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My research is in the general area of molecular biological physics. Often, conformational flexibility and dynamics is the key connection between the structure of a protein and its biological function. We are developing analytical and computational approaches to understand the mechanisms controlling large-scale structural changes in proteins. Examples include protein folding, allostery, and conformational changes induced from interactions with molecular surfaces. These questions are addressed using theoretical concepts and approaches from within statistical physics, soft condensed matter physics, and chemical physics, as well as molecular dynamics simulation.

Selected Publications

• Prithviraj Nandigrami and John J. Portman, Coarse-grained molecular simulations of allosteric cooperativity, J. Chem. Phys.144, 105101 (2016). 
• P. Nandigrami and J. J. Portman, Comparing allosteric transitions in the domains of calmodulin through coarse-grained simulations, J. Chem. Phys. 144, 105102 (2016).
• Swarnendu Tripathi and John J. Portman, Allostery and Folding of the N-Terminal Receiver Domain of Protein NtrC, J. Phys.Chem. B (2013). 
• Swarnendu Tripathi and John J. Portman, Conformational flexibility and the mechanisms of allosteric transitions in topologically similar proteins, J. Chem. Phys. 135, 075104 (2011).
• John J. Portman, Cooperativity and protein folding rates, Curr. Opin. Struct. Biol. 20, 11–15 (2010).
• Swandendu Tripathi and John J. Portman, Inherent flexibility determines the transition mechanisms of the EF-hands of Calmodulin, Proc. Natl. Acad. Sci. USA 106:2104-2109 (2009).
• Swarnendu Tripathi and John J. Portman, “Inherent flexibility and conformational transition in calmodulin N-Terminal domain from a variational approach”, J. Chem. Phys. 128, 205104 (2008).
• Xiangong Qi and John J. Portman, “Capillarity-like growth of protein folding nuclei” Proc. Natl. Acad. Sci. USA 105, 11164–11169 (2008).
• Tongye Shen, Chenghang Zong, John J. Portman, and Peter G. Wolynes, “Variationally determined free energy profiles for structural models of proteins: Characteristic Temperatures for folding and trapping”, J. Phys. Chem. B 10.1021/jp076280n (2008).
• Xianghong Qi and John J. Portman, “Excluded volume , local structural cooperativity , and the polymer physics of protein folding rates”, Proc. Natl. Acad. Sci. USA 104, 10841–10846 (2007).