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Patrick Charbonneau

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Published work

54 published item(s)

preprint2026arXiv

The critical slowing down in diffusion models

Computational sampling has been central to the sciences since the mid-20th century. While machine-learning-based approaches have recently enabled major advances, their behavior remains poorly understood, with limited theoretical control over when and why they succeed. Here we provide such insight for diffusion models-a class of generative schemes highly effective in practice-by analyzing their application to the $O(n)$ model of statistical field theory in the Gaussian limit $n \to \infty$. In this analytically tractable setting, we show that training a score model with a one-layer network architecture matching the exact solution exhibits a form of critical slowing down in parameter learning. This slowing down also impacts the generation process, indicating that the well-known difficulties of sampling near criticality persist even for learned generative models. To overcome this bottleneck, we demonstrate the power of combining architectural depth with physical locality. We find that using a two-layer architecture drastically reduces the critical slowing down, with the training time scaling logarithmically rather than quadratically with system size. By introducing a local score approximation we show that this acceleration in training time can be achieved without increasing the number of neural network parameters. Taken together, these results demonstrate that diffusion models can overcome the critical slowing down through appropriate architectural design, and establish a controlled framework for understanding and improving learned sampling methods in statistical physics and beyond.

preprint2022arXiv

Equilibrium Fluctuations in Mean-field Disordered Models

Mean-field models of glasses that present a random first order transition exhibit highly non-trivial fluctuations. Building on previous studies that focused on the critical scaling regime, we here obtain a fully quantitative framework for all equilibrium conditions. By means of the replica method we evaluate Gaussian fluctuations of the overlaps around the thermodynamic limit, decomposing them in thermal fluctuations inside each state and heterogeneous fluctuations between different states. We first test and compare our analytical results with numerical simulation results for the p-spin spherical model and the random orthogonal model, and then analyze the random Lorentz gas. In all cases, a strong quantitative agreement is obtained. Our analysis thus provides a robust scheme for identifying the key finite-size (or finite-dimensional) corrections to the mean-field treatment of these paradigmatic glass models.

preprint2022arXiv

Local dynamical heterogeneity in glass formers

We study the local dynamical fluctuations in glass-forming models of particles embedded in $d$-dimensional space, in the mean-field limit of $d\to\infty$. Our analytical calculation reveals that single-particle observables, such as squared particle displacements, display divergent fluctuations around the dynamical (or mode-coupling) transition, due to the emergence of nontrivial correlations between displacements along different directions. This effect notably gives rise to a divergent non-Gaussian parameter, $α_2$. The $d\to\infty$ local dynamics therefore becomes quite rich upon approaching the glass transition. The finite-$d$ remnant of this phenomenon further provides a long sought-after, first-principle explanation for the growth of $α_2$ around the glass transition that is \emph{not based on multi-particle correlations}.

preprint2021arXiv

The dimensional evolution of structure and dynamics in hard sphere liquids

The formulation of the mean-field, infinite-dimensional solution of hard sphere glasses is a significant milestone for theoretical physics. How relevant this description might be for understanding low-dimensional glass-forming liquids, however, remains unclear. These liquids indeed exhibit a complex interplay between structure and dynamics, and the importance of this interplay might only slowly diminish as dimension $d$ increases. A careful numerical assessment of the matter has long been hindered by the exponential increase of computational costs with $d$. By revisiting a once common simulation technique involving the use of periodic boundary conditions modeled on $D_d$ lattices, we here partly sidestep this difficulty, thus allowing the study of hard sphere liquids up to $d=13$. Parallel efforts by Mangeat and Zamponi [Phys. Rev. E 93, 012609 (2016)] have expanded the mean-field description of glasses to finite $d$ by leveraging standard liquid-state theory, and thus help bridge the gap from the other direction. The relatively smooth evolution of both structure and dynamics across the $d$ gap allows us to relate the two approaches, and to identify some of the missing features that a finite-$d$ theory of glasses might hope to include to achieve near quantitative agreement.

preprint2021arXiv

Thermodynamic stability of hard sphere crystals in dimensions 3 through 10

Although much is known about the metastable liquid branch of hard spheres--from low dimension $d$ up to ${d\to\infty}$--its crystal counterpart remains largely unexplored for $d>3$. In particular, it is unclear whether the crystal phase is thermodynamically stable in high dimensions and thus whether a mean-field theory of crystals can ever be exact. In order to determine the stability range of hard sphere crystals, their equation of state is here estimated from numerical simulations, and fluid-crystal coexistence conditions are determined using a generalized Frenkel-Ladd scheme to compute absolute crystal free energies. The results show that the crystal phase is stable at least up to $d=10$, and the dimensional trends suggest that crystal stability likely persists well beyond that point.

