Scholars@Duke
Patrick Charbonneau

Patrick Charbonneau

Professor of Chemistry
Chemistry
patrick.charbonneau@duke.edu
Box 90347, Durham, NC 27708-0347
5329 French Science, 124 Science Drive, Durham, NC 27708

Selected Publications

Simple Fluctuations in Simple Glass Formers.

Journal Article The journal of physical chemistry. B · November 2024 Critical single-particle fluctuations associated with particle displacements are inherent to simple glass-forming liquids in the limit of large dimensions and leave a pseudocritical trace across all finite dimensions. This characteristic could serve as a c ... Full text Cite

Colloidal hard spheres: Triumphs, challenges, and mysteries

Journal Article Reviews of Modern Physics · October 1, 2024 The simplicity of hard spheres as a model system is deceptive. Although the particles interact solely through volume exclusion, that nevertheless suffices for a wealth of static and dynamical phenomena to emerge, making the model an important target for ac ... Full text Cite

Notochord segmentation in zebrafish controlled by iterative mechanical signaling.

Journal Article Dev Cell · July 22, 2024 In bony fishes, patterning of the vertebral column, or spine, is guided by a metameric blueprint established in the notochord sheath. Notochord segmentation begins days after somitogenesis concludes and can occur in its absence. However, somite patterning ... Full text Link to item Cite

Pralines des Voyageurs: An Iconic Intercultural Food

Journal Article Cuizine : the Journal of Canadian Food Cultures · June 27, 2024 Pralines are well-known French and New Orleans delicacies synonymous with both high-calorie count and refinement. In the 18th and early 19th centuries, the confection also had a rougher edge. After substituting almonds and refined sugar by indigenous ingre ... Full text Open Access Cite

Dynamics and fluctuations of minimally structured glass formers.

Journal Article Physical review. E · May 2024 The mean-field theory (MFT) of simple structural glasses, which is exact in the limit of infinite spatial dimensions, d→∞, offers theoretical insight as well as quantitative predictions about certain features of d=3 systems. In order to more systematically ... Full text Cite

Data from: Dynamics and fluctuations of minimally-structured glass formers

Dataset · April 26, 2024 The mean-field theory (MFT) of simple structural glasses, which is exact in the limit of infinite spatial dimensions, d→∞, offers theoretical insight as well as quantitative predictions about certain features of d=3 systems. In order to more systematically ... Full text Cite

Glasslike caging with random planes.

Journal Article Physical review. E · February 2024 The richness of the mean-field solution of simple glasses leaves many of its features challenging to interpret. A minimal model that illuminates glass physics in the same way that the random energy model clarifies spin glass behavior would therefore be ben ... Full text Open Access Cite

Jamming, relaxation, and memory in a minimally structured glass former.

Journal Article Physical review. E · November 2023 Structural glasses form through various out-of-equilibrium processes, including temperature quenches, rapid compression (crunches), and shear. Although each of these processes should be formally understandable within the recently formulated dynamical mean- ... Full text Open Access Cite

Axial segmentation by iterative mechanical signaling.

Journal Article bioRxiv · March 28, 2023 In bony fishes, formation of the vertebral column, or spine, is guided by a metameric blueprint established in the epithelial sheath of the notochord. Generation of the notochord template begins days after somitogenesis and even occurs in the absence of so ... Full text Link to item Cite

From Panocha to Fudge

Journal Article Gastronomica · February 1, 2023 Although the origins of the popular candy called fudge have been traced to American industrial processed foods of the 1880s, an early version known as panochita de leche was made in eighteenth-century Mexico using only rustic brown sugar and milk. ... Full text Open Access Cite

Recreating Colonial Mexican Fudge

Journal Article Gastronomica · February 1, 2023 Full text Open Access Cite

Preface

Book · January 1, 2023 Cite

Spin Glass Theory and Far Beyond: Replica Symmetry Breaking After 40 Years

Book · January 1, 2023 About sixty years ago, the anomalous magnetic response of certain magnetic alloys drew the attention of theoretical physicists. It soon became clear that understanding these systems, now called spin glasses, would give rise to a new branch of statistical p ... Full text Cite

Communication: Weakening the critical dynamical slowing down of models with SALR interactions.

Journal Article The Journal of chemical physics · November 2022 In systems with frustration, the critical slowing down of the dynamics severely impedes the numerical study of phase transitions for even the simplest of lattice models. In order to help sidestep the gelation-like sluggishness, a clearer understanding of t ... Full text Open Access Cite

Gardner-like crossover from variable to persistent force contacts in granular crystals.

Journal Article Physical review. E · November 2022 We report experimental evidence of a Gardner-like crossover from variable to persistent force contacts in a two-dimensional bidisperse granular crystal by analyzing the variability of both particle positions and force networks formed under uniaxial compres ... Full text Open Access Cite

From the replica trick to the replica symmetry-breaking technique

Journal Article IAMP News Bulletin · October 2022 Among the various remarkable contributions of Giorgio Parisi to physics, his for- mulation of the replica symmetry breaking solution for the Sherrington-Kirkpatrick model stands out. In this article, different historical sources are used to reconstruct the ... Open Access Link to item Cite

Equilibrium fluctuations in mean-field disordered models.

