%% Books
@book{fds373522,
Author = {Charbonneau, P and Marinariy, E and Mézardz, M and Ricci-Tersenghiy,
F and Sicurox, G and Zamponi, F},
Title = {Preface},
Pages = {vii-viii},
Year = {2023},
Month = {January},
ISBN = {9789811273919},
Key = {fds373522}
}
@book{fds373523,
Author = {Charbonneau, P and Marinari, E and Mézard, M and Parisi, G and Ricci-Tersenghi, F and Sicuro, G and Zamponi, F},
Title = {Spin Glass Theory and Far Beyond: Replica Symmetry Breaking
After 40 Years},
Pages = {1-740},
Year = {2023},
Month = {January},
ISBN = {9789811273919},
url = {http://dx.doi.org/10.1142/13341},
Abstract = {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 physics. As physical materials, spin
glasses were found to be as useless as they were exotic.
They have nevertheless been recognized as paradigmatic
examples of complex systems with applications to problems as
diverse as neural networks, amorphous solids, biological
molecules, social and economic interactions, information
theory and constraint satisfaction problems. This book
presents an encyclopaedic overview of the broad range of
these applications. More than 30 contributions are compiled,
written by many of the leading researchers who have
contributed to these developments over the last few decades.
Some timely and cutting-edge applications are also
discussed. This collection serves well as an introduction
and summary of disordered and glassy systems for advanced
undergraduates, graduate students and practitioners
interested in the topic. Sample Chapter(s) Preface Chapter
1: Simulated Annealing, Optimization, Searching for Ground
States Chapter 34: Future Perspectives Contents: Simulated
Annealing, Optimization, Searching for Ground States (Sergio
Caracciolo, Alexander Hartmann, Scott Kirkpatrick and Martin
Weigel) Beyond the Ising Spin Glass I: m-Vector, Potts,
p-Spin, Spherical, Induced Moment, Random Graphs (David
Sherrington and Jairo R L de Almeida) Beyond the Ising Spin
Glass II: Spin Glass Without Replicas (J Michael Kosterlitz)
Renormalization Group in Spin Glasses (Tom Lubensky, Tamás
Temesvári, Imre Kondor and Maria Chiara Angelini) Numerical
Simulations and Replica Symmetry Breaking (Víctor
Martín-Mayor, Juan J Ruiz-Lorenzo, Beatriz Seoane and A
Peter Young) The High-dimensional Landscape Paradigm:
Spin-Glasses, and Beyond (Valentina Ros and Yan V Fyodorov)
Universal Aspects of the Structural Glass Transition from
Density Functional Theory (Theodore R Kirkpatrick and Dave
Thirumalai) Non-Perturbative Processes in Glasses (Peter G
Wolynes and Tommaso Rizzo) Dynamical Mean-Field Theory and
the Aging Dynamics (Andrea Crisanti, Silvio Franz, Jorge
Kurchan and Andrea Maiorano) Dynamical Heterogeneity in
Glass-Forming Liquids (Giulio Biroli, Kunimasa Miyazaki and
David R Reichman) The Kauzmann Transition to an Ideal Glass
Phase (Chiara Cammarota, Misaki Ozawa and Gilles Tarjus) The
Gardner Glass (Pierfrancesco Urbani, Yuliang Jin and Hajime
Yoshino) The Jamming Transition and the Marginally Stable
Solid (Francesco Arceri, Eric I Corwin and Corey S O'Hern)
From Polymers to the KPZ Equation (Victor Dotsenko, Pierre
Le Doussal and Henri Orland) Emergent Dynamics in Glasses
and Disordered Systems: Correlations and Avalanches (Annette
Zippelius, Matthias Fuchs, Alberto Rosso, James P Sethna and
Matthieu Wyart) Replica Symmetry Breaking in Random Lasers:
Experimental Measurement of the Overlap Distribution
(Claudio Conti, Neda Ghofraniha, Luca Leuzzi and Giancarlo
Ruocco) Anderson Localization on the Bethe Lattice (Saverio
Pascazio, Antonello Scardicchio and Marco Tarzia) Quantum
Glasses (Leticia F Cugliandolo and Markus Müller) The
Cavity Method: From Exact Solutions to Algorithms (Alfredo
Braunstein and Guilhem Semerjian) Message Passing and Its
Applications (Florent Krzakala, Manfred Opper and David
Saad) Information and Communication (Yoshiyuki Kabashima and
Toshiyuki Tanaka) The Mighty Force: Statistical Inference
and High-Dimensional Statistics (Erik Aurell, Jean Barbier,
Aurélien Decelle and Roberto Mulet) Disordered Systems
Insights on Computational Hardness (David Gamarnik, Cris
Moore and Lenka Zdeborová) Neural Networks: From the
Perceptron to Deep Nets (Marylou Gabrié, Surya Ganguli,
Carlo Lucibello and Riccardo Zecchina) From the Statistical
Physics of Disordered Systems to Neuroscience (Nicolas
Brunel, Rémi Monasson, Haim Sompolinsky and J Leo van
Hemmen) Statistical Physics of Biological Molecules (Simona
Cocco, Andrea De Martino, Andrea Pagnani, Martin Weigt and
Felix Ritort) Application of Spin Glass Ideas in Social
Sciences, Economics and Finance (Jean-Philippe Bouchaud,
Matteo Marsili and Jean-Pierre Nadal) Complex Dynamics in
Ecological Systems and Animal Behavior (M Cristina
Marchetti, Irene Giardina and A Altieri) Optimization of
Random High-Dimensional Functions: Structure and Algorithms
(Antonio Auffinger, Andrea Montanari and Eliran Subag)
Rigorous Results in the Sherrington–Kirkpatrick Model
(Wei-Kuo Chen, Dmitry Panchenko and Francesco Guerra) Random
Energy Models: Broken Replica Symmetry and Activated
Dynamics (Bernard Derrida, Peter Mottishaw and Véronique
Gayrard) Rigorous Results: Random Constraint Satisfaction
Problems (Amin Coja-Oghlan, Allan Sly and Nike Sun)
Metastates and Replica Symmetry Breaking (C M Newman, N Read
and D L Stein) Future Perspectives (Giorgio Parisi)
Readership: Advanced undergraduate and graduate students,
researchers and practitioners in the fields of statistical
physics and its applications, with a particular focus on
glassy and disordered systems, both classical and quantum,
and computer science, ecological, biological and financial
applications.},
Doi = {10.1142/13341},
Key = {fds373523}
}
%% Papers Published
@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},
Publisher = {AMER CHEMICAL SOC},
Year = {2001},
Month = {November},
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}
}
@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},
Number = {1-3},
Pages = {85-91},
Publisher = {Elsevier BV},
Year = {2001},
Month = {November},
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 = {Barden, CJ and Charbonneau, P and Schaefer, HF},
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},
Publisher = {American Chemical Society (ACS)},
Year = {2002},
Month = {August},
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 = {Chamon, C and Charbonneau, P and Cugliandolo, LF and Reichman, DR and Sellitto, M},
Title = {Out-of-equilibrium dynamical fluctuations in glassy
systems.},
Journal = {The Journal of chemical physics},
Volume = {121},
Number = {20},
Pages = {10120-10137},
Year = {2004},
Month = {November},
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 sigma model
approach.},
Doi = {10.1063/1.1809585},
Key = {UNKNOWN}
}
@article{UNKNOWN,
Author = {Reichman, DR and Charbonneau, P},
Title = {Mode-coupling theory},
Journal = {Journal of Statistical Mechanics: Theory and
Experiment},
Volume = {2005},
Number = {5},
Pages = {267-289},
Publisher = {IOP Publishing},
Year = {2005},
Month = {May},
url = {http://arxiv.org/abs/cond-mat/0511407},
Abstract = {In this set of lecture notes we review the mode-coupling
theory of the glass transition from several perspectives.
First, we derive mode-coupling equations for the description
of density fluctuations from microscopic considerations with
the use the Mori-Zwanzig projection operator technique. We
also derive schematic mode-coupling equations of a similar
form from a field-theoretic perspective. We review the
successes and failures of mode-coupling theory, and discuss
recent advances in the applications of the theory. © IOP
Publishing Ltd.},
Doi = {10.1088/1742-5468/2005/05/P05013},
Key = {UNKNOWN}
}
@article{UNKNOWN,
Author = {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 Pt 1},
Pages = {011507},
Year = {2007},
Month = {January},
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.},
Doi = {10.1103/physreve.75.011507},
Key = {UNKNOWN}
}
@article{UNKNOWN,
Author = {Charbonneau, P and Frenkel, D},
Title = {Gas-solid coexistence of adhesive spheres.},
Journal = {The Journal of chemical physics},
Volume = {126},
Number = {19},
Pages = {196101},
Year = {2007},
Month = {May},
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 Pt 1},
Pages = {050401},
Year = {2007},
Month = {May},
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.},
Doi = {10.1103/physreve.75.050401},
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},
Month = {September},
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.},
Doi = {10.1103/physrevlett.99.135701},
Key = {UNKNOWN}
}
@article{UNKNOWN,
Author = {Mladek, BM and Charbonneau, P and Frenkel, D},
Title = {Phase coexistence of cluster crystals: beyond the Gibbs
phase rule.},
Journal = {Physical review letters},
Volume = {99},
Number = {23},
Pages = {235702},
Year = {2007},
Month = {December},
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.},
Doi = {10.1103/physrevlett.99.235702},
Key = {UNKNOWN}
}
@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 Pt 1},
Pages = {011505},
Year = {2008},
Month = {July},
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 sigma rigidly joined at their midpoints. In an
earlier study [W. van Ketel, Phys. Rev. Lett. 94, 135703
(2005)] 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.},
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 = {494245-494245},
Publisher = {IOP Publishing},
Year = {2008},
Month = {December},
ISSN = {0953-8984},
url = {http://dx.doi.org/10.1088/0953-8984/20/49/494245},
Abstract = {Recently, particular interest has been placed in the study
of a strikingly counter-intuitive phenomenon: the clustering
of purely repulsive soft particles. This contribution serves
the purpose of both reviewing our current understanding of
the multiple occupancy crystals and presenting details of
recently developed tailor-cut approaches to the problem. We
first indicate, by use of analytically tractable examples,
how such a phenomenon can arise at all. We then show that
the thermodynamic formalism has to be adapted when studying
such systems and present a novel computer simulation
technique apt to do so. Finally, we discuss the intriguing
mechanical and structural responses of such systems upon
increasing the density. © 2008 IOP Publishing
Ltd.},
Doi = {10.1088/0953-8984/20/49/494245},
Key = {fds232096}
}
@article{fds232090,
Author = {van Meel, JA and Frenkel, D and Charbonneau, P},
Title = {Geometrical frustration: a study of four-dimensional hard
spheres.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {79},
Number = {3 Pt 1},
Pages = {030201},
Year = {2009},
Month = {March},
ISSN = {1539-3755},
url = {http://arxiv.org/abs/0809.1775},
Abstract = {The smallest maximum-kissing-number Voronoi polyhedron of
three-dimensional (3D) Euclidean spheres is the icosahedron,
and the tetrahedron is the smallest volume that can show up
in Delaunay tessellation. No periodic lattice is consistent
with either, and hence these dense packings are
geometrically frustrated. Because icosahedra can be
assembled from almost perfect tetrahedra, the terms
"icosahedral" and "polytetrahedral" packing are often used
interchangeably, which leaves the true origin of geometric
frustration unclear. Here we report a computational study of
freezing of 4D Euclidean hard spheres, where the densest
Voronoi cluster is compatible with the symmetry of the
densest crystal, while polytetrahedral order is not. We
observe that, under otherwise comparable conditions, crystal
nucleation in four dimensions is less facile than in three
dimensions, which is consistent with earlier observations
[M. Skoge, Phys. Rev. E 74, 041127 (2006)]. We conclude that
it is the geometrical frustration of polytetrahedral
structures that inhibits crystallization.},
Doi = {10.1103/physreve.79.030201},
Key = {fds232090}
}
@article{fds339883,
Author = {Ikeda, A and Charbonneau, P and van, MJA and Miyazaki,
K},
Title = {28aQL-4 Simulation and theoretical study of glass transition
of 4d hard sphere},
Journal = {Meeting abstracts of the Physical Society of
Japan},
Volume = {64},
Number = {2},
Pages = {293 pages},
Publisher = {The Physical Society of Japan (JPS)},
Year = {2009},
Month = {August},
Key = {fds339883}
}
@article{fds232088,
Author = {van Meel, JA and Charbonneau, B and Fortini, A and Charbonneau,
P},
Title = {Hard-sphere crystallization gets rarer with increasing
dimension.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {80},
Number = {6 Pt 1},
Pages = {061110},
Year = {2009},
Month = {December},
ISSN = {1539-3755},
url = {http://hdl.handle.net/10161/4283 Duke open
access},
Abstract = {We recently found that crystallization of monodisperse hard
spheres from the bulk fluid faces a much higher free-energy
barrier in four than in three dimensions at equivalent
supersaturation, due to the increased geometrical
frustration between the simplex-based fluid order and the
crystal [J. A. van Meel, D. Frenkel, and P. Charbonneau,
Phys. Rev. E 79, 030201(R) (2009)]. Here, we analyze the
microscopic contributions to the fluid-crystal interfacial
free energy to understand how the barrier to crystallization
changes with dimension. We find the barrier to grow with
dimension and we identify the role of polydispersity in
preventing crystal formation. The increased fluid stability
allows us to study the jamming behavior in four, five, and
six dimensions and to compare our observations with two
recent theories [C. Song, P. Wang, and H. A. Makse, Nature
(London) 453, 629 (2008); G. Parisi and F. Zamponi, Rev.
