Sharif Digital Repository

In this paper, the atomic-scale interactions between metallic tips and samples in noncontact atomic force microscopy (NC-AFM) are studied using molecular dynamics simulations. The effects of the tip and sample materials, the surface plane direction and the lateral position of the tip with respect to the sample, on the interaction force and the dissipated energy, are investigated. The simulations conducted demonstrate that, generally, we can classify the possible outcomes for the dynamics due to the tip-surface interactions into four major categories. The first category includes all cases in which there are no considerable instabilities in tip-surface interactions, leading to negligible... 

High Density Lipoprotein (HDL) is a lipid-protein complex responsible for transporting cholesterol and triglyceride molecules, as these compounds are unable to dissolve in aqueous environments such as a bloodstream. Among the most well-known possible structures, the belt-like structure is the most common shape proposed for this vital bimolecular complex. In this structure, the protein scaffold encompasses the lipid bilayer and a planar circular structure is formed. Several HDL simulations with embedded components in the lipid section were performed. Here, we applied a series of molecular dynamic simulations using the MARTINI coarse grain force field to investigate an HDL model, with pores of... 

Classical continuum mechanics fails to give accurate solution near the crack tip, moreover, it implies that a solid is able to sustain an infinite stress at the Griffith-Inglis crack tips. Among other critical issues is the inability of the classical approach to sense the size effect. For these reasons, for more in-depth understandings and accurate behavioral predictions, it is essential to develop some atomistic methods which properly accounts, not only for the structure but also the long and short range atomic interactions effectively. In this work the interaction of inhomogeneity and crack under polynomial loading is simulated by using the many body Rafii-Tabar and Sutton potential...