|
%% Papers Published
@booklet{Gollub80,
Author = {Gollub, JP and Romer, EJ and Socolar, JE},
Title = {Trajectory divergence for coupled relaxation oscillators:
Measurements and models},
Journal = {Journal of Statistical Physics},
Volume = {23},
Number = {3},
Pages = {321-333},
Publisher = {Springer Nature},
Year = {1980},
Month = {September},
ISSN = {0022-4715},
url = {http://dx.doi.org/10.1007/BF01011372},
Abstract = {The exponential divergence of nearby phase space
trajectories is a hallmark of nonperiodic (chaotic) behavior
in dynamical systems. We present the first laboratory of
measurements of divergence rates (or characteristic
exponents), using a system of coupled tunnel diode
relaxation oscillators. This property of sensitive
dependence on initial conditions is reliably associated with
broadband spectra, and both methods are used to characterize
the motion as a function of the coupling strength and
natural frequency ratio of the two oscillators. A simple
piecewise linear model correctly predicts the major periodic
and non-periodic regions of the parameter space, thus
confirming that the chaotic behavior involves only a few
degrees of freedom. © 1980 Plenum Publishing
Corporation.},
Doi = {10.1007/BF01011372},
Key = {Gollub80}
}
@article{fds248316,
Author = {Mele, EJ and Socolar, J},
Title = {Numerical integration of the time evolution operator:
Excited‐state dynamics in conjugated molecules},
Journal = {International Journal of Quantum Chemistry},
Volume = {26},
Series = {Quantum Chemistry Symposium},
Number = {18 S},
Pages = {347-358},
Publisher = {WILEY},
Year = {1984},
Month = {January},
ISSN = {0020-7608},
url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1984ACF7600031&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
Abstract = {Two simple and manageable schemes for integrating the time
evolution operator e−iHt are discussed and applied to
study vibronic effects in photoemission and optical
excitation of model conjugated molecules. Copyright © 1984
John Wiley & Sons, Inc.},
Doi = {10.1002/qua.560260832},
Key = {fds248316}
}
@article{fds248318,
Author = {Socolar, JE and Steinhardt, PJ and Levine, D},
Title = {Quasicrystals with arbitrary orientational
symmetry.},
Journal = {Physical review. B, Condensed matter},
Volume = {32},
Series = {Rapid Communication},
Number = {8},
Pages = {5547-5550},
Year = {1985},
Month = {October},
ISSN = {0163-1829},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9937798},
Doi = {10.1103/physrevb.32.5547},
Key = {fds248318}
}
@article{fds248356,
Author = {Socolar, JES and Steinhardt, PJ},
Title = {Quasicrystals II: Unit Cell Structures},
Journal = {Phys. Rev. B},
Volume = {34},
Pages = {617-647},
Year = {1986},
url = {http://dx.doi.org/10.1103/PhysRevB.34.617},
Doi = {10.1103/PhysRevB.34.617},
Key = {fds248356}
}
@article{fds248359,
Author = {Socolar, JES},
Title = {Phason Strain in Quasicrystals},
Journal = {Journal de Physique},
Volume = {C3},
Number = {C3},
Pages = {217-227},
Publisher = {E D P SCIENCES},
Year = {1986},
url = {http://dx.doi.org/10.1051/jphyscol:1986323},
Doi = {10.1051/jphyscol:1986323},
Key = {fds248359}
}
@article{fds248319,
Author = {Socolar, JE and Steinhardt, PJ},
Title = {Quasicrystals. II. Unit-cell configurations.},
Journal = {Physical review. B, Condensed matter},
Volume = {34},
Number = {2},
Pages = {617-647},
Year = {1986},
Month = {July},
ISSN = {0163-1829},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9939668},
Doi = {10.1103/physrevb.34.617},
Key = {fds248319}
}
@article{fds248357,
Author = {Socolar, JE and Lubensky, TC and Steinhardt, PJ},
Title = {Phonons, phasons, and dislocations in quasicrystals.},
Journal = {Physical review. B, Condensed matter},
Volume = {34},
Number = {5},
Pages = {3345-3360},
Year = {1986},
Month = {September},
ISSN = {0163-1829},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9940073},
Doi = {10.1103/physrevb.34.3345},
Key = {fds248357}
}
@article{fds248358,
Author = {Lubensky, TC and Socolar, JE and Steinhardt, PJ and Bancel, PA and Heiney, AP},
Title = {Distortion and peak broadening in quasicrystal diffraction
patterns.},
Journal = {Physical review letters},
Volume = {57},
Number = {12},
Pages = {1440-1443},
Year = {1986},
Month = {September},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10033450},
Doi = {10.1103/physrevlett.57.1440},
Key = {fds248358}
}
@article{fds248360,
Author = {Socolar, JE and Wright, DC},
Title = {Explanation of peak shapes observed in diffraction from
icosahedral quasicrystals.},
Journal = {Physical review letters},
Volume = {59},
Number = {2},
Pages = {221-224},
Year = {1987},
Month = {July},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10035483},
Doi = {10.1103/physrevlett.59.221},
Key = {fds248360}
}
@article{fds248361,
Author = {Onoda, GY and Steinhardt, PJ and DiVincenzo, DP and Socolar,
JE},
Title = {Growing perfect quasicrystals.},
Journal = {Physical review letters},
Volume = {60},
Number = {25},
Pages = {2653-2656},
Year = {1988},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10038414},
Doi = {10.1103/physrevlett.60.2653},
Key = {fds248361}
}
@article{fds248362,
Author = {Onoda, GY and Steinhardt, PJ and DiVincenzo, DP and Socolar,
JES},
Title = {Reply to Comment on PRL},
Journal = {Phys. Rev. Lett.},
Volume = {62},
Number = {10},
Pages = {1210},
Year = {1989},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10039608},
Doi = {10.1103/PhysRevLett.62.1210},
Key = {fds248362}
}
@article{fds37541,
Author = {J.E.S. Socolar},
Title = {Locality Constraints and 2D Quasicrystals},
Booktitle = {Quasicrystals - Adriatico Anniversary Research
Conference},
Publisher = {World Scientific, Singapore},
Editor = {M.V. Jaric and S. Lundqvist},
Year = {1989},
Key = {fds37541}
}
@article{fds303751,
Author = {Onoda, G and Steinhardt, PJ and DiVincenzo, D and Socolar,
JE},
Title = {Onoda etal. reply.},
Journal = {Physical review letters},
Volume = {62},
Number = {10},
Pages = {1210},
Year = {1989},
Month = {March},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10039608},
Doi = {10.1103/physrevlett.62.1210},
Key = {fds303751}
}
@article{fds248363,
Author = {Socolar, JE},
Title = {Simple octagonal and dodecagonal quasicrystals.},
Journal = {Physical review. B, Condensed matter},
Volume = {39},
Number = {15},
Pages = {10519-10551},
Year = {1989},
Month = {May},
ISSN = {0163-1829},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9947860},
Doi = {10.1103/physrevb.39.10519},
Key = {fds248363}
}
@article{fds353964,
Author = {Socolar, JES},
Title = {The Alternation Condition and 2D Quasicrystals},
Volume = {93},
Series = {Springer Series in Solid-State Sciences},
Pages = {101-111},
Booktitle = {Springer Series in Solid-State Sciences},
Publisher = {Springer Berlin Heidelberg},
Editor = {T. Fujiwara and T. Ogawa},
Year = {1990},
ISBN = {9783642842559},
url = {http://dx.doi.org/10.1007/978-3-642-84253-5_11},
Doi = {10.1007/978-3-642-84253-5_11},
Key = {fds353964}
}
@article{fds248364,
Author = {Socolar, JES},
Title = {Weak matching rules for quasicrystals},
Journal = {Communications in Mathematical Physics},
Volume = {129},
Number = {3},
Pages = {599-619},
Publisher = {Springer Nature},
Year = {1990},
Month = {May},
ISSN = {0010-3616},
url = {http://dx.doi.org/10.1007/BF02097107},
Abstract = {Weak matching rules for a quasicrystalline tiling are local
rules that ensure that fluctuations in "perp-space" are
uniformly bounded. It is shown here that weak matching rules
exist for N-fold symmetric tilings, where N is any integer
not divisible by four. The result suggests that, contrary to
previous indications, quasicrystalline ground states are not
confined to those symmetries for which the incommensurate
ratios of wavevectors are quadratic irrationals. An explicit
method of constructing weak matching rules for N-fold
symmetric tilings in two dimensions is presented. It is
shown that the generalization of the construction yields
weak matching rules in the case of icosahedral symmetry as
well. © 1990 Springer-Verlag.},
Doi = {10.1007/BF02097107},
Key = {fds248364}
}
@article{fds353963,
Author = {Socolar, JES},
Title = {Growth Rules For Quasicrystals},
Pages = {213-238},
Booktitle = {Series on Directions in Condensed Matter
Physics},
Publisher = {WORLD SCIENTIFIC},
Editor = {D. DiVincenzo and P. Steinhardt},
Year = {1991},
Month = {October},
ISBN = {9789810205225},
url = {http://dx.doi.org/10.1142/9789814503532_0008},
Doi = {10.1142/9789814503532_0008},
Key = {fds353963}
}
@article{fds248367,
Author = {Krug, J and Socolar, JES and Grinstein, G},
Title = {Surface Fluctuations and Criticality in a Class of 1D
Sandpile Models},
Journal = {Phys. Rev. A (RC)},
Volume = {46},
Number = {8},
Pages = {4479},
Year = {1992},
ISSN = {1050-2947},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9908766},
Key = {fds248367}
}
@article{fds248366,
Author = {Krug, J and Socolar, JE},
Title = {Comment on "Scalings of growing self-organized
surfaces"},
Journal = {Physical review letters},
Volume = {68},
Number = {5},
Pages = {722},
Year = {1992},
Month = {February},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10045973},
Doi = {10.1103/physrevlett.68.722},
Key = {fds248366}
}
@article{fds248365,
Author = {Socolar, JES},
Title = {Theory of Packings of Identical Hard Disks Generated by
Ballistic Deposition},
Journal = {Europhysics Letters (EPL)},
Volume = {18},
Number = {1},
Pages = {39-44},
Publisher = {IOP Publishing},
Year = {1992},
Month = {February},
url = {http://dx.doi.org/10.1209/0295-5075/18/1/008},
Abstract = {Recent simulations of the deposition of hard disks in a box
according to a rule in which each added disk seeks a
gravitationally stable position yielded several surprising
results. The packings exhibit an asymptotic approach to a
topologically ordered state at large heights, a rapid decay
of topological defects with height, and nontrivial
periodicities induced by periodic or hard-wall boundary
conditions. It is shown here that much of the observed
phenomenology can be understood via simple analysis of local
configurations of disks. It is also demonstrated that
deposition of identical disks onto an initially bare, flat
floor does not result in a close-packed crystalline
structure in the large system limit. © 1992 IOP Publishing
Ltd.},
Doi = {10.1209/0295-5075/18/1/008},
Key = {fds248365}
}
@article{fds303752,
Author = {Krug, J and Socolar, JE and Grinstein, G},
Title = {Surface fluctuations and criticality in a class of
one-dimensional sandpile models.},
Journal = {Physical review. A, Atomic, molecular, and optical
physics},
Volume = {46},
Number = {8},
Pages = {R4479-R4482},
Year = {1992},
Month = {October},
ISSN = {1050-2947},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9908766},
Doi = {10.1103/physreva.46.r4479},
Key = {fds303752}
}
@article{fds248368,
Author = {SOCOLAR, JES and GRINSTEIN, G and JAYAPRAKASH,
C},
Title = {ON SELF-ORGANIZED CRITICALITY IN NONCONSERVING
