The Charbonneau Group pursues frontier research in soft matter using simulation and theory. We tackle questions ranging from the molecular to the colloidal scale, such as the glass problem, protein crystallization, and nano- and microscale particle assembly.
Explaining how a liquid turns into solid glass is one of the most challenging problems in the theory of matter. By changing the dimension of space in simulations, my group first showed that the liquid structure is important in preventing crystallization, but that simple geometrical frustration does not cause the dynamical slowdown. In order to further elucidate how rugged free-energy landscapes relate to glassiness, we helped set up the Simons Collaboration on Cracking the Glass Problem: https://scglass.uchicago.edu. As part of this effort, we specifically use numerical simulations, mean-field theory, and renormalization group approaches to understand glassiness. Through numerical simulations, we have shown that the amorphous order is intimately related to the rarefaction of metastable states in the landscape, and is universally responsible for rapid dynamical slowdown observed in glass-forming liquids. Through mean-field theory, we have discovered a critical transition upon cooling/compressing glasses. Through simulations and renormalization group studies, we have further revealed that this phenomenon persists even in the presence of violent fluctuations. We are currently trying to understand the remarkable universality and dimensional robustness of the jamming transition in deeply quenched glasses.
 P. Charbonneau, E. I. Corwin, G. Parisi, A. Poncet, and F. Zamponi, Phys. Rev. Lett. 117, 045503 (2016).
 P. Charbonneau, J. Kurchan, G. Parisi, P. Urbani, and F. Zamponi, Annu. Rev. Condens. Matter Phys. 8, 265 (2017).
 P. Charbonneau and S. Yaida, Phys. Rev. Lett. 118, 215701 (2017).
 L. Berthier, P. Charbonneau, D. Coslovich, A. Ninarello, M. Ozawa, and S. Yaida, Proc. Nat. Acad. Sci. USA 114, 11356 (2017).
 L. Berthier, P. Charbonneau, E. Flenner, and F. Zamponi, Phys. Rev. Lett. 119, 188002 (2017).
Describing biological processes and drug design rely heavily on crystallographically-determined protein structures. Obtaining protein crystals, however, remains largely a trial-and-error endeavor. To understand the complex self-assembly of proteins, we have developed a hybrid approach that marries soft matter and structural biology. The resulting rationalization of the crystallization behavior of certain proteins allows us to make verifiable predictions about optimal crystallization conditions, and to constructively revisit physical and biological descriptions of the process. In collaboration with various protein crystallization facilities, we are also developing tools to analyze and interpret the results of crystallization experiments, and thus guide the formulation of appropriate experimental conditions.
In addition to phase behavior of proteins, we studied the structure of water around proteins, not only because biomolecular solvation affects protein phase behavior but also because water contributes to diffraction signals. The implication of the latter is that one needs to characterize the structure of water within protein crystals. We attempted to do this using molecular dynamics simulations and empirical water models and found that although these water models fall short of reproducing the water structure, information complementary to that obtained from diffraction data can be extracted via simulations.
 D. Fusco, P. Charbonneau, Phys. Rev. E 88, 012721 (2013).
 D. Fusco, J. Headd, J. J. Headd, A. de Simone, J. Wang, P. Charbonneau, Soft Matter 10, 290 (2014).
 J. McManus, P. Charbonneau, E. Zaccarelli, N. Asherie, Curr. Opin. Colloid Interface Sci. 22, 73-79 (2016).
 I. Altan, P. Charbonneau, E. H. Snell, Arch. Biochem. Biophys. 602, 12-20 (2016).
 I. Altan, D. Fusco, P. V. Afonine, P. Charbonneau, J. Phys. Chem B. 122(9), 2475-2486 (2018).
The self-assembly of nanoscale components is one of the most promising routes for designing ever smaller and more complex devices, such as organic photovoltaics and memory circuits. Microphase formers exhibit an exotic array of structures on the nanoscale, and these systems' relative simplicity makes them plausible experimental targets. Yet standard thermodynamic and kinetic descriptions provide insufficient guidance. Our novel simulation methodology for correctly treating lattices with fluctuating site occupancy allows us to obtain the equilibrium phase behavior of arbitrary microphase formers. Even the most basic of these models exhibit a surprisingly rich and novel behavior, such as softening due to clustering, reentrant transitions, and the formation of structure as varied as cluster crystals and double gyroid assemblies.
 K. Zhang and P. Charbonneau, Phys. Rev. Lett. 104, 195703 (2010).
 K. Zhang, P. Charbonneau, and B. M. Mladek, Phys. Rev. Lett. 105, 245701 (2010).
 Y. Zhuang, K. Zhang, and P. Charbonneau, Phys. Rev. Lett. 116, 098301 (2016).
 Y. Zhuang, P. Charbonneau, J. Phys. Chem. B 120, 6178 (2016).
 Y. Zhuang, P. Charbonneau, J. Chems. Phys. 147, 091102 (2017).
Colloidal Assembly in External Fields
Reliably tailored mesoscale structures have potential applications that range from photonic crystals to biological templates. Interestingly, tuning colloidal interactions through external fields can give rise in a wealth of different structures in that size scale. Understanding and controlling their assembly, however, remains challenging. In collaboration with various experimental groups we study the assembly of nano- and microscale colloidal suspensions in magnetic, gravitational and acoustic fields.
 Y. Yang, L. Fu, C. Marcoux, P. Charbonneau, J. E. S. Socolar and B. B. Yellen, Soft Matter 11, 2404 (2015).
 C. E. Owens, C. W. Shields IV, D. F. Cruz, P. Charbonneau and G. P. Lopez, Soft Matter 12, 717 (2016).
 L. Fu, W. Steinhardt, H. Zhao, J. E. S. Socolar and P. Charbonneau, Soft Matter 12, 2505 (2016).
 L. Fu, C. Bian, C. W. Shields IV, D. F. Cruz, G. P. Lopez, and Patrick Charbonneau, Soft Matter 13, 3296 (2017).
 A. T. Pham, Y. Zhuang, P. Detwiler, J. E. S. Socolar, P. Charbonneau and B. B. Yellen, Phys. Rev. E 95, 052607 (2017).