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Tongye Shen

Assistant Professor



Our focus is to understand the stability and the dynamics of mechanical structures of biological interests: from the level of single biomolecules to sub-cellular assembly for both equilibrium and far-from-equilibrium systems. Currently, by using advanced modeling methods and large scaling computer simulations, we study challenging problems such as biofuel & biomass conversion, non-equilibrium dynamics of cellular structures, statistics of biopolymer configurations in extreme environments, signaling by post-translational modifications.


  • PhD, Physics-Biophysics, University of California–San Diego (2002)
  • MS, Physics, University of California–San Diego (2000)
  • BS, Physics, Tsinghua University (1997)


Shen, T., Langan, P., French, A.D., Johnson, G.P., & Gnanakaran, S. Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence.  J. Am. Chem. Soc.  131, 14786-14794 (2009).

Lu, T., Shen, T., Bennett, M., Wolynes, P.G., & Hasty, J. Phenotypic variability of growing cellular populations,  Proc. Natl. Acad. Sci. USA  104, 18982-18987 (2007).

Shen, T., Zong, C., Hamelberg, D., McCammon, J.A., & Wolynes, P.G. The folding energy landscape and phosphorylation: Modeling the conformational switch of the NFAT regulatory domain,  FASEB J. 19, 1389-1395 (2005).

Shen, T. & Wolynes, P.G. Stability and dynamics of crystals and glasses of motorized particles, Proc. Natl. Acad. Sci. USA  101, 8547-8550 (2004).

Shen, T., Tai, K., Henchman, R.H., & McCammon, J.A. Molecular dynamics of acetylcholinesterase, Acc. Chem. Res.   35, 332-340 (2002).

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