MD simulations
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Recent papers in MD simulations
Constrained molecular dynamics (MD) computer simulations are presented for the solvation of Na+-Cl− ion-pair in supercritical methanol in an isothermal–isobaric ensemble (NPT) to understand the changes in the solvation structure of the... more
Constrained molecular dynamics (MD) computer simulations are presented for the solvation of Na+-Cl− ion-pair in supercritical methanol in an isothermal–isobaric ensemble (NPT) to understand the changes in the solvation structure of the... more
Metal nano-clusters (NCs) exhibit unique and interesting thermodynamic behaviour as compared to single molecule as well as bulk materials. Classical Molecular Dynamics (MD) simulations with Modified Embedded Atom Method (MEAM) model has... more
Following the recent emergence of SARS-CoV-2 or coronavirus disease 2019 (COVID-19), drug discovery and vaccine design to combat this fatal infection are critical. In this study, an essential enzyme in the SARS-CoV-2 replication... more
Ras-related protein (Rab-5a) is primarily involved in the regulation of early endosome fusion during endocytosis and takes part in the budding process. During GTP hydrolysis, Rab5a was spotted in the cytoplasmic side of early endo-somes... more
Ionic liquids (ILs) have shown great potential in the dissolution and stability of biomolecules when a low-to-moderate quantity of water is added. Hence, determining the thermophysical properties and understanding these novel mixtures at... more
Besides four Bcl-2 homology (BH1, BH2, BH3 and BH4) domains, the fl exible loop domain (FLD) of Bcl-2 is also important in regulating apoptosis. The FLD regulates apoptosis by interacting with JNK-1, PKC, PP2A phosphatase caspase-3,... more
We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamics (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane... more
Applying ab initio calculation and molecular dynamics simulation methods, we have been calculating and predicting the essential phase transition and self-assembly of two lower diamondoids (adamantane and diamantane), three of their... more