preprint2020arXiv

Memory formation in jammed hard spheres

Liquids equilibrated below an onset density share similar inherent states, while above that density their inherent states markedly differ. Although this phenomenon was first reported in simulations over 20 years ago, the physical origin of this memory remains controversial. Its absence from mean-field descriptions, in particular, has long cast doubt on its thermodynamic relevance. Motivated by a recent theoretical proposal, we reassess the onset phenomenology in simulations using a fast hard sphere jamming algorithm and find it both thermodynamically and dimensionally robust. Remarkably, we also uncover a second type of memory associated with a Gardner-like change in behavior along the jamming algorithm.

preprint2019arXiv

Finite-dimensional vestige of spinodal criticality above the dynamical glass transition

Finite-dimensional signatures of spinodal criticality are notoriously difficult to come by. The dynamical transition of glass-forming liquids, first described by mode-coupling theory, is a spinodal instability preempted by thermally activated processes that also limit how close the instability can be approached. We combine numerical tools to directly observe vestiges of the spinodal criticality in finite-dimensional glass formers. We use the swap Monte Carlo algorithm to efficiently thermalise configurations beyond the mode-coupling crossover, and analyze their dynamics using a scheme to screen out activated processes, in spatial dimensions ranging from $d=3$ to $d=9$. We observe a strong softening of the mean-field square-root singularity in $d=3$ that is progressively restored as $d$ increases above $d=8$, in surprisingly good agreement with perturbation theory.

preprint2019arXiv

Postponing the dynamical transition density using competing interactions

Systems of dense spheres interacting through very short-ranged attraction are known from theory, simulations and colloidal experiments to exhibit dynamical reentrance. The liquid state can thus be fluidized to higher densities than otherwise possible with interactions that are purely repulsive or long-ranged attractive. A recent mean-field, infinite-dimensional calculation predicts that the dynamical arrest of the fluid can be further delayed by adding a longer-ranged repulsive contribution to the short-ranged attraction. We examine this proposal by performing extensive numerical simulations in a three-dimensional system. We first find the short-ranged attraction parameters necessary to achieve the densest liquid state, and then explore the parameters space for an additional longer-ranged repulsion that could enhance the effect. In the family of systems studied, no significant (within numerical accuracy) delay of the dynamical arrest is observed beyond what is already achieved by the short-ranged attraction. Possible explanations are discussed.

preprint2019arXiv

Using schematic models to understand the microscopic basis for inverted solubility in $γ$D-crystallin

Inverted solubility--a crystal melting upon cooling--is observed in a handful of proteins, such as carbomonoxy hemoglobin and $γ$D-crystallin. In human $γ$D-crystallin, the phenomenon is associated with the mutation of the 23$^\mathrm{rd}$ residue, a proline, to a threonine, serine or valine. One proposed microscopic mechanism for this effect entails an increase in hydrophobicity upon mutagenesis. Recent crystal structures of a double mutant that includes the P23T mutation allows for a more careful investigation of this proposal. Here, we first measure the surface hydrophobicity of various mutant structures of this protein and determine that it does not discernibly increase upon the mutating the 23$^\mathrm{rd}$ residue. We then investigate the solubility inversion regime with a schematic patchy particle model that includes one of three models for temperature-dependent patch energies: two of the hydrophobic effect, and a more generic description. We conclude that while solubility inversion due to the hydrophobic effect may be possible, microscopic evidence to support it in $γ$D-crystallin is weak. More generally, we find that solubility inversion requires a fine balance between patch strengths and the temperature-dependent contribution, which may explain why inverted solubility is not commonly observed in proteins. In any event, we also find that the temperature-dependent interaction has only a negligible impact on the critical properties of the $γ$D-crystallin, in line with previous experimental observations.

preprint2018arXiv

Clustering and assembly dynamics of a one-dimensional microphase former

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 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 guide further study of three-dimensional microphase formers.

preprint2018arXiv

Correlation lengths in quasi-one-dimensional systems via transfer matrices

Using transfer matrices up to next-nearest-neighbour (NNN) interactions, we examine the structural correlations of quasi-one-dimensional systems of hard disks confined by two parallel lines and hard spheres confined in cylinders. Simulations have shown that the non-monotonic and non-smooth growth of the correlation length in these systems accompanies structural crossovers (Fu et al., Soft Matter, 2017, 13, 3296). Here, we identify the theoretical basis for these behaviour. In particular, we associate kinks in the growth of correlation lengths with eigenvalue crossing and splitting. Understanding the origin of such structural crossovers answers questions raised by earlier studies, and thus bridges the gap between theory and simulations for these reference models.

preprint2018arXiv

Temperature-dependent non-covalent protein-protein interactions explain normal and inverted solubility in a mutant of human gamma D-crystallin

Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) of the protein surface due to the variety of amino acid side chains in contact with solvent, contributes to protein protein contact formation in the crystal lattice is a major obstacle to predicting and optimising crystallization. The relative scarcity of sophisticated theoretical models that include sufficient detail to link collective behaviour, captured in protein phase diagrams, and molecular level details, determined from high-resolution structural information is a further barrier. Here we present two crystals structures for the P23TR36S mutant of gamma D-crystallin, each with opposite solubility behaviour, one melts when heated, the other when cooled. When combined with the protein phase diagram and a tailored patchy particle model we show that a single temperature dependent interaction is sufficient to stabilise the inverted solubility crystal. This contact, at the P23T substitution site, relates to a genetic cataract and reveals at a molecular level, the origin of the lowered and retrograde solubility of the protein. Our results show that the approach employed here may present an alternative strategy for the rationalization of protein crystallization.

preprint2017arXiv

Phase diagram and aggregation dynamics of a monolayer of paramagnetic colloids

We have developed a tunable colloidal system and a corresponding simulation model for studying the phase behavior of particles assembling under the influence of long-range magnetic interactions. A monolayer of paramagnetic particles is subjected to a spatially uniform magnetic field with a static perpendicular component and rapidly rotating in-plane component. The sign and strength of the interactions vary with the tilt angle $θ$ of the rotating magnetic field. For a purely in-plane field, $θ=90^{\circ}$, interactions are attractive and the experimental results agree well with both equilibrium and out-of-equilibrium predictions based on a two-body interaction model. For tilt angles $50^{\circ}\lesssim θ\lesssim 55^{\circ}$, the two-body interaction gives a short-range attractive and long-range repulsive (SALR) interaction, which predicts the formation of equilibrium microphases. In experiments, however, a different type of assembly is observed. Inclusion of three-body (and higher-order) terms in the model does not resolve the discrepancy. We thus further characterize the anomalous behavior by measuring the time-dependent cluster size distribution.

preprint2016arXiv

Assembly of hard spheres in a cylinder: a computational and experimental study

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 spheres of diameter $σ$ within cylinders of diameter $σ\leq D\leq 2.82σ$. 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 Péclet 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.

preprint2016arXiv

Efficient measurement of point-to-set correlations and overlap fluctuations in glass-forming liquids

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 remains, however, a major computational challenge. Here, we develop a general parallel-tempering method that provides orders-of-magnitude improvement for sampling and equilibrating configurations within cavities. We apply this improved scheme to the canonical Kob-Andersen binary Lennard-Jones model for temperatures down to the mode-coupling theory crossover. Most significant improvements are noted for small cavities, which have thus far been the most difficult to study. This methodological advance also enables us to study a broader range of physical observables associated with thermodynamic fluctuations. We measure the probability distribution of overlap fluctuations in cavities, which displays a non-trivial temperature evolution. The corresponding overlap susceptibility is found to provide a robust quantitative estimate of the point-to-set length scale requiring no fitting. By resolving spatial fluctuations of the overlap in the cavity, we also obtain quantitative information about the geometry of overlap fluctuations. We can thus examine in detail how the penetration length as well as its fluctuations evolve with temperature and cavity size.

preprint2016arXiv

Equilibrium Phase Behavior of a Continuous-Space Microphase Former

Periodic microphases universally emerge in systems for which short-range inter-particle attraction is frustrated by long-range repulsion. The morphological richness of these phases makes them desirable material targets, but our relatively coarse understanding of even simple models limits our grasp of their assembly. We report here the solution of the equilibrium phase behavior of a microscopic microphase former through specialized Monte Carlo simulations. The results for the ordered regime qualitatively agree with a Landau-type free energy description and highlight the nontrivial dynamical interplay between micelle, gel and microphase formation.

preprint2016arXiv

Equilibrium phase behavior of the square-well linear microphase-forming model

We have recently developed a simulation approach to calculate the equilibrium phase diagram of particle-based microphase formers. Here, this approach is used to calculate the phase behavior of the square-well linear model for different strengths and ranges of the linear long-range repulsive component. The results are compared with various theoretical predictions for microphase formation. The analysis further allows us to better understand the mechanism for microphase formation in colloidal suspensions.

preprint2016arXiv

Growing timescales and lengthscales characterizing vibrations of amorphous solids

