Search results for "Molecular Dynamic"
showing 10 items of 1090 documents
Liquid–solid interfaces: structure and dynamics from spectroscopy and simulations
2014
Liquid–solid interfaces play an important role in a number of phenomena encountered in biological, chemical and physical processes. Surface-induced changes of the material properties are not only important for the solid support but also for the liquid itself. In particular, it is now well established that water at the interface is substantially different from bulk water, even in the proximity of apparently inert surfaces such as a simple metal. The complex chemistry at liquid–solid interfaces is typically fundamental to heterogeneous catalysis and electrochemistry, and has become especially topical in connection with the search for new materials for energy production. A quite remarkable exa…
Interpretation of the Cu K-edge EXAFS spectra of Cu3N using ab initio molecular dynamics
2020
Financial support provided by ERDF project No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity “Post-doctoral research aid” realized at the Institute of Solid State Physics, University of Latvia is greatly acknowledged. This work was supported by a grant from the Swiss National Supercomputing Centre (CSCS) under the project ID s681 .
Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment.
2018
We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayer and sodium dodecyl sulfate (SDS) surfactant in an aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolytes. According to the hybrid approach, the intramolecular interactions are treated by a standard molecular Hamiltonian, and the nonelectrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure, as recently proposed [Zhu et al. Phys. Chem. Chem. Phys.…
Molecular dynamics investigation of the premelting effects of Lennard-Jones (111) surfaces
1987
Molecular dynamics simulations have been performed to study the premelting effects of noble-gas surfaces (argon) close to but below the bulk melting temperature. In particular, the increase of disorder as a function of temperature at (111) surface has been considered. The truncated Lennard-Jones (6-12) potential is used to describe the interactions between particles. Surface premelting has been analyzed by means of total energies, trajectory plots, mean sequare displacement functions, diffusion coefficients, vacancy concentrations and two-dimensional order parameters. The (111) surface starts to disorder by vacancy formation, which leads to the premelting of the surface layer far below the …
Structural features of selected protic ionic liquids based on a super-strong base
2019
Protic ionic liquids (PIL) were prepared from a super-strong base 1,7-diazabicyclo[5.4.0]undec-7-ene (DBU) and super-strong acids, trifluoromethane sulfonic acid (TfOH), and (trifluoromethanesulfonyl)-(nonafluorobutylsulfonyl)imide, (IM14H), ([DBUH][TfO] and [DBUH][IM14], respectively; the latter for the first time) and their chemical and physical properties and structural features have been explored using a synergy of experimental and computational tools. The short range order in neat DBU, as well as the long range structural correlations induced by charge correlation and hydrogen bonding interactions in the ionic liquids, have been explored under ambient conditions, where these compounds …
Modeling the Interaction of Carbon Monoxide with Flexible Graphene: From Coupled Cluster Calculations to Molecular-Dynamics Simulations
2018
The interaction of CO with graphene was studied at different theoretical levels. Quantum-mechanical calculations on finite graphene models with the use of coronene for coupled cluster calculations and circumcoronene for B97D calculations showed that there was no preferential site for adsorption and that the most important factor was the orientation of CO relative to graphene. The parallel orientation was preferred, with binding energies around 9 kJ mol-1 at the CCSD(T) and B97D levels, which was in good agreement with experimental findings. From a large number of CO-circumcoronene and CO-CO interactions, computed at different distances and randomly generated orientations, parameters were fi…
Effect of melting on ionization potential of sodium clusters
2003
The effect of melting transition on the ionization potential has been studied for sodium clusters with 40, 55, 142, and 147 atoms, using ab initio and classical molecular dynamics. Classical and ab initio simulations were performed to determine the ionization potential of Na142 and Na147 for solid, partly melted, and liquid structures. The results reveal no correlation between the vertical ionization potential and the degree of surface disorder, melting, or the total energy of the cluster obtained with the ab initio method. However, in the case of 40 and 55 atom clusters, the ionization potential seems to decrease when the cluster melts.
Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection
2013
Bioprotection by sugars, and in particular trehalose peculiarity, is a relevant topic due to the implications in several fields. The underlying mechanisms are not yet clearly elucidated, and remain the focus of current investigations. Here we revisit data obtained at our lab on binary sugar/water and ternary protein/sugar/water systems, in wide ranges of water content and temperature, in the light of the current literature. The data here discussed come from complementary techniques (Infrared Spectroscopy, Molecular Dynamics simulations, Small Angle X-ray Scattering and Calorimetry), which provided a consistent description of the bioprotection by sugars from the atomistic to the macroscopic …
Water orientation and hydrogen-bond structure at the fluorite/water interface
2016
AbstractWater in contact with mineral interfaces is important for a variety of different processes. Here, we present a combined theoretical/experimental study which provides a quantitative, molecular-level understanding of the ubiquitous and important CaF2/water interface. Our results show that, at low pH, the surface is positively charged, causing a substantial degree of water ordering. The surface charge originates primarily from the dissolution of fluoride ions, rather than from adsorption of protons to the surface. At high pH we observe the presence of Ca-OH species pointing into the water. These OH groups interact remarkably weakly with the surrounding water and are responsible for the…
Piezoelectric coefficients by molecular dynamics simulations in the constant stress ensemble: A case study of quartz
2006
Piezoelectric (strain) coefficients dij of quartz are calculated in terms of molecular dynamics as a function of pressure and temperature. We review the necessary formulas for the computation of electromechanical materials coefficients obtained at constant stress and temperature, and discuss how to overcome complications of the definition of polarization variations due to fluctuating box geometries. A method is employed suppressing significantly stochastic fluctuations of the estimators for piezoelectric coefficients. A recently suggested force field for the simulation of SiO2 reproduces available experimental data quite accurately. Predictions are made for the pressure dependence of dij of…