Publications

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    2020

  1. C. Floyd, H. Levine, C. Jarzynski* and G. A. Papoian* "Driven-dissipative dynamics of active cytoskeletal networks underlie near-critical energy fluctuations" submitted 2020, arXiv:2006.01884

  2. S. Jin, V. G. Contessoto, M. Chen, N. P. Schafer, W. Lu, X. Chen, C. Bueno, A. Hajitaheri, B. J. Sirovetz, A. Davtyan, G. A. Papoian, M.Y. Tsai, and P. G. Wolynes "AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes" Nucleic Acids Res; 2020, [Article]

  3. Xiaona Li, Qin Ni, Xiuxiu He, Jun Kong, Soon-Mi Lim, Garegin A. Papoian, Jerome P Trzeciakowski, Andreea Trache and Yi Jiang "Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry" PLOS Comp Biol; 2020, 16 (6), e1007693, [Article]

  4. Carlos Floyd, Garegin A. Papoian* and Christophe Jarzynski* "Gibbs free energy change of a discrete chemical reaction event" JCP; 2020, 152 (8), 084116, [Article]

  5. Mary Pitman, Yamini Dalal* and Garegin A. Papoian* "Minimal Cylinder Analysis Reveals the Mechanical Properties of Oncogenic Nucleosomes" Biophysical Journal; 2020, 118, 2309-2318, [Article]

  6. 2019

  7. Daniël P. Melters, Mary Pitman, Tatini Rakshit, Emilios K. Dimitriadis, Minh Bui, Garegin A. Papoian* and Yamini Dalal* "Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners" PNAS; 2019, 10.1073/pnas.1911880116 [Article]

  8. Qin Ni, Garegin A. Papoian* "Turnover versus treadmilling in actin network assembly and remodeling" Cytoskeleton; 2019, 10.1002/cm.21564 [Article]

  9. Aravind Chandrasekaran, Arpita Upadhyaya*, Garegin A. Papoian* "Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling" PLoS Comp Bio; 2019, 10.1371/journal.pcbi.1007156 [ Article ]

  10. Carlos Floyd, Garegin A. Papoian*, Christopher Jarzynski* "Quantifying dissipation in actomyosin networks" Interface Focus; 2019, 10.1098/rsfs.2018.0078 [ Article ]

  11. Haiqing Zhao, David Winogradoff, Yamini Dalal*, Garegin A. Papoian* "The Oligomerization Landscape of Histones" Biophysical Journal; 2019, 10.1016/j.bpj.2019.03.021 [ Article ]


  12. 2018

  13. H. Wu, P. G. Wolynes* and G. A. Papoian* "AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins" The Journal of Physical Chemistry B; 2018, 10.1021/acs.jpcb.8b05791 [Article]

  14. J. E. Komianos and G. A. Papoian * "Stochastic Ratcheting on a Funneled Energy Landscape Is Necessary for Highly Efficient Contractility of Actomyosin Force Dipoles" Phys Rev X; 2018, 10.1103/PhysRevX.8.021006 [Article]


  15. 2017

  16. G. A. Papoian and P. G. Wolynes * "AWSEM-MD: From Neural Networks to Protein Structure Predic- tion and Functional Dynamics of Complex Biomolecular Assemblies"; Contributed Book Chapter in "Coarse-Grained Modeling of Biomolecules", Publisher CRC Press, edited by G. A. Papoian; 2017, ISBN-10: 1466576065 [ Book]

  17. D. Potoyan and G. A. Papoian * "The Need for Computational Speed: State of the Art in DNA Coarse Graining"; Contributed Book Chapter in "Coarse-Grained Modeling of Biomolecules", Publisher CRC Press , edited by G. A. Papoian; 2017, ISBN-10: 1466576065 [ Book]

  18. G. A. Papoian * "A Brief Historical Survey of Coarse-Graining of Biomolecules"; Contributed Book Chapter in "Coarse-Grained Modeling of Biomolecules", Publisher CRC Press, edited by G. A. Papoian; 2017, ISBN-10: 1466576065 [ Book]