SYSTEMS},
Journal = {PHYSICAL REVIEW E},
Volume = {47},
Number = {4},
Pages = {2366-2376},
Publisher = {AMERICAN PHYSICAL SOC},
Year = {1993},
Month = {April},
ISSN = {1063-651X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9960267},
Doi = {10.1103/PhysRevE.47.2366},
Key = {fds248368}
}
@article{fds248369,
Author = {Grinstein, G and Jayaprakash, C and Socolar, JE},
Title = {Scale invariance of nonconserved quantities in driven
systems.},
Journal = {Physical review. E, Statistical physics, plasmas, fluids,
and related interdisciplinary topics},
Volume = {48},
Number = {2},
Pages = {R643-R646},
Year = {1993},
Month = {August},
ISSN = {1063-651X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9960763},
Doi = {10.1103/physreve.48.r643},
Key = {fds248369}
}
@article{fds248371,
Author = {SOCOLAR, JES},
Title = {[title field missing]},
Journal = {Phys. Rev. E},
Volume = {50},
Number = {4},
Pages = {3245-3248},
Year = {1994},
ISSN = {1063-651X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9962372},
Doi = {10.1103/PhysRevE.50.3245},
Key = {fds248371}
}
@article{fds248370,
Author = {Gauthier, DJ and Sukow, DW and Concannon, HM and Socolar,
JE},
Title = {Stabilizing unstable periodic orbits in a fast diode
resonator using continuous time-delay autosynchronization.},
Journal = {Physical review. E, Statistical physics, plasmas, fluids,
and related interdisciplinary topics},
Volume = {50},
Number = {3},
Pages = {2343-2346},
Year = {1994},
Month = {September},
ISSN = {1063-651X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9962244},
Doi = {10.1103/physreve.50.2343},
Key = {fds248370}
}
@article{fds248372,
Author = {Bleich, ME and Socolar, JES},
Title = {Stability of periodic orbits controlled by time-delay
feedback},
Journal = {Physics Letters, Section A: General, Atomic and Solid State
Physics},
Volume = {210},
Number = {1-2},
Pages = {87-94},
Publisher = {Elsevier BV},
Year = {1996},
Month = {January},
url = {http://dx.doi.org/10.1016/0375-9601(95)00827-6},
Abstract = {Extended time-delay auto-synchronization (ETDAS) is a
promising technique for stabilizing unstable periodic orbits
in low-dimensional dynamical systems. The technique involves
continuous feedback of signals delayed by multiples of the
orbit's period in a manner that is especially well-suited
for fast systems and optical implementation. We show how to
analyze the stability of a given implementation of ETDAS
without explicit integration of time-delay equations. To
illustrate the method and point out some nontrivial features
of ETDAS, we obtain the domain of control for a period-one
orbit of the driven, damped pendulum.},
Doi = {10.1016/0375-9601(95)00827-6},
Key = {fds248372}
}
@article{fds248373,
Author = {Bleich, ME and Socolar, JES},
Title = {Controlling spatiotemporal dynamics with time-delay
feedback},
Journal = {Physical Review E},
Volume = {54},
Number = {1},
Pages = {R17-R20},
Publisher = {American Physical Society (APS)},
Year = {1996},
Month = {July},
ISSN = {1063-651X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/9965164},
Doi = {10.1103/physreve.54.r17},
Key = {fds248373}
}
@article{fds248387,
Author = {Gauthier, DJ and Socolar, JES},
Title = {Comment on Dynamic Control of Cardiac Alternans},
Journal = {Physical Review Letters},
Volume = {79},
Number = {24},
Pages = {4938},
Publisher = {American Physical Society (APS)},
Year = {1997},
url = {http://dx.doi.org/10.1103/PhysRevLett.79.4938},
Abstract = {A Comment on the Letter by Keven Hall, et al., Phys. Rev.
Lett. 78, 4518 (1997). © 1997 The American Physical
Society.},
Doi = {10.1103/PhysRevLett.79.4938},
Key = {fds248387}
}
@article{fds248375,
Author = {Bleich, ME and Hochheiser, D and Moloney, JV and Socolar,
JES},
Title = {Controlling extended systems with spatially filtered,
time-delayed feedback},
Journal = {Physical Review E - Statistical Physics, Plasmas, Fluids,
and Related Interdisciplinary Topics},
Volume = {55},
Number = {3},
Pages = {2119-2126},
Publisher = {American Physical Society (APS)},
Year = {1997},
Month = {January},
url = {http://dx.doi.org/10.1103/PhysRevE.55.2119},
Abstract = {We investigate a control technique for spatially extended
systems combining spatial filtering with a previously
studied form of time-delay feedback. The scheme is naturally
suited to real-time control of optical systems. We apply the
control scheme to a model of a transversely extended
semiconductor laser in which a desirable, coherent
traveling-wave state exists, but is a member of a nowhere
stable family. Our scheme stabilizes this state and directs
the system towards it from realistic, distant, and noisy
initial conditions. As confirmed by numerical simulation, a
linear stability analysis about the controlled state
accurately predicts when the scheme is successful and
illustrates some key features of the control including the
individual merit of, and interplay between, the spatial and
temporal degrees of freedom in the control. © 1997 The
American Physical Society.},
Doi = {10.1103/PhysRevE.55.2119},
Key = {fds248375}
}
@article{fds248374,
Author = {Sukow, DW and Bleich, ME and Gauthier, DJ and Socolar,
JES},
Title = {Controlling chaos in a fast diode resonator using extended
time-delay autosynchronization: Experimental observations
and theoretical analysis.},
Journal = {Chaos (Woodbury, N.Y.)},
Volume = {7},
Number = {4},
Pages = {560-576},
Year = {1997},
Month = {December},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12779682},
Abstract = {We stabilize unstable periodic orbits of a fast diode
resonator driven at 10.1 MHz (corresponding to a drive
period under 100 ns) using extended time-delay
autosynchronization. Stabilization is achieved by feedback
of an error signal that is proportional to the difference
between the value of a state variable and an infinite series
of values of the state variable delayed in time by integral
multiples of the period of the orbit. The technique is easy
to implement electronically and it has an all-optical
counterpart that may be useful for stabilizing the dynamics
of fast chaotic lasers. We show that increasing the weights
given to temporally distant states enlarges the domain of
control and reduces the sensitivity of the domain of control
on the propagation delays in the feedback loop. We determine
the average time to obtain control as a function of the
feedback gain and identify the mechanisms that destabilize
the system at the boundaries of the domain of control. A
theoretical stability analysis of a model of the diode
resonator in the presence of time-delay feedback is in good
agreement with the experimental results for the size and
shape of the domain of control. (c) 1997 American Institute
of Physics.},
Doi = {10.1063/1.166256},
Key = {fds248374}
}
@article{fds248379,
Author = {Egolf, DA and Socolar, JES},
Title = {Failure of linear control in noisy coupled map
lattices},
Journal = {Physical Review E - Statistical Physics, Plasmas, Fluids,
and Related Interdisciplinary Topics},
Volume = {57},
Number = {5},
Pages = {5271-5275},
Publisher = {American Physical Society (APS)},
Year = {1998},
Month = {January},
url = {http://dx.doi.org/10.1103/PhysRevE.57.5271},
Abstract = {We study a one-dimensional ring of diffusively coupled
logistic maps in the vicinity of an unstable, spatially
homogeneous fixed point. The failure of linear controllers
due to additive noise is discussed with the aim of
clarifying the failure mechanism. A criterion is suggested
for estimating the noise level that can be tolerated by the
given controller. The criterion implies the loss of control
for surprisingly low noise levels in certain cases of
interest, and accurately accounts for the results of
numerical experiments over a broad range of parameter
values. Previous results of Grigoriev et al. [Phys. Rev.
Lett. 79, 2795 (1997)] are reviewed and compared with our
numerical and analytic results.© 1998 The American Physical
Society.},
Doi = {10.1103/PhysRevE.57.5271},
Key = {fds248379}
}
@article{fds248380,
Author = {Socolar, JES and Gauthier, DJ},
Title = {Analysis and comparison of multiple-delay schemes for
controlling unstable fixed points of discrete
maps},
Journal = {Physical Review E - Statistical Physics, Plasmas, Fluids,
and Related Interdisciplinary Topics},
Volume = {57},
Number = {6},
Pages = {6589-6595},
Publisher = {American Physical Society (APS)},
Year = {1998},
Month = {January},
url = {http://dx.doi.org/10.1103/PhysRevE.57.6589},
Abstract = {We investigate theoretically the stabilization of a fixed
point of a discrete one-dimensional nonlinear map by
applying small perturbations to an accessible system
parameter or variable. The size of the perturbations is
determined in real time using feedback schemes incorporating
only the dynamical state of the system and its state at
previous iterates without making a comparison to a reference
state. In particular, we compare and contrast two
algorithms: extended time-delay autosynchronization, which
uses an infinite series of past iterates with weights that
decay by a factor of [formula presented] with each time
step, and [formula presented]-time-delay
autosynchronization, which uses an average of [formula
presented] past iterates with equal weights. The range of
feedback parameters that successfully stabilize the fixed
point and the robustness of the schemes to noise are
determined. It is found that the domain of control for the
two schemes is similar for appropriately matched values of
[formula presented] and [formula presented], and that
[formula presented]-time-delay autosynchronization tends to
be less sensitive to noise. © 1998 The American Physical
Society.},
Doi = {10.1103/PhysRevE.57.6589},
Key = {fds248380}
}
@article{fds303753,
Author = {Socolar, JES},
Title = {Average stresses and force fluctuations in noncohesive
granular materials},
Journal = {PHYSICAL REVIEW E},
Volume = {57},
Number = {3},
Pages = {3204-3215},
Publisher = {AMERICAN PHYSICAL SOC},
Year = {1998},
Month = {March},
url = {http://arxiv.org/abs/cond-mat/9710089v1},
Abstract = {A lattice model is presented for investigating the
fluctuations in static granular materials under
gravitationally induced stress. The model is similar in
spirit to the scalar [formula presented] modelof Coppersmith
et al. [Phys. Rev. E 53, 4673 (1996)], but ensures balance
of all components of forces and torques at each site. The
geometric randomness in real granular materials is modeled
by choosing random variables at each site, consistent with
the assumption of cohesionless grains. Configurations of the
model can be generated rapidly, allowing the statistical
study of relatively large systems. For a two-dimensional
(2D) system with rough walls, the model generates
configurations consistent with continuum theories for the
average stresses (unlike the [formula presented] model)
without requiring the assumption of a constitutive relation.
