Myoglobin is an important protein for the study of structure and dynamics. Three conformational substates have been identified for the carbonmonoxy form of myoglobin (MbCO). These are manifested as distinct peaks in the IR absorption spectrum of the CO stretching mode. Ultrafast 2D IR vibrational echo chemical exchange experiments are used to observed switching between two of these substates, A...

Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine...

In this paper, we briefly review the boxed molecular dynamics (BXD) method which allows analysis of thermodynamics and kinetics in complicated molecular systems. BXD is a multiscale technique, in which thermodynamics and long-time dynamics are recovered from a set of short-time simulations. In this paper, we review previous applications of BXD to peptide cyclization, solution phase organic reac...

First principles molecular dynamics (MD) simulations, of water adsorption on the MgOf100g surface, was performed to determine the molecular structure and chemical nature of the adsorbed water at varying coverage. Dissociative adsorption was stabilized by hydrogen bond donation from neighboring water molecules. The dissociation barrier had a strong dependence on coverage. Spontaneous dissociatio...

Molecular-dynamics (MD) simulations are playing an increasingly important role in research into the modes of action of G-protein coupled receptors (GPCRs). In this field, MD simulations are unusually important as, because of the difficult experimental situation, they often offer the only opportunity to determine structural and mechanistic features in atomistic detail. Modern combinations of sof...

Cyclodextrins are widely used nowadays in many fields, including therapeutic systems, due to their ability to form inclusion complexes with a wide variety of compounds. In this study we present a series of molecular dynamics (MD) simulations on β-cyclodextrin/propiconazole inclusion complexes in order to gain insights on the inclusion process. The data obtained from constraint-free molecular dy...

the overall aim of this study is to calculate some water properties in the single wall carbon naotubes (swcnt) and compare them to the bulk water properties to investigate the deviation of water properties inside the swcnt from those in the bulk. here some physical and transport properties of water molecules in the single wall carbon nanotube were reported by performing molecular dynamics (md) ...

based on the fact the manipulation of fine nanoclusters calls for more precise modeling, the aim of this paper is to conduct an atomistic investigation for interaction analysis of particle-substrate system for pushing and positioning purposes. in the present research, 2d molecular dynamics simulations have been used to investigate such behaviors. performing the planar simulations can provide a ...

A simulation is reliable when the simulation time is much longer than the relaxation time of the quantities in question. The aim of this work is to address the question when Molecular Dynamics (MD) simulation is reliable and how it depends on the integration algorithms and optimal time step. There were certain problems related to the choice of integration algorithms on Molecular Dynamics simula...

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...