Publications of Peter G. Wolynes - The Journal of Physical Chemistry

Special Issue Preface pubs.acs.org/JPCB

Publications of Peter G. Wolynes 20. Hubbard, J. B.; Colonomos, P.; Wolynes, P. G. Molecular Theory of Solvated Ion Dynamics III: The Kinetic Dielectric Decrement. J. Chem. Phys. 1979, 71, 2652− 2661. 21. Wolynes, P. G. (Transl.: T. Fujiyama) What’s Simple about Complex Fluids? Kagaku no Ryoiki [J. Jpn. Chem.] 1979, 33, 897−905. 22. Calef, D. F.; Wolynes, P. G. Flow Birefringence and Hydrodynamic Boundary Conditions. J. Chem. Phys. 1980, 72, 535−540. 23. Skinner, J. L.; Wolynes, P. G. General Kinetic Models of Activated Processes in Condensed Phases. J. Chem. Phys. 1980, 72, 4913−4927. 24. Wolynes, P. G. Dynamics of Electrolyte Solutions. Ann. Rev. Phys. Chem. 1980, 31, 345−376. 25. Skinner, J. L.; Wolynes, P. G. Transition State and Brownian Motion Theories of Solitons. J. Chem. Phys. 1980, 73, 4015−1021. 26. Skinner, J. L.; Wolynes, P. G. Solitons, Defect Diffusion, and Dielectric Relaxation of Polymers. J. Chem. Phys. 1980, 73, 4022−4025. 27. Berne, B. J.; Skinner, J. L.; Wolynes, P. G. Impulsive Stochastic Models of Molecular Relaxation and Isomerization Reactions. J. Chem. Phys. 1980, 73, 4314−4320. 28. Chandler, D.; Wolynes P. G. Exploiting the Isomorphism between Quantum Theory and Classical Statistical Mechanics of Polyatomic Fluids. J. Chem. Phys. 1981, 74, 4078−4095. 29. Hynes, J. T.; Wolynes, P. G. A Continuum Theory for Quadrupole Relaxation of Ions in Solution. J. Chem. Phys. 1981, 75, 395−401. 30. Schweizer, K.; Stratt, R.; Chandler, D.; Wolynes, P. G. Convenient and Accurate Discretized Path Integral Methods for Equilibrium Quantum Mechanical Calculations. J. Chem. Phys. 1981, 75, 1347−1364. 31. Wolynes, P. G. Quantum Theory of Activated Events in Condensed Phases. Phys. Rev. Lett. 1981, 47, 968−971. 32. Hubbard, J. B.; Wolynes, P. G. An Electrohydrodynamic Contribution to the Hall Effect in Electrolyte Solutions. J. Chem. Phys. 1981, 775, 3051−3054. 33. Levy, R. M.; Karplus, M.; Wolynes, P. G. NMR Relaxation Parameters in Molecules with Internal Motion: Exact Langevin Trajectory Results Compared with Simplified Relaxation Models, J. Am. Chem. Soc. 1981, 103, 5998−6011. 34. Wolynes, P. G. Book Review: Functional Integration: Theory and Applications. J. Stat. Phys. 1982, 28, 409. 35. Wolynes, P. G. Quantum Statistical Mechanics of Solvation. In Ions and Molecules in Solution: a Collection of Invited Papers Presented at the Session Lectures and Microsymposia during the VI International Symposium on Solute−Solute−Solvent Interactions, Minoo, Japan, 4−10

1. Wolynes, P. G. Bounds for Convective Contributions to Transport Coefficients. Phys. Rev. A 1975, 11, 1700− 1705. 2. Wolynes, P. G. Hydrodynamic Boundary Conditions and Mode−Mode Coupling Theory. Phys. Rev. A 1976, 13, 1235−1250. 3. Wolynes, P. G. Osmotic Effects near the Critical Point. J. Phys. Chem. 1976, 80, 1570−1572. 4. Wolynes, P. G.; Deutch, J. M. Slip Boundary Conditions and the Hydrodynamic Effect on Diffusion Controlled Reactions. J. Chem. Phys. 1976, 65, 450−454. 5. Wolynes, P. G.; Deutch, J. M. Hydrodynamic Boundary Conditions and Polymer Dynamics. J. Chem. Phys. 1976, 65, 2030−2031. 6. McCammon, J. A.; Gelin, B. R.; Karplus, M.; Wolynes, P. G. The Hinge-Bending Mode of Lysozyme. Nature 1976, 262, 325−326. 7. Wolynes, P. G.; McCammon, J. A. Hydrodynamic Effect on the Coagulation of Porous Biopolymers. Macromolecules 1977, 10, 86−87. 8. McCammon, J. A.; Wolynes, P. G. Nonsteady Hydrodynamics of Biopolymer Motions. J. Chem. Phys. 1977, 66, 1452−1456. 9. Wolynes, P. G.; Deutch, J. M. Dynamical Orientation Correlations in Solution. J. Chem. Phys. 1977, 67, 733− 741. 10. Montgomery, J. A., Jr.; Berne, B. J.; Wolynes, P. G.; Deutch, J. M. On the Effects of Translation-Rotation Coupling on Hydrodynamic Diffusion Tensors. J. Chem. Phys. 1977, 67, 5971−5972. 11. Wolynes, P. G. Molecular Theory of Solvated Ion Dynamics. J. Chem. Phys. 1978, 68, 473−483. 12. Wolynes, P. G.; Roberts, R. E. Molecular Interpretation of the Infrared Water Vapor Continuum. Appl. Opt. 1978, 17, 1484−1485. 13. Schulten, K.; Wolynes, P. G. Semiclassical Description of Electron Spin Motion in Radicals Including the Effect of Electron Hopping. J. Chem. Phys. 1978, 68, 3292−3297. 14. Hubbard, J. B.; Wolynes, P. G. Dielectric Friction and Molecular Reorientation. J. Chem. Phys. 1978, 69, 998− 1006. 15. Skinner, J. L.; Wolynes, P. G. Relaxation Processes and Chemical Kinetics. J. Chem. Phys. 1978, 69, 2143−2150. 16. McCammon, J. A.; Wolynes, P. G.; Karplus, M. Picosecond Dynamics of Tyrosine Side Chains in Proteins. Biochemistry 1979, 18, 927−942. 17. Evans, D. F.; Tominaga, T.; Hubbard, J. B.; Wolynes, P. G. Ionic Mobility: Theory Meets Experiment. J. Phys. Chem. 1979, 83, 2669−2677. 18. Skinner, J. L.; Wolynes, P. G. Derivation of Smoluchowski Equations with Corrections for Fokker−Planck and BGK Collision Models. Physica A 1979, 96, 561−572. 19. Colonomos, P.; Wolynes, P. G. Molecular Theory of Solvated Ion Dynamics II: Fluid Structure and Ionic Mobilities. J. Chem. Phys. 1979, 71, 2644−2651. © 2013 Peter G. Wolynes