Journal Article Physical review. E · August 2022 Mean-field models of glasses that present a random first order transition exhibit highly nontrivial fluctuations. Building on previous studies that focused on the critical scaling regime, we here obtain a fully quantitative framework for all equilibrium co ... Full text Open Access Cite

Data from: Equilibrium fluctuations in mean-field disordered models

Dataset · July 22, 2022 Mean-field models of glasses that present a random first order transition exhibit highly nontrivial fluctuations. Building on previous studies that focused on the critical scaling regime, we here obtain a fully quantitative framework for all equilibrium co ... Full text Cite

The dimensional evolution of structure and dynamics in hard sphere liquids.

Journal Article The Journal of chemical physics · April 2022 The formulation of the mean-field infinite-dimensional solution of hard sphere glasses is a significant milestone for theoretical physics. How relevant this description might be for understanding low-dimensional glass-forming liquids, however, remains uncl ... Full text Open Access Cite

Local Dynamical Heterogeneity in Simple Glass Formers.

Journal Article Physical review letters · April 2022 We study the local dynamical fluctuations in glass-forming models of particles embedded in d-dimensional space, in the mean-field limit of d→∞. Our analytical calculation reveals that single-particle observables, such as squared particle displacements, dis ... Full text Open Access Cite

Data from: The dimensional evolution of structure and dynamics in hard sphere liquids

Dataset · March 30, 2022 The formulation of the mean-field infinite-dimensional solution of hard sphere glasses is a significant milestone for theoretical physics. How relevant this description might be for understanding low-dimensional glass-forming liquids, however, remains uncl ... Full text Cite

Data and scripts from: Local dynamical heterogeneity in simple glass formers

Dataset · March 18, 2022 We study the local dynamical fluctuations in glass-forming models of particles embedded in d-dimensional space, in the mean-field limit of d→∞. Our analytical calculation reveals that single-particle observables, such as squared particle displacements, dis ... Full text Cite

ADVANCES IN THE MOLECULAR SIMULATION OF MICROPHASE FORMERS

Chapter · January 1, 2022 This chapter details the different experimental microphase formers and provides a minimal theoretical framework to present the simulation challenges associated with studying model microphase formers. Block copolymers are by far the most studied microphase ... Full text Open Access Cite

Data from: Three simple scenarios for high-dimensional sphere packings

Dataset · December 9, 2021 Based on results from the physics and mathematics literature which suggest a series of clearly defined conjectures, we formulate three simple scenarios for the fate of hard sphere crystallization in high dimension: in scenario A, crystallization is impeded ... Full text Cite

Three simple scenarios for high-dimensional sphere packings.

Journal Article Physical review. E · December 2021 Based on results from the physics and mathematics literature which suggest a series of clearly defined conjectures, we formulate three simple scenarios for the fate of hard sphere crystallization in high dimension: in scenario A, crystallization is impeded ... Full text Open Access Cite

The dimensional evolution of structure and dynamics in hard sphere liquids

Journal Article J. Chem. Phys. · November 26, 2021 The formulation of the mean-field, infinite-dimensional solution of hard sphere glasses is a significant milestone for theoretical physics. How relevant this description might be for understanding low-dimensional glass-forming liquids, however, remains unc ... Open Access Link to item Cite

Numerical transfer matrix study of frustrated next-nearest-neighbor Ising models on square lattices

Journal Article Physical Review B · October 1, 2021 Ising models with frustrated next-nearest-neighbor interactions present a rich array of modulated phases. These phases, however, assemble and relax slowly, which hinders their computational study. In two dimensions, strong fluctuations further hamper deter ... Full text Open Access Cite

Local dynamical heterogeneity in glass formers

Journal Article Phys. Rev. Lett. · September 24, 2021 We study the local dynamical fluctuations in glass-forming models of particles embedded in $d$-dimensional space, in the mean-field limit of $d\to\infty$. Our analytical calculation reveals that single-particle observables, such as squared particle displac ... Open Access Link to item Cite

Comment on "kosterlitz-Thouless-type caging-uncaging transition in a quasi-one-dimensional hard disk system"

Journal Article Physical Review Research · September 1, 2021 Huerta [Phys. Rev. Research 2, 033351 (2020)2643-156410.1103/PhysRevResearch.2.033351] report a power-law decay of positional order in numerical simulations of hard disks confined within hard parallel walls, which they interpret as a Kosterlitz-Thouless (K ... Full text Open Access Cite

High-dimensional percolation criticality and hints of mean-field-like caging of the random Lorentz gas.

Journal Article Physical review. E · August 2021 The random Lorentz gas (RLG) is a minimal model for transport in disordered media. Despite the broad relevance of the model, theoretical grasp over its properties remains weak. For instance, the scaling with dimension d of its localization transition at th ... Full text Open Access Cite

Thermodynamic stability of hard sphere crystals in dimensions 3 through 10.

Journal Article The European physical journal. E, Soft matter · August 2021 Although much is known about the metastable liquid branch of hard spheres-from low dimension d up to [Formula: see text]-its crystal counterpart remains largely unexplored for [Formula: see text]. In particular, it is unclear whether the crystal phase is t ... Full text Open Access Cite

Data from: Thermodynamic stability of hard sphere crystals in dimensions 3 through 10

Dataset · July 28, 2021 Although much is known about the metastable liquid branch of hard spheres--from low dimension d up to the infinite dimensional limit--its crystal counterpart remains largely unexplored for d>3. In particular, it is unclear whether the crystal phase is ther ... Full text Cite

Data and scripts from: High-dimensional percolation criticality and hints of mean-field-like caging of the random Lorentz gas

Dataset · July 2, 2021 The random Lorentz gas (RLG) is a minimal model for transport in disordered media. Despite the broad relevance of the model, theoretical grasp over its properties remains weak. For instance, the scaling with dimension $d$ of its localization transition at ... Full text Cite

Finite-size effects in the microscopic critical properties of jammed configurations: A comprehensive study of the effects of different types of disorder.

