# Browsing by Author "Charbonneau, Patrick"

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Item Open Access A microscopic model of the Stokes-Einstein relation in arbitrary dimension.(The Journal of chemical physics, 2018-06) Charbonneau, Benoit; Charbonneau, Patrick; Szamel, GrzegorzThe 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 hydrodynamic derivation. Here, we revisit the work of Masters and Madden [J. Chem. Phys. 74, 2450-2459 (1981)], who first solved a statistical mechanics model of the SER using the projection operator formalism. By generalizing their analysis to all spatial dimensions and to partially structured solvents, we identify a potential microscopic origin of some of these deviations. We also reproduce the SER-like result from the exact dynamics of infinite-dimensional fluids.Item Restricted Application of Edwards' statistical mechanics to high-dimensional jammed sphere packings.(Phys Rev E Stat Nonlin Soft Matter Phys, 2010-11) Jin, Yuliang; Charbonneau, Patrick; Meyer, Sam; Song, Chaoming; Zamponi, FrancescoThe 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. The asymptotic high-dimensional behavior of the self-consistent relation is obtained by saddle-point evaluation and checked numerically. The resulting random close packing density scaling ϕ∼d2(-d) is consistent with that of other approaches, such as replica theory and density-functional theory. The validity of various structural approximations is assessed by comparing with three- to six-dimensional isostatic packings obtained from simulations. These numerical results support a growing accuracy of the theoretical approach with dimension. The approach could thus serve as a starting point to obtain a geometrical understanding of the higher-order correlations present in jammed packings.Item Open Access Assembly of hard spheres in a cylinder: a computational and experimental study(2017-03-10) Fu, Lin; Bian, Ce; Shields, C Wyatt; Cruz, Daniela F; López, Gabriel P; Charbonneau, PatrickHard 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 spheres of diameter $\sigma$ within cylinders of diameter $\sigma\leq D\leq 2.82\sigma$. Although in such a system phase transitions formally do not exist, marked structural crossovers are observed. In simulations, we find that the resulting pressure-diameter structural diagram echoes the densest packing sequence obtained at infinite pressure in this range of $D$. We also observe that the out-of-equilibrium self-assembly depends on the compression rate. Slow compression approximates equilibrium results, while fast compression can skip intermediate structures. Crossovers for which no continuous line-slip exists are found to be dynamically unfavorable, which is the source of this difference. Results from colloidal sedimentation experiments at high P\'eclet number are found to be consistent with the results of fast compressions, as long as appropriate boundary conditions are used. The similitude between compression and sedimentation results suggests that the assembly pathway does not here sensitively depend on the nature of the out-of-equilibrium dynamics.Item Open Access Bypassing sluggishness: SWAP algorithm and glassiness in high dimensionsBerthier, Ludovic; Charbonneau, Patrick; Kundu, JoyjitThe 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 $d=2$ and $3$. Here, we consider suitably optimized systems in $d=2, 3,\dots, 8$, to obtain insights into the performance and underlying physics of SWAP. We show that the speedup obtained decays rapidly with increasing the dimension. SWAP nonetheless delays systematically the onset of the activated dynamics by an amount that remains finite in the limit $d \to \infty$. This shows that the glassy dynamics in high dimensions $d>3$ is now computationally accessible using SWAP, thus opening the door for the systematic consideration of finite-dimensional deviations from the mean-field description.Item Open Access Caging and Transport in Simple Disordered Systems(2021) Hu, YiRecent advances on the glass problem motivate reexamining classical models of caging and transport. In particular, seemingly incompatible percolation and mean-field caging descriptions on the localization transition call for better understanding both. In light of this fundamental inconsistency, we study the caging and transport of a series of simple disordered systems.

We first consider the dynamics of site percolation on hypercubic lattices. Using theory and simulations, we obtain that both caging and subdiffusion scale logarithmically for dimension d ≥ d_u, the upper critical dimension of percolation. The theoretical derivation on Bethe lattice and a random graph confirm that logarithmic scalings should persist in the limit d→∞. The computational validation evaluates directly the dynamical critical exponents below d_u as well as their logarithmic scaling above d_u. Our numerical results improve various earlier estimates and are fully consistent with our theoretical predictions.