Mod. Phys. (to be published)].},
Doi = {10.1103/physreve.80.061110},
Key = {fds232088}
}
@article{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{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{fds232085,
Author = {Jin, Y and Charbonneau, P and Meyer, S and Song, C and Zamponi,
F},
Title = {Application of Edwards' statistical mechanics to
high-dimensional jammed sphere packings.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {82},
Number = {5 Pt 1},
Pages = {051126},
Year = {2010},
Month = {November},
ISSN = {1539-3755},
url = {http://hdl.handle.net/10161/4290 Duke open
access},
Abstract = {The isostatic jamming limit of frictionless spherical
particles from Edwards' statistical mechanics [Song et al.,
Nature (London) 453, 629 (2008)] is generalized to arbitrary
dimension d using a liquid-state description. The asymptotic
high-dimensional behavior of the self-consistent relation is
obtained by saddle-point evaluation and checked numerically.
The resulting random close packing density scaling
ϕ∼d2(-d) is consistent with that of other approaches,
such as replica theory and density-functional theory. The
validity of various structural approximations is assessed by
comparing with three- to six-dimensional isostatic packings
obtained from simulations. These numerical results support a
growing accuracy of the theoretical approach with dimension.
The approach could thus serve as a starting point to obtain
a geometrical understanding of the higher-order correlations
present in jammed packings.},
Doi = {10.1103/physreve.82.051126},
Key = {fds232085}
}
@article{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{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},
Publisher = {American Physical Society (APS)},
Year = {2011},
Month = {June},
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{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{fds232095,
Author = {Bergin, SM and Rathmell, AR and Chen, YH and Charbonneau, P and Li, ZY 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},
Year = {2012},
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{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},
Month = {January},
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.},
Doi = {10.1103/physrevlett.108.035701},
Key = {fds232082}
}
@article{fds232094,
Author = {Zhang, K and Charbonneau, P},
Title = {[N]pT Monte Carlo simulations of the cluster-crystal-forming
penetrable sphere model.},
Journal = {The Journal of chemical physics},
Volume = {136},
Number = {21},
Pages = {214106},
Year = {2012},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22697529},
Abstract = {Certain models with purely repulsive pair interactions can
form cluster crystals with multiply-occupied lattice sites.
Simulating these models' equilibrium properties is, however,
quite challenging. Here, we develop an expanded
isothermal-isobaric [N]pT ensemble that surmounts this
problem by allowing both particle number and lattice spacing
to fluctuate. It is particularly efficient at high T, where
particle insertion is facile. Using this expanded ensemble
and thermodynamic integration, we solve the phase diagram of
a prototypical cluster-crystal former, the penetrable sphere
model, and compare the results with earlier theoretical
predictions. At high temperatures and densities, the
equilibrium occupancy n(c)(eq) of face-centered cubic
crystal increases linearly. At low temperatures, although
n(c)(eq) plateaus at integer values, the crystal behavior
changes continuously with density. The previously ambiguous
crossover around T ~ 0.1 is resolved.},
Doi = {10.1063/1.4723869},
Key = {fds232094}
}
@article{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 the
United States of America},
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{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 Pt 1},
Pages = {042501},
Year = {2012},
Month = {October},
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 [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 = {fds232080}
}
@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{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},
Publisher = {American Physical Society (APS)},
Year = {2012},
Month = {December},
ISSN = {1539-3755},
url = {http://dx.doi.org/10.1103/PhysRevE.86.069902},
Doi = {10.1103/PhysRevE.86.069902},
Key = {fds232077}
}
@article{fds232072,
Author = {Fusco, D and Charbonneau, P},
Title = {Crystallization of asymmetric patchy models for globular
proteins in solution},
Journal = {PHYSICAL REVIEW E},
Volume = {88},
Number = {1},
Pages = {012721},
Year = {2013},
ISSN = {1539-3755},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000322082800005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Asymmetric patchy particle models have recently been shown
to describe the crystallization of small globular proteins
with near-quantitative accuracy. Here, we investigate how
asymmetry in patch geometry and bond energy generally
impacts the phase diagram and nucleation dynamics of this
family of soft matter models. We find the role of the
geometry asymmetry to be weak, but the energy asymmetry to
markedly interfere with the crystallization thermodynamics
and kinetics. These results provide a rationale for the
success and occasional failure of the proposal of George and
Wilson for protein crystallization conditions as well as
physical guidance for developing more effective protein
crystallization strategies.},
Doi = {10.1103/PhysRevE.88.012721},
Key = {fds232072}
}
@article{fds232076,
Author = {Charbonneau, P and Tarjus, G},
Title = {Decorrelation of the static and dynamic length scales in
hard-sphere glass formers},
Journal = {PHYSICAL REVIEW E},
Volume = {87},
Number = {4},
Pages = {042305},
Year = {2013},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23679412},
Abstract = {We show that, in the equilibrium phase of glass-forming
hard-sphere fluids in three dimensions, the static length
scales tentatively associated with the dynamical slowdown
and the dynamical length characterizing spatial
heterogeneities in the dynamics unambiguously decorrelate.
The former grow at a much slower rate than the latter when
density increases. This observation is valid for the
dynamical range that is accessible to computer simulations,
which roughly corresponds to that accessible in colloidal
experiments. We also find that, in this same range, no
one-to-one correspondence between relaxation time and
point-to-set correlation length exists. These results point
to the coexistence of several relaxation mechanisms in the
dynamically accessible regime of three-dimensional
hard-sphere glass formers.},
Doi = {10.1103/PhysRevE.87.042305},
Key = {fds232076}
}
@article{fds232075,
Author = {Charbonneau, B and Charbonneau, P and Tarjus, G},
Title = {Geometrical frustration and static correlations in
hard-sphere glass formers.},
Journal = {The Journal of chemical physics},
Volume = {138},
Number = {12},
Pages = {12A515},
Year = {2013},
Month = {March},
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.},
Doi = {10.1063/1.4770498},
Key = {fds232075}
}
@article{fds232071,
Author = {Charbonneau, B and Charbonneau, P and Jin, Y and Parisi, G and Zamponi,
F},
Title = {Dimensional dependence of the Stokes-Einstein relation and
its violation.},
Journal = {The Journal of chemical physics},
Volume = {139},
Number = {16},
Pages = {164502},
Year = {2013},
Month = {October},
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.},
Doi = {10.1063/1.4825177},
Key = {fds232071}
}
@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{fds232070,
Author = {Fusco, D and Headd, JJ and De Simone and A and Wang, J and Charbonneau,
P},
Title = {Characterizing protein crystal contacts and their role in
crystallization: rubredoxin as a case study.},
Journal = {Soft matter},
Volume = {10},
Number = {2},
Pages = {290-302},
Year = {2014},
Month = {January},
ISSN = {1744-683X},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000327849300006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {The fields of structural biology and soft matter have
independently sought out fundamental principles to
rationalize protein crystallization. Yet the conceptual
differences and the limited overlap between the two
disciplines have thus far prevented a comprehensive
understanding of the phenomenon to emerge. We conduct a
computational study of proteins from the rubredoxin family
that bridges the two fields. Using atomistic simulations, we
characterize the protein crystal contacts, and accordingly
parameterize patchy particle models. Comparing the phase
diagrams of these schematic models with experimental results
enables us to critically examine the assumptions behind the
two approaches. The study also reveals features of
protein–protein interactions that can be leveraged to
crystallize proteins more generally.},
Doi = {10.1039/c3sm52175c},
Key = {fds232070}
}
@article{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 = {April},
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{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. B},
Volume = {118},
Number = {28},
Pages = {8034-8041},
Year = {2014},
Month = {July},
ISSN = {1520-6106},
url = {http://pubs.acs.org/doi/abs/10.1021/jp5011428},
Abstract = {Advances in experimental techniques and in theoretical
models have improved our understanding of protein
crystallization. However, they have also left open questions
regarding the protein phase behavior and self-assembly
kinetics, such as why (nearly) identical crystallization
conditions can sometimes result in the formation of
different crystal forms. Here, we develop a patchy particle
model with competing sets of patches that provides a
microscopic explanation of this phenomenon. We identify
different regimes in which one or two crystal forms can
coexist with a low-density fluid. Using analytical
approximations, we extend our findings to different crystal
phases, providing a general framework for treating protein
crystallization when multiple crystal forms compete. Our
results also suggest different experimental routes for
targeting a specific crystal form, and for reducing the
dynamical competition between the two forms, thus
facilitating protein crystal assembly.},
Doi = {10.1021/jp5011428},
Key = {fds232069}
}
@article{fds232063,
Author = {Charbonneau, P and Kurchan, J and Parisi, G and Urbani, P and Zamponi,
F},
Title = {Exact theory of dense amorphous hard spheres in high
dimension. III. the full replica symmetry breaking
solution},
Journal = {Journal of Statistical Mechanics: Theory and
Experiment},
Volume = {2014},
Number = {10},
Pages = {P10009-P10009},
Publisher = {IOP Publishing},
Year = {2014},
Month = {October},
url = {http://arxiv.org/abs/1310.2549},
Abstract = {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 similar to the ones that have
been derived for spin glass models, thus showing that the
analogy between spin glasses and structural glasses
conjectured by Kirkpatrick, Thirumalai and Wolynes is
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. In the
second part of the paper, we discuss the solution of these
equations and we derive from it a number of physical
predictions. 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 that jammed packings are isostatic, and allows one
to compute analytically the critical exponents associated
with the jamming transition, which are missed by the 1RSB
solution. We show that these predictions compare very well
with numerical results.},
Doi = {10.1088/1742-5468/2014/10/P10009},
Key = {fds232063}
}
@article{fds232064,
Author = {Charbonneau, P and Jin, Y and Parisi, G and Zamponi,
F},
Title = {Hopping and the Stokes-Einstein relation breakdown in simple
glass formers.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {111},
Number = {42},
Pages = {15025-15030},
Year = {2014},
Month = {October},
ISSN = {0027-8424},
url = {http://arxiv.org/abs/1407.5677},
Abstract = {One of the most actively debated issues in the study of the
glass transition is whether a mean-field description is a
reasonable starting point for understanding experimental
glass formers. Although the mean-field theory of the glass
transition--like that of other statistical systems--is exact
when the spatial dimension d → ∞, the evolution of
systems properties with d may not be smooth.
Finite-dimensional effects could dramatically change what
happens in physical dimensions,d = 2, 3. For standard phase
transitions finite-dimensional effects are typically
captured by renormalization group methods, but for glasses
the corrections are much more subtle and only partially
understood. Here, we investigate hopping between localized
cages formed by neighboring particles in a model that allows
to cleanly isolate that effect. By bringing together results
from replica theory, cavity reconstruction, void
percolation, and molecular dynamics, we obtain insights into
how hopping induces a breakdown of the Stokes-Einstein
relation and modifies the mean-field scenario in
experimental systems. Although hopping is found to supersede
the dynamical glass transition, it nonetheless leaves a
sizable part of the critical regime untouched. By providing
a constructive framework for identifying and quantifying the
role of hopping, we thus take an important step toward
describing dynamic facilitation in the framework of the
mean-field theory of glasses.},
Doi = {10.1073/pnas.1417182111},
Key = {fds232064}
}
@article{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{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{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{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{fds232057,
Author = {Tavarone, R and Charbonneau, P and Stark, H},
Title = {Phase ordering of zig-zag and bow-shaped hard needles in two
dimensions.},
Journal = {The Journal of chemical physics},
Volume = {143},
Number = {11},
Pages = {114505},
Year = {2015},
Month = {September},
ISSN = {0021-9606},
url = {http://dx.doi.org/10.1063/1.4930886},
Abstract = {We perform extensive Monte Carlo simulations of a
two-dimensional bent hard-needle model in both its chiral
zig-zag and its achiral bow-shape configurations and present
their phase diagrams. We find evidence for a variety of
stable phases: isotropic, quasi-nematic, smectic-C,
anti-ferromorphic smectic-A, and modulated-nematic. This
last phase consists of layers formed by supramolecular
arches. They create a modulation of the molecular polarity
whose period is sensitively controlled by molecular
geometry. We identify transition densities using correlation
functions together with appropriately defined order
parameters and compare them with predictions from Onsager
theory. The contribution of the molecular excluded area to
deviations from Onsager theory and simple liquid crystal
phase morphology is discussed. We demonstrate the
isotropic-quasi-nematic transition to be consistent with a
Kosterlitz-Thouless disclination unbinding
scenario.},
Doi = {10.1063/1.4930886},
Key = {fds232057}
}
@article{fds232059,
Author = {Fusco, D and Charbonneau, P},
Title = {Soft matter perspective on protein crystal
assembly.},
Journal = {Colloids and surfaces. B, Biointerfaces},
Volume = {137},
Pages = {22-31},
Year = {2016},
Month = {January},
ISSN = {0927-7765},
url = {http://dx.doi.org/10.1016/j.colsurfb.2015.07.023},
Abstract = {Crystallography may be the gold standard of protein
structure determination, but obtaining the necessary
high-quality crystals is also in some ways akin to
prospecting for the precious metal. The tools and models
developed in soft matter physics to understand colloidal
assembly offer some insights into the problem of
crystallizing proteins. This topical review describes the
various analogies that have been made between proteins and
colloids in that context. We highlight the explanatory power
of patchy particle models, but also the challenges of
providing guidance for crystallizing specific proteins. We
conclude with a presentation of possible future research
directions. This review is intended for soft matter
scientists interested in protein crystallization as a
self-assembly problem, and as an introduction to the
pertinent physics literature for protein scientists more
generally.},
Doi = {10.1016/j.colsurfb.2015.07.023},
Key = {fds232059}
}
@article{fds311998,
Author = {Berthier, L and Charbonneau, P and Yaida, S},
Title = {Efficient measurement of point-to-set correlations and
overlap fluctuations in glass-forming liquids.},
Journal = {The Journal of chemical physics},
Volume = {144},
Number = {2},
Pages = {024501},
Year = {2016},
Month = {January},
ISSN = {0021-9606},
url = {http://dx.doi.org/10.1063/1.4939640},
Abstract = {Cavity point-to-set correlations are real-space tools to
detect the roughening of the free-energy landscape that
accompanies the dynamical slowdown of glass-forming liquids.