Journal Article Physical review. E · July 2021 Jamming criticality defines a universality class that includes systems as diverse as glasses, colloids, foams, amorphous solids, constraint satisfaction problems, neural networks, etc. A particularly interesting feature of this class is that small interpar ... Full text Open Access Cite

Solution of disordered microphases in the Bethe approximation.

Journal Article The Journal of chemical physics · July 2021 The periodic microphases that self-assemble in systems with competing short-range attractive and long-range repulsive (SALR) interactions are structurally both rich and elegant. Significant theoretical and computational efforts have thus been dedicated to ... Full text Open Access Cite

Data from: Solution of disordered microphases in the Bethe approximation

Dataset · June 29, 2021 The periodic microphases that self-assemble in systems with competing short-range attractive and long-range repulsive (SALR) interactions are structurally both rich and elegant. Significant theoretical and computational efforts have thus been dedicated to ... Full text Cite

Data and scripts from: Characterization and efficient Monte Carlo sampling of disordered microphases

Dataset · June 7, 2021 The disordered microphases that develop in the high-temperature phase of systems with competing short- range attractive and long-range repulsive (SALR) interactions result in a rich array of distinct morphologies, such as cluster, void cluster and percolat ... Full text Cite

Data and scripts from: Percolation thresholds on high-dimensional D_n and E_8-related lattices

Dataset · June 2, 2021 The site and bond percolation problems are conventionally studied on (hyper)cubic lattices, which afford straightforward numerical treatments. The recent implementation of efficient simulation algorithms for high-dimensional systems now also facilitates th ... Full text Cite

Mean-Field Caging in a Random Lorentz Gas.

Journal Article The journal of physical chemistry. B · June 2021 The random Lorentz gas (RLG) is a minimal model of both percolation and glassiness, which leads to a paradox in the infinite-dimensional, d → ∞ limit: the localization transition is then expected to be continuous for the former and discont ... Full text Open Access Cite

Percolation thresholds on high-dimensional D_{n} and E_{8}-related lattices.

Journal Article Physical review. E · June 2021 The site and bond percolation problems are conventionally studied on (hyper)cubic lattices, which afford straightforward numerical treatments. The recent implementation of efficient simulation algorithms for high-dimensional systems now also facilitates th ... Full text Open Access Cite

Characterization and efficient Monte Carlo sampling of disordered microphases.

Journal Article The Journal of chemical physics · June 2021 The disordered microphases that develop in the high-temperature phase of systems with competing short-range attractive and long-range repulsive (SALR) interactions result in a rich array of distinct morphologies, such as cluster, void cluster, and percolat ... Full text Open Access Cite

Data from: Mean-field caging in a random Lorentz gas

Dataset · May 25, 2021 The random Lorentz gas (RLG) is a minimal model of both percolation and glassiness, which leads to a paradox in the infinite-dimensional limit: the localization transition is then expected to be continuous for the former and discontinuous for the latter. A ... Full text Cite

Resolving the two-dimensional axial next-nearest-neighbor Ising model using transfer matrices

Journal Article Physical Review B · March 25, 2021 Some features of the phase diagram of the two-dimensional axial next-nearest-neighbor Ising model have long been debated. The extended structural correlations and long relaxation times associated with its Kosterlitz-Thouless phase indeed result in analytic ... Full text Open Access Cite

Interplay between percolation and glassiness in the random Lorentz gas.

Journal Article Physical review. E · March 2021 The random Lorentz gas (RLG) is a minimal model of transport in heterogeneous media that exhibits a continuous localization transition controlled by void space percolation. The RLG also provides a toy model of particle caging, which is known to be relevant ... Full text Open Access Cite

Data and Scripts from: Interplay between percolation and glassiness in the random Lorentz gas

Dataset · March 1, 2021 The random Lorentz gas (RLG) is a minimal model of transport in heterogeneous media that exhibits a continuous localization transition controlled by void space percolation. The RLG also provides a toy model of particle caging, which is known to be relevant ... Full text Cite

Engaging Researchers in Data Dialogues: Designing Collaborative Programming to Promote Research Data Sharing

Journal Article Journal of eScience Librarianship · March 1, 2021 A range of regulatory pressures emanating from funding agencies and scholarly journals increasingly encourage researchers to engage in formal data sharing practices. As academic libraries continue to refine their role in supporting researchers in t ... Full text Open Access Cite

Memory Formation in Jammed Hard Spheres.

Journal Article Physical review letters · February 2021 Liquids equilibrated below an onset condition share similar inherent states, while those above that onset have inherent states that markedly differ. Although this type of materials memory was first reported in simulations over 20 years ago, its physical or ... Full text Open Access Cite

Sugars: Soft Caramel and Sucre à la Crème--an Undergraduate Experiment about Sugar Crystallization

Chapter · 2021 A comprehensive reference to molecular gastronomy, this book highlights techniques that have enabled chefs to achieve new and better ways of preparing food. ... Open Access Link to item Cite

Finite Dimensional Vestige of Spinodal Criticality above the Dynamical Glass Transition.

