Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chlorid...

This paper is designed to examine the binding behavior of Coumarin with bovine -casein (βCN) through fluorescence spectroscopy and molecular modeling techniques. The data analysis on fluorescence titration experiments at various temperatures represents the enthalpy driven nature for the formation of Coumarin–βCN complex and the prevailed role of hydrogen bonds and van der Waals interactions in...

Molecular dynamics simulations of a model main-chain liquid-crystalline polymer (LCP), and a low molecular weight analogue, have been carried out using an efficient parallel algorithm. Amain-chain LCP is formed with the help of Gay-Berne mesogenic units connected to each other through flexible methylene spacers. We have studied the effect of varying the spacer length, and have examined the regi...

in this study the operations of melting of au15ag40 nanoalloy have been studied using the molecular dynamic simulations through the gupta multiparticle potential and the nonergodicity of simulations is eliminated by the multiple histogram method. the melting characteristics are determined by the analysis of variations in the potential energy. the calculations indicate that the melting of au15ag...

the interaction between propranolol (prop) and human serum albumin (hsa) was studied in the presence of dimethyl methylphosphonate (dmmp). dmmp is usually considered as a simulant for chemical warfare agents (cwas). for this purpose fluorescence quenching, resonance light scattering (rls), synchronous, three-dimensional fluorescence spectroscopy and molecular dynamics (md) simulation were emplo...

Dynamic wetting on the flexible hydrophilic pillar-arrays is studied using large scale molecular dynamics simulations. For the first time, the combined effect of the surface topology, the intrinsic wettability and the elasticity of a solid on the wetting process is taken into consideration. The direction-dependent dynamics of both liquid and pillars, especially at the moving contact line (MCL),...

ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mono- and bis-spirooxindole-hexahydropyrrolizines as potent butyrylcholinestrase (BuChE) inhibitors were carried out using statistical methods, molecular dynamics and molecular docking simulation. QSAR methodologies, including classification and regression tree (CART), multiple linear regression (MLR),...

Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (P(ced)) which is involved in tetramerization using disorder analysis and m...

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...