Shape effects on the yield stress and deformation of silicon nanowires: A molecular dynamics simulation

The tension and compression of single-crystalline silicon nanowires (SiNWs) with different cross-sectional shapes are studied systematically using molecular dynamics simulation. The shape effects on the yield stresses are characterized. For the same surface to volume ratio, the circular cross-sectional SiNWs are stronger than the square cross-sectional ones under tensile loading, but reverse happens in compressive loading. With the atoms colored by least-squares atomic local shear strain, the deformation processes reveal that the failure modes of incipient yielding are dependent on the loading directions. The SiNWs under tensile loading slip in {111} surfaces, while the compressive loading leads the SiNWs to slip in the {110} surfaces. The present results are expected to contribute to the design of the silicon devices in nanosystems.

Splitting the fast and slow motions in molecular dynamics simulations based on the change of cold potential well bottom

Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

Molecular dynamics research of G249 and S249 substitutions of p53 protein.

,The molecular dynamics research of the core domain of p53 protein crystal structure shows that besides the stability in biochemistry this domain also shows a high stability in molecular mechanics. Based on that work, the residue R249 was substituted with amino acids Gly and Ser respectively, and molecular dynamics researches were performed separately. The results show that these substitutions cause a relax tendency between loop2 and 3 domains, leading to an alteration of the whole conformation of p53 core domain and ruining its stability. The results visually explains the mechanism of p53 changes in immunological and biochemical reactions, which are caused by 249 residue substitutions from 3-D structure variations.

Molecular evolution study in China: progress and future promise

China has a large land area with highly diverse topography, climate and vegetation, and animal resources and is ranked eighth in the world and first in the Northern Hemisphere on richness of biodiversity. Even though little work on molecular evolution had

Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Molecular dynamics simulation on the complex of the tobramycin and 16S rRNA a site

A 3. 6 ns molecular dynamics simulation was carried out on the complex system of tobramycin and 16S rRNA in order to understand the speciality recognition mechanism between tobramycin and 16S rRNA at the molecular level. The results demonstrate that two l

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Molecular Dynamics Simulation on Characteristics of Decomposition of Methane Hydrate in the Presence of Hydrogen Peroxide Solution

In this work, the characteristics of the decomposition of methane hydrate Structure I (SI) in the presence of hydrogen peroxide solution is investigated using the molecular dynamics simulation. The mechanism of the transformation process from the solid hydrate to the liquid is analyzed with the effect of hydrogen peroxide (HP) solution. In addition, the effect of ethylene glycol (EG) with the same molar concentration with HP on the methane hydrate dissociation is also studied. The results illustrate that both HP and EG promote well the hydrate dissociation. The work provides the important reference value for the experimental investigation into the promotion effect of HP on the hydrate dissociation.