Low-temperature properties of crystalline solids can be understood using harmonic perturbations around a perfect lattice, as in Debye's theory. Low-temperature properties of amorphous solids, however, strongly depart from such descriptions, displaying enhanced transport, activated slow dynamics across energy barriers, excess vibrational modes with respect to Debye's theory (i.e., a Boson Peak), and complex irreversible responses to small mechanical deformations. These experimental observations indirectly suggest that the dynamics of amorphous solids becomes anomalous at low temperatures. Here, we present direct numerical evidence that vibrations change nature at a well-defined location deep inside the glass phase of a simple glass former. We provide a real-space description of this transition and of the rapidly growing time and length scales that accompany it. Our results provide the seed for a universal understanding of low-temperature glass anomalies within the theoretical framework of the recently discovered Gardner phase transition.

preprint2016arXiv

Kinetic Monte Carlo Simulations for Birefringence Relaxation of Photo-Switchable Molecules on a Surface

Recent experiments have demonstrated that in a dense monolayer of photo-switchable dye Methyl-Red molecules the relaxation of an initial birefringence follows a power-law decay, typical for glass-like dynamics. The slow relaxation can efficiently be controlled and accelerated by illuminating the monolayer with circularly polarized light, which induces trans-cis isomerization cycles. To elucidate the microscopic mechanism, we develop a two-dimensional molecular model in which the trans and cis isomers are represented by straight and bent needles, respectively. As in the experimental system, the needles are allowed to rotate and to form overlaps but they cannot translate. The out-of-equilibrium rotational dynamics of the needles is generated using kinetic Monte Carlo simulations. We demonstrate that, in a regime of high density and low temperature, the power-law relaxation can be traced to the formation of spatio-temporal correlations in the rotational dy- namics, i.e., dynamic heterogeneity. We also show that the nearly isotropic cis isomers can prevent dynamic heterogeneity from forming in the monolayer and that the relaxation then becomes exponential.

preprint2016arXiv

Linking dynamical heterogeneity to static amorphous order

Glass-forming liquids grow dramatically sluggish upon cooling. This slowdown has long been thought to be accompanied by a growing correlation length. Characteristic dynamical and static length scales, however, have been observed to grow at different rates, which perplexes the relationship between the two and with the slowdown. Here, we show the existence of a direct link between dynamical sluggishness and static point-to-set correlations, holding at the local level as we probe different environments within a liquid. This link, which is stronger and more general than that observed with locally preferred structures, suggests the existence of an intimate relationship between structure and dynamics in a broader range of glass-forming liquids than previously thought.

preprint2016arXiv

Point-to-set lengths, local structure, and glassiness

The growing sluggishness of glass-forming liquids is thought to be accompanied by growing structural order. The nature of such order, however, remains hotly debated. A decade ago, point-to-set (PTS) correlation lengths were proposed as measures of amorphous order in glass formers, but recent results raise doubts as to their generality. Here, we extend the definition of PTS correlations to agnostically capture any type of growing order in liquids, be it local or amorphous. This advance enables the formulation of a clear distinction between slowing down due to conventional critical ordering and that due to glassiness, and provides a unified framework to assess the relative importance of specific local order and generic amorphous order in glass formation.

preprint2016arXiv

Recent Advances in the Theory and Simulation of Model Colloidal Microphase Formers

This mini-review synthesizes our understanding of the equilibrium behavior of particle models with short-range attractive and long-range repulsive (SALR) interactions. These models, which can form stable periodic microphases, aim to reproduce the essence of colloidal suspensions with competing interactions. Ordered structures, however, have yet to be obtained in experiments. In order to better understand the hurdles to periodic microphase assembly, marked theoretical and simulation advances have been made over the last few years. Here, we present recent progress in the study of microphases in models with SALR interactions using liquid-state theory and density-functional theory as well as numerical simulations. Combining these various approaches provides a description of periodic microphases, and give insights into the rich phenomenology of the surrounding disordered regime. Three additional ongoing research directions in the thermodynamics of models with SALR interactions are also presented.

preprint2016arXiv

The Physics of Protein Self-Assembly

Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed phases associated with diseases, such as amyloid fibrils. Although seemingly different, these assemblies all originate from fundamental protein interactions and are driven by similar thermodynamic and kinetic factors. Here we review recent advances in understanding protein self-assembly through a soft condensed matter perspective with an emphasis on three specific systems: globular proteins, viruses and amyloid fibers. We conclude with a discussion of unanswered questions in the field.

preprint2015arXiv

Computational Crystallization

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 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.

preprint2015arXiv

Dimensional study of the dynamical arrest in a random Lorentz gas

The random Lorentz gas 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. Comparing 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.

