Now showing items 1-20 of 54

    • A microscopic model of the Stokes-Einstein relation in arbitrary dimension. 

      Charbonneau, Benoit; Charbonneau, Patrick; Szamel, Grzegorz (The Journal of chemical physics, 2018-06)
      The Stokes-Einstein relation (SER) is one of the most robust and widely employed results from the theory of liquids. Yet sizable deviations can be observed for self-solvation, which cannot be explained by the standard ...
    • Application of Edwards' statistical mechanics to high-dimensional jammed sphere packings. 

      Jin, Yuliang; Charbonneau, Patrick; Meyer, Sam; Song, Chaoming; Zamponi, Francesco (Phys Rev E Stat Nonlin Soft Matter Phys, 2010-11)
      The isostatic jamming limit of frictionless spherical particles from Edwards' statistical mechanics [Song et al., Nature (London) 453, 629 (2008)] is generalized to arbitrary dimension d using a liquid-state description. ...
    • Assembly of hard spheres in a cylinder: a computational and experimental study 

      Fu, Lin; Bian, Ce; Shields, C Wyatt; Cruz, Daniela F; López, Gabriel P; Charbonneau, Patrick (2017-03-10)
      Hard spheres are an important benchmark of our understanding of natural and synthetic systems. In this work, colloidal experiments and Monte Carlo simulations examine the equilibrium and out-of-equilibrium assembly of hard ...
    • Bypassing sluggishness: SWAP algorithm and glassiness in high dimensions 

      Berthier, Ludovic; Charbonneau, Patrick; Kundu, Joyjit
      The recent implementation of a swap Monte Carlo algorithm (SWAP) for polydisperse mixtures fully bypasses computational sluggishness and closes the gap between experimental and simulation timescales in physical dimensions ...
    • Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study. 

      Fusco, Diana; Headd, Jeffrey J; De Simone, Alfonso; Wang, Jun; Charbonneau, Patrick (Soft Matter, 2014-01-14)
      The fields of structural biology and soft matter have independently sought out fundamental principles to rationalize protein crystallization. Yet the conceptual differences and the limited overlap between the two disciplines ...
    • Classification of crystallization outcomes using deep convolutional neural networks. 

      Bruno, Andrew E; Charbonneau, Patrick; Newman, Janet; Snell, Edward H; So, David R; Vanhoucke, Vincent; Watkins, Christopher J; ... (9 authors) (PloS one, 2018-01)
      The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art ...
    • Clustering and assembly dynamics of a one-dimensional microphase former. 

      Hu, Yi; Charbonneau, Patrick (Soft matter, 2018-03-26)
      Both ordered and disordered microphases ubiquitously form in suspensions of particles that interact through competing short-range attraction and long-range repulsion (SALR). While ordered microphases are more appealing materials ...
    • Competition between monomeric and dimeric crystals in schematic models for globular proteins. 

      Fusco, Diana; Charbonneau, Patrick (J Phys Chem B, 2014-07-17)
      Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. However, they have also left open questions regarding the protein phase behavior and self-assembly ...
    • Computational crystallization. 

      Altan, Irem; Charbonneau, Patrick; Snell, Edward H (Arch Biochem Biophys, 2016-07-15)
      Crystallization is a key step in macromolecular structure determination by crystallography. While a robust theoretical treatment of the process is available, due to the complexity of the system, the experimental process ...
    • Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling. 

      Berthier, Ludovic; Charbonneau, Patrick; Coslovich, Daniele; Ninarello, Andrea; Ozawa, Misaki; Yaida, Sho (Proceedings of the National Academy of Sciences of the United States of America, 2017-10-10)
      Liquids relax extremely slowly on approaching the glass state. One explanation is that an entropy crisis, because of the rarefaction of available states, makes it increasingly arduous to reach equilibrium in that regime. ...
    • Crystallization of asymmetric patchy models for globular proteins in solution. 

