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College of Arts and Sciences

Sima Setayeshgar

Sima Setayeshgar Professor

B.S., Massachusetts Institute of Technology (1990)
Ph.D., California Institute of Technology (1998)

Office: Swain West 306
Phone: (812) 855-9127
Email: simas at

I am a physicist with interests at the interface between physics and biology on scales ranging from the molecular and cellular to the macroscopic. Powerful experimental methods, such as genetic tools, microfluidics, two-photon and fluorescence microscopy and single molecule techniques have made biological systems an exciting area for quantitative research. In approaching such problems, a physicist must contend with the sheer complexity of biological systems and the limitations arising from the difficulties in carrying out reproducible experiments. The fact that problems and their methods of solution are common across different biological systems - for example, phototransduction in the retina and chemotactic signal transduction in E. coli - points to the existence of organizing principles, making this quest especially rewarding.

Cellular biophysics: The cells biological functions - growth, differentiation and the generation of specialized properties - are carried out by networks of biochemical reactions comprising the cellular hardware. I am interested in understanding the limits set by physics, such as thermal and diffusive noise, on the accuracy of biochemical signaling which can to be considered the most basic and fundamental level of information processing in biology. Comparison of theoretical limits with recent experiments, for example on gene expression and chemotactic response in bacteria, suggests that for these crucial tasks the cells performance approaches limits set by physical laws.

Sustained nonequilibrium systems: Nonlinear processes leading to instabilities in systems far from equilibrium are responsible for the spatiotemporal phenomena that occur all around us, from fluids to chemical and biological systems, with striking similarities between macroscopic patterns in systems with different microscopic descriptions. Most of the observed patterns in nature are nonequilibrium, dissipative structures which cannot be understood in terms of minimizing a free energy, unlike their equilibrium counterparts, such as crystals. Nonetheless, common mechanisms underlying the formation of such patterns can be identified: linear instability, slaving to marginal modes near onset, and nonlinear saturation. Theoretical approaches are focused on understanding generic properties of pattern-forming systems by building simple mathematical models of controlled and reproducible experimental systems, such as Rayleigh-Benard convection or spiral waves in chemical systems, with the hope of extending these findings to more complicated systems, such as the climate or the heart. There is growing experimental evidence that the formation and subsequent breakdown of spiral waves of electric potential in the heart, leading to a spatiotemporally disorganized state of electrical excitation, is related to fatal arrhythmias. I am interested in applying analytical and numerical tools to better understanding scroll wave instabilities in physiologically realistic domains.

Selected Publications

  • S. Setayeshgar and M. C. Cross, "Turing instability in a boundary-fed system," Physical Review E 58, 4485 (1998).
  • S. Setayeshgar and M. C. Cross, "Numerical bifurcation diagram for the two dimensional boundary-fed chlorine-dioxide-iodine-malonic acid system," Physical Review E 59, 4258 (1998).
  • S. Setayeshgar and A. J. Bernoff, "Scroll wave dynamics in the presence of slowly varying anisotropy," Physical Review Letters 88, 028101 (2002).
  • S. Setayeshgar, C. W. Gear, H. G. Othmer, and I. G. Kevrekidis,"Application of coarse integration to bacterial chemotaxis," Multiscale Modeling and Simulation, 4307 (2005).
  • W. Bialek and S. Setayeshgar, "Physical limits to biochemical signaling," Proceedings of the National Academy of Sciences, USA 102, 10040 (2005).
  • J. Wagner, S. Setayeshgar, L. A. Sharon, J. P. Reilly and Y. V. Brun, "A Role in Nutrient Uptake for Bacterial Cell Envelope Extensions," Proceedings of the National Academy of Sciences, USA 103, 11772 (2006).
  • W. Bialek and S. Setayeshgar, "Cooperativity, sensitivity and noise in biochemical signaling," Physical Review Letters 100, 258101 (2008).
  • C. Berne, X. Ma, N. Licata, B. Neves, S. Setayeshgar, Y.V. Brun, and B. Dragnea, "Physiochemical Properties of Caulobacter crescentus Holdfast: A Localized Bacterial Adhesive," Journal of Physical Chemistry B 117, 10492 (2013).
  • B. Mohari, N. A. Licata, D. T. Kysela, P. M. Merritt, S. Mukhopadhyay, Y. V. Brun, S. Setayeshgar, and C. Fuqua, "Novel Pseudotaxis Mechanisms Improve Migration of Straight Swimming Bacterial Mutants through a Porous Environment," mBio 6, e00005 (2015).
  • N. A. Licata, B. Mohari, C. Fuqua, and S. Setayeshgar, "Bacterial Diffusion in Porous Media," Biophysical Journal 110 247 (2016).
  • M. Hernando-Perez, S. Setayeshgar, Y. Hou, R. Temam, Y. V. Brun, B. Dragnea, and C. Berne, "Layered Structure and Complex Mechanochemistry Underlie Strength and Versatility in a Bacterial Adhesive," mBio 9, e02359-17 (2018).
  • K. Hagner, S. Setayeshgar, and M. Lynch, "Stochastic Protein Multimerization, Activity, and Fitness," Physical Review E 98, 062401 (2018).
  • W. J. Zabel, K. P. Hagner, B. J. Livesey, J. A. Marsh, S. Setayeshgar, M. Lynch, and P. G. Higgs, "Evolution of Protein Interfaces in Multimers and Fibrils," Journal of Chemical Physics 150, 225102 (2019).