Alumnus
Nitin Rathore

Education

• Ph.D., Chemical and Biological Engineering, University of Wisconsin-Madison, 2005
• B.Tech., Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi, India, 2000

Research

Protein structure prediction by Monte Carlo Simulations: Understanding of Protein Folding Mechanisms and Their Application to Proteomics / Bioinformatics

My research focused on the understanding of the protein folding mechanisms and the various lattice and off-lattice models to simulate them. Proteomics--the study of proteins and their functions and interactions--is a new field with myriad variables to be accounted for, as scientists convert gene sequence data into primary protein structures. This has only contributed to the increasing gap between the number of available protein sequences and known 3D structures. Gene-sequencing projects, high-throughput screening, combinatorial chemical synthesis and proteomics studies are creating massive volumes and multiple sources of biological and chemical data. With this staggering amount of structural and physicochemical information about biomolecules available, it is indeed an intellectually challenging task for the engineer to use their insights most efficiently to relate and turn this increasingly complex data into useful information and knowledge. Computer simulations have proved to be invaluable tools in the modeling and understanding of condensed matter. My research concerned with this in-silico approach of studying thermodynamic, kinetic and structural details and its application to develop better algorithms and models for solving the protein structure prediction problem.

Publication

• Nitin Rathore, Thomas A. Knotts IV, and Juan J. de Pablo.
  "Confinement Effects on the Thrmodynamics of Protein Folding: Monte Carlo Simulations".
  Biophysical Journal, 90(5):1767-1773, March 1, 2006. [doi:10.1529/biophysj.105.071076] [BiophysJ]
• Nitin Rathore, Manan Chopra, and Juan J. de Pablo.
  "Optimal allocation of replicas in parallel tempering simulations".
  Journal of Chemical Physics 122(2):024111, 2005 January 8. [doi:10.1063/1.1831273] [AIP/JCP]
• Nitin Rathore, Qiliang Yan, and Juan J. de Pablo.
  "Molecular simulation of the reversible mechanical unfolding of proteins".
  Journal of Chemical Physics 120(12):5781-5788, 2004 March 22. [DOI] [AIP/JCP]
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• Nitin Rathore, Thomas A. Knotts IV, and Juan J. de Pablo.
  "Density of states simulations of proteins".
  Journal of Chemical Physics 118(9) 4285--4290, 2003 March 1. [DOI] [AIP/JCP]
  Erratum: Journal of Chemical Physics 118(20) 9460--9461, 2003 May 22. [DOI] [AIP/JCP]
• Nitin Rathore and Juan J. de Pablo.
  "Monte Carlo simulations of proteins through a random walk in energy space".
  Journal of Chemical Physics 116(16):7225-7230, April 22, 2002. [doi:10.1063/1.1463059] [AIP/JCP]

Presentations

• N. Rathore and J. J. de Pablo. "Monte Carlo simulations of proteins through a random walk in energy space", Emerging Technology Symposium, 224th American Chemical Society National Meeting, Boston, MA, U.S.A., 2002. Best presentation award by Schrödinger Inc.