For a 2D system with periodic boundary conditions, the model
generates single-grain force distributions similar to those
obtained from the [formula presented] modelwith a singular
distribution of [formula presented]’s. © 1998 The
American Physical Society.},
Doi = {10.1103/PhysRevE.57.3204},
Key = {fds303753}
}
@article{fds248381,
Author = {Sexton, MG and Socolar, JE and Schaeffer, DG},
Title = {Force distribution in a scalar model for noncohesive
granular material.},
Journal = {Physical review. E, Statistical physics, plasmas, fluids,
and related interdisciplinary topics},
Volume = {60},
Number = {2 Pt B},
Pages = {1999-2008},
Year = {1999},
Month = {August},
ISSN = {1063-651X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11969992},
Abstract = {We study a scalar lattice model for intergrain forces in
static, noncohesive, granular materials, obtaining two
primary results: (i) The applied stress as a function of
overall strain shows a power law dependence with a
nontrivial exponent, which moreover varies with system
geometry; and (ii) probability distributions for forces on
individual grains appear Gaussian at all stages of
compression, showing no evidence of exponential tails. With
regard to both results, we identify correlations responsible
for deviations from previously suggested
theories.},
Doi = {10.1103/physreve.60.1999},
Key = {fds248381}
}
@article{fds248388,
Author = {Richards, SA and Wilson, WG and Socolar, JE},
Title = {Selection for intermediate mortality and reproduction rates
in a spatially structured population.},
Journal = {Proceedings. Biological sciences},
Volume = {266},
Number = {1436},
Pages = {2383-2388},
Year = {1999},
Month = {December},
ISSN = {0962-8452},
url = {http://www.ncbi.nlm.nih.gov/pubmed/10643082},
Abstract = {How local interactions influence both population and
evolutionary dynamics is currently a key topic in
theoretical ecology. We use a 'well-mixed' analytical model
and spatially explicit individual-based models to
investigate a system where a population is subject to rare
disturbance events. The disturbance can only propagate
through regions of the population where the density of
individuals is sufficiently high and individuals affected by
the disturbance die shortly after. We find that populations
where individuals are sessile often exhibit very different
dynamic behaviour when compared to populations where
individuals are mobile and spatially well mixed. When
mutations are allowed which affect either offspring birth
rates or mortality rates, the well-mixed populations always
evolve to a state where a single disturbance event leads to
extinction. Populations often persist substantially longer
if individuals are sessile and they disperse their offspring
locally. We also find that for sessile populations selection
may favour short-lived individuals with limited offspring
production. Population dynamics are found to be strongly
influenced by the host characters that are evolving and the
rate at which host variation is introduced into the
system.},
Doi = {10.1098/rspb.1999.0935},
Key = {fds248388}
}
@article{fds248382,
Author = {Bleich, ME and Socolar, JES},
Title = {Delayed feedback control of a paced excitable
oscillator},
Journal = {International Journal of Bifurcation and Chaos in Applied
Sciences and Engineering},
Volume = {10},
Number = {3},
Pages = {603-609},
Publisher = {World Scientific Pub Co Pte Lt},
Year = {2000},
Month = {January},
url = {http://dx.doi.org/10.1142/S0218127400000414},
Abstract = {A simple numerical experiment on Fitzhugh-Nagumo equations
demonstrates that time-delay feedback methods can stabilize
regular behavior in a paced, excitable oscillator without
using large applied pulses. The method is robust against
slow variations in the pacing rate and can be used to track
an orbit into a parameter regime where it is unstable.
Moreover, the method requires no information about the
desired orbit other than period, which is determined
directly by the observation of the pacing signal. Results
are presented for feedback stabilization of a nonspiking
orbit in the rapid pacing regime.},
Doi = {10.1142/S0218127400000414},
Key = {fds248382}
}
@article{fds3758,
Author = {J.E.S Socolar},
Title = {Chaos},
Series = {3rd Edition},
Booktitle = {Encyclopedia of Physical Science and Technology},
Publisher = {Academic Press},
Editor = {R. Meyers},
Year = {2001},
Key = {fds3758}
}
@article{fds248322,
Author = {Socolar, JE and Richards, S and Wilson, WG},
Title = {Evolution in a spatially structured population subject to
rare epidemics.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {63},
Number = {4 Pt 1},
Pages = {041908},
Year = {2001},
Month = {April},
url = {http://dx.doi.org/10.1103/physreve.63.041908},
Abstract = {We study a model that gives rise to spatially inhomogeneous
population densities in a system of host individuals subject
to rare, randomly distributed disease events. For stationary
hosts that disperse offspring over short distances,
evolutionary dynamics can lead to persistent populations
with a variety of spatial structures. A mean-field analysis
is shown to account for the behavior observed in simulations
of a one-dimensional system, where the evolutionarily stable
state corresponds to the solution of a straightforward
optimization problem. In two dimensions, evolution drives
the system to a stable critical state that is less well
understood.},
Doi = {10.1103/physreve.63.041908},
Key = {fds248322}
}
@article{fds248383,
Author = {Harrington, I and Socolar, JE},
Title = {Limitation on stabilizing plane waves via time-delay
feedback.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {64},
Number = {5 Pt 2},
Pages = {056206},
Year = {2001},
Month = {November},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/11736053},
Abstract = {Previous work has demonstrated the possibility of
stabilizing plane wave solutions of one-dimensional systems
using a spatially local form of time-delayed feedback. We
show that the natural extension of this method to
two-dimensional systems fails due to the presence of
torsion-free unstable perturbations. Linear stability
analysis of the complex Ginzburg-Landau equation reveals
that long wavelength, transverse wave instabilities cannot
be suppressed by the method of extended time-delay
autosynchronization. The conclusion follows from symmetry
considerations and therefore applies to a wide class of
models with simple plane wave solutions.},
Doi = {10.1103/physreve.64.056206},
Key = {fds248383}
}
@article{fds248323,
Author = {Socolar, JES and Schaeffer, DG and Claudin, P},
Title = {Erratum: Directed force chain networks and stress response
in static granular materials (The European Physical Journal
E (2002) 7 (353-370))},
Journal = {European Physical Journal E},
Volume = {8},
Number = {4},
Pages = {453},
Year = {2002},
Month = {January},
url = {http://dx.doi.org/10.1140/epje/i2002-10030-4},
Doi = {10.1140/epje/i2002-10030-4},
Key = {fds248323}
}
@article{fds248389,
Author = {Socolar, JES and Schaeffer, DG and Claudin, P},
Title = {Directed force chain networks and stress response in static
granular materials.},
Journal = {The European physical journal. E, Soft matter},
Volume = {7},
Number = {4},
Pages = {353-370},
Year = {2002},
Month = {April},
url = {http://xxx.lanl.gov/abs/cond-mat/0201242},
Abstract = {A theory of stress fields in two-dimensional granular
materials based on directed force chain networks is
presented. A general Boltzmann equation for the densities of
force chains in different directions is proposed and a
complete solution is obtained for a special case in which
chains lie along a discrete set of directions. The analysis
and results demonstrate the necessity of including nonlinear
terms in the Boltzmann equation. A line of nontrivial
fixed-point solutions is shown to govern the properties of
large systems. In the vicinity of a generic fixed point, the
response to a localized load shows a crossover from a
single, centered peak at intermediate depths to two
propagating peaks at large depths that broaden
diffusively.},
Doi = {10.1140/epje/i2002-10011-7},
Key = {fds248389}
}
@article{fds344682,
Author = {Beck, O and Amann, A and Schöll, E and Socolar, JES and Just,
W},
Title = {Comparison of time-delayed feedback schemes for
spatiotemporal control of chaos in a reaction-diffusion
system with global coupling.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {66},
Number = {1 Pt 2},
Pages = {016213},
Year = {2002},
Month = {July},
url = {http://dx.doi.org/10.1103/physreve.66.016213},
Abstract = {Time-delayed feedback control for stabilizing time periodic
spatial patterns is investigated in a generic
reaction-diffusion system with global coupling. We focus on
the case of low-dimensional chaos where unstable patterns
admit only a single unstable mode. Spatial degrees of
freedom are taken into account to define different control
schemes. The efficiency of these schemes is discussed, where
control forces are motivated by physical requirements as
well as by the possibility of obtaining analytically exact
results. We find that control schemes that contain the full
feedback of the inhibitor variable may finally destroy the
control performance. Thus schemes that omit the inhibitor
might be more efficient. Our numerical findings are
explained in terms of Floquet spectra and compared with
analytical solutions of particular coupling
schemes.},
Doi = {10.1103/physreve.66.016213},
Key = {fds344682}
}
@article{fds248384,
Author = {Beck, O and Amann, A and Schoell, E and Socolar, JES},
Title = {`Comparison of time-delayed feedback schemes for
spatio-temporal control of chaos},
Journal = {Phys. Rev. E},
Volume = {66},
Number = {1},
Pages = {016213},
Year = {2002},
Month = {December},
ISSN = {1539-3755},
url = {http://dx.doi.org/10.1103/PhysRevE.66.016213},
Abstract = {Time-delayed feedback control for stabilizing time periodic
spatial patterns is investigated in a generic
reaction-diffusion system with global coupling. We focus on
the case of low-dimensional chaos where unstable patterns
admit only a single unstable mode. Spatial degrees of
freedom are taken into account to define different control
schemes. The efficiency of these schemes is discussed, where
control forces are motivated by physical requirements as
well as by the possibility of obtaining analytically exact
results. We find that control schemes that contain the full
feedback of the inhibitor variable may finally destroy the
control performance. Thus schemes that omit the inhibitor
might be more efficient. Our numerical findings are
explained in terms of Floquet spectra and compared with
analytical solutions of particular coupling schemes. ©
2002 The American Physical Society.},
Doi = {10.1103/PhysRevE.66.016213},
Key = {fds248384}
}
@article{fds318470,
Author = {Hövel, P and Socolar, JES},
Title = {Stability domains for time-delay feedback control with
latency},
Journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {68},
Number = {3 2},
Pages = {362061-362067},
Year = {2003},
Abstract = {The stability of periodic orbits controlled by time-delay
feedback methods with latency was determined. Floquet theory
and first order theory were used to derive nonlinear shapes
from parametrized plane. It was found that Floquet modes,
that contributed significantly to the overall stability
picture, reduced the domain control substantially.},
Key = {fds318470}
}
@article{fds248326,
Author = {Otto, M and Bouchaud, JP and Claudin, P and Socolar,
JES},
Title = {Anisotropy in granular media: Classical elasticity and
directed-force chain network},
Journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {67},
Number = {3 1},
Pages = {031302/1-031302/24},
Year = {2003},
ISSN = {1063-651X},
url = {http://arxiv.org/abs/cond-mat/0211015v2},
Abstract = {A general framework that covers both classical anisotropic
elasticity theory and a generally anisotropic
"pseudoelasticity" theory, that appears within a linearized
treatment of directed-force chain networks is presented. It
is shown how the formalism applies to the example of a
triangular ball-and-spring network, indicating how spring
stiffnesses must be chosen to access all possible regions of
the general parameter space.},
Doi = {10.1103/PhysRevE.67.031302},
Key = {fds248326}
}
@article{fds353962,
Author = {Socolar, J},
Title = {Chaos},
Pages = {637-665},
Booktitle = {Encyclopedia of Physical Science and Technology},
Publisher = {Elsevier},
Year = {2003},
ISBN = {9780122274107},
url = {http://dx.doi.org/10.1016/b0-12-227410-5/00094-6},
Doi = {10.1016/b0-12-227410-5/00094-6},
Key = {fds353962}
}
@article{fds248385,
Author = {Socolar, JES},
Title = {Discrete models of force chain networks},
Journal = {Discrete and Continuous Dynamical Systems - Series
B},
Volume = {3},
Number = {4},
Pages = {601-618},
Publisher = {American Institute of Mathematical Sciences
(AIMS)},
Year = {2003},
Month = {January},
ISSN = {1531-3492},
url = {http://xxx.lanl.gov/abs/cond-mat/0212162},
Abstract = {A fundamental property of any material is its response to a
localized stress applied at a boundary. For granular
materials consisting of hard, cohesionless particles, not
even the general form of the stress response is known.
