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Peter G. Wolynes
Professor
Bullard-Welch Foundation Professor of Science, Professor of Chemistry and Materials Science & NanoEngineering, Professor of Physics & Astronomy
 
e-mail:pwolynes@rice.edu
 
  • A.M. Chemistry (1972) Harvard University
  • A.B. Chemistry (Honors) (1971) Indiana University
  • Ph.D. Chemical Physics (1976) Harvard University
 
Primary Department
   Department of Chemistry
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Department Affiliations
 
  • Department of BioSciences
  • Department of Chemistry
  • Department of Materials Science and NanoEngineering
  • Department of Physics and Astronomy
  • Institute of Biosciences and Bioengineering
  •  
    Other Affiliations
     
  • Baylor College of Medicine
  •  
    Websites
     Group page
     Rice faculty page
     Group Page
     Rice Chemistry
     Group Page
     
    Research Areas
     Theoretical chemical physics; protein folding and function; glasses and stochastic cell biology
     

    Research

     

    The research in my group is broadly concerned with many-body phenomena in biology, chemistry and physics. A major theme is understanding systems where a large diversity of long-lived states is involved, necessitating the use of a statistical characterization of an energy or attractor landscape. The most notable examples are glasses, liquids, biomolecules and biomolecular regulatory networks. In the area of protein folding we are interested both in describing folding kinetics in the laboratory and the development of bioinformatically based schemes for predicting structure from sequence using computer simulation. A key concept is that the energy landscape of a foldable protein looks like a rugged funnel. This idea guides the development of both simple folding kinetics models and structure prediction algorithms. Similar issues of attractor landscapes also arise in higher order biological processes, such as gene recognition and genetic network regulation, which we also study. The energy landscapes of supercooled liquids and glasses also present interesting problems. We have shown how a new approach based on "random first order transitions" explains many quantitative relations found empirically both in liquids and under cryogenic conditions where quantum effects play a role. The same ideas show promise in the study of systems as different as high temperature superconductors, polymer assemblies, and microemulsions. They are also useful for describing the three dimensional structure and dynamics of the interior of living cells.

     
    Teaching Areas
     Theoretical chemical physics; physical chemistry
     
    Selected Publications
     Refereed articles
     

    Bai, X.; Wolynes, P.G. On the Hydrodynamics of Swimming Enzymes. J. Chem. Phys.  2015, 143, 165101.

     
     

    Potoyan, D.A; Wolynes, P.G. Dichotomous Noise Models of Gene Switches. J. Chem. Phys. 2015 143:195101.

     
     

    Schafer, N. P.; Kim, B. L.; Zheng, W.; Wolynes, P. G. Learning to Fold Proteins Using Energy Landscape Theory. Isr. J. Chem. 2014. 54, 1311-1337. doi:10.1002/ijch.201300145.

     
     

    Schafer, N. P.; Kim, B. L.; Zheng, W.; Wolynes, P. G. Learning to Fold Proteins Using Energy Landscape Theory. Isr. J. Chem. 2014. 54, 1311-1337. doi:10.1002/ijch.201300145.

     
     

    Schafer, N. P.; Kim, B. L.; Zheng, W.; Wolynes, P. G. Learning to Fold Proteins Using Energy Landscape Theory. Isr. J. Chem. 2014. 54, 1311-1337. doi:10.1002/ijch.201300145.

     
     

    Sirovetz, B.J.; Schafer, N.P.; Wolynes, P.G. Water Mediated Interactions and the Protein Folding Phase Diagram in the Temperature-Pressure Plane. J. Phys. Chem. B. 2015, 119, 11416-11427.

     
     

    Truong, H.H.; Kim, B.L., Schafer, N.P., Wolynes, P.G. Predictive Energy Landscapes for Folding Membrane Protein Assemblies. J. Chem. Phys. 2015, 143, 243101.

