The Computational Microscope

University Of Illinois At Urbana-Champaign, Urbana IL

Investigators

Abstract

This proposal is for a provisional allocation of time on the Blue Waters computer system, due to become operational in 2011, and for travel funds to support technical coordination by various collaborators with the Blue Waters project team and vendor technical team. The project involves molecular dynamics simulations of three cellular systems and processes: viral infection, morphogenesis of intra-cellular membranes, and the photosynthetic chromatophore. The actions of these biological processes unfold in time and it is difficult to follow such evolution with crystallography. Molecular dynamics simulations will provide insights into the evolution of these processes. Planned work with the poliovirus involves the use of numerical simulation to study the changes at the atomic level that are responsible for the process by which a poliovirus enters a cell. It is thought that this will be representative of this process for a class of viruses, the non-enveloped RNA viruses, that include the agents of diseases such as hepatitis A, the common cold, and viral meningitis. The planned studies of how proteins shape intracellular membranes will provide insights into an important aspect of organelle and vesicle formation. The work on photosynthesis involves studies of the chromatophore in purple bacteria, a system involving over 200 proteins and a step along the route of being able to model an organelle. This will allow researchers to determine the statistically preferred routes for quinones as they couple distant proteins, and how the light-generated electrical potential spreads as it drives ATP synthesis and cellular transport. The molecular simulation codes used in this work will be made widely available, providing tools for other researchers in the chemistry, biochemistry and materials research communities. There will be substantial involvement of post-doctoral researchers and graduate students in the projects for which the allocation is requested. The results of the work should be of use in medicine and bio-engineering.