preprint2015arXiv

Hard sphere packings within cylinders

The packing of hard spheres (HS) of diameter $σ$ in a cylinder has been used to model experimental systems, such as fullerenes in nanotubes and colloidal wire assembly. Finding the densest packings of HS under this type of confinement, however, grows increasingly complex with the cylinder diameter, $D$. Little is thus known about the densest achievable packings for $D>2.873σ$. In this work, we extend the identification of the packings up to $D=4.00σ$ by adapting Torquato-Jiao's adaptive-shrinking-cell formulation and sequential-linear-programming (SLP) technique. We identify 17 new structures, almost all of them chiral. Beyond $D\approx2.85σ$, most of the structures consist of an outer shell and an inner core that compete for being close packed. In some cases, the shell adopts its own maximum density configuration, and the stacking of core spheres within it is quasiperiodic. In other cases, an interplay between the two components is observed, which may result in simple periodic structures. In yet other cases, the very distinction between core and shell vanishes, resulting in more exotic packing geometries, including some that are three-dimensional extensions of structures obtained from packing hard disks in a circle.

preprint2015arXiv

Highly Parallel Acoustic Assembly of Microparticles into Well-Ordered Colloidal Crystallites

The precise arrangement of microscopic objects is critical to the development of functional materials and ornately patterned surfaces. Here, we present an acoustics-based method for the rapid arrangement of microscopic particles into organized and programmable architectures, which are periodically spaced within a square assembly chamber. This macroscale device employs two-dimensional bulk acoustic standing waves to propel particles along the base of the chamber toward pressure nodes or antinodes, depending on the acoustic contrast factor of the particle, and is capable of simultaneously creating thousands of size-limited, isotropic and anisotropic assemblies within minutes. We pair experiments with Brownian dynamics simulations to model the migration kinetics and assembly patterns of spherical microparticles. We use these insights to predict and subsequently validate the onset of buckling of the assemblies into three-dimensional clusters by experiments upon increasing the acoustic pressure amplitude and the particle concentration. The simulations are also used to inform our experiments for the assembly of non-spherical particles, which are then recovered via fluid evaporation and directly inspected by electron microscopy. This method for assembly of particles offers several notable advantages over other approaches (e.g., magnetics, electrokinetics and optical tweezing) including simplicity, speed and scalability and can also be used in concert with other such approaches for enhancing the types of assemblies achievable.

preprint2015arXiv

Numerical detection of the Gardner transition in a mean-field glass former

Recent theoretical advances predict the existence, deep into the glass phase, of a novel phase transition, the so-called Gardner transition. This transition is associated with the emergence of a complex free energy landscape composed of many marginally stable sub-basins within a glass metabasin. In this study, we explore several methods to detect numerically the Gardner transition in a simple structural glass former, the infinite-range Mari-Kurchan model. The transition point is robustly located from three independent approaches: (i) the divergence of the characteristic relaxation time, (ii) the divergence of the caging susceptibility, and (iii) the abnormal tail in the probability distribution function of cage order parameters. We show that the numerical results are fully consistent with the theoretical expectation. The methods we propose may also be generalized to more realistic numerical models as well as to experimental systems.

preprint2015arXiv

Phase ordering of zig-zag and bow-shaped hard needles in two dimensions

We perform extensive Monte Carlo simulations of a two-dimensional bent hard-needle model in both its chiral zig-zag and its achiral bow-shape configurations and present their phase diagrams. We find evidence for a variety of stable phases: isotropic, quasi-nematic, smectic-C, anti-ferromorphic smectic-A, and modulated-nematic. This last phase consists of layers formed by supramolecular arches. They create a periodic modulation of the molecular polarity whose period is sensitively controlled by molecular geometry. We identify transition densities using correlation functions together with appropriately defined order parameters and compare them with predictions from Onsager theory. The contribution of the molecular excluded area to deviations from Onsager theory and simple liquid crystal phase morphology is discussed. We demonstrate the isotropic--quasi-nematic transition to be consistent with a Kosterlitz-Thouless disclination unbinding scenario.

preprint2015arXiv

Phase Transformations in Binary Colloidal Monolayers

Phase transformations can be difficult to characterize at the microscopic level due to the inability to directly observe individual atomic motions. Model colloidal systems, by contrast, permit the direct observation of individual particle dynamics and of collective rearrangements, which allows for real-space characterization of phase transitions. Here, we study a quasi-two-dimensional, binary colloidal alloy that exhibits liquid-solid and solid-solid phase transitions, focusing on the kinetics of a diffusionless transformation between two crystal phases. Experiments are conducted on a monolayer of magnetic and nonmagnetic spheres suspended in a thin layer of ferrofluid and exposed to a tunable magnetic field. A theoretical model of hard spheres with point dipoles at their centers is used to guide the choice of experimental parameters and characterize the underlying materials physics. When the applied field is normal to the fluid layer, a checkerboard crystal forms; when the angle between the field and the normal is sufficiently large, a striped crystal assembles. As the field is slowly tilted away from the normal, we find that the transformation pathway between the two phases depends strongly on crystal orientation, field strength, and degree of confinement of the monolayer. In some cases, the pathway occurs by smooth magnetostrictive shear, while in others it involves the sudden formation of martensitic plates.

