Patrick Charbonneau | Scholars@Duke

Patrick Charbonneau
Associate Professor of Chemistry

Professor Charbonneau studies soft matter. His work combines theory and simulation to understand the glass problem, protein crystallization, microphase formation, and colloidal assembly in external fields.

Current Appointments & Affiliations

Associate Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2015
Associate Chair of Chemistry, Chemistry, Trinity College of Arts & Sciences 2017
Associate Professor of Physics, Physics, Trinity College of Arts & Sciences 2016

Contact Information

5329 French Science, 124 Science Drive, Durham, NC 27708
Box 90347, Durham, NC 27708-0347
patrick.charbonneau@duke.edu (919) 613-6261
Charbonneau Research Group

Background
Education, Training, & Certifications
- Ph.D., Harvard University 2006
- B.S., McGill University (Canada) 2001
Duke Appointment History
- Assistant Professor in the Department of Physics, Physics, Trinity College of Arts & Sciences 2013 - 2016
- Assistant Professor of Chemistry, Chemistry, Trinity College of Arts & Sciences 2008 - 2015
- Assistant Professor in the Department of Physics, Physics, Trinity College of Arts & Sciences 2009 - 2012
Recognition
In the News
- APR 13, 2018 Duke Research Blog
  
  Looking at Cooking as a Science Experiment
- NOV 2, 2017 Duke Research Blog
  
  Cheating Time to Watch Liquids do the Slow Dance
- MAY 30, 2017
  
  Breaking Glass in Infinite Dimensions
- APR 13, 2016
  
  Duke Professor Teams Up to Crack the Glass Problem
- MAR 3, 2015
  
  Visualizing how matter changes from one state to another, on an atomic level
- NOV 12, 2014
  
