%% Papers Published @article{fds338465, Author = {Norman, J and Sorrell, EL and Hu, Y and Siripurapu, V and Garcia, J and Bagwell, J and Charbonneau, P and Lubkin, SR and Bagnat, M}, Title = {Tissue self-organization underlies morphogenesis of the notochord.}, Journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, Volume = {373}, Number = {1759}, Year = {2018}, Month = {September}, url = {http://dx.doi.org/10.1098/rstb.2017.0320}, Abstract = {The notochord is a conserved axial structure that in vertebrates serves as a hydrostatic scaffold for embryonic axis elongation and, later on, for proper spine assembly. It consists of a core of large fluid-filled vacuolated cells surrounded by an epithelial sheath that is encased in extracellular matrix. During morphogenesis, the vacuolated cells inflate their vacuole and arrange in a stereotypical staircase pattern. We investigated the origin of this pattern and found that it can be achieved purely by simple physical principles. We are able to model the arrangement of vacuolated cells within the zebrafish notochord using a physical model composed of silicone tubes and water-absorbing polymer beads. The biological structure and the physical model can be accurately described by the theory developed for the packing of spheres and foams in cylinders. Our experiments with physical models and numerical simulations generated several predictions on key features of notochord organization that we documented and tested experimentally in zebrafish. Altogether, our data reveal that the organization of the vertebrate notochord is governed by the density of the osmotically swelling vacuolated cells and the aspect ratio of the notochord rod. We therefore conclude that self-organization underlies morphogenesis of the vertebrate notochord.This article is part of the Theo Murphy meeting issue on 'Mechanics of development'.}, Doi = {10.1098/rstb.2017.0320}, Key = {fds338465} } @article{fds335288, Author = {Reyes, C and Fu, L and Suthanthiraraj, PPA and Owens, CE and Shields, CW and López, GP and Charbonneau, P and Wiley, BJ}, Title = {The Limits of Primary Radiation Forces in Bulk Acoustic Standing Waves for Concentrating Nanoparticles}, Journal = {Particle & Particle Systems Characterization}, Volume = {35}, Number = {7}, Pages = {1700470-1700470}, Year = {2018}, Month = {July}, url = {http://dx.doi.org/10.1002/ppsc.201700470}, Doi = {10.1002/ppsc.201700470}, Key = {fds335288} } @article{fds337003, Author = {Hu, Y and Fu, L and Charbonneau, P}, Title = {Correlation lengths in quasi-one-dimensional systems via transfer matrices}, Journal = {Molecular Physics}, Pages = {1-10}, Year = {2018}, Month = {June}, url = {http://dx.doi.org/10.1080/00268976.2018.1479543}, Doi = {10.1080/00268976.2018.1479543}, Key = {fds337003} } @article{fds337552, Author = {Charbonneau, B and Charbonneau, P and Szamel, G}, Title = {A microscopic model of the Stokes-Einstein relation in arbitrary dimension.}, Journal = {The Journal of Chemical Physics}, Volume = {148}, Number = {22}, Pages = {224503}, Year = {2018}, Month = {June}, url = {http://dx.doi.org/10.1063/1.5029464}, Abstract = {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.}, Doi = {10.1063/1.5029464}, Key = {fds337552} } @article{fds333301, Author = {Hu, Y and Charbonneau, P}, Title = {Clustering and assembly dynamics of a one-dimensional microphase former.}, Journal = {Soft Matter}, Year = {2018}, Month = {March}, url = {http://dx.doi.org/10.1039/c8sm00315g}, Abstract = {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 inspire further study of three-dimensional microphase formers.}, Doi = {10.1039/c8sm00315g}, Key = {fds333301} } @article{fds333302, Author = {Altan, I and Fusco, D and Afonine, PV and Charbonneau, P}, Title = {Learning about Biomolecular Solvation from Water in Protein Crystals.}, Journal = {Journal of Physical Chemistry B}, Volume = {122}, Number = {9}, Pages = {2475-2486}, Year = {2018}, Month = {March}, url = {http://dx.doi.org/10.1021/acs.jpcb.7b09898}, Abstract = {Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are not localized and are thus difficult to assign to specific density peaks. The intricateness of the protein-water interface compounds this difficulty. This information has, therefore, not often been used to study biomolecular solvation. Here, we develop a methodology to surmount in part this difficulty. More specifically, we compare the solvent structure obtained from diffraction data for which experimental phasing is available to that obtained from constrained molecular dynamics (MD) simulations. The resulting spatial density maps show that commonly used MD water models are only partially successful at reproducing the structural features of biomolecular solvation. The radial distribution of water is captured with only slightly higher accuracy than its angular distribution, and only a fraction of the water molecules assigned with high reliability to the crystal structure is recovered. These differences are likely due to shortcomings of both the water models and the protein force fields. Despite these limitations, we manage to infer protonation states of some of the side chains utilizing MD-derived densities.}, Doi = {10.1021/acs.jpcb.7b09898}, Key = {fds333302} } @article{fds337004, Author = {Bruno, AE and Charbonneau, P and Newman, J and Snell, EH and So, DR and Vanhoucke, V and Watkins, CJ and Williams, S and Wilson, J}, Title = {Classification of crystallization outcomes using deep convolutional neural networks.}, Journal = {Plos One}, Volume = {13}, Number = {6}, Pages = {e0198883}, Year = {2018}, Month = {January}, url = {http://dx.doi.org/10.1371/journal.pone.0198883}, Abstract = {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.}, Doi = {10.1371/journal.pone.0198883}, Key = {fds337004} } @article{fds331333, Author = {Berthier, L and Charbonneau, P and Flenner, E and Zamponi, F}, Title = {Origin of Ultrastability in Vapor-Deposited Glasses.}, Journal = {Physical Review Letters}, Volume = {119}, Number = {18}, Pages = {188002}, Year = {2017}, Month = {November}, url = {http://dx.doi.org/10.1103/physrevlett.119.188002}, Abstract = {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 ultrastable 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.}, Doi = {10.1103/physrevlett.119.188002}, Key = {fds331333} } @article{fds329889, Author = {Berthier, L and Charbonneau, P and Coslovich, D and Ninarello, A and Ozawa, M and Yaida, S}, Title = {Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling.}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Volume = {114}, Number = {43}, Pages = {11356-11361}, Year = {2017}, Month = {October}, url = {http://dx.doi.org/10.1073/pnas.1706860114}, Abstract = {Liquids relax extremely slowly on approaching the glass state. One explanation is that an entropy crisis, because of the rarefaction of available states, makes it increasingly arduous to reach equilibrium in that regime. Validating this scenario is challenging, because experiments offer limited resolution, while numerical studies lag more than eight orders of magnitude behind experimentally relevant timescales. In this work, we not only close the colossal gap between experiments and simulations but manage to create in silico configurations that have no experimental analog yet. Deploying a range of computational tools, we obtain four estimates of their configurational entropy. These measurements consistently confirm that the steep entropy decrease observed in experiments is also found in simulations, even beyond the experimental glass transition. Our numerical results thus extend the observational window into the physics of glasses and reinforce the relevance of an entropy crisis for understanding their formation.}, Doi = {10.1073/pnas.1706860114}, Key = {fds329889} } @article{fds328992, Author = {Charbonneau, P and Li, YC and Pfister, HD and Yaida, S}, Title = {Cycle-expansion method for the Lyapunov exponent, susceptibility, and higher moments.}, Journal = {Physical Review. E}, Volume = {96}, Number = {3-1}, Pages = {032129}, Year = {2017}, Month = {September}, url = {http://dx.doi.org/10.1103/physreve.96.032129}, Abstract = {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 ζ function for one-dimensional systems. We further show that, for systems governed by sequences of random matrices, the cycle expansion of the ζ 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.