15. Inherrent flexibility determines the transition mechanisms of the EF-hands of Calmodulin, Swarnendu Tripathi, Proc. Natl. Acad. Sci. (In Review).[Abstract]

14. Cross-Disciplinary Molecular Science Education in Introductory Science Courses: An NSDL MatDL Collection, D. J. Yaron, J. L Davenport, M. Karabinos, G. Leinhardt, L. M Bartolo, J. J. Portman, C. S. Lowe, D. R. Sadowy, W. C. Carter, and C. Ashe, Proceedings of the 8th ACM/IEEE-CS Joint Conference on Digital Libraries (2008). [Abstract]

13. Inherent flexibility and protein function: the open/closed conformational transition of the N-terminal domain of calmodulin, Swandendu Tripathi and John J. Portman, J. Chem. Phys. 128, 205104 (2008). [Abstract]

12. Capillarity-like growth of protein folding nuclei, Xianghong Qi and John J. Portman, Proc. Natl. Acad. Sci. USA 105, 11164--11169 . [Abstract]

11. Variationally determined free energy profiles for structural models of proteins: Characteristic Temperatures for folding and trapping,Tongye Shen, Chenghang Zong, John J. Portman, and Peter G. Wolynes, J. Phys. Chem. B, 10.1021/jp076280n (2008). [Abstract] [Cited by]

10. Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates, Xianghong Qi and John J. Portman, Proc. Natl. Acad. Sci. USA 104, 10841--10846 (2007). [Abstract] [Cited by]

9. Peptide Folding Simulations, S. Gnanakaran, Hugh Nymeyer, John Portman, Kevin Y. Sanbonmatsu, and Angel E. Garcia, Curr. Opin. Struct. Biol. 13(2), 168--174 (2003). [Abstract] [Cited by]

8. Non-Gaussian Dynamics from a Simulation of a Short Peptide: Loop Closure rates and Effective Diffusion Coefficients, John J. Portman, J. Chem. Phys. 118, 2381--2391 (2003). [Abstract] [Cited by]

7. Microscopic Theory of Protein Folding Rates.II: Local Reaction Coordinates and Chain Dynamics, John J. Portman, Shoji Takada, and Peter G. Wolynes, J. Chem. Phys. 114, 5082--5096 (2001). [Abstract] [Cited by]

6. Microscopic Theory of Protein Folding Rates.I: Fine Structure of the Free Energy Profile and Folding Routes from a Variational Approach, John J. Portman, Shoji Takada, and Peter G.Wolynes, J. Chem. Phys. 144, 5069--5081 (2001). [Abstract] [Cited by]

5. Speeding Molecular Recognition by Using the Folding Funnel: The Fly-casting Mechanism', Benjamin A.Shoemaker, John J.Portman, and Peter G. Wolynes, Proc. Natl. Acad. Sci. USA 97, 8868--8873 (2000). [Abstract] [Cited by]

4. Complementary Variational Approximations for Intermittency and Reaction Dynamics in Fluctuating Environments, John J. Portman and Peter G. Wolynes, J. Phys. Chem. A 103,10602--10610 (1999). [Abstract] [Cited by]

3. Variational Theory of Site Resolved Protein Folding Free Energy Surfaces, J. J . Portman, S. Takada, P.~ G. Wolynes, Phys. Rev. Lett. 81(23), 5237--5240 (1998). [Abstract] [Cited by]

2. An Elementary Mode Coupling Theory of Random Heteropolymer Dynamics, Shoji Takada, John J. Portman, Peter G. Wolynes, Proc. Natl. Acad. Sci. USA 94, 2318 (1997). [Abstract] [Cited by]

1. Theoretical Investigations of Collisions of Aligned Atoms: $Ca(4s4f^1F)$ + He, A.~P. Hickman, J.~J. Portman, S. Krebs, and W. Meyer, Phys. Rev. Lett. 72 (12), 1814--1818 (1994). [Abstract] [Cited by]