Title of Talk

Modelling the dynamics of chemical noise in yeast cell cycle

 

Abstract

A population of genetically identical cells exposed to same conditions shows significant cell-to-cell variation in characteristics. This cell-to-cell variability is linked to stochasticity in gene expression.Statistical physical models of gene expression indicate that due to low cellular abundances of various molecular species,the rates ofvarious biochemical reactions become discrete function of time, leading to noisy protein production over time. In order to understand the dynamics and consequence of noise, one has to make model for the whole cell. But the theoretical studies of chemical noise in cellular systems have mostly been concentrated on a single gene or a small genetic network. Towards this, we have recently built a mathematical model of yeast cell cycle control network to understand/predict the outcome of noise in various properties of cell cycle, e.g., cycle times, cell size at birth and division, durations in various phases of the cell cycle etc. The simulated results from the model compare favorably with the behavior of individual yeast cells observed experimentally. Our model provides understanding on how the cell cycle regulatory network works more or less accurately under the stochastic fluctuations of proteins and mRNAs.

 

References:

1. David A. Ball, Neil R. Adames, Nadine Reischmann, Debashis Barik, Christopher T. Franck, John J. Tyson, Jean Peccoud, Cell Cycle 2013, 12, 3203

2. Debashis Barik, William T. Baumann, Mark R. Paul, BelaNovak, John J Tyson, Mol. Sys. Biol. 2010, 6, 405

3. Orsolya Kapuy, Debashis Barik, Maria R. D. Sananes, John J. Tyson, Bela Novak, Prog. Biophys. Mol. Biol. 2009, 100, 47

Debashis Barik, Assistant Professor

 

School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad, 500046, AP, INDIA

e-mail: dbariksc@uohyd.ac.in

Profile. Debashis Barik is an assistant professor in the School of Chemistry, University of Hyderabad, India. He received Ph. D. in theoretical physical chemistry from Indian Association for the Cultivation of Science, Jadavpur University, India. His Ph. D. researchwas focused on applicationof statistical mechanical methods to understand the dynamics of chemical reactions in condensed phases, transport of matter under periodic potentials and thermal conduction in low dimensional lattices. He used a c-number formulation of quantum Brownian motion to calculate time dependent reaction rate, Kramers’ turnover rate etc. For the last six years his main interest is to understand the origin and consequences of chemical noise in cellular systems. During his postdoctoral research at Virginia Tech, USA, he developed a mathematical model for yeast cell cycle to help quantify the noise propagation in biochemical reaction network. His current goal is to understand how the molecular fluctuations are modulated by different kinds of feedback regulations to help predict the topology of a biochemical reaction network. He uses theories/tools from statistical mechanics, stochastic calculus, chemical kinetics, non-linear dynamics and experimental data from published literature on living cell for his research.

 

Selected Publications

1. Debashis Barik, William T. Baumann, Mark R. Paul, Bela Novak, John J Tyson, Mol. Sys. Biol. 2010, 6, 405

2. Debashis Barik, Mark R. Paul, William T. Baumann, Yang Cao, John J. Tyson, Biophys. J. 2008, 95, 3563

3. Debashis Barik, Euro. Phys. J. B 2007, 56, 229

4. Debashis Barik, Europhys. Lett. 2006, 75, 42

5. Debashis Barik, Suman K. Banik, Deb Shankar Ray, J. Chem. Phys. 2003, 119, 680