a national resource for computational science education

HOME BWPEP Shodor Blue Waters

View Position
Project TitleSimulations of Gas diffusion in Hydrogenases
SummaryHydrogenases are biological catalysts that can both generate H2 using cheap metals such as Nickel and Iron for catalysis. However, these proteins get poisoned due to exposure to oxygen. We plan to perform long-time scale simulations of these proteins on Blue Waters to understand the mechanism by which oxygen diffuses and inhibits the catalyst.
Job DescriptionThe selected intern will work to perform MD simulations of Hydrogenase in the presence of oxygen on Blue Waters Supercomputer. The intern will also learn about Markov state models (MSMBuilder software package) built using the collected simulation data for understanding the effect of protein conformations on oxygen diffusion. The goal of this summer internship is to identify the key bottlenecks in the diffusion of oxygen within the protein matrix and identification of mutations that could block the diffusion.
Conditions/QualificationsMust be an undergrad at U of Illinois at Urbana-Champaign; Students with Biochemistry, Chemistry, Biophysics or Chemical engineering background are preferred.
Start Date05/16/2015
End Date05/31/2016
LocationUniversity of Illinois, Urbana-Champaign, IL
Qingyuan Liu