Potassium Channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. Potassium Channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. Realistic studies of ion current in biologic channels present a major challenge for compu...

Over the past years, two-dimensional materials such as graphene, phosphorene, silicene, and boron-nitride have attracted the attention of many researchers. After the successful synthesis of graphene, due to its many new applications, researches began to produce nanosheets from other elements, and among these elements, boron was one of the options. In the periodic table of elements, boron is ahe...

A novel computational fluid dynamics and molecular kinetic theory (CFD-MK) method was developed to simulate the impingement of a nanodroplet onto a solid surface. A numerical solution of the Navier–Stokes equation using a volume-of-fluid (VOF) technique was used to model nanodroplet deformation. Dynamic contact angle during droplet impact was obtained by molecular kinetic theory. This dynamic c...

Human epidermal growth factor receptor 2 (HER2) is a member of the epidermal growth factor receptor family having tyrosine kinase activity. Overexpression of HER2 usually causes malignant transformation of cells and is responsible for the breast cancer. In this work, the virtual screening, molecular docking, quantum mechanics and molecular dynamics methods were employed to study protein–ligand ...

Studying the interaction of pharmaceutical ionic liquids with human serum albumin (HSA) can help investigating whether or not ionic liquid formation can enhance pharmacological profile of the discrete ingredients. In this respect, in the present work, the interactions of Benzalkonium Ibuprofenate, as a well-known active pharmaceutical ionic liquid, Benzalkonium Chloride, and also Sodium Ibuprof...

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...

The effect of sample size on the melting parameter of simulated potassium chloride microcrystal is investigated by molecular dynamics simulation. The size of microcrystal is varied from 8 to 4096 ions. The increase in melting temperature with sample size was found to be in good agreement with the theory.

Human serum albumin (HSA) is the most abundant protein in the blood plasma. Drug binding to HSA is crucial to study the absorption, distribution, metabolism, efficiency and bioavailability of drug molecules. In this study, isothermal titration calorimetry and molecular dynamics simulation of HSA and its complex with indometacin (IM) were performed to investigate thermodynamics parameters and th...

Alzheimer's disease is an irreversible and progressive brain disorder that slowly destroys memory and thinking skills and ultimately the ability to do the simplest things and can lead to death. Cholinesterases (ChEs) play an important role in controlling cholinergic transmission, and subsequently, by inhibiting CHEs, acetylcholine levels in the brain are elevated. Coumarins have been shown to e...

Experiences designing and deploying NAMD-G, an infrastructure for executing biomolecular simulations using the parallel molecular dynamics code NAMD within the context of a Computational Grid, are described. The effort is motivated by a general outline of the tasks involved in conducting research of this class as traditionally undertaken, followed by a description of the enhancements offered by...