preprint2015arXiv

Soft Matter Perspective on Protein Crystal Assembly

Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter physics to understand colloidal assembly offer some insights into the problem of crystallizing proteins. This topical review describes the various analogies that have been made between proteins and colloids in that context. We highlight the explanatory power of patchy particle models, but also the challenges of providing guidance for crystallizing specific proteins. We conclude with a presentation of possible future research directions. This article is intended for soft matter scientists interested in protein crystallization as a self-assembly problem, and as an introduction to the pertinent physics literature for protein scientists more generally.

preprint2015arXiv

Universal non-Debye scaling in the density of states of amorphous solids

At the jamming transition, amorphous packings are known to display anomalous vibrational modes with a density of states (DOS) that remains constant at low frequency. The scaling of the DOS at higher densities remains, however, unclear. One might expect to find simple Debye scaling, but recent results from effective medium theory and the exact solution of mean-field models both predict an anomalous, non-Debye scaling. Being mean-field solutions, however, these solutions are only strictly applicable to the limit of infinite spatial dimension, and it is unclear what value they have for finite-dimensional systems. Here, we study packings of soft spheres in dimensions 3 through 7 and find, far from jamming, a universal non-Debye scaling of the DOS that is consistent with the mean-field predictions. We also consider how the soft mode participation ratio converges to the mean-field prediction as dimension increases.

preprint2014arXiv

Competition between monomeric and dimeric crystals in schematic models for globular proteins

Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why (nearly) identical crystallization conditions 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.

preprint2014arXiv

Emergence of limit-periodic order in tiling models

A 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 that state during a slow quench through an infinite sequence of phase transitions. We study the model as a function of the strength of the next-nearest-neighbor interactions, and introduce closely related 3D models with only nearest-neighbor interactions that exhibit limit-periodic phases. For models with no next-nearest-neighbor interactions of the Taylor-Socolar type, there is a large degenerate classes of ground states, including crystalline patterns and limit-periodic ones, but a slow quench still yields the limit-periodic state. For the Taylor-Socolar lattice model, we present calculations of the diffraction pattern for a particular decoration of the tile that permits exact expressions for the amplitudes, and identify domain walls that slow the relaxation times in the ordered phases. For one of the 3D models, we show that the phase transitions are first order, with equilibrium structures that can be more complex than in the 2D case, and we include a proof of aperiodicity for a geometrically simple tile with only nearest-neighbor matching rules.

preprint2014arXiv

Exact theory of dense amorphous hard spheres in high dimension. III. The full RSB solution

In the first part of this paper, we derive the general replica equations that describe infinite-dimensional hard spheres at any level of replica symmetry breaking (RSB) and in particular in the fullRSB scheme. We show that these equations are formally very similar to the ones that have been derived for spin glass models, thus showing that the analogy between spin glasses and structural glasses conjectured by Kirkpatrick, Thirumalai, and Wolynes is realized in a strong sense in the mean field limit. We also suggest how the computation could be generalized in an approximate way to finite dimensional hard spheres. In the second part of the paper, we discuss the solution of these equations and we derive from it a number of physical predictions. We show that, below the Gardner transition where the 1RSB solution becomes unstable, a fullRSB phase exists and we locate the boundary of the fullRSB phase. Most importantly, we show that the fullRSB solution predicts correctly that jammed packings are isostatic, and allows one to compute analytically the critical exponents associated with the jamming transition, which are missed by the 1RSB solution. We show that these predictions compare very well with numerical results.

preprint2014arXiv

Fractal free energy landscapes in structural glasses

Glasses are amorphous solids whose constituent particles are caged by their neighbors and thus cannot flow. This sluggishness is often ascribed to the free energy landscape containing multiple minima (basins) separated by high barriers. Here we show, using theory and numerical simulation, that the landscape is much rougher than is classically assumed. Deep in the glass, it undergoes a "roughness transition" to fractal basins. This brings about isostaticity at jamming and marginality of glassy states near jamming. Critical exponents for the basin width, the weak force distribution, and the spatial spread of quasi-contacts at jamming can be analytically determined. Their value is found to be compatible with numerical observations. This advance therefore incorporates the jamming transition of granular materials into the framework of glass theory. Because temperature and pressure control which features of the landscape are experienced, glass mechanics and transport are expected to reflect the features of the topology we discuss here. Hitherto mysterious properties of low-temperature glasses could be explained by this approach.