Special Issue: Peter G. Wolynes Festschrift Published: October 24, 2013 12678

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53. Wolynes, P. G. Microscopic Theory of Aperiodic Crystals: Approaches for the Hard Sphere Glass Transition. J. Non-Cryst. Solids 1985, 75, 443−448. 54. Cooper, K.; Jakobsson, E.; Wolynes, P. G. The Theory of Ion Transport through Membrane Channels. Prog. Biophys. Mol. Biol. 1985, 46, 51−96. 55. Behrman, E. C.; Wolynes, P. G. Dynamics of a TwoLevel System Coupled to a Dissipative Bath: Comparisons of Analytical Theories with Monte Carlo Simulation. J. Chem. Phys. 1985, 83, 5863−5869. 56. Wolynes, P. G. Dissipation, Tunneling and Adiabaticity Criteria for Curve Crossing Problems in the Condensed Phase. J. Chem. Phys. 1987, 86, 1957−1966. 57. Hall, R. W.; Wolynes, P. G. Quantum Monte Carlo Study of a Lattice-Atom Model for Excitonic Fluids. Phys. Rev. B 1986, 33, 7879−7881. 58. Logan, D. E.; Wolynes, P. G. Anderson Localization in Topologically Disordered Systems: The Effects of Band Structure. J. Chem. Phys. 1986, 85, 937−948. 59. Hall, R. W.; Wolynes, P. G. G. N. Lewis’ Atom and Quantum Monte Carlo Studies of Liquids. J. Stat. Phys. 1986, 43, 935−948. 60. Wolynes, P. G. Adiabaticity Criteria in Biomolecular Reactions. In Proceedings in Life Sciences: Protein Structure: Molecular and Electronic Reactivity; Austin, R., Buhks, E., Chance, B., De Vault, D., Dutton, P. L., Frauenfelder, H., Gol’danskii, V. I., Eds.; Springer-Verlag: Berlin, 1987; pp 201−209. 61. Wolynes, P. G. Computational Hurdles in Chemistry-Classical Simulations, Quantum Simulations, and Beyond. In High-Speed Computing: Scientif ic Applications and Algorithm Design; Wilhelmson, R., Ed.; University of Illinois Press: Champaign, IL, 1988; pp 164−165. 62. Kirkpatrick, T. R.; Wolynes, P. G. Connections between Some Kinetic and Equilibrium Theories of the Glass Transition. Phys. Rev. A 1987, 35, 3072−3080. 63. Cline, R. E., Jr.; Wolynes, P. G. Stochastic Dynamic Models of Curve Crossing Phenomena in Condensed Phases. J. Chem. Phys. 1987, 86, 3836−3844. 64. Wolynes, P. G. Linearized Microscopic Theories of Nonequilibrium Solvation. J. Chem. Phys. 1987, 86, 5133−5136. 65. Morgan, J. D.; Wolynes, P. G. Adiabaticity of Electron Transfer at an Electrode. J. Phys. Chem. 1987, 91, 874− 883. 66. Mason, B. A.; Hess, K.; Cline, R. E., Jr.; Wolynes, P. G. A New Technique for the Calculation of Real-Time Path Integrals and Applications to Electron Transport. Superlattices and Microstructures 1987, 3, 421−428. 67. Hall, R. W.; Wolynes, P. G. The Aperiodic Crystal Picture and Free Energy Barriers in Glasses. J. Chem. Phys. 1987, 86, 2943−2948. 68. Kuki, A.; Wolynes, P. G. Electron Tunneling Paths in Proteins. Science 1987, 236, 1647−1652. 69. Bryngelson, J. D.; Wolynes, P. G. Spin Glasses and the Statistical Mechanics of Protein Folding. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 7524−7528. 70. Logan, D. E.; Wolynes, P. G. Dephasing and Anderson Localization in Topologically Disordered Systems. Phys. Rev. B 1987, 36, 4135−4147. 71. Wolynes, P. G. Imaginary Time Path Integral Monte Carlo Route to Rate Coefficients for Nonadiabatic Barrier Crossing. J. Chem. Phys. 1987, 87, 6559−6561.

July 1982; Tanaka, N., Ohtaki, H., Tamamushi, R., Eds.; Elsevier Press: Amsterdam, The Netherlands, 1983; pp 127−136. Calef, D. F.; Wolynes, P. G. Classical Solvent Dynamics and Electron Transfer I. Continuum Theory. J. Phys. Chem. 1983, 87, 3387−3400. Chandler, D.; Schweizer, K. S.; Wolynes, P. G. Electronic States of a Topologically Disordered System: Exact Solution of the Mean Spherical Model for Liquids. Phys. Rev. Lett. 1982, 49, 1100−1103. Calef, D.; Wolynes, P. G. Smoluchowski-Vlasov Theory of Charge Solvation Dynamics. J. Chem. Phys. 1983, 78, 4145−4153. Calef, D. F.; Wolynes, P. G. Classical Solvent Dynamics and Electron Transfer II. Molecular Aspects. J. Chem. Phys. 1983, 78, 470−482. Jongeward, G. A.; Wolynes, P. G. Renormalization Group Studies of Tunneling Systems in the Condensed Phase. J. Chem. Phys. 1983, 79, 3517−3528. Behrman, E. C.; Jongeward, G. A.; Wolynes, P. G. A Monte Carlo Approach for the Real Time Dynamics of Tunneling Systems in Condensed Phases. J. Chem. Phys. 1983, 79, 6277−6281. Wolynes, P. G. Chemical Physics of Molecular Systems in Condensed Phases. In Monte Carlo Methods in Quantum Problems; Kalos, M. H., Ed.; D. Reidel Publishing Company: Dordrecht, The Netherlands, 1984; pp 71−104. Logan, D. E.; Wolynes, P. G. Self-Consistent Theory of Localization in Topologically Disordered Systems. Phys. Rev. B 1984, 29, 6560−6562. Chiles, R. A.; Jongeward, G. A.; Bolton, M. A.; Wolynes, P. G. A Monte Carlo Approach to Chemical Bonding in Condensed Phases. J. Chem. Phys. 1984, 81, 2039−2046. Stoessel, J. P.; Wolynes, P. G. Linear Excitations and the Stability of the Hard Sphere Glass. J. Chem. Phys. 1984, 80, 4502−4512. Frauenfelder, H.; Wolynes, P. G. Rate Theories and Puzzles of Hemeprotein Kinetics. Science 1985, 229, 337−345. Hubbard, J. B.; Wolynes, P. G. Theories of Solvated Ion Dynamics. In The Chemical Physics of Solvation; Dogonadze, R. R., Kalman, E., Kornyshev, A. A., Ulstrup, J., Eds.; Elsevier Science Ltd.: Amsterdam, The Netherlands, 1986; pp 33−112. Logan, D. E.; Wolynes, P. G. Anderson Localization in Topologically Disordered Systems. Phys. Rev. B 1985, 31, 2437−2450. Singh, Y.; Stoessel, J. P.; Wolynes, P. G. Hard-Sphere Glass and the Density-Functional Theory of Aperiodic Crystals. Phys. Rev. Lett. 1985, 54, 1059−1062. Wahlstrand, K. J.; Wolynes, P. G. Simulation of a Relativistic Soliton Model of Crystalline Polymer Dynamics. J. Chem. Phys. 1985, 82, 5259−5263. Behrman, E. C.; Jongeward, G. A.; Wolynes, P. G. An Optimized Random Phase Approximation for the Dynamics of Tunneling Systems in Condensed Phases. J. Chem. Phys. 1985, 83, 668−673. Hall, R. W.; Wolynes, P. G. Solvent Influence on Atomic Spectra: The Effect of Finite Size. J. Chem. Phys. 1985, 83, 3214−3221. 12679




