(4dm) Cloud-Based Simulations On Google Exacycle Provide Novel Mechanistic Insights Into Transitions in Complex Chemical and Biological Systems

Complex chemical and biological processes lie at the heart of some of the most challenging problems in science and engineering. The molecular-level description of these processes is required not only understanding the physical phenomena but also for engineering novel solutions of the associated problem. 

Multi-scale approaches are required for facing the challenging task of describing such processes that span several orders of magnitude in both length and time scales. These processes are being investigated by a spectrum of computational techniques ranging from quantum mechanics, molecular dynamics to multi-scale coarse graining and bridging between relevant scales. I have used computational methodologies such as world-wide distributed computing on platforms such as Google exacycle and Folding@home, rare event simulation techniques, GPU computing, network models etc. to study long time and length scale phenomena. In this poster, I have discussed the applications of these techniques to problems related to human health (such as conformational changes in G-Protein Coupled Receptors and Kinases, which are key signaling enzymes involved in diseases such as Cancer), materials (Biomineralization; Growth of inorganic crystals in presence of proteins), and energy (transport of small molecules in NiFe Hydrogeneases, which are involved in reversible oxidation and production of hydrogen).

More details can be found on my website: http://www.stanford.edu/~shukla