Measuring these correlations in model glass formers remains,
however, a major computational challenge. Here, we develop a
general parallel-tempering method that provides
orders-of-magnitude improvement for sampling and
equilibrating configurations within cavities. We apply this
improved scheme to the canonical Kob-Andersen binary
Lennard-Jones model for temperatures down to the
mode-coupling theory crossover. Most significant
improvements are noted for small cavities, which have thus
far been the most difficult to study. This methodological
advance also enables us to study a broader range of physical
observables associated with thermodynamic fluctuations. We
measure the probability distribution of overlap fluctuations
in cavities, which displays a non-trivial temperature
evolution. The corresponding overlap susceptibility is found
to provide a robust quantitative estimate of the
point-to-set length scale requiring no fitting. By resolving
spatial fluctuations of the overlap in the cavity, we also
obtain quantitative information about the geometry of
overlap fluctuations. We can thus examine in detail how the
penetration length as well as its fluctuations evolve with
temperature and cavity size.},
Doi = {10.1063/1.4939640},
Key = {fds311998}
}
@article{fds311999,
Author = {Owens, CE and Shields, CW and Cruz, DF and Charbonneau, P and López,
GP},
Title = {Highly parallel acoustic assembly of microparticles into
well-ordered colloidal crystallites.},
Journal = {Soft matter},
Volume = {12},
Number = {3},
Pages = {717-728},
Year = {2016},
Month = {January},
ISSN = {1744-683X},
url = {http://dx.doi.org/10.1039/c5sm02348c},
Abstract = {The precise arrangement of microscopic objects is critical
to the development of functional materials and ornately
patterned surfaces. Here, we present an acoustics-based
method for the rapid arrangement of microscopic particles
into organized and programmable architectures, which are
periodically spaced within a square assembly chamber. This
macroscale device employs two-dimensional bulk acoustic
standing waves to propel particles along the base of the
chamber toward pressure nodes or antinodes, depending on the
acoustic contrast factor of the particle, and is capable of
simultaneously creating thousands of size-limited, isotropic
and anisotropic assemblies within minutes. We pair
experiments with Brownian dynamics simulations to model the
migration kinetics and assembly patterns of spherical
microparticles. We use these insights to predict and
subsequently validate the onset of buckling of the
assemblies into three-dimensional clusters by experiments
upon increasing the acoustic pressure amplitude and the
particle concentration. The simulations are also used to
inform our experiments for the assembly of non-spherical
particles, which are then recovered via fluid evaporation
and directly inspected by electron microscopy. This method
for assembly of particles offers several notable advantages
over other approaches (e.g., magnetics, electrokinetics and
optical tweezing) including simplicity, speed and
scalability and can also be used in concert with other such
approaches for enhancing the types of assemblies
achievable.},
Doi = {10.1039/c5sm02348c},
Key = {fds311999}
}
@article{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
(Physical Review E - Statistical, Nonlinear, and Soft Matter
Physics (2014) 90 (012136))},
Journal = {Physical Review E},
Volume = {93},
Number = {2},
Publisher = {American Physical Society (APS)},
Year = {2016},
Month = {February},
url = {http://dx.doi.org/10.1103/PhysRevE.93.029902},
Doi = {10.1103/PhysRevE.93.029902},
Key = {fds318069}
}
@article{fds311996,
Author = {Fu, L and Steinhardt, W and Zhao, H and Socolar, JES and Charbonneau,
P},
Title = {Hard sphere packings within cylinders.},
Journal = {Soft matter},
Volume = {12},
Number = {9},
Pages = {2505-2514},
Year = {2016},
Month = {March},
ISSN = {1744-683X},
url = {http://dx.doi.org/10.1039/c5sm02875b},
Abstract = {Arrangements of identical hard spheres confined to a
cylinder with hard walls have been used to model
experimental systems, such as fullerenes in nanotubes and
colloidal wire assembly. Finding the densest configurations,
called close packings, of hard spheres of diameter σ in a
cylinder of diameter D is a purely geometric problem that
grows increasingly complex as D/σ increases, and little is
thus known about the regime for D > 2.873σ. In this work,
we extend the identification of close packings up to D =
4.00σ by adapting Torquato-Jiao's adaptive-shrinking-cell
formulation and sequential-linear-programming (SLP)
technique. We identify 17 new structures, almost all of them
chiral. Beyond D ≈ 2.85σ, most of the structures consist
of an outer shell and an inner core that compete for being
close packed. In some cases, the shell adopts its own
maximum density configuration, and the stacking of core
spheres within it is quasiperiodic. In other cases, an
interplay between the two components is observed, which may
result in simple periodic structures. In yet other cases,
the very distinction between the core and shell vanishes,
resulting in more exotic packing geometries, including some
that are three-dimensional extensions of structures obtained
from packing hard disks in a circle.},
Doi = {10.1039/c5sm02875b},
Key = {fds311996}
}
@article{fds318067,
Author = {Tavarone, R and Charbonneau, P and Stark, H},
Title = {Kinetic Monte Carlo simulations for birefringence relaxation
of photo-switchable molecules on a surface.},
Journal = {The Journal of chemical physics},
Volume = {144},
Number = {10},
Pages = {104703},
Year = {2016},
Month = {March},
url = {http://dx.doi.org/10.1063/1.4943393},
Abstract = {Recent experiments have demonstrated that in a dense
monolayer of photo-switchable dye methyl-red molecules the
relaxation of an initial birefringence follows a power-law
decay, typical for glass-like dynamics. The slow relaxation
can efficiently be controlled and accelerated by
illuminating the monolayer with circularly polarized light,
which induces trans-cis isomerization cycles. To elucidate
the microscopic mechanism, we develop a two-dimensional
molecular model in which the trans and cis isomers are
represented by straight and bent needles, respectively. As
in the experimental system, the needles are allowed to
rotate and to form overlaps but they cannot translate. The
out-of-equilibrium rotational dynamics of the needles is
generated using kinetic Monte Carlo simulations. We
demonstrate that, in a regime of high density and low
temperature, the power-law relaxation can be traced to the
formation of spatio-temporal correlations in the rotational
dynamics, i.e., dynamic heterogeneity. We also show that the
nearly isotropic cis isomers can prevent dynamic
heterogeneity from forming in the monolayer and that the
relaxation then becomes exponential.},
Doi = {10.1063/1.4943393},
Key = {fds318067}
}
@article{fds318068,
Author = {Zhuang, Y and Zhang, K and Charbonneau, P},
Title = {Equilibrium Phase Behavior of a Continuous-Space Microphase
Former.},
Journal = {Physical review letters},
Volume = {116},
Number = {9},
Pages = {098301},
Year = {2016},
Month = {March},
url = {http://dx.doi.org/10.1103/physrevlett.116.098301},
Abstract = {Periodic microphases universally emerge in systems for which
short-range interparticle attraction is frustrated by
long-range repulsion. The morphological richness of these
phases makes them desirable material targets, but our
relatively coarse understanding of even simple models
hinders controlling their assembly. We report here the
solution of the equilibrium phase behavior of a microscopic
microphase former through specialized Monte Carlo
simulations. The results for cluster crystal, cylindrical,
double gyroid, and lamellar ordering qualitatively agree
with a Landau-type free energy description and reveal the
nontrivial interplay between cluster, gel, and microphase
formation.},
Doi = {10.1103/physrevlett.116.098301},
Key = {fds318068}
}
@article{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 and Interface
Science},
Volume = {22},
Pages = {73-79},
Publisher = {Elsevier BV},
Year = {2016},
Month = {April},
url = {http://dx.doi.org/10.1016/j.cocis.2016.02.011},
Abstract = {Understanding protein self-assembly is important for many
biological and industrial processes. Proteins can
self-assemble into crystals, filaments, gels, and other
amorphous aggregates. The final forms include virus capsids
and condensed phases associated with diseases such as
amyloid fibrils. Although seemingly different, these
assemblies all originate from fundamental protein
interactions and are driven by similar thermodynamic and
kinetic factors. Here we review recent advances in
understanding protein self-assembly through a soft condensed
matter perspective with an emphasis on three specific
systems: globular proteins, viruses, and amyloid fibrils. We
conclude with a discussion of unanswered questions in the
field.},
Doi = {10.1016/j.cocis.2016.02.011},
Key = {fds318066}
}
@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{fds318062,
Author = {Charbonneau, P and Corwin, EI and Parisi, G and Poncet, A and Zamponi,
F},
Title = {Universal Non-Debye Scaling in the Density of States of
Amorphous Solids.},
Journal = {Physical review letters},
Volume = {117},
Number = {4},
Pages = {045503},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1103/physrevlett.117.045503},
Abstract = {At the jamming transition, amorphous packings are known to
display anomalous vibrational modes with a density of states
(DOS) that remains constant at low frequency. The scaling of
the DOS at higher packing fractions remains, however,
unclear. One might expect to find a simple Debye scaling,
but recent results from effective medium theory and the
exact solution of mean-field models both predict an
anomalous, non-Debye scaling. Being mean-field in nature,
however, these solutions are only strictly valid in the
limit of infinite spatial dimension, and it is unclear what
value they have for finite-dimensional systems. Here, we
study packings of soft spheres in dimensions 3 through 7 and
find, away from jamming, a universal non-Debye scaling of
the DOS that is consistent with the mean-field predictions.
We also consider how the soft mode participation ratio
evolves as dimension increases.},
Doi = {10.1103/physrevlett.117.045503},
Key = {fds318062}
}
@article{fds318063,
Author = {Berthier, L and Charbonneau, P and Jin, Y and Parisi, G and Seoane, B and Zamponi, F},
Title = {Growing timescales and lengthscales characterizing
vibrations of amorphous solids.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {113},
Number = {30},
Pages = {8397-8401},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1073/pnas.1607730113},
Abstract = {Low-temperature properties of crystalline solids can be
understood using harmonic perturbations around a perfect
lattice, as in Debye's theory. Low-temperature properties of
amorphous solids, however, strongly depart from such
descriptions, displaying enhanced transport, activated slow
dynamics across energy barriers, excess vibrational modes
with respect to Debye's theory (i.e., a boson peak), and
complex irreversible responses to small mechanical
deformations. These experimental observations indirectly
suggest that the dynamics of amorphous solids becomes
anomalous at low temperatures. Here, we present direct
numerical evidence that vibrations change nature at a
well-defined location deep inside the glass phase of a
simple glass former. We provide a real-space description of
this transition and of the rapidly growing time- and
lengthscales that accompany it. Our results provide the seed
for a universal understanding of low-temperature glass
anomalies within the theoretical framework of the recently
discovered Gardner phase transition.},
Doi = {10.1073/pnas.1607730113},
Key = {fds318063}
}
@article{fds318064,
Author = {Charbonneau, P and Dyer, E and Lee, J and Yaida, S},
Title = {Linking dynamical heterogeneity to static amorphous
order},
Journal = {Journal of Statistical Mechanics: Theory and
Experiment},
Volume = {2016},
Number = {7},
Pages = {074004-074004},
Publisher = {IOP Publishing},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1088/1742-5468/2016/07/074004},
Abstract = {Glass-forming liquids grow dramatically sluggish upon
cooling. This slowdown has long been thought to be
accompanied by a growing correlation length. Characteristic
dynamical and static length scales, however, have been
observed to grow at different rates, which perplexes the
relationship between the two and with the slowdown. Here, we
show the existence of a direct link between dynamical
sluggishness and static point-to-set correlations, holding
at the local level as we probe different environments within
a liquid. This link, which is stronger and more general than
that observed with locally preferred structures, suggests
the existence of an intimate relationship between structure
and dynamics in a broader range of glass-forming liquids
than previously thought.},
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. B},
Volume = {120},
Number = {26},
Pages = {6178-6188},
Year = {2016},
Month = {July},
url = {http://dx.doi.org/10.1021/acs.jpcb.6b02167},
Abstract = {We have recently developed a simulation approach to
calculate the equilibrium phase diagram of particle-based
microphase formers. Here, this approach is used to calculate
the phase behavior of the square-well linear model for
different strengths and ranges of the linear long-range
repulsive component. The results are compared with various
theoretical predictions for microphase formation. The
analysis further allows us to better understand the
mechanism for microphase formation in colloidal
suspensions.},
Doi = {10.1021/acs.jpcb.6b02167},
Key = {fds318065}
}
@article{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. B},
Volume = {120},
Number = {32},
Pages = {7775-7782},
Year = {2016},
Month = {August},
url = {http://dx.doi.org/10.1021/acs.jpcb.6b05471},
Abstract = {This mini-review synthesizes our understanding of the
equilibrium behavior of particle-based models with
short-range attractive and long-range repulsive (SALR)
interactions. These models, which can form stable periodic
microphases, aim to reproduce the essence of colloidal
suspensions with competing interparticle interactions.