     
     

    Tsai, M-Y.; Zheng, W.; Balamurugan, D.; Schafer, N.P.; Kim, B.L.; Cheung, M.S.; Wolynes, P.G. Electrostatics, Structure Prediction and the Energy Landscapes for Protein Folding and Binding. 2015 online publication, Prot. Sci. doi:10.1002/pro.2751.

     
     

    Wolynes, P. Evolution, Energy Landscapes and the Paradoxes of Protein Folding. Biochimie, 2015 119: 218-230.

     
     

    Zhang, B.; Wolynes, P.G. Topology, structures, and energy landscapes of human chromosomes. Proc. Natl. Acad. Sci. U.S.A. 2015,  112, 6062-6067.

     
     

    A. Wisitsorasak, P.G. Wolynes, "Dynamical Heterogeneity of the Glassy State," J. Phys. Chem. B118, 7835-7848, 2014.

     
     

    B. Zhang, P.G. Wolynes, "Stem cell differentiation as a many-body problem," Proc. Natl. Acad. Sci. U.S.A. 111, 10185-10190, 2014.

     
     

    B.L. Kim, N.P. Schafer, P.G. Wolynes, "Predictive energy landscapes for folding alpha-helical transmembrane proteins," Proc. Natl. Acad. Sci. U.S.A., 111, 11031-11036, 2014.

     
     

    D.U. Ferreiro, E.A. Komives, P.G. Wolynes, "Frustration in Biomolecules," Q. Rev. Biophys. 47, 285-363, 2014.

     
     

    F. Morcos, N.P. Schafer, R.R. Cheng, J.N. Onuchic, P.G. Wolynes, "Coevolutionary information, protein folding landscapes and the thermodynamics of natural selection," Proc. Natl. Acad. Sci. U.S.A.111, 12408-12413.

     
     

    M. Tsytlonok, P.O. Craig, E. Sivertsson, D. Serquera, S. Perrett, R.B. Best, P.G. Wolynes, L.S. Itzhaki, "Complex energy landscape of a giant repeat protein," Structure, 21:1954, 2013.

     
     

    N.P. Schafer, B.L. Kim, W. Zheng, Wolynes, P.G., "Learning to Fold Proteins Using Energy Landscape Theory," Isr. J. Chem. 54, 1311-1337, 2014.

     
     

    A. Wisitsorasak and P.G. Wolynes, "Fluctuating mobility generation and transport in glasses," Phys. Rev. E 88:022308, 2013.

     
     

    H.Truong, B. Kim, N.P. Schafer, P.G. Wolynes, "Funneling and frustration in the energy landscapes of some designed and simplified proteins," J. Chem. Phys.  139:121908, 2013.

     
     

    P. Rabochiy, P.G. Wolynes, V. Lubchenko, "Microscopically based calculations of the free energy barrier and dynamic length scale in supercooled liquids: The comparative role of configurational entropy and elasticity," J. Phys. Chem. 117:15204-15219, 2013.

     
     

    S. Wang and P.G. Wolynes, "Microscopic theory of the glassy dynamics of passive and active network materials," J. Chem. Phys. 138:12A521-1/10, 2013.

     
     

    S. Wang, P.G. Wolynes, "Active patterning and asymmetric transport in a model actomyosin network," J. Chem. Phys. 139:235103-1/11, 2013.

     
     

    W. Zheng, N.P. Schafer, P.G. Wolynes, "Free energy landscapes for initiation and branching of protein aggregation," Proc. Natl. Acad. Sci. .S.A. 110:20515-20520, 2013.

     
     

    A. Wisitsorasak and P.G. Wolynes, “On the Strength of Glasses.” Proc. Natl. Acad. Sci. USA  109:16068-16072, 2012.

     
     

    A. Wisitsorasak and P.G. Wolynes, “On the Strength of Glasses.” Proc. Natl. Acad. Sci. USA  109:16068-16072, 2012.

     
     

    M. Jenik, R. Gonzalo Parra, L.G.Radusky, A.Turjanski, P.G. Wolynes, D.U. Ferreiro, “Protein frustratometer: a tool to localize energetic frustration in protein molecules,"  Nucl. Acids Res., 40: 348-351, 2012.

