Search results for "molecular dynamics"
showing 10 items of 1075 documents
Multiscale modeling of polymers at interfaces
2009
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this process, degrees of freedom on smaller scales are eliminated to the favor of a model suitable for efficient study of the system behavior on larger length and time scales. We emphasize the need to distinguish between dynamic and static properties regarding the model validation. A model which accurately reproduces static properties may fail completely, when it comes to the dynamic behavior of the system. Furthermore, we comment on the use of Monte Carlo method i…
Detection of planar defects caused by ion irradiation in Si using molecular dynamics
2007
We have analyzed the evolution of defects caused by self-irradiation of crystalline silicon. A classical molecular dynamics simulation was followed by defect analysis using the Pixel Mapping (PM) method. The PM identified {311} planar defects and long-chain structures of the so-called interstitial chains following low energy (1 keV) ion impact. The areal density obtained from simulation of self-interstitial atoms was about two thirds of that of experiments reported in the literature [Jpn. J. Appl. Phys. 30 (1991) L639], while the atomic configuration on respective planes agreed exactly.
Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles
2017
International audience; Nanophase segregation of a bi-component thiol self-assembled monolayer is predicted using atomistic molecular dynamics simulations and experimentally confirmed. The simulations suggest the formation of domains rich in acid-terminated chains, on one hand, and of domains rich in amide-functionalized ethylene glycol oligomers, on the other hand. In particular, within the amide-ethylene glycol oligomers region, a key role is played by the formation of inter-chain hydrogen bonds. The predicted phase segregation is experimentally confirmed by the synthesis of 35 and 15 nm gold nanoparticles functionalized with several binary mixtures of ligands. An extensive study by trans…
Elastic Properties and Line Tension of Self-Assembled Bilayer Membranes
2013
The elastic properties of a self-assembled bilayer membrane are studied using the self-consistent field theory, applied to a model system composed of flexible amphiphilic chains dissolved in hydrophilic polymeric solvents. Examining the free energy of bilayer membranes with different geometries allows us to calculate their bending modulus, Gaussian modulus, two fourth-order membrane moduli, and the line tension. The dependence of these parameters on the microscopic characteristics of the amphiphilic chain, characterized by the volume fraction of the hydrophilic component, is systematically studied. The theoretical predictions are compared with the results from a simple monolayer model, whic…
Melting and multipole deformation of sodium clusters
1999
Melting and multipole deformations of sodium clusters with up to 55 atoms are studied using an ab initio molecular dynamics method. The melting temperature regions for Na20, Na40, and Na 55 + are estimated. The melting temperature region determined here for Na 55 + agrees with the one determined experimentally. The dominating deformation type observed at the liquid phase for Na20 and Na40 is octupole deformation and for Na14 and Na 55 + quadrupole deformation.
Force probe simulations using an adaptive resolution scheme
2021
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute a…
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…