Ordered structures, however, have yet to be obtained in
experiments. In order to better understand the hurdles to
periodic microphase assembly, marked theoretical and
simulation advances have been made over the past few years.
Here, we present recent progress in the study of microphases
in models with SALR interactions using liquid-state theory
and density-functional theory as well as numerical
simulations. Combining these various approaches provides a
description of periodic microphases, and gives insights into
the rich phenomenology of the surrounding disordered regime.
Ongoing research directions in the thermodynamics of models
with SALR interactions are also presented.},
Doi = {10.1021/acs.jpcb.6b05471},
Key = {fds318061}
}
@article{fds318060,
Author = {Yaida, S and Berthier, L and Charbonneau, P and Tarjus,
G},
Title = {Point-to-set lengths, local structure, and
glassiness.},
Journal = {Physical review. E},
Volume = {94},
Number = {3-1},
Pages = {032605},
Year = {2016},
Month = {September},
url = {http://dx.doi.org/10.1103/physreve.94.032605},
Abstract = {The growing sluggishness of glass-forming liquids is thought
to be accompanied by growing structural order. The nature of
such order, however, remains hotly debated. A decade ago,
point-to-set (PTS) correlation lengths were proposed as
measures of amorphous order in glass formers, but recent
results raise doubts as to their generality. Here, we extend
the definition of PTS correlations to agnostically capture
any type of growing order in liquids, be it local or
amorphous. This advance enables the formulation of a clear
distinction between slowing down due to conventional
critical ordering and that due to glassiness, and provides a
unified framework to assess the relative importance of
specific local order and generic amorphous order in glass
formation.},
Doi = {10.1103/physreve.94.032605},
Key = {fds318060}
}
@article{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},
Publisher = {ANNUAL REVIEWS},
Year = {2017},
Month = {March},
url = {http://dx.doi.org/10.1146/annurev-conmatphys-031016-025334},
Abstract = {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 model in the
mean-field limit of infinite spatial dimension. Numerical
simulations have remarkably confirmed the dimensional
robustness of some of the predictions. This review describes
these latest advances. More specifically, we consider the
dynamical and thermodynamic descriptions of hard spheres
around the dynamical, Gardner, and jamming transitions.
Comparing mean-field predictions with the finite-dimensional
simulations, we identify robust aspects of the theory and
uncover its more sensitive features. We conclude with a
brief overview of ongoing research.},
Doi = {10.1146/annurev-conmatphys-031016-025334},
Key = {fds325416}
}
@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{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{fds361583,
Author = {Charbonneau, P},
Title = {Lecture Notes on the Statistical Mechanics of Disordered
Systems},
Year = {2017},
Month = {May},
Abstract = {This material complements David Chandler's Introduction to
Modern Statistical Mechanics (Oxford University Press, 1987)
in a graduate-level, one-semester course I teach in the
Department of Chemistry at Duke University. Students enter
this course with some knowledge of statistical
thermodynamics and quantum mechanics, usually acquired from
undergraduate physical chemistry at the level of D. A.
McQuarrie & J. D. Simon's Physical Chemistry: A Molecular
Approach (University Science Books, 1997). These notes,
which introduce students to a modern treatment of glassiness
and to the replica method, build on the material and
problems contained in the eight chapters of Chandler's
textbook.},
Key = {fds361583}
}
@article{fds328992,
Author = {Charbonneau, P and Li, YC and Pfister, HD and Yaida,
S},
Title = {Cycle-expansion method for the Lyapunov exponent,
susceptibility, and higher moments.},
Journal = {Physical review. E},
Volume = {96},
Number = {3-1},
Pages = {032129},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1103/physreve.96.032129},
Abstract = {Lyapunov exponents characterize the chaotic nature of
dynamical systems by quantifying the growth rate of
uncertainty associated with the imperfect measurement of
initial conditions. Finite-time estimates of the exponent,
however, experience fluctuations due to both the initial
condition and the stochastic nature of the dynamical path.
The scale of these fluctuations is governed by the Lyapunov
susceptibility, the finiteness of which typically provides a
sufficient condition for the law of large numbers to apply.
Here, we obtain a formally exact expression for this
susceptibility in terms of the Ruelle dynamical ζ function
for one-dimensional systems. We further show that, for
systems governed by sequences of random matrices, the cycle
expansion of the ζ function enables systematic computations
of the Lyapunov susceptibility and of its higher-moment
generalizations. The method is here applied to a class of
dynamical models that maps to static disordered spin chains
with interactions stretching over a varying distance and is
tested against Monte Carlo simulations.},
Doi = {10.1103/physreve.96.032129},
Key = {fds328992}
}
@article{fds328993,
Author = {Zhuang, Y and Charbonneau, P},
Title = {Communication: Microphase equilibrium and assembly
dynamics.},
Journal = {The Journal of chemical physics},
Volume = {147},
Number = {9},
Pages = {091102},
Year = {2017},
Month = {September},
url = {http://dx.doi.org/10.1063/1.4996904},
Abstract = {Despite many attempts, ordered equilibrium microphases have
yet to be obtained in experimental colloidal suspensions.
The recent computation of the equilibrium phase diagram of a
microscopic, particle-based microphase former [Zhuang et
al., Phys. Rev. Lett. 116, 098301 (2016)] has nonetheless
found such mesoscale assemblies to be thermodynamically
stable. Here, we consider their equilibrium and assembly
dynamics. At intermediate densities above the order-disorder
transition, we identify four different dynamical regimes and
the structural changes that underlie the dynamical
crossovers from one disordered regime to the next. Below the
order-disorder transition, we also find that periodic
lamellae are the most dynamically accessible of the periodic
microphases. Our analysis thus offers a comprehensive view
of the dynamics of disordered microphases and a route to the
assembly of periodic microphases in a putative
well-controlled, experimental system.},
Doi = {10.1063/1.4996904},
Key = {fds328993}
}
@article{fds329889,
Author = {Berthier, L and Charbonneau, P and Coslovich, D and Ninarello, A and Ozawa, M and Yaida, S},
Title = {Configurational entropy measurements in extremely
supercooled liquids that break the glass
ceiling.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {114},
Number = {43},
Pages = {11356-11361},
Year = {2017},
Month = {October},
url = {http://dx.doi.org/10.1073/pnas.1706860114},
Abstract = {Liquids relax extremely slowly on approaching the glass
state. One explanation is that an entropy crisis, because of
the rarefaction of available states, makes it increasingly
arduous to reach equilibrium in that regime. Validating this
scenario is challenging, because experiments offer limited
resolution, while numerical studies lag more than eight
orders of magnitude behind experimentally relevant
timescales. In this work, we not only close the colossal gap
between experiments and simulations but manage to create in
silico configurations that have no experimental analog yet.
Deploying a range of computational tools, we obtain four
estimates of their configurational entropy. These
measurements consistently confirm that the steep entropy
decrease observed in experiments is also found in
simulations, even beyond the experimental glass transition.
Our numerical results thus extend the observational window
into the physics of glasses and reinforce the relevance of
an entropy crisis for understanding their
formation.},
Doi = {10.1073/pnas.1706860114},
Key = {fds329889}
}
@article{fds331333,
Author = {Berthier, L and Charbonneau, P and Flenner, E and Zamponi,
F},
Title = {Origin of Ultrastability in Vapor-Deposited
Glasses.},
Journal = {Physical review letters},
Volume = {119},
Number = {18},
Pages = {188002},
Year = {2017},
Month = {November},
url = {http://dx.doi.org/10.1103/physrevlett.119.188002},
Abstract = {Glass films created by vapor-depositing molecules onto a
substrate can exhibit properties similar to those of
ordinary glasses aged for thousands of years. It is believed
that enhanced surface mobility is the mechanism that allows
vapor deposition to create such exceptional glasses, but it
is unclear how this effect is related to the final state of
the film. Here we use molecular dynamics simulations to
model vapor deposition and an efficient Monte Carlo
algorithm to determine the deposition rate needed to create
ultrastable glassy films. We obtain a scaling relation that
quantitatively captures the efficiency gain of vapor
deposition over bulk annealing, and demonstrates that
surface relaxation plays the same role in the formation of
vapor-deposited glasses as bulk relaxation does in ordinary
glass formation.},
Doi = {10.1103/physrevlett.119.188002},
Key = {fds331333}
}
@article{fds337004,
Author = {Bruno, AE and Charbonneau, P and Newman, J and Snell, EH and So, DR and Vanhoucke, V and Watkins, CJ and Williams, S and Wilson,
J},
Title = {Classification of crystallization outcomes using deep
convolutional neural networks.},
Journal = {PloS one},
Volume = {13},
Number = {6},
Pages = {e0198883},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.1371/journal.pone.0198883},
Abstract = {The Machine Recognition of Crystallization Outcomes (MARCO)
initiative has assembled roughly half a million annotated
images of macromolecular crystallization experiments from
various sources and setups. Here, state-of-the-art machine
learning algorithms are trained and tested on different
parts of this data set. We find that more than 94% of the
test images can be correctly labeled, irrespective of their
experimental origin. Because crystal recognition is key to
high-density screening and the systematic analysis of
crystallization experiments, this approach opens the door to
both industrial and fundamental research
applications.},
Doi = {10.1371/journal.pone.0198883},
Key = {fds337004}
}
@article{fds333302,
Author = {Altan, I and Fusco, D and Afonine, PV and Charbonneau,
P},
Title = {Learning about Biomolecular Solvation from Water in Protein
Crystals.},
Journal = {The journal of physical chemistry. B},
Volume = {122},
Number = {9},
Pages = {2475-2486},
Year = {2018},
Month = {March},
url = {http://dx.doi.org/10.1021/acs.jpcb.7b09898},
Abstract = {Water occupies typically 50% of a protein crystal and thus
significantly contributes to the diffraction signal in
crystallography experiments. Separating its contribution
from that of the protein is, however, challenging because
most water molecules are not localized and are thus
difficult to assign to specific density peaks. The
intricateness of the protein-water interface compounds this
difficulty. This information has, therefore, not often been
used to study biomolecular solvation. Here, we develop a
methodology to surmount in part this difficulty. More
specifically, we compare the solvent structure obtained from
diffraction data for which experimental phasing is available
to that obtained from constrained molecular dynamics (MD)
simulations. The resulting spatial density maps show that
commonly used MD water models are only partially successful
at reproducing the structural features of biomolecular
solvation. The radial distribution of water is captured with
only slightly higher accuracy than its angular distribution,
and only a fraction of the water molecules assigned with
high reliability to the crystal structure is recovered.
These differences are likely due to shortcomings of both the
water models and the protein force fields. Despite these
limitations, we manage to infer protonation states of some
of the side chains utilizing MD-derived densities.},
Doi = {10.1021/acs.jpcb.7b09898},
Key = {fds333302}
}
@article{fds333301,
Author = {Hu, Y and Charbonneau, P},
Title = {Clustering and assembly dynamics of a one-dimensional
microphase former.},
Journal = {Soft matter},
Volume = {14},
Number = {20},
Pages = {4101-4109},
Year = {2018},
Month = {May},
url = {http://dx.doi.org/10.1039/c8sm00315g},
Abstract = {Both ordered and disordered microphases ubiquitously form in
suspensions of particles that interact through competing
short-range attraction and long-range repulsion (SALR).