Journal Article Physical review letters · September 2020 Finite dimensional signatures of spinodal criticality are notoriously difficult to come by. The dynamical transition of glass-forming liquids, first described by mode-coupling theory, is a spinodal instability preempted by thermally activated processes tha ... Full text Open Access Cite

Data from: Finite-dimensional vestige of spinodal criticality above the dynamical glass transition

Dataset · August 5, 2020 Finite-dimensional signatures of spinodal criticality are notoriously difficult to come by. The dynamical transition of glass-forming liquids, first described by mode-coupling theory, is a spinodal instability preempted by thermally activated processes tha ... Full text Cite

Postponing the dynamical transition density using competing interactions

Journal Article Granular Matter · August 1, 2020 Systems of dense spheres interacting through very short-ranged attraction are known from theory, simulations and colloidal experiments to exhibit dynamical reentrance. Their liquid state can thus be fluidized at higher densities than possible in systems wi ... Full text Open Access Cite

Data from: Postponing the dynamical transition density using competing interactions

Dataset · February 24, 2020 Systems of dense spheres interacting through very short-ranged attraction are known from theory, simulations and colloidal experiments to exhibit dynamical reentrance. Their liquid state can thus be fluidized at higher densities than possible in systems wi ... Full text Cite

Using Schematic Models to Understand the Microscopic Basis for Inverted Solubility in γD-Crystallin.

Journal Article The journal of physical chemistry. B · November 2019 Inverted solubility-melting a crystal by cooling-is observed in a handful of proteins, such as carbomonoxy hemoglobin C and γD-crystallin. In human γD-crystallin, the phenomenon is associated with the mutation of the 23rd residue, a proline, to a threonine ... Full text Open Access Cite

Data from: Front-mediated melting of isotropic ultrastable glasses

Dataset · October 8, 2019 Ultrastable vapor-deposited glasses display uncommon material properties. Most remarkably, upon heating they are believed to melt via a liquid front that originates at the free surface and propagates over a mesoscopic crossover length, before crossing over ... Full text Cite

Front-Mediated Melting of Isotropic Ultrastable Glasses.

Journal Article Physical review letters · October 2019 Ultrastable vapor-deposited glasses display uncommon material properties. Most remarkably, upon heating they are believed to melt via a liquid front that originates at the free surface and propagates over a mesoscopic crossover length, before crossing over ... Full text Open Access Cite

Data and scripts from: Using Schematic Models to Understand the Microscopic Basis for Inverted Solubility in gammaD-crystallin

Dataset · September 30, 2019 Featured Publication Inverted solubility--melting a crystal by cooling--is observed in a handful of proteins, such as carbomonoxy hemoglobin and gammaD-crystallin. In human gammaD-crystallin, the phenomenon is associated with the mutation of the 23rd residue, a proline, to a t ... Full text Cite

Temperature-Dependent Interactions Explain Normal and Inverted Solubility in a γD-Crystallin Mutant.

Journal Article Biophysical journal · September 2019 Protein crystal production is a major bottleneck in the structural characterization of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) of ... Full text Open Access Cite

Data and scripts from: temperature-dependent interactions explain normal and inverted solubility in a γD-crystallin mutant

Dataset · July 17, 2019 Protein crystal production is a major bottleneck in the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy (or patchiness) of ... Full text Cite

Gardner physics in amorphous solids and beyond.

Journal Article The Journal of chemical physics · July 2019 Featured Publication One of the most remarkable predictions to emerge out of the exact infinite-dimensional solution of the glass problem is the Gardner transition. Although this transition was first theoretically proposed a generation ago for certain mean-field spin glass mod ... Full text Open Access Cite

Zero-temperature glass transition in two dimensions.

Journal Article Nature communications · April 2019 Liquids cooled towards the glass transition temperature transform into amorphous solids that have a wide range of applications. While the nature of this transformation is understood rigorously in the mean-field limit of infinite spatial dimensions, the pro ... Full text Open Access Cite

Bypassing sluggishness: SWAP algorithm and glassiness in high dimensions.

Journal Article Physical review. E · March 2019 The recent implementation of a swap Monte Carlo algorithm (SWAP) for polydisperse glass forming mixtures bypasses computational sluggishness and closes the gap between experimental and simulation timescales in physical dimensions d=2 and 3. Here, we consid ... Full text Open Access Cite

Data and scripts from: Zero-temperature glass transition in two dimensions

Dataset · February 26, 2019 Liquids cooled towards the glass transition temperature transform into amorphous solids that have a wide range of applications. While the nature of this transformation is understood rigorously in the mean-field limit of infinite spatial dimensions, the pro ... Full text Cite

Data and scripts from: Bypassing sluggishness: SWAP algorithm and glassiness in high dimensions

Dataset · February 22, 2019 The recent implementation of a swap Monte Carlo algorithm (SWAP) for polydisperse mixtures fully bypasses computational sluggishness and closes the gap between experimental and simulation timescales in physical dimensions d=2 and 3. Here, we consider suita ... Full text Cite

Data and scripts from: Morphology of renormalization-group flow for the de Almeida–Thouless–Gardner universality class

