Molecular dynamics (MD) simulation is an established method for studying the conformational changes that are important for protein function. Recent advances in hardware and software have allowed MD simulations over the same timescales as experiment, improving the agreement between theory and experiment to a large extent. However, running such simulations are costly, in terms of resources, stora...

In this work, a procedure to simulate the MD (molecular distillation) process for lactic acid purification was developed. The simulation was carried out with the aid of the Aspen Plus Process Simulator. Flash vessel was used to represent the MD process since the software does not present this unit operation. The simulation results with efficiency factors were in agreement with previously report...

A combined theoretical and molecular dynamics (MD) simulation study of the collective modes and their dispersion in a two-dimensional Yukawa system in the strongly coupled liquid state is presented. The theoretical analysis relies upon the quasilocalized charge approximation; the MD simulation generates static pair correlation functions and dynamical current-current correlation spectra.

Atomistic molecular dynamics (MD) simulations of druglike molecules embedded in lipid bilayers are of considerable interest as models for drug penetration and positioning in biological membranes. Here we analyze partitioning of coumarin in dioleoylphosphatidylcholine (DOPC) bilayer, based on both multiple, unbiased 3 μs MD simulations (total length) and free energy profiles along the bilayer no...

In this work, molecular dynamics (MD) simulations were employed to investigate the effects of duty cycle changes and utilization of tantalum nitride interlayer on the surface roughness and adhesion of Ta coating deposited by pulsed-DC plasma assisted chemical vapor deposition. To examine the simulation results, some selected deposition conditions were experimentally implemented and characterize...

Abstract. Efforts to use molecular dynamics (MD) to develop both non-equilibrium dissociation models required in the shock layer as well as gas-surface interaction models specifically for surface catalysis will be summarized. First, an accelerated MD algorithm for dilute gases is presented, called the Event-Driven/Time-Driven (ED/TD) MD method. The method detects and moves molecules directly to...

A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtain...

A hexagonal liquid crystal of DNA fragments (double-stranded, 150 basepairs) with tetramethylammonium (TMA) counterions was investigated with small angle neutron scattering (SANS). We obtained the structure factors pertaining to the DNA and counterion density correlations with contrast matching in the water. Molecular dynamics (MD) computer simulation of a hexagonal assembly of nine DNA molecul...

We have developed a parallel program for molecular dynamics (MD) simulation on clusters of personal computers (PCs). The program implements the Split Integration Symplectic Method (SISM) for MD integration that analytically treats high-frequency motions in molecules, allowing the simulation time step to be longer than in standard methods. The program is designed to run on parallel clusters of p...