While ordered microphases are more appealing materials
targets, understanding the rich structural and dynamical
properties of their disordered counterparts is essential to
controlling their mesoscale assembly. Here, we study the
disordered regime of a one-dimensional (1D) SALR model,
whose simplicity enables detailed analysis by transfer
matrices and Monte Carlo simulations. We first characterize
the signature of the clustering process on macroscopic
observables, and then assess the equilibration dynamics of
various simulation algorithms. We notably find that cluster
moves markedly accelerate the mixing time, but that event
chains are of limited help in the clustering regime. These
insights will inspire further study of three-dimensional
microphase formers.},
Doi = {10.1039/c8sm00315g},
Key = {fds333301}
}
@article{fds337552,
Author = {Charbonneau, B and Charbonneau, P and Szamel, G},
Title = {A microscopic model of the Stokes-Einstein relation in
arbitrary dimension.},
Journal = {The Journal of chemical physics},
Volume = {148},
Number = {22},
Pages = {224503},
Year = {2018},
Month = {June},
url = {http://dx.doi.org/10.1063/1.5029464},
Abstract = {The Stokes-Einstein relation (SER) is one of the most robust
and widely employed results from the theory of liquids. Yet
sizable deviations can be observed for self-solvation, which
cannot be explained by the standard hydrodynamic derivation.
Here, we revisit the work of Masters and Madden [J. Chem.
Phys. 74, 2450-2459 (1981)], who first solved a statistical
mechanics model of the SER using the projection operator
formalism. By generalizing their analysis to all spatial
dimensions and to partially structured solvents, we identify
a potential microscopic origin of some of these deviations.
We also reproduce the SER-like result from the exact
dynamics of infinite-dimensional fluids.},
Doi = {10.1063/1.5029464},
Key = {fds337552}
}
@article{fds335288,
Author = {Reyes, C and Fu, L and Suthanthiraraj, PPA and Owens, CE and Shields,
CW and López, GP and Charbonneau, P and Wiley, BJ},
Title = {The Limits of Primary Radiation Forces in Bulk Acoustic
Standing Waves for Concentrating Nanoparticles},
Journal = {Particle and Particle Systems Characterization},
Volume = {35},
Number = {7},
Pages = {1700470-1700470},
Publisher = {WILEY},
Year = {2018},
Month = {July},
url = {http://dx.doi.org/10.1002/ppsc.201700470},
Abstract = {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 model for predicting the
distribution of nanoparticles around the node of a 1D bulk
acoustic standing wave over time as a function of pressure
amplitude, acoustic contrast factor (i.e., nanoparticle and
fluid composition), and size of the nanoparticles.
Predictions from this model are systematically compared to
results from experiments on gold nanoparticles of different
sizes to determine the model's accuracy in estimating both
the rate and the degree of nanoparticle focusing across a
range of pressure amplitudes. The model is further used to
predict the minimum particle size that can be focused for
different nanoparticle and fluid compositions, and those
predictions are tested with gold, silica, and polystyrene
nanoparticles in water. A procedure combining UV-light and
photoacid is used to induce the aggregation of nanoparticles
to illustrate the effect of nanoparticle aggregation on the
observed degree of acoustic focusing. Overall, these
findings clarify the extent to which acoustic resonating
devices can be used to manipulate, pattern, and enrich
nanoparticles suspended in liquids.},
Doi = {10.1002/ppsc.201700470},
Key = {fds335288}
}
@article{fds338465,
Author = {Norman, J and Sorrell, EL and Hu, Y and Siripurapu, V and Garcia, J and Bagwell, J and Charbonneau, P and Lubkin, SR and Bagnat,
M},
Title = {Tissue self-organization underlies morphogenesis of the
notochord.},
Journal = {Philos Trans R Soc Lond B Biol Sci},
Volume = {373},
Number = {1759},
Pages = {20170320},
Year = {2018},
Month = {September},
url = {http://dx.doi.org/10.1098/rstb.2017.0320},
Abstract = {The notochord is a conserved axial structure that in
vertebrates serves as a hydrostatic scaffold for embryonic
axis elongation and, later on, for proper spine assembly. It
consists of a core of large fluid-filled vacuolated cells
surrounded by an epithelial sheath that is encased in
extracellular matrix. During morphogenesis, the vacuolated
cells inflate their vacuole and arrange in a stereotypical
staircase pattern. We investigated the origin of this
pattern and found that it can be achieved purely by simple
physical principles. We are able to model the arrangement of
vacuolated cells within the zebrafish notochord using a
physical model composed of silicone tubes and
water-absorbing polymer beads. The biological structure and
the physical model can be accurately described by the theory
developed for the packing of spheres and foams in cylinders.
Our experiments with physical models and numerical
simulations generated several predictions on key features of
notochord organization that we documented and tested
experimentally in zebrafish. Altogether, our data reveal
that the organization of the vertebrate notochord is
governed by the density of the osmotically swelling
vacuolated cells and the aspect ratio of the notochord rod.
We therefore conclude that self-organization underlies
morphogenesis of the vertebrate notochord.This article is
part of the Theo Murphy meeting issue on 'Mechanics of
development'.},
Doi = {10.1098/rstb.2017.0320},
Key = {fds338465}
}
@article{fds337003,
Author = {Hu, Y and Fu, L and Charbonneau, P},
Title = {Correlation lengths in quasi-one-dimensional systems via
transfer matrices},
Journal = {Molecular Physics},
Volume = {116},
Number = {21-22},
Pages = {3345-3354},
Publisher = {Informa UK Limited},
Year = {2018},
Month = {November},
url = {http://dx.doi.org/10.1080/00268976.2018.1479543},
Abstract = {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 non-monotonic and non-smooth
growth of the correlation length in these systems
accompanies structural crossovers [Fu et al., Soft Matter
13, 3296 (2017)]. Here, we identify the theoretical basis
for these behaviours. In particular, we associate kinks in
the growth of correlation lengths with eigenvalue crossing
and splitting. Understanding the origin of such structural
crossovers answers questions raised by earlier studies, and
thus bridges the gap between theory and simulations for
these reference models.},
Doi = {10.1080/00268976.2018.1479543},
Key = {fds337003}
}
@article{fds345659,
Author = {Altan, I and Charbonneau, P},
Title = {Obtaining Soft Matter Models of Proteins and their Phase
Behavior.},
Journal = {Methods in molecular biology (Clifton, N.J.)},
Volume = {2039},
Pages = {209-228},
Year = {2019},
Month = {January},
url = {http://dx.doi.org/10.1007/978-1-4939-9678-0_15},
Abstract = {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 biomolecule to a patchy model requires
simplifying effective protein-protein interactions, which in
turn provides a microscopic understanding of the protein
solution behavior. The patchy model can indeed be fully
analyzed, including its phase diagram. In this chapter, we
detail the methodology of mapping a given protein to a
patchy model and of determining the phase diagram of the
latter. We also briefly describe the theory upon which the
methodology is based, provide practical information, and
discuss potential pitfalls. Data and scripts relevant to
this work have been archived and can be accessed at
https://doi.org/10.7924/r4ww7bs1p .},
Doi = {10.1007/978-1-4939-9678-0_15},
Key = {fds345659}
}
@article{fds350499,
Author = {Altan, I and Charbonneau, P},
Title = {Correction to: Obtaining Soft Matter Models of Proteins and
their Phase Behavior.},
Journal = {Methods in molecular biology (Clifton, N.J.)},
Volume = {2039},
Pages = {C1},
Year = {2019},
Month = {January},
url = {http://dx.doi.org/10.1007/978-1-4939-9678-0_18},
Abstract = {The acknowledgement section text has been updated in the
chapter.},
Doi = {10.1007/978-1-4939-9678-0_18},
Key = {fds350499}
}
@article{fds341577,
Author = {Charbonneau, P and Corwin, EI and Fu, L and Tsekenis, G and van der
Naald, M},
Title = {Glassy, Gardner-like phenomenology in minimally polydisperse
crystalline systems.},
Journal = {Physical review. E},
Volume = {99},
Number = {2-1},
Pages = {020901},
Year = {2019},
Month = {February},
url = {http://dx.doi.org/10.1103/physreve.99.020901},
Abstract = {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 jamming features akin to those observed
in amorphous solids. Structurally, they exhibit a power-law
scaling in their probability distribution of weak forces and
small interparticle gaps as well as a flat density of
vibrational states. Dynamically, they display anomalous
aging above a characteristic pressure. Quantitatively, this
disordered crystal phase has much in common with the
Gardner-like phase seen in maximally disordered solids. Near
crystals should be amenable to experimental realizations in
commercially available particulate systems and are to be
indispensable in verifying the theory of amorphous
materials.},
Doi = {10.1103/physreve.99.020901},
Key = {fds341577}
}
@article{fds341477,
Author = {Biroli, G and Charbonneau, P and Hu, Y},
Title = {Dynamics around the site percolation threshold on
high-dimensional hypercubic lattices.},
Journal = {Physical review. E},
Volume = {99},
Number = {2-1},
Pages = {022118},
Year = {2019},
Month = {February},
url = {http://dx.doi.org/10.1103/physreve.99.022118},
Abstract = {Recent advances on the glass problem motivate reexamining
classical models of percolation. Here we consider the
displacement of an ant in a labyrinth near the percolation
threshold on cubic lattices both below and above the upper
critical dimension of simple percolation, d_{u}=6. Using
theory and simulations, we consider the scaling regime and
obtain that both caging and subdiffusion scale
logarithmically for d≥d_{u}. The theoretical derivation,
which considers Bethe lattices with generalized connectivity
and a random graph model, confirms that logarithmic scalings
should persist in the limit d→∞. The computational
validation employs accelerated random walk simulations with
a transfer-matrix description of diffusion to evaluate
directly the dynamical critical exponents below d_{u} as
well as their logarithmic scaling above d_{u}. Our numerical
results improve various earlier estimates and are fully
consistent with our theoretical predictions.},
Doi = {10.1103/physreve.99.022118},
Key = {fds341477}
}
@article{fds341867,
Author = {Charbonneau, P and Hu, Y and Raju, A and Sethna, JP and Yaida,
S},
Title = {Morphology of renormalization-group flow for the de
Almeida-Thouless-Gardner universality class.},
Journal = {Physical review. E},
Volume = {99},
Number = {2-1},
Pages = {022132},
Year = {2019},
Month = {February},
url = {http://dx.doi.org/10.1103/physreve.99.022132},
Abstract = {A replica-symmetry-breaking phase transition is predicted in
a host of disordered media. The criticality of the
transition has, however, long been questioned below its
upper critical dimension, six, due to the absence of a
critical fixed point in the renormalization-group flows at
one-loop order. A recent two-loop analysis revealed a
possible strong-coupling fixed point, but given the
uncontrolled nature of perturbative analysis in the
strong-coupling regime, debate persists. Here we examine the
nature of the transition as a function of spatial dimension
and show that the strong-coupling fixed point can go through
a Hopf bifurcation, resulting in a critical limit cycle and
a concomitant discrete scale invariance. We further
investigate a different renormalization scheme and argue
that the basin of attraction of the strong-coupling fixed
point (or limit cycle) may stay finite for all
dimensions.},
Doi = {10.1103/physreve.99.022132},
Key = {fds341867}
}
@article{fds342189,
Author = {Berthier, L and Charbonneau, P and Kundu, J},
Title = {Bypassing sluggishness: SWAP algorithm and glassiness in
high dimensions.},
Journal = {Physical review. E},
Volume = {99},
Number = {3-1},
Pages = {031301},
Year = {2019},
Month = {March},
url = {http://dx.doi.org/10.1103/physreve.99.031301},
Abstract = {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 consider suitably optimized
systems in d=2,3,⋯,8 to obtain insights into the
performance and underlying physics of SWAP. We show that the
speedup obtained decays rapidly with increasing the
dimension. SWAP nonetheless delays systematically the onset
of the activated dynamics by an amount that remains
seemingly finite in the limit d→∞. This shows that the
glassy dynamics in high dimensions d>3 is now
computationally accessible using SWAP, thus opening the door
for the systematic consideration of finite-dimensional
deviations from the mean-field description.},
Doi = {10.1103/physreve.99.031301},
Key = {fds342189}
}
@article{fds342344,
Author = {Berthier, L and Charbonneau, P and Ninarello, A and Ozawa, M and Yaida,
S},
Title = {Zero-temperature glass transition in two
dimensions.},
Journal = {Nature communications},
Volume = {10},
Number = {1},
Pages = {1508},
Year = {2019},
Month = {April},
url = {http://dx.doi.org/10.1038/s41467-019-09512-3},
Abstract = {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 problem remains wide open in
physical dimensions. Nontrivial finite-dimensional
fluctuations are hard to control analytically, and
experiments fail to provide conclusive evidence regarding
the nature of the glass transition. Here, we develop Monte
Carlo methods for two-dimensional glass-forming liquids that
allow us to access equilibrium states at sufficiently low
temperatures to directly probe the glass transition in a
regime inaccessible to experiments. We find that the liquid
state terminates at a thermodynamic glass transition which
occurs at zero temperature and is associated with an entropy
crisis and a diverging static correlation length. Our
results thus demonstrate that a thermodynamic glass
transition can occur in finite dimensional
glass-formers.},
Doi = {10.1038/s41467-019-09512-3},
Key = {fds342344}
}
@article{fds344711,
Author = {Berthier, L and Biroli, G and Charbonneau, P and Corwin, EI and Franz,
S and Zamponi, F},
Title = {Gardner physics in amorphous solids and beyond.},
Journal = {The Journal of chemical physics},
Volume = {151},
Number = {1},
Pages = {010901},
Year = {2019},
Month = {July},
url = {http://dx.doi.org/10.1063/1.5097175},
Abstract = {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 models, its materials relevance was
only realized when a systematic effort to relate glass
formation and jamming was undertaken. A number of nontrivial
physical signatures associated with the Gardner transition
have since been considered in various areas, from models of
structural glasses to constraint satisfaction problems. This
perspective surveys these recent advances and discusses the
novel research opportunities that arise from
them.},
Doi = {10.1063/1.5097175},
Key = {fds344711}
}
@article{fds345658,
Author = {Khan, AR and James, S and Quinn, MK and Altan, I and Charbonneau, P and McManus, JJ},
Title = {Temperature-Dependent Interactions Explain Normal and
Inverted Solubility in a γD-Crystallin Mutant.},
Journal = {Biophysical journal},
Volume = {117},
Number = {5},
Pages = {930-937},
Publisher = {Elsevier BV},
Year = {2019},
Month = {September},
url = {http://dx.doi.org/10.1016/j.bpj.2019.07.019},
Abstract = {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 the protein surface, due to
the variety of amino-acid side chains in contact with
solvent, contributes to protein-protein contact formation in
the crystal lattice is a major obstacle to predicting and
optimizing crystallization. The relative scarcity of
sophisticated theoretical models that include sufficient
detail to link collective behavior, captured in protein
phase diagrams, and molecular-level details, determined from
high-resolution structural information, is a further
barrier. Here, we present two crystal structures for the
P23T + R36S mutant of γD-crystallin, each with opposite
solubility behavior: one melts when heated, the other when
cooled. When combined with the protein phase diagram and a
tailored patchy particle model, we show that a single
temperature-dependent interaction is sufficient to stabilize
the inverted solubility crystal. This contact, at the P23T
substitution site, relates to a genetic cataract and reveals
at a molecular level the origin of the lowered and
retrograde solubility of the protein. Our results show that
the approach employed here may present a productive strategy
for the rationalization of protein crystallization.},
Doi = {10.1016/j.bpj.2019.07.019},
Key = {fds345658}
}
@article{fds347015,
Author = {Flenner, E and Berthier, L and Charbonneau, P and Fullerton,
CJ},
Title = {Front-Mediated Melting of Isotropic Ultrastable
Glasses.},
Journal = {Physical review letters},
Volume = {123},
Number = {17},
Pages = {175501},
Year = {2019},
Month = {October},
url = {http://dx.doi.org/10.1103/physrevlett.123.175501},
Abstract = {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 to bulk melting. We combine
swap Monte Carlo with molecular dynamics simulations to
prepare and melt isotropic amorphous films of unprecedendtly
high kinetic stability. We are able to directly observe both
bulk and front melting, and the crossover between them. We
measure the front velocity over a broad range of conditions,
and a crossover length scale that grows to nearly 400
particle diameters in the regime accessible to simulations.