}, Doi = {10.1103/physreve.96.032129}, Key = {fds328992} } @article{fds328993, Author = {Zhuang, Y and Charbonneau, P}, Title = {Communication: Microphase equilibrium and assembly dynamics.}, Journal = {The Journal of Chemical Physics}, Volume = {147}, Number = {9}, Pages = {091102}, Year = {2017}, Month = {September}, url = {http://dx.doi.org/10.1063/1.4996904}, Abstract = {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 dynamics of disordered microphases and a route to the assembly of periodic microphases in a putative well-controlled, experimental system.}, Doi = {10.1063/1.4996904}, Key = {fds328993} } @article{fds326546, Author = {Charbonneau, P and Yaida, S}, Title = {Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions.}, Journal = {Physical Review Letters}, Volume = {118}, Number = {21}, Pages = {215701}, Year = {2017}, Month = {May}, url = {http://dx.doi.org/10.1103/physrevlett.118.215701}, Abstract = {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.}, Doi = {10.1103/physrevlett.118.215701}, Key = {fds326546} } @article{fds326691, Author = {Pham, AT and Zhuang, Y and Detwiler, P and Socolar, JES and Charbonneau, P and Yellen, BB}, Title = {Phase diagram and aggregation dynamics of a monolayer of paramagnetic colloids.}, Journal = {Physical Review. E}, Volume = {95}, Number = {5-1}, Pages = {052607}, Year = {2017}, Month = {May}, url = {http://dx.doi.org/10.1103/physreve.95.052607}, Abstract = {We have developed a tunable colloidal system and a corresponding theoretical 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 a 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^{∘}, 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^{∘}≲θ≲55^{∘}, the two-body interaction gives a short-range attractive and long-range repulsive 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 further characterize the anomalous regime by measuring the time-dependent cluster size distribution.}, Doi = {10.1103/physreve.95.052607}, Key = {fds326691} } @article{fds325814, Author = {Fu, L and Bian, C and Shields, CW and Cruz, DF and López, GP and Charbonneau, P}, Title = {Assembly of hard spheres in a cylinder: a computational and experimental study.}, Journal = {Soft Matter}, Volume = {13}, Number = {18}, Pages = {3296-3306}, Year = {2017}, Month = {May}, url = {http://dx.doi.org/10.1039/c7sm00316a}, Abstract = {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≤D≤ 2.82σ. Although phase transitions formally do not exist in such systems, marked structural crossovers can nonetheless be observed. Over this range of D, we find in simulations that structural crossovers echo the structural changes in the sequence of densest packings. 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 main source of this difference. Results from colloidal sedimentation experiments at low diffusion rate are found to be consistent with the results of fast compressions, as long as appropriate boundary conditions are used.}, Doi = {10.1039/c7sm00316a}, Key = {fds325814} } @article{fds325416, Author = {Charbonneau, P and Kurchan, J and Parisi, G and Urbani, P and Zamponi, F}, Title = {Glass and Jamming Transitions: From Exact Results to Finite-Dimensional Descriptions}, Journal = {Annual Review of Condensed Matter Physics}, Volume = {8}, Number = {1}, Pages = {265-288}, Year = {2017}, Month = {March}, url = {http://dx.doi.org/10.1146/annurev-conmatphys-031016-025334}, Doi = {10.1146/annurev-conmatphys-031016-025334}, Key = {fds325416} } @article{fds318060, Author = {Yaida, S and Berthier, L and Charbonneau, P and Tarjus, G}, Title = {Point-to-set lengths, local structure, and glassiness.}, Journal = {Physical Review. E}, Volume = {94}, Number = {3-1}, Pages = {032605}, Year = {2016}, Month = {September}, url = {http://dx.doi.org/10.1103/physreve.94.032605}, Abstract = {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.}, Doi = {10.1103/physreve.94.032605}, Key = {fds318060} } @article{fds318061, Author = {Zhuang, Y and Charbonneau, P}, Title = {Recent Advances in the Theory and Simulation of Model Colloidal Microphase Formers.}, Journal = {Journal of Physical Chemistry B}, Volume = {120}, Number = {32}, Pages = {7775-7782}, Year = {2016}, Month = {August}, url = {http://dx.doi.org/10.1021/acs.jpcb.6b05471}, Abstract = {This mini-review synthesizes our understanding of the equilibrium behavior of particle-based 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 interparticle 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 past 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 gives insights into the rich phenomenology of the surrounding disordered regime. Ongoing research directions in the thermodynamics of models with SALR interactions are also presented.}, Doi = {10.1021/acs.jpcb.6b05471}, Key = {fds318061} } @article{fds318062, Author = {Charbonneau, P and Corwin, EI and Parisi, G and Poncet, A and Zamponi, F}, Title = {Universal Non-Debye Scaling in the Density of States of Amorphous Solids.}, Journal = {Physical Review Letters}, Volume = {117}, Number = {4}, Pages = {045503}, Year = {2016}, Month = {July}, url = {http://dx.doi.org/10.1103/physrevlett.117.045503}, Abstract = {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 packing fractions remains, however, unclear. One might expect to find a 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 in nature, however, these solutions are only strictly valid in 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, away 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 evolves as dimension increases.}, Doi = {10.1103/physrevlett.117.045503}, Key = {fds318062} } @article{fds318063, Author = {Berthier, L and Charbonneau, P and Jin, Y and Parisi, G and Seoane, B and Zamponi, F}, Title = {Growing timescales and lengthscales characterizing vibrations of amorphous solids.}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Volume = {113}, Number = {30}, Pages = {8397-8401}, Year = {2016}, Month = {July}, url = {http://dx.doi.org/10.1073/pnas.1607730113}, Abstract = {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 lengthscales 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.}, Doi = {10.1073/pnas.1607730113}, Key = {fds318063} } @article{fds311997, Author = {Altan, I and Charbonneau, P and Snell, EH}, Title = {Computational crystallization.}, Journal = {Archives of Biochemistry and Biophysics}, Volume = {602}, Pages = {12-20}, Year = {2016}, Month = {July}, ISSN = {0003-9861}, url = {http://dx.doi.org/10.1016/j.abb.2016.01.004}, Abstract = {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.}, Doi = {10.1016/j.abb.2016.01.004}, Key = {fds311997} } @article{fds318064, Author = {Charbonneau, P and Dyer, E and Lee, J and Yaida, S}, Title = {Linking dynamical heterogeneity to static amorphous order}, Journal = {Journal of Statistical Mechanics: Theory and Experiment}, Volume = {2016}, Number = {7}, Pages = {074004-074004}, Year = {2016}, Month = {July}, url = {http://dx.doi.org/10.1088/1742-5468/2016/07/074004}, Doi = {10.1088/1742-5468/2016/07/074004}, Key = {fds318064} } @article{fds318065, Author = {Zhuang, Y and Charbonneau, P}, Title = {Equilibrium Phase Behavior of the Square-Well Linear Microphase-Forming Model.}, Journal = {Journal of Physical Chemistry B}, Volume = {120}, Number = {26}, Pages = {6178-6188}, Year = {2016}, Month = {July}, url = {http://dx.doi.org/10.1021/acs.jpcb.6b02167}, Abstract = {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.}, Doi = {10.1021/acs.jpcb.6b02167}, Key = {fds318065} } @article{fds318066, Author = {McManus, JJ and Charbonneau, P and Zaccarelli, E and Asherie, N}, Title = {The physics of protein self-assembly}, Journal = {Current Opinion in Colloid & Interface Science}, Volume = {22}, Pages = {73-79}, Year = {2016}, Month = {April}, url = {http://dx.doi.org/10.1016/j.cocis.2016.02.011}, Doi = {10.1016/j.cocis.2016.02.011}, Key = {fds318066} } @article{fds311996, Author = {Fu, L and Steinhardt, W and Zhao, H and Socolar, JES and Charbonneau, P}, Title = {Hard sphere packings within cylinders.}, Journal = {Soft Matter}, Volume = {12}, Number = {9}, Pages = {2505-2514}, Year = {2016}, Month = {March}, ISSN = {1744-683X}, url = {http://dx.doi.org/10.1039/c5sm02875b}, Abstract = {Arrangements of identical hard spheres confined to a cylinder with hard walls have been used to model experimental systems, such as fullerenes in nanotubes and colloidal wire assembly. Finding the densest configurations, called close packings, of hard spheres of diameter σ in a cylinder of diameter D is a purely geometric problem that grows increasingly complex as D/σ increases, and little is thus known about the regime for D > 2.873σ. In this work, we extend the identification of close 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 ≈ 2.85σ, 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 the 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.