Center for Biophysics and Quantitative Biology

Diwakar Shukla

Associate Professor

The long-term research goal of Shukla group is to combine theory, computation, and experiments to develop quantitative models of molecular processes relevant for health, energy and climate change. We integrate ideas from a wide range of disciplines and aim to investigate the functional role of the “Dynamics” in molecular processes.

Research Description

Shukla group is developing computational and experimental methods to enable the investigation of biological systems in atomistic detail. As we move from a static structural picture to a dynamic ensemble view of protein structure and function, novel computational and experimental paradigms are required for obtaining quantitative understanding of biological phenomena.

The key research areas include: 1. Computational Methods Development: Develop AI/ML and molecular dynamics simulation based methods for mechanistic understanding and design of molecular systems. 2. High-Throughout Experiments: Engineer proteins and chemicals using high-throughput experimental techniques in synergy with machine learning methods. 3. Mechanistic understanding of molecular systems: Develop and employ computational and experimental tools to elucidate mechanistic principles that regulate function at the molecular scale. In particular, our group is focused on two specific problems of chemical perception and molecular transport.

Education

B.Tech., 2006, Indian Institute of Technology, Bombay (Chemical Engineering)
Ph.D., 2011, Massachusetts Institute of Technology (Chemical Engineering)
Postdoc., 2011-14,, Stanford University

Awards

2024 Stanley H. Pierce Award for Excellence in Mentoring, College of Engineering, University of Illinois
2024 Dean’s Award for Excellence in Research, College of Engineering, University of Illinois
2024 Engineering Council Outstanding Advising Award, University of Illinois
2022 Pivot Fellowship, Simons Foundation
2022 Editorial Advisory Board, Journal of Physical Chemistry, ACS
2022 Frontiers of Engineering, US National Academy of Engineering
2021 Maximizing Investigator Research Award (MIRA), NIGMS, NIH
2021 J. Phys. Chem. & PHYS Division Lectureship Award, ACS
2021 Lincoln Excellence for Assistant Professors Scholar, University of Illinois
2020 Dean’s Award for Excellence in Research, University of Illinois
2019 Alfred P. Sloan Research Fellowship in Chemistry, Sloan Foundation
2019 SCS Excellence in Teaching Award, School of Chemical Sciences, University of Illinois
2018 NSF Early Career Award, National Science Foundation
2018 OpenEye Outstanding Junior Faculty in Computational Chemistry, ACS
2018 CoMSEF Young Investigator Award, American Institute of Chemical Engineers
2017 New Innovator Award in Food and Agriculture Research, Foundation for Food & Agriculture Research
2015 Engineering Council Outstanding Advising Award, University of Illinois

Representative Publications

1. Anh T. P. Nguyen, Austin T. Weigle and Diwakar Shukla*, Functional Regulation of Aquaporin Dynamics by Lipid Bilayer Composition. Nature Communications, Volume 15, Article number: 1848, 2024.

2. Diego E. Kleiman and Diwakar Shukla*, Active Learning of the Conformational Ensemble of Proteins using Maximum Entropy VAMPNets. Journal of Chemical Theory and Computation, Volume 19, Issue 14, Pages 4377–4388, 2023.

3. Matthew C Chan, Balaji Selvam, Heather J Young, Erik Procko and Diwakar Shukla*, The substrate import mechanism of the human serotonin transporter, Biophysical Journal, Volume 121, Issue 5, Pages 715-730, 2022.

4. Balaji Selvam, Ya-Chi Yu, Li-Qing Chen and Diwakar Shukla*, Molecular basis of the glucose transport mechanism in plants, ACS Central Science, Volume 5, Issue 6, Pages 1085-1096, 2019.

5. Balaji Selvam, Zahra Shamsi and Diwakar Shukla*, Universality of the sodium ion binding mechanism in class AG‐protein‐coupled receptors, Angewandte Chemie, Volume 12, Pages 3102-3107, 2018.