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Diwakar Shukla

University of Illinois at Urbana-Champaign

Molecular Biosciences

2018

Mittal S., Chen J., Selvam B., and Shukla D. (2018): Leveraging computational simulations to understand the activation mechanism of strigolactone receptor in Arabidopsis thaliana, (manuscript in preparation)
Saurabh Shukla, Chuankai Zhao, and Diwakar Shukla (2018): Complex dynamics of ABA binding and receptor activation revealed by kinetic network models, (in review)
Balaji Pannerselvam, Shriyaa Mittal, and Diwakar Shukla (2018): Free energy landscape of the complete transport cycle in a key bacterial transporter, (in review)
Chen Q., Mittal S., Shamsi Z., and Shukla D. (2018): Molecular dynamics simulations reveal the conformational heterogeneity of a strigolactone receptor in parasitic plants, (manuscript in preparation)
Shriyaa Mittal, and Diwakar Shukla (2018): Recruiting Machine Learning Methods for Molecular Simulations of Proteins, Molecular Simulation, Informa UK Limited, pp1-14
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, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 122, Num 3, pp1017-1025
Alexander S. Moffett, and Diwakar Shukla (2018): Using Molecular Simulation to Explore the Nanoscale Dynamics of the Plant Kinome, Biochemical Journal, Portland Press Ltd., Vol 475, Num 5, pp905-921

2017

Z. Shamsi and D. Shukla (2017): Concestor kinase activation mechanism uncovers the Cyclin dependence of CDK family kinases, (submitted)
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
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, The Journal of Physical Chemistry B, American Chemical Society (ACS), Vol 121, Num 42, pp9761-9770
Saurabh Shukla, Zahra Shamsi, Alexander S. Moffett, Balaji Selvam, and Diwakar Shukla (2017): Application of Hidden Markov Models in Biomolecular Simulations, Methods in Molecular Biology, Springer New York, Hidden Markov Models, pp29--41
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

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

2013

Kai J. Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding, Dan Belov, Russ B. Altman, and Vijay S. Pande (2013): Cloud-Based Simulations on Google Exacycle Reveal Ligand Modulation of GPCR Activation Pathways, Nature Chemistry, Nature Publishing Group, Vol 6, Num 1, pp15--21

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

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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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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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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