Meeting Information

Modeling Biomolecular Structure and Dynamics by Blending Ideas from Machine Learning and Physics

March 16, 2022
Virtual

Date: Wednesday, March 16, 2022
Speaker: Dr. Garegin Papoian
Title: Modeling Biomolecular Structure and Dynamics by Blending Ideas from Machine Learning and Physics
Time: 1:00 p.m. Eastern Time (US and Canada) Talk goes from 1:00 - 3:00 p.m. Attendees can sign in any time after 12:30 p.m.

Abstract: AWSEM, which stands for the Associative memory, Water mediated, Structure and Energy Model, is a coarse-grained protein simulation package that is being developed and maintained by the Papoian lab at the University of Maryland and the Wolynes lab at Rice University. It arose from one of the earliest applications of neural network theories to structural modeling of proteins, however, evolving over time into a Hamiltonian containing both physical and knowledge-based potentials. In this talk, I will first give a brief historical overview of the development of various potentials that enter the AWSEM Hamiltonian followed by recent applications. In particular, I will highlight AWSEM’s applications in structure prediction and dynamical behaviors of various macromolecular complexes, such as histone dimers, tetramers, octamers, histone chaperones and whole nucleosomes. Also, I will discuss some recent extensions and variations of AWSEM, such as AWSEM-IDP, addressing the general challenge of modeling intrinsically disordered proteins (IDPs).

Biography: Dr. Garegin Papoian was born in Yerevan, Armenia. He did his graduate work with Professor Roald Hoffmann at Cornell University, a Nobel Laureate in Chemistry, on quantum chemistry of intermetallic alloys and heterogenous catalysis. His postdoctoral researches were guided by Professor Michael Klein at the University of Pennsylvania and Professor Peter Wolynes at University of California, San Diego, on various topics in biophysics, from enzyme catalysis to protein folding. He started his independent group in 2004 as an Assistant Professor of Chemistry at the University of North Carolina at Chapel Hill, where he received tenure in 2010. He subsequently moved to the University of Maryland as the first Monroe Martin Professor with appointments in the Department of Chemistry and Biochemistry and the Institute for Physical Science and Technology. He supervised several graduate programs at UMD, including serving as Director of the Chemical Physics Graduate Program. He is interested in bringing tools of physics, chemistry and machine learning to shed light on complex biological processes at the molecular and cellular levels. He develops computational methods to study the fundamental principles governing self-assembly and dynamics of cellular cytoskeletons comprised of actin filaments, microtubules and various other associated proteins. His group is also investigating physical processes behind genomic DNA self-assembly, emphasizing the role intrinsically disordered proteins, electrostatics and elasticity.

He received an National Science Foundation CAREER Award, Camille Dreyfus Teacher-Scholar Award, Beckman Young Investigator Award, Camille and Henry Dreyfus New Faculty Award and National Institutes of Health Postdoctoral Fellowship among a number of honors.

For additional information on the subject of this talk see: (https://www.amazon.science/research-awards/success-stories/garegin-papoians-quest-to-model-an-elusive-class-of-proteins).

Questions regarding the meeting? Please email units@aps.org for assistance.

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