  19. C. Floyd, C. Jarzynski, and G. A. Papoian * "Low-dimensional manifold of actin polymerization dynamics"; New Journal of Physics; 2017, 10.1088/1367-2630/aa9641 [ Article]

  20. M. Bui , M. Pitman , A. Nuccio, S. Roque, P. Donlin-Asp, A. Nita-Lazar, G. A. Papoian *, and Y. Dalal * "Internal Modifications in the CENP-A Nucleosome Modulate Centromeric Dynamics"; Epigenetics Chromatin; 2017, 10.1186/s13072-017-0124-6 [ Article]

  21. S. M. Avdoshenko, A. Das, R. Satija, G. A. Papoian, and D. E. Makarov * "Theoretical and Computational Validation of the Kuhn Barrier Friction Mechanism in Unfolded Proteins"; Scientific Reports; 2017, 10.1038/s41598-017-00287-5 [ Article]

  22. I. Echeverria and G A. Papoian * "Perspectives on the Coarse-Grained Models of DNA"; Contributed Book Chapter in "Many-Body Effects and Electrostatics in Biomolecules", Publisher Pan Stanford; edited by Qiang Cui and Markus Meuwly; 2017, ISBN-10:9814613924



  23. 2016


  24. H. Zhao, D. Winogradoff, M. Bui, Y. Dalal, and G. A. Papoian * "Promiscuous histone mis-assembly is actively prevented by chaperones"; JACS; 2016, 10.1021/jacs.6b05355 [ Article]

  25. B. Zhang, W. Zheng, G. A. Papoian, and P. G. Wolynes * "Exploring the Free Energy Landscape of Nucleosomes"; JACS; 2016, 10.1021/jacs.6b02893 [ Article]

  26. K. Popov, J. Komianos, and G. A. Papoian * "MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks"; PLoS Comp Bio; 2016, doi:10.1371/journal.pcbi.1004877 [ Article]

  27. U. Dobramysl, G. A. Papoian *, and R. Erban *, "Steric Effects Induce Geometric Remodeling of Actin Bundles in Filopodia"; Biophys J; 2016, doi:10.1016/j.bpj.2016.03.013 [ Article]

  28. A. Davtyan, M. Platkov, M. Gruebele *, G. A. Papoian *, "Stochastic Resonance in Protein Folding Dynamics"; ChemPhysChem; 2016, doi:10.1002/cphc.201501125 [ Article]

  29. K. Dave, A. Davtyan, G. A. Papoian *, M. Gruebele *, M. Platkov, "Environmental Fluctuations and Stochastic Resonance in Protein Folding"; ChemPhysChem; 2016, doi:10.1002/cphc.201501041 [ Article]


    2015


  30. D. Winogradoff, H. Zhao, Y. Dalal *, G. A. Papoian *, "Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome"; Sci Rep; 2015, 5, 17038 DOI: 10.1038/srep17038 [ PDF]

  31. D. Winogradoff, I. Echeverria, D. A. Potoyan, G A. Papoian *, "The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects" ; J Am Chem Soc; 2015, 137, 6245-6253 [ PDF]

  32. I. Echeverria and G. A. Papoian * "DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates" PLOS Comp. Bio.; 2015, DOI: 10.1371/journal.pcbi.1003980 [ PDF]


  33. 2014


  34. I. Echeverria and G. A. Papoian * "Structural Heterogeneity and Dynamics of the Unfolded Ensemble" Israel J. Chem.; 2014, 54, 1293–1301 [ PDF]

  35. I. Echeverria, D. E. Makarov * and G. A. Papoian * "Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins" J. Am. Chem. Soc.; 2014, 136, 8708–8713 [ PDF]

  36. R. Erban *, M. Flegg and G. A. Papoian * "Multiscale Stochastic Reaction-Diffusion Modeling: Application to Actin Dynamics in Filopodia" Bulletin of Mathematical Biology; 2014, 76, 799–818 [ PDF]


  37. 2013


  38. K. Popov and G. A. Papoian * "Capsid Deformations Reveal Complex Mechano-Chemistry" Biophysical Journal; 2013, 105, 2233–2234 [ PDF]