Recent implementation of efficient simulation algorithms for high-dimensional systems also facilitates the study of dense packing lattices beyond the conventional hypercubic ones. Here, we consider the percolation problem on checkerboard D_d lattices and on E_8 relatives for d=6 to 9. Precise estimates for both site and bond percolation thresholds obtained from invasion percolation simulations are compared with dimensional series expansion based on lattice animal enumeration for D_d lattices. As expected, the bond percolation threshold rapidly approaches the Bethe lattice limit as d increases for these high-connectivity lattices. Corrections, however, exhibit clear yet unexplained trends.

The random Lorentz gas (RLG) is a minimal model for transport in disordered media. Despite the broad relevance of the model, theoretical grasp over its properties remains weak. Here, we first extend analytical expectations for asymptotic high-d bounds on the void percolation threshold, and then computationally evaluate both the threshold and its criticality in various d. A simple modification of the RLG is found to bring the mean-field-like caging down to d=3.

The RLG also provides a toy model of particle caging, which is known to be relevant for describing the discontinuous dynamical transition of glasses. Following the percolation studies, we consider its exact mean-field solution in the d→∞ limit and perform simulation in d=2...20. We find that for sufficiently high d the mean-field caging transition precedes and prevents the percolation transition, which only happens on timescales diverging with d. This perturbative correction is associated with the cage heterogeneity. We further show that activated processes related to rare cage escapes destroy the glass transition in finite dimensions, leading to a rich interplay between glassiness and percolation physics. This advance suggests that the RLG can be used as a toy model to develop a first-principle description of particle hopping in structural glasses.

While the cages in the RLG are formed by non-interacting obstacles, cage structure is important for the hopping process in three-dimensional glasses. As a final note and also a future direction, a study on the three-dimensional polydisperse hard spheres with modification, named as the Mari-Kurchan-Krzakala (MKK) model was proposed. This consideration provides a controllable way to interpolate between the mean-field and the real space glasses. These insights help chart a path toward a complete description of finite-dimensional glasses.