  Through the Theoretical Glass
- APR 24, 2014
  
  When Things Get Glassy, Molecules Go Fractal
- NOV 15, 2013 Duke Research Blog
  
  Spherical Cows Help Turn Proteins to Crystals
- JUL 15, 2013 Smithsonian
  
  Scientists get best view yet of the structure of glass
- APR 10, 2013
  
  Chemistry in the Kitchen, Cooking in the Classroom
- FEB 15, 2013
  
  Sloan Foundation Names Charbonneau, Lu as 2013 Research Fellows
Awards & Honors
- Top 20 Reviewers for 2012. Journal of Chemical Physics. April 9, 2013
- Alfred P. Sloan Research Fellow. Alfred P. Sloan Foundation. February 14, 2013
- Mention of Teaching Excellence. Duke University. June 1, 2012
- Open Eye Award. American Chemical Society. November 14, 2011
- Faculty Early Career Development (CAREER) Program. National Science Foundation. 2011
- Ralph E. Powe Junior Faculty Enhancement Award. Oak Ridge National Laboratory. 2009
Research
Selected Grants
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Soft Matter Simulation and Theory of the Crystal Assembly of Globular and Membrane Proteins awarded by National Science Foundation 2018 - 2021
- SUPPLEMENT: Cracking the Glass Problem awarded by Simons Foundation 2016 - 2019
- GAANN - Department of Chemistry awarded by Department of Education 2015 - 2018
- Continuous Acoustofluidic Confinement for the Manufacture of Functional, Entropically Ordered awarded by National Science Foundation 2014 - 2017
- CAREER: Soft Matter Self-Assembly: Protein Crystallization and Collodial Microphase Formation awarded by National Science Foundation 2011 - 2016
- Structural Biology and Biophysics Training Program awarded by National Institutes of Health 1994 - 2015
Publications & Artistic Works
Selected Publications
- Journal Articles
  - Hu, Y, and Charbonneau, P. "Clustering and assembly dynamics of a one-dimensional microphase former." Soft matter (March 26, 2018). Full Text
  - Altan, I, Fusco, D, Afonine, PV, and Charbonneau, P. "Learning about Biomolecular Solvation from Water in Protein Crystals." Journal of Physical Chemistry B 122, no. 9 (March 8, 2018): 2475-2486. Full Text
  - Berthier, L, Charbonneau, P, Flenner, E, and Zamponi, F. "Origin of Ultrastability in Vapor-Deposited Glasses." Physical review letters 119, no. 18 (November 2017): 188002-. Full Text
  - Berthier, L, Charbonneau, P, Flenner, E, and Zamponi, F. "Origin of Ultrastability in Vapor-Deposited Glasses." Physical Review Letters 119, no. 18 (November 2017). Full Text
  - Berthier, L, Charbonneau, P, Coslovich, D, Ninarello, A, Ozawa, M, and Yaida, S. "Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling." Proceedings of the National Academy of Sciences of the United States of America 114, no. 43 (October 10, 2017): 11356-11361. Full Text
  - Charbonneau, P, Li, YC, Pfister, HD, and Yaida, S. "Cycle-expansion method for the Lyapunov exponent, susceptibility, and higher moments." Physical review. E 96, no. 3-1 (September 18, 2017): 032129-. Full Text
  - Zhuang, Y, and Charbonneau, P. "Communication: Microphase equilibrium and assembly dynamics." The Journal of chemical physics 147, no. 9 (September 2017): 091102-. Full Text Open Access Copy
  - Berthier, L, Charbonneau, P, Flenner, E, and Zamponi, F. "How to create equilibrium vapor-deposited glasses." (August 23, 2017). Open Access Copy
  - Charbonneau, P, Li, Y, Pfister, H, and Yaida, S. "Lyapunov exponent and susceptibility." (August 23, 2017). Open Access Copy
  - Berthier, L, Charbonneau, P, Coslovich, D, Ninarello, A, Ozawa, M, and Yaida, S. "Breaking the glass ceiling: Configurational entropy measurements in extremely supercooled liquids." (June 1, 2017). Open Access Copy
  - Charbonneau, P, and Yaida, S. "Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions." Physical review letters 118, no. 21 (May 26, 2017): 215701-. Full Text Open Access Copy
  - Pham, AT, Zhuang, Y, Detwiler, P, Socolar, JES, Charbonneau, P, and Yellen, BB. "Phase diagram and aggregation dynamics of a monolayer of paramagnetic colloids." Physical review. E 95, no. 5-1 (May 12, 2017): 052607-. Full Text Open Access Copy