Directed force chain networks (DFCNs) provide a theoretical
frame-work for addressing this issue, and analysis of
simplified DFCN models reveal both rich mathematical
structure and surprising properties. We review some basic
elements of DFCN models and present a class of homogeneous
solutions for cases in which force chains are restricted to
lie on a discrete set of directions.},
Doi = {10.3934/dcdsb.2003.3.601},
Key = {fds248385}
}
@article{fds248386,
Author = {Socolar, JES and Kauffman, SA},
Title = {Scaling in ordered and critical random boolean
networks.},
Journal = {Physical review letters},
Volume = {90},
Number = {6},
Pages = {068702},
Year = {2003},
Month = {February},
ISSN = {0031-9007},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12633339},
Abstract = {Random Boolean networks, originally invented as models of
genetic regulatory networks, are simple models for a broad
class of complex systems that show rich dynamical
structures. From a biological perspective, the most
interesting networks lie at or near a critical point in
parameter space that divides "ordered" from "chaotic"
attractor dynamics. We study the scaling of the average
number of dynamically relevant nodes and the median number
of distinct attractors in such networks. Our calculations
indicate that the correct asymptotic scalings emerge only
for very large systems.},
Doi = {10.1103/physrevlett.90.068702},
Key = {fds248386}
}
@article{fds303750,
Author = {Otto, M and Bouchaud, J-P and Claudin, P and Socolar,
JES},
Title = {Anisotropy in granular media: classical elasticity and
directed-force chain network.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {67},
Number = {3 Pt 1},
Pages = {031302},
Year = {2003},
Month = {March},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/12689059},
Abstract = {A general approach is presented for understanding the stress
response function in anisotropic granular layers in two
dimensions. The formalism accommodates both classical
anisotropic elasticity theory and linear theories of
anisotropic directed-force chain networks. Perhaps
surprisingly, two-peak response functions can occur even for
classical, anisotropic elastic materials, such as triangular
networks of springs with different stiffnesses. In such
cases, the peak widths grow linearly with the height of the
layer, contrary to the diffusive spreading found in
"stress-only" hyperbolic models. In principle,
directed-force chain networks can exhibit the two-peak,
diffusively spreading response function of hyperbolic
models, but all models in a particular class studied here
are found to be in the elliptic regime.},
Doi = {10.1103/physreve.67.031302},
Key = {fds303750}
}
@article{fds248378,
Author = {Hövel, P and Socolar, JES},
Title = {Stability domains for time-delay feedback control with
latency.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {68},
Number = {3 Pt 2},
Pages = {036206},
Year = {2003},
Month = {September},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/14524867},
Abstract = {We generalize a known analytical method for determining the
stability of periodic orbits controlled by time-delay
feedback methods when latencies associated with the
generation and injection of the feedback signal cannot be
ignored. We discuss the case of extended time-delay
autosynchronization and show that nontrivial qualitative
features of the domain of control observed in experiments
can be explained by taking into account the effects of both
the unstable eigenmode and a single stable eigenmode in the
Floquet theory.},
Doi = {10.1103/physreve.68.036206},
Key = {fds248378}
}
@article{fds304615,
Author = {Harrington, I and Socolar, JES},
Title = {Design and robustness of delayed feedback controllers for
discrete systems.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {69},
Number = {5 Pt 2},
Pages = {056207},
Year = {2004},
Month = {May},
ISSN = {1539-3755},
url = {http://dx.doi.org/10.1103/physreve.69.056207},
Abstract = {We study a matrix form of time-delay feedback control in the
context of discrete time maps of high dimension. In almost
all cases where standard proportional feedback control
methods can achieve control, time-delay feedback controllers
containing only static elements can be designed to achieve
identical linear stability properties. Analysis of an
example involving a ring of coupled maps that can be
controlled at only two sites demonstrates that the
time-delay controller equivalent to a standard optimal
controller can be equally robust in the presence of noise,
except at special points in parameter space where the
uncontrolled system has a mode with Floquet multiplier
exactly equal to 1. Numerical simulations confirm the
results of the analysis.},
Doi = {10.1103/physreve.69.056207},
Key = {fds304615}
}
@article{fds248354,
Author = {Dealy, S and Kauffman, S and Socolar, J},
Title = {Modeling pathways of differentiation in genetic regulatory
networks with Boolean networks},
Journal = {Complexity},
Volume = {11},
Number = {1},
Pages = {52-60},
Publisher = {WILEY},
Year = {2005},
Month = {January},
ISSN = {1076-2787},
url = {http://dx.doi.org/10.1002/cplx.20100},
Abstract = {We have carried out the first examination of pathways of
cell differentiation in model genetic networks in which cell
types are assumed to be attractors of the nonlinear
dynamics, and differentiation corresponds to a transition of
the cell to a new basin of attraction, which may be induced
by a signal or noise perturbation. The associated flow along
a transient to a new attractor corresponds to a pathway of
differentiation. We have measured a variety of features of
such model pathways of differentiation, most of which should
be observable using gene array techniques. © 2005 Wiley
Periodicals, Inc.},
Doi = {10.1002/cplx.20100},
Key = {fds248354}
}
@article{fds248355,
Author = {Tighe, BP and Socolar, JES and Schaeffer, DG and Mitchener, WG and Huber, ML},
Title = {Force distributions in a triangular lattice of rigid
bars.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {72},
Number = {3 Pt 1},
Pages = {031306},
Year = {2005},
Month = {September},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16241425},
Abstract = {We study the uniformly weighted ensemble of force balanced
configurations on a triangular network of nontensile contact
forces. For periodic boundary conditions corresponding to
isotropic compressive stress, we find that the probability
distribution for single-contact forces decays faster than
exponentially. This superexponential decay persists in
lattices diluted to the rigidity percolation threshold. On
the other hand, for anisotropic imposed stresses, a broader
tail emerges in the force distribution, becoming a pure
exponential in the limit of infinite lattice size and
infinitely strong anisotropy.},
Doi = {10.1103/physreve.72.031306},
Key = {fds248355}
}
@inbook{fds26115,
Author = {J.E.S. Socolar},
Title = {Nonlinear Dynamical Systems},
Booktitle = {Complex Systems Science and Biomedicine},
Publisher = {Kluwer},
Editor = {Deisboeck and Kresh},
Year = {2006},
Month = {February},
Key = {fds26115}
}
@article{fds248352,
Author = {Foster, DV and Kauffman, SA and Socolar, JES},
Title = {Network growth models and genetic regulatory
networks.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {73},
Number = {3 Pt 1},
Pages = {031912},
Year = {2006},
Month = {March},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/16605563},
Abstract = {We study a class of growth algorithms for directed graphs
that are candidate models for the evolution of genetic
regulatory networks. The algorithms involve partial
duplication of nodes and their links, together with the
innovation of new links, allowing for the possibility that
input and output links from a newly created node may have
different probabilities of survival. We find some
counterintuitive trends as the parameters are varied,
including the broadening of the in-degree distribution when
the probability for retaining input links is decreased. We
also find that both the scaling of transcription factors
with genome size and the measured degree distributions for
genes in yeast can be reproduced by the growth algorithm if
and only if a special seed is used to initiate the
process.},
Doi = {10.1103/physreve.73.031912},
Key = {fds248352}
}
@article{fds248353,
Author = {Samuelsson, B and Socolar, JES},
Title = {Exhaustive percolation on random networks.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {74},
Number = {3 Pt 2},
Pages = {036113},
Publisher = {American Physical Society (APS)},
Year = {2006},
Month = {September},
ISSN = {1539-3755},
url = {http://link.aps.org/abstract/PRE/v74/e036113},
Abstract = {We consider propagation models that describe the spreading
of an attribute, called "damage," through the nodes of a
random network. In some systems, the average fraction of
nodes that remain undamaged vanishes in the large system
limit, a phenomenon we refer to as exhaustive percolation.
We derive scaling law exponents and exact results for the
distribution of the number of undamaged nodes, valid for a
broad class of random networks at the exhaustive percolation
transition and in the exhaustive percolation regime. This
class includes processes that determine the set of frozen
nodes in random Boolean networks with in-degree
distributions that decay sufficiently rapidly with the
number of inputs. Connections between our calculational
methods and previous studies of percolation beginning from a
single initial node are also pointed out. Central to our
approach is the observation that key aspects of damage
spreading on a random network are fully characterized by a
single function, specifying the probability that a given
node will be damaged as a function of the fraction of
damaged nodes. In addition to our analytical investigations
of random networks, we present a numerical example of
exhaustive percolation on a directed lattice.},
Doi = {10.1103/physreve.74.036113},
Key = {fds248353}
}
@article{fds248350,
Author = {Socolar, JES},
Title = {The hexagonal parquet tiling k-isohedral monotiles with
arbitrarily large k},
Journal = {Mathematical Intelligencer},
Volume = {29},
Number = {2},
Pages = {33-38},
Publisher = {Springer Nature},
Year = {2007},
Month = {March},
ISSN = {0343-6993},
url = {http://www.phy.duke.edu/~socolar/hexparquet.pdf},
Abstract = {The interplay between local constraints and global structure
of mathematical and physical systems is both subtle and
important. This paper shows how to construct a single tile
that can fill the Euclidean plane only with a tiling that
contains k distinct isohedral sets of tiles, where k can be
made arbitrarily large. It is shown that the construction
cannot work for a simply connected 2D tile with matching
rules for adjacent tiles enforced by shape alone. It is also
shown that any of the following modifications allows the
construction to work: (1) coloring the edges of the tiling
and imposing rules on which colors can touch; (2) allowing
the tile to be multiply connected; (3) requiring maximum
density rather than space-filling; (4) allowing the tile to
have a thickness in the third dimension.},
Doi = {10.1007/BF02986203},
Key = {fds248350}
}
@article{fds248348,
Author = {Shreim, A and Grassberger, P and Nadler, W and Samuelsson, B and Socolar, JES and Paczuski, M},
Title = {Network analysis of the state space of discrete dynamical
systems.},
Journal = {Physical review letters},
Volume = {98},
Number = {19},
Pages = {198701},
Year = {2007},
Month = {May},
ISSN = {0031-9007},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17677672},
Abstract = {We study networks representing the dynamics of elementary 1D
cellular automata (CA) on finite lattices. We analyze
scaling behaviors of both local and global network
properties as a function of system size. The scaling of the
largest node in-degree is obtained analytically for a
variety of CA including rules 22, 54, and 110. We further
define the path diversity as a global network measure. The
coappearance of nontrivial scaling in both the hub size and
the path diversity separates simple dynamics from the more
complex behaviors typically found in Wolfram's class IV and
some class III CA.},
Doi = {10.1103/physrevlett.98.198701},
Key = {fds248348}
}
@article{fds248328,
Author = {Socolar, JES},
Title = {Erratum: The hexagonal parquet tiling, k-isohedral monotiles
with arbitrarily large k (The Mathematical Intelligencer
29:2 (33-38))},
Journal = {Mathematical Intelligencer},
Volume = {29},
Number = {4},
Pages = {6},
Publisher = {Springer Nature},
Year = {2007},
Month = {September},
ISSN = {0343-6993},
url = {http://dx.doi.org/10.1007/BF02986167},
Doi = {10.1007/BF02986167},
Key = {fds248328}
}
@article{fds248349,
Author = {Norrell, J and Samuelsson, B and Socolar, JES},
Title = {Attractors in continuous and Boolean networks.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {76},
Number = {4 Pt 2},
Pages = {046122},
Year = {2007},
Month = {October},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17995075},
Abstract = {We study the stable attractors of a class of continuous
dynamical systems that may be idealized as networks of
Boolean elements, with the goal of determining which Boolean
attractors, if any, are good approximations of the
attractors of generic continuous systems. We investigate the
dynamics in simple rings and rings with one additional
self-input. An analysis of switching characteristics and
pulse propagation explains the relation between attractors
of the continuous systems and their Boolean approximations.