90. Bryngelson, J. D.; Wolynes, P. G. A Simple Statistical Field Theory of Heteropolymer Collapse with Application to Protein Folding. Biopolymers 1990, 30, 177−188. 91. Wolynes, P. G. Spin Glass Ideas and the Protein Folding Problems. In Spin Glasses and Biology; Stein, D., Ed.; World Scientific Press: Singapore, 1992; pp 225−259. 92. Logan, D. E.; Wolynes, P. G. Quantum Localization and Energy Flow in Many-Dimensional Fermi Resonant Systems. J. Chem. Phys. 1990, 93, 4994−5012. 93. Friedrichs, M. S.; Wolynes, P. G. Molecular Dynamics of Associative Memory Hamiltonians for Protein Tertiary Structure Recognition. Tetrahedron Comput. Methodol. 1990, 3, 175−190. 94. Fleming, G. R.; Wolynes, P. G. Chemical Dynamics in Solution. Phys. Today 1990, 43, 36−43. 95. Sasai, M.; Wolynes, P. G. Molecular Theory of Associative Memory Hamiltonian Models of Protein Folding. Phys. Rev. Lett. 1990, 65, 2740−2743. 96. Wolynes, P. G. Search and Recognition: Spin Glass Engineering as an Approach to Protein Structure Prediction. In Biologically Inspired Physics; Proceedings of a NATO Advanced Research Workshop on Biologically Inspired Physics, Cargese, France, September 3−13, 1990; Peliti, L., Ed.; Plenum Press: New York, 1991; pp 15−37. 97. Wong, C. F.; Zheng, C.; Shen, J.; McCammon, J. A.; Wolynes, P. G. Cytochrome c: A Molecular Proving Ground for Computer Simulations. J. Phys. Chem. 1993, 97, 3100−3110. 98. Tanimura, Y.; Wolynes, P. G. Quantum and Classical Fokker−Planck Equations for a Gaussian-Markovian Noise Bath. Phys. Rev. A 1991, 43, 4131−4142. 99. Friedrichs, M.: Goldstein, R.; Wolynes, P. G. Generalized Protein Tertiary Structure Recognition Using Associative Memory Hamiltonians. J. Mol. Biol. 1991, 222, 1013− 1034. 100. Zheng, C.; McCammon, J. A.; Wolynes, P. G. Quantum Simulations of Conformation Reorganization in the Electron Transfer Reactions of Tuna Cytochrome c. Chem. Phys. 1991, 158, 261−270. 101. Goldstein, R.; Wolynes, P. G. Protein Tertiary Structure Prediction Using Associative Memory Hamiltonians--A Progress Report. In AIP Conference Proceedings 239, Advances in Biomolecular Simulations International Conference, Obernai, France, 1991; Lavery, R., Rivail, J.-L., Smith, J., Eds.; American Institute of Physics: New York, 1991; pp 200−209. 102. Frauenfelder, H.; Sligar, S.; Wolynes, P. G. The Energy Landscapes and Motions of Proteins. Science 1991, 254, 1598−1603. 103. Bohr, H.; Goldstein, R.; Wolynes, P. G. Predicting Surface Structures of Proteins by Neural Networks. Modell., Meas. Control, C 1992, 31, 53−63. 104. Bohr, H. G.; Wolynes, P. G. Protein Folding: A Physical View of Neural Network Approaches. In Proceedings of Workshop on Neural Networks: From Biology to High Energy Physics; Proceedings of Workshop on Neural Networks, Elba International Physics Center, Italy, June 5−14, 1991; Benhar, O., Bosio, C., Del Giudice, P., Tabet, E., Eds.; ETS Editrice: Pisa, Italy, 1992; pp 261− 275. 105. Tanimura, Y.; Wolynes, P. G. The Interplay of Tunneling, Resonance and Dissipation in Quantum

72. Kirkpatrick, T. R.; Wolynes, P. G. Stable and Metastable States of Mean-Field Potts and Structural Glasses. Phys. Rev. B 1987, 35, 8552−8564. 73. Logan, D. E.; Wolynes, P. G. Localizability and Dephasing of Dipolar Excitons in Topologically Disordered Systems. J. Chem. Phys. 1987, 87, 7199−7207. 74. Morgan, J. D.; Wolynes, P. G. The Supersymmetric Diffusional Influence Functional: General Theory. J. Chem. Phys. 1988, 88, 7781−7790. 75. Cline, R. E., Jr.; Wolynes, P. G. Monte Carlo Methods for Real-Time Quantum Dynamics of Dissipative Systems. J. Chem. Phys. 1988, 88, 4334−4350. 76. Zheng, C.; Wong, C.; McCammon, J. A.; Wolynes, P. G. Quantum Simulation of Ferrocytochrome c. Nature 1988, 334, 726−728. 77. Mertz, J. E.; Wolynes, P. G. Self-Consistent Phonon Theories of One- and Two-Component Quasicrystals. Unpublished work, 1988. 78. Wolynes, P. G. Aperiodic Crystals: Biology, Chemistry and Physics in a Fugue with Stretto. In Proceedings of the International Symposium on Frontiers in Science; AIP Conference Proceedings Number 180; Chan, S., DeBrunner, P. G., Eds.; Am. Inst. Physics: College Park, MD, 1989; pp 39−65. 79. Onuchic, J. N.; Wolynes, P. G. Classical and Quantum Pictures of Reaction Dynamics in Condensed Matter: Resonances, Dephasing and All That. J. Phys. Chem. 1988, 92, 6495−6503. 80. Wolynes, P. G. Dynamics of Proteins and Nucleic Acids. Phys. Today 1988, 41, 105−106. 81. Ohmine, I.; Tanaka, H.; Wolynes, P. G. Large Local Energy Fluctuations in Water: (II) Cooperative Motions and Fluctuations. J. Chem. Phys. 1988, 89, 5852−5860. 82. Wolynes, P. G. Chemical Reaction Dynamics in Complex Molecular Systems. In Complex Systems, SFI Studies in the Sciences of Complexity; Stein, D., Ed.; Addison-Wesley Longman Publishing: New York, 1989; pp 355−387. 83. Zheng, C.; Wong, C. F.; McCammon, J. A.; Wolynes, P. G. Classical and Quantum Aspects of Ferrocytochrome c. Chem. Scr. 1989, 29A, 171−179. 84. Zheng, C.; McCammon, J. A.; Wolynes, P. G. Quantum Simulation of Nuclear Rearrangement in Electron Transfer Reactions. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 6441−6444. 85. Bryngelson, J. D.; Wolynes, P. G. Intermediates and Barrier Crossing in a Random Energy Model (with Applications to Protein Folding). J. Phys. Chem. 1989, 93, 6902−6915. 86. Friedrichs, M. S.; Wolynes, P. G. Genetic Algorithms for Model Biomolecular Optimization Problems. Unpublished work, 1989. 87. Kirkpatrick, T. R., Thirumalai, D.; Wolynes, P. G. Scaling Concepts for the Dynamics of Viscous Liquids near an Ideal Glassy State. Phys. Rev. A 1989, 40, 1045−1054. 88. Friedrichs, M. S.; Wolynes, P. G. Toward Protein Tertiary Structure Recognition by Means of Associative Memory Hamiltonians. Science 1989, 246, 371−373. 89. Evensky, D. A.; Scalletar, R. T.; Wolynes, P. G. Localization and Dephasing Effects in a Time Dependent Anderson Hamiltonian. J. Phys. Chem. 1990, 94, 1149− 1154. 12680



