Authored by
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Title

Sudeep Bhattacharyay, Ph.D.

Pronouns
he/him/his
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Professor
Content type
College of Arts and Sciences
Chemistry and Biochemistry Department
Blugold Center for High Performance Computing

Contact Information

Office
Phillips Hall 455
105 Garfield Avenue
Eau Claire, WI 54702-4004
Phone
715-836-2278
Email
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Education

Education

  • Ph.D. Indian Association for the Cultivation of Science, Jadavpur, India (Chemistry)
  • M.S. Indian Institute of Technology, Kharagpur, India (Chemistry)
  • B.S. Indian Institute of Technology, Kharagpur, India (Chemistry)
Teaching and Research Interests

Teaching and Research Interests

  • General Chemistry
  • Physical Chemistry
  • Biophysical Chemistry
  • Computational Chemistry
  • Artificial Intelligence in Healthcare

One of my main interests is to foster active learning through discovery-guided projects. In the past few semesters, classroom research projects have been designed and introduced in biophysical and physical chemistry courses, mostly with senior students. These projects are computational and are being carried out using either a remote server or the in-house Blugold Super-Computing Cluster.

  • Theoretical chemistry to probe molecules and their chemical reactivities
  • Dynamics of protein and its role in the enzyme catalysis
  • Interactions between protein and crowder
  • Artificial intelligence-mediated screening of enzyme inhibitors
  • Disordered proteins

We use theory, concepts of physical chemistry, and advanced computer simulation methods to explore these questions. In addition, we also collaborate with experimentalists to validate the theoretical findings.

