arXiv subjects

Patrick Charbonneau

Publications and source records attributed to Patrick Charbonneau.

At least 55 records · Page 3Linked to original sources

arXiv2019

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.

cond-mat.stat-mech↗

arXiv2018

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.

q-bio.BM↗

arXiv2018

Dynamics around the Site Percolation Threshold on High-Dimensional Hypercubic Lattices

Recent advances on the glass problem motivate reexamining classical models of percolation. Here, we consider the displacement of an ant in a labyrinth near the percolation threshold on cubic lattices both below and above the upper critical dimension of simple percolation, d_u=6. Using theory and simulations, we consider the scaling regime part, and obtain that both caging and subdiffusion scale logarithmically for d >= d_u. The theoretical derivation considers Bethe lattices with generalized connectivity and a random graph model, and employs a scaling analysis to confirm that logarithmic scalings should persist in the infinite dimension limit. The computational validation employs accelerated random walk simulations with a transfer-matrix description of diffusion to evaluate 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.

cond-mat.stat-mech↗

arXiv2018

Bypassing sluggishness: SWAP algorithm and glassiness in high dimensions

The recent implementation of a swap Monte Carlo algorithm (SWAP) for polydisperse mixtures fully bypasses computational sluggishness and closes the gap between experimental and simulation timescales in physical dimensions $d=2$ 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.

cond-mat.stat-mech↗

arXiv2018

Morphology of renormalization-group flow for the de Almeida-Thouless-Gardner universality class

A replica-symmetry-breaking phase transition is predicted in a host of disordered media. The criticality of the transition has, however, long been questioned below its upper critical dimension, six, due to the absence of a critical fixed point in the renormalization-group flows at one-loop order. A recent two-loop analysis revealed a possible strong-coupling fixed point but, given the uncontrolled nature of perturbative analysis in the strong-coupling regime, debate persists. Here we examine the nature of the transition as a function of spatial dimension and show that the strong-coupling fixed point can go through a Hopf bifurcation, resulting in a critical limit cycle and a concomitant discrete scale invariance. We further investigate a different renormalization scheme and argue that the basin of attraction of the strong-coupling fixed point/limit cycle may thus stay finite for all dimensions.

cond-mat.stat-mech↗

arXiv2018

Glassy, Gardner-like Phenomenology in Minimally Polydisperse Crystalline Systems

We report on a non-equilibrium phase of matter, the minimally disordered crystal phase, which we find exists between the maximally amorphous glasses and the ideal crystal. Even though these near crystals appear highly ordered, they display glassy and jamming features akin to those observed in amorphous solids. Structurally, they exhibit a power-law scaling in their probability distribution of weak forces and small interparticle gaps as well as a flat density of vibrational states. Dynamically, they display anomalous aging above a characteristic pressure. Quantitatively this disordered crystal phase has much in common with the Gardner-like phase seen in maximally disordered solids. Near crystals should be amenable to experimental realizations in commercially-available particulate systems and are to be indispensable in verifying the theory of amorphous materials.

cond-mat.soft↗

arXiv2018

A Microscopic Model of the Stokes-Einstein Relation in Arbitrary Dimension

The Stokes-Einstein relation (SER) is one of the most robust and widely employed results from the theory of liquids. Yet sizable deviations can be observed for self-solvation, which cannot be explained by the standard 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.

cond-mat.stat-mech↗

arXiv2018

Classification of crystallization outcomes using deep convolutional neural networks

The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art 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.

q-bio.BM↗

arXiv2018

Zero-temperature glass transition in two dimensions

The nature of the glass transition is theoretically understood in the mean-field limit of infinite spatial dimensions, but the problem remains totally open in physical dimensions. Nontrivial finite-dimensional fluctuations are hard to control analytically, and experiments fail to provide conclusive evidence regarding the nature of the glass transition. Here, we use Monte Carlo simulations that fully bypass the glassy slowdown, and access equilibrium states in two-dimensional glass-forming liquids at low enough temperatures to directly probe the transition. We find that the liquid state terminates at a thermodynamic glass transition at zero temperature, which is associated with an entropy crisis and a diverging static correlation length.

cond-mat.stat-mech↗

arXiv2018

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.

cond-mat.soft↗

arXiv2018

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.

cond-mat.soft↗

arXiv2017

Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling

Liquids relax extremely slowly upon approaching the glass state. One explanation is that an entropy crisis, due to 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 new observational window into the physics of glasses and reinforce the relevance of an entropy crisis for understanding their formation.