Item Open Access Characterization and efficient Monte Carlo sampling of disordered microphases.(The Journal of chemical physics, 2021-06) Zheng, Mingyuan; Charbonneau, PatrickThe disordered microphases that develop in the high-temperature phase of systems with competing short-range attractive and long-range repulsive (SALR) interactions result in a rich array of distinct morphologies, such as cluster, void cluster, and percolated (gel-like) fluids. These different structural regimes exhibit complex relaxation dynamics with marked heterogeneity and slowdown. The overall relationship between these structures and configurational sampling schemes, however, remains largely uncharted. Here, the disordered microphases of a schematic SALR model are thoroughly characterized, and structural relaxation functions adapted to each regime are devised. The sampling efficiency of various advanced Monte Carlo sampling schemes-Virtual-Move (VMMC), Aggregation-Volume-Bias (AVBMC), and Event-Chain (ECMC)-is then assessed. A combination of VMMC and AVBMC is found to be computationally most efficient for cluster fluids and ECMC to become relatively more efficient as density increases. These results offer a complete description of the equilibrium disordered phase of a simple microphase former as well as dynamical benchmarks for other sampling schemes.Item Open Access Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study.(Soft Matter, 2014-01-14) Fusco, Diana; Headd, Jeffrey J; De Simone, Alfonso; Wang, Jun; Charbonneau, PatrickThe 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 have thus far prevented a comprehensive understanding of the phenomenon to emerge. We conduct a computational study of proteins from the rubredoxin family that bridges the two fields. Using atomistic simulations, we characterize the protein crystal contacts, and accordingly parameterize patchy particle models. Comparing the phase diagrams of these schematic models with experimental results enables us to critically examine the assumptions behind the two approaches. The study also reveals features of protein–protein interactions that can be leveraged to crystallize proteins more generally.Item Open Access Classification of crystallization outcomes using deep convolutional neural networks.(PloS one, 2018-01) Bruno, Andrew E; Charbonneau, Patrick; Newman, Janet; Snell, Edward H; So, David R; Vanhoucke, Vincent; Watkins, Christopher J; Williams, Shawn; Wilson, JulieThe 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 machine learning algorithms are trained and tested on different parts of this data set. We find that more than 94% of the test images can be correctly labeled, irrespective of their experimental origin. Because crystal recognition is key to high-density screening and the systematic analysis of crystallization experiments, this approach opens the door to both industrial and fundamental research applications.Item Open Access Clustering and assembly dynamics of a one-dimensional microphase former.(Soft matter, 2018-03-26) Hu, Yi; Charbonneau, PatrickBoth 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 targets, understanding the rich structural and dynamical properties of their disordered counterparts is essential to controlling their mesoscale assembly. Here, we study the disordered regime of a one-dimensional (1D) SALR model, whose simplicity enables detailed analysis by transfer matrices and Monte Carlo simulations. We first characterize the signature of the clustering process on macroscopic observables, and then assess the equilibration dynamics of various simulation algorithms. We notably find that cluster moves markedly accelerate the mixing time, but that event chains are of limited help in the clustering regime. These insights will inspire further study of three-dimensional microphase formers.Item Open Access Communication: Weakening the critical dynamical slowing down of models with SALR interactions.(The Journal of chemical physics, 2022-11) Zheng, Mingyuan; Tarzia, Marco; Charbonneau, PatrickIn systems with frustration, the critical slowing down of the dynamics severely impedes the numerical study of phase transitions for even the simplest of lattice models. In order to help sidestep the gelation-like sluggishness, a clearer understanding of the underlying physics is needed. Here, we first obtain generic insight into that phenomenon by studying one-dimensional and Bethe lattice versions of a schematic frustrated model, the axial next-nearest neighbor Ising (ANNNI) model. Based on these findings, we formulate two cluster algorithms that speed up the simulations of the ANNNI model on a 2D square lattice. Although these schemes do not eliminate the critical slowing own, speed-ups of factors up to 40 are achieved in some regimes.Item Open Access Competition between monomeric and dimeric crystals in schematic models for globular proteins.(J Phys Chem B, 2014-07-17) Fusco, Diana; Charbonneau, PatrickAdvances 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 kinetics, such as why (nearly) identical crystallization conditions can sometimes result in the formation of different crystal forms. Here, we develop a patchy particle model with competing sets of patches that provides a microscopic explanation of this phenomenon. We identify different regimes in which one or two crystal forms can coexist with a low-density fluid. Using analytical approximations, we extend our findings to different crystal phases, providing a general framework for treating protein crystallization when multiple crystal forms compete. Our results also suggest different experimental routes for targeting a specific crystal form, and for reducing the dynamical competition between the two forms, thus facilitating protein crystal assembly.Item Open Access Computational crystallization.(Arch Biochem Biophys, 2016-07-15) Altan, Irem; Charbonneau, Patrick; Snell, Edward HCrystallization 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 is still largely one of trial and error. In this article, efforts in the field are discussed together with a theoretical underpinning using a solubility phase diagram. Prior knowledge has been used to develop tools that computationally predict the crystallization outcome and define mutational approaches that enhance the likelihood of crystallization. For the most part these tools are based on binary outcomes (crystal or no crystal), and the full information contained in an assembly of crystallization screening experiments is lost. The potential of this additional information is illustrated by examples where new biological knowledge can be obtained and where a target can be sub-categorized to predict which class of reagents provides the crystallization driving force. Computational analysis of crystallization requires complete and correctly formatted data. While massive crystallization screening efforts are under way, the data available from many of these studies are sparse. The potential for this data and the steps needed to realize this potential are discussed.Item Open Access 