The next Biophysics and Development Seminar will take place on
Monday, March 8, 2021
1:00pm Eastern Time US and Canada
Gregory A. Voth, Ph.D., FRSC
Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics,
The University of Chicago
Overcoming the Multiscale Simulation Challenge for Biomolecular Systems
Advances in theoretical and computational methodology will be presented that are designed to simulate complex (biomolecular and other soft matter) systems across multiple length and timescales. The approach provides a systematic connection between all-atom molecular dynamics, coarse-grained modeling, and mesoscopic phenomena. At the heart of these concepts are methods for deriving coarse-grained (CG) models from molecular structures and their underlying atomic-scale interactions. This particular aspect of the work has strong connections to the procedure of renormalization in physics, but in the context of CG models, it is developed and implemented for more heterogeneous systems. An important new component of our work has also been the concept of the “ultra-coarse-grained” (UCG) model and its associated computational implementation. In the UCG approach, the CG sites or“beads” can have internal states, much like quantum mechanical states. These internal states help to self-consistently quantify a more complicated set of possible interactions within and between the CG sites, while still maintaining a high degree of coarse-graining in the modeling. The presence of the UCG site internal states greatly expands the possible range of systems amenable to accurate CG modeling, i.e., quite heterogeneous systems, including complex self-assembly processes involving large multi-protein complexes. Applications to experimentally important targets such as cytoskeleton actin filaments and virus particles (virions) will be given.
Gregory A. Voth is the Haig P. PapazianDistinguished Service Professor of Chemistry at The University of Chicago. He is also a Professor of the James Franck Institute and the Institute for Biophysical Dynamics. He received a Ph.D. in Theoretical Chemistry from the California Institute of Technology in 1987 and was an IBM Postdoctoral Fellow at the University of California, Berkeley from 1987-89. He is the author or co-author of approximately560 peer-reviewed scientific articles that have been cited more than 46,000times with a current h-index of 108. Voth is a Fellow of the American Chemical Society, American Physical Society, The Biophysical Society, the Royal Society of Chemistry, and the American Association for the Advancement of Science. He has received a number of awards and other forms of recognition for his work, including most recently the Innovation Award from the Biophysical Society, the Joel Henry Hildebrand National AmericanChemical Society Award in the Theoretical and Experimental Chemistry of Liquids, the Royal Society of Chemistry S.F. Boys-A. Rahman Award for Outstanding Innovative Research inComputational Chemistry, the American Chemical Society Division of Physical Chemistry Award in Theoretical Chemistry, and Election to theInternational Academy of Quantum Molecular Science. He has mentored nearly 200postdoctoral fellows and graduate students.
Professor Voth is a leader in the development and application of theoretical and computational methods to study problems involving the structure and dynamics of complex condensed phase systems, including proteins, membranes, liquids, and materials. He has pioneered a method known as “multiscale coarse-graining” in which the resolution of the molecular-scale entities is reduced into simpler structures, but key information on their interactions is accurately retained (or renormalized) so the resulting computer simulation can accurately and efficiently predict the properties of large assemblies of complex molecules such as lipids and proteins. This method is multiscale, meaning it describes complex condensed phase and biomolecular systems from the molecular scale to the mesoscale and ultimately to the macroscopic scale. Professor Voth’s other research interests include the study of charge transport (protons and electrons) in water and biomolecules – a fundamental process in living organisms and other systems that has been poorly understood because of its complexity. He also studies the exotic behavior of room-temperature ionic liquids and other complex materials such nanoparticle self-assembly, polymer electrolyte membranes for fuel cells, and electrode-electrolyte interfaces in energy storage devices. In the earlier part of his career, Professor Voth extensively developed and applied new methods to study quantum and electron transfer dynamics in condensed phase systems-much of this work was based on the Feynman path integral description of quantum mechanics.