- Qin Ni, Garegin A. Papoian* "Turnover versus treadmilling in actin network assembly and remodeling" Cytoskeleton; 2019, 10.1002/cm.21564 [Article]
- 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 ]
- Carlos Floyd, Garegin A. Papoian*, Christopher Jarzynski* "Quantifying dissipation in actomyosin networks" Interface Focus; 2019, 10.1098/rsfs.2018.0078 [ Article ]
- 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 ]
- 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 ]
- 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 ]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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
- 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]
- 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]
- 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]
- 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]
- A. Davtyan, M. Platkov, M. Gruebele *, G. A. Papoian *, "Stochastic Resonance in Protein Folding Dynamics"; ChemPhysChem; 2016, doi:10.1002/cphc.201501125 [ Article]
- 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]
- 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]
- 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]
- 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]
- I. Echeverria and G. A. Papoian *, "Structural Heterogeneity and Dynamics of the Unfolded Ensemble"; Israel J. Chem.; 2014, 54, 1293–1301 [ PDF]
- 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]
- 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]
- K. Popov and G. A. Papoian *, "Capsid Deformations Reveal Complex Mechano-Chemistry"; Biophysical Journal; 2013, 105, 2233–2234 [ PDF]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- M. Rubinstein and G. A. Papoian *, "Polyelectrolytes in biology and soft matter" ; Soft Matter; 2012, 8, 9265–9267 [ PDF]
- 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]
- 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]
- 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]
- 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]
- 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)
- 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)
- 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]
- 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]
- 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]
- A. Savelyev and G. A. Papoian *, "Chemically accurate coarse graining of double-stranded DNA"; Proc. Natl. Acad. Sci. USA; 2010, 107, 20340–5 [ PDF]
- 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]
- 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]
- 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]
- 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]
- L. Hu and G. A. Papoian *, "Mechano-Chemical Feedbacks Regulate Actin Mesh Growth in Lamellipodial Protrusions" ; Biophys. J.; 2010, 98,1375–1384 [ PDF]
- 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]
- P. I. Zhuravlev and G. A. Papoian *, "Functional vs. Folding Landscapes: The Same yet Different"; Curr. Opin. Struct. Biol.; 2010, 20, 16–20 [ PDF]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- Y. Lan, T. Elston *, and G. A. Papoian *, "Elimination of Fast Variables in Chemical Langevin Equations" ; J. Chem. Phys.; 2008, 129, 214115 [ PDF]
- 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]
- 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]
- 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.)
- Y. Lan and G. A. Papoian *, "The Stochastic Dynamics of Filopodial Growth", Biophysical Journal; 2008, 94, 3839-3852[ PDF]
- Y. Lan and G. A. Papoian *, "Stochastic Resonant Signaling in Enzyme Cascades", Physical Review Letters; 2007, 98 , 228301 [ PDF]
- 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]
- Y. Lan and G. A. Papoian *, "Evolution of Complex Probability Distributions in Enzyme Cascades", Journal of Theoretical Biology; 2007, 248, 537-545 [ PDF]
- 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]
- 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]
- 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]
- 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]
- 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, [ PDF]
UCSD & UPenn
- 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]
- 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 ]
- 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]
- 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]
- 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]
- 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
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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
- 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
- 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