The objective of this project was the development and performance optimisation of a coupling application. The coupler library is intended for interfacing massively-parallel algorithms for multi-physics simulations. The development of the coupler library adopted the same philosophy of the Message Passing Interface (MPI) library: The coupler was engineered as a set of libraries that are accessibl...

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...

A series of molecular dynamics (MD) simulations of nonlinear molecules has been performed to test the efficiency of newly introduced semianalytical second-order symplectic time-reversible MD integrators that combine MD and the standard theory of molecular vibrations. The simulation results indicate that for the same level of accuracy, the new algorithms allow significantly longer integration ti...

Molecular dynamics (MD) simulation is used to study effects from moisture at cellulose nanofibril (CNF)–graphene oxide (GO) interfaces adhering in the wet state.

efficiency of enzymes which are used in industrial or environmental applications is highly dependent on their thermal stability. in this study, the stability of dfpase has been evaluated after introducing disulfide bonds to the structure. the results obtained from a series of protein design software were subjected to molecular dynamics simulation at different temperature to test the performance...

We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, approximately 250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and...

in this report, we describe a procedure for in-silico design of a novel haloalkane dehalogenase protein that exhibits luciferase property which can be potentially used in biosensor applications. from a pdb blast search, the selected haloalkane dehalogenase (pdb code: 1ede) had a close structural homology with a lucifearse (pdb code: 2psj chain a) sharing an identity of 33%. initially, the amino...

Atomic motions in protein molecules have been studied by molecular dynamics (MD) simulations; dynamics simulation methods have also been employed in conformational studies of polypeptide molecules. It was found that when atomic masses are weighted, the molecular dynamics method can significantly increase the sampling of dihedral conformation space in such studies, compared to a conventional MD ...

Fragment molecular orbital molecular dynamics (FMO-MD) with periodic boundary conditions is performed on liquid water using the analytic energy gradient, the electrostatic potential point charge approximation, and the electrostatic dimer approximation. Compared to previous FMO-MD simulations of water that used an approximate energy gradient, inclusion of the response terms to provide a fully an...