cond-mat.stat-mech↗

arXiv2017

Origin of ultrastability in vapor-deposited glasses

Glass films created by vapor-depositing molecules onto a substrate can exhibit properties similar to those of ordinary glasses aged for thousands of years. It is believed that enhanced surface mobility is the mechanism that allows vapor deposition to create such exceptional glasses, but it is unclear how this effect is related to the final state of the film. Here we use molecular dynamics simulations to model vapor deposition and an efficient Monte Carlo algorithm to determine the deposition rate needed to create ultra-stable glassy films. We obtain a scaling relation that quantitatively captures the efficiency gain of vapor deposition over bulk annealing, and demonstrates that surface relaxation plays the same role in the formation of vapor-deposited glasses as bulk relaxation does in ordinary glass formation.

cond-mat.soft↗

arXiv2017

Cycle-expansion method for the Lyapunov exponent, susceptibility, and higher moments

Lyapunov exponents characterize the chaotic nature of dynamical systems by quantifying the growth rate of uncertainty associated with the imperfect measurement of initial conditions. Finite-time estimates of the exponent, however, experience fluctuations due to both the initial condition and the stochastic nature of the dynamical path. The scale of these fluctuations is governed by the Lyapunov susceptibility, the finiteness of which typically provides a sufficient condition for the law of large numbers to apply. Here, we obtain a formally exact expression for this susceptibility in terms of the Ruelle dynamical zeta function for one-dimensional systems. We further show that, for systems governed by sequences of random matrices, the cycle expansion of the zeta function enables systematic computations of the Lyapunov susceptibility and of its higher-moment generalizations. The method is here applied to a class of dynamical models that maps to static disordered spin chains with interactions stretching over a varying distance, and is tested against Monte Carlo simulations.

cond-mat.stat-mech↗

arXiv2017

Microphase Equilibrium and Assembly Dynamics

Despite many attempts, ordered equilibrium microphases have yet to be obtained in experimental colloidal suspensions. The recent computation of the equilibrium phase diagram of a microscopic, particle-based microphase former [Zhuang et al., Phys. Rev. Lett. 116, 098301 (2016)] has nonetheless found such mesoscale assemblies to be thermodynamically stable. Here, we consider their equilibrium and assembly dynamics. At intermediate densities above the order-disorder transition, we identify four different dynamical regimes and the structural changes that underlie the dynamical crossovers from one disordered regime to the next. Below the order-disorder transition, we also find that periodic lamellae are the most dynamically accessible of the periodic microphases. Our analysis thus offers a comprehensive view of the disordered microphase dynamics and a route to the assembly of periodic microphases in a putative well-controlled, experimental system.

cond-mat.soft↗

arXiv2017

Lecture Notes on the Statistical Mechanics of Disordered Systems

This material complements David Chandler's Introduction to Modern Statistical Mechanics (Oxford University Press, 1987) in a graduate-level, one-semester course I teach in the Department of Chemistry at Duke University. Students enter this course with some knowledge of statistical thermodynamics and quantum mechanics, usually acquired from undergraduate physical chemistry at the level of D. A. McQuarrie & J. D. Simon's Physical Chemistry: A Molecular Approach (University Science Books, 1997). These notes, which introduce students to a modern treatment of glassiness and to the replica method, build on the material and problems contained in the eight chapters of Chandler's textbook.

cond-mat.stat-mech↗

arXiv2017

Nontrivial critical fixed point for replica-symmetry-breaking transitions

The transformation of the free-energy landscape from smooth to hierarchical is one of the richest features of mean-field disordered systems. A well-studied example is the de Almeida-Thouless transition for spin glasses in a magnetic field, and a similar phenomenon--the Gardner transition--has recently been predicted for structural glasses. The existence of these replica-symmetry-breaking phase transitions has, however, long been questioned below their upper critical dimension, d_u=6. Here, we obtain evidence for the existence of these transitions in d<d_u using a two-loop calculation. Because the critical fixed point is found in the strong-coupling regime, we corroborate the result by resumming the perturbative series with inputs from a three-loop calculation and an analysis of its large-order behavior. Our study offers a resolution of the long-lasting controversy surrounding phase transitions in finite-dimensional disordered systems.

cond-mat.stat-mech↗

arXiv2017

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.

cond-mat.soft↗