Our results disentangle the relative roles of kinetic
stability and vapor deposition in the physical properties of
stable glasses.},
Doi = {10.1103/physrevlett.123.175501},
Key = {fds347015}
}
@article{fds358430,
Author = {Altan, I and Khan, AR and James, S and Quinn, MK and McManus, JJ and Charbonneau, P},
Title = {Using Schematic Models to Understand the Microscopic Basis
for Inverted Solubility in γD-Crystallin.},
Journal = {The journal of physical chemistry. B},
Volume = {123},
Number = {47},
Pages = {10061-10072},
Year = {2019},
Month = {November},
url = {http://dx.doi.org/10.1021/acs.jpcb.9b07774},
Abstract = {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, serine, or valine. One proposed
microscopic mechanism entails an increase in surface
hydrophobicity upon mutagenesis. Recent crystal structures
of a double mutant that includes the P23T mutation allow for
a more careful investigation of this proposal. Here, we
first measure the surface hydrophobicity of various mutant
structures of γD-crystallin and discern no notable increase
in hydrophobicity upon mutating the 23rd residue. We then
investigate the solubility inversion regime with a schematic
patchy particle model that includes one of three variants of
temperature-dependent patch energies: two of the hydrophobic
effect, and one of a more generic nature. We conclude that,
while solubility inversion due to the hydrophobic effect may
be possible, microscopic evidence to support it in
γD-crystallin is weak. More generally, we find that
solubility inversion requires a fine balance between patch
strengths and their temperature-dependent component, which
may explain why inverted solubility is not commonly observed
in proteins. We also find that the temperature-dependent
interaction has only a negligible impact on liquid-liquid
phase boundaries of γD-crystallin, in line with previous
experimental observations.},
Doi = {10.1021/acs.jpcb.9b07774},
Key = {fds358430}
}
@article{fds349734,
Author = {Charbonneau, P and Kundu, J},
Title = {Postponing the dynamical transition density using competing
interactions},
Journal = {Granular Matter},
Volume = {22},
Number = {3},
Year = {2020},
Month = {August},
url = {http://dx.doi.org/10.1007/s10035-020-0998-z},
Abstract = {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 with pure repulsion or with
long-ranged attraction. A recent mean-field,
infinite-dimensional calculation predicts that the dynamical
arrest of the fluid can be further delayed by adding a
longer-ranged repulsive contribution to the short-ranged
attraction. We examine this proposal by performing extensive
numerical simulations in a three-dimensional system. We
first find the short-ranged attraction parameters necessary
to achieve the densest liquid state, and then explore the
parameter space for an additional longer-ranged repulsion
that could further enhance reentrance. In the family of
systems studied, no significant (within numerical accuracy)
delay of the dynamical arrest is observed beyond what is
already achieved by the short-ranged attraction. Possible
explanations are discussed.},
Doi = {10.1007/s10035-020-0998-z},
Key = {fds349734}
}
@article{fds352376,
Author = {Berthier, L and Charbonneau, P and Kundu, J},
Title = {Finite Dimensional Vestige of Spinodal Criticality above the
Dynamical Glass Transition.},
Journal = {Physical review letters},
Volume = {125},
Number = {10},
Pages = {108001},
Year = {2020},
Month = {September},
url = {http://dx.doi.org/10.1103/physrevlett.125.108001},
Abstract = {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 that also limit how close the
instability can be approached. We combine numerical tools to
directly observe vestiges of the spinodal criticality in
finite dimensional glass formers. We use the swap
Monte Carlo algorithm to efficiently thermalize
configurations beyond the mode-coupling crossover, and
analyze their dynamics using a scheme to screen out
activated processes, in spatial dimensions ranging from d=3
to d=10. We observe a strong softening of the mean-field
square-root singularity in d=3 that is progressively
restored as d increases above d=8, in surprisingly good
agreement with perturbation theory.},
Doi = {10.1103/physrevlett.125.108001},
Key = {fds352376}
}
@article{fds358428,
Author = {Charbonneau, P and Morse, PK},
Title = {Memory Formation in Jammed Hard Spheres.},
Journal = {Physical review letters},
Volume = {126},
Number = {8},
Pages = {088001},
Year = {2021},
Month = {February},
url = {http://dx.doi.org/10.1103/physrevlett.126.088001},
Abstract = {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 origin remains controversial. Its absence from
mean-field descriptions, in particular, has long cast doubt
on its thermodynamic relevance. Motivated by a recent
theoretical proposal, we reassess the onset phenomenology in
simulations using a fast hard sphere jamming algorithm and
find it to be both thermodynamically and dimensionally
robust. Remarkably, we also uncover a second type of memory
associated with a Gardner-like regime of the jamming
algorithm.},
Doi = {10.1103/physrevlett.126.088001},
Key = {fds358428}
}
@article{fds355940,
Author = {Biroli, G and Charbonneau, P and Corwin, EI and Hu, Y and Ikeda, H and Szamel, G and Zamponi, F},
Title = {Interplay between percolation and glassiness in the random
Lorentz gas.},
Journal = {Physical review. E},
Volume = {103},
Number = {3},
Pages = {L030104},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.1103/physreve.103.l030104},
Abstract = {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 for describing the
discontinuous dynamical transition of glasses. In order to
clarify the interplay between the seemingly incompatible
percolation and caging descriptions of the RLG, we consider
its exact mean-field solution in the infinite-dimensional
d→∞ limit and perform numerics in d=2...20. We find that
for sufficiently high d the mean-field caging transition
precedes and prevents the percolation transition, which only
happens on timescales diverging with d. We further show that
activated processes related to rare cage escapes destroy the
glass transition in finite dimensions, leading to a rich
interplay between glassiness and percolation physics. This
advance suggests that the RLG can be used as a toy model to
develop a first-principle description of particle hopping in
structural glasses.},
Doi = {10.1103/physreve.103.l030104},
Key = {fds355940}
}
@article{fds365295,
Author = {Downey, M and Lafferty-Hess, S and Charbonneau, P and Zoss,
A},
Title = {Engaging Researchers in Data Dialogues: Designing
Collaborative Programming to Promote Research Data
Sharing},
Journal = {Journal of eScience Librarianship},
Volume = {10},
Number = {2},
Publisher = {University of Massachusetts Medical School},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.7191/jeslib.2021.1193},
Abstract = {<jats:p>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 this data sharing space,
one particular challenge has been finding new ways to
meaningfully engage with campus researchers. Libraries help
shape norms and encourage data sharing through education and
training, and there has been significant growth in the
services these institutions are able to provide and the ways
in which library staff are able to collaborate and
communicate with researchers. Evidence also suggests that
within disciplines, normative pressures and expectations
around professional conduct have a significant impact on
data sharing behaviors (Kim and Adler 2015; Sigit Sayogo and
Pardo 2013; Zenk-Moltgen et al. 2018). Duke University
Libraries' Research Data Management program has recently
centered part of its outreach strategy on leveraging peer
networks and social modeling to encourage and normalize
robust data sharing practices among campus researchers. The
program has hosted two panel discussions on issues related
to data management—specifically, data sharing and research
reproducibility. This paper reflects on some lessons learned
from these outreach efforts and outlines next
steps.</jats:p>},
Doi = {10.7191/jeslib.2021.1193},
Key = {fds365295}
}
@article{fds355939,
Author = {Hu, Y and Charbonneau, P},
Title = {Resolving the two-dimensional axial next-nearest-neighbor
Ising model using transfer matrices},
Journal = {Physical Review B},
Volume = {103},
Number = {9},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.1103/PhysRevB.103.094441},
Abstract = {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 analytical and numerical treatments
making contradictory predictions. Here, we introduce a
numerical transfer matrix approach that bypasses these
problems and thus clears up various ambiguities. In
particular, we confirm the transition temperatures and the
order of the transition to the floating incommensurate
phase. Our approach motivates considering transfer matrices
for solving long-standing problems in related
models.},
Doi = {10.1103/PhysRevB.103.094441},
Key = {fds355939}
}
@article{fds356930,
Author = {Biroli, G and Charbonneau, P and Hu, Y and Ikeda, H and Szamel, G and Zamponi, F},
Title = {Mean-Field Caging in a Random Lorentz Gas.},
Journal = {The journal of physical chemistry. B},
Volume = {125},
Number = {23},
Pages = {6244-6254},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.1021/acs.jpcb.1c02067},
Abstract = {The random Lorentz gas (RLG) is a minimal model of both
percolation and glassiness, which leads to a paradox in the
infinite-dimensional, <i>d</i> → ∞ limit: the
localization transition is then expected to be
<i>continuous</i> for the former and <i>discontinuous</i>
for the latter. As a putative resolution, we have recently
suggested that, as <i>d</i> increases, the behavior of the
RLG converges to the glassy description and that percolation
physics is recovered thanks to finite-<i>d</i> perturbative
and nonperturbative (instantonic) corrections [Biroli et al.
<i>Phys. Rev. E</i> 2021, 103, L030104]. Here, we expand on
the <i>d</i> → ∞ physics by considering a simpler static
solution as well as the dynamical solution of the RLG.
Comparing the 1/<i>d</i> correction of this solution with
numerical results reveals that even perturbative corrections
fall out of reach of existing theoretical descriptions.
Comparing the dynamical solution with the mode-coupling
theory (MCT) results further reveals that, although key
quantitative features of MCT are far off the mark, it does
properly capture the discontinuous nature of the <i>d</i>
→ ∞ RLG. These insights help chart a path toward a
complete description of finite-dimensional
glasses.},
Doi = {10.1021/acs.jpcb.1c02067},
Key = {fds356930}
}
@article{fds357297,
Author = {Hu, Y and Charbonneau, P},
Title = {Percolation thresholds on high-dimensional D_{n} and
E_{8}-related lattices.},
Journal = {Physical review. E},
Volume = {103},
Number = {6-1},
Pages = {062115},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.1103/physreve.103.062115},
Abstract = {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 the study of
D_{n} root lattices in n dimensions as well as E_{8}-related
lattices. Here, we consider the percolation problem on D_{n}
for n=3 to 13 and on E_{8} relatives for n=6 to 9. Precise
estimates for both site and bond percolation thresholds
obtained from invasion percolation simulations are compared
with dimensional series expansion based on lattice animal
enumeration for D_{n} lattices. As expected, the bond
percolation threshold rapidly approaches the Bethe lattice
limit as n increases for these high-connectivity lattices.