Dataset · February 13, 2019 A replica-symmetry-breaking phase transition is predicted in a host of disordered media. The criticality of the transition has, however, long been questioned below its upper critical dimension, six, due to the absence of a critical fixed point in the renor ... Full text Cite

Data and scripts from: Glassy, Gardner-like phenomenology in minimally polydisperse crystalline systems

Dataset · February 5, 2019 We report on a nonequilibrium phase of matter, the minimally disordered crystal phase, which we find exists between the maximally amorphous glasses and the ideal crystal. Even though these near crystals appear highly ordered, they display glassy and jammin ... Full text Cite

Data and scripts from: Dynamics around the site percolation threshold on high-dimensional hypercubic lattices

Dataset · February 5, 2019 Recent advances on the glass problem motivate reexamining classical models of percolation. Here, we consider the displacement of an ant in a labyrinth near the percolation threshold on cubic lattices both below and above the upper critical dimension of sim ... Full text Cite

Data and scripts from: Obtaining soft matter models of proteins and their phase behavior

Dataset · February 4, 2019 Globular proteins are roughly spherical biomolecules with attractive, and highly directional interactions. This microscopic observation motivates describing these proteins as patchy particles: hard spheres with attractive surface patches. Mapping a biomole ... Full text Cite

Glassy, Gardner-like phenomenology in minimally polydisperse crystalline systems.

Journal Article Physical review. E · February 2019 We report on a nonequilibrium phase of matter, the minimally disordered crystal phase, which we find exists between the maximally amorphous glasses and the ideal crystal. Even though these near crystals appear highly ordered, they display glassy and jammin ... Full text Open Access Cite

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

Journal Article Physical review. E · February 2019 A replica-symmetry-breaking phase transition is predicted in a host of disordered media. The criticality of the transition has, however, long been questioned below its upper critical dimension, six, due to the absence of a critical fixed point in the renor ... Full text Open Access Cite

Dynamics around the site percolation threshold on high-dimensional hypercubic lattices.

Journal Article Physical review. E · February 2019 Recent advances on the glass problem motivate reexamining classical models of percolation. Here we consider the displacement of an ant in a labyrinth near the percolation threshold on cubic lattices both below and above the upper critical dimension of simp ... Full text Open Access Cite

Obtaining Soft Matter Models of Proteins and their Phase Behavior.

Journal Article Methods in molecular biology (Clifton, N.J.) · January 2019 Globular proteins are roughly spherical biomolecules with attractive and highly directional interactions. This microscopic observation motivates describing these proteins as patchy particles: hard spheres with attractive surface patches. Mapping a biomolec ... Full text Open Access Cite

Correction to: Obtaining Soft Matter Models of Proteins and their Phase Behavior.

Journal Article Methods in molecular biology (Clifton, N.J.) · January 2019 The acknowledgement section text has been updated in the chapter. ... Full text Open Access Cite

Correlation lengths in quasi-one-dimensional systems via transfer matrices

Journal Article Molecular Physics · November 17, 2018 Using transfer matrices up to next-nearest-neighbour interactions, we examine the structural correlations of quasi-one-dimensional systems of hard disks confined by two parallel lines and hard spheres confined in cylinders. Simulations have shown that the ... Full text Open Access Cite

Data and scripts from: Equilibrium phase behavior of the square-well linear microphase-forming model

Dataset · October 9, 2018 The data files in this collection are associated with the paper "Equilibrium phase behavior of the square-well linear microphase-forming model", Y. Zhuang, P. Charbonneau, PRL, 2016. They include .dat, .gle and .eps files with associated raw data and gener ... Full text Cite

Data and scripts from: Nontrivial critical fixed point for replica-symmetry-breaking transitions

Dataset · October 8, 2018 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 ph ... Full text Cite

Data and scripts from: Universal non-Debye scaling in the density of states of amorphous solids

Dataset · October 4, 2018 The data files in this collection are associated with the paper "Universal Non-Debye Scaling in the Density of States of Amorphous Solids", A. Poncet, P. Charbonneau, E. I. Corwin, G. Parisi, and F. Zamponi, PRL, 2016. They include .dat, .pdf, .gnu, .eps a ... Full text Cite

Tissue self-organization underlies morphogenesis of the notochord.

Journal Article Philos Trans R Soc Lond B Biol Sci · September 24, 2018 The notochord is a conserved axial structure that in vertebrates serves as a hydrostatic scaffold for embryonic axis elongation and, later on, for proper spine assembly. It consists of a core of large fluid-filled vacuolated cells surrounded by an epitheli ... Full text Open Access Link to item Cite

The Limits of Primary Radiation Forces in Bulk Acoustic Standing Waves for Concentrating Nanoparticles

Journal Article Particle and Particle Systems Characterization · July 1, 2018 Acoustic waves are increasingly used to concentrate, separate, and pattern nanoparticles in liquids, but the extent to which nanoparticles of different size and composition can be focused is not well-defined. This article describes a simple analytical mode ... Full text Open Access Cite

A microscopic model of the Stokes-Einstein relation in arbitrary dimension.

