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BIOE Seminar Series: Cameron Abrams
Friday, March 17, 2017
9:00 a.m.-10:00 a.m.
Pepco Room (1105), Jeong H. Kim Engineering Building
For More Information:
Dr. Silvina Matysiak

Cameron Abrams
Department of Chemical and Biological Engineering
Drexel University

New Rare-Event Methods in Molecular Simulations:  Applications to Ligand Entry Kinetics and Protein Conformational Changes

All-atom molecular dynamics (MD) simulations provide a powerful way to guide our thinking about links between molecular structure and macroscopic properties, but only if we continue to explore our understanding of, and overcome, its limitations.  The most important limitation of MD is arguably the “rare-event” problem:  transitions between recognizable metastable states occur too infrequently for MD simulation to statistically characterize.  In this talk, I’ll highlight two recent methods developed in our group to address the rare-event problem in MD.  The first, Markovian Milestoning, permits computation of rate constants associated with relatively slow processes in all-atom systems.  We show its application to the problem of structurally understanding the influence of substrate binding on the entry and exit kinetics of oxygen in flavoenzymes.   The second, replica-exchange on-the-fly free-energy parameterization, overcomes the classical “hidden-variable” problem prevalent in rare-event methods in biomolecular simulations.  We show its application in the understanding of the effects of phenotypically distinct mutations in the human prion protein, the etiological agent of Creutzfeldt-Jakob disease and other neurodegenerative diseases.  The talk will end with some perspectives on the future of rare-event methods in furthering our structural understanding of biomolecular kinetics.

About the Speaker

Cameron F. Abrams earned a BS in Chemical Engineering from NC State University in 1995 and a PhD in Chemical Engineering from UC-Berkeley in 2000.  After two years of postdoctoral work at the Max-Planck-Institute for Polymer Research in Mainz, Germany, he joined the Department of Chemical and Biological Engineering at Drexel University.  Abrams is the recipient of an NSF CAREER award, an ONR Young Investigator Award, and is the 2015 Impact Awardee in Computational Molecular Sciences and Engineering from the American Institute of Chemical Engineers.  In additional to novel molecular simulation methods, Abrams’ research interests include high-performance materials, protein-related kinetics and thermodynamics, and HIV-1 entry inhibitor design.  


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