Dr. Harshwardhan Katkar's Talk

Mar 28, 2019 - 17:00

Mar 28, 2019 - 18:00

Room 118, Chemical Engg Dept

Seminars

Dr. Harshwardhan Katkar, University of Chicago

Abstract: Processes that span multiple length scales and timescales are common in nature, and this multiscale nature often limits our knowledge of many biological systems. Systematic models based on a strong basis often serve as powerful tools to probe such systems for aspects that lie outside the current experimental limits, and complement our understanding of these systems. Developing such systematic modeling frameworks can assist in manipulating the structure and dynamics of biological macromolecules such as DNA, RNA and protein assemblies for designing applications related to healthcare.In this talk, I will introduce the idea of using biological and synthetic nanopores as rapid low-cost DNA sequencing devices and discuss about the design challenges involved in transforming this idea into a commercial technique. Modeling the process can aid in optimizing the design of these devices, but is complicated due to the rich phenomenology and the multiple timescales involved in the translocation process. I will describe a theoretical model for the translocation process that we developed based on the Fokker-Planck formalism and the parameter window of validity for the model. The model highlights the important role that the pore interactions play in governing the kinetics of translocation, which we also observed in our extensive coarse-grained simulations of DNA as a polyelectrolyte translocating through nanopores. I will also discuss potential uses of nanopores to read single molecule level characteristics such as charge sequences and topology of polymers. The second part of my talk will focus on describing the development of systematic coarse-grained models for biologically relevant polymers and protein assemblies. I will introduce the multiscale modeling framework developed for studying filament networks of actin- a highly conserved protein and a key constituent of the cell cytoskeleton. I will discuss the discovery of underlying mechanism of hydrolysis of the ATP bound to filamentous actin using this framework. Using the actin cytoskeleton as an example, I will demonstrate how tools such as multiscale modeling and enhanced free energy sampling techniques can be employed to gain insights into complex biological phenomena. Bio: Harshwardhan H. Katkar is a postdoctoral scholar in the Department of Chemistry at The University of Chicago, where he joined in June, 2016. He received a Ph.D. in Chemical Engineering at the University of Massachusetts Amherst, an M. Tech. in Chemical Engineering at Indian Institute of Technology Bombay and studied Polymer Engineering at Institute of Chemical Technology, Mumbai. His work during Ph.D. and his postdoctoral research focuses on development and application of theoretical and computational models for biologically relevant systems, and include modeling the dynamics of cytoskeletal proteins and the transport of polyelectrolytes through nanopores. His research interests lie in the areas of fluid mechanics, and multiscale modeling and simulations of biological and soft matter. This seminar is compulsory for students registered for course CL 702 or CL 704.