}, Doi = {10.1039/c5sm02875b}, Key = {fds311996} } @article{fds318067, Author = {Tavarone, R and Charbonneau, P and Stark, H}, Title = {Kinetic Monte Carlo simulations for birefringence relaxation of photo-switchable molecules on a surface.}, Journal = {The Journal of Chemical Physics}, Volume = {144}, Number = {10}, Pages = {104703}, Year = {2016}, Month = {March}, url = {http://dx.doi.org/10.1063/1.4943393}, Abstract = {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 dynamics, 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.}, Doi = {10.1063/1.4943393}, Key = {fds318067} } @article{fds318068, Author = {Zhuang, Y and Zhang, K and Charbonneau, P}, Title = {Equilibrium Phase Behavior of a Continuous-Space Microphase Former.}, Journal = {Physical Review Letters}, Volume = {116}, Number = {9}, Pages = {098301}, Year = {2016}, Month = {March}, url = {http://dx.doi.org/10.1103/physrevlett.116.098301}, Abstract = {Periodic microphases universally emerge in systems for which short-range interparticle 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 hinders controlling 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 cluster crystal, cylindrical, double gyroid, and lamellar ordering qualitatively agree with a Landau-type free energy description and reveal the nontrivial interplay between cluster, gel, and microphase formation.}, Doi = {10.1103/physrevlett.116.098301}, Key = {fds318068} } @article{fds318069, Author = {Marcoux, C and Byington, TW and Qian, Z and Charbonneau, P and Socolar, JES}, Title = {Erratum: Emergence of limit-periodic order in tiling models [Phys. Rev. E 90 , 012136 (2014)]}, Journal = {Physical Review. E}, Volume = {93}, Number = {2}, Year = {2016}, Month = {February}, url = {http://dx.doi.org/10.1103/PhysRevE.93.029902}, Doi = {10.1103/PhysRevE.93.029902}, Key = {fds318069} } @article{fds232059, Author = {Fusco, D and Charbonneau, P}, Title = {Soft matter perspective on protein crystal assembly.}, Journal = {Colloids and Surfaces. B, Biointerfaces}, Volume = {137}, Pages = {22-31}, Year = {2016}, Month = {January}, ISSN = {0927-7765}, url = {http://dx.doi.org/10.1016/j.colsurfb.2015.07.023}, Abstract = {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 review 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.}, Doi = {10.1016/j.colsurfb.2015.07.023}, Key = {fds232059} } @article{fds311998, Author = {Berthier, L and Charbonneau, P and Yaida, S}, Title = {Efficient measurement of point-to-set correlations and overlap fluctuations in glass-forming liquids.}, Journal = {The Journal of Chemical Physics}, Volume = {144}, Number = {2}, Pages = {024501}, Year = {2016}, Month = {January}, ISSN = {0021-9606}, url = {http://dx.doi.org/10.1063/1.4939640}, Abstract = {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.}, Doi = {10.1063/1.4939640}, Key = {fds311998} } @article{fds311999, Author = {Owens, CE and Shields, CW and Cruz, DF and Charbonneau, P and López, GP}, Title = {Highly parallel acoustic assembly of microparticles into well-ordered colloidal crystallites.}, Journal = {Soft Matter}, Volume = {12}, Number = {3}, Pages = {717-728}, Year = {2016}, Month = {January}, ISSN = {1744-683X}, url = {http://dx.doi.org/10.1039/c5sm02348c}, Abstract = {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.}, Doi = {10.1039/c5sm02348c}, Key = {fds311999} } @article{fds232057, Author = {Tavarone, R and Charbonneau, P and Stark, H}, Title = {Phase ordering of zig-zag and bow-shaped hard needles in two dimensions.}, Journal = {The Journal of Chemical Physics}, Volume = {143}, Number = {11}, Pages = {114505}, Year = {2015}, Month = {September}, ISSN = {0021-9606}, url = {http://dx.doi.org/10.1063/1.4930886}, Abstract = {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 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.}, Doi = {10.1063/1.4930886}, Key = {fds232057} } @article{fds232060, Author = {Jin, Y and Charbonneau, P}, Title = {Dimensional study of the dynamical arrest in a random Lorentz gas.}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {91}, Number = {4}, Pages = {042313}, Year = {2015}, Month = {April}, ISSN = {1539-3755}, url = {http://dx.doi.org/10.1103/physreve.91.042313}, Abstract = {The random Lorentz gas (RLG) is a minimal model for transport in heterogeneous media. Upon increasing the obstacle density, it exhibits a growing subdiffusive transport regime and then a dynamical arrest. Here, we study the dimensional dependence of the dynamical arrest, which can be mapped onto the void percolation transition for Poisson-distributed point obstacles. We numerically determine the arrest in dimensions d=2-6. Comparison of the results with standard mode-coupling theory reveals that the dynamical theory prediction grows increasingly worse with d. In an effort to clarify the origin of this discrepancy, we relate the dynamical arrest in the RLG to the dynamic glass transition of the infinite-range Mari-Kurchan-model glass former. Through a mixed static and dynamical analysis, we then extract an improved dimensional scaling form as well as a geometrical upper bound for the arrest. The results suggest that understanding the asymptotic behavior of the random Lorentz gas may be key to surmounting fundamental difficulties with the mode-coupling theory of glasses.}, Doi = {10.1103/physreve.91.042313}, Key = {fds232060} } @article{fds232061, Author = {Charbonneau, P and Corwin, EI and Parisi, G and Zamponi, F}, Title = {Jamming criticality revealed by removing localized buckling excitations.}, Journal = {Physical Review Letters}, Volume = {114}, Number = {12}, Pages = {125504}, Year = {2015}, Month = {March}, ISSN = {0031-9007}, url = {http://dx.doi.org/10.1103/physrevlett.114.125504}, Abstract = {Recent theoretical advances offer an exact, first-principles theory of jamming criticality in infinite dimension as well as universal scaling relations between critical exponents in all dimensions. For packings of frictionless spheres near the jamming transition, these advances predict that nontrivial power-law exponents characterize the critical distribution of (i) small interparticle gaps and (ii) weak contact forces, both of which are crucial for mechanical stability. The scaling of the interparticle gaps is known to be constant in all spatial dimensions d-including the physically relevant d=2 and 3, but the value of the weak force exponent remains the object of debate and confusion. Here, we resolve this ambiguity by numerical simulations. We construct isostatic jammed packings with extremely high accuracy, and introduce a simple criterion to separate the contribution of particles that give rise to localized buckling excitations, i.e., bucklers, from the others. This analysis reveals the remarkable dimensional robustness of mean-field marginality and its associated criticality.}, Doi = {10.1103/physrevlett.114.125504}, Key = {fds232061} } @article{fds232062, Author = {Yang, Y and Fu, L and Marcoux, C and Socolar, JES and Charbonneau, P and Yellen, BB}, Title = {Phase transformations in binary colloidal monolayers.}, Journal = {Soft Matter}, Volume = {11}, Number = {12}, Pages = {2404-2415}, Year = {2015}, Month = {March}, ISSN = {1744-683X}, url = {http://dx.doi.org/10.1039/c5sm00009b}, Abstract = {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.}, Doi = {10.1039/c5sm00009b}, Key = {fds232062} } @article{fds226206, Author = {Ye Yang and Lin Fu and Catherine Marcoux and Joshua E. S. Socolar and Patrick Charbonneau and Benjamin B. Yellen}, Title = {Martensitic Transformations in Binary Colloidal Monolayers}, Journal = {Soft Matter}, Year = {2015}, url = {http://dx.doi.org/10.1039/C5SM00009B}, Abstract = {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.}, Doi = {10.1039/C5SM00009B}, Key = {fds226206} } @article{fds232064, Author = {Charbonneau, P and Jin, Y and Parisi, G and Zamponi, F}, Title = {Hopping and the Stokes-Einstein relation breakdown in simple glass formers.