Next HPCViz seminar will be held Wednesday December 5: starting at 9:00 in the VIC studio. We are happy to announce the following speakers: Rossen Apostolov and Ali Gholami. See below for more information.
See you there!
Title: Ensemble Computing and Markov State Models in Molecular Dynamics Simulations
Molecular Dynamics (MD) simulations are extensively used for atomistic level studies of structural changes in molecules, inter-molecular interactions, phase transitions etc. A single MD simulation follows the time evolution of a stochastic system and is in practice unable to fully explore all possible states of the system, as needed for achieving statistical significance. The system can reach meta-stable states that it cannot escape or some events of interest may occur on timescales far beyond what is achievable with current methodology. In addition, most of the supercomputers nowadays have capabilities far beyond the hard-scaling limits of many bio-molecular systems of interest.
Being inherently embarrassingly parallel in nature, ensemble computing presents opportunities for improving the sampling of system states by staging thousands of system replicas to run in parallel. However extracting meaningful information from the vast amount of this trajectory data is not an easy task. Markov State Models (MSM) generate kinetic
models based on collected large-scale simulation data. They can help greatly in understanding the evolution of investigated system while allowing to reach timescales larger than those of the individual simulation runs.
Title: Security of the Biobank Cloud