  39. L. Hu and G. A. Papoian * "Molecular Transport Modulates the Adaptive Response of Branched Actin Networks to an External Force" J. Phys. Chem. B.; 2013, 117, 13388–13396 [ PDF]

  40. D. Ma, S. Bettis, K. Hanson, M. Minakova, L. Alibabaei, W. Fondrie, D. Ryan, G. A. Papoian, T. J. Meyer, M. L. Waters and J. M. Papanikolas,  "Interfacial Energy Conversion in Ru II Polypyridyl-Derivatized Oligoproline Assemblies on TiO 2" J. Am. Chem. Soc.; 2013, 135, 5250–5253 [ PDF]

  41. D. A. Potoyan, A. Savelyev and G. A. Papoian *"Recent successes in coarse-grained modeling of DNA"WIREs Comput. Mol. Sci.; 2013, 3, 69–83 [ PDF]


  42. 2012


  43. W. Zheng, N. Schafer, A. Davtyan, G. A. Papoian * and P. G. Wolynes *"Predictive Energy Landscapes for Protein-Protein Association"Proc. Natl. Acad. Sci. USA; 2012, 109, 19244–19429 [ PDF]

  44. D. A. Potoyan and G. A. Papoian * "Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation" Proc. Natl. Acad. Sci. USA; 2012, 109, 17857-17862 [ PDF]

  45. P. I. Zhuravlev, Y. Lan, M. S. Minakova and G. A. Papoian * "Theory of active transport in filopodia and stereocilia" Proc. Natl. Acad. Sci. USA; 2012, 109, 10849–10854 [ PDF]

  46. M. Rubinstein and G. A. Papoian * "Polyelectrolytes in biology and soft matter" Soft Matter; 2012, 8, 9265–9267 [ PDF]

  47. D. J. Wilger, S. E. Bettis, C. K. Materese, M. S. Minakova, G. A. Papoian *, J. M. Panpanikolas and M. L. Waters,  "Tunable Energy Transfer Rates via Control of Primary, Secondary, and Tertiary Structure of a Coiled Coil Peptide Scaffold"Inorganic Chemistry; 2012, 51, 11324 [ PDF]

  48. A. Davtyan, W. Zheng, N. Schafer, C. Clementi, P. G. Wolynes * and G. A. Papoian *"AWSEM-MD: Protein Structure Prediction Using Coarse-grained Physical Potentials and Bioinformatically Based Local Structure Biasing"J. Phys. Chem. B.; 2012, 116, 8494–8503 [ PDF]

  49. D. A. Potoyan, P. I. Zhuravlev and G. A. Papoian *"Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase using All Atom Explicit Solvent Simulations"J. Phys. Chem. B.; 2012,116, 1709–1715 [ PDF]

  50. P. I. Zhuravlev, L. Hu, and G. A. Papoian *"Computer Simulations of Mechano-Chemical Networks Choreographing Actin Dynamics in Cell Motility" Contributed Book Chapter in “Computational Modeling of Biological Systems: From Molecules to Pathways”, Publisher: Springer, edited by N. Dokholyan; 2012, ISBN-10: 1461421454 [ Publisher's Site][ Amazon]


  51. 2011


  52. A. Savelyev, C. K. Materese and G. A. Papoian *"Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?"J. Am. Chem. Soc.; 2011, 133, 19290–19293 [ PDF]
    ( This work was highlighted by "Chemistry World", which is an RSC publication)

  53. P. I. Zhuravlev and G. A. Papoian * "Protein fluxes along the filopodium as a framework for understanding the growth-retraction dynamics: The interplay between diffusion and active transport"Cell Adhesion & Migration; 2011, 5, 448–456 [ Article][ PDF] (Note: Special Issue on Filopodia- This article has a review section summarizing our recent works on modeling filopodia)

  54. L. Hu and G. A. Papoian *"How does the Antagonism Between Capping and Anti-Capping Proteins Control Actin Network Dynamics?";  J. Phys.: Condens. Matter (Special Issue on “Cooperative dynamics in cells) ”; 2011, 23, 374101 [ PDF]

