Peptides are frequently used model systems for protein folding. They are also gaining increased importance as therapeutics. Here, the ability of molecular dynamics (MD) simulation for describing the structure and dynamics of β-hairpin peptides was investigated, with special attention given to the impact of a single interstrand sidechain to sidechain interaction. The MD trajectories were compare...

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. ...

in this paper, we use molecular dynamics and finite element simulations to determine the mechanical properties of single-crystal metal of silver (ag) with nano-holes. the lattice transition method from 3-dimensions into 2-dimentions in molecular dynamics simulation as well as plane stress model in finite element method, is used to lessen the simulation time consuming. elasticity module reductio...

A new local ab initio molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atom's nucleus in the active region are calculate...

We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (ADM·Na and DIM·Na) are studied separately ...

In this contribution we will present the survey of our past and current endeavor on parallel approaches in molecular modeling algorithm development, for example, molecular dynamics (MD) simulation. In particular, we will describe the new split integration symplectic method for the numerical solution of molecular dynamics equations and methods for the determination of vibrational frequencies and...

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cann...

Density Functional Theory (DFT) which is based on quantum mechanics theory has been broadly used to compute the energy and the structure of molecules and solids. However, the DFT method is limited when running calculations for a large system and only thousands of atoms can be solved. Alternatively, Molecular Dynamics (MD) simulation can be used to investigate the properties of the atomic system...

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...

Abstract The microscopic mechanism of metal ablation induced by ultrashort laser pulse irradiation is investigated. A two-temperature model scheme combined with molecular dynamics (TTM-MD) developed to incorporate electronic entropy effects into the simulation while satisfying energy conservation law. Simulation TTM-MD reveals that near threshold causes high-energy atom/ion emission and sub-nan...