the mechanical properties including elastic stiffness constants as well as bulk modulus of palladium (pd) nanowire were calculated in the constant temperature and pressure (npt), ensemble by molecular dynamics (md) simulation technique. the quantum sutton-chen (q-sc) many-body potential was used to calculate the cohesive energy as well as forces experience by every atoms. the temperature and pr...

A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is for...

This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality techniques for intuitive bio-nanorobotic prototyping. Using molecular dynamic simulations the operator can design, characterize and prototype the behavior of bio-nanorobotic components and structures. The main novelty of the proposed simulations is based on the characterization ...

advanced technologies in molecular biology and modern experimental biophysics heavily rely not only on the knowledge of structure of essential proteins but also on their structural dynamics. the function of these bimolecular systems and the pathways along which the biological phenomena take place can be determined based on the knowledge of the molecular structure and behavior. as such, the simp...

graphene sheet including single vacancy, double vacancy and stone-wales with armchair and zigzag structure was simulated using molecular dynamics simulation. the effect of defects on shear’s modulus, shear strength and fracture  strain was investigated. results showed that these shear properties reduce when the degrees of all kinds of defects increase. the dangling bond in sv and dv defected gr...

microtubules, the active filaments with tubular shapes, play important roles in a wide range of cellular functions, including structural supports, mitosis, cytokinesis, and vesicular transport, which are essential for the growth and division of eukaryotic cells. finding properties of microtubules is one of the main concerns of scientists. this work helps to obtain mechanical properties of micro...

in this study, we have investigated radius dependence of hydrogen storage within armchair (n,n) single walled carbon nanotubes (swcnt) in a square arrays. to this aim, we have employed equilibrium molecular dynamics (md) simulation. our simulations results reveal that radius of carbon nanotubes are an important and influent factor in hydrogen distribution inside carbon nanotubes and consequentl...