  - Fu, L, Bian, C, Shields, CW, Cruz, DF, López, GP, and Charbonneau, P. "Assembly of hard spheres in a cylinder: a computational and experimental study." Soft matter 13, no. 18 (May 2017): 3296-3306. Full Text Open Access Copy
  - Charbonneau, P, Kurchan, J, Parisi, G, Urbani, P, and Zamponi, F. "Glass and Jamming Transitions: From Exact Results to Finite-Dimensional Descriptions." Annual Review of Condensed Matter Physics 8, no. 1 (March 31, 2017): 265-288. Full Text Open Access Copy
  - Yaida, S, Berthier, L, Charbonneau, P, and Tarjus, G. "Point-to-set lengths, local structure, and glassiness." Physical review. E 94, no. 3-1 (September 22, 2016): 032605-. Full Text Open Access Copy
  - Zhuang, Y, and Charbonneau, P. "Recent Advances in the Theory and Simulation of Model Colloidal Microphase Formers." The journal of physical chemistry. B 120, no. 32 (August 2016): 7775-7782. Full Text Open Access Copy
  - Charbonneau, P, Corwin, EI, Parisi, G, Poncet, A, and Zamponi, F. "Universal Non-Debye Scaling in the Density of States of Amorphous Solids." Physical review letters 117, no. 4 (July 22, 2016): 045503-. Full Text Open Access Copy
  - Berthier, L, Charbonneau, P, Jin, Y, Parisi, G, Seoane, B, and Zamponi, F. "Growing timescales and lengthscales characterizing vibrations of amorphous solids." Proceedings of the National Academy of Sciences of the United States of America 113, no. 30 (July 8, 2016): 8397-8401. Full Text Open Access Copy
  - Altan, I, Charbonneau, P, and Snell, EH. "Computational crystallization." Archives of biochemistry and biophysics 602 (July 2016): 12-20. (Review) Full Text Open Access Copy
  - Charbonneau, P, Dyer, E, Lee, J, and Yaida, S. "Linking dynamical heterogeneity to static amorphous order." Journal of Statistical Mechanics: Theory and Experiment 2016, no. 7 (July 1, 2016): 074004-074004. Full Text Open Access Copy
  - Zhuang, Y, and Charbonneau, P. "Equilibrium Phase Behavior of the Square-Well Linear Microphase-Forming Model." The journal of physical chemistry. B 120, no. 26 (July 2016): 6178-6188. Full Text Open Access Copy
  - McManus, JJ, Charbonneau, P, Zaccarelli, E, and Asherie, N. "The physics of protein self-assembly." Current Opinion in Colloid & Interface Science 22 (April 2016): 73-79. Full Text Open Access Copy
  - Fu, L, Steinhardt, W, Zhao, H, Socolar, JES, and Charbonneau, P. "Hard sphere packings within cylinders." Soft matter 12, no. 9 (March 2016): 2505-2514. Full Text Open Access Copy
  - Tavarone, R, Charbonneau, P, and Stark, H. "Kinetic Monte Carlo simulations for birefringence relaxation of photo-switchable molecules on a surface." The Journal of chemical physics 144, no. 10 (March 2016): 104703-. Full Text Open Access Copy
  - Zhuang, Y, Zhang, K, and Charbonneau, P. "Equilibrium Phase Behavior of a Continuous-Space Microphase Former." Physical review letters 116, no. 9 (March 2016): 098301-. Full Text Open Access Copy
  - Marcoux, C, Byington, TW, Qian, Z, Charbonneau, P, and Socolar, JES. "Erratum: Emergence of limit-periodic order in tiling models [Phys. Rev. E 90 , 012136 (2014)]." Physical Review E 93, no. 2 (February 2016). Full Text Open Access Copy
  - Berthier, L, Charbonneau, P, and Yaida, S. "Efficient measurement of point-to-set correlations and overlap fluctuations in glass-forming liquids." The Journal of chemical physics 144, no. 2 (January 2016): 024501-. Full Text Open Access Copy
  - Fusco, D, and Charbonneau, P. "Soft matter perspective on protein crystal assembly." Colloids and surfaces. B, Biointerfaces 137 (January 2016): 22-31. (Review) Full Text Open Access Copy
  - Owens, CE, Shields, CW, Cruz, DF, Charbonneau, P, and López, GP. "Highly parallel acoustic assembly of microparticles into well-ordered colloidal crystallites." Soft matter 12, no. 3 (January 2016): 717-728. Full Text Open Access Copy