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124. Schofield, S. A.; Wolynes, P. G. Quantum Dynamics and Microcanonical Rate Theory. J. Chem. Phys. 1994, 100, 350−356. 125. Goldstein, R. A.; Luthey-Schulten, Z.; Wolynes, P. G. Protein Tertiary Structure Recognition Using Optimized Associative Memory Hamiltonians. In Proceedings of the 26th Hawaii International Conference on System Sciences; Manoa, HI, 1993; Mudge, T. N., Milutinovic V., Hunter, L., Eds.; IEEE Computer Society Press: Los Alamitos, CA, 1993; pp 699−707. 126. Goldstein, R. A.; Luthey-Schulten, Z.; Wolynes, P. G. A Bayesian Approach to Sequence Alignment Algorithms for Protein Structure Recognition. In Proceedings of the 27th Hawaii International Conference on System Sciences; Manoa, HI, 1994; Hunter, L., Ed.; IEEE Computer Society Press: Los Alamitos, CA, 1994; pp 306−315. 127. Frauenfelder, H.; Wolynes, P. G. Biomolecules: Where the Physics of Complexity and Simplicity Meet. Phys. Today 1994, 47, 58−64. 128. Schofield, S. A.; Wolynes, P. G. Rate Theory and NonRRKM Quantum Dynamics Described by Local Random Matrix Models. Chem. Phys. Lett. 1994, 217, 497−502. 129. Schofield, S. A.; Gentile, A. C.; Wolynes, P. G. The Statistics of Reaction Rates in Quantum Chaotic Systems Described by Local Random Matrix Models. In Fluctuations and Order: The New Synthesis; Millonas, M. M., Ed.; Springer-Verlag: New York, 1996. 130. Caliri, A.; Bohr, H.; Wolynes, P. G. Two-Dimensional Chain Folding-Random Energy Interaction. Phys. Lett. A 1993, 183, 327−331. 131. Gulukota, K.; Wolynes, P. G. Statistical Mechanics of Kinetic Proof-Reading in Protein Folding In Vivo. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 9292−9296. 132. Schofield, S. A.; Wolynes, P. G. Rate Theory and Quantum Energy Flow in Molecules: Modeling the Effects of Anisotropic Diffusion and of Dephasing. J. Phys. Chem. 1995, 99, 2753−2763. 133. Bohr, H.; Wang, J.; Wolynes, P. G. Growth of Domains in Distance Geometry through Protein Folding. In Protein Structure by Distance Analysis; Bohr, H., Brunak, S., Eds.; IOS Press: Amsterdam, The Netherlands, 1994; pp 98−109. 135. Bryngelson, J.; Onuchic, J., Socci, N.; Wolynes, P. G. Funnels, Pathways, and the Energy Landscape of Protein Folding: A Synthesis. Proteins: Struct., Funct., Genet. 1995, 21, 167−195. 136. Luthey-Schulten, Z.; Ramirez, B. E.; Wolynes, P. G. Helix−Coil, Liquid Crystal and Spin Glass Transitions of a Collapsed Heteropolymer. J. Phys. Chem. 1995, 99, 2177−2185. 137. Saven, J. G.; Wang, J.; Wolynes, P. G. Kinetics of Protein Folding: The Dynamics of Globally Connected Rough Energy Landscapes with Biases. J. Chem. Phys. 1994, 101, 11037−11043. 138. Panchenko, A. R.; Wang, J.; Nienhaus G. U.; Wolynes, P. G. Analysis of Ligand Binding to Heme Proteins Using a Fluctuating Path Description. J. Phys. Chem. 1995, 99, 9278−9282. 139. Wang, J.; Wolynes, P. G. Intermittency of Single Molecule Reaction Dynamics in Fluctuating Environments. Phys. Rev. Lett. 1995, 74, 4317−4320. 140. Schofield, S. A.; Wolynes, P. G.; Wyatt, R. E. Computational Study of Many-Dimensional Quantum Energy

Barrier Crossing: A Numerical Study. J. Chem. Phys. 1992, 96, 8485−8496. Goldstein, R.; Luthey-Schulten, Z.; Wolynes, P. G. Optimal Protein-Folding Codes from Spin-Glass Theory. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4918−4922. Wolynes, P. G. Randomness and Complexity in Chemical Physics. Acc. Chem. Res. 1992, 25, 513−519. Wolynes, P. G. Book Review: Advances in Chemical Physics, Volume LXXVII; Prigogine, I., Rice, S. A., Eds.; John Wiley & Sons: New York, 1990. Wolynes, P. G. Will Computer Design Become a Matter of Evolution? Comput. Phys. 1992, 6, 296. Schofield, S.; Wolynes, P. G. A Scaling Perspective on Quantum Energy Flow in Molecules. J. Chem. Phys. 1993, 98, 1123−1131. Onuchic, J.; Wolynes, P. G. Energy Landscapes, Glass Transitions and Chemical Reaction Dynamics in Biomolecular or Solvent Environments. J. Chem. Phys. 1993, 98, 2218−2224. Schofield, S. A.; Wolynes, P. G.; Gentile, A. C. NonRRKM Dynamics and the Statistics of Reaction Rates in Chaotic Systems. J. Chem. Phys. 1993, 98, 7898−7902. Wade, R. C.; Bohr, H.; Wolynes, P. G. Prediction of Water Binding Sites on Proteins by Neural Networks. J. Am. Chem. Soc. 1992, 114, 8284−8285. Sasai, M.; Wolynes, P. G. Unified Theory of Collapse, Folding and Glass Transitions in Associative-Memory Hamiltonian Models of Proteins. Phys. Rev. A 1992, 46, 7979−7997. Goldstein, R. A.; Luthey-Schulten, Z. A.; Wolynes, P. G. Protein Tertiary Structure Recognition Using Optimized Hamiltonians with Local Interactions. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 9029−9033. Bohr, H.; Wolynes, P. G. Initial Events of Protein Folding from an Information-Processing Viewpoint. Phys. Rev. A 1992, 46, 5242−5248. Weissman, M. B.; Wolynes, P. G. Hopfield Models and Spin-Density Waves in Metallic Spin Glasses. Phys. Rev. B 1992, 46, 14209−14212. Irwin, J.; Bohr, H.; Mochizuki, K.; Wolynes, P. G. Classification and Prediction of Protein Side Chains by Neural Network Techniques. J. Neural Syst. 1993, 3, 177. Evensky, D. A.; Wolynes, P. G. Transport of Dipolar Excitons in Disordered Systems. Chem. Phys. Lett. 1993, 209, 185−189. Wang, J.; Wolynes, P. G. Passage Through Fluctuating Geometrical Bottlenecks: The General Gaussian Fluctuating Case. Chem. Phys. Lett. 1993, 212, 427−433. Goldstein, R. A.; Luthey-Schulten, Z.; Wolynes, P. G. The Statistical Mechanical Basis of Sequence Alignment Algorithms for Protein Structure Recognition. In New Developments in Theoretical Studies of Proteins, Advanced Series in Physical Chemistry; Elber, R., Ed.; World Scientific: Singapore, 1996; Vol. 7, pp 359−388. Wang, J.; Wolynes, P. G. Survival Paths for Reaction Dynamics in Fluctuating Environments. Chem. Phys. 1994, 180, 141−156. Goldstein, R. A.; Katzenellenbogen, J. A.; LutheySchulten, Z. A.; Seielstad, D. A.; Wolynes, P. G. ThreeDimensional Model for the Hormone Binding Domains of Steroid Receptors. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 9949−9953. 12681