}, Journal = {Proceedings of the National Academy of Sciences of the United States of America}, Volume = {111}, Number = {42}, Pages = {15025-15030}, Year = {2014}, Month = {October}, ISSN = {0027-8424}, url = {http://arxiv.org/abs/1407.5677}, Abstract = {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 → ∞, 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 toward describing dynamic facilitation in the framework of the mean-field theory of glasses.}, Doi = {10.1073/pnas.1417182111}, Key = {fds232064} } @article{fds232063, Author = {Charbonneau, P and Kurchan, J and Parisi, G and Urbani, P and Zamponi, F}, Title = {Exact theory of dense amorphous hard spheres in high dimension. III. The full replica symmetry breaking solution}, Journal = {Journal of Statistical Mechanics: Theory and Experiment}, Volume = {2014}, Number = {10}, Pages = {P10009-P10009}, Year = {2014}, Month = {October}, url = {http://arxiv.org/abs/1310.2549}, Abstract = {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 glass models and structural glasses conjectured by Kirkpatrick, Thirumalai, and Wolynes is indeed 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. We present preliminary results obtained from the solution of these equations. 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 the critical exponents associated to scaling around the jamming transition, which are missed by the 1RSB solution.}, Doi = {10.1088/1742-5468/2014/10/P10009}, Key = {fds232063} } @article{fds232065, Author = {Marcoux, C and Byington, TW and Qian, Z and Charbonneau, P and Socolar, JES}, Title = {Emergence of limit-periodic order in tiling models.}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {90}, Number = {1}, Pages = {012136}, Year = {2014}, Month = {July}, ISSN = {1539-3755}, url = {http://arxiv.org/abs/1406.2905}, Abstract = {A two-dimensional (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 class of ground states, including crystalline patterns and limit-periodic ones, but a slow quench still yields the limit-periodic state. For the Taylor-Socolar lattic 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.}, Doi = {10.1103/physreve.90.012136}, Key = {fds232065} } @article{fds232069, Author = {Fusco, D and Charbonneau, P}, Title = {Competition between monomeric and dimeric crystals in schematic models for globular proteins.}, Journal = {Journal of Physical Chemistry B}, Volume = {118}, Number = {28}, Pages = {8034-8041}, Year = {2014}, Month = {July}, ISSN = {1520-6106}, url = {http://pubs.acs.org/doi/abs/10.1021/jp5011428}, Abstract = {Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. However, they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why (nearly) identical crystallization conditions can sometimes result in the formation of different crystal forms. Here, we develop a patchy particle model with competing sets of patches that provides a microscopic explanation of this phenomenon. We identify different regimes in which one or two crystal forms can coexist with a low-density fluid. Using analytical approximations, we extend our findings to different crystal phases, providing a general framework for treating protein crystallization when multiple crystal forms compete. Our results also suggest different experimental routes for targeting a specific crystal form, and for reducing the dynamical competition between the two forms, thus facilitating protein crystal assembly.}, Doi = {10.1021/jp5011428}, Key = {fds232069} } @article{fds232067, Author = {Fusco, D and Barnum, TJ and Bruno, AE and Luft, JR and Snell, EH and Mukherjee, S and Charbonneau, P}, Title = {Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.}, Journal = {Plos One}, Volume = {9}, Number = {7}, Pages = {e101123}, Year = {2014}, Month = {January}, url = {http://hdl.handle.net/10161/10578 Duke open access}, Abstract = {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.}, Doi = {10.1371/journal.pone.0101123}, Key = {fds232067} } @article{fds232068, Author = {Charbonneau, P and Kurchan, J and Parisi, G and Urbani, P and Zamponi, F}, Title = {Fractal free energy landscapes in structural glasses.}, Journal = {Nature Communications}, Volume = {5}, Pages = {3725}, Year = {2014}, Month = {January}, url = {http://dx.doi.org/10.1038/ncomms4725}, Abstract = {Glasses are amorphous solids whose constituent particles are caged by their neighbours 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, which brings about isostaticity and marginal stability on approaching jamming. Critical exponents for the basin width, the weak force distribution and the spatial spread of quasi-contacts near jamming can be analytically determined. Their value is found to be compatible with numerical observations. This advance incorporates the jamming transition of granular materials into the framework of glass theory. Because temperature and pressure control what features of the landscape are experienced, glass mechanics and transport are expected to reflect the features of the topology we discuss here.}, Doi = {10.1038/ncomms4725}, Key = {fds232068} } @article{fds232070, Author = {Fusco, D and Headd, JJ and De Simone and A and Wang, J and Charbonneau, P}, Title = {Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study.}, Journal = {Soft Matter}, Volume = {10}, Number = {2}, Pages = {290-302}, Year = {2014}, Month = {January}, ISSN = {1744-683X}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000327849300006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Abstract = {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 the protein crystal contacts, and accordingly parameterize patchy particle models. Comparing the phase diagrams of these schematic models with experimental results enables us to critically examine the assumptions behind the two approaches. The study also reveals features of protein–protein interactions that can be leveraged to crystallize proteins more generally.}, Doi = {10.1039/C3SM52175C}, Key = {fds232070} } @article{fds232072, Author = {Fusco, D and Charbonneau, P}, Title = {Crystallization of asymmetric patchy models for globular proteins in solution}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {88}, Number = {1}, Pages = {012721}, Year = {2013}, Month = {July}, ISSN = {1539-3755}, url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000322082800005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92}, Abstract = {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 impacts the phase diagram and nucleation dynamics of this family of soft matter models. We find the role of the geometry asymmetry to be weak, but the energy asymmetry to markedly interfere with the crystallization thermodynamics and kinetics. These results provide a rationale for the success and occasional failure of the proposal of George and Wilson for protein crystallization conditions as well as physical guidance for developing more effective protein crystallization strategies.}, Doi = {10.1103/PhysRevE.88.012721}, Key = {fds232072} } @article{fds232076, Author = {Charbonneau, P and Tarjus, G}, Title = {Decorrelation of the static and dynamic length scales in hard-sphere glass formers}, Journal = {Physical Review. E}, Volume = {87}, Number = {4}, Pages = {042305}, Year = {2013}, Month = {April}, ISSN = {1539-3755}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23679412}, Abstract = {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 accessible in colloidal experiments. We also find that, in this same range, no one-to-one correspondence between relaxation time and point-to-set correlation length exists. These results point to the coexistence of several relaxation mechanisms in the dynamically accessible regime of three-dimensional hard-sphere glass formers.}, Doi = {10.1103/PhysRevE.87.042305}, Key = {fds232076} } @article{fds232071, Author = {Charbonneau, B and Charbonneau, P and Jin, Y and Parisi, G and Zamponi, F}, Title = {Dimensional dependence of the Stokes-Einstein relation and its violation}, Journal = {The Journal of Chemical Physics}, Volume = {139}, Number = {16}, Pages = {164502}, Year = {2013}, ISSN = {0021-9606}, url = {http://arxiv.org/abs/1210.6073}, Abstract = {We generalize to higher spatial dimensions the Stokes-Einstein relation (SER) as well as the leading correction to diffusivity in finite systems with periodic boundary conditions, and validate these results with numerical simulations. We then investigate the evolution of the high-density SER violation with dimension in simple hard sphere glass formers. The analysis suggests that this SER violation disappears around dimension du= 8, above which it is not observed. The critical exponent associated with the violation appears to evolve linearly in 8 - d, below d = 8, as predicted by Biroli and Bouchaud [J. Phys.: Condens. Matter 19, 205101 (2007)], but the linear coefficient is not consistent with the prediction. The SER violation with d establishes a new benchmark for theory, and its complete description remains an open problem. © 2013 AIP Publishing LLC.