For simple rings, "reliable" Boolean attractors correspond
to stable continuous attractors. For networks with more
complex logic, the qualitative features of continuous
attractors are influenced by inherently non-Boolean
characteristics of switching events.},
Doi = {10.1103/physreve.76.046122},
Key = {fds248349}
}
@article{fds248351,
Author = {Berger, CM and Cain, JW and Socolar, JES and Gauthier,
DJ},
Title = {Control of electrical alternans in simulations of paced
myocardium using extended time-delay autosynchronization.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {76},
Number = {4 Pt 1},
Pages = {041917},
Year = {2007},
Month = {October},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/17995036},
Abstract = {Experimental studies have linked alternans, an abnormal
beat-to-beat alternation of cardiac action potential
duration, to the genesis of lethal arrhythmias such as
ventricular fibrillation. Prior studies have considered
various closed-loop feedback control algorithms for
perturbing interstimulus intervals in such a way that
alternans is suppressed. However, some experimental cases
are restricted in that the controller's stimuli must preempt
those of the existing waves that are propagating in the
tissue, and therefore only shortening perturbations to the
underlying pacing are allowed. We present results
demonstrating that a technique known as extended time-delay
autosynchronization (ETDAS) can effectively control
alternans locally while operating within the above
constraints. We show that ETDAS, which has already been used
to control chaos in physical systems, has numerous
advantages over previously proposed alternans control
schemes.},
Doi = {10.1103/physreve.76.041917},
Key = {fds248351}
}
@inbook{fds70496,
Author = {J.E.S. Socolar},
Title = {Time-delay control for discrete maps},
Booktitle = {Handbook of Chaos Control},
Publisher = {Wiley-VCH Verlag GmbH},
Editor = {E. Scholl and H. G. Schuster},
Year = {2007},
Month = {December},
url = {http://www.wiley.com/WileyCDA/WileyTitle/productCd-3527406050,descCd-tableOfContents.html},
Abstract = {A pedagogical introduction to discrete time-delayed feedback
methods. It is neither a comprehensive review, nor a
presentation of dramatic new results. It does, on the other
hand, organize known results in a self-contained manner that
emphasizes the conceptual points that have proven to be
important, where much of the original literature focuses on
historically important points and rigorous mathematical
proofs. The present work also contains examples and one
generalization that have not appeared elsewhere.},
Key = {fds70496}
}
@article{fds248338,
Author = {Ribeiro, AS and Kauffman, SA and Lloyd-Price, J and Samuelsson, B and Socolar, JES},
Title = {Mutual information in random Boolean models of regulatory
networks.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {77},
Number = {1 Pt 1},
Pages = {011901},
Year = {2008},
Month = {January},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18351870},
Abstract = {The amount of mutual information contained in the time
series of two elements gives a measure of how well their
activities are coordinated. In a large, complex network of
interacting elements, such as a genetic regulatory network
within a cell, the average of the mutual information over
all pairs, <I>, is a global measure of how well the system
can coordinate its internal dynamics. We study this average
pairwise mutual information in random Boolean networks
(RBNs) as a function of the distribution of Boolean rules
implemented at each element, assuming that the links in the
network are randomly placed. Efficient numerical methods for
calculating <I> show that as the number of network nodes, N,
approaches infinity, the quantity N<I> exhibits a
discontinuity at parameter values corresponding to critical
RBNs. For finite systems it peaks near the critical value,
but slightly in the disordered regime for typical parameter
variations. The source of high values of N<I> is the
indirect correlations between pairs of elements from
different long chains with a common starting point. The
contribution from pairs that are directly linked approaches
zero for critical networks and peaks deep in the disordered
regime.},
Doi = {10.1103/physreve.77.011901},
Key = {fds248338}
}
@article{fds248337,
Author = {Tighe, BP and Socolar, JES},
Title = {Nonlinear elastic stress response in granular
packings.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {77},
Number = {3 Pt 1},
Pages = {031303},
Year = {2008},
Month = {March},
ISSN = {1539-3755},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18517366},
Abstract = {We study the nonlinear elastic response of a two-dimensional
material to a localized boundary force, with the particular
goal of understanding the differences observed between
isotropic granular materials and those with hexagonal
anisotropy. Corrections to the classical Boussinesq result
for the stresses in an infinite half space of a linear,
isotropic material are developed in a power series in
inverse distance from the point of application of the force.
The breakdown of continuum theory on scales of order of the
grain size is modeled with phenomenological parameters
characterizing the strengths of induced multipoles near the
point of application of the external force. We find that the
data of Geng [Phys. Rev. Lett. 87, 035506 (2001)] on
isotropic and hexagonal packings of photoelastic grains can
be fitted within this framework. Fitting the hexagonal
packings requires a choice of elastic coefficients with
hexagonal anisotropy stronger than that of a simple
ball-and-spring model. For both the isotropic and hexagonal
cases, induced dipole and quadrupole terms produce
propagation of stresses away from the vertical direction
over short distances. The scale over which such propagation
occurs is significantly enhanced by the nonlinearities that
generate hexagonal anisotropy.},
Doi = {10.1103/physreve.77.031303},
Key = {fds248337}
}
@article{fds145241,
Author = {D.A. Orlando and C.Y. Lin and A. Bernard and J.Y. Wang and J.E.S.
Socolar, E.S. Iversen and A.J. Hartemink and S.B.
Haase},
Title = {Global control of cell-cycle transcription by coupled CDK
and network oscillators},
Journal = {Nature},
Year = {2008},
Month = {May},
url = {http://dx.doi.org/doi:10.1038/nature06955},
Doi = {doi:10.1038/nature06955},
Key = {fds145241}
}
@article{fds248314,
Author = {Socolar, JES},
Title = {Time-Delay Control for Discrete Maps},
Pages = {29-45},
Publisher = {Wiley-VCH Verlag GmbH & Co. KGaA},
Year = {2008},
Month = {May},
url = {http://dx.doi.org/10.1002/9783527622313.ch2},
Abstract = {This chapter is intended as a pedagogical introduction to
discrete time delayed feedback methods. It is neither a
comprehensive review, nor a presentation of dramatic new
results. It does, on the other hand, organize known results
in a self-contained manner that emphasizes the conceptual
points that have proven to be important, where much of the
original literature focuses on historically important points
and rigorous mathematical proofs. The present work also
contains examples and one generalization that have not
appeared elsewhere. The goal is to provide a conceptual
foundation for readers who wonder whether discrete time
delay feedback methods are up to the task they have in mind.
Since the study of discrete methods foreshadows many (but
not all!) of the important questions that arise in studies
of continuous versions of delayed feedback control, the
present chapter may also serve as a useful prequel to
chapters on continuous methods. © 2008 Wiley-VCH Verlag
GmbH & Co. KGaA.},
Doi = {10.1002/9783527622313.ch2},
Key = {fds248314}
}
@article{fds248339,
Author = {Orlando, DA and Lin, CY and Bernard, A and Wang, JY and Socolar, JES and Iversen, ES and Hartemink, AJ and Haase, SB},
Title = {Global control of cell-cycle transcription by coupled CDK
and network oscillators.},
Journal = {Nature},
Volume = {453},
Number = {7197},
Pages = {944-947},
Year = {2008},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18463633},
Abstract = {A significant fraction of the Saccharomyces cerevisiae
genome is transcribed periodically during the cell division
cycle, indicating that properly timed gene expression is
important for regulating cell-cycle events. Genomic analyses
of the localization and expression dynamics of transcription
factors suggest that a network of sequentially expressed
transcription factors could control the temporal programme
of transcription during the cell cycle. However, directed
studies interrogating small numbers of genes indicate that
their periodic transcription is governed by the activity of
cyclin-dependent kinases (CDKs). To determine the extent to
which the global cell-cycle transcription programme is
controlled by cyclin-CDK complexes, we examined genome-wide
transcription dynamics in budding yeast mutant cells that do
not express S-phase and mitotic cyclins. Here we show that a
significant fraction of periodic genes are aberrantly
expressed in the cyclin mutant. Although cells lacking
cyclins are blocked at the G1/S border, nearly 70% of
periodic genes continued to be expressed periodically and on
schedule. Our findings reveal that although CDKs have a
function in the regulation of cell-cycle transcription, they
are not solely responsible for establishing the global
periodic transcription programme. We propose that periodic
transcription is an emergent property of a transcription
factor network that can function as a cell-cycle oscillator
independently of, and in tandem with, the CDK
oscillator.},
Doi = {10.1038/nature06955},
Key = {fds248339}
}
@article{fds344681,
Author = {Norrell, J and Socolar, JES},
Title = {Boolean modeling of collective effects in complex
networks.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {79},
Number = {6 Pt 1},
Pages = {061908},
Year = {2009},
Month = {June},
url = {http://dx.doi.org/10.1103/physreve.79.061908},
Abstract = {Complex systems are often modeled as Boolean networks in
attempts to capture their logical structure and reveal its
dynamical consequences. Approximating the dynamics of
continuous variables by discrete values and Boolean logic
gates may, however, introduce dynamical possibilities that
are not accessible to the original system. We show that
large random networks of variables coupled through
continuous transfer functions often fail to exhibit the
complex dynamics of corresponding Boolean models in the
disordered (chaotic) regime, even when each individual
function appears to be a good candidate for Boolean
idealization. A suitably modified Boolean theory explains
the behavior of systems in which information does not
propagate faithfully down certain chains of nodes. Model
networks incorporating calculated or directly measured
transfer functions reported in the literature on
transcriptional regulation of genes are described by the
modified theory.},
Doi = {10.1103/physreve.79.061908},
Key = {fds344681}
}
@article{fds248335,
Author = {Zhang, R and de S Cavalcante and HLD and Gao, Z and Gauthier, DJ and Socolar, JES and Adams, MM and Lathrop, DP},
Title = {Boolean chaos.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {80},
Number = {4 Pt 2},
Pages = {045202},
Year = {2009},
Month = {October},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19905381},
Abstract = {We observe deterministic chaos in a simple network of
electronic logic gates that are not regulated by a clocking
signal. The resulting power spectrum is ultrawide band,
extending from dc to beyond 2 GHz. The observed behavior is
reproduced qualitatively using an autonomously updating
Boolean model with signal propagation times that depend on
the recent history of the gates and filtering of pulses of
short duration, whose presence is confirmed experimentally.
Electronic Boolean chaos may find application as an
ultrawide-band source of radio waves.},
Doi = {10.1103/physreve.80.045202},
Key = {fds248335}
}
@article{fds248334,
Author = {Cavalcante, HLDDS and Gauthier, DJ and Socolar, JES and Zhang,
R},
Title = {On the origin of chaos in autonomous Boolean
networks.},
Journal = {Philosophical transactions. Series A, Mathematical,
physical, and engineering sciences},
Volume = {368},
Number = {1911},
Pages = {495-513},
Year = {2010},
Month = {January},
ISSN = {1364-503X},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20008414},
Abstract = {We undertake a systematic study of the dynamics of Boolean
networks to determine the origin of chaos observed in recent
experiments. Networks with nodes consisting of ideal logic
gates are known to display either steady states, periodic
behaviour or an ultraviolet catastrophe where the number of
logic-transition events circulating in the network per unit
time grows as a power law. In an experiment, the non-ideal
behaviour of the logic gates prevents the ultraviolet
catastrophe and may lead to deterministic chaos. We identify
certain non-ideal features of real logic gates that enable
chaos in experimental networks. We find that short-pulse
rejection and asymmetry between the logic states tend to
engender periodic behaviour, at least for the simplest
networks. On the other hand, we find that a memory effect
termed 'degradation' can generate chaos. Our results
strongly suggest that deterministic chaos can be expected in
a large class of experimental Boolean-like networks. Such
devices may find application in a variety of technologies
requiring fast complex waveforms or flat power spectra, and
can be used as a test-bed for fundamental studies of
real-world Boolean-like networks.},
Doi = {10.1098/rsta.2009.0235},
Key = {fds248334}
}
@article{fds248345,
Author = {Sevim, V and Gong, X and Socolar, JES},
Title = {Reliability of transcriptional cycles and the yeast
cell-cycle oscillator},
Journal = {PLoS Computational Biology},
Volume = {6},
Number = {7},
Pages = {18},
Year = {2010},
Month = {January},
ISSN = {1553-7358},
url = {http://www.ncbi.nlm.nih.gov/pubmed/20628620},
Abstract = {A recently published transcriptional oscillator associated
with the yeast cell cycle provides clues and raises
questions about the mechanisms underlying autonomous cyclic
processes in cells. Unlike other biological and synthetic
oscillatory networks in the literature, this one does not
seem to rely on a constitutive signal or positive
auto-regulation, but rather to operate through stable
transmission of a pulse on a slow positive feedback loop
that determines its period. We construct a continuous-time
Boolean model of this network, which permits the modeling of
noise through small fluctuations in the timing of events,
and show that it can sustain stable oscillations. Analysis
of simpler network models shows how a few building blocks
can be arranged to provide stability against fluctuations.