Corrections, however, exhibit clear yet unexplained trends.
Interestingly, the finite-size scaling exponent for invasion
percolation is found to be lattice and percolation-type
specific.},
Doi = {10.1103/physreve.103.062115},
Key = {fds357297}
}
@article{fds357540,
Author = {Zheng, M and Charbonneau, P},
Title = {Characterization and efficient Monte Carlo sampling of
disordered microphases.},
Journal = {The Journal of chemical physics},
Volume = {154},
Number = {24},
Pages = {244506},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.1063/5.0052114},
Abstract = {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 percolated (gel-like) fluids.
These different structural regimes exhibit complex
relaxation dynamics with marked heterogeneity and slowdown.
The overall relationship between these structures and
configurational sampling schemes, however, remains largely
uncharted. Here, the disordered microphases of a schematic
SALR model are thoroughly characterized, and structural
relaxation functions adapted to each regime are devised. The
sampling efficiency of various advanced Monte Carlo sampling
schemes-Virtual-Move (VMMC), Aggregation-Volume-Bias
(AVBMC), and Event-Chain (ECMC)-is then assessed. A
combination of VMMC and AVBMC is found to be computationally
most efficient for cluster fluids and ECMC to become
relatively more efficient as density increases. These
results offer a complete description of the equilibrium
disordered phase of a simple microphase former as well as
dynamical benchmarks for other sampling schemes.},
Doi = {10.1063/5.0052114},
Key = {fds357540}
}
@article{fds357866,
Author = {Charbonneau, P and Tarzia, M},
Title = {Solution of disordered microphases in the Bethe
approximation.},
Journal = {The Journal of chemical physics},
Volume = {155},
Number = {2},
Pages = {024501},
Year = {2021},
Month = {July},
url = {http://dx.doi.org/10.1063/5.0052111},
Abstract = {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 untangling their properties. By contrast,
disordered microphases, which are structurally just as rich
but nowhere near as elegant, have not been as carefully
considered. Part of the difficulty is that simple mean-field
descriptions make a homogeneity assumption that washes away
all of their structural features. Here, we study disordered
microphases by exactly solving a SALR model on the Bethe
lattice. By sidestepping the homogenization assumption, this
treatment recapitulates many of the key structural regimes
of disordered microphases, including particle and void
cluster fluids as well as gelation. This analysis also
provides physical insight into the relationship between
various structural and thermal observables, between
criticality and physical percolation, and between glassiness
and microphase ordering.},
Doi = {10.1063/5.0052111},
Key = {fds357866}
}
@article{fds357947,
Author = {Charbonneau, P and Corwin, EI and Dennis, RC and Díaz Hernández
Rojas and R and Ikeda, H and Parisi, G and Ricci-Tersenghi,
F},
Title = {Finite-size effects in the microscopic critical properties
of jammed configurations: A comprehensive study of the
effects of different types of disorder.},
Journal = {Physical review. E},
Volume = {104},
Number = {1-1},
Pages = {014102},
Year = {2021},
Month = {July},
url = {http://dx.doi.org/10.1103/physreve.104.014102},
Abstract = {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 interparticle forces (f) and gaps (h)
are distributed according to nontrivial power laws. A
recently developed mean-field (MF) theory predicts the
characteristic exponents of these distributions in the limit
of very high spatial dimension, d→∞ and, remarkably,
their values seemingly agree with numerical estimates in
physically relevant dimensions, d=2 and 3. These exponents
are further connected through a pair of inequalities derived
from stability conditions, and both theoretical predictions
and previous numerical investigations suggest that these
inequalities are saturated. Systems at the jamming point are
thus only marginally stable. Despite the key physical role
played by these exponents, their systematic evaluation has
yet to be attempted. Here, we carefully test their value by
analyzing the finite-size scaling of the distributions of f
and h for various particle-based models for jamming. Both
dimension and the direction of approach to the jamming point
are also considered. We show that, in all models,
finite-size effects are much more pronounced in the
distribution of h than in that of f. We thus conclude that
gaps are correlated over considerably longer scales than
forces. Additionally, remarkable agreement with MF
predictions is obtained in all but one model, namely
near-crystalline packings. Our results thus help to better
delineate the domain of the jamming universality class. We
furthermore uncover a secondary linear regime in the
distribution tails of both f and h. This surprisingly robust
feature is understood to follow from the (near) isostaticity
of our configurations.},
Doi = {10.1103/physreve.104.014102},
Key = {fds357947}
}
@article{fds359023,
Author = {Charbonneau, B and Charbonneau, P and Hu, Y and Yang,
Z},
Title = {High-dimensional percolation criticality and hints of
mean-field-like caging of the random Lorentz
gas.},
Journal = {Physical review. E},
Volume = {104},
Number = {2-1},
Pages = {024137},
Year = {2021},
Month = {August},
url = {http://dx.doi.org/10.1103/physreve.104.024137},
Abstract = {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 the void percolation threshold is
not well controlled analytically nor computationally. A
recent study [Biroli et al., Phys. Rev. E 103, L030104
(2021)2470-004510.1103/PhysRevE.103.L030104] of the caging
behavior of the RLG motivated by the mean-field theory of
glasses has uncovered physical inconsistencies in that
scaling that heighten the need for guidance. Here we first
extend analytical expectations for asymptotic high-d bounds
on the void percolation threshold and then computationally
evaluate both the threshold and its criticality in various
d. In high-d systems, we observe that the standard
percolation physics is complemented by a dynamical slowdown
of the tracer dynamics reminiscent of mean-field caging. A
simple modification of the RLG is found to bring the
interplay between percolation and mean-field-like caging
down to d=3.},
Doi = {10.1103/physreve.104.024137},
Key = {fds359023}
}
@article{fds358389,
Author = {Charbonneau, P and Gish, CM and Hoy, RS and Morse,
PK},
Title = {Thermodynamic stability of hard sphere crystals in
dimensions 3 through 10.},
Journal = {The European physical journal. E, Soft matter},
Volume = {44},
Number = {8},
Pages = {101},
Year = {2021},
Month = {August},
url = {http://dx.doi.org/10.1140/epje/s10189-021-00104-y},
Abstract = {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 thermodynamically stable in high
dimensions and thus whether a mean-field theory of crystals
can ever be exact. In order to determine the stability range
of hard sphere crystals, their equation of state is here
estimated from numerical simulations, and fluid-crystal
coexistence conditions are determined using a generalized
Frenkel-Ladd scheme to compute absolute crystal free
energies. The results show that the crystal phase is stable
at least up to [Formula: see text], and the dimensional
trends suggest that crystal stability likely persists well
beyond that point.},
Doi = {10.1140/epje/s10189-021-00104-y},
Key = {fds358389}
}
@article{fds359461,
Author = {Hu, Y and Charbonneau, P},
Title = {Comment on "kosterlitz-Thouless-type caging-uncaging
transition in a quasi-one-dimensional hard disk
system"},
Journal = {Physical Review Research},
Volume = {3},
Number = {3},
Year = {2021},
Month = {September},
url = {http://dx.doi.org/10.1103/PhysRevResearch.3.038001},
Abstract = {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
(KT)-type caging-uncaging transition. The proposed existence
of such a transition in a quasi-one-dimensional system,
however, contradicts long-held physical expectations. To
clarify if the proposed ordering persists in the
thermodynamic limit, we introduce an exact transfer matrix
approach to expeditiously generate configurations of very
large subsystems that are typical of equilibrium
thermodynamic (infinite-size) systems. The power-law decay
of positional order is found to extend only over finite
distances. We conclude that the numerical simulation results
reported are associated with a crossover unrelated to
KT-type physics, and not with a proper thermodynamic phase
transition.},
Doi = {10.1103/PhysRevResearch.3.038001},
Key = {fds359461}
}
@article{fds361441,
Author = {Biroli, G and Charbonneau, P and Folena, G and Hu, Y and Zamponi,
F},
Title = {Local dynamical heterogeneity in glass formers},
Journal = {Phys. Rev. Lett.},
Volume = {128},
Pages = {175501},
Year = {2021},
Month = {September},
Abstract = {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 displacements, display divergent
fluctuations around the dynamical (or mode-coupling)
transition, due to the emergence of nontrivial correlations
between displacements along different directions. This
effect notably gives rise to a divergent non-Gaussian
parameter, $\alpha_2$. The $d\to\infty$ local dynamics
therefore becomes quite rich upon approaching the glass
transition. The finite-$d$ remnant of this phenomenon
further provides a long sought-after, first-principle
explanation for the growth of $\alpha_2$ around the glass
transition that is \emph{not based on multi-particle
correlations}.},
Key = {fds361441}
}
@article{fds359876,
Author = {Hu, Y and Charbonneau, P},
Title = {Numerical transfer matrix study of frustrated
next-nearest-neighbor Ising models on square
lattices},
Journal = {Physical Review B},
Volume = {104},
Number = {14},
Year = {2021},
Month = {October},
url = {http://dx.doi.org/10.1103/PhysRevB.104.144429},
Abstract = {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 determining their equilibrium
phase behavior from theoretical approximations. The exact
numerical transfer matrix (TM) method, which bypasses both
difficulties, can serve as a benchmark method once its own
numerical challenges are surmounted. Building on our recent
study [Hu and Charbonneau, Phys. Rev. B 103, 094441
(2021)2469-995010.1103/PhysRevB.103.094441], in which we
evaluated the two-dimensional axial next-nearest-neighbor
Ising model with transfer matrices, we here extend the
effective usage of the TM method to Ising models with
biaxial, diagonal, and third-nearest-neighbor frustration
models. The high-accuracy TM numerics help resolve various
physical ambiguities about these reference models, thus
providing a clearer overview of modulated phase formation in
two dimensions.},
Doi = {10.1103/PhysRevB.104.144429},
Key = {fds359876}
}
@article{fds361440,
Author = {Charbonneau, P and Hu, Y and Kundu, J and Morse, PK},
Title = {The dimensional evolution of structure and dynamics in hard
sphere liquids},
Journal = {J. Chem. Phys.},
Volume = {156},
Pages = {134502},
Year = {2021},
Month = {November},
Abstract = {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 unclear. These liquids indeed exhibit a
complex interplay between structure and dynamics, and the
importance of this interplay might only slowly diminish as
dimension $d$ increases. A careful numerical assessment of
the matter has long been hindered by the exponential
increase of computational costs with $d$. By revisiting a
once common simulation technique involving the use of
periodic boundary conditions modeled on $D_d$ lattices, we
here partly sidestep this difficulty, thus allowing the
study of hard sphere liquids up to $d=13$. Parallel efforts
by Mangeat and Zamponi [Phys. Rev. E 93, 012609 (2016)] have
expanded the mean-field description of glasses to finite $d$
by leveraging standard liquid-state theory, and thus help
bridge the gap from the other direction. The relatively
smooth evolution of both structure and dynamics across the
$d$ gap allows us to relate the two approaches, and to
identify some of the missing features that a finite-$d$
theory of glasses might hope to include to achieve near
quantitative agreement.},
Key = {fds361440}
}
@article{fds361334,
Author = {Charbonneau, P and Morse, PK and Perkins, W and Zamponi,
F},
Title = {Three simple scenarios for high-dimensional sphere
packings.},
Journal = {Physical review. E},
Volume = {104},
Number = {6-1},
Pages = {064612},
Year = {2021},
Month = {December},
url = {http://dx.doi.org/10.1103/physreve.104.064612},
Abstract = {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 and the glass phase constitutes
the densest packing; in scenario B, crystallization from the
liquid is possible, but takes place much beyond the
dynamical glass transition and is thus dynamically
implausible; and in scenario C, crystallization is possible
and takes place before (or just after) dynamical arrest,
thus making it plausibly accessible from the liquid state.
