Theory of Polymer–Nanopore Interactions Refined Using Molecular Dynamics Simulations

Molecular dynamics simulations for plasma-surface interactions

Molecular Dynamics Simulations of Freezing Behavior of Pure Water and 14% Water-NaCl Mixture Using the Coarse-Grained Model

 We performed molecular dynamics simulations using the coarse-grained model to study the freezing behavior of pure water and 14% water-salt mixture in a wide range of temperatures for a very long time around 50 nanoseconds. For the salty water, an interface in nanoscale was used. For both systems, the f...

Modeling of annexin A2—Membrane interactions by molecular dynamics simulations

The annexins are a family of Ca2+-regulated phospholipid binding proteins that are involved in membrane domain organization and membrane trafficking. Although they are widely studied and crystal structures are available for several soluble annexins their mode of membrane association has never been studied at the molecular level. Here we obtained molecular information on the annexin-membrane int...

Observation and description of phonon interactions in molecular dynamics simulations

Three-phonon interactions are identified and analyzed in nonequilibrium molecular dynamics simulations of the Lennard-Jones face-centered cubic crystal. The small simulation cells studied and the classical nature of the simulations lead to a different description of the phonon transport than the quantum-particle model. The selection process is strictly governed by the mode wave vectors. In dete...

Large Scale Molecular Dynamics Simulations of Lipid-Drug Interactions

Molecular dynamics is a powerful computational technique for studying biochemical systems at the atomic resolution. We will present the results of several recent studies in our laboratory that apply molecular dynamics to the distribution and behaviour of small molecules within lipid bilayer environments similar to the membrane surrounding all cells. Specifically, we have studied the distributio...