Published Research

Published Research

Selected Publications

  1. Conformational Fluidity of Intrinsically Disordered Proteins in Crowded Environment: A Molecular Dynamics Simulation Study
    Shult, C.*, Gunderson, K.*, Coffey, S. J.*, McNally, B.*, Brandt, M.*, Smith, L.*, Steczynski, J.*, Olerich, E. R.*, Schroeder, S. E.*, Severson, N. J.*, Hati, S. and Bhattacharyya, S. J. Biomol. Struct. Dyn. , in the press. 
  2. Polyethylene Glycol Impacts Conformation and Dynamics of Escherichia coli Prolyl-tRNA Synthetase via Crowding and Confinement Effects
    Liebau, J.*, Laatsch, B. F.*, Rusnak, J.*, Gunderson, K.*, Finke, B.*, Bargender, K.*, Narkiewicz-Jodko, A.*, Weeks, K.*, Williams, M. T.*, Shulgina, I.*, Musier-Forsyth, K., Bhattacharyya, S., and Hati, S. Biochemistry, 2024. (DOI: 10.1021/acs.biochem.3c00719).
  3. High-performance computing in undergraduate education at primarily undergraduate institutions in Wisconsin: progress, challenges, and opportunities Hebert, J.*, Hratisch, R.*, Gomes, R., Kunkel, W., Marshall, D., Ghosh, A., Doss, I.*, Ma, Y., Stedman, D., Stinson, B., Varghese, A., Mohr, M.*, Rozario, P.* ·Bhattacharyya, S. Educ. Inf. Technol, 2024. (DOI: 10.1007/s10639-024-12582-6) .
  4. Writing a Literature Review as a Class Project in an Upper-Level Undergraduate Biochemistry Course
    Hati, S. and Bhattacharyya, S. Biochem. Mol. Biol. Educ. 2024, 52, 1-6. (DOI: 10.1002/bmb.21814).
  5. Insight into the Mechanism of Tryptophan Fluorescence Quenching due to Synthetic Crowding Agents: A Combined Experimental and Computational Study Fossum, C. J.*, Johnson, B. O. V.*, Golde, S. T.*, Kielman, A. J.*, Finke, B.*, Lowater, H. R.*, Laatsch, B.*, Bhattacharyya, S. and Hati, S. ACS Omega, 2023, 8, 44820-44830. (DOI:10.1021/acsomega.3c06006).  
  6. Inter-institutional Resource Sharing in Undergraduate HPC Education: Interviews with University Administrators Ghosh, A., Kunkel, W., Varghese, A., Ma, Y., Gomes, R., Bhattacharyya, S., Mohr, M.*, Doss, I.*, and Hebert, J.* SIGCSE 2023: Proc. ACM Tech. Sympos. Comp. Sci. Edu V, 2023, 848–853. (DOI:10.1145/3545945.3569784). 
  7. Polyethylene Glycol 20k. Does it Fluoresce? Laatsch, B.*; Brandt, M.*, Finke, B.*,Fossum, C. J.*,Wackett, M. J.*, Lowater, H.R.*, Narkiewicz-Jodko, A.*, Le, C. N.*, Yang, T., Glowgowski, E. M., Bailey-Hartsel, S.C., Hati, S. and Bhattacharyya, S. ACS Omega, 2023, 8, 14208–14218. (DOI:10.1021/acsomega.3c01124). 
  8. Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations Wozney, A. J.*, Smith, M. A.*, Abdrabbo, M.*, Birch, C. M.*, Cicigoi, K. A.*, Dolan, C. C.*, Gerzema, A. E. L.*, Hansen, A.*, Henseler, E. J.*, LaBerge, B.*, Leavens, C. M.*, Le, C. N.*, Lindquist, A. C.*, Ludwig, R. K.*, O'Reilly, M. G.*, Reynolds, J. H.*, Sherman, B. A.*, Sillman, H. W.*, Smith, M. A.*, Snortheim, M. J.*, Svaren, L. M.*, Vanderpas, E. C.*, Wackett, M. J.*, Weiss, M. M.*, Hati, S. and Bhattacharyya, S. Protein J. , 2022 , 41 , 444-456. (DOI: 10.1007/s10930-022-10065-6). 
  9. Pre-Existing Oxidative Stress Creates a Docking-Ready Conformation of the SARS-CoV-2 Receptor-Binding Domain Fossum, C. J.*, Laatsch, B. F.*, Lowater, H. R.* Narkiewicz-Jodko*, A. R.*, Lonzarich, L.*, Hati S. and Bhattacharyya, S. ACS Bio & Med Chem Au , 2022, 2 , 84-93. (DOI: 10.1021/acsbiomedchemau.1c00040). 
  10. Vitamin D and COVID-19: A Review on the Role of Vitamin D in Preventing and Reducing the Severity of COVID-19 Infection Abdrabbo, M., Birch, C. M., Brandt, M.*, K. A., Coffey, S. J.*, Dolan, C. C.*, Dvorak, H.*, Gehrke, A. C.*, Gerzema, A. E. L.*, Hansen, A.*, Henseler, E. J.*, Huelsbeck, A. C.*, LaBerge, B.*, Leavens, C. M.*, Le, C. N.*, Lindquist, A. C.*, Ludwig, R. K.*, Reynolds, J. H.*, Severson, N. J.*, Sherman, B. A.*, Sillman, H. W.*, Smith, M. A.*, Smith, M. A.*, Snortheim, M. J.*, Svaren, L. M.*, Vanderpas, E. C.*, Wackett, M. J.*, Wozney, A. J.*, Bhattacharyya, S., and Hati, S.* Protein Science , 2021 , 30 , 2206-2220. (DOI: 10.1002/pro.4190). 
  11. Role of Oxidative Stress on SARS-CoV (SARS) and SARS-CoV-2 (COVID-19) Infection: A Review Suhail, S.*; Zajac, Z.*; Fossum, C.*; Lowater, H.*; McCracken, C.*; Severson, N.*; Laatsch, B.*; Narkiewicz-Jodko, A.*; Johnson, B.*; Liebau, J.*; Bhattacharyya, S.; and Hati, S. Protein J., 2020, 39,644-656. (DOI: 10.1007/s10930-020-09935-8).
  12. Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase Hu, Q. H.*; Williams, M. T.*; Shulgina, I.*; Fossum, C.*; Weeks, K.*; Adams, L.A.*; Reinhardt, C. R.*; Musier-Forsyth K.; Hati, S.; and Bhattacharyya, S. ACS Catal., 2020, 10, 10229-10242. (DOI:10.1021/acscatal.0c02381).37. Effects of Distal Mutations on Prolyl-Adenylate Formation of Escherichia coli Prolyl-tRNA Synthetase Zajac, J.*; Anderson, H.*; Adams, L. A.*; Wangmo, D.*; Suhail, S.*; Almen, A.*; Berns, L.*; Coerber, B.*; Dawson, L.*; Hunger, A.*; Jehn, J.*; Johnson, J.*; Plack, N.*; Strasser, S.*; Williams, M. T.*; Bhattacharyya, S.; and Hati, S. Protein J. 2020, 39,542-553. (DOI:10.1007/s10930-020-09910-3).
