Presenter 1: Thomas Lee (Research Fellow, Mark group, SCMB)
Title: Large-scale validation of force fields
Abstract: The application of molecular dynamics simulations to drug design, protein structure determination, and biophysics research more generally, depend critically on the quality of protein force fields. These force fields must be validated by demonstrating that they reproduce experimental properties of proteins. To validate and compare recent versions of the GROMOS force field, a set of 52 protein structures obtained from the Protein Data Bank (PDB) has been simulated, each for 3 replicates of 15 ns. The results show that the force fields reproduce the results of crystallographic and NMR experiments. However, despite improvements to the parameters in newer versions of the force field, no difference in their ability to reproduce experimental observations was detected on the time scale simulated. In order to simulate longer time scales using graphics processing units (GPUs), we have developed software to support the use of GROMOS force fields in the Amber molecular dynamics software package. The 52 structures in the validation set have each been simulated for 400 ns. These simulations further validate the ability of the force field to reproduce experimental observations of proteins. The simulations also reveal potentially inappropriate side-chain conformations in structures deposited in the PDB.
Presenter 2: Fariba Asadi (PhD student, Nguyen group, SoCE)
Title: The link between the kinetics of gas hydrate formation and surface ion distribution in the low salt concentration regime
Abstract: Gas hydrates are ice-like solids that form when nonpolar gas molecules with the proper size are encased in cages of water molecules at low temperature (less than 300K) and high pressure (more than 0.6 MPa). Clathrate hydrates are crucial from the point of view of flow assurance, future energy resource as well as promising innovative and sustainable applications such as gas separation, CO2 sequestration, seawater desalination and natural gas storage. Under the presence of appropriate additives, the formation of Gas hydrates can be controlled in desired manners. Depending on their properties, additives can thermodynamically and/or kinetically influence gas hydrate formation and promote/inhibit this process. One of the most common additives are inorganic salts, which can thermodynamically inhibit hydrate formation. However, some inorganic salts at low concentration can act as a kinetic hydrate promoter. I show the link between ion distribution at the gas/water interface and gas dissolution is one of the possible reasons for this unexpected behaviour of salts at low concentration on gas hydrate formation.