preprint2014arXiv

Hopping and the Stokes-Einstein relation breakdown in simple glass formers

One of the most actively debated issues in the study of the glass transition is whether a mean-field description is a reasonable starting point for understanding experimental glass formers. Although the mean-field theory of the glass transition -- like that of other statistical systems -- is exact when the spatial dimension $d\rightarrow\infty$, the evolution of systems properties with $d$ may not be smooth. Finite-dimensional effects could dramatically change what happens in physical dimensions, $d=2,3$. For standard phase transitions finite-dimensional effects are typically captured by renormalization group methods, but for glasses the corrections are much more subtle and only partially understood. Here, we investigate hopping between localized cages formed by neighboring particles in a model that allows to cleanly isolate that effect. By bringing together results from replica theory, cavity reconstruction, void percolation, and molecular dynamics, we obtain insights into how hopping induces a breakdown of the Stokes--Einstein relation and modifies the mean-field scenario in experimental systems. Although hopping is found to supersede the dynamical glass transition, it nonetheless leaves a sizable part of the critical regime untouched. By providing a constructive framework for identifying and quantifying the role of hopping, we thus take an important step towards describing dynamic facilitation in the framework of the mean-field theory of glasses.

preprint2014arXiv

Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

preprint2013arXiv

Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study

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 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 their 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.

preprint2013arXiv

Decorrelation of the static and dynamic length scales in hard-sphere glass-formers

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 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 of 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 accessible dynamical regime of three-dimensional hard-sphere glass formers.

preprint2013arXiv

Dimensional dependence of the Stokes--Einstein relation and its violation

We generalize to higher spatial dimensions the Stokes--Einstein relation (SER) and the leading correction to diffusivity in periodic systems, and validate them using numerical simulations. Using these results, we investigate the evolution of the SER violation with dimension in simple hard sphere glass formers. The analysis suggests that the SER violation disappears around dimension d=8, above which SER is not violated. The critical exponent associated to the violation appears to evolve linearly in 8-d below d=8, as predicted by Biroli and Bouchaud [J. Phys.: Cond. Mat. 19, 205101 (2007)], but the linear coefficient is not consistent with their prediction. The SER violation evolution with d establishes a new benchmark for theory, and a complete description remains an open problem.

preprint2013arXiv

Geometrical Frustration and Static Correlations in Hard-Sphere Glass Formers

We analytically and numerically characterize the structure of hard-sphere fluids in order to review various geometrical frustration scenarios of the glass transition. We find generalized polytetrahedral order to be correlated with increasing fluid packing fraction, but to become increasingly irrelevant with increasing dimension. We also find the growth in structural correlations to be modest in the dynamical regime accessible to computer simulations.

preprint2013arXiv

The crystallization of asymmetric patchy models for globular proteins in solution

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 generally impact 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 George and Wilson's proposal for protein crystallization conditions as well as physical guidance for developing more effective protein crystallization strategies.

preprint2012arXiv

[N]pT ensemble and finite-size scaling study of the GEM-4 critical isostructural transition

First-order transitions of system where both lattice site occupancy and lattice spacing fluctuate, such as cluster crystals, cannot be efficiently studied by traditional simulation methods. These methods necessarily fix one of these two degrees of freedom, but this difficulty is surmounted by the generalized [N]pT ensemble [J. Chem. Phys. 136, 214106 (2012)]. Here it is shown that histogram reweighting and the [N]pT ensemble can be used to study an isostructural transition between cluster crystals of different occupancy in the generalized exponential model of index 4 (GEM-4). Extending this scheme to finite-size scaling studies also allows to accurately determine the critical point parameters and to verify that it belongs to the Ising universality class.

preprint2012arXiv

[N]pT Monte Carlo Simulations of the Cluster-Crystal-Forming Penetrable Sphere Model

Certain models with purely repulsive pair interactions can form cluster crystals with multiply-occupied lattice sites. Simulating these models' equilibrium properties is, however, quite challenging. Here, we develop an expanded isothermal-isobaric $[N]pT$ ensemble that surmounts this problem by allowing both particle number and lattice spacing to fluctuate. We apply the method with a Monte Carlo simulation scheme to solve the phase diagram of a prototypical cluster-crystal former, the penetrable sphere model (PSM), and compare the results with earlier theoretical predictions. At high temperatures and densities, the equilibrium occupancy $n_{\mathrm{c}}^{\mathrm{eq}}$ of face-centered cubic (FCC) crystal increases linearly. At low temperatures, although $n_{\mathrm{c}}^{\mathrm{eq}}$ plateaus at integer values, the crystal behavior changes continuously with density. The previously ambiguous crossover around $T\sim0.1$ is resolved.