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243. Sasai, M.; Wolynes, P. G. Stochastic Gene Expression as a Many Body Problem. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 2374−2379. 244. Eastwood, M. P.; Hardin, C.; Luthey-Schulten, Z.; Wolynes, P. G. Statistical Mechanical Refinement of Protein Structure Prediction Schemes II: Mayer Cluster Expansion Approach. J. Chem. Phys. 2003, 118, 8500− 8512. 245. Papoian, G. A.; Ulander, J.; Wolynes, P. G. The Role of Water Mediated Interactions in Protein−Protein Recognition Landscapes. J. Am. Chem. Soc. 2003, 125, 9170− 9178. 246. Plotkin, S. S.; Wolynes, P. G. Buffed Energy Landscapes: Another Solution to the Kinetic Paradoxes of Protein Folding. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 4417− 4422. 248. Hardin, C.; Eastwood, M. P.; Prentiss, M. C.; LutheySchulten, Z.; Wolynes, P. G. Associative Memory Hamiltonians for Protein Structure Prediction without Homology: Alpha/Beta Proteins. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1679−1684. 249. Miyashita, O. M.; Onuchic, J. N.; Wolynes, P. G. Nonlinear Elasticity, Protein Quakes and the Energy Landscapes of Functional Transitions in Proteins. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 1679−1684. 250. Leitner, D. M.; Levine, B.; Quenneville, J.; Martinez, T. J.; Wolynes, P. G. Quantum Energy Flow and transStilbene Photoisomerization: An Example of a nonRRKM Reaction. J. Phys. Chem. 2004, 105, 10706− 10716. 251. Gruebele, M.; Wolynes, P. G. Vibrational Energy Flow and Chemical Reactions. Acc. Chem. Res. 2004, 37, 261− 267. 252. Levy, Y.; Onuchic, J. N.; Wolynes, P. G. Protein Topology Determines Binding Mechanism. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 13786−13791. 253. Levy, Y.; Papoian, G. A.; Onuchic, J. N.; Wolynes, P. G. Energy Landscape Analysis of Protein Dimers. Isr. J. Chem. 2004, 44, 281−297. 254. Lubchenko, V.; Wolynes, P. G. Barrier Softening near the Onset of Nonactivated Transport in Supercooled Liquids: Implications for Establishing Detailed Connection between Thermodynamic and Kinetic Anomalies in Supercooled Liquids. J. Chem. Phys. 2004, 119, 9088− 9105. 255. Onuchic, J. N.; Wolynes, P. G. Theory of Protein Folding. Curr. Opin. Struct. Biol. 2004, 14, 70−75. 256. Papoian, G. A.; Ulander, J.; Eastwood, M. P.; LutheySchulten, Z.; Wolynes, P. G. Water in Protein Structure Prediction. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3352− 3357. 257. Lubchenko, V.; Wolynes, P. G. Theory of Aging in Structural Glasses. J. Chem. Phys. 2004, 121, 2852−2865. 258. Levy, Y.; Caflisch, A.; Onuchic, J. N.; Wolynes, P. G. The Folding and Dimerization of HIV-1 Protease: Evidence for a Stable Monomer from Simulations. J. Mol. Biol. 2004, 340, 67−79. 259. Lubchenko, V.; Silbey R. J.; Wolynes, P. G. Electrodynamics of Amorphous Media at Low Temperatures. Mol. Phys. 2006, 104, 1325−1335. 260. Shen, T.; Wolynes, P. G. Stability and Dynamics of Motorized Crystals and Glasses. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 8547−8550.

261. Wolynes, P. G. Latest Folding Game Results: Protein A, 10, Computationalists 7. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 6837−6838. 262. Wu, S.; Schmalian, J.; Kotliar, G.; Wolynes, P. G. Solution of Local Field Equations for Self-Generated Glasses. Phys. Rev. B 2004, 70, 024207. 263. Yang, S. C.; Cho, S. S.; Levy, Y.; Cheung, M. S.; Levine, H.; Wolynes, P. G.; Onuchic, J. N. Domain Swapping Is a Consequence of Minimal Frustration. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 13786−13791. 264. Miyashita, O.; Wolynes, P. G.; Onuchic, J. N. Simple Energy Landscape Model for the Kinetics of Functional Transitions in Proteins. J. Phys. Chem. B 2005, 109, 1959−1969. 265. Wolynes, P. G. Energy Landscapes and Solved Protein Folding Problems. Philos. Trans. R. Soc., A 2005, 363, 453−467. Comments in other discussions, pp 431; 490. 266. Lubchenko, V.; Wolynes, P. G.; Frauenfelder, H. The Mosaic Energy Landscapes of Liquids and the Control of Protein Conformational Dynamics by Glass Forming Solvents. J. Phys. Chem. B 2005, 109, 7488−7499. 267. Walczak, A. M.; Sasai, M.; Wolynes, P. G. Self-Consistent Proteomic Field Theory of Stochastic Gene Switches. Biophys. J. 2005, 88, 828−850. 268. Shen, T.; Zong, C.; Hamelberg, D.; McCammon, J. A.; Wolynes, P. G. The Folding Energy Landscape and Phosphorylation: Modeling the Conformational Switch of the NFAT Regulatory Domain. FASEB J. 2005, 19, 1389−1395. 269. Ferreiro, D. U.; Cho, S. S.; Komives, E.; Wolynes, P. G. The Energy Landscape of Modular Repeat Proteins: Topology Determines the Folding Mechanism in the Ankyrin Family. J. Mol. Biol. 2005, 354, 679−692. 270. Hornos, J. E. M.; Schultz, D.; Innocentini, G. C. P.; Walczak, A. M.; Wang, J.; Onuchic, J. N.; Wolynes, P. G. The Self-Regulating Gene: An Exact Solution. Phys. Rev. E 2005, 72, 051907-1/5. 271. Levy, Y.; Cho, S. S.; Shen, T.; Onuchic, J. N.; Wolynes, P. G. Symmetry and Frustration in Protein Energy Landscapes: A Near-Degeneracy Resolves the ROP Dimer Folding Mystery. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2373−2378. 272. Shen, T.; Hoffman, C. P.; Oliveberg. M.; Wolynes, P. G. Scanning Malleable Transition State Ensembles: Coupling Theory and Experiment for Folding Protein U1A. Biochemistry 2005, 44, 6433−6439. 273. Schmalian, J.; Wolynes, P. G. Electronic Mayonnaise: Uniting the Sciences of Hard and Soft Matter. Mater. Res. Soc. Bull. 2005, 30, 433−436. 274. Bhattacharya, S. M.; Bagchi, B.; Wolynes, P. G. Bridging the Gap between the Mode Coupling and the Random First Order Transition Theories of Structural Relaxation in Liquids. Phys. Rev. E 2005, 72, 031509-1/12. 275. Stevenson, J.; Wolynes, P. G. Thermodynamic-Kinetic Correlations in Supercooled Liquids: A Critical Survey of Experimental Data and Predictions of the Random First Order Transition Theory of Glasses. J. Phys. Chem. B 2005, 109, 15093−15097. 276. Levy, Y.; Cho, S.; Onuchic, J. N.; Wolynes, P. G. A Survey of Flexible Binding Mechanisms and Their Transition States Using Native Topology Based Energy Landscapes. J. Mol. Biol. 2005, 346, 1121−1145. 12685




