Research Interests

Statistical Thermodynamics and Kinetics of RNA and Protein Folding

We are studying the statistical thermodynamics and kinetics and computer  modeling of biomolecules and polymers, particularly RNA & protein folding.

Biological molecules are large organic molecules composed of hundreds or thousands of atoms bound together by covalent bonds into a chain-like structure. One of the best known challenges in biology is to understand how biomolecules fold properly into compact structures to perform biological functions and how they mis-fold to cause disease. A fundamental problem we are pursuing is the study of the physical principles that govern folding-unfolding of bio-molecules. Based on the physical principles, we are developing statistical mechanical theories and computational models that can make accurate predictions for the sequence-structure and structure-activity relationships for  biomolecules. This involves statistical physics, computer simulations and, of course, mathematics.

Zhang, Wenbing and Shi-Jie Chen. Master equation approach to finding the rate-limiting steps in biopolymer folding, Journal of Chemical Physics, Vol. 118, pp. 3413-3420 , 2003.

Zhang, Wenbing and Shi-Jie Chen. RNA hairpin-folding kinetics, Proc. National Academy of Sciences U.S.A., Vol. 99, pp. 1931-1936 , 2002.

Zhang, Wenbing and Shi-Jie Chen. A Three-Dimensional Statistical Mechanical Model of Folding Double-Stranded Chain Molecules, Journal of Chemical Physics, Vol. 114, pp. 7669-7681 , 2001.

Tostesen, Eivind and Shi-Jie Chen and Ken A. Dill. RNA Folding Transitions and Cooperativity, Journal of Physical Chemistry, Vol. 105, pp. 1618-1630 , 2001.

Zhang, Wenbing and Shi-Jie Chen. Predicting Free Energy Landscapes for Complexes of Double Stranded Chain Molecules, Journal of Chemical Physics, Vol. 114, pp. 4253-4266 , 2001.

Chen, Shi-Jie and Ken A. Dill. RNA Folding Energy Landscapes, Proc. National Academy of Sciences U.S.A, Vol. 97, pp. 646-651 , 2000.