  - Tavarone, R, Charbonneau, P, and Stark, H. "Phase ordering of zig-zag and bow-shaped hard needles in two dimensions." The Journal of chemical physics 143, no. 11 (September 2015): 114505-. Full Text Open Access Copy
  - Charbonneau, P, Jin, Y, Parisi, G, Rainone, C, Seoane, B, and Zamponi, F. "Numerical detection of the Gardner transition in a mean-field glass former." Physical review. E, Statistical, nonlinear, and soft matter physics 92, no. 1 (July 21, 2015): 012316-. Full Text Open Access Copy
  - Jin, Y, and Charbonneau, P. "Dimensional study of the dynamical arrest in a random Lorentz gas." Physical review. E, Statistical, nonlinear, and soft matter physics 91, no. 4 (April 27, 2015): 042313-. Full Text Open Access Copy
  - Charbonneau, P, Corwin, EI, Parisi, G, and Zamponi, F. "Jamming criticality revealed by removing localized buckling excitations." Physical review letters 114, no. 12 (March 27, 2015): 125504-. Full Text Open Access Copy
  - Yang, Y, Fu, L, Marcoux, C, Socolar, JES, Charbonneau, P, and Yellen, BB. "Phase transformations in binary colloidal monolayers." Soft matter 11, no. 12 (March 2015): 2404-2415. Full Text Open Access Copy
  - Charbonneau, P, Jin, Y, Parisi, G, and Zamponi, F. "Hopping and the Stokes-Einstein relation breakdown in simple glass formers." Proceedings of the National Academy of Sciences of the United States of America 111, no. 42 (October 6, 2014): 15025-15030. Full Text Open Access Copy
  - Charbonneau, P, Kurchan, J, Parisi, G, Urbani, P, and Zamponi, F. "Exact theory of dense amorphous hard spheres in high dimension. III. The full replica symmetry breaking solution." Journal of Statistical Mechanics: Theory and Experiment 2014, no. 10 (October 1, 2014): P10009-P10009. Full Text Open Access Copy
  - Marcoux, C, Byington, TW, Qian, Z, Charbonneau, P, and Socolar, JES. "Emergence of limit-periodic order in tiling models." Physical review. E, Statistical, nonlinear, and soft matter physics 90, no. 1 (July 29, 2014): 012136-. Full Text Open Access Copy
  - Fusco, D, and Charbonneau, P. "Competition between monomeric and dimeric crystals in schematic models for globular proteins." The journal of physical chemistry. B 118, no. 28 (July 2014): 8034-8041. Full Text Open Access Copy
  - Charbonneau, P, Kurchan, J, Parisi, G, Urbani, P, and Zamponi, F. "Fractal free energy landscapes in structural glasses." Nature communications 5 (January 2014): 3725-. Full Text Open Access Copy
  - Fusco, D, Barnum, TJ, Bruno, AE, Luft, JR, Snell, EH, Mukherjee, S, and Charbonneau, P. "Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms." PloS one 9, no. 7 (January 2014): e101123-. Full Text Open Access Copy
  - Fusco, D, Headd, JJ, De Simone, A, Wang, J, and Charbonneau, P. "Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study." SOFT MATTER 10, no. 2 (2014): 290-302. Full Text Open Access Copy Link to Item
  - Charbonneau, B, Charbonneau, P, Jin, Y, Parisi, G, and Zamponi, F. "Dimensional dependence of the Stokes-Einstein relation and its violation." Journal of Chemical Physics 139, no. 16 (October 28, 2013). Full Text
  - Charbonneau, B, Charbonneau, P, Jin, Y, Parisi, G, and Zamponi, F. "Dimensional dependence of the Stokes-Einstein relation and its violation." Journal of Chemical Physics 139, no. 16 (2013). Open Access Copy
  - Charbonneau, B, Charbonneau, P, and Tarjus, G. "Geometrical frustration and static correlations in hard-sphere glass formers." Journal of Chemical Physics 138, no. 12 (2013). Full Text
  - Martinez, H, Miró, P, Charbonneau, P, Hillmyer, MA, and Cramer, CJ. "Selectivity in Ring-Opening Metathesis Polymerization of Z -Cyclooctenes Catalyzed by a Second-generation Grubbs Catalyst." ACS Catalysis 2, no. 12 (December 7, 2012): 2547-2556. Full Text
  - Charbonneau, P, Corwin, EI, Parisi, G, and Zamponi, F. "Universal microstructure and mechanical stability of jammed packings." Phys Rev Lett 109, no. 20 (November 16, 2012): 205501-. Full Text Open Access Copy Link to Item