}, Doi = {10.1063/1.4825177}, Key = {fds232071} } @article{fds232075, Author = {Charbonneau, B and Charbonneau, P and Tarjus, G}, Title = {Geometrical frustration and static correlations in hard-sphere glass formers}, Journal = {The Journal of Chemical Physics}, Volume = {138}, Number = {12}, Pages = {12A515}, Year = {2013}, ISSN = {0021-9606}, url = {http://arxiv.org/abs/1210.4445}, Abstract = {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. © 2013 American Institute of Physics.}, Doi = {10.1063/1.4770498}, Key = {fds232075} } @article{fds232079, Author = {Charbonneau, P and Corwin, EI and Parisi, G and Zamponi, F}, Title = {Universal microstructure and mechanical stability of jammed packings.}, Journal = {Physical Review Letters}, Volume = {109}, Number = {20}, Pages = {205501}, Year = {2012}, Month = {November}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23215504}, Abstract = {The mechanical properties of jammed packings 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.}, Doi = {10.1103/physrevlett.109.205501}, Key = {fds232079} } @article{fds303174, Author = {Zhang, K and Charbonneau, P}, Title = {[N]pT ensemble and finite-size-scaling study of the critical isostructural transition in the generalized exponential model of index 4.}, Journal = {Phys Rev E Stat Nonlin Soft Matter Phys}, Volume = {86}, Number = {4 Pt 1}, Pages = {042501}, Year = {2012}, Month = {October}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23214631}, Abstract = {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, which necessarily fix one of these two degrees of freedom. The difficulty, however, can be surmounted by the generalized [N]pT ensemble [J. Chem. Phys. 136, 214106 (2012)]. Here we show 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 us to accurately determine the critical point parameters and to verify that it belongs to the Ising universality class.}, Doi = {10.1103/PhysRevE.86.042501}, Key = {fds303174} } @article{fds232081, Author = {Charbonneau, P and Ikeda, A and Parisi, G and Zamponi, F}, Title = {Dimensional study of the caging order parameter at the glass transition.}, Journal = {Proc Natl Acad Sci U S A}, Volume = {109}, Number = {35}, Pages = {13939-13943}, Year = {2012}, Month = {August}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22891303}, Abstract = {The glass problem is notoriously hard and controversial. Even at the mean-field level, little is agreed upon regarding why a fluid becomes sluggish while exhibiting but unremarkable structural changes. It is clear, however, that the process involves self-caging, which provides an order parameter for the transition. It is also broadly assumed that this cage should have a gaussian shape in the mean-field limit. Here we show that this ansatz does not hold. By performing simulations as a function of spatial dimension d, we find the cage to keep a nontrivial form. Quantitative mean-field descriptions of the glass transition, such as mode-coupling theory, density functional theory, and replica theory, all miss this crucial element. Although the mean-field random first-order transition scenario of the glass transition is qualitatively supported here and non-mean-field corrections are found to remain small on decreasing d, reconsideration of its implementation is needed for it to result in a coherent description of experimental observations.}, Doi = {10.1073/pnas.1211825109}, Key = {fds232081} } @article{fds232094, Author = {Zhang, K and Charbonneau, P}, Title = {[N]pT Monte Carlo simulations of the cluster-crystal-forming penetrable sphere model.}, Journal = {The Journal of Chemical Physics}, Volume = {136}, Number = {21}, Pages = {214106}, Year = {2012}, Month = {June}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22697529}, Abstract = {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. It is particularly efficient at high T, where particle insertion is facile. Using this expanded ensemble and thermodynamic integration, we solve the phase diagram of a prototypical cluster-crystal former, the penetrable sphere model, and compare the results with earlier theoretical predictions. At high temperatures and densities, the equilibrium occupancy n(c)(eq) of face-centered cubic crystal increases linearly. At low temperatures, although n(c)(eq) plateaus at integer values, the crystal behavior changes continuously with density. The previously ambiguous crossover around T ~ 0.1 is resolved.}, Doi = {10.1063/1.4723869}, Key = {fds232094} } @article{fds232095, Author = {Bergin, SM and Chen, Y-H and Rathmell, AR and Charbonneau, P and Li, Z-Y and Wiley, BJ}, Title = {The effect of nanowire length and diameter on the properties of transparent, conducting nanowire films.}, Journal = {Nanoscale}, Volume = {4}, Number = {6}, Pages = {1996-2004}, Year = {2012}, Month = {March}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22349106}, Abstract = {This article describes how the dimensions of nanowires affect the transmittance and sheet resistance of a random nanowire network. Silver nanowires with independently controlled lengths and diameters were synthesized with a gram-scale polyol synthesis by controlling the reaction temperature and time. Characterization of films composed of nanowires of different lengths but the same diameter enabled the quantification of the effect of length on the conductance and transmittance of silver nanowire films. Finite-difference time-domain calculations were used to determine the effect of nanowire diameter, overlap, and hole size on the transmittance of a nanowire network. For individual nanowires with diameters greater than 50 nm, increasing diameter increases the electrical conductance to optical extinction ratio, but the opposite is true for nanowires with diameters less than this size. Calculations and experimental data show that for a random network of nanowires, decreasing nanowire diameter increases the number density of nanowires at a given transmittance, leading to improved connectivity and conductivity at high transmittance (>90%). This information will facilitate the design of transparent, conducting nanowire films for flexible displays, organic light emitting diodes and thin-film solar cells.}, Doi = {10.1039/c2nr30126a}, Key = {fds232095} } @article{fds232077, Author = {Zhang, K and Charbonneau, P}, Title = {Erratum: [N]pT ensemble and finite-size-scaling study of the critical isostructural transition in the generalized exponential model of index 4}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {86}, Number = {6}, Year = {2012}, ISSN = {1539-3755}, url = {http://dx.doi.org/10.1103/PhysRevE.86.069902}, Doi = {10.1103/PhysRevE.86.069902}, Key = {fds232077} } @article{fds232080, Author = {Zhang, K and Charbonneau, P}, Title = {[N]pT ensemble and finite-size-scaling study of the critical isostructural transition in the generalized exponential model of index 4}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {86}, Number = {4}, Pages = {042501}, Year = {2012}, ISSN = {1539-3755}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23214631}, Abstract = {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, which necessarily fix one of these two degrees of freedom. The difficulty, however, can be surmounted by the generalized [N]pT ensemble. Here we show 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 us to accurately determine the critical point parameters and to verify that it belongs to the Ising universality class. © 2012 American Physical Society.}, Doi = {10.1103/PhysRevE.86.042501}, Key = {fds232080} } @article{fds232082, Author = {Charbonneau, B and Charbonneau, P and Tarjus, G}, Title = {Geometrical frustration and static correlations in a simple glass former}, Journal = {Physical Review Letters}, Volume = {108}, Number = {3}, Pages = {035701}, Year = {2012}, ISSN = {0031-9007}, url = {http://arxiv.org/abs/1108.2494}, Abstract = {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. © 2012 American Physical Society.}, Doi = {10.1103/PhysRevLett.108.035701}, Key = {fds232082} } @article{fds232083, Author = {Charbonneau, P and Ikeda, A and Parisi, G and Zamponi, F}, Title = {Glass transition and random close packing above three dimensions.