Journal Article The Journal of chemical physics · June 2018 The Stokes-Einstein relation (SER) is one of the most robust and widely employed results from the theory of liquids. Yet sizable deviations can be observed for self-solvation, which cannot be explained by the standard hydrodynamic derivation. Here, we revi ... Full text Open Access Cite

Data from: A microscopic model of the Stokes-Einstein Relation in arbitrary dimension

Dataset · May 29, 2018 The Stokes--Einstein relation (SER) is one of most robust and widely employed results from the theory of liquids. Yet sizable deviations can be observed for selfsolvation, which cannot be explained by the standard hydrodynamic derivation. Here, we revisit ... Full text Cite

Data and scripts from: Correlation lengths in quasi-one-dimensional systems via transfer matrices

Dataset · May 29, 2018 Using transfer matrices up to next-nearest-neighbour (NNN) interactions, we examine the structural correlations of quasi-one-dimensional systems of hard disks confined by two parallel lines and hard spheres confined in cylinders. Simulations have shown tha ... Full text Cite

Clustering and assembly dynamics of a one-dimensional microphase former.

Journal Article Soft matter · May 2018 Both ordered and disordered microphases ubiquitously form in suspensions of particles that interact through competing short-range attraction and long-range repulsion (SALR). While ordered microphases are more appealing materials targets, understanding the ... Full text Open Access Cite

Data and scripts from: Clustering and assembly dynamics of a one-dimensional microphase former

Dataset · March 14, 2018 We study the disordered regime of a one-dimensional (1D) short-range attraction and long-range repulsion (SALR) model, whose simplicity enables detailed analysis by transfer matrices and Monte Carlo simulations. We first characterize the signature of the c ... Full text Cite

Learning about Biomolecular Solvation from Water in Protein Crystals.

Journal Article The journal of physical chemistry. B · March 2018 Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are no ... Full text Open Access Cite

Data and Scripts from: Learning about biomolecular solvation from water in protein crystals

Dataset · February 6, 2018 Water occupies typically 50% of a protein crystal, and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are n ... Full text Cite

Classification of crystallization outcomes using deep convolutional neural networks.

Journal Article PloS one · January 2018 The Machine Recognition of Crystallization Outcomes (MARCO) initiative has assembled roughly half a million annotated images of macromolecular crystallization experiments from various sources and setups. Here, state-of-the-art machine learning algorithms a ... Full text Open Access Cite

Origin of Ultrastability in Vapor-Deposited Glasses.

Journal Article Physical review letters · November 2017 Glass films created by vapor-depositing molecules onto a substrate can exhibit properties similar to those of ordinary glasses aged for thousands of years. It is believed that enhanced surface mobility is the mechanism that allows vapor deposition to creat ... Full text Open Access Cite

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

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2017 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 challen ... Full text Open Access Cite

Data and scripts from: The origin of ultrastability in vapor-deposited glasses

Dataset · September 21, 2017 Glass films created by vapor-depositing molecules onto a substrate can exhibit properties similar to those of ordinary glasses aged for thousands of years. It is believed that enhanced surface mobility is the mechanism that allows vapor deposition to creat ... Full text Cite

Data and scripts from: Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling

Dataset · September 19, 2017 The data files in this collection are associated with "Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling", Berthier, Ludovic; Charbonneau, Patrick; Coslovich, Daniele; Ninarello, Andrea; Ozawa, Misaki; Yaida ... Full text Cite

Data and scripts from: Cycle-expansion method for the Lyapunov exponent, susceptibility, and higher moments

Dataset · September 15, 2017 Lyapunov exponents characterize the chaotic nature of dynamical systems by quantifying the growth rate of uncertainty associated with the imperfect measurement of initial conditions. Finite-time estimates of the exponent, however, experience fluctuations d ... Full text Cite

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

Journal Article Physical review. E · September 2017 Lyapunov exponents characterize the chaotic nature of dynamical systems by quantifying the growth rate of uncertainty associated with the imperfect measurement of initial conditions. Finite-time estimates of the exponent, however, experience fluctuations d ... Full text Open Access Cite

Communication: Microphase equilibrium and assembly dynamics.

Journal Article The Journal of chemical physics · September 2017 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 ... Full text Open Access Cite

Data and scripts from: Microphase equilibrium and assembly dynamics

Dataset · August 25, 2017 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.~Let ... Full text Cite

Lecture Notes on the Statistical Mechanics of Disordered Systems

Journal Article · May 19, 2017 This material complements David Chandler's Introduction to Modern Statistical Mechanics (Oxford University Press, 1987) in a graduate-level, one-semester course I teach in the Department of Chemistry at Duke University. Students enter this course with some ... Open Access Link to item Cite

Data and scripts from: Phase diagram and aggregation dynamics of a monolayer of paramagnetic colloids

Dataset · May 4, 2017 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 spat ... Full text Cite

Phase diagram and aggregation dynamics of a monolayer of paramagnetic colloids.

Journal Article Physical review. E · May 2017 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 spat ... Full text Open Access Cite

Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions.

Journal Article Physical review letters · May 2017 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 ph ... Full text Open Access Cite

Assembly of hard spheres in a cylinder: a computational and experimental study.

