Abhishek Jha, Ph.D.

2007 University of Chicago, Chicago, IL 
statistical mechanics of polymers in the liquid phase, protein dynamics aggregation, and folding, equilibrium aggregation phenomena, and molecular electronic structure
"Abhishek Jha"
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Karl F. Freed grad student 2007 Chicago
 (Reduced computational models for structure and dynamics of unfolded proteins and other stories.)
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Baxa MC, Haddadian EJ, Jha AK, et al. (2012) Context and force field dependence of the loss of protein backbone entropy upon folding using realistic denatured and native state ensembles. Journal of the American Chemical Society. 134: 15929-36
Debartolo J, Jha A, Freed KF, et al. (2012) Local Backbone Preferences and Nearest-Neighbor Effects in the Unfolded and Native States Protein and Peptide Folding, Misfolding, and Non-Folding. 79-98
Haddadian EJ, Gong H, Jha AK, et al. (2011) Automated real-space refinement of protein structures using a realistic backbone move set. Biophysical Journal. 101: 899-909
DeBartolo J, Colubri A, Jha AK, et al. (2009) Mimicking the folding pathway to improve homology-free protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 106: 3734-9
Kosmrlj A, Jha AK, Huseby ES, et al. (2008) How the thymus designs antigen-specific and self-tolerant T cell receptor sequences. Proceedings of the National Academy of Sciences of the United States of America. 105: 16671-6
Kent A, Jha AK, Fitzgerald JE, et al. (2008) Benchmarking implicit solvent folding simulations of the amyloid β(10-35) fragment Journal of Physical Chemistry B. 112: 6175-6186
Jha AK, Freed KF. (2008) Solvation effect on conformations of 1,2:dimethoxyethane: Charge-dependent nonlinear response in implicit solvent models Journal of Chemical Physics. 128
Fitzgerald JE, Jha AK, Colubri A, et al. (2007) Reduced C(beta) statistical potentials can outperform all-atom potentials in decoy identification. Protein Science : a Publication of the Protein Society. 16: 2123-39
Fitzgerald JE, Jha AK, Sosnick TR, et al. (2007) Polypeptide motions are dominated by peptide group oscillations resulting from dihedral angle correlations between nearest neighbors. Biochemistry. 46: 669-82
Colubri A, Jha AK, Shen MY, et al. (2006) Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. Journal of Molecular Biology. 363: 835-57
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