  - Zhang, K, and Charbonneau, P. "[N]pT ensemble and finite-size-scaling study of the critical isostructural transition in the generalized exponential model of index 4." Phys Rev E Stat Nonlin Soft Matter Phys 86, no. 4 Pt 1 (October 2012): 042501-. Full Text Link to Item
  - Charbonneau, P, Ikeda, A, Parisi, G, and Zamponi, F. "Dimensional study of the caging order parameter at the glass transition." Proc Natl Acad Sci U S A 109, no. 35 (August 28, 2012): 13939-13943. Full Text Open Access Copy Link to Item
  - Zhang, K, and Charbonneau, P. "[N]pT Monte Carlo simulations of the cluster-crystal-forming penetrable sphere model." J Chem Phys 136, no. 21 (June 7, 2012): 214106-. Full Text Open Access Copy Link to Item
  - Bergin, SM, Chen, Y-H, Rathmell, AR, Charbonneau, P, Li, Z-Y, and Wiley, BJ. "The effect of nanowire length and diameter on the properties of transparent, conducting nanowire films." Nanoscale 4, no. 6 (March 21, 2012): 1996-2004. Full Text Open Access Copy Link to Item
  - Charbonneau, B, Charbonneau, P, and Tarjus, G. "Geometrical frustration and static correlations in a simple glass former." Physical Review Letters 108, no. 3 (2012). Full Text Open Access Copy
  - Zhang, K, and Charbonneau, P. "[N]pT ensemble and finite-size-scaling study of the critical isostructural transition in the generalized exponential model of index 4." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 86, no. 4 (2012). Full Text Open Access Copy
  - Zhang, K, and Charbonneau, P. "Erratum: [N]pT ensemble and finite-size-scaling study of the critical isostructural transition in the generalized exponential model of index 4." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 86, no. 6 (2012). Full Text Open Access Copy
  - Charbonneau, P, Ikeda, A, Parisi, G, and Zamponi, F. "Glass transition and random close packing above three dimensions." Phys Rev Lett 107, no. 18 (October 28, 2011): 185702-. Full Text Open Access Copy Link to Item
  - Zhang, K, and Charbonneau, P. "Monte Carlo approach for studying microphases applied to the axial next-nearest-neighbor Ising and the Ising-Coulomb models." Physical Review B - Condensed Matter and Materials Physics 83, no. 21 (2011). Full Text Open Access Copy
  - Zhang, K, Charbonneau, P, and Mladek, BM. "Reentrant and isostructural transitions in a cluster-crystal former." Phys Rev Lett 105, no. 24 (December 10, 2010): 245701-. Full Text Open Access Copy Link to Item
  - Zhang, K, and Charbonneau, P. "Monte carlo study of the axial next-nearest-neighbor Ising model." Phys Rev Lett 104, no. 19 (May 14, 2010): 195703-. Full Text Open Access Copy Link to Item
  - Charbonneau, P, Ikeda, A, van Meel, JA, and Miyazaki, K. "Numerical and theoretical study of a monodisperse hard-sphere glass former." Phys Rev E Stat Nonlin Soft Matter Phys 81, no. 4 Pt 1 (April 2010): 040501-. Full Text Open Access Copy Link to Item
  - Jin, Y, Charbonneau, P, Meyer, S, Song, C, and Zamponi, F. "Application of Edwards' statistical mechanics to high-dimensional jammed sphere packings." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82, no. 5 (2010). Full Text Open Access Copy
  - Meel, JAV, Charbonneau, B, Fortini, A, and Charbonneau, P. "Hard-sphere crystallization gets rarer with increasing dimension." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 80, no. 6 (2009). Full Text Open Access Copy
  - Meel, JAV, Frenkel, D, and Charbonneau, P. "Geometrical frustration: A study of four-dimensional hard spheres." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 79, no. 3 (2009). Full Text Open Access Copy
  - Charbonneau, P, Das, C, and Frenkel, D. "Dynamical heterogeneity in a glass-forming ideal gas." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 78, no. 1 (2008). Full Text Open Access Copy
  - Mladek, BM, Charbonneau, P, Likos, CN, Frenkel, D, and Kahl, G. "Multiple occupancy crystals formed by purely repulsive soft particles." Journal of Physics Condensed Matter 20, no. 49 (2008). Full Text
  - Charbonneau, P, and Frenkel, D. "Gas-solid coexistence of adhesive spheres." Journal of Chemical Physics 126, no. 19 (2007). Full Text Open Access Copy