277. Dzero, M.; Schmalian, J.; Wolynes, P. G. Activated Events in Glasses: the Structure of Entropic Droplets. Phys. Rev. B 2005, 72, 100201−100204. 278. Cho, S. S.; Levy, Y.; Onuchic, J. N.; Wolynes, P. G. Overcoming Residual Frustration in Domain Swapping: The Roles of Disulfide Bonds in Dimerization and Aggregation. Phys. Biol. 2005, 1, 544−555. 279. Lubchenko, V.; Wolynes, P. G. The Microscopic Quantum Theory of Low Temperature Amorphous Solids. Adv. Chem. Phys. 2007, 136, 95−206. 280. Zong, C.; Lu, T.; Shen, T.; Wolynes, P. G. Nonequilibrium Self-Assembly of Linear Fibers: Microscopic Treatment of Growth, Decay, Catastrophe and Rescue. Phys. Biol. 2006, 3, 83−92. 281. Lätzer, J.; Papoian, G.; Prentiss, M.; Komives, E.; Wolynes, P. G. Induced Fit, Folding, and Recognition of the NF-κB-Nuclear Localization Signals by IκBα and IκBβ. J. Mol. Biol. 2007, 367, 262−274. 282. Shen, T.; Wolynes, P. G. Nonequilibrium Statistical Mechanical Models for Cytoskeletal Assembly: Toward Understanding Tensegrity in Cells. Phys. Rev. E 2005, 72, 041927-1/11. 283. Weinkam, P.; Zong, C.; Wolynes, P. G. A Funneled Energy Landscape for Cytochrome c Directly Predicts the Sequential Folding Route Inferred from Hydrogen Exchange Experiments. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 12401−12406. 284. Stevenson, J. D.; Schmalian, J.; Wolynes, P. G. The Shapes of Cooperatively Rearranging Regions in Glass Forming Liquids. Nat. Phys. 2006, 21, 268−274. 285. Oliveberg. M.; Wolynes, P. G. The Experimental Survey of Protein Folding Energy Landscapes. Q. Rev. Biophys. 2005, 38, 245−288. 286. Wolynes, P. G. Recent Successes of the Energy Landscape Theory of Protein Folding and Function. Q. Rev. Biophys. 2005, 38, 405−410. 287. Walczak, A. M.; Onuchic, J. N.; Wolynes, P. G. Absolute Rate Theories of Epigenetic Stability. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 18926−18931. 288. Cho, S.; Levy, Y.; Wolynes, P. G. P vs Q: Structural Reaction Coordinates Capture Protein Folding on Smooth Landscapes. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 586−591. 289. Prentiss, M. C.; Hardin, C.; Eastwood, M. P.; Zong, C.; Wolynes, P. G. Protein Structure Prediction: The Next Generation. J. Chem. Theory Comput. 2006, 2, 705−716. 290. Zong, C.; Wilson, C. J.; Shen, T.; Wolynes, P. G.; Wittung-Stafshede, P. ϕ-Value Analysis of Apo-Azurin Folding: Comparison between Experiment and Theory. Biochemistry 2006, 45, 6458−6466. 291. Lu, T.; Hasty, J; Wolynes, P. G. Effective Temperature in Stochastic Kinetics and Gene Networks. Biophys. J. 2006, 91, 1−11. 292. Wolynes, P. G. Counterfactual Biochemistry: Protein Folding and Molecular Recognition in Water and Other Fluid Environments. In Water and Life: The Unique Properties of H20; Lynden-Bell, R. M., Morris, S. C., Barrow, J. D., Finney, J. L., Harper, C. L., Eds.; CRC Press/Taylor & Francis Group: Boca Raton, FL, 2010; pp 13−218. 293. Wolynes, P. G. The Protein Folding Energy Landscape: A Primer. In Protein Folding, Misfolding and Aggregation;

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Muñoz, V., Ed.; Royal Society of Chemistry: Cambridge, U.K., 2008; pp 49−69. Zong, C.; Papoian, G. A.; Ulander, J.; Wolynes, P. G. The Role of Topology, Nonadditivity and Water Mediated Interactions in Predicting the Structures of α/β Proteins. J. Am. Chem. Soc. 2006, 128, 5168−5176. Leitner, D. M.; Wolynes, P. G. Quantum Theory of Enhanced Unimolecular Reaction Rates below the Ergodicity Threshold. Chem. Phys. 2006, 329, 163−167. Okazaki, K.; Koga, N.; Takada, S.; Onuchic, J. N.; Wolynes, P. G. Multiple-Basin Energy Landscapes for Large Amplitude Conformational Motions of Proteins: Structure-Based Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 11944−11849. Lubchenko, V.; Wolynes, P. G. Theory of Structural Glasses and Supercooled Liquids. Annu. Rev. Phys. Chem. 2007, 58, 235−266. Shen, T.; Wolynes, P. G. Statistical Mechanics of a Cat’s Cradle. New J. Phys. 2006, 8, 73-1/8. Lan, Y.; Wolynes, P. G.; Papoian, G. A. A Variational Approach to the Stochastic Aspects of Cellular Signal Transduction. J. Chem. Phys. 2006, 125, 124106-1/11. Levy, Y.; Onuchic, J. N.; Wolynes, P. G. Fly-Casting in Protein−DNA Binding: Frustration between Protein Folding and Electrostatics Facilitates Target Recognition. J. Am. Chem. Soc. 2007, 3, 738−739. Lu, T.; Shen, T.; Zong, C.; Hasty, J.; Wolynes, P. G. The Statistics of Cellular Signal Transduction as a Race to the Nucleus by Multiple Random Walkers in Compartment/ Phosphorylation Space. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 16752−16757. Lätzer, J.; Eastwood, M.; Wolynes, P. G. Simulation Studies of the Fidelity of Biomolecular Structure Ensemble Recreation. J. Chem. Phys. 2006, 125, 214905-1/12. Wolynes, P. G. Lectures on Biomolecular Energy Landscapes. Proceedings of the International School of Physics ‘Enrico Fermi’ Course CLXV, ‘Protein Folding and Drug Design’, Varenna, Italy, July 4−14, 2006; Broglia, R. A., Serrano, L., Tiana, G., Eds.; IOS Press: Amsterdam, The Netherlands, 2007; pp 27−46. Fereirro, D. U.; Cervantes, C. F.; Truhlar, S. M. E.; Cho, S. S.; Wolynes, P. G.; Komives, E. A. Stabilizing IκBα by Consensus Design. J. Mol. Biol. 2007, 365, 1201−1216. Bhattracharyya, S. M.; Bagchi, B.; Wolynes, P. G. Dynamical Heterogeneity and the Interplay between Activated and Mode Coupling Dynamics in Supercooled Liquids. 2007, http://arxiv.org/abs/cond-mat/ 0702435v1. arXiv.org e-Print archive. Kwac, K.; Wolynes, P. G. Protein Structure Prediction Using an Associated Memory Hamiltonian and All-Atom Molecular Dynamics Simulations. Bull. Korean Chem. Soc. 2008, 29, 2172−2182. Zong, C.; Wilson, C. J.; Shen, T.; Wittung-Staffshede, P.; Mayo, S.; Wolynes, P. G. Establishing the Entatic State in Folding Metalated Pseudomonas aeruginosa Azurin. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 3159−3164. Stevenson, J. D.; Wolynes, P. G. Comparison of Some Recent Excitation Chain Arguments with the Random First Order Transition Theory of Supercooled Liquids and Experiment. 2006, http://arxiv.org/abs/cond-mat/ 0609677. arXiv.org e-Print archive. dx.doi.org/10.1021/jp407074y | J. Phys. Chem. B 2013, 117, 12678−12688



