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...

Supplementary Materials: The following are available online at http://www.mdpi.com/1999-4915/7/11/2919, Figure S1: DLS analysis of PV 3CD protein, Figure S2: PCA analysis reveal major motions of 3CD, Figure S3: MD simulations reveal multiple interfaces in WT and mutant 3CD, Figure S4: Mutations of 3CD in the crystal structure, Figure S5: Analysis of the 50 ns MD simulations of mutant PV 3CD, an...

Molecular dynamics (MD) simulations have been used to study surface reaction dynamics of Si and Si02 etching by halogens. To perform classical MD simulations for Si02 etching reaction by halogens (C1 or F), we have constructed new sets of twoand three-body interatomic potential functions based on potential energy data obtained from ab initio quantum mechanical calculations of the electronic sta...

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...

Complete determination of a membrane protein structure requires knowledge of the protein position within the lipid bilayer. As the number of determined structures of membrane proteins increases so does the need for computational methods which predict their position in the lipid bilayer. Here we present a coarse-grained molecular dynamics approach to lipid bilayer self-assembly around membrane p...

Molecular dynamics (MD) simulations were used to investigate the electroporation of archaeal lipid bilayers when subjected to high transmembrane voltages induced by a charge imbalance, mimicking therefore millisecond electric pulse experiments. The structural characteristics of the bilayer, a 9:91 mol% 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI) and 2,3-di-O-sesterterpanyl-s...

We present a simple method for calculating a continuum temperature field directly from a molecular dynamics (MD) simulation. Using the idea of a projection matrix previously developed for use in the bridging scale, we derive a continuum temperature equation which only requires information that is readily available from MD simulations, namely the MD velocity, atomic masses and Boltzmann constant...