      Fusco, Diana; Charbonneau, Patrick (Phys Rev E Stat Nonlin Soft Matter Phys, 2013-07)
      Asymmetric patchy particle models have recently been shown to describe the crystallization of small globular proteins with near-quantitative accuracy. Here, we investigate how asymmetry in patch geometry and bond energy ...
    • Decorrelation of the static and dynamic length scales in hard-sphere glass formers. 

      Charbonneau, Patrick; Tarjus, Gilles (Phys Rev E Stat Nonlin Soft Matter Phys, 2013-04)
      We show that, in the equilibrium phase of glass-forming hard-sphere fluids in three dimensions, the static length scales tentatively associated with the dynamical slowdown and the dynamical length characterizing spatial ...
    • Dimensional dependence of the Stokes-Einstein relation and its violation 

      Charbonneau, Benoit; Charbonneau, Patrick; Jin, Yuliang; Parisi, Giorgio; Zamponi, Francesco (Journal of Chemical Physics, 2013-10-28)
      We generalize to higher spatial dimensions the Stokes-Einstein relation (SER) as well as the leading correction to diffusivity in finite systems with periodic boundary conditions, and validate these results with numerical ...
    • Dimensional study of the caging order parameter at the glass transition. 

      Charbonneau, Patrick; Ikeda, Atsushi; Parisi, Giorgio; Zamponi, Francesco (Proc Natl Acad Sci U S A, 2012-08-28)
      The glass problem is notoriously hard and controversial. Even at the mean-field level, little is agreed upon regarding why a fluid becomes sluggish while exhibiting but unremarkable structural changes. It is clear, however, ...
    • Dimensional study of the dynamical arrest in a random Lorentz gas. 

      Jin, Yuliang; Charbonneau, Patrick (Phys Rev E Stat Nonlin Soft Matter Phys, 2015-04)
      The random Lorentz gas (RLG) is a minimal model for transport in heterogeneous media. Upon increasing the obstacle density, it exhibits a growing subdiffusive transport regime and then a dynamical arrest. Here, we study ...
    • Dynamical heterogeneity in a glass-forming ideal gas. 

      Charbonneau, Patrick; Das, Chinmay; Frenkel, Daan (Phys Rev E Stat Nonlin Soft Matter Phys, 2008-07)
      We conduct a numerical study of the dynamical behavior of a system of three-dimensional "crosses," particles that consist of three mutually perpendicular line segments of length sigma rigidly joined at their midpoints. In ...
    • Dynamics around the Site Percolation Threshold on High-Dimensional Hypercubic Lattices 

      Biroli, Giulio; Charbonneau, Patrick; Hu, Yi
      Recent advances on the glass problem motivate reexamining classical models of percolation. Here, we consider the displacement of an ant in a labyrinth near the percolation threshold on cubic lattices both below and above ...
    • Efficient measurement of point-to-set correlations and overlap fluctuations in glass-forming liquids. 

      Berthier, Ludovic; Charbonneau, Patrick; Yaida, Sho (J Chem Phys, 2016-01-14)
      Cavity point-to-set correlations are real-space tools to detect the roughening of the free-energy landscape that accompanies the dynamical slowdown of glass-forming liquids. Measuring these correlations in model glass formers ...
    • Emergence of limit-periodic order in tiling models. 

      Marcoux, Catherine; Byington, Travis W; Qian, Zongjin; Charbonneau, Patrick; Socolar, Joshua ES (Phys Rev E Stat Nonlin Soft Matter Phys, 2014-07)
      A two-dimensional (2D) lattice model defined on a triangular lattice with nearest- and next-nearest-neighbor interactions based on the Taylor-Socolar monotile is known to have a limit-periodic ground state. The system reaches ...
    • Equilibrium Phase Behavior of a Continuous-Space Microphase Former. 

      Zhuang, Yuan; Zhang, Kai; Charbonneau, Patrick (Phys Rev Lett, 2016-03-04)
      Periodic microphases universally emerge in systems for which short-range interparticle attraction is frustrated by long-range repulsion. The morphological richness of these phases makes them desirable material targets, but ...