  13. Impact of Thiol-Disulfide Balance on the Binding of Covid-19 Spike Protein with Angiotensin-Converting Enzyme 2 Receptor Hati, S. and Bhattacharyya, S. ACS Omega 2020, 5, 16292-16298. (DOI:10.1021/acsomega.0c02125). 
  14. Crowder-induced Conformational Ensemble Shift in Escherichia Coli Prolyl-tRNA Synthetase Adams, L. A.*, Andrews, R. J.*, Hu, Q. H.*, Smit, H. L.*, Hati, S., and Bhattacharyya, S. Biophys. J. 2019 , 117, 1269-1284. (DOI:10.1016/j.bpj.2019.08.033).
  15. Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations Reinhardt, C. R.*, Hu, Q. H.*, Bresnahan, C. G.*, Hati, S., Bhattacharyya, S. ACS Catal. 2018, 12, 12015-12029. (doi:10.1021/acscatal.8b04193). 
  16. Integrating Research into the Curriculum: A Low-Cost Strategy for Promoting Undergraduate Research. Hati, S. and Bhattacharyya, S. in ACS Symposium Series "Best Practices for Supporting and Expanding Undergraduate Research in Chemistry" Eds. Gourley, B. L. and Jones, R. M. 2018, 119-141 (doi:10.1021/bk-2018-1275.ch008). 
  17. Insight into the Kinetics and Thermodynamics of the Hydride Transfer Reactions between Quinones and Lumiflavin: A Density Functional Theory Study Reinhardt, C. R.*, Jaglinski, T. C.*, Kastenschmidt, A. M.*, Song, E. H.*, Krause, A. J.*, Gollmar, J. M.*, Meise, K. J.*, Stenerson, Z. S.*, Weibel, T. J.*, Dison, A.*, Finnegan, M. R.*, Griesi, D. S.*, Gross, A. K.*, Heltne, M. D.*, Hughes, T. G.*, Hunt, C. D.*, Jansen, K. A.*, Xiong, A. H.*, Hati, S., and Bhattacharyya, S. J. Mol. Model. 2016, 22, 199 (doi: 10.1007/s00894-016-3074-1).
  18. Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins Hati, S. and Bhattacharyya, S. Biochem. Mol. Biol. Ed. 2016, 44, 140-159 (doi:10.1002/bmb.20942).
  19. Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol Bresnahan, C. G.*, Reinhardt, C. R.*, Bartholow, T. *, Rumpel, J. P.*, North, M. A.*, and Bhattacharyya, S.J. Phys. Chem. A2015, 119, 172–182. (doi:10.1021/jp510020v).
  20. Probing the Global and Local Dynamics of Aminoacyl-tRNA Synthetases using All atom and Coarse-grained Simulations Strom, A.,* Fehling, S.*, Bhattacharyya, S., Hati, S.J. Mol. Mod.2014,20, 2245 (doi:10.1007/s00894-014-2245-1).
  21. Comparison of the Intrinsic Dynamics of Aminoacyl-tRNA Synthetases *Warren, N.*,  Strom, A.*, Nicolet, B.*, Albin, K.*, Albrecht, J.,* Bausch, B.* Dobbe, M.*, Dudek, M.*, Firgens, S.*, Fritsche, C.*, Gunderson, A.*, Heimann, J.*, Her, C.*, Hurt, J. * Konorev, D.*, Lively, M.*, Meacham, S.*, Rodriguez, V*, Tadayon, S.*, Trcka, D.*, Yang, Y.*, Bhattacharyya, S., and Hati, S. The Protein Journal2014,33,184-98. (doi:10.1007/s10930-014-9548-z).
  22. Strictly Conserved Lysine of Prolyl-tRNA Synthetase Editing Domain Facilitates Binding and Positioning of Misacylated tRNAPro Bartholow, T. G.,* Sanford, B. L., Cao, B.V.,* Schmidt, H. L., Johnson, J. M., Meitzner, J. Bhattacharyya, S., Musier-Forsyth, K. M., Hati, S. Biochemistry 2014, 53, 1059-68:doi:10.1021/bi401279r.
  23. Multiple pathways promote dynamical coupling between catalytic domains in escherichia coli prolyl-tRNA synthetase, Johnson, J. M., Sanford, B. L., Strom, A. S,* Tadayon, S.,* Brent, L., Zirbes, A., Bhattacharyya, S., Musier-Forsyth, K. M., Hati, S. Biochemistry2013,52, 4399-4412.
  24. Role of coupled-dynamics in the catalytic activity of prokaryotic-like prolyl-tRNA synthetases Sanford, B.L., Cao, B.V.,* Johnson, J., Zimmerman, C., Strom, A. S.,* Mueller, R. M.,* Bhattacharyya, S., Musier-Forsyth, K. M., Hati, S.Biochemistry2012,51,2146-2156.
  25. Interplay of flavin's redox states and protein dynamics: an insight from QM/MM simulations of dihydronicotinamide ribosidequinone oxidoreductase 2Mueller, R. M.,* North, M. A.,*Yang, C.,*Hati, S., Bhattacharyya, S.J. Phys. Chem.2011,115, 3632-3641.
  26. Improved density functional description of the electrochemistry and structure-property descriptors of substituted flavins North, M. A.,*Bhattacharyya, S., and Truhlar, D. G.J. Phys. Chem.2010,114, 14907–14915.
  27. Theoretical determination of the redox potentials of NRH:quinone oxidoreductase 2 using quantum mechanical/molecular mechanical simulations Rauschnot, J. C. Jr.,*Yang, C.,*Yang, V.,*and Bhattacharyya, S.J. Phys. Chem.2009,113,8149-8157.
  28. Evolutionary basis for the coupled-domain motions inThermus thermophilus leucyl-tRNA synthetase Weimer, K. M. E.,* Shane, B. L., Brunetto, M., Bhattacharyya, S. and Hati, S.J. Biol. Chem.2009,284, 10088-99.