     
     

    S. Wang and P.G. Wolynes,  “Tensegrity and Motor-Driven Effective Interactions in a Model Cytoskeleton,” J. Chem. Phys. 136: 145102/1-18, 2012.

     
     

    A. Burger, A. Walczak and P.G. Wolynes,  “Influence of Decoys on the noise and Dynamics of Gene Expression,” Phys. Rev.E. 86:041920-1/7, 2012.

     
     

    A. Davytan, N. Schafer, W. Zheng, C. Clementi, P.G. Wolynes, G.A. Papoian, "AWSEM-MD: Protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing," J. Phys. Chem. 116:9494-8503, 2012.

     
     

    H. Lammert, P.G. Wolynes, J.N. Onuchic, "The Role of Atomic Level Steric Effects and Attractive Forces in Protein Folding," Proteins 80:362-372, 2012.

     
     

    N.P. Schafer, R.M.B. Hoffman, A. Burger, P.O. Craig, E.A. Komives, P.G. Wolynes, “Discrete Kinetic Models from Funneled Energy Landscape Simulations,” PLOS ONE 7(12):e50635, 2012. [doi:10.137/journal.pone.0050635]

     
     

    P.G. Wolynes, W.A. Eaton, A. Fersht, “Chemical Physics of Protein Folding,” Proc. Natl. Acad. Sci. USA 109:17770-17771, 2012.

     
     

    S. Wang and P.G. Wolynes,  “Active Contractility in Actomyosin Networks,” Proc. Natl. Acad. Sci. USA 109: 6446-6451, 2012.

     
     

    W. Zheng, N. Schafer, A Davtyan, G.A. Papoian, P.G. Wolynes, “Predictive Energy Landscapes for Protein-Protein Association,” Proc. Natl. Acad. Sci. USA 109, 19244-19247, 2012.

     
     

    W. Zheng, N.P. Schafer, P.G. Wolynes, "Frustration in the energy landscapes of multidomain protein misfolding," Proc. Natl. Acad. Sci. USA 110:1680-1685, 2013.

     
     

    D.U.  Ferreiro, J.A. Hegler, E.A.Komives, and P.G. Wolynes, "On the role of frustration in the energy landscapes of allosteric proteins," Proc. Natl. Acad. Sci. USA 108:3499-3505, 2011.

     
     

    P.O. Craig, J. Lätzer, P. Weinkam, R.M.B. Hoffman, D.U. Ferreiro, E.A. Komives, P.G. Wolynes, "Prediction of native state hydrogen exchange from perfectly funneled energy landscapes" J. Am. Chem. Soc. 133:17463-17472, 2011.

     
     

    S. Wang and P.G. Wolynes, “On the spontaneous collective motion of active matter,” Proc. Natl. Acad. Sci. USA 108:15184-15189, 2011.

     
     

    S. Wang and P.G. Wolynes, “Effective temperature and glassy dynamics of active matter,” J. Chem. Phys. 135: 051101/1-4, 2011.

     
     

    S. Wang, T. Shen, and P.G. Wolynes, "The Interplay of Nonlinearity and Architecture in Equilibrium Cytoskeletal Mechanics," J. Chem. Phys. 134:014510-1-16, 2011.

     
     

    W. Li, P.G. Wolynes, S. Takada, "Frustration, specific sequence dependence and nonlinearity in large-amplitude fluctuations of allosteric proteins," Proc. Natl. Acad. Sci. USA 108: 3504-3509, 2011.

     
     

    J.A. Hegler, J. Laetzer, A. Shehu, C. Clementi, and P.G. Wolynes, "Restriction versus guidance in protein structure prediction.” Proc. Natl. Acad. Sci. USA 106:15302-15307, 2009.

