Detecting Events in Molecular Dynamics Simulations

Gyration Radius and Energy Study at Different Temperatures for Acetylcholine Receptor Protein in Gas Phase by Monte Carlo, Molecular and Langevin Dynamics Simulations

The determination of gyration radius is a strong research for configuration of a Macromolecule. Italso reflects molecular compactness shape. In this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. We studiedthe changes of these factors as a function of temperature for Acetylcholine receptor protein in gasphase with n...

Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations

Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...

Planar Molecular Dynamics Simulation of Au Clusters in Pushing Process

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 ...

Effects of Dimethyl Sulfoxide and Mutations on the Folding of Abeta(25-35) Peptide: Molecular Dynamics Simulations

The 25-35 fragment of the amyloid β (Aβ) peptide is a naturally occurring proteolytic by-product of its larger parent molecule that retains the amyloid characteristics and toxicity of the full length parent molecule. Aggregation of this peptide occurs rapidly in aqueous solutions and thus characterization of its folding process is very difficult. In the present study, early stages of Aβ(25–35) ...

Long Range Corrections to the Vapor-Liquid Equilibrium and Surface Tension of Methane with NVT Molecular Dynamics Simulations

Mechanical Characteristics and Failure Mechanism of Nano-Single Crystal Aluminum Based on Molecular Dynamics Simulations: Strain Rate and Temperature Effects

Besides experimental methods, numerical simulations bring benefits and great opportunities to characterize and predict mechanical behaviors of materials especially at nanoscale. In this study, a nano-single crystal aluminum (Al) as a typical face centered cubic (FCC) metal was modeled based on molecular dynamics (MD) method and by applying tensile and compressive strain loadings its mechanical ...