arXiv subjects

Patrick Charbonneau

Publications and source records attributed to Patrick Charbonneau.

At least 91 records · Page 5Linked to original sources

arXiv2015

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.

cond-mat.dis-nn↗

arXiv2015

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.

cond-mat.soft↗

arXiv2014

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.

cond-mat.dis-nn↗

arXiv2014

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.

cond-mat.dis-nn↗

arXiv2014

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.

cond-mat.stat-mech↗

arXiv2014

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.

q-bio.BM↗

arXiv2014

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.

cond-mat.dis-nn↗

arXiv2014

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.

cond-mat.soft↗

arXiv2013

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.

cond-mat.soft↗

arXiv2013

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.

cond-mat.stat-mech↗

arXiv2013

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.

cond-mat.soft↗

arXiv2013

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.

cond-mat.dis-nn↗

arXiv2013

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.

cond-mat.stat-mech↗

arXiv2012

[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.

cond-mat.soft↗

arXiv2012

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.

cond-mat.stat-mech↗

arXiv2012

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.

cond-mat.stat-mech↗

arXiv2012

[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.

cond-mat.soft↗

arXiv2012

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.

cond-mat.soft↗