Dr. Rajesh K. Murarka

Computational Biophysics and Chemistry

  • Designation : Assistant Professor
  • Phone : +91 755 269 1319, 669 1319
  • Email : rkm@iiserb.ac.in
  • Fax : +91 755 669 2392
Academic Details

Assistant Professor (Since Jan 2009), Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal.

Post-doc. (Jan 2006 – Nov 2008), Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, with Prof. Harold A. Scheraga.

Post-doc. (Jan 2004 - Dec 2005), Department of Bioengineering, University of California, Berkeley, CA, with Prof. Teresa Head-Gordon.

Ph.D. (1997 - 2003), Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Advisor: Prof. Biman Bagchi.

Profile Details

    Our research program aims at development and application of state-of-the-art molecular simulation methods based on principles of statistical mechanics and quantum chemistry to understand various problems in contemporary Biophysics and Chemical Physics / Physical Chemistry.

    It is well recognised that the function of a biological macromolecule (proteins and nucleic acids) is made possible through fluctuations of varying amplitude and duration around the folded conformation of the molecule. These motions are not simply the inherent property of molecules held together by relatively weak interactions, but rather evolve along paths that enhance their biological effectiveness. Our research focuses on deciphering the microscopic correlations between structure, conformational dynamics (operating at different lengh and time scales) and functions of these molecules, and the molecular mechanism underlying the coupling of their motions with the surrounding solvent environments.

    Many eukaryotic proteins under physiological condition are structurally disordered in their isolated state (known as intrinsically disordered proteins, IDPs) and adopts well-defined tertiary structures only upon binding to their partner molecules. We are currently trying to understand the mechanism of this coupled folding and binding process exhibited by IDPs and the role of intrinsic structural disorder in determining numerous vital biological functions implicated in cell signalling and disease.

    Furthermore, our group is actively involved in understanding of the structural and dynamical properties of the environmentally benign green-solvents, such as pure and hydrated ionic liquids, and the nature of solvation energetics and dynamics in these solvents, both under bulk and confined conditions. Other research activities in the group include multi-scale modeling and simulations of protein folding/unfolding, aggregation, and protein-drug interactions.


    • Rajesh K. Murarka, Sarika Bhattacharyya, Ranjit Biswas, and Biman Bagchi, “Isomerization dynamics in viscous liquids: Microscopic investigation of the coupling and decoupling of the rate to and from solvent viscosity and dependence on the intermolecular potential”, Journal of Chemical Physics, 110: 7365-7375 (1999).

    • Rajesh K. Murarka, and Biman Bagchi, “Heterogeneous relaxation in supercooled liquids: A density functional theory analysis”, Journal of Chemical Physics, 115: 5513- 5520 (2001).

    • Rajesh K. Murarka, and Biman Bagchi, “Local composition fluctuations in strongly nonideal binary mixtures”, Journal of Chemical Physics, 117: 1155-1165 (2002).

    • Rajesh K. Murarka, Sarika Bhattacharyya, and Biman Bagchi, “Diffusion of small light particles in a solvent of large massive molecules”, Journal of Chemical Physics, 117: 10730-10738 (2002).

    • Rajesh K. Murarka, and Biman Bagchi, “Pair dynamics in a glass forming binary mixture: Simulations and theory”, Physical Review E, 67: 041501 (2003).

    • Rajesh K. Murarka, and Biman Bagchi, “Diffusion and viscosity in a supercooled polydisperse system”, Physical Review E, 67: 051504 (2003).

    • Daniela Russo†, Rajesh K. Murarka†, G. Hura, E. Verschell, John R. D. Copley, and Teresa Head-Gordon, “Evidence of anomalous hydration dynamics near a model hydrophobic peptide”, Journal of Physical Chemistry B, 108: 19885-19893 (2004). [†contributed equally]

    • Daniela Russo*, Rajesh K. Murarka*, John R. D. Copley, and Teresa Head-Gordon, “Molecular view of water dynamics near model peptides”, Journal of Physical Chemistry B, 109: 12966-12975 (2005). [*corresponding author]

    • Rajesh K. Murarka* and Teresa Head-Gordon, “Single-particle and collective hydration dynamics for hydrophobic and hydrophilic peptides”, Journal of Chemical Physics 126: 215101 (2007). Selected for Virtual Journal of Biological Physics Research, 13 (12) (2007); one of the top 20 most downloaded research articles published in Journal of Chemical Physics during the month of June 2007. [*corresponding author]

    • Rajesh K. Murarka, Adam Liwo, and Harold A. Scheraga, “Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone”, Journal of Chemical Physics, 127: 155103(1-16) (2007). Selected for Virtual Journal of Biological Physics Research, 14 (9) (2007).

    • A. Liwo, C. Czaplewski, S. Oldziej, M. Chinchio, A. V. Rojas, M. Khalili, M. Makowski, S. Kalinowski, U. Kozlowska, Rajesh K. Murarka, and Harold A. Scheraga, “Mesoscopic dynamics with the UNRES force field - a tool for studying the kinetics and thermodynamics of protein folding”, in “From Computational Biophysics to Systems Biology”, edited by U. H. E. Hansmann, John von Neumann Institute of Computing, Julich, NIC Series, 36: 31-36 (2007).

    • Rajesh K. Murarka, and Teresa Head-Gordon, “Dielectric relaxation of aqueous solutions of hydrophilic versus amphiphilic peptides”, Journal of Physical Chemistry B, 112: 179-186 (2008).

    • C. Malardier-Jugroot, Margaret E. Johnson, Rajesh. K. Murarka, and Teresa HeadGordon, “Aqueous peptides as experimental models for hydration water dynamics near protein surfaces”, Physical Chemistry Chemical Physics, 10: 4903-4908 (2008).

    • Margaret E. Johnson, C. Malardier-Jugroot, Rajesh K. Murarka, and Teresa HeadGordon, “Hydration water dynamics near biological surfaces”, Journal of Physical Chemistry B, 113: 4082-4092 (2009).

    • A. Liwo, C. Czaplewski, S. Oldziej, A. V. Rojas, R. Kazmierkiewicz, M. Makowski, Rajesh K. Murarka, and Harold A. Scheraga, “Simulation of protein structure and dynamics with the coarse-grained UNRES force field”, in “Coarse-Graining of Condensed Phase and Biomolecular Systems”, edited by G. A. Voth, Taylor and Francis Publ., pp. 107-122 (2009).

    • Navjeet Ahalawat and Rajesh K. Murarka*, “On the role of solvent in protein dynamical transition: A molecular dynamics simulation study” (manuscript in preparation).

    • Navjeet Ahalawat, Simran Arora and Rajesh K. Murarka*, "Structural ensemble of CD4 cytoplasmic tail (402-419) reveals a nearly flat free energy landscape with local alpha-helical order in aqueous solution", Journal of Physical Chemistry B (Biman Bagchi Festschrift) 119: 11229-11242 (2015).

    • Rajesh Singh, Navjeet Ahalawat and Rajesh K. Murarka*, "Activation of corticotropin-releasing factor 1 receptor: Insights from molecular dynamics simulations", Journal of Physical Chemistry B, 119: 2806-2817 (2015).

    • Navjeet Ahalawat and Rajesh K. Murarka*, "Conformational changes and allosteric communications in human serum albumin due to ligand binding", Journal of Bimolecular Structure and Dynamics, 33: 2192-2204 (2015).