     
     

    D. Ferreiro, J. Hegler, E. Komives, and P.G. Wolynes, "Localizing Frustration in Native Proteins and Protein Assemblies," Proc. Nat. Acad. Sci. USA 104:19819-19824, 2007.

     
     

    M. Gruebele and P. Wolynes, "Quantizing Ulam's Control Conjecture," Phys. Rev. Lett. 99:060201/1-4, 2007.

     
     

    P.G. Wolynes, “Energy Landscapes and Solved Protein Folding Problems,” Phil. Trans. Roy. Soc. AA363, 453-464, 2005.

     
     

    G.A. Papoian, J. Ulander, M.P. Eastwood, Z. Luthey-Schulten and P.G. Wolynes, "Water in Protein Structure Prediction," Proc. Natl. Acad. Sci. USA 101:3352-3357, 2004.

     
     

    M. Gruebele and P. G. Wolynes, “Vibrational Energy Flow and Chemical Reactions,” Acc. Chem. Res., 37:261-267, 2004.

     
     

    M. Sasai and P. G. Wolynes, “Stochastic Gene Expression as a Many Body Problem”, Proc. Natl. Acad. Sci. USA, 100:2374-2379, 2003.

     
     

    V. Lubchenko and P.G. Wolynes, “The Intrinsic Quantum Excitations of Low Temperature Glasses,” Phys. Rev. Lett., 87, 195901, 2001.

     
     

    B. A. Shoemaker, John J. Portman, and Peter G. Wolynes, “Speeding molecular recognition by using the folding funnel: The fly-casting mechanism, Proc. Natl. Acad. Sci. USA 97, 8868-8873, 2000.

     
     

    X. Y. Xia and P. G. Wolynes, “Fragilities of Liquids Predicted from the Random First Order Transition Theory of Glasses,” Proc. Natl. Acad. Sci. 97(7):2990-2994, 2000.

     
     

    J. Bryngelson, J. Onuchic, N. Socci and P. G. Wolynes, “Funnels, Pathways, and the Energy Landscape of Protein Folding: A Synthesis,” Proteins: Structure, Function, and Genetics 21:167-195, 1995.

     
     

    R. Goldstein, Z. Luthey-Schulten and P. G. Wolynes, “Optimal Protein-Folding Codes from Spin-Glass Theory,”  Proc. Natl. Acad. Sci. USA 89:4918-4922, 1992.

     
     

    H. Frauenfelder, S. Sligar and P. G. Wolynes, “The Energy Landscapes and Motions of Proteins,” Science 254:1598-1603, 1991.

     
     

    J. D. Bryngelson and P. G. Wolynes, “Spin Glasses and the Statistical Mechanics of Protein Folding,” Proc. Natl. Acad. Sci. USA 84:7524-7528, 1987.

     
     

    T. R. Kirkpatrick, D. Thirumalai and P. G. Wolynes, “Scaling Concepts for the Dynamics of Viscous Liquids Near an Ideal Glassy State,” Phys. Rev. A 40(2):1045-1054, 1989.

     
     Book chapters
     

    M. Dzero, J. Schmalian, P.G. Wolynes, "Glassiness in Uniformly Frustrated Systems" in Structural Glasses and Supercooled Liquids" Eds. V. Lubchenko and P.G. Wolynes (John Wiley & Sons, 2012), pp. 193-221.

     
     

    V. Lubchenko and P.G. Wolynes, "Theories of Structural Glass Dynamics: Mosaics, Jamming, and All That" in Structural Glasses and Supercooled Liquids, Eds. V. Lubchenko and P.G. Wolynes (John Wiley and Sons, 2012) pp. 341-379.

     
     

    J. Kurchan, J.S. Langer, T.A. Witten, and P.G. Wolynes, “Scientific Interview” in Dynamical heteroteneities in glasses, colloids, and granular media," Eds. L. Berthier, G. Biroli, j-P Bouchaud, L. Cipelletti and W. van Saarloos (Oxford University Press, 2011) pp. 1-38. [cond.mat arXiv:1010.295v1].

