Dhruva Chakravorty - Texas A&M University (TAMU) Scholar

HR job title

Director for User Services and Research

selected publications

academic article
- Chakravorty, D., & Pham, M. T. (2020). Evaluating the Effectiveness of an Online Learning Platform in Transitioning Users from a High Performance Computing to a Commercial Cloud Computing Environment. Journal of Computational Science Education. 11(1), 93-99.
- Chakravorty, D. K., Pennings, M. M., Liu, H., Thomas, X., Rodriguez, D., & Perez, L. M. (2020). Incorporating Complexity in Computing Camps for High School Students A Report on the Summer Computing Academy Program at Texas A&M University. Journal of Computational Science Education. 11(1), 12-20.
- Chakravorty, D. K., Pennings, M. M., Liu, H., Wei, Z. S., Rodriguez, D. M., Jordan, L. T., ... Le, S. D. (2019). Effectively Extending Computational Training Using Informal Means at Larger Institutions. Journal of Computational Science Education. 10(1), 40-47.
- Chakravorty, D. K., Pennings, M. M., Liu, H., Wei, Z. S., Rodriguez, D. M., Jordan, L. T., ... Gober, N. (2019). Evaluating Active Learning Approaches for Teaching Intermediate Programming at an Early Undergraduate Level. Journal of Computational Science Education. 10(1), 61-66.
- Chakravorty, D. K., Li, P., Tran, T. T., Bayse, C. A., & Merz, K. M. (2016). Metal Ion Capture Mechanism of a Copper Metallochaperone. Biochemistry. 55(3), 501-509.
- Bayden, A. S., Gomez, E. F., Audie, J., Chakravorty, D. K., & Diller, D. J. (2015). A combined cheminformatic and bioinformatic approach to address the proteolytic stability challenge in peptide-based drug discovery. Biopolymers. 104(6), 775-789.
- Ucisik, M. N., Chakravorty, D. K., & Merz, K. M. (2015). Models for the Metal Transfer Complex of the N-Terminal Region of CusB and CusF. Biochemistry. 54(27), 4226-4235.
- Chakravorty, D. K., & Merz, K. M. (2015). Role of substrate dynamics in protein prenylation reactions. Accounts of Chemical Research. 48(2), 439-448.
- Carter, J. D., Mathias, J. D., Gomez, E. F., Ran, Y., Xu, F., Galiano, L., ... Fanucci, G. E. (2014). Characterizing solution surface loop conformational flexibility of the GM2 activator protein. Journal of Physical Chemistry B. 118(36), 10607-10617.
- Ucisik, M. N., Chakravorty, D. K., & Merz, K. M (2013). Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB. Biochemistry. 52(39), 6911-6923.
- Chakravorty, D. K., Parker, T. M., Guerra, A. J., Sherrill, C. D., Giedroc, D. P., & Merz, K. M. (2013). Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins. Journal of the American Chemical Society. 135(1), 30-33.
- Li, P., Roberts, B. P., Chakravorty, D. K., & Merz, K. M. (2013). Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent. Journal of Chemical Theory and Computation. 9(6), 2733-2748.
- Chakravorty, D. K., Wang, B., Lee, C. W., Guerra, A. J., Giedroc, D. P., & Merz, K. M. (2013). Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. Journal of Biomolecular NMR. 56(2), 125-137.
- Lee, C. W., Chakravorty, D. K., Chang, F., Reyes-Caballero, H., Ye, Y., Merz, K. M., & Giedroc, D. P. (2012). Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery. Biochemistry. 51(12), 2619-2629.
- Chakravorty, D. K., Wang, B., Lee, C. W., Giedroc, D. P., & Merz, K. M. (2012). Simulations of allosteric motions in the zinc sensor CzrA. Journal of the American Chemical Society. 134(7), 3367-3376.
- Chakravorty, D. K., Wang, B., Ucisik, M. N., & Merz, K. M. (2011). Insight into the cation- interaction at the metal binding site of the copper metallochaperone CusF. Journal of the American Chemical Society. 133(48), 19330-19333.
- Chakravorty, D. K., & Hammes-Schiffer, S (2010). Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations. Journal of the American Chemical Society. 132(21), 7549-7555.
- Yang, Y., Chakravorty, D. K., & Merz, K. M. (2010). Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry. 49(44), 9658-9666.
- Chakravorty, D. K., Soudackov, A. V., & Hammes-Schiffer, S (2009). Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: analysis of hydrogen bonding, conformational motions, and electrostatics. Biochemistry. 48(44), 10608-10619.
- Chakravorty, D. K., Kumarasiri, M., Soudackov, A. V., & Hammes-Schiffer, S. (2008). Implementation of umbrella integration within the framework of the empirical valence bond approach. Journal of Chemical Theory and Computation. 4(11), 1974-1980.
- Seo, J. H., Bruner, M., Payne, A., Gober, N., McMullen, D. R., & Chakravorty, D. K. Using Virtual Reality to Enforce Principles of Cybersecurity. Journal of Computational Science Education. 10(1), 81-87.
chapter
- Chakravorty, D. K., & Merz, K. M. (2014). Studying allosteric regulation in metal sensor proteins using computational methods. Advances in protein chemistry and structural biology. Karabencheva-Christova, T. (Eds.), Biomolecular Modelling and Simulations. (pp. 181-218). Elsevier.
patent
- Chakravorty, D., & Merz Jr, K. M. (2016). Pharmacogenic therapies targeting the metal-ion transcriptional regulation machinery in bacteria

principal investigator on

co-principal investigator on

ACES - Accelerating Computing for Emerging Sciences awarded by National Science Foundation - (Arlington, Virginia, United States) 2021 - 2026

education and training

Ph.D. in Mixed Quantum/Classical Methods in Computational Chemistry, Pennsylvania State University - (State College, Pennsylvania, United States) 2010
M.S. in Physical Chemistry, University of Delhi - (New Delhi, India) 2004
B.S. in Chemistry (with Honors), University of Delhi - (New Delhi, India) 2002

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Dhruva

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Chakravorty

mailing address

222 Jones St.

College Station, TX 77843

USA

email

chakravorty@tamu.edu

Chakravorty, Dhruva Director for User Services and Research

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