Hernan Bernabe

Student: Hernan Bernabe, Graduate Student in Biomedical Engineering, University of Iowa
Faculty Advisor: Dr. Michael Schnieders

My research project with Michael J. Schnieders at the University of Iowa, in the Department of Biomedical Engineering, focuses on efficient exploration of free energy differences between molecular states using novel GPU accelerated molecular dynamics algorithms. Free energy differences between molecular states have important implications for understanding fundamental biochemical processes and for the design of new organic materials. Our novel GPU powered algorithm is capable of dramatically accelerating the calculation of van der Waals and electrostatics interactions between atoms in a system. Such “n-body” energy and force evaluations are a recognized performance bottleneck during both molecular dynamics simulations and in the context of simulating gravitational systems. Our state-of-the-art simulation algorithms are being used to understand and design biomolecules with new functions. For example, our atomic resolution simulation algorithms of biomolecular interactions are needed to help elucidate how biological systems respond to changes in gravitational force in terms of cellular growth, metabolism, repair of DNA damage and response to infection.