     
    Presentations
     Invited Talks
     

    "Evolution and Protein Folding Landscapes,." Conference: Significance of Knotted Structures for Function of Proteins and Nucleic Acids, Warsaw, Poland. (September 18, 2014)

     
     

    "Evolution, Frustration and the Energy Landscape of Biomolecules,." Nobel Conference, Stockholm, Sweden. (June 3, 2014)

     
     

    "Evolution, Frustration and the Energy Landscape of Biomolecules,." University of Wisconsin, Madison, Wisconsin. (May 5, 2014)

     
     

    "Landscapes and Beyond--Glasses, Proteins and the Cell,." Gateways to Emergent Behavior in Science and Society, Workshop: Santa Fe Institute, Santa Fe, New Mexico. (September 24, 2014)

     
     

    "Supercooled Liquids, Glasses and their Ultimate Fates,." Indian Institute of Technology, Kanpur, India. (February 17)

     
     

    "The Protein Folding Problem,." Charles Edison Lecture, University of Notre Dame, South Bend, Indiana. (October 9, 2014)

     
     

    ""Landscapes and Beyond--Glasses, Proteins, and the Cell"." Gateways to Emergent Behavior in Science and Society, Santa Fe, NM. (09/24/2013)

     
     

    ""Learning to Live with Frustration in Biochemistry"." Weizmann Institute, Rehoboth, Israel. (05/07/2013)

     
     

    ""Motorized Glasses and Crystals" Microscopic Models of Active Matter and the Cytoskeleton,"." American Physical Society Annual Meeting, Baltimore, MD. (03/22/2013)

     
     

    ""Protein Folding: Function, Frustration and Misfolding"." University of Rome "La Sapienza", Rome, Italy. (06/07/2013)

     
     

    ""Protein Folding: The Basics of Energy Landscape Theory"." University of Rome "La Sapienza", Rome, Italy. (06/07/2013)

     
     

    ""Recent Successes of the Energy Landscape Theory of Protein Folding"." University of Michigan: The Oncley Lecture, Ann Arbor, MI. (01/10/2013)

     
     

    ""Recent Successes of the Energy Landscape Theory of Protein Folding"." K21 Member Luncheon, Rice University,, Houston, TX. (10/04/2013)

     
     

    ""Supercooled Liquids, Glasses and their Ultimate Fates"." University of Rome "La Sapienza", Rome, Italy. (06/27/2013)

     
     

    "Funnels, Frustration, Flycasting and Cracking: The Overlapping Energy Landscapes of Folding and Function" Protein Folding: Moving Beyond Simple Model Systems, Weizmann Institute, Rehovot, Israel (May 14, 2012)

     
     

    "Glasses, Supercooled Liquids and Their Ultimate Fate" Materials Research Society Spring Meeting, San Francisco, CA (April 11, 2012)

     
     

    "Innovation in Science." 22nd Annual Keck Research Conference, Houston, TX. (October 19, 2012)

     
     

    "Landscapes and Beyond: From Physics and Protein Folding to Modeling Active Biological Matter." National Science Foundation, MPS, Washington, DC. (March 19, 2012)

     
     

    "Landscapes of Matter." ESF-LFUI Conference on Energy Landscapes, Obergurgl, Austria. (July 17, 2012)

     
     

    "Landscapes of Matter." American Chemical Society, San Diego, CA. (March 27, 2012)

     
     

    "Landscapes of Matter, Energy and Life" Pacific Institute of Theoretical Physics: Quantum Phenomena Lecture Series, University of British Columbia, Vancouver, B.C. (March 14, 2012)

     
     

    "Recent Advances in the Theory of Glasses" American Chemical Society Annual Meeting, Philadelphia, PA (August 22, 2012)

     
     

    "The Energy Landscape Theory of Protein Folding" Seminar Course Lecture, University of Tennessee, Knoxville, TN (January 25, 2012)

     
     

