Multiscale computational approach that combines different methods to study laser ablation phenomenon is presented. The methods include the molecular dynamics (MD) breathing sphere model for simulation of the initial stage of laser ablation, a combined MD finite element method (FEM) approach for simulation of propagation of the laser-induced pressure waves out from the MD computational cell, and...

Ab4'uci.t — The structures and reactivities of proteins are markedly influenced by water. In conformational energy calculations, the hydration of proteins is treated by a hydration-shell model. Originally, the shell model was parameterized with exoerimental data, but more recently empirical potentials were introduced to obtain these parameters by Monte Carlo and molecular dynamics techniques. T...

Using GROMACS (a molecular dynamics package) we simulate ionic copolymers and compare the numerical results with those obtained by the lattice Monte Carlo simulations. While the results are qualitatively similar for both methods, the simulation times are significantly longer for the molecular dynamics simulations than those for the corresponding Monte Carlo runs.

Single-crystal diffuse scattering (SCDS) reveals detailed structural insights into materials. In particular, it is sensitive to two-body correlations, whereas traditional Bragg peak-based methods are sensitive to single-body correlations. This means that diffuse scattering is sensitive to ordering that persists for just a few unit cells: nanoscale order, sometimes referred to as “local structur...

A numerical method that combines molecular dynamics simulation and finite element analysis to simulate the mechanical behaviors of materials and structures at nano-scale is proposed. In this combined method, the initial atomistic model is transformed to continuum model, and an approximate solution is first obtained with the finite element method for the system under the specified boundary condi...

The melting of a 64 ion microcrystal of KCI was studied by means of a molecular dynamics computer simulation. We used a central pair interaction with an inverse power law repulsion. The thermodynamics, kinetic and structural properties such as melting temperature, latent heat, mean square displacement, diffusion constant, radial distribution function and bond angle distribution are calculated. ...

This paper is designed to examine the binding behavior of Coumarin with bovine -casein (βCN) through fluorescence spectroscopy and molecular modeling techniques. The data analysis on fluorescence titration experiments at various temperatures represents the enthalpy driven nature for the formation of Coumarin–βCN complex and the prevailed role of hydrogen bonds and van der Waals interactions in...

A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is for...

the interaction between propranolol (prop) and human serum albumin (hsa) was studied in the presence of dimethyl methylphosphonate (dmmp). dmmp is usually considered as a simulant for chemical warfare agents (cwas). for this purpose fluorescence quenching, resonance light scattering (rls), synchronous, three-dimensional fluorescence spectroscopy and molecular dynamics (md) simulation were emplo...