We present results from molecular dynamics simulations for the non-equilibrium evolution of a binary fluid in the presence of a wetting surface. We study the pattern dynamics which results when a homogeneous fluid mixture is quenched to temperatures both above and below the critical temperature. Our extensive computer simulation results are in agreement with arguments based on Ginzburg-Landau t...

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...

All atom molecular dynamics simulations have become a standard method for mapping equilibrium protein dynamics and non-equilibrium events like folding and unfolding. Here, we present detailed methods for performing such simulations. Generic protocols for minimization, solvation, simulation, and analysis derived from previous studies are also presented. As a measure of validation, our water mode...

A simulation is reliable when the simulation time is much longer than the relaxation time of the quantities in question. The aim of this work is to address the question when Molecular Dynamics (MD) simulation is reliable and how it depends on the integration algorithms and optimal time step. There were certain problems related to the choice of integration algorithms on Molecular Dynamics simula...

in this report, we describe a procedure for in-silico design of a novel haloalkane dehalogenase protein that exhibits luciferase property which can be potentially used in biosensor applications. from a pdb blast search, the selected haloalkane dehalogenase (pdb code: 1ede) had a close structural homology with a lucifearse (pdb code: 2psj chain a) sharing an identity of 33%. initially, the amino...

the aim of this research is to calculate the elastic constants and bulk modulus of cu-20 wt% ni random nanoalloy. the molecular dynamics simulation technique was used to calculate the mechanical properties in npt ensemble. the interaction between atoms as well as cohesive energy in the nanoalloy modeled systems was calculated by morse et al. two body potential. also the temperature of the syste...

the overall aim of this study is to calculate some water properties in the single wall carbon naotubes (swcnt) and compare them to the bulk water properties to investigate the deviation of water properties inside the swcnt from those in the bulk. here some physical and transport properties of water molecules in the single wall carbon nanotube were reported by performing molecular dynamics (md) ...

the aim of this study is investigating the transport mechanism of ibuprofen chiral isomers inside singlewall carbon nano tube (swcnt) using mathematical modeling. to achieve this goal, molecular dynamicssimulation has been performed to evaluate the interactions of ibuprofen isomers with swcnt in an aqueoussolution. results show that both chiral forms of ibuprofen molecules enter and remain insi...

As shown by Jarzynski, free energy differences between equilibrium states can be expressed in terms of the statistics of work carried out on a system during non-equilibrium transformations. This exact result, as well as the related Crooks fluctuation theorem, provide the basis for the computation of free energy differences from fast switching molecular dynamics simulations, in which an external...