Journal Article Soft matter · May 2017 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 cyli ... Full text Open Access Cite

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

Journal Article Annual Review of Condensed Matter Physics · March 31, 2017 Despite decades of work, gaining a first-principles understanding of amorphous materials remains an extremely challenging problem. However, recent theoretical breakthroughs have led to the formulation of an exact solution of a microscopic glass-forming mod ... Full text Open Access Cite

Data and scripts from: Hard sphere packings within cylinders

Dataset · March 21, 2017 The data files in this collection are associated with the paper "Hard sphere packings within cylinders", L. Fu, W. Steinhardt, Y. Zhao, J.E.S Socolar and P. Charbonneau, Soft Matter, 2016. They include .dat and .m files with associated raw data and generat ... Full text Cite

Data and scripts from: Assembly of hard spheres in a cylinder: a computational and experimental study

Dataset · March 20, 2017 The data files in this collection are associated with the paper "Assembly of hard spheres in a cylinder: a computational and experimental study", L. Fu, C. Bian, W. Shields, D. Cruz, G. Lopez and P. Charbonneau, Soft Matter (2017). They include .dat and .m ... Full text Cite

Data and scripts from: Point-to-set lengths, local structure, and glassiness

Dataset · September 14, 2016 The data files in this collection are associated with the paper "Point-to-set lengths, local structure, and glassiness", S. Yaida, P. Charbonneau, L. Berthier, and G. Tarjus, Phys. Rev. E, 2016. They include .dat, .eps and .m files with associated raw data ... Full text Cite

Point-to-set lengths, local structure, and glassiness.

Journal Article Physical review. E · September 2016 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 amorphou ... Full text Open Access Cite

Recent Advances in the Theory and Simulation of Model Colloidal Microphase Formers.

Journal Article The journal of physical chemistry. B · August 2016 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 ess ... Full text Open Access Cite

Data and scripts from: Growing timescales and lengthscales characterizing vibrations of amorphous solids

Dataset · July 5, 2016 The data files in this collection are associated with the paper "Growing timescales and lengthscales characterizing vibrations of amorphous solids", Y. Jin, L. Berthier, P. Charbonneau, G. Parisi, B. Seoane, and F. Zamponi, PNAS, 2016. They include .dat, . ... Full text Cite

Computational crystallization.

Journal Article Archives of biochemistry and biophysics · July 2016 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 er ... Full text Open Access Cite

Equilibrium Phase Behavior of the Square-Well Linear Microphase-Forming Model.

Journal Article The journal of physical chemistry. B · July 2016 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 ... Full text Open Access Cite

Growing timescales and lengthscales characterizing vibrations of amorphous solids.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · July 2016 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 enha ... Full text Open Access Cite

Universal Non-Debye Scaling in the Density of States of Amorphous Solids.

Journal Article Physical review letters · July 2016 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 ex ... Full text Open Access Cite

Linking dynamical heterogeneity to static amorphous order

Journal Article Journal of Statistical Mechanics: Theory and Experiment · July 1, 2016 Glass-forming liquids grow dramatically sluggish upon cooling. This slowdown has long been thought to be accompanied by a growing correlation length. Characteristic dynamical and static length scales, however, have been observed to grow at different rates, ... Full text Open Access Cite

Data and scripts from: Linking dynamical heterogeneity to static amorphous order

Dataset · May 16, 2016 The data files in this collection are associated with the paper "Linking dynamical heterogeneity to static amorphous order", P. Charbonneau, S. Yaida, E. Dyer, and J. Lee, J. Stat. Mech., 2016. They include .dat, .eps, and .m files with associated raw data ... Full text Cite

The physics of protein self-assembly

Journal Article Current Opinion in Colloid and Interface Science · April 1, 2016 Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed phases associated ... Full text Open Access Cite

Hard sphere packings within cylinders.

Journal Article Soft matter · March 2016 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 sphe ... Full text Open Access Cite

Kinetic Monte Carlo simulations for birefringence relaxation of photo-switchable molecules on a surface.

Journal Article The Journal of chemical physics · March 2016 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 contro ... Full text Open Access Cite

Equilibrium Phase Behavior of a Continuous-Space Microphase Former.

Journal Article Physical review letters · March 2016 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 understandi ... Full text Open Access Cite

Soft matter perspective on protein crystal assembly.

Journal Article Colloids and surfaces. B, Biointerfaces · January 2016 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 underst ... Full text Open Access Cite

Highly parallel acoustic assembly of microparticles into well-ordered colloidal crystallites.

Journal Article Soft matter · January 2016 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 programm ... Full text Open Access Cite

Efficient measurement of point-to-set correlations and overlap fluctuations in glass-forming liquids.

Journal Article The Journal of chemical physics · January 2016 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 comp ... Full text Open Access Cite

Phase ordering of zig-zag and bow-shaped hard needles in two dimensions.

Journal Article The Journal of chemical physics · September 2015 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 ... Full text Open Access Cite

Numerical detection of the Gardner transition in a mean-field glass former.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · July 2015 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 sta ... Full text Open Access Cite

Dimensional study of the dynamical arrest in a random Lorentz gas.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · April 2015 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 dy ... Full text Open Access Cite

Phase transformations in binary colloidal monolayers.

Journal Article Soft matter · March 2015 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 c ... Full text Open Access Cite

Jamming criticality revealed by removing localized buckling excitations.

Journal Article Physical review letters · March 2015 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 tran ... Full text Open Access Cite

Hopping and the Stokes-Einstein relation breakdown in simple glass formers.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2014 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 ... Full text Open Access Cite

Exact theory of dense amorphous hard spheres in high dimension. III. the full replica symmetry breaking solution

Journal Article Journal of Statistical Mechanics: Theory and Experiment · October 1, 2014 In the first part of this paper, we derive the general replica equations that describe infinite-dimensional hard spheres at any level of replica symmetry breaking (RSB) and in particular in the fullRSB scheme. We show that these equations are formally very ... Full text Open Access Cite

Competition between monomeric and dimeric crystals in schematic models for globular proteins.

