June 11, 2018
Congratulations to Blue Waters Assistant Professor Diwakar Shukla, who has been chosen to receive the 2018 ComMSEF Young Investigator Award for Modeling & Simulation.
This award, from the Computational Molecular Science and Engineering Forum of the American Institute of Chemical Engineers, recognizes outstanding research in computational molecular science and engineering, encompassing both methods and applications.
This fall Shukla will deliver a presentation within the CoMSEF plenary session of the AIChE Annual Meeting. His talk is entitled, “Methodologies for enhanced unbiased sampling of the free energy landscapes of proteins.” The abstract follows.
“Protein function is inextricably linked to protein dynamics. As we move from a static structural picture to a dynamic ensemble view of protein structure and function, novel computational paradigms are required for observing and understanding conformational dynamics of proteins and its functional implications. In principle, molecular dynamics simulations can provide the time evolution of atomistic models of proteins, but the long time scales associated with functional dynamics make it difficult to observe rare dynamical transitions on the free energy landscapes associated with protein function. One approach to surmount this challenge is to use reaction coordinate that characterize the rare conformational transitions to sample conformational landscapes more effectively. However, it is not possible to identify reaction coordinate for systems a priori, especially for proteins with limited availability of structural information. Furthermore, different reaction coordinates characterize the free energy barriers at different points on the free energy landscapes. Here, we discuss a set of methodologies outlined in a series of papers from our group, which use evolutionarily coupling between protein residues and machine learning methods to adaptively guide sampling with no alterations to potential energy functions in order to expedite exploration of the free energy landscapes.”
Shukla joined the University of Illinois Department of Chemical and Biomolecular Engineering in 2015. He also is an affiliate faculty member in the Center for Biophysics and Computational Biology, Computational Science & Engineering Program, Department of Plant Biology and National Center for Supercomputing Applications. He started his research career at the Indian Institute of Technology (IIT) Bombay, India, where he received B. Tech and M. Tech. degrees in chemical engineering. He then joined Massachusetts Institute of Technology where he received MS and PhD degrees in chemical engineering under guidance of Prof. Bernhardt Trout followed by a postdoc at Stanford University with Prof. Vijay Pande. He has received several awards for his research including the CoMSEF Graduate student award from AIChE, Peterson award from the American Chemical Society, Innovation in Biotechnology award from American Association of Pharmaceutical Scientists, OpenEye outstanding junior faculty award in computational chemistry from ACS and the New Innovator Award from the Foundation for Food and Agriculture Research.