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Diwakar Shukla

University of Illinois at Urbana-Champaign

Molecular Biosciences

2020

Zahra Shamsi and Diwakar Shukla (2020): How does evolution design functional free energy landscapes of proteins? A case study on the emergence of regulation in the Cyclin Dependent Kinase family, Molecular Systems Design & Engineering, Royal Society of Chemistry, Vol 5, Num 1, pp392-400
Faisal Aldukhi, Aniket Deb, Chuankai Zhao, Alexander S. Moffett, and Diwakar Shukla (2020): Molecular Mechanism of Brassinosteroid Perception by the Plant Growth Receptor BRI1, Journal of Physical Chemistry B, American Chemical Society, Vol 124, Num 2, pp355-365

2019

Luke Cuculis, Chuankai Zhao, Zhanar Abil, Huimin Zhao, Diwakar Shukla, and Charles M. Schroeder (2019): Divalent cations promote TALE DNA-binding specificity, Nucleic Acids Research, Oxford University Press
Balaji Selvam, Ya-Chi Yu, Li-Qing Chen, and Diwakar Shukla (2019): Molecular Basis of Glucose Transport Mechanism in Plants, ACS Central Science, American Chemical Society, Vol 5, Num 6, pp1085-1096
Saurabh Shukla, Chuankai Zhao, and Diwakar Shukla (2019): Dewetting Controls Plant Hormone Perception and Initiation of Drought Resistance Signaling, Structure, Elsevier BV, Vol 27, pp1-11
Drishti Guin, Shriyaa Mittal, Brian Bozymski, Diwakar Shukla, and Martin Gruebele (2019): Dodine as a Kosmo-Chaotropic Agent, Journal of Physical Chemistry Letters, American Chemical Society, Vol 10, Num 10, pp2600-2605

2018

Shriyaa Mittal and Diwakar Shukla (2018): Recruiting Machine Learning Methods for Molecular Simulations of Proteins, Molecular Simulation, Informa UK Limited, pp1-14
Qihua Chen, Jiangyan Feng, Shriyaa Mittal, and Diwakar Shukla (2018): Automatic Feature Selection in Markov State Models Using Genetic Algorithm, Journal of Computational Science Education, Shodor Education Foundation, Vol 9, Num 2, pp14-22
Balaji Selvam, Zahra Shamsi, and Diwakar Shukla (2018): Universality of the Sodium Ion Binding Mechanism in Class A G-Protein-Coupled Receptors, Angewandte Chemie International Edition, Wiley-Blackwell, Vol 57, Num 12, pp3048-3053
Jiangyan Feng and Diwakar Shukla (2018): Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings, Journal of Physical Chemistry B, American Chemical Society, Vol 122, Num 3, pp1017-1025
Balaji Selvam, Shriyaa Mittal, and Diwakar Shukla (2018): Free Energy Landscape of the Complete Transport Cycle in a Key Bacterial Transporter, ACS Central Science, American Chemical Society, Vol 4, Num 9, pp1146-1154
Zahra Shamsi, Kevin J. Cheng, and Diwakar Shukla (2018): Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes, Journal of Physical Chemistry B, American Chemical Society, Vol 122, Num 35, pp8386-8395
Chuankai Zhao and Diwakar Shukla (2018): SAXS-Guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes, Scientific Reports, Springer Nature, Vol 8, Num 1

2017

Shamsi, Zahra and Moffett, Alexander S. and Shukla, Diwakar (2017): Enhanced unbiased sampling of protein dynamics using evolutionary coupling information, Scientific Reports, Springer Nature, Vol 7, Num 1
Amy Marshall-Colon, Stephen P. Long, Douglas K. Allen, Gabrielle Allen, Daniel A. Beard, Bedrich Benes, Susanne von Caemmerer, A. J. Christensen, Donna J. Cox, John C. Hart, Peter M. Hirst, Kavya Kannan, Daniel S. Katz, Jonathan P. Lynch, Andrew J. Millar, Balaji Panneerselvam, Nathan D. Price, Przemyslaw Prusinkiewicz, David Raila, Rachel G. Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Matthew J. Turk, Eberhard O. Voit, Yu Wang Xinyou Yin, and Xin-Guang Zhu (2017): Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform, Frontiers in Plant Science, Frontiers, Vol 8, pp786
Alexander S. Moffett, Kyle W. Bender, Steven C. Huber, and Diwakar Shukla (2017): Allosteric Control of a Plant Receptor Kinase Through S-Glutathionylation, Biophysical Journal, Elsevier BV, Vol 113, Num 11, pp2354-2363
Shriyaa Mittal and Diwakar Shukla (2017): Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity, Journal of Physical Chemistry B, American Chemical Society, Vol 121, Num 42, pp9761-9770
Alexander S. Moffett, Kyle W. Bender, Steven C. Huber, and Diwakar Shukla (2017): Molecular Dynamics Simulations Reveal the Conformational Dynamics of Arabidopsis thaliana BRI1 and BAK1 Receptor-Like Kinases, Journal of Biological Chemistry, American Society for Biochemistry & Molecular Biology (ASBMB), Vol 292, Num 30, pp12643-12652
Saurabh Shukla, Zahra Shamsi, Alexander S. Moffett, Balaji Selvam, and Diwakar Shukla (2017): Application of Hidden Markov Models in Biomolecular Simulations, Springer New York, Hidden Markov Models: Methods and Protocols, pp29-41