  - Charbonneau, P, and Reichman, DR. "Phase behavior and far-from-equilibrium gelation in charged attractive colloids." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 75, no. 5 (2007). Full Text Open Access Copy
  - Charbonneau, P, and Reichman, DR. "Systematic characterization of thermodynamic and dynamical phase behavior in systems with short-ranged attraction." Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 75, no. 1 (2007). Full Text Open Access Copy
  - Charbonneau, P, and Reichman, DR. "Dynamical heterogeneity and nonlinear susceptibility in supercooled liquids with short-range attraction." Physical Review Letters 99, no. 13 (2007). Full Text Open Access Copy
  - Mladek, BM, Charbonneau, P, and Frenkel, D. "Phase coexistence of cluster crystals: Beyond the gibbs phase rule." Physical Review Letters 99, no. 23 (2007). Full Text Open Access Copy
  - Reichman, DR, and Charbonneau, P. "Mode-coupling theory." Journal of Statistical Mechanics: Theory and Experiment , no. 5 (2005): 267-289. Full Text Open Access Copy
  - Chamon, C, Charbonneau, P, Cugliandolo, LF, Reichman, DR, and Sellitto, M. "Out-of-equilibrium dynamical fluctuations in glassy systems." Journal of Chemical Physics 121, no. 20 (2004): 10120-10137. Full Text Open Access Copy
  - Barden, CJ, Charbonneau, P, and III, HFS. "Group 13-group 16 heterocubanes [RM(μ₃-E)]₄ (R = H, CH₃; M = Al, Ga, In; E = O, S, Se, Te) and group 13 cubanes [RM(μ₃-M)]₄ (R = F, Cl, CH₃, NO₂; M = Al, Ga, In): A structural study." Organometallics 21, no. 17 (2002): 3605-3609. Full Text
  - Spivey, AC, Charbonneau, P, Fekner, T, Hochmuth, DH, Maddaford, A, Malardier-Jugroot, C, Redgrave, AJ, and Whitehead, MA. "Energy barriers to rotation in axially chiral analogues of 4-(dimethylamino)pyridine." JOURNAL OF ORGANIC CHEMISTRY 66, no. 22 (November 2, 2001): 7394-7401. Full Text Link to Item
  - Charbonneau, P, Jean-Claude, B, and Whitehead, MA. "Synthesis of a prodrug: A semi-empirical PM3 study." Journal of Molecular Structure: THEOCHEM 574 (2001): 85-91. Full Text
  - Spivey, AC, Charbonneau, P, Fekner, T, Hochmuth, DH, Maddaford, A, Malardier-Jugroot, C, Redgrave, AJ, and Whitehead, MA. "Energy barriers to rotation in axially chiral analogues of 4-(dimethylamino)pyridine." Journal of Organic Chemistry 66, no. 22 (2001): 7394-7401. Full Text
  - Berthier, L, Charbonneau, P, Coslovich, D, Ninarello, A, Ozawa, M, and Yaida, S. "Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling." PNAS 114: 11356-11361. Full Text Link to Item
  - Bruno, AE, Charbonneau, P, Newman, J, Snell, EH, So, DR, Vanhoucke, V, Williams, S, and Wilson, J. "Classification of crystallization outcomes using deep convolutional neural networks." Link to Item
  - Charbonneau, B, Charbonneau, P, and Szamel, G. "A Microscopic Model of the Stokes-Einstein Relation in Arbitrary Dimension." Link to Item
  - Charbonneau, P, Corwin, EI, Fu, L, Tsekenis, G, and Naald, MVD. "Gardner Phenomenology in Minimally Polydisperse Crystalline Systems." Link to Item
  - Charbonneau, P. "Lecture Notes on the Statistical Mechanics of Disordered Systems." Open Access Copy Link to Item
Teaching & Mentoring
Recent Courses
- CHEM 393: Research Independent Study 2018
- CHEM 394: Research Independent Study 2018
- CHEM 493: Research Independent Study 2018
- CHEM 494: Research Independent Study 2018
- CHEM 543: Statistical Thermodynamics 2018
- CHEM 544: Statistical Mechanics 2018
- CHEM 81S: Introduction to Research in Chemistry 2016
- CHEM 89S: First-Year Seminar 2016
- CHEM 990-4: Special Topics in Physical Chemistry 2016
Scholarly, Clinical, & Service Activities
Presentations & Appearances
Service to the Profession

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Education, Training, & Certifications

Duke Appointment History

In the News

Awards & Honors

Selected Grants

Selected Publications

Journal Articles

Recent Courses

Presentations & Appearances

Service to the Profession