Contact Information
University of Illinois
200 RAL, Box C-3
600 S Mathews Ave
Urbana, IL 61801
Biography
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 and Honors
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
Additional Campus Affiliations
Professor, Chemical and Biomolecular Engineering
James W. Westwater Scholar, Chemical and Biomolecular Engineering
Affiliate, Chemistry
Professor, Bioengineering
Professor, National Center for Supercomputing Applications (NCSA)
Professor, Center for Digital Agriculture, National Center for Supercomputing Applications (NCSA)
Affiliate, Carl R. Woese Institute for Genomic Biology
Highlighted 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.
Recent Publications
Barrett, S. E., Yin, S., Jordan, P., Brunson, J. K., Gordon-Nunez, J., Costa Machado da Cruz, G., Rosario, C., Okada, B. K., Anderson, K., Pires, T. A., Wang, R., Shukla, D., Burk, M. J., & Mitchell, D. A. (2025). Substrate interactions guide cyclase engineering and lasso peptide diversification. Nature chemical biology, 21(3), 412-419. https://doi.org/10.1038/s41589-024-01727-w
Chan, M. C., Alfawaz, Y., Paul, A., & Shukla, D. (2025). Molecular insights into the elevator-type mechanism of the cyanobacterial bicarbonate transporter BicA. Biophysical journal, 124(2), 379-392. https://doi.org/10.1016/j.bpj.2024.12.013
Cui, H., Su, Y., Dean, T. J., Yu, T., Zhang, Z., Peng, J., Shukla, D., & Zhao, H. (2025). Enzyme specificity prediction using cross attention graph neural networks. Nature, 647(8090), 639-647. https://doi.org/10.1038/s41586-025-09697-2
Dutta, S., & Shukla, D. (2025). Characterization of binding kinetics and intracellular signaling of new psychoactive substances targeting cannabinoid receptor using transition-based reweighting method. eLife, 13. https://doi.org/10.7554/eLife.98798.3
Long, S. P., Wang, Y., Carmo-Silva, E., Cavanagh, A. P., Jonikas, M. C., Kromdijk, J., Long, B. M., Marshall-Colón, A., Shukla, D., Wilson, R. H., Zhu, X. G., & Ainsworth, E. A. (2025). Feeding from the sun—Successes and prospects in bioengineering photosynthesis for food security. Cell, 188(24), 6700-6719. https://doi.org/10.1016/j.cell.2025.10.033