Our findings suggest that the transcriptional oscillator in
yeast belongs to a new class of biological oscillators. ©
2010 Sevim et al.},
Doi = {10.1371/journal.pcbi.1000842},
Key = {fds248345}
}
@article{Socolar:2011:AHT:2027468.2027502,
Author = {Socolar Joshua and ES and Taylor Joan and M},
Title = {An aperiodic hexagonal tile},
Journal = {J. Comb. Theory Ser. A},
Volume = {118},
Number = {8},
Pages = {2207-2231},
Publisher = {Academic Press, Inc.},
Address = {Orlando, FL, USA},
Year = {2011},
Month = {November},
ISSN = {0097-3165},
url = {http://dx.doi.org/10.1016/j.jcta.2011.05.001},
Keywords = {Aperiodic, Matching rules, Substitution,
Tiling},
Abstract = {We show that a single prototile can fill space uniformly but
not admit a periodic tiling. A two-dimensional, hexagonal
prototile with markings that enforce local matching rules is
proven to be aperiodic by two independent methods. The
space-filling tiling that can be built from copies of the
prototile has the structure of a union of honeycombs with
lattice constants of 2na, where a sets the scale of the most
dense lattice and n takes all positive integer values. There
are two local isomorphism classes consistent with the
matching rules and there is a nontrivial relation between
these tilings and a previous construction by Penrose.
Alternative forms of the prototile enforce the local
matching rules by shape alone, one using a prototile that is
not a connected region and the other using a
three-dimensional prototile. © 2011 Elsevier
Inc.},
Doi = {10.1016/j.jcta.2011.05.001},
Key = {Socolar:2011:AHT:2027468.2027502}
}
@article{fds248332,
Author = {Socolar, JES},
Title = {Local action, global impact: forcing nonperiodicity with a
single structural unit.},
Journal = {Chaos (Woodbury, N.Y.)},
Volume = {21},
Number = {4},
Pages = {041106},
Year = {2011},
Month = {December},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22225336},
Abstract = {This is a presentation, with explanation, of an image of a
nonperiodic tiling whose structure is forced by local rules
governing how nearest and next-nearest neighbors can
align.},
Doi = {10.1063/1.3668192},
Key = {fds248332}
}
@article{fds248331,
Author = {Sun, M and Socolar, JES},
Title = {Comparison of autonomous Boolean network dynamics and ODE
models},
Journal = {Chaos},
Year = {2012},
Key = {fds248331}
}
@article{fds248347,
Author = {Khalil, KS and Sagastegui, A and Li, Y and Tahir, MA and Socolar, JES and Wiley, BJ and Yellen, BB},
Title = {Binary colloidal structures assembled through Ising
interactions},
Journal = {Nature Communications},
Volume = {3},
Pages = {794},
Year = {2012},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22531179},
Abstract = {New methods for inducing microscopic particles to assemble
into useful macroscopic structures could open pathways for
fabricating complex materials that cannot be produced by
lithographic methods. Here we demonstrate a colloidal
assembly technique that uses two parameters to tune the
assembly of over 20 different pre-programmed structures,
including kagome, honeycomb and square lattices, as well as
various chain and ring configurations. We programme the
assembled structures by controlling the relative
concentrations and interaction strengths between spherical
magnetic and non-magnetic beads, which behave as
paramagnetic or diamagnetic dipoles when immersed in a
ferrofluid. A comparison of our experimental observations
with potential energy calculations suggests that the lowest
energy configuration within binary mixtures is determined
entirely by the relative dipole strengths and their relative
concentrations.},
Doi = {10.1038/ncomms1798},
Key = {fds248347}
}
@article{fds248343,
Author = {Byington, TW and Socolar, JES},
Title = {Hierarchical freezing in a lattice model.},
Journal = {Physical review letters},
Volume = {108},
Number = {4},
Pages = {045701},
Year = {2012},
Month = {January},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22400863},
Abstract = {A certain two-dimensional lattice model with nearest and
next-nearest neighbor interactions is known to have a
limit-periodic ground state. We show that during a slow
quench from the high temperature, disordered phase, the
ground state emerges through an infinite sequence of phase
transitions. We define appropriate order parameters and show
that the transitions are related by renormalizations of the
temperature scale. As the temperature is decreased,
sublattices with increasingly large lattice constants become
ordered. A rapid quench results in a glasslike state due to
kinetic barriers created by simultaneous freezing on
sublattices with different lattice constants.},
Doi = {10.1103/physrevlett.108.045701},
Key = {fds248343}
}
@article{fds248341,
Author = {Durrett, R and Gleeson, JP and Lloyd, AL and Mucha, PJ and Shi, F and Sivakoff, D and Socolar, JES and Varghese, C},
Title = {Graph fission in an evolving voter model.},
Journal = {Proceedings of the National Academy of Sciences of the
United States of America},
Volume = {109},
Number = {10},
Pages = {3682-3687},
Year = {2012},
Month = {March},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22355142},
Abstract = {We consider a simplified model of a social network in which
individuals have one of two opinions (called 0 and 1) and
their opinions and the network connections coevolve. Edges
are picked at random. If the two connected individuals hold
different opinions then, with probability 1 - α, one
imitates the opinion of the other; otherwise (i.e., with
probability α), the link between them is broken and one of
them makes a new connection to an individual chosen at
random (i) from those with the same opinion or (ii) from the
network as a whole. The evolution of the system stops when
there are no longer any discordant edges connecting
individuals with different opinions. Letting ρ be the
fraction of voters holding the minority opinion after the
evolution stops, we are interested in how ρ depends on α
and the initial fraction u of voters with opinion 1. In case
(i), there is a critical value α(c) which does not depend
on u, with ρ ≈ u for α > α(c) and ρ ≈ 0 for
α < α(c). In case (ii), the transition point α(c)(u)
depends on the initial density u. For α > α(c)(u),
ρ ≈ u, but for α < α(c)(u), we have
ρ(α,u) = ρ(α,1/2). Using simulations and approximate
calculations, we explain why these two nearly identical
models have such dramatically different phase
transitions.},
Doi = {10.1073/pnas.1200709109},
Key = {fds248341}
}
@article{fds248344,
Author = {Socolar, JES and Taylor, JM},
Title = {Forcing nonperiodicity with a single tile},
Journal = {The Mathematical Intelligencer},
Volume = {34},
Number = {1},
Pages = {18-28},
Publisher = {Springer Nature},
Year = {2012},
Month = {Spring},
ISSN = {0343-6993},
url = {http://dx.doi.org/10.1007/s00283-011-9255-y},
Abstract = {An aperiodic prototile is a shape for which infinitely many
copies can be arranged to fill Euclidean space completely
with no overlaps, but not in a periodic pattern. Tiling
theorists refer to such a prototile as an "einstein" (a
German pun on "one stone"). The possible existence of an
einstein has been pondered ever since Berger's discovery of
large set of prototiles that in combination can tile the
plane only in a nonperiodic way. In this article we review
and clarify some features of a prototile we recently
introduced that is an einstein according to a reasonable
definition.},
Doi = {10.1007/s00283-011-9255-y},
Key = {fds248344}
}
@article{fds248340,
Author = {Gong, X and Socolar, JES},
Title = {Quantifying the complexity of random Boolean
networks.},
Journal = {Physical review. E, Statistical, nonlinear, and soft matter
physics},
Volume = {85},
Number = {6 Pt 2},
Pages = {066107},
Year = {2012},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23005162},
Abstract = {We study two measures of the complexity of heterogeneous
extended systems, taking random Boolean networks as
prototypical cases. A measure defined by Shalizi et al. for
cellular automata, based on a criterion for optimal
statistical prediction [Shalizi et al., Phys. Rev. Lett. 93,
118701 (2004)], does not distinguish between the spatial
inhomogeneity of the ordered phase and the dynamical
inhomogeneity of the disordered phase. A modification in
which complexities of individual nodes are calculated yields
vanishing complexity values for networks in the ordered and
critical regimes and for highly disordered networks, peaking
somewhere in the disordered regime. Individual nodes with
high complexity are the ones that pass the most information
from the past to the future, a quantity that depends in a
nontrivial way on both the Boolean function of a given node
and its location within the network.},
Doi = {10.1103/physreve.85.066107},
Key = {fds248340}
}
@article{fds248342,
Author = {Byington, T and Socolar, JES},
Title = {Hierarchical freezing of limit-periodic structure},
Journal = {Physical Review E},
Year = {2012},
Month = {November},
Key = {fds248342}
}
@article{fds304616,
Author = {Cheng, X and Sun, M and Socolar, JES},
Title = {Autonomous Boolean modelling of developmental gene
regulatory networks.},
Journal = {Journal of the Royal Society, Interface},
Volume = {10},
Number = {78},
Pages = {20120574},
Year = {2013},
Month = {January},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23034351},
Abstract = {During early embryonic development, a network of regulatory
interactions among genes dynamically determines a pattern of
differentiated tissues. We show that important timing
information associated with the interactions can be
faithfully represented in autonomous Boolean models in which
binary variables representing expression levels are updated
in continuous time, and that such models can provide a
direct insight into features that are difficult to extract
from ordinary differential equation (ODE) models. As an
application, we model the experimentally well-studied
network controlling fly body segmentation. The Boolean model
successfully generates the patterns formed in normal and
genetically perturbed fly embryos, permits the derivation of
constraints on the time delay parameters, clarifies the
logic associated with different ODE parameter sets and
provides a platform for studying connectivity and robustness
in parameter space. By elucidating the role of regulatory
time delays in pattern formation, the results suggest new
types of experimental measurements in early embryonic
development.},
Doi = {10.1098/rsif.2012.0574},
Key = {fds304616}
}
@article{fds353916,
Author = {Yellen, B and Yang, Y and Yu, L and Charbonneau, P and Socolar, J and Lopez, G},
Title = {Magnetically directed assembly and dynamic manipulation of
binary colloidal crystals},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL
SOCIETY},
Volume = {245},
Pages = {1 pages},
Publisher = {AMER CHEMICAL SOC},
Year = {2013},
Month = {April},
Key = {fds353916}
}
@article{fds248315,
Author = {Sun, M and Cheng, X and Socolar, JES},
Title = {Causal structure of oscillations in gene regulatory
networks: Boolean analysis of ordinary differential equation
attractors.},
Journal = {Chaos (Woodbury, N.Y.)},
Volume = {23},
Number = {2},
Pages = {025104},
Year = {2013},
Month = {June},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23822502},
Abstract = {A common approach to the modeling of gene regulatory
networks is to represent activating or repressing
interactions using ordinary differential equations for
target gene concentrations that include Hill function
dependences on regulator gene concentrations. An alternative
formulation represents the same interactions using Boolean
logic with time delays associated with each network link. We
consider the attractors that emerge from the two types of
models in the case of a simple but nontrivial network: a
figure-8 network with one positive and one negative feedback
loop. We show that the different modeling approaches give
rise to the same qualitative set of attractors with the
exception of a possible fixed point in the ordinary
differential equation model in which concentrations sit at
intermediate values. The properties of the attractors are
most easily understood from the Boolean perspective,
suggesting that time-delay Boolean modeling is a useful tool
for understanding the logic of regulatory
networks.},
Doi = {10.1063/1.4807733},
Key = {fds248315}
}
@article{PhysRevE.90.012136,
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},
Publisher = {American Physical Society},
Year = {2014},
Month = {July},
ISSN = {1539-3755},
url = {http://link.aps.org/doi/10.1103/PhysRevE.90.012136},
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 = {PhysRevE.90.012136}
}
@article{fds248313,
Author = {Cheng, X and Lyons, DC and Socolar, JES and McClay,
DR},
Title = {Delayed transition to new cell fates during cellular
reprogramming.},
Journal = {Developmental biology},
Volume = {391},
Number = {2},
Pages = {147-157},
Year = {2014},
Month = {July},
ISSN = {0012-1606},
url = {http://www.sciencedirect.com/science/article/pii/S001216061400222X},
Abstract = {In many embryos specification toward one cell fate can be
diverted to a different cell fate through a reprogramming
process. Understanding how that process works will reveal
insights into the developmental regulatory logic that
emerged from evolution. In the sea urchin embryo, cells at
gastrulation were found to reprogram and replace missing
cell types after surgical dissections of the embryo.
