Ranjith, P

Dr. Ranjith Padinhateeri

Professor

Phone: +(91-22) 2576 7761
Fax: +(91-22) 2572 7760
E-mail: ranjithp [at] iitb.ac.in
Location: Room No. 306, BSBE Building
Lab web page

Research Interest

My broad areas of interest are biophysics and soft-matter physics. I do theoretical studies to understand various physical and biological phenomena, using a variety of tools from physics including equilibrium and non-equilibrium statistical mechanics, polymer physics, and soft-matter theory. I tackle research problems using a combination of computational (numerical) and analytical methods. My specific areas of interest include: (i) Organisation of Chromatin, (ii) Self-assembly of proteins, and (iii) Decision-making in cellular processes.

More details of the work can be found in the lab webpage

Academic Background

  • B. Sc.  : Physics, 1997, Zamorin’s Guruvayurappan College, University of Calicut, Kerala.
  • M. Sc. : Physics, 2000, Indian Institute of Technology Madras, Chennai, India
  • Ph.D. : Physics, 2005, Indian Institute of Technology Madras, Chennai, India

Teaching

Biological thermodynamics, Mathematical methods  for Biologists, Biostatistics, Modeling Biological Systems and Processes

Professional Experience

  • Professor : Indian Institute of Technology Bombay, 2018-
  • Associate Professor : Indian Institute of Technology Bombay, 2014-2018
  • Assistant Professor : Indian Institute of Technology Bombay, 2009-2014
  • Post-doctoral fellow : Institut Curie, Paris, France, 2007 — 2009.
  • Post-doctoral fellow : University of Illinois at Chicago/Northwestern University,Evanston, USA, 2005 — 2007.

Awards

  • Excellence in Teaching award – IIT Bombay, 2014
  • Senior Innovative Young Biotechnologist Award (Sr. IYBA) 2013-14, Department of Biotechnology, India.
  • Innovative Young Biotechnologist Award (IYBA) 2009-10, Department of Biotechnology, India.
  • Award for the best Ph. D. thesis, Physics, IIT Madras, 2005


Selected Publications

  • Coupling of replisome movement with nucleosome dynamics can contribute to parent-daughter information transfer; Tripti Bameta, Dibyendu Das & Ranjith Padinhateeri; Nucleic Acids Research, 46, 4991-5000 (2018)
  • Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure; Gaurav Bajpai, Ishutesh Jain, Mandar Inamdar, Dibyendu Das & Ranjith Padinhateeri; PLoS Computational Biology, 13, e1005365 (2017)
  • Defining a physical basis for diversity in protein self-assemblies using a minimal model; Srivastav Ranganathan, Samir Maji andRanjith PadinhateeriJ. Am. Chem. Soc.  138, 13911— 13922, (2016)
  • Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics; Jyotsana Parmar, Dibyendu Das, and Ranjith Padinhateeri; Nucleic Acids Research, 44, 1630-1641,  (2016)
  • Statistical mechanics provides novel insights into microtubule stability and mechanism of shrinkage; IshuteshJain, Mandar Inamdar, and Ranjith Padinhateeri; PLOS Computational Biology 11(2): e1004099 (2015)
  • Collectiveforce generated by multiple biolfilamentscan exceed the sum of forces due to individual filaments; Dipjyoti Das, Dibyendu Das, and Ranjith Padinhateeri; New J. Phys., 16, 063032 (2014)
  • Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplaybetween active remodeling and DNA sequence; Jyotsana Parmar, John F Marko, and Ranjith Padinhateeri, Nucleic Acids Research, 42, 128-146, (2014)
  • Stretching and bending fluctuations of short DNA molecules; Ranjith Padinhateeri and Gautam I. MenonBiophys. J., 104, 463-271 (2013)
  • History-dependent depolymerization of actin filaments; Ishutesh Jain, David Lacoste, Dulal Panda and Ranjith PadinhateeriBiochemistry, 51, 7580-7587 (2012)
  • Random hydrolysis controls the dynamicsinstability of microtubules; Ranjith Padinhateeri, A. B. Kolomeisky, and David LacosteBiophys. J., 102, 1274-1283 (2012)
  • Molecular interpretation of ACTH–endorphin coaggregation: relevance to  secretory granule biogenesis; S Ranganathan P. K. Singh, U. Singh, P. S. Singru, R. Padinhateeri and S. K. MajiPLoS ONE, 7, e31924 (2012)
  • Nucleosome positioning in a model of active chromatin remodeling enzymes; Ranjith Padinhateeri and John F. Marko, Proc. Natl. Acad. Sci. USA, 108, 7799-7803 (2011)
  • Non-equilibrium self-assembly of a filament coupled to ATP/GTP hydrolysis; P. Ranjith, D. Lacoste, K. Mallick and J-F. Joanny, Biophysical Journal 96, 2146-2159, (2009)
  • Nucleosome hopping and sliding kinetics determined from dynamics of single ,chromatin fibers in Xenopus egg extracts; P. Ranjith, J. Yan and John F. Marko, Proc. Natl. Acad. Sci. USA, 104, 13649-13654 (2007)
  • Distribution Functions, Loop Formation Probabilities andForce-Extension Relations in a Model for Short Double-Stranded DNA Molecules; P. Ranjith, P. B. Sunil Kumar and Gautam I. Menon, Phys. Rev. Lett. 94, 138102 (2005)
  • Dynamics of folding in Semiflexible filaments; P. Ranjith and P. B. Sunil Kumar, Phys. Rev. Lett. 89, 018302 (2002)

List of ongoing projects:

  • Force generation by Actin and Microtubules: In this project we are studying non-equilibrium dynamics of actin and microtubules, and the resulting force generation.
  • Nucleosome dynamics: In this project we are investigating sequence-dependent kinetics of nucleosomes along DNA.