Jaydeb Chakrabarti
    Professor








   jaydeb@bose.res.in
   www.bose.res.in
   Telephone +91-33-2335 5706/07/08

I. Educational Background:

  • B. Sc.: Presidency College, Calcutta University , India (1987)
  • M. Sc.: Rajabazar Science College, Calcutta University, India (1989)
  • Ph D: Department of Physics, IISc, Bangalore (1995), India (1995)
  • II. Professional Experience:

  • Post-Doctoral Reseach: AMOLF, Amsterdam, The Netherlands (1999)
  • Faculty – S.N. Bose National Centre for Basic Sciences, Kolkata (since Nov., 1999)
  • Visiting Scientist in SFB-TR6 project under Germany-The Netherlands collaboration
  • III. Broad Area of Research:

  • Statics and Dynamics of soft matter systems including colloids, biomacromolecules and so on:The primary methods are: (1) computer simulations based on Molecular Dynamics, Monte Carlo and Brownian Dynamics; (2) Mean field calculations based on classical density functional theories.
  • IV. Problems currently undergoing:

    The problems can be largely categorized into three classes as described below:

    A. Studies on Bio-macromolecular complexes:

    We perform detailed computation and theoretical analysis on conformational changes in biomacromolecular complexes, like, protein-metal ion, protein-protein, protein-ligand structures which forms the heart of allbiochemical activities.
    1. Microscopic insight on protein functions:We have developed a method for calculating the thermodynamics of conformational changes in bio-molecular complexes based on the distribution of the dihedral angles. Based on this we seek microscopic view of protein functions.
    2. Dynamic aspects of conformational fluctuations:We probe in detail how the time dependent fluctuations of the dihedral angles are correlated to show the connection between the structure and dynamics. In particular, we examine the long distance communication in proteins based on simulations and theoretical modeling.
    3. Quantum Mechanical effects:The coordination of metal ions to a protein leads to substantial electronic redistribution which governs the stability of metallo-proteins. This leads us to undertake ab-initio calculations for metal binding regions, using density functional theory.
    B. Modeling large scale behavior of bio-macromolecular systems:

    The behavior of a system comprising of bio-nacroemolecules are addressed by statistical mecahanical theories.

     
    1. The aggregation behavior and dynamics of proteins investigated by statistical mechanical theories and computer simulations.
    2. The kinetics of bio-molecular reactions by theoretical modeling and computer simulations.
    C. Equilibrium and non-equilibrium studies on colloidal systems:

    Colloidal systems represent a model soft matter system which can be used to study the condensed matter properties both in equilibrium and out of equilibrium.

    1. Effective forces:The medium generated effective forces on the colloids add to the direct interaction between them, resulting in mutual effective pair interaction which controls their phase behaviour and dynamics. We study the effective colloidal forces, their tenability and consequences in phase behaviours in the presence of an external potential.
    2. Probing dynamics in colloids under external perturbations:Colloidal particle dynamics probed via the time dependent probability distributions of the particle displacement under a variety of external perturbations, like external potentials and confinement.

    Significant recent publications:

    • Quantum chemical studies on the role of residues in calcium ion binding to Calmodulin. S.Sikdar, M.Ghosh, M. De Raychaudhury and J. Chakrabarti, Chem Phys Lett, 2014, 605, 103 (2014).
    • A microscopic insight from conformational thermodynamics to functional ligand binding in proteins. S.Sikdar, J.Chakrabarti and M. Ghosh, Mol Biosyst, 10, 3280 (2014).
    • Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation Amit Das, J. Chakrabarti and Mahua Ghosh Biophysical Journal, 104, 1274 (2013).
    • Cross-over between central and non-central conservative effective forces in a modulated colloidal fluid C. Basu Chaudhuri, S. Chakrabarty and J. Chakrabarti, J. Chem. Phys. , 139, 204903 (2013).
    • Dimensional crossover in fluids under nanometer-scale confinement A. Das and J. Chakrabarti, Phys. Rev. E (rapid comm), 85, 050601(R) (2012).
    • High-Affinity Quasi-Specific Sites in the Genome: How the DNA-Binding Proteins Cope with them J. Chakrabarti, Navin Chandra, Paromita Raha, and Siddhartha Roy, Biophysical Journal, 101, 1123 (2011).
     
     
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