  55. M. Minakova, A. Savelyev and G. A. Papoian *"Non-equilibrium Water Transport in a Nonionic Microemulsion System"J. Phys. Chem. B.; 2011, 115, 6503-6508 [ PDF]

  56. D. A. Potoyan and G. A. Papoian *"Energy Landscape Analyses of Disordered Histone Tails Reveal Special Organization of Their Conformational Dynamics"J. Am. Chem. Soc.; 2011,133,7405-7415 [ PDF]


  57. 2010


  58. A. Savelyev and G. A. Papoian *"Chemically accurate coarse graining of double-stranded DNA"Proc. Natl. Acad. Sci. USA; 2010, 107, 20340–5 [ PDF]

  59. V. Oklejas, C. Zong, G. A. Papoian, P. G. Wolynes *"Protein structure prediction: Do hydrogen bonding and water-mediated interactions suffice?" Methods; 2010, 52, 84–90 [ PDF]

  60. P. I. Zhuravlev and G. A. Papoian * "Protein functional landscapes, dynamics, allostery : a tortuous path towards a universal theoretical framework"Q Rev. Biophys.; 2010, 43(3),295–332 [ PDF]

  61. P. I. Zhuravlev, S. Wu, D. A. Potoyan, M. Rubinstein and G. A. Papoian * "Computing free energies of protein conformations from explicit solvent simulations" Methods; 2010, 52, 115–121[ PDF]

  62. P. I. Zhuravlev, B. Der and G. A. Papoian * "Design of Active Transport Must Be Highly Intricate: a Possible Role of Myosin and Ena/Vasp for G-Actin Transport in Filopodia"Biophys. J.; 2010, 98, 1439–1448 [ PDF]

  63. L. Hu and G. A. Papoian * "Mechano-Chemical Feedbacks Regulate Actin Mesh Growth in Lamellipodial Protrusions" Biophys. J.; 2010, 98,1375–1384 [ PDF]

  64. N. Tanaka and G. A. Papoian * "Reverse-Engineering of Biochemical Reaction Networks from Spatio-Temporal Correlations of Fluorescence Fluctuations"J. Theor. Biol.; 2010, 264, 490–500 [ PDF]

  65. P. I. Zhuravlev and G. A. Papoian * "Functional vs. Folding Landscapes: The Same yet Different"Curr. Opin. Struct. Biol.; 2010, 20, 16–20 [ PDF]


    2009


  66. 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 [ PDF]

  67. 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 (28), 11570-11575 [ PDF]

  68. 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 [ PDF]

  69. 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 [ PDF]

  70. 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 [ PDF]


    2008


  71. 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 [ PDF]

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

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

  74. 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[ PDF]

  75. 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 [ PDF]
    (This article accompanied by V. Lubchenko's Commentary and highlighted on the Cover of August 5th issue of PNAS.)

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


    2007


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

  78. 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 [ PDF]

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

  80. 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 [ PDF]

  81. 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 [ PDF]


    2006


  82.  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 [ PDF]

  83. 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, [ PDF]

  84. Y. Lan and G. A. Papoian * "The Interplay between Discrete Noise and Nonlinear Chemical Kinetics in a Signal Amplification Cascade", Journal of Chemical Physics; 2006125, 154901, [ PDF]

    UCSD & UPenn

  85. 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 [ PDF]

    2004

  86. 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 [ PDF][ Commentary PDF ]

  87. 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 [ PDF]

  88. 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 [ PDF]

    2003

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

  90. 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 [ PDF]

    Cornell University

  91. 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 [ PDF]

  92. 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 [ PDF]

  93. 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 [ PDF][Popular Press: Science Daily]

  94. G. A. Papoian, J. K. N�rskov, 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 [ PDF]

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

  96. 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 [ PDF]

  97. G. A. Papoian and R. Hoffmann "Building up complexity from strips and sheets --- the electronic structure of the La 12Mn 2Sb 30 alloy." Journal of Solid State Chemistry; 1998 , 139 , 8-21 [ PDF]

  98. 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

  99. 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 [ PDF]

    Russian Academy of Sciences, Higher Chemical College

  100. 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:   August 15, 2018