We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD) scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained ...

Non-equilibrium steady state systems do not obey the equipartition theorem in that the distribution of the random kinetic energy among the three directions is not independent of the mechanism which removes the dissipative heat. This becomes important beyond the linear regime because system properties will be functions of the thermostatting mechanism as well. For homogeneous non-equilibrium mole...

Molecular Dynamics (MD) simulation and Density Functional Theory (DFT) methods have been used to evaluate the efficiency of four quinoline derivatives on corrosion inhibition in the aqueous phase. Some quantum chemical parameters such as hardness (η), electrophilicity (w), polarizability (a), energy of the highest occupied molecular orbital (EHOMO), energy of th...

Equilibrium formally can be represented as an ensemble of uncoupled systems undergoing unbiased dynamics in which detailed balance is maintained. Many nonequilibrium processes can be described by suitable subsets of the equilibrium ensemble. Here, we employ the "weighted ensemble" (WE) simulation protocol [Huber and Kim, Biophys. J.1996, 70, 97-110] to generate equilibrium trajectory ensembles ...

phage elisa is a common method to confirm binding of obtained phages from phage display technique to related antigens. enzyme-conjugated antibody directed against the major capsid protein (pviii) or enzyme-conjugated secondary antibody against the primary antibody is used as a detection system in phage elisa. we have suggested to express an acid phosphatase (sapm) enzyme on m13 pix minor coat p...

Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chlorid...

Surfactant molecules are used as interesting tools to study the structure, function and stability of proteins. Protonation states of amino acids may be changed in the presence of surfactants. In this work, using experimental observations and molecular dynamic simulation, the effects of sodium dodecyl sulfate on the acid dissociation constants of tryptophan was examined. The acid–base equilibriu...

In this study, an evaporation coefficient representing the rate of vapor molecules was calculated in a vapor–gas binary mixture and non-equilibrium system using molecular dynamics simulation. The herein refers to state which net occurs, calculation is composed non-condensable (NC) gas molecules. demonstrated have almost same value as that equilibrium state. number density NC around gas–liquid i...

We simulate the far-from-equilibrium irreversible expansion of a compressed ideal gas in two space dimensions. For this problem the particle trajectories from conventional Smooth Particle Applied Mechanics are isomorphic to those from a corresponding molecular dynamics simulation. The smooth-particle \weight function", used to describe the expanding gas, is identical to the pair potential gover...