Publications of Patrick Charbonneau    :chronological  alphabetical  by type listing:

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@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
             USA},
   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},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1103/PhysRevE.96.032129},
   Doi = {10.1103/PhysRevE.96.032129},
   Key = {fds328992}
}

@article{fds328993,
   Author = {Zhuang, Y and Charbonneau, P},
   Title = {Communication: Microphase equilibrium and assembly
             dynamics.},
   Journal = {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},
   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.},
   Key = {fds318060}
}

@article{fds318061,
   Author = {Zhuang, Y and Charbonneau, P},
   Title = {Recent Advances in the Theory and Simulation of Model
             Colloidal Microphase Formers.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   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
             USA},
   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 (Online)},
   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 = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   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 = {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 = {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 = {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{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{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{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}
}

@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
             USA},
   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 (Online)},
   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 = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   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{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}
}

@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},
   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 their crystal contacts, and accordingly
             parameterize patchy particle models. Comparing the phase
             diagrams of these schematic models with experimental results
             enables us to critically examine the assumptions behind the
             two approaches. The study also reveals features of
             protein-protein interactions that can be leveraged to
             crystallize proteins more generally.},
   Doi = {10.1039/c3sm52175c},
   Key = {fds232070}
}

@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 = {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 d u = 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 = {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 = {Physical Review E - Statistical, Nonlinear, and Soft Matter
             Physics},
   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 = {Proceedings of the National Academy of Sciences of
             USA},
   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 = {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 = {Physical Review Letters},
   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 - Condensed Matter and Materials
             Physics},
   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{fds232087,
   Author = {Zhang, K and Charbonneau, P},
   Title = {Monte carlo study of the axial next-nearest-neighbor Ising
             model.},
   Journal = {Physical Review Letters},
   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 = {Physical Review E - Statistical, Nonlinear, and Soft Matter
             Physics},
   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{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},
   Pages = {051126},
   Year = {2010},
   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 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 ∼d 2 -d is consistent with
             that of other approaches, such as replica theory and
             density-functional theory. The validity of various
             structural approximations is assessed by comparing with
             three- to six-dimensional isostatic packings obtained from
             simulations. These numerical results support a growing
             accuracy of the theoretical approach with dimension. The
             approach could thus serve as a starting point to obtain a
             geometrical understanding of the higher-order correlations
             present in jammed packings. © 2010 The American Physical
             Society.},
   Doi = {10.1103/PhysRevE.82.051126},
   Key = {fds232085}
}

@article{fds232088,
   Author = {Meel, JAV 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},
   Pages = {061110},
   Year = {2009},
   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. 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. © 2009 The
             American Physical Society.},
   Doi = {10.1103/PhysRevE.80.061110},
   Key = {fds232088}
}

@article{fds232090,
   Author = {Meel, JAV 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},
   Pages = {030201(R)},
   Year = {2009},
   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.
             We conclude that it is the geometrical frustration of
             polytetrahedral structures that inhibits crystallization. ©
             2009 The American Physical Society.},
   Doi = {10.1103/PhysRevE.79.030201},
   Key = {fds232090}
}

@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{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},
   Volume = {20},
   Number = {49},
   Pages = {494245},
   Year = {2008},
   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 = {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 = {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},
   Number = {5},
   Pages = {267-289},
   Year = {2005},
   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 = {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(μ3-E)]4
             (R = H, CH3; M = Al, Ga, In; E = O, S, Se, Te)
             and group 13 cubanes [RM(μ3-M)]4 (R =
             F, Cl, CH3, NO2; 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}
}