Non-skeletogenic mesoderm (NSM) cells reprogrammed to
replace missing skeletogenic mesoderm cells and animal caps
reprogrammed to replace all endomesoderm. In both cases
evidence of reprogramming onset was first observed at the
early gastrula stage, even if the cells to be replaced were
removed earlier in development. Once started however, the
reprogramming occurred with compressed gene expression
dynamics. The NSM did not require early contact with the
skeletogenic cells to reprogram, but the animal cap cells
gained the ability to reprogram early in gastrulation only
after extended contact with the vegetal halves prior to that
time. If the entire vegetal half was removed at early
gastrula, the animal caps reprogrammed and replaced the
vegetal half endomesoderm. If the animal caps carried
morpholinos to either hox11/13b or foxA (endomesoderm
specification genes), the isolated animal caps failed to
reprogram. Together these data reveal that the emergence of
a reprogramming capability occurs at early gastrulation in
the sea urchin embryo and requires activation of early
specification components of the target tissues.},
Doi = {10.1016/j.ydbio.2014.04.015},
Key = {fds248313}
}
@article{fds248311,
Author = {Sun, M and Cheng, X and Socolar, JES},
Title = {Regulatory logic and pattern formation in the early sea
urchin embryo.},
Journal = {Journal of theoretical biology},
Volume = {363},
Pages = {80-92},
Year = {2014},
Month = {December},
ISSN = {0022-5193},
url = {http://dx.doi.org/10.1016/j.jtbi.2014.07.023},
Abstract = {We model the endomesoderm tissue specification process in
the vegetal half of the early sea urchin embryo using
Boolean models with continuous-time updating to represent
the regulatory network that controls gene expression. Our
models assume that the network interaction rules remain
constant over time and the dynamics plays out on a
predetermined program of cell divisions. An exhaustive
search of two-node models, in which each node may represent
a module of several genes in the real regulatory network,
yields a unique network architecture that can accomplish the
pattern formation task at hand--the formation of three
latitudinal tissue bands from an initial state with only two
distinct cell types. Analysis of an eight-gene model
constructed from available experimental data reveals that it
has a modular structure equivalent to the successful
two-node case. Our results support the hypothesis that the
gene regulatory network provides sufficient instructions for
producing the correct pattern of tissue specification at
this stage of development (between the fourth and tenth
cleavages in the urchin embryo).},
Doi = {10.1016/j.jtbi.2014.07.023},
Key = {fds248311}
}
@article{fds248310,
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 = {fds248310}
}
@article{fds312774,
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},
ISSN = {2470-0045},
url = {http://dx.doi.org/10.1103/PhysRevE.93.029902},
Doi = {10.1103/PhysRevE.93.029902},
Key = {fds312774}
}
@article{fds311987,
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 = {fds311987}
}
@article{fds311986,
Author = {Marcoux, C and Socolar, JES},
Title = {Sparse phonon modes of a limit-periodic structure},
Journal = {Physical Review B - Condensed Matter and Materials
Physics},
Volume = {93},
Number = {17},
Publisher = {American Physical Society},
Year = {2016},
Month = {May},
ISSN = {0163-1829},
url = {http://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.174102},
Abstract = {Limit-periodic structures are well ordered but nonperiodic,
and hence have nontrivial vibrational modes. We study a ball
and spring model with a limit-periodic pattern of spring
stiffnesses and identify a set of extended modes with
arbitrarily low participation ratios, a situation that
appears to be unique to limit-periodic systems. The balls
that oscillate with large amplitude in these modes live on
periodic nets with arbitrarily large lattice constants. By
studying periodic approximants to the limit-periodic
structure, we present numerical evidence for the existence
of such modes, and we give a heuristic explanation of their
structure.},
Doi = {10.1103/PhysRevB.93.174102},
Key = {fds311986}
}
@article{fds315560,
Author = {Hann, CT and Socolar, JES and Steinhardt, PJ},
Title = {Local growth of icosahedral quasicrystalline
tilings},
Journal = {Physical Review B},
Volume = {94},
Number = {1},
Publisher = {American Physical Society (APS)},
Year = {2016},
Month = {July},
url = {http://arxiv.org/abs/1604.02479v1},
Abstract = {Icosahedral quasicrystals (IQCs) with extremely high degrees
of translational order have been produced in the laboratory
and found in naturally occurring minerals, yet questions
remain about how IQCs form. In particular, the fundamental
question of how locally determined additions to a growing
cluster can lead to the intricate long-range correlations in
IQCs remains open. In answer to this question, we have
developed an algorithm that is capable of producing a
perfectly ordered IQC yet relies exclusively on local rules
for sequential, face-to-face addition of tiles to a cluster.
When the algorithm is seeded with a special type of cluster
containing a defect, we find that growth is forced to
infinity with high probability and that the resultant IQC
has a vanishing density of defects. The geometric features
underlying this algorithm can inform analyses of
experimental systems and numerical models that generate
highly ordered quasicrystals.},
Doi = {10.1103/PhysRevB.94.014113},
Key = {fds315560}
}
@article{fds323248,
Author = {Rutkowski, DM and Marcoux, C and Socolar, JES and Hall,
CK},
Title = {Formation of limit-periodic structures by quadrupole
particles confined to a triangular lattice},
Journal = {Physical Review E - Statistical, Nonlinear, and Soft Matter
Physics},
Volume = {95},
Number = {1-1},
Pages = {012604},
Publisher = {American Physical Society},
Year = {2017},
Month = {January},
url = {http://dx.doi.org/10.1103/PhysRevE.95.012604},
Abstract = {We have performed Monte Carlo (MC) simulations on
two-dimensional systems of quadrupole particles confined to
a triangular lattice in order to determine the conditions
that permit the formation of a limit-periodic phase. We have
found that limit-periodic structures form only when the
rotations of the particles are confined to a set of six
orientations aligned with the lattice directions. Related
structures including striped and unidirectional rattler
phases form when π/6 rotations or continuous rotations are
allowed. Order parameters signaling the formation of the
limit-periodic structure and related structures are measured
as a function of temperature. Our findings on the formation
of the limit-periodic structure elucidate features relevant
to the experimental creation of such a structure, which is
expected to have interesting vibrational and electromagnetic
modes.},
Doi = {10.1103/PhysRevE.95.012604},
Key = {fds323248}
}
@article{fds325482,
Author = {Socolar, JES and Lubensky, TC and Kane, CL},
Title = {Mechanical graphene},
Journal = {New Journal of Physics},
Volume = {19},
Number = {2},
Pages = {025003-025003},
Publisher = {IOP Publishing},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1088/1367-2630/aa57bb},
Abstract = {We present a model of a mechanical system with a vibrational
mode spectrum identical to the spectrum of electronic
excitations in a tight-binding model of graphene. The model
consists of point masses connected by elastic couplings,
called 'tri-bonds', that implement certain three-body
interactions, which can be tuned by varying parameters that
correspond to the relative hopping amplitudes on the
different bond directions in graphene. In the mechanical
model, this is accomplished by varying the location of a
pivot point that determines the allowed rigid rotations of a
single tri-bond. The infinite system constitutes a Maxwell
lattice, with the number of degrees of freedom equal to the
number of constraints imposed by the tri-bonds. We construct
the equilibrium and compatibility matrices and analyze the
model's phase diagram, which includes spectra with Weyl
points for some placements of the pivot and topologically
polarized phases for others. We then discuss the edge modes
and associated states of self stress for strips cut from the
periodic lattice. Finally, we suggest a physical realization
of the tri-bond, which allows access to parameter regimes
not available to experiments on (strained) graphene and may
be used to create other two-dimensional mechanical
metamaterials with different spectral features.},
Doi = {10.1088/1367-2630/aa57bb},
Key = {fds325482}
}
@article{fds325483,
Author = {Oǧuz, EC and Socolar, JES and Steinhardt, PJ and Torquato,
S},
Title = {Hyperuniformity of quasicrystals},
Journal = {Physical Review B},
Volume = {95},
Number = {5},
Publisher = {American Physical Society (APS)},
Year = {2017},
Month = {February},
url = {http://dx.doi.org/10.1103/PhysRevB.95.054119},
Abstract = {Hyperuniform systems, which include crystals, quasicrystals,
and special disordered systems, have attracted considerable
recent attention, but rigorous analyses of the
hyperuniformity of quasicrystals have been lacking because
the support of the spectral intensity is dense and
discontinuous. We employ the integrated spectral intensity
Z(k) to quantitatively characterize the hyperuniformity of
quasicrystalline point sets generated by projection methods.
The scaling of Z(k) as k tends to zero is computed for
one-dimensional quasicrystals and shown to be consistent
with independent calculations of the variance, σ2(R), in
the number of points contained in an interval of length 2R.
