X. Hu, S.L. Crick, G. Bu, C. Frieden, R.V. Pappu, J-M. Lee. Amyloid seeds formed by cellular uptake, concentration, and aggregation of the amyloid-beta peptide. Proc. Natl. Acad. Sci. USA (2009) In press.

A.A. Chen, M. Marucho, N.A. Baker, R.V. Pappu . Simulations of RNA interactions with monovalent ions. Methods Enzymol. 469: 406-426 (2009) Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B. [Download PDF]

D.T. Thomas, R.V. Pappu, N.A. Baker . NPO: Ontology for Cancer Nanotechnology Research. Nature Precedings. (2009) http://dx.doi.org/10.1038/npre.2009.3514.1 [Download PDF]

H.A. Lashuel, R.V. Pappu. Amyloids Go Genomic: Insights Regarding the Sequence Determinants of Prion Formation from Genome-Wide Studies. ChemBioChem 10: 1951-1954 (2009). [Download PDF]

A. Vitalis, N. Lyle, R.V. Pappu . Thermodynamics of beta sheet formation in polyglutamine. Biophys. J. 97: 303-311. (2009) Feature Article [Download PDF] .

A.A. Chen, D.E. Draper, R.V. Pappu Molecular simulation studies of monovalen counterion-mediated interactions in a model RNA kissing loop. J. Mol. Biol. . 390: 805-819 (2009). [Download PDF]

A. Vitalis, R.V. Pappu. Methods for Monte Carlo Simulations of Biomacromolecules. Annu. Rep. Comput. Chem. 5: 49-76 (2009). [Download PDF].

R.V. Pappu, R. Nussinov. Protein folding: Lessons learned and new frontiers. Phys. Biol. 6: 010301 (2009) [Download PDF] .

A. Vitalis, R.V. Pappu. ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions. J. Comput. Chem. 30: 673-700, (2009). Cover picture [Download PDF] .

A. Vitalis, X. Wang, R.V. Pappu. Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization. J.Mol. Biol. 384: 279-297 (2008). [Download PDF] .

H.T. Tran, A. Mao, R.V. Pappu. Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered polypeptides. J.Am. Chem. Soc. 130: 7380-7392 (2008). [Download PDF] .

M. A. Wyczalkowski, R.V. Pappu. Satisfying the fluctuation theorem in free energy calculations with Hamiltonian Replica Exchange. Phys. Rev. E. . 77, 026104, (2008). [Download PDF] . Erratum: Phys. Rev. E. 029905 E, (2008). [Download PDF] .

R.V. Pappu, X. Wang, A. Vitalis, S.L. Crick. A polymer physics perspective on driving forces and mechanisms for protein aggregation. Arch. Biochem. Biophys. 469, 132-141 (2008). [Download PDF] .

A.A. Chen, R.V. Pappu. Parameters of monovalent ions in the AMBER-99 forcefield: Assessment of inaccuracies and proposed improvements. J. Phys. Chem. B. 111, 11884-11887, (2007). [Download PDF] .

A. Vitalis, X. Wang, R.V. Pappu. Quantitative characterization of intrinsic disorder in polyglutamine: Insights from analysis based on polymer theories. Biophys. J. 93, 1923-1937 (2007). [Download PDF] .

A.A. Chen, R.V. Pappu. Quantitative Characterization of Ion Pairing and Cluster Formation in Strong 1:1 Electrolytes. J. Phys. Chem. B. 111, 6469-6478, (2007). [Download PDF] .

S.L. Crick, M. Jayaraman, C. Frieden, R. Wetzel, R.V. Pappu. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc. Natl. Acad. Sci. USA. 103, 1674-1679, (2006). [Download PDF] .

H.T. Tran, R.V. Pappu. Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions. Biophys. J. 91, 1868-1886, (2006). [Download PDF] .

X. Wang, A. Vitalis, M.A. Wyczalkowski, R.V. Pappu. Characterizing the conformational ensemble of monomeric polyglutamine. Proteins: Struc., Func. Bioinform. 63 , 297-311, (2006). [Download PDF] .

H.T. Tran, X. Wang, R.V. Pappu. Reconciling observations of sequence-specific conformational preferences with the generic behavior of denatured proteins. Biochemistry. 44, 11369-11380 (2005). [Download PDF] . [Supplementary Information]

A. Patriciu, G.S. Chirikjian, R.V. Pappu. Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints. J. Chem. Phys. 121, 12708-12720 (2004). [Download PDF]

A.N. Drozdov, A. Grossfield, R.V. Pappu. The Role of Solvent in Determining Conformational Preferences of Alanine Dipeptide in Water. J. Am. Chem. Soc. 126, 2574-2581 (2004). [Download PDF]

R.V. Pappu, G.D.Rose. A Simple Model for polyproline II structure in Unfolded States of Alanine-Based Peptides. Protein Sci. 11, 2437-2455 (2002). [Download PDF]

R.V. Pappu, R. Srinivasan, G.D. Rose. The Flory Isolated Pair Hypothesis is not Valid for Polypeptide Chains: Implications for Protein Folding. Proc. Natl. Acad. Sci. USA 97, 12565-12570 (2000). [Download PDF]

R.K. Hart, R.V. Pappu, J.W. Ponder. Exploring the Similarities Between Potential Smoothing and Simulated Annealing. J. Comput. Chem. 97, 12565-12570 (2000). [Download PDF]

R.V. Pappu Review of the Fourth Johns Hopkins Protein Folding Meeting. Proteins: Struct. Func. Genet. 36, 263-269 (1999). [Download PDF]

R.V. Pappu, G.R. Marshall, J.W. Ponder. A Potential Smoothing Algorithm Accurately Predicts Transmembrane Helix Packing. Nature Struct. Biol. 6, 50-55 (1999). [Download PDF] [Erratum]

R.V. Pappu, R.K. Hart, J.W. Ponder. Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization. J. Phys. Chem. B 102, 9725-9742 (1998). [Download PDF]

E.S. Huang, P. Koehl, M. Levitt, R.V. Pappu, J.W. Ponder. Accuracy of Side-Chain Prediction Upon Near-Native Protein Backbones Generated by Ab Initio Folding Methods. Proteins: Struct. Func. Genet. 33, 204-217 (1998). [Download PDF]

R.V. Pappu, D.L. Weaver. The Early Folding Kinetics of Apomyoglobin. Protein Sci. 7, 480-9742 (1998). [Download PDF]

R.V. Pappu, W.J. Schneller, D.L. Weaver. Electrostatic Multipole Representation of a Polypeptide Chain: An Algorithm for Simulation of Polypeptide Properties. J. Comput. Chem. 17, 1033-1045 (1996). [Download PDF]