}, Journal = {Phys Rev Lett}, Volume = {107}, Number = {18}, Pages = {185702}, Year = {2011}, Month = {October}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22107645}, Abstract = {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 dimensions.}, Doi = {10.1103/PhysRevLett.107.185702}, Key = {fds232083} } @article{fds232089, Author = {Zhang, K and Charbonneau, P}, Title = {Monte Carlo approach for studying microphases applied to the axial next-nearest-neighbor Ising and the Ising-Coulomb models}, Journal = {Physical Review B}, Volume = {83}, Number = {21}, Pages = {214303}, Year = {2011}, ISSN = {1098-0121}, url = {http://arxiv.org/abs/1102.1405}, Abstract = {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. Simple phases are not found to play a particularly significant role in the devil's flowers and interfacial roughening plays at most a small role in the ANNNI layered regime. 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. © 2011 American Physical Society.}, Doi = {10.1103/PhysRevB.83.214303}, Key = {fds232089} } @article{fds232084, Author = {Zhang, K and Charbonneau, P and Mladek, BM}, Title = {Reentrant and isostructural transitions in a cluster-crystal former.}, Journal = {Physical Review Letters}, Volume = {105}, Number = {24}, Pages = {245701}, Year = {2010}, Month = {December}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21231534}, Abstract = {We study the low-temperature behavior of a simple cluster-crystal forming system through simulation. We find the phase diagram to be hybrid between the Gaussian core model and the penetrable sphere model. The system additionally exhibits S-shaped doubly reentrant phase sequences as well as critical isostructural transitions between crystals of different average lattice site occupancy. Because of the possible annihilation of lattice sites and accompanying clustering, the system moreover shows an unusual softening upon compression.}, Doi = {10.1103/physrevlett.105.245701}, Key = {fds232084} } @article{fds232085, Author = {Jin, Y and Charbonneau, P and Meyer, S and Song, C and Zamponi, F}, Title = {Application of Edwards' statistical mechanics to high-dimensional jammed sphere packings.}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {82}, Number = {5 Pt 1}, Pages = {051126}, Year = {2010}, Month = {November}, ISSN = {1539-3755}, url = {http://hdl.handle.net/10161/4290 Duke open access}, Abstract = {The isostatic jamming limit of frictionless spherical particles from Edwards' statistical mechanics [Song et al., Nature (London) 453, 629 (2008)] is generalized to arbitrary dimension d using a liquid-state description. The asymptotic high-dimensional behavior of the self-consistent relation is obtained by saddle-point evaluation and checked numerically. The resulting random close packing density scaling ϕ∼d2(-d) is consistent with that of other approaches, such as replica theory and density-functional theory. The validity of various structural approximations is assessed by comparing with three- to six-dimensional isostatic packings obtained from simulations. These numerical results support a growing accuracy of the theoretical approach with dimension. The approach could thus serve as a starting point to obtain a geometrical understanding of the higher-order correlations present in jammed packings.}, Doi = {10.1103/physreve.82.051126}, Key = {fds232085} } @article{fds232087, Author = {Zhang, K and Charbonneau, P}, Title = {Monte carlo study of the axial next-nearest-neighbor Ising model.}, Journal = {Phys Rev Lett}, Volume = {104}, Number = {19}, Pages = {195703}, Year = {2010}, Month = {May}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20866979}, Abstract = {The equilibrium phase behavior of microphase-forming systems is notoriously difficult to obtain because of the extended metastability of the modulated phases. We develop a simulation method based on free-energy integration that surmounts this problem and with which we describe the modulated regime of the canonical three-dimensional axial next-nearest-neighbor Ising model. Equilibrium order parameters are obtained and the critical behavior beyond the Lifshitz point is examined. The absence of widely extended bulging modulated phases illustrates the limitations of various approximation schemes used to analyze microphase-forming models.}, Doi = {10.1103/PhysRevLett.104.195703}, Key = {fds232087} } @article{fds232086, Author = {Charbonneau, P and Ikeda, A and van Meel, JA and Miyazaki, K}, Title = {Numerical and theoretical study of a monodisperse hard-sphere glass former.}, Journal = {Phys Rev E Stat Nonlin Soft Matter Phys}, Volume = {81}, Number = {4 Pt 1}, Pages = {040501}, Year = {2010}, Month = {April}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20481668}, Abstract = {There exists a variety of theories of the glass transition and many more numerical models. But because the models need built-in complexity to prevent crystallization, comparisons with theory can be difficult. We study the dynamics of a deeply supersaturated monodisperse four-dimensional (4D) hard-sphere fluid, which has no such complexity, but whose strong intrinsic geometrical frustration inhibits crystallization, even when deeply supersaturated. As an application, we compare its behavior to the mode-coupling theory (MCT) of glass formation. We find MCT to describe this system better than any other structural glass formers in lower dimensions. The reduction in dynamical heterogeneity in 4D suggested by a milder violation of the Stokes-Einstein relation could explain the agreement. These results are consistent with a mean-field scenario of the glass transition.}, Doi = {10.1103/PhysRevE.81.040501}, Key = {fds232086} } @article{fds232088, Author = {van Meel, JA and Charbonneau, B and Fortini, A and Charbonneau, P}, Title = {Hard-sphere crystallization gets rarer with increasing dimension.}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {80}, Number = {6 Pt 1}, Pages = {061110}, Year = {2009}, Month = {December}, ISSN = {1539-3755}, url = {http://hdl.handle.net/10161/4283 Duke open access}, Abstract = {We recently found that crystallization of monodisperse hard spheres from the bulk fluid faces a much higher free-energy barrier in four than in three dimensions at equivalent supersaturation, due to the increased geometrical frustration between the simplex-based fluid order and the crystal [J. A. van Meel, D. Frenkel, and P. Charbonneau, Phys. Rev. E 79, 030201(R) (2009)]. Here, we analyze the microscopic contributions to the fluid-crystal interfacial free energy to understand how the barrier to crystallization changes with dimension. We find the barrier to grow with dimension and we identify the role of polydispersity in preventing crystal formation. The increased fluid stability allows us to study the jamming behavior in four, five, and six dimensions and to compare our observations with two recent theories [C. Song, P. Wang, and H. A. Makse, Nature (London) 453, 629 (2008); G. Parisi and F. Zamponi, Rev. Mod. Phys. (to be published)].}, Doi = {10.1103/physreve.80.061110}, Key = {fds232088} } @article{fds339883, Author = {Ikeda, A and Charbonneau, P and van, MJA and Miyazaki, K}, Title = {28aQL-4 Simulation and theoretical study of glass transition of 4d hard sphere}, Journal = {Meeting Abstracts of the Physical Society of Japan}, Volume = {64}, Number = {2}, Pages = {293 pages}, Publisher = {The Physical Society of Japan (JPS)}, Year = {2009}, Month = {August}, Key = {fds339883} } @article{fds232090, Author = {van Meel, JA and Frenkel, D and Charbonneau, P}, Title = {Geometrical frustration: a study of four-dimensional hard spheres.}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {79}, Number = {3 Pt 1}, Pages = {030201}, Year = {2009}, Month = {March}, ISSN = {1539-3755}, url = {http://arxiv.org/abs/0809.1775}, Abstract = {The smallest maximum-kissing-number Voronoi polyhedron of three-dimensional (3D) Euclidean spheres is the icosahedron, and the tetrahedron is the smallest volume that can show up in Delaunay tessellation. No periodic lattice is consistent with either, and hence these dense packings are geometrically frustrated. Because icosahedra can be assembled from almost perfect tetrahedra, the terms "icosahedral" and "polytetrahedral" packing are often used interchangeably, which leaves the true origin of geometric frustration unclear. Here we report a computational study of freezing of 4D Euclidean hard spheres, where the densest Voronoi cluster is compatible with the symmetry of the densest crystal, while polytetrahedral order is not. We observe that, under otherwise comparable conditions, crystal nucleation in four dimensions is less facile than in three dimensions, which is consistent with earlier observations [M. Skoge, Phys. Rev. E 74, 041127 (2006)]. We conclude that it is the geometrical frustration of polytetrahedral structures that inhibits crystallization.