preprint2012arXiv

Dimensional Study of the Caging Order Parameter at the Glass Transition

The glass problem is notoriously hard and controversial. Even at the mean-field level, little is agreed about how a fluid turns 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, we find the cage to keep a non-trivial 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 here qualitatively supported and non-mean-field corrections are found to remain small on decreasing dimension, reconsideration of its implementation is needed for it to result in a coherent description of experimental observations.

preprint2012arXiv

Geometrical Frustration and Static Correlations in a Simple Glass Former

We study the geometrical frustration scenario of glass formation for simple hard sphere models. We find that the dual picture in terms of defects brings little insight and no theoretical simplification for the understanding of the slowing down of relaxation, because of the strong frustration characterizing these systems. The possibility of a growing static length is furthermore found to be physically irrelevant in the regime that is accessible to computer simulations.

preprint2012arXiv

Reentrant and Isostructural Transitions in a Cluster-Crystal Former

We study the low-temperature behavior of a simple cluster-crystal forming system through simulation. The phase behavior is found to be hybrid between the Gaussian core and penetrable sphere models. The system additionally exhibits a series of reentrant crystallization and melting loops as well as critical isostructural transitions between crystals of different occupancy. Due to the creation and annihilation of lattice sites, the system further shows an unusual and intriguing softening upon compression.

preprint2012arXiv

Universal microstructure and mechanical stability of jammed packings

Jammed packings' mechanical properties depend sensitively on their detailed local structure. Here we provide a complete characterization of the pair correlation close to contact and of the force distribution of jammed frictionless spheres. In particular we discover a set of new scaling relations that connect the behavior of particles bearing small forces and those bearing no force but that are almost in contact. By performing systematic investigations for spatial dimensions d=3-10, in a wide density range and using different preparation protocols, we show that these scalings are indeed universal. We therefore establish clear milestones for the emergence of a complete microscopic theory of jamming. This description is also crucial for high-precision force experiments in granular systems.

preprint2011arXiv

A Monte Carlo Approach for Studying Microphases Applied to the Axial Next-Nearest-Neighbor Ising and the Ising-Coulomb Models

The equilibrium phase behavior of microphase-forming systems is notoriously difficult to obtain because of the extended metastability of their modulated phases. In this paper we present a systematic simulation methodology for studying layered microphases and apply the approach to two prototypical lattice-based systems: the three-dimensional axial next-nearest-neighbor Ising (ANNNI) and Ising-Coulomb (IC) models. The method involves thermodynamically integrating along a reversible path established between a reference system of free spins under an ordering field and the system of interest. The resulting free energy calculations unambiguously locate the phase boundaries. The simple phases are not observed to play a particularly significant role in the devil's flowers. With the help of generalized order parameters, the paramagnetic-modulated critical transition of the ANNNI model is also studied. We confirm the XY universality of the paramagnetic-modulated transition and its isotropic nature. Interfacial roughening is found to play at most a small role in the ANNNI layered regime.

preprint2011arXiv

Glass transition and random close packing above three dimensions

Motivated by a recently identified severe discrepancy between a static and a dynamic theory of glasses, we numerically investigate the behavior of dense hard spheres in spatial dimensions 3 to 12. Our results are consistent with the static replica theory, but disagree with the dynamic mode-coupling theory, indicating that key ingredients of high-dimensional physics are missing from the latter. We also obtain numerical estimates of the random close packing density, which provides new insights into the mathematical problem of packing spheres in large dimension.

preprint2010arXiv

Application of Edwards' statistical mechanics to high dimensional jammed sphere packings

The isostatic jamming limit of frictionless spherical particles from Edwards' statistical mechanics [Song \emph{et al.}, Nature (London) {\bf 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 $ϕ\sim d\,2^{-d}$ 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.

preprint2010arXiv

Monte Carlo Study of the Axial Next-Nearest-Neighbor Ising Model

The equilibrium phase behavior of microphase-forming substances and models is notoriously difficult to obtain because of the extended metastability of the modulated phases. We develop a simulation method based on thermodynamic integration that avoids this problem and with which we obtain the phase diagram of the canonical three-dimensional axial next-nearest-neighbor Ising model. The equilibrium devil's staircase, magnetization, and susceptibility are obtained. The critical exponents confirm the XY nature of the disorder-modulated phase transition beyond the Lifshitz point. The results identify the limitations of various approximation schemes used to analyze this basic microphase-forming model.

preprint2005arXiv

Mode-Coupling Theory (MCT) Lecture Notes

In this set of lecture notes we review the mode-coupling theory of the glass transition from several perspectives. First, we derive mode-coupling equations for the description of density fluctuations from microscopic considerations with the use the Mori-Zwanzig projection operator technique. We also derive schematic mode-coupling equations of a similar form from a field-theoretic perspective. We review the successes and failures of mode-coupling theory, and discuss recent advances in the applications of the theory.