(6cn) Multi-Scale Modeling of Biophysical Systems and Soft Matter

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 fundamental basis often serve as powerful tools to probe such systems in aspects that lie outside the current experimental limits, and complement our understanding of these systems. My research interests lie in developing systematic modeling frameworks to understand and manipulate the structure and dynamics of biological macromolecules such as DNA, RNA and proteins and synthetic polymers by manipulating their environments, and to use such modeling frameworks for designing commercial applications.

My graduate work at University of Massachusetts Amherst (UMass Amherst) introduced me to the idea of using nanopores as rapid low-cost DNA sequencing devices and the design challenges involved in transforming this idea into a commercial technique. Using extensive coarse-grained simulations of DNA as a polyelectrolyte translocating through biological and synthetic nanopores, I was able to highlight the important role of electrostatic interactions in the kinetics involved. I also developed simple design principles for using nanopores to characterize polyelectrolytes based on their architectures. I implemented the Multi-Particle Collision Dynamics technique on a GPU architecture as a part of this work. I constructed a theoretical model for the translocation process based on the Fokker-Planck formalism and established the parameter window for validity of the model. After advancing to a postdoctoral position at the University of Chicago, I focused on developing systematic coarse-grained models for biologically relevant polymers. I developed a multi-scale coarse-grained modeling framework for studying filament networks in the cell. I discovered the underlying mechanism of hydrolysis of the nucleotide bound to the filamentous protein actin using this framework, and used enhanced sampling simulation methods to aid modeling of actin associating proteins.

In the near future, I plan to combine the expertise I have developed through these research experiences to propose application based nanopore design strategies. I will start by developing an efficient multi-scale modeling and simulation framework to allow for rapid screening of nanopore designs to control the transport of important biological and synthetic polymers. I will then extend this framework to study the design of nanopores as commercial devices to characterize protein folding. My broader goal is to develop a strong research program in the area of biophysics and soft matter using systematic modeling and simulation techniques, with a balance between efforts aimed at developing a fundamental understanding of biological systems and those aimed at developing technologies of commercial importance.

Teaching Interests:

I have had a pleasant experience as a teaching assistant for many courses while I was a graduate student in the Departments of Chemical Engineering at both, UMass Amherst and at Indian Institute of Technology Bombay (IIT Bombay). At IIT Bombay, I conducted laboratory sessions involving heat exchangers for the undergraduate Chemical Engineering Laboratory and was involved in constructing problems aimed at understanding the design principles of heat exchangers for the laboratory sessions and the for final examination. I also conducted experiments and examinations for pneumatic conveying of granular materials for the undergraduate Laboratory. I graded assignments and exams for undergraduate courses at both these institutions and enjoyed the experience of helping individual students to confidently solve assignment problems by providing them just enough information to trigger their thought process. At UMass Amherst, I had the additional opportunity to conduct weekly, hour-long tutorial sessions that complemented the lectures by the course instructor for the undergraduate Fluid Mechanics course, and had a first-hand experience conducting tutorials for the graduate Transport Process course. I also value the opportunity I had as a mentor at both these institutes, to my colleagues and to undergraduate summer interns.

Through my experience as a student of some outstanding teachers, and as a teaching assistant for the courses mentioned above, I have learnt simple principles that make a course easy to learn. I will provide a course outline and make references to it during my lectures. I will provide peer-learning opportunities through the use of group assignments. I will strive to make efficient use of chalk boards or white boards for the delivery of suitable parts of the course material, especially those containing important mathematical derivations. Based on my teaching experience and my research expertise, I propose to teach the following courses.

Core Courses: Transport Processes, Fluid Mechanics, Chemical Reaction Engineering, Chemical Engineering Analysis, Numerical and Computational Methods in Chemical Engineering.

Advanced Courses: Modeling and Simulations, aimed at imparting Chemical Engineers with basic skills required to construct systematic models and perform simulations from molecular scale up to the process scale.