309. Schultz, D.; Onuchic, J. N.; Wolynes, P. G. Understanding Stochastic Simulations of the Smallest Genetic Networks. J. Chem. Phys. 2007, 126, 245102-1/11. 310. Gruebele, M.; Wolynes, P. G. Quantizing Ulam’s Control Conjecture. Phys. Rev. Lett. 2007, 99, 060201-1/4. 311. Hall, R. W.; Wolynes, P. G. Intermolecular Forces and the Glass Transition. J. Phys. Chem. B 2008, 112, 301− 312. 312. Schultz, D.; Ben Jacob, E.; Onuchic, J. N.; Wolynes, P. G. Molecular Level Stochastic Model for Competence Cycles in Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 17582−17587. 313. Lu, T.; Shen, T.; Bennett, M.; Wolynes, P. G.; Hasty, J. Phenotypic Variability of Growing Cellular Populations. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 18982−18987. 314. Ferreiro, D.; Hegler, J.; Komives, E.; Wolynes, P. G. Localizing Frustration in Native Proteins and Protein Assemblies. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 19819−19824. 315. Sutto, L.; Lätzer, J.; Hegler, J.; Ferreiro, D.; Wolynes, P. G. Consequences of Localized Frustration for the Folding Mechanism of the IM7 Protein. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 19825−19830. 316. Cho, S. S.; Weinkam, P.; Wolynes, P. G. Origins of Barriers and Barrierless Folding in BBL. Proc. Natl. Acad. Sci. U.S.A. 2008, 104, 112−123. 317. Lätzer, J., Shen, T.; Wolynes, P. G. Conformational Switching upon Phosphorylation: A Predictive Framework Based on Energy Landscape Principles. Biochemistry 2008, 47, 2110−2122. 318. Wolynes, P. G. Protein Folding and Beyond: Energy Landscapes and the Organization of Living Matter in Space and Time. In Physical Biology f rom Atoms to Medicine; Zewail, A. H., Ed.; World Scientific: Singapore, 2008; pp 267−288. 319. Shen, T.; Zong, C.; Portman, J.; Wolynes, P. G. Variationally Determined Free Energy Profiles for Structural Models of Proteins: Characteristic Temperatures for Folding and Trapping. J. Phys. Chem. B 2008, 112, 6074−6082. 320. Ferreiro, D. U.; Walczak, A. M.; Komives, E. A.; Wolynes, P. G. The Energy Landscapes of RepeatContaining Proteins: Topology, Cooperativity and the Folding Funnels of One-Dimensional Architectures. PLoS Comput. Biol. 2008, 4, e1000070. 321. Whitford, P. G.; Onuchic, J. N.; Wolynes, P. G. The Energy Landscape along an Enzymatic Reaction Trajectory: Hinges or Cracks? HFSP J. 2008, 2, 61−64. 322. Itzhaki, L. S.; Wolynes, P. G. The Quest to Understand Protein Folding. Curr. Opin. Struct. Biol. 2008, 18, 1−3. 323. Prentiss, M. C.; Wales, D. J.; Wolynes, P. G. Protein Structure Prediction Using Basin Hopping. J. Chem. Phys. 2008, 128, 225106-1/9. 324. Ferreiro, D. U.; Wolynes, P. G. The Capillarity Picture and the Kinetics of One-Dimensional Protein Folding. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9853−9854. 325. Wolynes, P. G. Gene Regulation: Single Molecule Chemical Physics in a Natural Context. In Single Molecule Spectroscopy in Chemistry, Physics and Biology, Springer Series in Chemistry Vol 96; Proceedings of Nobel Symposium Single Molecular Spectroscopy in Chemistry, Physics and Biology, Sånga-Säby Kurs & Konferens,

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Sweden, June 2008; Gräslund, A., Rigler, R., Widengren, J., Eds.; Springer Verlag: Berlin, 2010; pp 553−560. Stevenson, J. D.; Walczak, A. M.; Hall, R. W.; Wolynes, P. G. Constructing Explicit Magnetic Analogies for the Dynamics of Glass Forming Liquids. J. Chem. Phys. 2008, 129, 194505-1/6. Stevenson, J. D.; Wolynes, P. G. On the Surface of Glasses. J. Chem. Phys. 2008, 129, 234514-1/4. Bhattacharyya, S.; Bagchi, B.; Wolynes, P. G. Facilitation, Complexity Growth, Mode Coupling and Activated Dynamics in Supercooled Liquids. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 16067−16082. Hegler, J. A.; Weinkam, P.; Wolynes, P. G. The Spectrum of Biomolecular States and Motions. HFSP J. 2008, 2, 307−313. Wang, W.; Xu, W. X.; Levy, Y.; Trizac, E.; Wolynes, P. G. Confinement Effects on the Kinetics and Thermodynamics of Protein Dimerization. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 5517−5522. Cho, S. S.; Levy, Y.; Wolynes, P. G. Quantitative Criteria for Native Energetic Heterogeneity Influences in the Prediction of Protein Folding Kinetics Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 434−439. Schultz, D.; Walczak, A.M.; Onuchic, J. N.; Wolynes, P. G. Extinction and Resurrection in Gene Networks. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 19165−19170. Walczak, A. M.; Wolynes, P. G. Gene−Gene Cooperativity in Small Networks. Biophys. J. 2009, 96, 4525− 4541. Wolynes, P. G. Spatiotemporal Structures in Aging and Rejuvenating Glasses. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 1353−1358. Dzero, M.; Schmalian, J.; Wolynes, P. G. Replica Theory for Fluctuations of the Activation Barriers in Glassy Systems. Phys. Rev. B 2009, 80, 024204-1/15. Lenz, P.; Cho, S. S.; Wolynes, P. G. Analysis of Single Molecule Folding Studies with Replica Correlation Functions. Chem. Phys. Lett. 2009, 471, 310−314. Weinkam, P.; Pletneva, E. V.; Gray, H. B.; Winkler, J. R.; Wolynes, P. G. Electrostatic Effects on Funneled Landscapes and Structural Diversity in Denatured Protein Ensembles. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 1797−1801. Weinkam, P.; Romesberg, F. E.; Wolynes, P. G. Chemical Frustration in the Protein Folding Landscape: Grand Canonial Ensemble Simulations of Cytochrome c. Biochemistry 2009, 48, 2394−2404. Weinkam, P.; Zimmerman, J.; Sagle, L. B.; Matsuda, S.; Dawson, P. E.; Wolynes, P. G.; Romesberg, F. E. Characterization of Alkaline Transitions in Ferricytochrome c Using Carbon-Deuterium Infrared Probes. Biochemistry 2009, 47, 13470−13480. Stevenson, J. D.; Wolynes, P. G. A Universal Origin for Secondary Relaxations in Supercooled Liquids and Structural Glasses. Nat. Phys. 2010, 6, 62−68. Hegler, J. A.; Laetzer, J.; Shehu, A.; Clementi, C; Wolynes, P. G. Restriction versus Guidance in Protein Structure Prediction. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 15302−15307. Wolynes, P. G. Some Quantum Weirdness in Physiology. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 17247−17248. Weinkam, P.; Wolynes, P. G. The Folding Landscapes of Metalloproteins. In Protein Folding and Metal Ions-dx.doi.org/10.1021/jp407074y | J. Phys. Chem. B 2013, 117, 12678−12688


