Chapter 5: Molecular Simulation in the Energy Biosciences

Molecular simulation can be used to understand key physical processes in the energy biosciences. Both molecular mechanical (MM) and quantum mechanical (QM) simulation techniques provide atomic-detailed insight into mechanisms at the core of research in bioenergy and bioremediation. The present article describes molecular simulation in the energy biosciences in two sections: Methods and Applications. In the Methods section, we provide a synopsis of current progress in developing simulation techniques that make efficient use of large-scale supercomputers. This is done with two examples: scalable implicit solvation models and scaling molecular dynamics (MD) to O(100k) cores. In the Applications section, we discuss modeling and simulation of cellulosic biomass, an effort aimed at shedding light on biomass recalcitrance to hydrolysis (a bottleneck in biofuel production) and simulations describing the fate of mercury in contaminated biogeochemical systems. We outline research aimed at understanding the dynamics and function of the proteins and enzymes that confer mercury resistance to bacteria.