    "Beyond Landscapes--The Far-from-Equilibrium Cell" Linnett Professorship Lecture,  University of Cambridge, U.K. (November 11, 2011)

     
     

     “Frustration and the Functional and Folding Landscapes of Proteins” American Physical Society Annual Meeting, Dallas, TX.  (March 21, 2011)

     
     

    “Frustration in Condensed Matter Physics" CIFAR/MEXT Joint Meeting, Vancouver, B.C.  (May 29, 2011)

     
     

    "Landscapes of Matter, Energy and Life" Linnett Professorship Lecture, University of Cambridge, U.K. (November 3, 2011)

     
     

    “RNA and protein folding and beyond: A vision for the next decade” National Science Foundation workshop, Washington, D.C. (September 11-13, 2011)

     
     

    "Recent Successes in the Energy Landscape Theory of Protein Folding" 7th International Conference on Biological Physics, La Jolla, CA. (June 23-25, 2011)

     
     

    "Recent Successes of the Energy Landscape Theory of Protein Folding" Linnett Professorship Lecture, University of Cambridge, U.K. (November 8, 2011)

     
     

    "The Theory of the Structural Glass Transition" Linnett Professorship Lecture, University of Cambridge, U.K. (November 9, 2011)

     
     

    “The Theory of the Structural Glass Transition" Unifying Concepts in Glass Physics V, Institut Henri Poincare, Paris. (December 12-16, 2011)

     
     

    "Water-mediated interactions in protein folding and structure." The Biophysical Society Annual Meeting, Baltimore, MD. (March 5, 2011)

     
     Keynote Speaker
     

    "Recent Successes of the Energy Landscape Theory of Protein Folding,." Dynamics of Complex Chemical and Biological Systems Symposium, Kanpur, India. (February 13, 2014)

     
     

    "Protein Folding Dynamics." GRC Protein Folding Dynamics , Ventura, CA. (January 8, 2012 )

     
     Seminar Speaker
     

    "Harvesting the Fruits of the Energy Landscape Theory of Protein Folding,." University of Texas San Antonio, San Antonio, Texas. (March 28, 2014)

     
     

    "The Protein Folding Problem, ." University of Houston, Houston, Texas. (September 30, 2014)

     
     

    Bio-X Program Seminar, Stanford University, Palo Alto, CA, May 2011.

     
     

    Colloquium, Department of Chemistry, Pennsylvania State University, State College, PA.  February 2011.

     
    Editorial Positions
     Member of the Editorial Board, Advances in Physics. (2011 - 2014)

     Member of the Editorial Board, Advances in Physics. Taylor and Francis. (2015 - 2016)

    Supervised Theses & Dissertations
     Apiwat Wisitsorasak, Ph.D. Dynamical Heterogeneity of the Glassy State. (2014) (Thesis or Dissertation Director)

     Nicholas Peter Schafer, Ph.D. Folding, Binding, Misfolding and Aggregation with AWSEM. (2014) (Thesis or Dissertation Director)

     Bobby Kim, PhD Optimization of coats-grained molecular dynamics potentials for protein folding. (2015) (Thesis or Dissertation Director)

    Awards, Prizes, & Fellowships
     Flygare Memorial Award Lecturer, University of Illinois at Urbana-champaign (2015)

     American Chemical Society Award in Theoretical Chemistry, American Chemical Society (2011)

     Linnett Professorship at Sidney Sussex College, University of Cambridge, (Fall 2011)

    Positions Held
     Science Board, The Santa Fe Institute. (2011 - 2014)

     Advisory Council, National Academy of Sciences. (2013 - 2016)

     Board of Directors, The Academy of Medicine, Engineering and Sciences of Texas (TAMEST). (2013 - 2016)

     Committee on Science, Engineering and Public Policy (COSEPUP), National Academy of Sciences. (2013 - 2016)

     Foreign Advisory Council, Institute for Molecular Science, Okazaki, Japan. (2011 - 2011)