-conductivity dominate the spectra at high temperatures and low frequency. The CMC concentration affects the morphological structure of cellulose and subsequently alters its physical properties. X-ray diffractometry measurements show that increasing the concentration of CMC promote…