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, 2017-10-10) Berthier, Ludovic; Charbonneau, Patrick; Coslovich, Daniele; Ninarello, Andrea; Ozawa, Misaki; Yaida, ShoLiquids 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. Validating this scenario is challenging, because experiments offer limited resolution, while numerical studies lag more than eight orders of magnitude behind experimentally relevant timescales. In this work, we not only close the colossal gap between experiments and simulations but manage to create in silico configurations that have no experimental analog yet. Deploying a range of computational tools, we obtain four estimates of their configurational entropy. These measurements consistently confirm that the steep entropy decrease observed in experiments is also found in simulations, even beyond the experimental glass transition. Our numerical results thus extend the observational window into the physics of glasses and reinforce the relevance of an entropy crisis for understanding their formation.Item Open Access Correction to: Obtaining Soft Matter Models of Proteins and their Phase Behavior.(Methods in molecular biology (Clifton, N.J.), 2019-01) Altan, Irem; Charbonneau, PatrickThe acknowledgement section text has been updated in the chapter.Item Open Access Crystallization of asymmetric patchy models for globular proteins in solution.(Phys Rev E Stat Nonlin Soft Matter Phys, 2013-07) Fusco, Diana; Charbonneau, PatrickAsymmetric 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 generally impacts the phase diagram and nucleation dynamics of this family of soft matter models. We find the role of the geometry asymmetry to be weak, but the energy asymmetry to markedly interfere with the crystallization thermodynamics and kinetics. These results provide a rationale for the success and occasional failure of the proposal of George and Wilson for protein crystallization conditions as well as physical guidance for developing more effective protein crystallization strategies.Item Open Access Decorrelation of the static and dynamic length scales in hard-sphere glass formers.(Phys Rev E Stat Nonlin Soft Matter Phys, 2013-04) Charbonneau, Patrick; Tarjus, GillesWe 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 heterogeneities in the dynamics unambiguously decorrelate. The former grow at a much slower rate than the latter when density increases. This observation is valid for the dynamical range that is accessible to computer simulations, which roughly corresponds to that accessible in colloidal experiments. We also find that, in this same range, no one-to-one correspondence between relaxation time and point-to-set correlation length exists. These results point to the coexistence of several relaxation mechanisms in the dynamically accessible regime of three-dimensional hard-sphere glass formers.Item Open Access Dimensional dependence of the Stokes-Einstein relation and its violation(Journal of Chemical Physics, 2013-10-28) Charbonneau, Benoit; Charbonneau, Patrick; Jin, Yuliang; Parisi, Giorgio; Zamponi, FrancescoWe 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 simulations. We then investigate the evolution of the high-density SER violation with dimension in simple hard sphere glass formers. The analysis suggests that this SER violation disappears around dimension d u = 8, above which it is not observed. The critical exponent associated with the violation appears to evolve linearly in 8 - d, below d = 8, as predicted by Biroli and Bouchaud [J. Phys.: Condens. Matter 19, 205101 (2007)], but the linear coefficient is not consistent with the prediction. The SER violation with d establishes a new benchmark for theory, and its complete description remains an open problem. © 2013 AIP Publishing LLC.Item Open Access Dimensional study of the caging order parameter at the glass transition.(Proc Natl Acad Sci U S A, 2012-08-28) Charbonneau, Patrick; Ikeda, Atsushi; Parisi, Giorgio; Zamponi, FrancescoThe 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, that the process involves self-caging, which provides an order parameter for the transition. It is also broadly assumed that this cage should have a gaussian shape in the mean-field limit. Here we show that this ansatz does not hold. By performing simulations as a function of spatial dimension d, we find the cage to keep a nontrivial form. Quantitative mean-field descriptions of the glass transition, such as mode-coupling theory, density functional theory, and replica theory, all miss this crucial element. Although the mean-field random first-order transition scenario of the glass transition is qualitatively supported here and non-mean-field corrections are found to remain small on decreasing d, reconsideration of its implementation is needed for it to result in a coherent description of experimental observations.Item Open Access Dimensional study of the dynamical arrest in a random Lorentz gas.(Phys Rev E Stat Nonlin Soft Matter Phys, 2015-04) Jin, Yuliang; Charbonneau, PatrickThe 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 the dimensional dependence of the dynamical arrest, which can be mapped onto the void percolation transition for Poisson-distributed point obstacles. We numerically determine the arrest in dimensions d=2-6. Comparison of the results with standard mode-coupling theory reveals that the dynamical theory prediction grows increasingly worse with d. In an effort to clarify the origin of this discrepancy, we relate the dynamical arrest in the RLG to the dynamic glass transition of the infinite-range Mari-Kurchan-model glass former. Through a mixed static and dynamical analysis, we then extract an improved dimensional scaling form as well as a geometrical upper bound for the arrest. The results suggest that understanding the asymptotic behavior of the random Lorentz gas may be key to surmounting fundamental difficulties with the mode-coupling theory of glasses.Item Open Access Dynamical heterogeneity in a glass-forming ideal gas.(Phys Rev E Stat Nonlin Soft Matter Phys, 2008-07) Charbonneau, Patrick; Das, Chinmay; Frenkel, DaanWe 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 an earlier study [W. van Ketel, Phys. Rev. Lett. 94, 135703 (2005)] we showed that this model has the structural properties of an ideal gas, yet the dynamical properties of a strong glass former. In the present paper we report an extensive study of the dynamical heterogeneities that appear in this system in the regime where glassy behavior sets in. On the one hand, we find that the propensity of a particle to diffuse is determined by the structure of its local environment. The local density around mobile particles is significantly less than the average density, but there is little clustering of mobile particles, and the clusters observed tend to be small. On the other hand, dynamical susceptibility results indicate that a large dynamical length scale develops even at moderate densities. This suggests that propensity and other mobility measures are an incomplete measure of the dynamical length scales in this system.