Debashis Barik

Assistant Professor School of Chemistry University of Hyderabad Gachibowli, Hyderabad, 500046, AP, India Email: dbariksc@uohyd.ac.in
barikdd@gmail.com
Tel: +91-040-2313-4821(Office) +91-040-2313-4921(Lab)

Link to Debashis at Uohyd
Profile in Google Scholar
Previous position at VT: Postdoctoral Fellow, 2007-10.

Research Pages: Tyson Lab

Current Research Interests

I am a postdoc in labs of both Prof. John J. Tyson and Dr. Mark R. Paul (Dept. Mechanical Engineering) since March, 2007.

Chemical reactions are intrinsically noisy due to the inherent uncertainty in the collision event of the reacting molecules. In general, the amount of noise is inversely proportional to the square root of the size of the system (here the number of reacting molecules). A living cell is like a reaction chamber, where chemical reactions are occurring at every instant of time. In a typical yeast cell, the population of proteins, on average, varies from a couple of hundreds to several thousands molecules and the number of mRNA varies ranges from one to ten molecules. Due to the low copy number of mRNA and the low abundance of transcription factors, protein expression levelfluctuates a lot. Simple model of gene expression reveals that the noise in gene expression also critically depends on the times scales of transcription and translation and on the average life times of mRNAs and translated proteins. The fluctuations in the gene expressions level are reflected in the phenotypic behavior of a cell.

Recent single cell measurements on budding yeast cells have quantified not only the average cell cycle time, the durations of the G1 phase and the S/G2/M phases and the durations of several other critical events in the cellcycle, but also the variability of those durations both for the mother and the daughter cells in various growth conditions. For the last two years I have been involved in building mathematical model of budding yeast cell cycle (stochastic model) to explore how the protein-protein and gene-protein interaction networks and noise in individual gene expression contribute to the over variability in the cell cycle.

Education

Ph. D. 2006 Indian Association for the Cultivation of Science, Kolkata, India,
Theoretical Chemical Physics.
M. Sc. 2001 University of Calcutta, Chemistry.
B. Sc. 1999 R. K. Mission Residential College, Narendrapur,
University of Calcutta, India

Publications

Barik, D., Ball, D. A., Peccoud, J. and Tyson, J. J. (2016). A stochastic model of the yeast cell cycle reveals roles for feedback regulation in limiting cell viability. PLoS Comput. Biol. 12:e1005230.
[Abstract] [Article]
Ball, D.A., Adames, N.R., Reischmann, N., Barik, D., Franck, C.T., Tyson, J.J., and Peccoud, J. (2013). Measurement and modeling of transcriptional noise in the cell cycle regulatory network. Cell Cycle 12: 3203-3218.
[Abstract] [Article]
Barik, D., Baumann, W.T., Paul, M.R., Novak, B., and Tyson, J.J. (2010). A model of yeast cell cycle regulation based on multisite phosphorylation. Mol. Syst. Biol. 6:405.
[Abstract] [Article]
Kapuy, O., Barik, D., Domingo Sananes, M.R., Tyson, J.J., and Novak, B. (2009). Bistability by multiple phosphorylation of regulatory proteins. Prog Biophys Mol Biol 100:47-56.
[Abstract] [Article]
Barik, D., Paul, M.R., Baumann, W.T., Cao, Y., and Tyson, J.J. (2008). Stochastic simulation of enzyme-catalyzed reactions with disparate time scales. Biophys. J. 95: 3563-3574.
[Abstract] [Article]
Chaudhuri, J.R., and Barik, D. (2008). State-dependent diffusion in a periodic potential for a nonequilibrium open system. Euro. Phys. J. B 63:117-126.
[Abstract] [Article]
Barik, D. (2007). Anomalous heat conduction in a 2d Frenkel-Kontorova lattice. Euro. Phys. J. B 63:229-234.
[Abstract] [Article]
Chaudhuri, J.R., Barik, D., and Banik, S. K. (2007). Nonequilibrium fluctuation induced escape from a metastable state. Euro. Phys. J. B 63:333-336.
[Abstract] [Article]
Chaudhuri, J.R., Barik, D., and Banik, S. K. (2007). Directed motion generated by heat bath nonlinearly driven by external noise. J. Phys. A: Math. Theor. 40:14715-14723.
[Abstract] [Article]
Barik, D., Ghosh, P. K., and Ray, D. S. (2006). Langevin dynamics with dichotomous noise; direct simulation and applications. J. Stat. Mech. P03010.
[Abstract] [Article]
Barik, D., and Ray, D. S. (2006). Quantum equilibrium factor in the decay of a metastable state at low temperature. J. Stat. Mech. P06001.
[Abstract] [Article]
Barik, D. (2006). Heat conduction in 2d harmonic lattices with on-site potential. Europhys. Lett. 75:42-48.
[Abstract] [Article]
Chaudhuri, J.R., Barik, D., and Banik, S. K. (2006). Dynamics of a metastable state nonlinearly coupled to a heat bath driven by an external noise. Phys. Rev. E. 74:061119-061120.
[Abstract] [Article]
Chaudhuri, J.R., Barik, D., and Banik, S. K. (2006). Escape rate from a metastable state weakly interacting with heat bath driven by external noise. Phys. Rev. E. 73:051101-051110.
[Abstract] [Article]
Ghosh,P. K., Barik, D., and Ray, D. S. (2006). Inhomogeneous quantum diffusion and decay of a meta-stable state. Phys. Lett. A 360:35-43.
[Abstract] [Article]
Barik, D., and Ray, D. S. (2005). Quantum state-dependent diffusion and multiplicative noise: a microscopic approach. J. Stat. Phys. 120:339-365 .
[Abstract] [Article]
Ghosh, P. K., Barik, D., and Ray, D. S. (2005). Noise induced transition in quantum system. Phys. Lett. A 342:12-21.
[Abstract] [Article]
Ghosh, P. K., Barik, D., and Ray, D. S. (2005). Noise induced quantum transport. Phys. Rev. E 71:041107-041116.
[Abstract] [Article]
Ghosh, P. K., Barik, D., Bag, B. C., and Ray, D. S. (2005). Quantum escape kinetics over a fluctuating barrier. J. Chem. Phys. 123:224104-224110.
[Abstract] [Article]
Barik, D., and Ray, D. S. (2004). Anharmonic quantum contribution to vibrational dephasing. J. Chem. Phys. 121:1681-1689.
[Abstract] [Article]
Barik, D., and Ray, D. S. (2003). Quantum phase-space function formulation of reactive flux theory. J. Chem. Phys. 119:680-695.
[Abstract] [Article]
Barik, D., and Ray, D. S. (2003). Numerical simulation of transmission coefficient using c-number Langevin equation. J. Chem. Phys. 119:12973-12980.
[Abstract] [Article]

Personal

Apart from my scientific efforts, I am really passionate about cooking. I enjoy cooking various Indian foods using American vegetables and fishes. I like going for car drive with my wife Durba (who is doing postdoc in Penn State) with music on (John Denver and Santana).