Publications

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* Denotes work initiated and completed after joining the faculty at the University of North Carolina at Chapel Hill

     UNC-Chapel Hill

       2009

  1. C. K. Materese, A. Savelyev and G. A. Papoian*,  "Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle"; J. Am. Chem. Soc.; 2009, 131, 15005–15013 [Article]

  2. P. I. Zhuravlev and G. A. Papoian*,  "Molecular Noise of Capping Protein Binding Induces Macroscopic Instability in Filopodial Dynamics" ; Proc. Natl. Acad. Sci. USA; 2009, 106, 11570-11575 [Article]

  3. P. I. Zhuravlev, C. K. Materese and G. A. Papoian*,  "Deconstructing the Native State: Energy Landscapes, Function and Dynamics of Globular Proteins";  J. Phys. Chem. B (Feature Article; July 2 2009 Journal Cover); 2009, 113, 8800–8812 [Article]

  4. A. Savelyev and G. A. Papoian*,  "Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl"; J. Phys. Chem. B.;2009, 113, 7785–7793 [Article]

  5. A. Savelyev and G. A. Papoian*,  "Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA";  Biophys. J.; 2009, 96, 4044-4052 [Article]

    2008

  6. S. Wu, P. I. Zhuravlev and G. A. Papoian*,  "High Resolution Approach to the Native State Ensemble Kinetics and Thermodynamics" ; Biophysical J.; 2008, 95, 5524-5532 [Article]

  7. Y. Lan, T. Elston, and G. A. Papoian*,  "Elimination of Fast Variables in Chemical Langevin Equations" ; J. Chem. Phys.; 2008, 129, 214115 [Article PDF]

  8. G. A. Papoian*,  "Proteins with Weakly Funneled Energy Landscapes Challenge the Classical Structure–Function Paradigm" ; Proc. Natl. Acad. Sci. USA; 2008, 105 , 14237–14238 [Article PDF]

  9. A. Savelyev and G. A. Papoian*,  "Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers";  The Journal of Physical Chemistry B; 2008, 112, 9135–9145[Article PDF]

  10. C. K. Materese, C. C. Goldmon and G. A. Papoian*,  "Hierarchical Organization of Eglin C Native State Dynamics Is Shaped by Competing Direct and Water-Mediated Interactions" ; Proc. Natl. Acad. Sci. USA; 2008, 105 , 10659 –10664 [Article PDF]
    (This article accompanied by V. Lubchenko's Commentary and highlighted on the Cover of August 5th issue of PNAS.)

  11. Y. Lan and G. A. Papoian*,  "The Stochastic Dynamics of Filopodial Growth", Biophysical Journal; 2008, 94, 3839-3852[Article PDF]

    2007

  12. Y. Lan and G. A. Papoian*,  "Stochastic Resonant Signaling in Enzyme Cascades", Physical Review Letters; 2007, 98 , 228301 [Article PDF]

  13. A. Savelyev and G. A. Papoian*,  "Inter-DNA Electrostatics from Explicit Solvent Molecular Dynamics Simulations" ;  Journal of the American Chemical Society; 2007, 129 , 6060-6061 [Article PDF]

  14. Y. Lan and G. A. Papoian*,  "Evolution of Complex Probability Distributions in Enzyme Cascades", Journal of Theoretical Biology; 2007, 248, 537-545 [Article PDF]

  15. J. Latzer, G. A. Papoian, M. C. Prentiss, E. A. Komives, and P. G. Wolynes, "Induced Fit, Folding, and Recognition of the NF-κB-Nuclear Localization Signals by IκBα and IκBβ"; Journal of Molecular Biology; 2007, 367, 262-274 [Article PDF]

  16. A. Savelyev and G. A. Papoian*,  "Free Energy Calculations of Na+ and K+ Partitioning between DNA and Chloride Solutions" ;  Mendeleev Communications;  2007, 17, 97-99 [Article PDF]

    2006

  17.  A. Savelyev and G. A. Papoian*,  "Electrostatic, Steric, and Hydration Interactions Favor Na+ Condensation around DNA Compared with K+" ;  Journal of the American Chemical Society;  2006, 128 , 14506-14518 [Article PDF]

  18. Y. Lan, P. G. Wolynes, and G. A. Papoian*, "A Variational Approach to the Stochastic Aspects of Cellular Signal Transduction", Journal of Chemical Physics; 2006, 125, 124106, [Article PDF]

  19. Y. Lan and G. A. Papoian*,  "The Interplay between Discrete Noise and Nonlinear Chemical Kinetics in a Signal Amplification Cascade", Journal of Chemical Physics; 2006, 125, 154901, [Article PDF]

