arXiv subjects

Patrick Charbonneau

Publications and source records attributed to Patrick Charbonneau.

At least 73 records · Page 4Linked to original sources

arXiv2017

Glass and Jamming Transitions: From Exact Results to Finite-Dimensional Descriptions

Despite decades of work, gaining a first-principle understanding of amorphous materials remains an extremely challenging problem. However, recent theoretical breakthroughs have led to the formulation of an exact solution in the mean-field limit of infinite spatial dimension, and numerical simulations have remarkably confirmed the dimensional robustness of some of the predictions. This review describes these latest advances. More specifically, we consider the dynamical and thermodynamic descriptions of hard spheres around the dynamical, Gardner and jamming transitions. Comparing mean-field predictions with the finite-dimensional simulations, we identify robust aspects of the description and uncover its more sensitive features. We conclude with a brief overview of ongoing research.

cond-mat.dis-nn↗

arXiv2016

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.

cond-mat.soft↗

arXiv2016

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.

cond-mat.stat-mech↗

arXiv2016

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.

cond-mat.dis-nn↗

arXiv2016

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.

cond-mat.soft↗

arXiv2016

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.

cond-mat.soft↗

arXiv2016

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.

cond-mat.soft↗

arXiv2016

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.

cond-mat.soft↗

arXiv2016

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.

cond-mat.soft↗

arXiv2016

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.

cond-mat.soft↗

arXiv2016

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.

cond-mat.stat-mech↗

arXiv2015

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.

cond-mat.dis-nn↗

arXiv2015

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.

q-bio.BM↗

arXiv2015

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.

cond-mat.soft↗

arXiv2015

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.

cond-mat.soft↗

arXiv2015

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.

cond-mat.soft↗

arXiv2015

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.

cond-mat.stat-mech↗

arXiv2015

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.

cond-mat.dis-nn↗