Molecular dynamic simulation is a powerful tool for finding dependencies in biological molecules. Correlation matrices can map out the nature of correlated movements performed by different regions within the molecule during their solution state simulations and provide a critical tool in understanding the interactions between different residues in a structure. Here we present a methodology to ex...

An integrated model based on the variant of Ba/Bt, is established to predict size-dependent melting point of nanoparticles by considering the geometric and energetic characteristics of Wulff construction. Ba is the rest bond number and Bt denotes the total bond number without broken bonds in a Wulff construction. Without any adjustable parameters, this model predicts a decreasing trend of melti...

the interaction between proteins and membranes has an important role in biological pro-cesses.we have calculated energies of interaction between melittin and dmpc bilayer in differenttemperatures. we have used the charmm software for md simulation under the canonical (n,v, e) ensemble at different temperatures. the computations have shown that water moleculeshave more penetration into the bilay...

background: recently, it has been indicated that x-ray coherent scatter from biological tissues can be used to access signature of tissue. some scientists are interested in studying this effect to get early detection of breast cancer. since experimental methods for optimization are time consuming and expensive, some scientists suggest using simulation. monte carlo (mc) codes are the best option...

aromatase inhibitors (ais) as effective candidates have been used in the treatment of hormone-dependent breast cancer. in this study, we have proposed 300 structures as potential ais and filtered them by lipinski’s rule of five using druglito software. subsequently, they were subjected to docking simulation studies to select the top 20 compounds based on their gibbs free energy changes and also...

We propose a local heating method via molecular dynamic simulation to investigate the charge transport efficiency along a polypeptide chain in the gas phase. In the protein charge transfer process, the carbonyl groups next to a Cα-hinge collide with each other. Within a critical contact distance between O–O atoms, charge starts to transfer otherwise the charge being at rest. This is termed a bi...

A new method is proposed for correctly modeling the long range interaction between a fluid and a bounding wall in atomistic simulations. This method incorporates the molecular structure of the solid substrate while allowing for a finite interaction cutoff by making a proper estimation of long range correction for the fluid-wall interaction. The method is then applied to a molecular dynamic simu...

insulin-like growth factor (igf-1) is an anti-apoptosis factor in multiple cell types associated with various cancers. computational methods allow investigating the systems between 50–100 atoms in the frame of quantum mechanics and up to 50,000 atoms with molecular dynamics. since there are specific interactions between the residues, the solvent could play an important role in the stability of ...

Supercooled liquids near the glass transition exhibit the phenomenon of heterogeneous relaxation; at any specific time, a nominally homogeneous equilibrium fluid undergoes dynamic fluctuations in its structure on a molecular distance scale with rates that are very different in different regions of the sample. Several theoretical and simulation studies have suggested a change in the nature of th...

abstract in the dynamic and competitive market, managers seek to find effective strategies for new products development. since there has not been a thorough research in this field, this study is based on a review on the risks exist in the npd process and an analysis of risks through fmea approach to prioritize the existent risks and a modeling behavior of the npd process and main risks using sy...