    UCSD & UPenn

  20. C. Zong, G. A. Papoian, J. Ulander, and P. G. Wolynes "The Role of Topology, Nonadditivity and Water Mediated Interactions in Predicting the Structures of α/β Proteins" ;  Journal of the American Chemical Society; 2006, 128 , 281-297 [Article PDF]

    2004

  21. G. A. Papoian, J. Ulander, M. E. Eastwood, Z. Luthey-Schulten, and P. G. Wolynes "Water in Protein Structure Prediction" ; Proc. Natl. Acad. Sci. USA; 2004, 101 , 3352-3357 [Article PDF][Commentary PDF]

  22. Y. Levy, G. A. Papoian, J. N. Onuchic, and P. G. Wolynes "The Energy Landscape Analysis of Protein Dimers" ; Israel J. Chem.; 2004 , 44 , 281-297 [Article PDF]

  23. G. A. Papoian, J. Ulander, and P. G. Wolynes "The Role of Water Mediated Interactions in Protein-Protein Recognition Landscapes." ; Journal of the American Chemical Society ; 2003 , 125 , 9170-9178 [Article PDF]

    2003

  24. G. A. Papoian and P. G. Wolynes "The Physics and Bioinformatics of Binding and Folding - an Energy Landscape Perspective" ; Biopolymers; 2003, 68 , 333-349 [Article PDF]

  25. G. A. Papoian, W. F. DeGrado, and M. L. Klein "Probing the Configurational Space of a Metalloprotein Core: An ab Initio Molecular Dynamics Study of Duo Ferro 1 binuclear Zn Cofactor."; Journal of the American Chemical Society; 2003 , 125, 560-569 [Article PDF]

    Cornell University

  26. G. A. Papoian and R. Hoffmann "Electron-rich Rods as Building Blocks for Sb Strips and Te sheets" ; Journal of the American Chemical Society; 2001 , 123 , 6600-6608 [Article PDF]

  27. A. Ienco, R. Hoffmann and G. A. Papoian "Electron-rich bonding and the Importance of s,p mixing as One Moves Across a Period: A Lesson from the LiSn System." Journal of the American Chemical Society; 2001 , 123 , 2317-2325 [Article PDF]

  28. G. A. Papoian and R. Hoffmann "Hypervalent Bonding in One, Two and Three Dimensions: Extending the Zintl-Klemm Concept to Nonclassical Electron-Rich Networks." Angewandte Chemie International Edition; 2000, 39 , 2408-2448 [Article PDF][Popular Press: Science Daily]

  29. G. A. Papoian, J. K. Nørskov, and R. Hoffmann "A comparative study of hydrogen, methyl, and ethyl chemisorption on the Pt (111) surface." Journal of the American Chemical Society; 2000 , 122 , 4129-4144 [Article PDF]

  30. D. -K. Seo, G. A. Papoian, and R. Hoffmann. "Generalized Perturbational Molecular Orbital (PMO) Theory." International Journal of Quantum Chemistry; 2000 , 77 , 408-420 [Article PDF]

  31. W. V. Glassey, G. A. Papoian and R. Hoffmann "Total energy partitioning within an extended Huckel framework: a Hamilton Population study of surface --- CO interaction in the c(2x2) --- CO/Ni(100) chemisorption system." Journal of Chemical Physics; 1999, 111 , 893-910 [Article PDF]

  32. G. A. Papoian and R. Hoffmann "Building up complexity from strips and sheets --- the electronic structure of the La12Mn2Sb30 alloy." Journal of Solid State Chemistry; 1998 , 139 , 8-21 [Article PDF]

  33. G. A. Papoian, K.P. Butin, R. Hoffmann, and V.I Rozenberg "Theoretical investigation of [2.2]paracyclophane as a donor toward Cr(CO)3 group." Russian Chemical Bulletin; 1998 , 47 , 153-159

    University of Kansas

  34. G. A. Papoian, K. Gu, J. Wiorkiewicz-Kuczera, K. Kuczera, and K. Bowman-James. "Molecular dynamics simulations of nitrate complexes with polyammonium macrocycles: insight on phosphoryl transfer catalysis." Journal of the American Chemical Society; 1996, 118 , 1354-64 [Article PDF]

    Russian Academy of Sciences, Higher Chemical College

  35. S. Nefedov, A. Pasynskii, I. Eremenko, G. A. Papoian, L. Rubinstein, A. Yanovskii, and Yu. Struchkov. "Electron control of metal-metal bond multiplicity in binuclear thiolate-bridged rhenium-molybdenum complexes." Russian Journal of Inorganic Chemistry; 1993 , 38 , 69-7 
Last updated:   October 17, 2009