Journal Article The journal of physical chemistry. B · July 2014 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) iden ... Full text Open Access Cite

Emergence of limit-periodic order in tiling models.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · July 2014 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 quenc ... Full text Open Access Cite

Fractal free energy landscapes in structural glasses.

Journal Article Nature communications · April 2014 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, usin ... Full text Open Access Cite

Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study.

Journal Article Soft matter · January 2014 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 compr ... Full text Open Access Cite

Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

Journal Article PloS one · January 2014 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 pr ... Full text Open Access Cite

Dimensional dependence of the Stokes-Einstein relation and its violation.

Journal Article The Journal of chemical physics · October 2013 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 t ... Full text Open Access Cite

Geometrical frustration and static correlations in hard-sphere glass formers.

Journal Article The Journal of chemical physics · March 2013 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 ... Full text Open Access Cite

Universal microstructure and mechanical stability of jammed packings.

Journal Article Physical review letters · November 2012 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 particu ... Full text Open Access Cite

[N]pT ensemble and finite-size-scaling study of the critical isostructural transition in the generalized exponential model of index 4.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · October 2012 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 dif ... Full text Open Access Cite

Dimensional study of the caging order parameter at the glass transition.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 2012 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-c ... Full text Open Access Cite

[N]pT Monte Carlo simulations of the cluster-crystal-forming penetrable sphere model.

Journal Article The Journal of chemical physics · June 2012 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 en ... Full text Open Access Cite

The effect of nanowire length and diameter on the properties of transparent, conducting nanowire films

Journal Article Nanoscale · 2012 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 c ... Full text Open Access Cite

Geometrical frustration and static correlations in a simple glass former.

Journal Article Physical review letters · January 2012 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 relaxatio ... Full text Open Access Cite

Glass transition and random close packing above three dimensions.

Journal Article Physical review letters · October 2011 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, ... Full text Open Access Cite

Monte Carlo approach for studying microphases applied to the axial next-nearest-neighbor Ising and the Ising-Coulomb models

Journal Article Physical Review B - Condensed Matter and Materials Physics · June 9, 2011 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 a ... Full text Open Access Cite

Reentrant and isostructural transitions in a cluster-crystal former.

Journal Article Physical review letters · December 2010 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 re ... Full text Open Access Cite

Application of Edwards' statistical mechanics to high-dimensional jammed sphere packings.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · November 2010 The isostatic jamming limit of frictionless spherical particles from Edwards' statistical mechanics [Song et al., Nature (London) 453, 629 (2008)] is generalized to arbitrary dimension d using a liquid-state description. The asymptotic high-dimensional beh ... Full text Open Access Cite

Monte carlo study of the axial next-nearest-neighbor Ising model.

Journal Article Physical review letters · May 2010 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 w ... Full text Open Access Cite

Numerical and theoretical study of a monodisperse hard-sphere glass former.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · April 2010 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 supersaturate ... Full text Open Access Cite

Hard-sphere crystallization gets rarer with increasing dimension.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · December 2009 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 ... Full text Open Access Cite

28aQL-4 Simulation and theoretical study of glass transition of 4d hard sphere

Journal Article Meeting abstracts of the Physical Society of Japan · August 18, 2009 Cite

Geometrical frustration: a study of four-dimensional hard spheres.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · March 2009 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 ... Full text Open Access Cite

Multiple occupancy crystals formed by purely repulsive soft particles

Journal Article Journal of Physics Condensed Matter · December 10, 2008 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 occ ... Full text Cite

Dynamical heterogeneity in a glass-forming ideal gas.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · July 2008 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 sigma rigidly joined at their midpoints. In an earlier study [W. van Ketel, Ph ... Full text Open Access Cite

Phase coexistence of cluster crystals: beyond the Gibbs phase rule.

Journal Article Physical review letters · December 2007 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 v ... Full text Open Access Cite

Dynamical heterogeneity and nonlinear susceptibility in supercooled liquids with short-range attraction.

Journal Article Physical review letters · September 2007 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 corre ... Full text Open Access Cite

Phase behavior and far-from-equilibrium gelation in charged attractive colloids.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · May 2007 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 techniqu ... Full text Open Access Cite

Gas-solid coexistence of adhesive spheres.

Journal Article The Journal of chemical physics · May 2007 Full text Open Access Cite

Systematic characterization of thermodynamic and dynamical phase behavior in systems with short-ranged attraction.

Journal Article Physical review. E, Statistical, nonlinear, and soft matter physics · January 2007 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 approa ... Full text Open Access Cite

Mode-coupling theory

Journal Article Journal of Statistical Mechanics: Theory and Experiment · May 1, 2005 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-Zw ... Full text Open Access Cite

Out-of-equilibrium dynamical fluctuations in glassy systems.

Journal Article The Journal of chemical physics · November 2004 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 sca ... Full text Open Access Cite

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 Article Organometallics · August 19, 2002 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. Geom ... Full text Cite

Synthesis of a prodrug: A semi-empirical PM3 study

Journal Article Journal of Molecular Structure: THEOCHEM · November 16, 2001 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-tetrazepinon ... Full text Cite

Energy barriers to rotation in axially chiral analogues of 4-(dimethylamino)pyridine.

Journal Article The Journal of organic chemistry · November 2001 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 ... Full text Cite