}, Doi = {10.1103/physreve.79.030201}, Key = {fds232090} } @article{fds232096, Author = {Mladek, BM and Charbonneau, P and Likos, CN and Frenkel, D and Kahl, G}, Title = {Multiple occupancy crystals formed by purely repulsive soft particles}, Journal = {Journal of Physics. Condensed Matter : an Institute of Physics Journal}, Volume = {20}, Number = {49}, Pages = {494245-494245}, Year = {2008}, Month = {December}, ISSN = {0953-8984}, url = {http://dx.doi.org/10.1088/0953-8984/20/49/494245}, Abstract = {Recently, particular interest has been placed in the study of a strikingly counter-intuitive phenomenon: the clustering of purely repulsive soft particles. This contribution serves the purpose of both reviewing our current understanding of the multiple occupancy crystals and presenting details of recently developed tailor-cut approaches to the problem. We first indicate, by use of analytically tractable examples, how such a phenomenon can arise at all. We then show that the thermodynamic formalism has to be adapted when studying such systems and present a novel computer simulation technique apt to do so. Finally, we discuss the intriguing mechanical and structural responses of such systems upon increasing the density. © 2008 IOP Publishing Ltd.}, Doi = {10.1088/0953-8984/20/49/494245}, Key = {fds232096} } @article{UNKNOWN, Author = {Charbonneau, P and Das, C and Frenkel, D}, Title = {Dynamical heterogeneity in a glass-forming ideal gas}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {78}, Number = {1}, Pages = {011505}, Year = {2008}, ISSN = {1539-3755}, url = {http://arxiv.org/abs/0804.3704}, Abstract = {We conduct a numerical study of the dynamical behavior of a system of three-dimensional "crosses," particles that consist of three mutually perpendicular line segments of length σ rigidly joined at their midpoints. In an earlier study we showed that this model has the structural properties of an ideal gas, yet the dynamical properties of a strong glass former. In the present paper we report an extensive study of the dynamical heterogeneities that appear in this system in the regime where glassy behavior sets in. On the one hand, we find that the propensity of a particle to diffuse is determined by the structure of its local environment. The local density around mobile particles is significantly less than the average density, but there is little clustering of mobile particles, and the clusters observed tend to be small. On the other hand, dynamical susceptibility results indicate that a large dynamical length scale develops even at moderate densities. This suggests that propensity and other mobility measures are an incomplete measure of the dynamical length scales in this system. © 2008 The American Physical Society.}, Doi = {10.1103/PhysRevE.78.011505}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Mladek, BM and Charbonneau, P and Frenkel, D}, Title = {Phase coexistence of cluster crystals: Beyond the gibbs phase rule}, Journal = {Physical Review Letters}, Volume = {99}, Number = {23}, Pages = {235702}, Year = {2007}, ISSN = {0031-9007}, url = {http://arxiv.org/abs/0708.2979}, Abstract = {We report a study of the phase behavior of multiple-occupancy crystals through simulation. We argue that in order to reproduce the equilibrium behavior of such crystals, it is essential to treat the number of lattice sites as a constraining thermodynamic variable. The resulting free-energy calculations thus differ considerably from schemes used for single-occupancy lattices. Using our approach, we obtain the phase diagram and the bulk modulus for a generalized exponential model that forms cluster crystals at high densities. We compare the simulation results with existing theoretical predictions. We also identify two types of density fluctuations that can lead to two sound modes and evaluate the corresponding elastic constants. © 2007 The American Physical Society.}, Doi = {10.1103/PhysRevLett.99.235702}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Charbonneau, P and Reichman, DR}, Title = {Dynamical heterogeneity and nonlinear susceptibility in supercooled liquids with short-range attraction}, Journal = {Physical Review Letters}, Volume = {99}, Number = {13}, Pages = {135701}, Year = {2007}, ISSN = {0031-9007}, url = {http://arxiv.org/abs/0706.1657}, Abstract = {Recent work has demonstrated the strong qualitative differences between the dynamics near a glass transition driven by short-ranged repulsion and one governed by short-ranged attraction. Here we study in detail the behavior of nonlinear, higher-order correlation functions that measure the growth of length scales associated with dynamical heterogeneity in both types of systems. We find that this measure is qualitatively different in the repulsive and attractive cases with regards to the wave vector dependence as well as the time dependence of the standard nonlinear four-point dynamical susceptibility. We discuss the implications of these results for the general understanding of dynamical heterogeneity in glass-forming liquids. © 2007 The American Physical Society.}, Doi = {10.1103/PhysRevLett.99.135701}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Charbonneau, P and Reichman, DR}, Title = {Systematic characterization of thermodynamic and dynamical phase behavior in systems with short-ranged attraction}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {75}, Number = {1}, Pages = {011507}, Year = {2007}, ISSN = {1539-3755}, url = {http://arxiv.org/abs/cond-mat/0604428}, Abstract = {In this paper we demonstrate the feasibility and utility of an augmented version of the Gibbs ensemble Monte Carlo method for computing the phase behavior of systems with strong, extremely short-ranged attractions. For generic potential shapes, this approach allows for the investigation of narrower attractive widths than those previously reported. Direct comparison to previous self-consistent Ornstein-Zernike approximation calculations is made. A preliminary investigation of out-of-equilibrium behavior is also performed. Our results suggest that the recent observations of stable cluster phases in systems without long-ranged repulsions are intimately related to gas-crystal and metastable gas-liquid phase separation. © 2007 The American Physical Society.}, Doi = {10.1103/PhysRevE.75.011507}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Charbonneau, P and Frenkel, D}, Title = {Gas-solid coexistence of adhesive spheres}, Journal = {The Journal of Chemical Physics}, Volume = {126}, Number = {19}, Pages = {196101}, Year = {2007}, ISSN = {0021-9606}, url = {http://arxiv.org/abs/cond-mat/0703378}, Abstract = {In this note, the authors investigate whether the gas-liquid critical point can remain stable with respect to solidification for narrow attractive interactions down to the Baxter limit. Using a crude cell theory, the authors estimate the necessary conditions for this to be true. Possible realizations are briefly discussed. © 2007 American Institute of Physics.}, Doi = {10.1063/1.2737051}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Charbonneau, P and Reichman, DR}, Title = {Phase behavior and far-from-equilibrium gelation in charged attractive colloids}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {75}, Number = {5}, Pages = {050401(R)}, Year = {2007}, ISSN = {1539-3755}, url = {http://arxiv.org/abs/cond-mat/0604430}, Abstract = {In this Rapid Communication we demonstrate the applicability of an augmented Gibbs ensemble Monte Carlo approach for the phase behavior determination of model colloidal systems with short-ranged depletion attraction and long-ranged repulsion. This technique allows for a quantitative determination of the phase boundaries and ground states in such systems. We demonstrate that gelation may occur in systems of this type as the result of arrested microphase separation, even when the equilibrium state of the system is characterized by compact microphase structures. © 2007 The American Physical Society.