We present a structural metric based on the Distribution of Reciprocal of Interatomic Distances (DRID) for evaluating geometrical similarity between two conformations of a molecule. A molecular conformation is described by a vector of 3N orientation-independent DRID descriptors where N is the number of molecular centroids, for example, the non-hydrogen atoms in all nonsymmetric groups of a pept...

In this paper, the stability characteristics of single-walled carbon nanotubes (SWCNTs) under the action of axial load are investigated. To this end, a nonlocal Flügge shell model is developed to accommodate the small length scale effects. The analytical Rayleigh-Ritz method with beam functions is applied to the variational statement derived from the Flügge-type buckling equations. Molecular dy...

The thermally induced order-to-disorder transition of a monolayer of krypton (Kr) atoms adsorbed on a graphite surface is studied based on a coarse molecular-dynamics (CMD) approach for the bracketing and location of the transition onset. A planar order parameter is identified as a coarse variable, psi, that can describe the macroscopic state of the system. Implementation of the CMD method enab...

The study of evaporation of water from biological macromolecules is important for the understanding of electrospray mass spectrometry experiments. In electrospray ionization (ESI), electrically charged nanoscale droplets are formed from solutions of, for example, proteins. Then evaporation of the solvent leads to dry protein ions that can be analyzed in the mass spectrometer. In this work the d...

The overall aim of this study is to calculate some water properties in the single wall carbon naotubes (SWCNT) and compare them to the bulk water properties to investigate the deviation of water properties inside the SWCNT from those in the bulk. Here some physical and transport properties of water molecules in the single wall carbon nanotube were reported by performing molecular dynamics (MD) ...

Molecular Dynamics (MD) simulations were applied to calculate self-diffusion coefficients (Di ) and heats of adsorption for ethane, propane and n-butane. The simulations were done in temperature range of 300-525 K for various concentrations inside the pores of silicalite type zeolite. The calculated values of self-diffusion coefficients and heats of adsorption resulted from the current wo...

I n a recent paper we reported non-equilibrium molecular dynamics simulations of liquid rubidium using the isokinetic sllod algorithm for the dynamics and the Price potential for the interactions. New and more extensive results are presented which confirm that the results exhibit normal square-root behaviour of the shear viscosity as a function of strain rate at the triple point.

In this work, the thermal reaction of aluminum (Al) and nickel oxide (NiO) was investigated by molecular dynamics simulations. Some effective features of reaction such as reaction temperature, the reaction mechanism, and diffusion rate of oxygen into aluminum structure were studied. ReaxFF force field was performed to study the Al/NiO thermite reaction behavior at five different temperatures (5...

Abstract In Alzheimer's disease (AD), neuroinflammation is detrimental in causing neurodegeneration. the central nervous system, inhibitor of nuclear factor kappa B kinase subunit beta (IKK2/IKKβ/IKKB/IKBKB) signaling linked to neuroinflammation-mediated learning and memory deficits through canonical pathway, while dopamine agonists have been known reverse such effects. Our silico analysis pred...

in this paper, the stability characteristics of single-walled carbon nanotubes (swcnts) under the action of axial load are investigated. to this end, a nonlocal flügge shell model is developed to accommodate the small length scale effects. the analytical rayleigh-ritz method with beam functions is applied to the variational statement derived from the flügge-type buckling equations. molecular dy...