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Srirupa Chakraborty

CNLS Postdoctoral Research Associate
T-6/CNLS

Computational modeling and simulations of biomolecules, theoretical biophysics

Srirupa Chakraborty

Office: TA-3, Bldg 1690, Room 115
Mail Stop: K710
Phone: (505) 667-5609
Fax: (505) 665-7652

srirupac@lanl.gov
home page

Research highlight
     Educational Background/Employment:
    • Ph.D. (2016) Biophysics, State University of New York, Buffalo, USA
    • M.Sc. (2009) Physics, Indian Institute of Technology, Guwahati, India
    • B.Sc. (2007) Physics, Presidency College, University of Calcutta, India
    • Employment:
      • 2018-present: Postdoctoral Research Associate, Los Alamos National Laboratory
      • 2016-2017: Visiting Scientist, IBM T. J. Watson Research Center, NY

    Research Interests:

    • I am interested in computer-aided structural modeling and simulations of biomolecules. My current research aims to elucidate the conformational dynamics of HIV envelope glycoproteins and ultimately aid in designing knowledge-based therapeutic strategies. Towards this goal, I am applying atomistic and coarse-grained molecular dynamics simulations and working on developing novel tools and techniques to bridge in silico models and experimental results through bioinformatics-based data mining and statistical analyses.

    Selected Recent Publications:

      Full publication list in Google Scholar

    1. Chakraborty, S., Das, P., Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors, Nature Scientific Reports 7.1,9941 (2017)
    2. Gupta, S., Chakraborty, S., Vij, R., Auerbach, A., A mechanism for acetylcholine receptor gating based on structure, coupling, phi, and flip” - Long- and short-range interactions with the M2-M3 linker suggest a mechanism for acetylcholine receptor gating, J. Gen. Physiol. 149(1),85-103 (2017)
    3. Nayak, T., Chakraborty, S., Zheng, W., Auerbach, A., Structural correlates of affinity in fetal versus adult endplate nicotinic receptors, Nature Communications 7,11352 (2016)
    4. Chakraborty, S., Zheng, W., Decrypting structural, dynamic and energetic basis of kinesin interacting with tubulin dimer in three ATPase states by all-atom molecular dynamics simulation, ACS Biochemistry 54,859-869 (2015)
    5. Purohit, P., Chakraborty, S., Auerbach, A., Function of the M1 pi-helix in endplate receptor activation and desensitization, Journal of Physiology 593,2851-2866 (2015)
    6. Nayak, T., Chakraborty, S., Bruhova, I., Gupta, S., Zheng, W., Auerbach, A., Structural correlates of affinity in fetal versus adult endplate nicotinic receptors, Proceedings of National Academy of Sciences, USA 111(49),17660-6 (2014)
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