}, Doi = {10.1103/PhysRevE.75.050401}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Reichman, DR and Charbonneau, P}, Title = {Mode-coupling theory}, Journal = {Journal of Statistical Mechanics: Theory and Experiment}, Volume = {2005}, Number = {05}, Pages = {P05013-P05013}, Year = {2005}, Month = {May}, url = {http://arxiv.org/abs/cond-mat/0511407}, Abstract = {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. © IOP Publishing Ltd.}, Doi = {10.1088/1742-5468/2005/05/P05013}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Chamon, C and Charbonneau, P and Cugliandolo, LF and Reichman, DR and Sellitto, M}, Title = {Out-of-equilibrium dynamical fluctuations in glassy systems}, Journal = {The Journal of Chemical Physics}, Volume = {121}, Number = {20}, Pages = {10120-10137}, Year = {2004}, ISSN = {0021-9606}, url = {http://arxiv.org/abs/cond-mat/0401326}, Abstract = {In this paper we extend the earlier treatment of out-of-equilibrium mesoscopic fluctuations in glassy systems in several significant ways. First, via extensive simulations, we demonstrate that models of glassy behavior without quenched disorder display scalings of the probability of local two-time correlators that are qualitatively similar to that of models with short-ranged quenched interactions. The key ingredient for such scaling properties is shown to be the development of a criticallike dynamical correlation length, and not other microscopic details. This robust data collapse may be described in terms of a time-evolving "extreme value" distribution. We develop a theory to describe both the form and evolution of these distributions based on a effective σ model approach. © 2004 American Institute of Physics.}, Doi = {10.1063/1.1809585}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Barden, CJ and Charbonneau, P and III, HFS}, Title = {Group 13-group 16 heterocubanes [RM(μ_{3}-E)]_{4}(R = H, CH_{3}; M = Al, Ga, In; E = O, S, Se, Te) and group 13 cubanes [RM(μ_{3}-M)]_{4}(R = F, Cl, CH_{3}, NO_{2}; M = Al, Ga, In): A structural study}, Journal = {Organometallics}, Volume = {21}, Number = {17}, Pages = {3605-3609}, Year = {2002}, ISSN = {0276-7333}, url = {http://dx.doi.org/10.1021/om0202672}, Abstract = {Twenty-four group 13-group 16 chalcogen heterocubanes [RM(μ3-E)]4 (R = H, CH3; M = Al, Ga, In; E = O, S, Se, Te) and 12 group 13-group 13 pure cubanes [RM(μ3-M)]4 (R = F, Cl, CH3, NO2; M = Al, Ga, In) have been studied using density functional theory. Geometries and thermodynamic properties were computed at the B3LYP/SRLC level. All structures were found to be true minima with at most 0.08 Å and 2.5° deviation from the limited experimental geometries. These chalcogen heterocubanes appear thermodynamically resistant to fragmentation. The M4E4 core for each structure proved to be insensitive to ligand choice for the group 13-group 16 heterocubanes. By contrast, the electron-deficient M8 cores of the pure cubanes were variously affected by the electronegativity of various R groups. The entropically disfavored nature of the synthesis may hold the key to the as-yet-unsynthesized [RAl(μ3-O)]4.}, Doi = {10.1021/om0202672}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Charbonneau, P and Jean-Claude, B and Whitehead, MA}, Title = {Synthesis of a prodrug: A semi-empirical PM3 study}, Journal = {Journal of Molecular Structure: Theochem}, Volume = {574}, Pages = {85-91}, Year = {2001}, ISSN = {0166-1280}, url = {http://dx.doi.org/10.1016/S0166-1280(01)00586-3}, Abstract = {The semi-empirical PM3 method is used to investigate the synthesis of a prodrug of type I which can regenerate the short-lived anti-tumoral tetrazepinone. The reaction pathway examined involves four consecutive steps: the ring opening of benzo-tetrazepinone (1 → 2), the diazonium coupling (2 → 3), the double-proton transfer (4 → 6) and the dissociation (7 → 8). Geometry PM3 optimisation of all starting material, reaction intermediates and products lead to a qualitative study of this solvent-dependent synthesis. Energetics and substituent effects are analysed using a simple electron-withdrawing, electron-donating argument based on calculated Hammett constants. © 2001 Published by Elsevier Science B.V.}, Doi = {10.1016/S0166-1280(01)00586-3}, Key = {UNKNOWN} } @article{UNKNOWN, Author = {Spivey, AC and Charbonneau, P and Fekner, T and Hochmuth, DH and Maddaford, A and Malardier-Jugroot, C and Redgrave, AJ and Whitehead, MA}, Title = {Energy barriers to rotation in axially chiral analogues of 4-(dimethylamino)pyridine}, Journal = {The Journal of Organic Chemistry}, Volume = {66}, Number = {22}, Pages = {7394-7401}, Year = {2001}, ISSN = {0022-3263}, url = {http://dx.doi.org/10.1021/jo015593q}, Abstract = {The barriers to enantiomerization of a series of axially chiral biaryl analogues of 4-(dimethylamino)-pyridine (DMAP) 1-10 were determined experimentally by means of dynamic HPLC measurements and racemization studies. The barriers to rotation in derivatives 1-6 (based on the bicyclic 5-azaindoline core) were lower than those in the corresponding derivatives 7-10 (based on the monocyclic DMAP core). Semiempirical (PM3), ab initio Hartree-Fock (HF/STO-3G), and density functional theory (DFT/B3LYP/6-31G*) calculations reveal that these differences in barriers to rotation are the result of differing degrees of hybridization of the non-pyridyl nitrogen in the enantiomerization transition states (TSs). The importance of heteroatom hybridization as a factor in determining nonsteric contributions to barriers to rotation in azabiaryls of this type is discussed.}, Doi = {10.1021/jo015593q}, Key = {UNKNOWN} } %% Papers Accepted @article{fds226361, Author = {Patrick Charbonneau and Eric I. Corwin and Giorgio Parisi and Francesco Zamponi}, Title = {Jamming Criticality Revealed by Removing “Bucklers”}, Journal = {Physical Review Letters}, Year = {2015}, url = {http://arxiv.org/abs/1411.3975v1}, Abstract = {Recent theoretical advances offer an exact, first-principle theory of jamming criticality in infinite dimension as well as universal scaling relations between critical exponents in all dimensions. For jammed packings of frictionless spheres, these advances predict that power-law exponents characterize the critical distribution of (i) small inter-particle gaps and (ii) weak contact forces, both of which are crucial for mechanical stability. The scaling of the inter-particle gaps is known to be constant in all spatial dimensions d – including the physically relevant d = 2 and 3, but the value of the weak force exponent remains the object of debate and confusion. Here, we resolve this ambiguity by numerical simulations. We construct isostatic jammed packings with extremely high accuracy, and introduce a simple criterion to separate the contribution of particles that give rise to localized excitations (the “bucklers”) from the others. This analysis reveals the remarkable dimensional robustness of mean-field marginality and its associated criticality.}, Key = {fds226361} } %% Papers Submitted @article{fds232058, Author = {Charbonneau, P and Jin, Y and Parisi, G and Rainone, C and Seoane, B and Zamponi, F}, Title = {Numerical detection of the Gardner transition in a mean-field glass former.}, Journal = {Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics}, Volume = {92}, Number = {1}, Pages = {012316}, Year = {2015}, Month = {July}, ISSN = {1539-3755}, url = {http://arxiv.org/abs/1501.07244}, Abstract = {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.}, Doi = {10.1103/physreve.92.012316}, Key = {fds232058} } @article{fds224956, Author = {Y. Jin and P. Charbonneau}, Title = {Mapping the arrest of the random Lorentz gas to the dynamical transition of simple glass formers}, Year = {2014}, url = {http://arxiv.org/abs/1409.0688}, Abstract = {The random Lorentz gas is a minimal model for transport in heterogeneous media. Here, we map its dynamical arrest at high obstacle density onto the dynamical transition of the Mari-Kurchan model glass former. The association provides quasi-rigorous bounds for void percolation, which together with numerical results in d=2-6 suggests an equivalence between the two transitions in the limit of high spatial dimension. This conjecture provides physical insights into the systematic difficulties that mode-coupling theory encounters in predicting the onset of both types of dynamical arrest.}, Key = {fds224956} }