Physics Colloquium, May 15, 2012
Systems biology of a simple organism: On E. coli's memory, computation, and energy cost Yuhai Tu

IBM T. J. Watson Research Center

Living organisms need to encode and process information accurately in order to make proper decisions critical for their survival. Although much progress have been made in identifying key components responsible for various biological functions, it remains a great challenge to understand system-level behaviors from the molecular-level knowledge of biology, and to unravel possible design principles for the underlying biochemical circuits. In this talk, we will present some of our recent theoretical/modeling work [1-6] in collaboration with several experimental groups to understand the chemo-sensory system in E. coli. Based on molecular biology and biochemistry of the E. coli chemotaxis pathway and by using mathematical models originated from statistical physics, we address several system-level questions on E. coli's information processing and decision making processes: 1) How does E. coli encode a memory of its past experience? 2) How does a cell compute chemical gradient accurately in a wide range of backgrounds? 3) How much is the energy cost of regulating the chemotaxis signaling circuit?

References:

[1] "The energy-speed-accuracy trade-off in sensory adaptation", G. Lan, P. Sartori, S. Neumann, V. Sourjik, Yuhai Tu, Nature Physics, March 2012.

[2] "Adapt locally and act globally: strategy to maintain high chemoreceptor sensitivity in complex environments", G. Lan, S. Schulmeister, V. Sourjik, Yuhai Tu, Molecular Systems Biology 7:475, 2011.

[3] "A modular gradient-sensing network for chemotaxis in E. coli revealed by responses to time-varying stimuli", T. S. Shimizu, Yuhai Tu, and Howard C. Berg, Molecular Systems Biology 6: 382, 2010.

[4] "Modeling the chemotactic response of E. coli to time-varying stimuli", Y. Tu, T. S. Shimizu and H. Berg, PNAS, 105(39), 14855-14860 (2008).

[5] "Nonequilibrium mechanism for a biological switch: Sensing by Maxwell's demons", Y. Tu, PNAS, 105(33), 11737-11741 (2008).

[6] "An allosteric model for heterogeneous receptor complexes: Understanding bacterial chemotaxis responses to multiple stimuli", B. Mello and Yuhai Tu, PNAS, 102(48), 17354-17359 (2005).

Dr. Tu's Web Site

4:00 p.m., Physics Research Building (PRB), Room 1080

Reception at 3:45 p.m., Atrium, PRB