In order to assess the underlying conjectures and thus
obtain insight into which scenario is most likely to be
realized, we investigate the densest sphere packings for
dimension d=3-10 using cell-cluster expansions as well as
numerical simulations. These resulting estimates of the
crystal entropy near close packing tend to support scenario
C. We additionally confirm that the crystal equation of
state is dominated by the free-volume expansion and that a
meaningful polynomial correction can be formulated.},
Doi = {10.1103/physreve.104.064612},
Key = {fds361334}
}
@article{fds362914,
Author = {Charbonneau, P and Hu, Y and Kundu, J and Morse, PK},
Title = {The dimensional evolution of structure and dynamics in hard
sphere liquids.},
Journal = {The Journal of chemical physics},
Volume = {156},
Number = {13},
Pages = {134502},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1063/5.0080805},
Abstract = {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 unclear. These liquids indeed exhibit a
complex interplay between structure and dynamics, and the
importance of this interplay might only slowly diminish as
dimension d increases. A careful numerical assessment of the
matter has long been hindered by the exponential increase in
computational costs with d. By revisiting a once common
simulation technique involving the use of periodic boundary
conditions modeled on D<sub>d</sub> lattices, we here partly
sidestep this difficulty, thus allowing the study of hard
sphere liquids up to d = 13. Parallel efforts by Mangeat and
Zamponi [Phys. Rev. E 93, 012609 (2016)] have expanded the
mean-field description of glasses to finite d by leveraging
the standard liquid-state theory and, thus, help bridge the
gap from the other direction. The relatively smooth
evolution of both the structure and dynamics across the d
gap allows us to relate the two approaches and to identify
some of the missing features that a finite-d theory of
glasses might hope to include to achieve near quantitative
agreement.},
Doi = {10.1063/5.0080805},
Key = {fds362914}
}
@article{fds366242,
Author = {Biroli, G and Charbonneau, P and Folena, G and Hu, Y and Zamponi,
F},
Title = {Local Dynamical Heterogeneity in Simple Glass
Formers.},
Journal = {Physical review letters},
Volume = {128},
Number = {17},
Pages = {175501},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1103/physrevlett.128.175501},
Abstract = {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, display divergent fluctuations
around the dynamical (or mode-coupling) transition, due to
the emergence of nontrivial correlations between
displacements along different directions. This effect
notably gives rise to a divergent non-Gaussian parameter,
α_{2}. The d→∞ local dynamics therefore becomes quite
rich upon approaching the glass transition. The finite-d
remnant of this phenomenon further provides a long
sought-after, first-principle explanation for the growth of
α_{2} around the glass transition that is not based on
multiparticle correlations.},
Doi = {10.1103/physrevlett.128.175501},
Key = {fds366242}
}
@article{fds365824,
Author = {Folena, G and Biroli, G and Charbonneau, P and Hu, Y and Zamponi,
F},
Title = {Equilibrium fluctuations in mean-field disordered
models.},
Journal = {Physical review. E},
Volume = {106},
Number = {2-1},
Pages = {024605},
Year = {2022},
Month = {August},
url = {http://dx.doi.org/10.1103/physreve.106.024605},
Abstract = {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 conditions. By means of the
replica method we evaluate Gaussian fluctuations of the
overlaps around the thermodynamic limit, decomposing them in
thermal fluctuations inside each state and heterogeneous
fluctuations between different states. We first test and
compare our analytical results with numerical simulation
results for the p-spin spherical model and the random
orthogonal model, and then analyze the random Lorentz gas.
In all cases, a strong quantitative agreement is obtained.
Our analysis thus provides a robust scheme for identifying
the key finite-size (or finite-dimensional) corrections to
the mean-field treatment of these paradigmatic glass
models.},
Doi = {10.1103/physreve.106.024605},
Key = {fds365824}
}
@article{fds367536,
Author = {Charbonneau, P},
Title = {From the replica trick to the replica symmetry-breaking
technique},
Journal = {IAMP News Bulletin},
Volume = {2022},
Number = {October},
Pages = {5-25},
Year = {2022},
Month = {October},
Abstract = {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 scientific and professional
contexts of this prodigious advance.},
Key = {fds367536}
}
@article{fds367801,
Author = {Zheng, M and Tarzia, M and Charbonneau, P},
Title = {Communication: Weakening the critical dynamical slowing down
of models with SALR interactions.},
Journal = {The Journal of chemical physics},
Volume = {157},
Number = {18},
Pages = {181103},
Year = {2022},
Month = {November},
url = {http://dx.doi.org/10.1063/5.0120634},
Abstract = {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 the underlying physics is needed.
Here, we first obtain generic insight into that phenomenon
by studying one-dimensional and Bethe lattice versions of a
schematic frustrated model, the axial next-nearest neighbor
Ising (ANNNI) model. Based on these findings, we formulate
two cluster algorithms that speed up the simulations of the
ANNNI model on a 2D square lattice. Although these schemes
do not eliminate the critical slowing own, speed-ups of
factors up to 40 are achieved in some regimes.},
Doi = {10.1063/5.0120634},
Key = {fds367801}
}
@article{fds368098,
Author = {Kool, L and Charbonneau, P and Daniels, KE},
Title = {Gardner-like crossover from variable to persistent force
contacts in granular crystals.},
Journal = {Physical review. E},
Volume = {106},
Number = {5-1},
Pages = {054901},
Publisher = {American Physical Society (APS)},
Year = {2022},
Month = {November},
url = {http://dx.doi.org/10.1103/physreve.106.054901},
Abstract = {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 compression. Starting from densities
just above the freezing transition and for variable amounts
of additional compression, we compare configurations to both
their own initial state and to an ensemble of equivalent
reinitialized states. This protocol shows that force
contacts are largely undetermined when the density is below
a Gardner-like crossover, after which they gradually
transition to being persistent, being fully so only above
the jamming point. We associate the disorder that underlies
this effect with the size of the microscopic asperities of
the photoelastic disks used, by analogy to other mechanisms
that have been previously predicted theoretically.},
Doi = {10.1103/physreve.106.054901},
Key = {fds368098}
}
@article{fds369827,
Author = {Charbonneau, P and Kilgore, K and Pilcher, JM},
Title = {Recreating Colonial Mexican Fudge},
Journal = {Gastronomica},
Volume = {23},
Number = {1},
Pages = {112-115},
Publisher = {University of California Press},
Year = {2023},
Month = {February},
url = {http://dx.doi.org/10.1525/gfc.2023.23.1.112},
Doi = {10.1525/gfc.2023.23.1.112},
Key = {fds369827}
}
@article{fds369826,
Author = {Charbonneau, P and Pilcher, JM},
Title = {From Panocha to Fudge},
Journal = {Gastronomica},
Volume = {23},
Number = {1},
Pages = {100-111},
Publisher = {University of California Press},
Year = {2023},
Month = {February},
url = {http://dx.doi.org/10.1525/gfc.2023.23.1.100},
Abstract = {<jats:p>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. The authors of this article
combined the methodologies of physical chemistry and food
history to examine the development of this dish using the
science of sugar refining as well as manuscript and
published cookbook recipes, memoirs, and travel accounts.
Given the lack of Old World confectionery antecedents to the
key technique of whisking the cooling sugar to induce
crystallization, they attribute panochita to vernacular
Mexican traditions of sugar refining and candy
making.</jats:p>},
Doi = {10.1525/gfc.2023.23.1.100},
Key = {fds369826}
}
@article{fds370445,
Author = {Wopat, S and Adhyapok, P and Daga, B and Crawford, JM and Peskin, B and Norman, J and Bagwell, J and Fogerson, SM and Di Talia and S and Kiehart,
DP and Charbonneau, P and Bagnat, M},
Title = {Axial segmentation by iterative mechanical
signaling.},
Journal = {bioRxiv},
Year = {2023},
Month = {March},
url = {http://dx.doi.org/10.1101/2023.03.27.534101},
Abstract = {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 somite segmentation. However,
patterning defects in the somites lead to imprecise
notochord segmentation, suggesting these processes are
linked. Here, we reveal that spatial coordination between
the notochord and the axial musculature is necessary to
ensure segmentation of the zebrafish spine both in time and
space. We find that the connective tissues that anchor the
axial skeletal musculature, known as the myosepta in
zebrafish, transmit spatial patterning cues necessary to
initiate notochord segment formation, a critical
pre-patterning step in spine morphogenesis. When an
irregular pattern of muscle segments and myosepta interact
with the notochord sheath, segments form non-sequentially,
initiate at atypical locations, and eventually display
altered morphology later in development. We determine that
locations of myoseptum-notochord connections are hubs for
mechanical signal transmission, which are characterized by
localized sites of deformation of the extracellular matrix
(ECM) layer encasing the notochord. The notochord sheath
responds to the external mechanical changes by locally
augmenting focal adhesion machinery to define the initiation
site for segmentation. Using a coarse-grained mathematical
model that captures the spatial patterns of
myoseptum-notochord interactions, we find that a
fixed-length scale of external cues is critical for driving
sequential segment patterning in the notochord. Together,
this work identifies a robust segmentation mechanism that
hinges upon mechanical coupling of adjacent tissues to
control patterning dynamics.},
Doi = {10.1101/2023.03.27.534101},
Key = {fds370445}
}
@article{fds374243,
Author = {Charbonneau, P and Morse, PK},
Title = {Jamming, relaxation, and memory in a minimally structured
glass former.},
Journal = {Physical review. E},
Volume = {108},
Number = {5-1},
Pages = {054102},
Year = {2023},
Month = {November},
url = {http://dx.doi.org/10.1103/physreve.108.054102},
Abstract = {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-field theory (DMFT) of glasses,
the numerical tools needed to solve the DMFT equations up
to the relevant physical regime do not yet exist. In this
context, numerical simulations of minimally structured (and
therefore mean-field-like) model glass formers can aid the
search for and understanding of such solutions, thanks to
their ability to disentangle structural from dimensional
effects. We study here the infinite-range Mari-Kurchan model
under simple out-of-equilibrium processes, and we compare
results with the random Lorentz gas [J. Phys. A 55, 334001
(2022)10.1088/1751-8121/ac7f06]. Because both models are
mean-field-like and formally equivalent in the limit of
infinite spatial dimensions, robust features are expected to
appear in the DMFT as well. The comparison provides insight
into temperature and density onsets, memory, as well as
anomalous relaxation. This work also further enriches the
algorithmic understanding of the jamming
density.},
Doi = {10.1103/physreve.108.054102},
Key = {fds374243}
}
@article{fds376237,
Author = {Bonnet, G and Charbonneau, P and Folena, G},
Title = {Glasslike caging with random planes.},
Journal = {Physical review. E},
Volume = {109},
Number = {2-1},
Pages = {024125},
Year = {2024},
Month = {February},
url = {http://dx.doi.org/10.1103/physreve.109.024125},
Abstract = {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 beneficial. Here we propose such a
real-space model that is amenable to infinite-dimensional
d→∞ analysis and is exactly solvable in finite d in some
regimes. By joining analysis with numerical simulations, we
uncover geometrical signatures of the dynamical and jamming
transitions and obtain insight into the origin of activated
processes. Translating these findings into the context of
standard glass formers further reveals the role played by
nonconvexity in the emergence of Gardner and jamming
physics.},
Doi = {10.1103/physreve.109.024125},
Key = {fds376237}
}
%% Papers Accepted
@article{fds226361,
Author = {Patrick Charbonneau and Eric I. Corwin and Giorgio Parisi and Francesco Zamponi},
Title = {Jamming Criticality Revealed by Removing
“Bucklers”},
Journal = {Physical Review Letters},
Year = {2015},
url = {http://arxiv.org/abs/1411.3975v1},
Abstract = {Recent theoretical advances offer an exact, first-principle
theory of jamming criticality in infinite dimension as well
as universal scaling relations between critical exponents in
all dimensions. For jammed packings of frictionless spheres,
these advances predict that power-law exponents characterize
the critical distribution of (i) small inter-particle gaps
and (ii) weak contact forces, both of which are crucial for
mechanical stability. The scaling of the inter-particle gaps
is known to be constant in all spatial dimensions d –
including the physically relevant d = 2 and 3, but the value
of the weak force exponent remains the object of debate and
confusion. Here, we resolve this ambiguity by numerical
simulations. We construct isostatic jammed packings with
extremely high accuracy, and introduce a simple criterion to
separate the contribution of particles that give rise to
localized excitations (the “bucklers”) from the others.
This analysis reveals the remarkable dimensional robustness
of mean-field marginality and its associated
criticality.},
Key = {fds226361}
}
%% Papers Submitted
@article{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}
}
%% Chapter in Book
@misc{fds363022,
Author = {Charbonneau, P and Altan, I and De Valicourt and J},
Title = {Sugars: Soft Caramel and Sucre à la Crème--an
Undergraduate Experiment about Sugar Crystallization},
Pages = {545-547},
Booktitle = {Handbook of Molecular Gastronomy: Scientific Foundations and
Culinary Applications},
Publisher = {CRC Press},
Editor = {Burke, RM and Kelly, AL and Lavelle, C and This vo Kientza,
H},
Year = {2021},
ISBN = {9781466594784},
Abstract = {A comprehensive reference to molecular gastronomy, this book
highlights techniques that have enabled chefs to achieve new
and better ways of preparing food.},
Key = {fds363022}
}
@misc{fds369677,
Author = {Charbonneau, P and Zhang, K},
Title = {ADVANCES IN THE MOLECULAR SIMULATION OF MICROPHASE
FORMERS},
Pages = {81-133},
Booktitle = {Reviews in Computational Chemistry: Volume
32},
Year = {2022},
Month = {January},
ISBN = {9781119625896},
url = {http://dx.doi.org/10.1002/9781119625933.ch3},
Abstract = {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 formers. The chapter focuses on the
phenomenological field theory description of the
universality of the microphase formation and of the nature
of the order-disorder transition. The chapter describes
molecular simulation methods that have been specifically
designed to achieve equilibrium in the periodic microphase
regime. It details the thermodynamic framework and a free
energy integration simulation method, followed by a concrete
introduction to the ghost particle/cluster switching method.
The chapter discusses several classical Monte Carlo
algorithms to enhance the efficiency of simulating
disordered microphases. It presents three models for which
quantitative results have been obtained: a one-dimensional,
a lattice, and an off-lattice microphase former. Fine-tuning
colloidal suspensions to allow the formation of periodic
microphases thus remains an open experimental
problem.},
Doi = {10.1002/9781119625933.ch3},
Key = {fds369677}
}