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Chemical and Biomolecular Engineering

Computational Chemical & Biomolecular Engineering

Faculty: Diwakar Shukla, Baron Peters, Charles Sing, Jonathan Higdon

Several research groups in our department are involved in scientific computing and modeling of complex chemical and biomolecular systems with the goal of elucidating their underlying design principles. For example, we are investigating how chemical reactions occur on catalyst surfaces, how enzymes convert substrates into products, how cellular signaling works at the molecular level and how materials self-assemble. The University of Illinois at Urbana-Champaign is one of the leading universities in the world in the field of scientific computing. Our campus is home to the Blue Waters Supercomputer and National Center for Supercomputing Applications, both of which provide unique resources and opportunities to our graduate students working on computational problems. Currently, there are four faculty members working in this research area.

Professor Diwakar Shukla

The long-term research interest of the Shukla Group is the combined use of theory, computation, and experiments to develop quantitative models of biological phenomena relevant for health, energy and environment. The main goals of the group’s projects are to develop a platform for integrating computational methods for understanding protein function; elucidating mechanistic insights to regulate plant growth and development within the context of global climate change; and understand complex manipulation of signaling networks in both plants and humans by small molecules. Under this broad umbrella of computational molecular sciences, the Shukla Group integrates ideas from a wide range of disciplines to answer questions that are tied together by a vision of “Dynamic” biology and its role in engineering products for human health, energy and environment. The figure below shows how the free energy landscape of the sugar transporter SWEET in plants changes during the substrate transport.

The figure above shows how the free energy landscape of the sugar transporter SWEET in plants changes during the substrate transport.

Professor Baron Peters

The Peters Group investigates the kinetics of nucleation, electron transfer, and catalytic reactions that depend on the properties of short-lived and infrequently-visited transition states. Researchers obtain insights into the properties of transition states by using special “rare events” methods from molecular simulation and quantum chemistry. The applications are focused on the kinetics of crystal nucleation and growth, on catalysis by amorphous materials, and on reactions in polar solvents and other complex environments. In each of these areas, the Peters Group develops state-of-the-art simulation techniques to overcome limitations of present-day simulation techniques. In particular, the group specializes in stochastic models that link molecular-scale dynamics and properties to phenomena at long time scales and continuum length scales.

The figure shows work from Peters Group (Knott et al. J. Am. Chem. Soc. 136:321–29) using quantum mechanics/molecular mechanics with explicit water in aimless shooting simulations of cellulose hydrolysis by the cellulase enzyme.

Professor Charles Sing

Research in the Sing Group is focused on charged polymers, polymer dynamics, and biophysics. Researchers use coarse-grained models to understand the emergent physics of polymer or biophysical systems, and then use the resulting insights to guide the design new materials. Current research efforts are focused on problems that are challenging because they span large length and time scales, and new theory or simulation methods are necessary to yield new fundamental physical principles. The figure below the competitive binding of multiple species that may couple to the properties of an underlying substrate.

The research in Sing group is focused on charged polymers, polymer dynamics, and biophysics. Sing research group uses coarse-grained models to understand the emergent physics of polymer or biophysical systems, and then use the resulting insights to guide the design new materials.

Professor Jonathan Higdon

The Higdon Research group investigates geophysical fluid dynamics associated with evolution of meandering rivers; develops simulations for large scale systems of hyperbolic partial differential equations for petroleum reservoirs and geophysical transport processes; and investigates the micro-scale dynamics of complex fluids.
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