Molecular dynamics simulations for plasma-surface interactions

Molecular Dynamics Simulation and Free Energy Studies on the Interaction of Salicylic Acid with Human Serum Albumin (HSA)

Human serum albumin (HSA) is the most abundant protein in the blood plasma. Molecular dynamics simulations of subdomain IIA of HSA and its complex with salicylic acid (SAL) were performed to investigate structural changes induced by the ligand binding. To estimate the binding affinity of SAL molecule to subdomains IB and IIA in HSA protein, binding free energies were calculated using the Molecu...

Energy study at different solvents for potassium Channel Protein by Monte Carlo, Molecular and Langevin Dynamics Simulations

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...

Long Range Corrections to the Vapor-Liquid Equilibrium and Surface Tension of Methane with NVT Molecular Dynamics Simulations

Plasma-surface interactions of hydrogenated carbon

We present a review of our study of interactions of plasma particles (atoms, molecules) with hydrogenated amorphous carbon surfaces typical of plasma-facing divertor tiles and deposited layers in magnetic-fusion reactors. Our computer simulations of these processes are based on classical molecular dynamics simulations, using the best currently available multibody bond-order hydrocarbon potentia...

MD-Simulation of Duty Cycle and TaN Interlayer Effects on the Surface Properties of Ta Coatings Deposited by Pulsed-DC Plasma Assisted Chemical Vapor Deposition

In this work, molecular dynamics (MD) simulations were employed to investigate the effects of duty cycle changes and utilization of tantalum nitride interlayer on the surface roughness and adhesion of Ta coating deposited by pulsed-DC plasma assisted chemical vapor deposition. To examine the simulation results, some selected deposition conditions were experimentally implemented and characterize...

Three new scorpion chloride channel toxins as potential anti-cancer drugs: Computational prediction of the interactions with hMMP-2 by docking and Steered Molecular Dynamics Simulations

Scorpion venom is a rich source of toxins which have great potential to develop new therapeutic agents. Scorpion chloride channel toxins (ClTxs), such as Chlorotoxin selectively inhibit human Matrix Methaloproteinase-2 (hMMP-2). The inhibitors of hMMP-2 have potential use in cancer therapy. Three new ClTxs, meuCl14, meuCl15 and meuCl16, derived from the venom transcriptome of Iranian scorpion, ...