2016

Diwakar Shukla, Ariana Peck, and Vijay S. Pande (2016): Conformational Heterogeneity of the Calmodulin Binding Interface, Nature Communications, Nature Publishing Group, Vol 7, pp10910

2014

Kai J. Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding, Dan Belov, Russ B. Altman, and Vijay S. Pande (2014): Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways, Nature Chemistry, Springer Nature Limited, Vol 6, Num 1, pp15-21

2019

Diwakar Shukla, Erik Procko (2019): Simulations Uncover the Mechanism of Serotonin Transport in the Brain, 2019 Blue Waters Annual Report, pp294-295
Diwakar Shukla, Aditi Das (2019): Elucidating the Ligand Selectivity and Activation Mechanisms of Cannabinoid Receptors, 2019 Blue Waters Annual Report, pp296-297
Diwakar Shukla (2019): Molecular Basis of the Nitrate Transport Mechanism in Plants, 2019 Blue Waters Annual Report, pp292-293

2018

Diwakar Shukla (2018): Unraveling the Molecular Magic of Witchweed, Blue Waters annual-book summary slide
Diwakar Shukla, Li-Qing Chen (2018): Molecular Simulations on Blue Waters Aid the Understanding of How Plants Transport Sugars between Cells, Blue Waters annual-book summary slide
Diwakar Shukla (2018): Unraveling the Molecular Magic of Witchweed, 2018 Blue Waters Annual Report, pp242-243
Diwakar Shukla, Li-Qing Chen (2018): Molecular Simulations on Blue Waters Aid the Understanding of How Plants Transport Sugars between Cells, 2018 Blue Waters Annual Report, pp244-245

2017

Diwakar Shukla (2017): Understanding The Protein Allostery in Kinases and GPCRS, 2017 Blue Waters Annual Report, pp236-237

2016

Diwakar Shukla (2016): Computational investigation of drought-resistance in plants, 2016 Blue Waters Annual Report, pp232-233
Matthew Chan, B. Selvam, and D. Shukla: Substrate-induced conformational transitions of the human serotonin transporter
American Chemical Society (ACS) Fall 2019 National Meeting; San Diego, Calif., Aug 29, 2019

Department celebrates scholarship recipients, winners of undergraduate research symposium


Apr 16, 2018

On Friday, April 13, 2018, the Department of Chemical and Biomolecular Engineering honored its outstanding students at the Undergraduate Awards Ceremony. At the annual event, faculty presented the 2017-2018 scholarships and Omega Chi Epsilon, the national honor society for chemical engineering, announced winners of the annual Undergraduate Research Symposium. This year, judges awarded three students the top award: Qihua Chen, Marko Ivancevic, and Eli Karvelis. Chen, a member of Dr. Diwakar Shukla’s research group, presented with, “Molecular Dynamics Simulations Reveal the Conformational Heterogeneity of a Strigolactone Receptor in Parasitic Plants.” Marko Ivancevic, who worked with the Paranthaman Research Group at Oak Ridge National Lab, presented, “Novel Carbon Electrodes Derived from Waste Tires for Capacitive Deionization of Brackish Water.” Eli Karvelis, a member of Dr. Brendan Harley’s research group, presented, “Modeling Glioblastoma Invasion with Microfluidic Chips.”


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18 students selected for Blue Waters Student Internship Program


Apr 17, 2017

Shodor and the Blue Waters project have selected 18 undergraduate students from across the country to participate in the Blue Waters Student Internship Program for 2017-2018. Interns will learn to apply high-performance computing to problems in science, mathematics, and engineering through the year-long program. Their experience will begin in late May with a two-week Petascale Institute at the National Center for Supercomputing Applications (NCSA).


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Blue Waters Illinois allocations awarded to 26 research teams


Mar 7, 2017

Twenty-six research teams at the University of Illinois at Urbana-Champaign have been allocated computation time on the National Center for Supercomputing Application's (NCSA) sustained-petascale Blue Waters supercomputer after applying in Fall 2016. These allocations range from 25,000 to 600,000 node-hours of compute time over a time span of either six months or one year. The research pursuits of these teams are incredibly diverse, ranging anywhere from physics to political science.


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22 students selected for Blue Waters Student Internship Program


May 4, 2015

Shodor and the Blue Waters project have selected 19 undergraduate students and three graduate students from across the country to participate in the Blue Waters Student Internship Program for 2015-2016. Interns will learn to apply high-performance computing to problems in science, mathematics, and engineering through the year-long program. Their experience will begin later this month with a two-week Petascale Institute at the National Center for Supercomputing Applications (NCSA).


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