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.
- 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, Inherrent 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).
- Theoretical Biological Physics
OFFICEDepartment of Physics
CONTACT INFOPhone: 330-672-9518
COURSES TEACHINGSpring 2014
- PHY 23101 - 001 General University Physics I
- PHY 40096 - 004 Individual Investigation
- PHY 80199 - 009 Dissertation I
- PHY 80299 - 013 Dissertation Ii
- PHY 60098 - 027 Research
- PHY 64101 - 020 Advanced Problem Solving
- PHY 74101 - 020 Advanced Problem Solving
- PHY 80199 - 050 Dissertation I
- PHY 80299 - 082 Dissertation Ii
- PHY 12000 - 001 Introductory Physics Seminar
- PHY 65301 - 001 Statistical Mechanics I