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Mechanisms, Biology and Disease, Gomes, C. M., WittungStafshede, P., Eds.; Taylor & Francis: Boca Raton, FL, 2010; pp 247−273. Weinkam, P.; Zimmerman, J.; Romesberg, F. E.; Wolynes, P. G. The Folding Energy Landscape and Free Energy Excitations of Cytochrome c. Acc. Chem. Res. 2010, 3, 652−660. Schultz, D.; Wolynes, P. G.; Ben-Jacob, E.; Onuchic, J. N. Deciding Fate in Adverse Times: Sporulation and Competence in Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 21027−21034. Bhattacharyya, S.; Bagchi B.; Wolynes, P. G. SubQuadratic Wave Number Dependence of the Structural Relaxation of Supercooled Liquids in the Crossover Regime. J. Chem. Phys. 2010, 132, 104503-1/6. Trizac, E.; Levy, Y.; Wolynes, P. G. Capillarity Theory for the Fly-Casting Mechanism. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 2746−2750. Burger, A.; Walczak, A.; Wolynes, P. G. Abduction and Asylum in the Lives of Transcription Factors. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 4016−4021. Prentiss, M. C.; Wales, D. J.; Wolynes, P. G. The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein. PLoS Comput. Biol. 2010, 6, e1000835. Oklejas, V.; Zong, C.; Papoian, G. A.; Wolynes, P. G. Protein Structure Prediction: Do Hydrogen Bonding and Water-Mediated Interactions Suffice? Methods 2010, 52, 84−90. Stevenson, J. D.; Wolynes, P. G. The Ultimate Fate of Supercooled Liquids. J. Phys. Chem. A 2011, 115, 3713− 3719. Kurchan, J.; Langer, J. S.; Witten, T. A.; Wolynes, P. G. Scientific Interview. In Dynamical Heterogeneities in Glasses, Colloids, and Granular Media; Berthier, L., Biroli, G., Bouchaud, J.-P., Cipelletti, L.; van Saarloos, W., Eds.; Oxford University Press: New York, 2011; pp 1−38. Wang, S.; Shen, T.; Wolynes, P. G. The Interplay of Nonlinearity and Architecture in Equilibrium Cytoskeletal Mechanics. J. Chem. Phys. 2011, 134, 014510-1/16. Ferreiro, D. U.; Hegler, J. A.; Komives, E. A.; Wolynes, P. G. On the Role of Frustration in the Energy Landscapes of Allosteric Proteins. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 3499−3505. Li, W.; Wolynes, P. G.; Takada, S.; Frustration, Specific Sequence Dependence and Nonlinearity in LargeAmplitude Fluctuations of Allosteric Proteins. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 3504−3509. Wolynes, P. G. Theories of Structural Glass Dynamics: Mosaics, Jamming, and All That. In Structural Glasses and Supercooled Liquids; Lubchenko, V., Wolynes, P. G., Eds.; John Wiley & Sons: New York, 2012; pp 341−379. Dzero, M.; Schmalian, J.; Wolynes, P. G. Glassiness in Uniformly Frustrated Systems. In Structural Glasses and Supercooled Liquids; Lubchenko, V., Wolynes, P. G., Eds.; John Wiley & Sons: New York, 2012; pp 193−221. Craig, P. O.; Lätzer, J.; Weinkam, P.; Hoffman, R. M. B.; Ferreiro, D. U.; Komives, E. A.; Wolynes, P. G. Prediction of Native State Hydrogen Exchange from Perfectly Funneled Energy Landscapes. J. Am. Chem. Soc. 2011, 133, 17463−17472. Wang, S.; Wolynes, P. G. Effective Temperature and Glassy Dynamics of Active Matter. J. Chem. Phys. 2011, 135, 051101-1/4.

360. Wang, S.; Wolynes, P. G. On the Spontaneous Collective Motion of Active Matter. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 15184−15189. 361. Lammert, H.; Wolynes, P. G.; Onuchic, J. N. The Role of Atomic Level Steric Effects and Attractive Forces in Protein Folding. Proteins 2012, 80, 362−373. 362. Davtyan, A.; Schafer, N.; Zheng, W.; Clementi, C;. Wolynes, P. G.; Papoian, G. A. AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing. J. Phys. Chem 2012, 116, 8494−8503. 363. Wang, S.; Wolynes, P. G. Active Contractility in Actomyosin Networks. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 6446−6451. 364. Wang, S.; Wolynes, P. G. Tensegrity and Motor-Driven Effective Interactions in a Model Cytoskeleton. J. Chem. Phys. 2012, 136, 145102-1/18. 365. Wisitsorasak, A.; Wolynes, P. G. On the Strength of Glasses. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 16068− 16072. 366. Jenik, M.; Gonzalo Parra, R.; Radusky, L. G.; Turjanski, A.; Wolynes, P. G.; Ferreiro, D. U. Protein Frustratometer: A Tool to Localize Energetic Frustration in Protein Molecules. Nucleic Acids Res. 2012, 40, 348−351. 367. Wolynes, P. G.; Eaton, W. A.; Fersht, A. Chemical Physics of Protein Folding. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17770−17771. 368. Burger, A.; Walczak, A.; Wolynes, P. G. Influence of Decoys on the Noise and Dynamics of Gene Expression Phys. Rev. E 2012, 86, 041920-1/7. 369. Zheng, W.; Schafer, N.; Davtyan, A.; Papoian, G. A.; Wolynes, P. G. Predictive Energy Landscapes for Protein−Protein Association. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 19244−19247. 370. Schafer, N. P.; Hoffman, R. M. B.; Burger, A.; Craig, P. O.; Komives, E. A.; Wolynes, P. G. Discrete Kinetic Models from Funneled Energy Landscape Simulations. PLoS One 2012, 7, e50635. 371. Wang, S.; Wolynes, P. G. Microscopic Theory of the Glassy Dynamics of Passive and Active Network Materials. J. Chem. Phys. 2013, 138, 12A521-1/10. 372. Zheng, W.; Schafer, N. P.; Wolynes, P. G. Frustration in the Energy Landscapes of Multidomain Protein Misfolding. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 1680−1685.

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Publications of Peter G. Wolynes - The Journal of Physical Chemistry

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