We find that one-dimensional quasicrystals produced by
projection from a two-dimensional lattice onto a line of
slope 1/τ fall into distinct classes determined by the
width of the projection window. For a countable dense set of
widths, Z(k)∼k4; for all others, Z(k)∼k2. This
distinction suggests that measures of hyperuniformity define
new classes of quasicrystals in higher dimensions as
well.},
Doi = {10.1103/PhysRevB.95.054119},
Key = {fds325483}
}
@article{fds326695,
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 = {fds326695}
}
@article{fds342627,
Author = {Goshaw, A and Greenside, H and Socolar, J and Schaeffer,
D},
Title = {Robert Paul Behringer},
Journal = {Physics Today},
Volume = {71},
Number = {12},
Pages = {60-60},
Publisher = {AIP Publishing},
Year = {2018},
Month = {December},
url = {http://dx.doi.org/10.1063/pt.3.4098},
Doi = {10.1063/pt.3.4098},
Key = {fds342627}
}
@article{fds340470,
Author = {Oğuz, EC and Socolar, JES and Steinhardt, PJ and Torquato,
S},
Title = {Hyperuniformity and anti-hyperuniformity in one-dimensional
substitution tilings.},
Journal = {Acta crystallographica. Section A, Foundations and
advances},
Volume = {75},
Number = {Pt 1},
Pages = {3-13},
Year = {2019},
Month = {January},
url = {http://dx.doi.org/10.1107/s2053273318015528},
Abstract = {This work considers the scaling properties characterizing
the hyperuniformity (or anti-hyperuniformity) of
long-wavelength fluctuations in a broad class of
one-dimensional substitution tilings. A simple argument is
presented which predicts the exponent α governing the
scaling of Fourier intensities at small wavenumbers, tilings
with α > 0 being hyperuniform, and numerical computations
confirm that the predictions are accurate for quasiperiodic
tilings, tilings with singular continuous spectra and
limit-periodic tilings. Quasiperiodic or singular continuous
cases can be constructed with α arbitrarily close to any
given value between -1 and 3. Limit-periodic tilings can be
constructed with α between -1 and 1 or with Fourier
intensities that approach zero faster than any power
law.},
Doi = {10.1107/s2053273318015528},
Key = {fds340470}
}
@article{fds343715,
Author = {Abed Zadeh and A and Barés, J and Socolar, JES and Behringer,
RP},
Title = {Seismicity in sheared granular matter.},
Journal = {Physical review. E},
Volume = {99},
Number = {5-1},
Pages = {052902},
Year = {2019},
Month = {May},
url = {http://dx.doi.org/10.1103/physreve.99.052902},
Abstract = {We report on experiments investigating the dynamics of a
slider that is pulled by a spring across a granular medium
consisting of a vertical layer of photoelastic disks. The
motion proceeds through a sequence of discrete events,
analogous to seismic shocks, in which elastic energy stored
in the spring is rapidly released. We measure the statistics
of several properties of the individual events: the energy
loss in the spring, the duration of the movement, and the
temporal profile of the slider motion. We also study certain
conditional probabilities and the statistics of
mainshock-aftershock sequences. At low driving rates, we
observe crackling with Omori-Utsu, Båth, and waiting time
laws similar to those observed in seismic dynamics. At
higher driving rates, where the sequence of events shows
strong periodicity, we observe scaling laws and asymmetrical
event shapes that are clearly distinguishable from those in
the crackling regime.},
Doi = {10.1103/physreve.99.052902},
Key = {fds343715}
}
@article{fds346749,
Author = {Kozlowski, R and Carlevaro, CM and Daniels, KE and Kondic, L and Pugnaloni, LA and Socolar, JES and Zheng, H and Behringer,
RP},
Title = {Dynamics of a grain-scale intruder in a two-dimensional
granular medium with and without basal friction.},
Journal = {Physical review. E},
Volume = {100},
Number = {3-1},
Pages = {032905},
Year = {2019},
Month = {September},
url = {http://dx.doi.org/10.1103/physreve.100.032905},
Abstract = {We report on a series of experiments in which a grain-sized
intruder is pushed by a spring through a two-dimensional
granular material composed of photoelastic disks in a
Couette geometry. We study the intruder dynamics as a
function of packing fraction for two types of supporting
substrates: A frictional glass plate and a layer of water
for which basal friction forces are negligible. We observe
two dynamical regimes: Intermittent flow, in which the
intruder moves freely most of the time but occasionally gets
stuck, and stick-slip dynamics, in which the intruder
advances via a sequence of distinct, rapid events. When
basal friction is present, we observe a smooth crossover
between the two regimes as a function of packing fraction,
and we find that reducing the interparticle friction
coefficient causes the stick-slip regime to shift to higher
packing fractions. When basal friction is eliminated, we
observe intermittent flow at all accessible packing
fractions. For all cases, we present results for the
statistics of stick events, the intruder velocity, and the
force exerted on the intruder by the grains. Our results
indicate the qualitative importance of basal friction at
high packing fractions and suggest a possible connection
between intruder dynamics in a static material and clogging
dynamics in granular flows.},
Doi = {10.1103/physreve.100.032905},
Key = {fds346749}
}
@article{fds346748,
Author = {Zhao, Y and Barés, J and Zheng, H and Socolar, JES and Behringer,
RP},
Title = {Shear-Jammed, Fragile, and Steady States in Homogeneously
Strained Granular Materials.},
Journal = {Physical review letters},
Volume = {123},
Number = {15},
Pages = {158001},
Year = {2019},
Month = {October},
url = {http://dx.doi.org/10.1103/physrevlett.123.158001},
Abstract = {We study the jamming phase diagram of sheared granular
material using a novel Couette shear setup with a multiring
bottom. The setup uses small basal friction forces to apply
a volume-conserving linear shear with no shear band to a
granular system composed of frictional photoelastic discs.
The setup can generate arbitrarily large shear strain due to
its circular geometry, and the shear direction can be
reversed, allowing us to measure a feature that
distinguishes shear-jammed from fragile states. We report
systematic measurements of the stress, strain, and contact
network structure at phase boundaries that have been
difficult to access by traditional experimental techniques,
including the yield stress curve and the jamming curve close
to ϕ_{SJ}≈0.75, the smallest packing fraction supporting
a shear-jammed state. We observe fragile states created
under large shear strain over a range of ϕ<ϕ_{SJ}. We also
find a transition in the character of the quasistatic steady
flow centered around ϕ_{SJ} on the yield curve as a
function of packing fraction. Near ϕ_{SJ}, the average
contact number, fabric anisotropy, and nonrattler fraction
all show a change of slope. Above ϕ_{F}≈0.7 the steady
flow shows measurable deviations from the basal linear shear
profile, and above ϕ_{b}≈0.78 the flow is localized in a
shear band.},
Doi = {10.1103/physrevlett.123.158001},
Key = {fds346748}
}
@article{fds346311,
Author = {Zhao, Y and Barés, J and Zheng, H and Bester, CS and Xu, Y and Socolar,
JES and Behringer, RP},
Title = {Jamming transition in non-spherical particle systems:
pentagons versus disks},
Journal = {Granular Matter},
Volume = {21},
Number = {4},
Year = {2019},
Month = {November},
url = {http://dx.doi.org/10.1007/s10035-019-0940-4},
Abstract = {We investigate the jamming transition in a quasi-2D granular
material composed of regular pentagons or disks subjected to
quasistatic uniaxial compression. We report six major
findings based on experiments with monodisperse photoelastic
particles with static friction coefficient μ≈ 1. (1) For
both pentagons and disks, the onset of rigidity occurs when
the average coordination number of non-rattlers, Znr,
reaches 3, and the dependence of Znr on the packing fraction
ϕ changes again when Znr reaches 4. (2) Though the packing
fractions ϕc1 and ϕc2 at these transitions differ from run
to run, for both shapes the data from all runs with
different initial configurations collapses when plotted as a
function of the non-rattler fraction. (3) The averaged
values of ϕc1 and ϕc2 for pentagons are around 1 % smaller
than those for disks. (4) Both jammed pentagons and disks
show Gamma distribution of the Voronoi cell area with same
parameters. (5) The jammed pentagons have similar
translational order for particle centers but slightly less
orientational order for contacting pairs compared to jammed
disks. (6) For jammed pentagons, the angle between edges at
a face-to-vertex contact point shows a uniform distribution
and the size of a cluster connected by face-to-face contacts
shows a power-law distribution.},
Doi = {10.1007/s10035-019-0940-4},
Key = {fds346311}
}
@article{fds346703,
Author = {Wang, M and Wang, D and Socolar, JES and Zheng, H and Behringer,
RP},
Title = {Jamming by shear in a dilating granular system},
Journal = {Granular Matter},
Volume = {21},
Number = {4},
Year = {2019},
Month = {November},
url = {http://dx.doi.org/10.1007/s10035-019-0951-1},
Abstract = {Jamming can occur in frictional granular materials
undergoing shear at a fixed packing fraction, ϕ, within a
range below the isotropic jamming point, with the amount of
strain required to induce jamming, γ, increasing with
decreasing ϕ. We are interested in how the shear jamming
process is affected when the system dilates as it is
sheared. We conduct experiments to shear a 2D granular
system while continuously increasing the system volume.
Below a certain dilation rate, the system is still able to
jam for ϕ smaller than the initial ϕ. We measure γ for
different dilation rates and initial packing fractions by
monitoring the coordination number of non-rattlers and the
system pressure. We find that γ is the same as the γ
required to jam a system with fixed packing fraction ϕ via
pure shear. Graphic abstract: [Figure not available: see
fulltext.].},
Doi = {10.1007/s10035-019-0951-1},
Key = {fds346703}
}
@article{fds348660,
Author = {Carlevaro, CM and Kozlowski, R and Pugnaloni, LA and Zheng, H and Socolar, JES and Kondic, L},
Title = {Intruder in a two-dimensional granular system: Effects of
dynamic and static basal friction on stick-slip and clogging
dynamics.},
Journal = {Physical review. E},
Volume = {101},
Number = {1-1},
Pages = {012909},
Year = {2020},
Month = {January},
url = {http://dx.doi.org/10.1103/physreve.101.012909},
Abstract = {We present simulation results for an intruder pulled through
a two-dimensional granular system by a spring using a model
designed to mimic the experiments described by Kozlowski et
al. [Phys. Rev. E 100, 032905 (2019)2470-004510.1103/PhysRevE.100.032905].
In that previous study the presence of basal friction
between the grains and the base was observed to change the
intruder dynamics from clogging to stick-slip. Here we first
show that our simulation results are in excellent agreement
with the experimental data for a variety of experimentally
accessible friction coefficients governing interactions of
particles with each other and with boundaries. We then use
simulations to explore a broader range of parameter space,
focusing on the friction between the particles and the base.
We consider both static and dynamic basal friction
coefficients, which are difficult to vary smoothly in
experiments. The simulations show that dynamic friction
strongly affects the stick-slip behavior when the
coefficient is decreased below 0.1, while static friction
plays only a marginal role.},
Doi = {10.1103/physreve.101.012909},
Key = {fds348660}
}
@article{fds348644,
Author = {Tian, Z and Shen, C and Li, J and Reit, E and Bachman, H and Socolar, J and Cummer, S and Huang, T},
Title = {Dispersion Tuning and Route Reconfiguration of Acoustic
Waves in Valley Topological Phononic Crystals},
Journal = {Nature Communications},
Volume = {11},
Number = {1},
Pages = {762},
Year = {2020},
Month = {February},
url = {http://dx.doi.org/10.1038/s41467-020-14553-0},
Abstract = {The valley degree of freedom in crystals offers great
potential for manipulating classical waves; however, few
studies have investigated valley states with complex
wavenumbers, valley states in graded systems, or dispersion
tuning for valley states. Here, we present tunable valley
phononic crystals (PCs) composed of hybrid channel-cavity
cells with three tunable parameters. Our PCs support valley
states and Dirac cones with complex wavenumbers. They can be
configured to form chirped valley PCs in which edge modes
are slowed to zero group velocity states, where the energy
at different frequencies accumulates at different designated
locations. They enable multiple novel functionalities,
including tuning of dispersion relations for valley states,
robust routing of surface acoustic waves, and spatial
modulation of group velocities. This work may spark future
investigations of topological states with complex
wavenumbers in other classical systems, further study of
topological states in graded materials, and the development
of novel acoustic devices.},
Doi = {10.1038/s41467-020-14553-0},
Key = {fds348644}
}
@article{fds350620,
Author = {Zhao, Y and Barés, J and Socolar, JES},
Title = {Yielding, rigidity, and tensile stress in sheared columns of
hexapod granules.},
Journal = {Physical review. E},
Volume = {101},
Number = {6-1},
Pages = {062903},
Year = {2020},
Month = {June},
url = {http://dx.doi.org/10.1103/physreve.101.062903},
Abstract = {Granular packings of nonconvex or elongated particles can
form freestanding structures like walls or arches. For some
particle shapes, such as staples, the rigidity arises from
interlocking of pairs of particles, but the origins of
rigidity for noninterlocking particles remains unclear. We
report on experiments and numerical simulations of sheared
columns of "hexapods," particles consisting of three
mutually orthogonal sphero-cylinders whose centers coincide.
We vary the length-to-diameter aspect ratio, α, of the
sphero-cylinders and subject the packings to quasistatic
direct shear. For small α, we observe a finite yield
stress. For large α, however, the column becomes rigid when
sheared, supporting stresses that increase sharply with
increasing strain. Analysis of x-ray microcomputed
tomography (micro-CT) data collected during the shear
reveals that the stiffening is associated with a tilted,
oblate cluster of hexapods near the nominal shear plane in
which particle deformation and average contact number both
increase. Simulation results show that the particles are
collectively under tension along one direction, even though
they do not interlock pairwise. These tensions comes from
contact forces carrying large torques, and they are
perpendicular to the compressive stresses in the packing.
They counteract the tendency to dilate, thus stabilizing the
particle cluster.},
Doi = {10.1103/physreve.101.062903},
Key = {fds350620}
}
@article{fds355199,
Author = {Jalali, P and Zhao, Y and Socolar, JES},
Title = {Static and dynamic features of granular material failure due
to upward pulling of a buried sphere by a slowly increasing
force.},
Journal = {Soft matter},
Volume = {17},
Number = {10},
Pages = {2832-2839},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.1039/d0sm01914c},
Abstract = {A spherical intruder embedded in a confined granular column
is extracted by pulling it upward by an attached string. As
the tension of the string gradually increases, a failure
event occurs at a certain pulling force, leading to rapid
upward acceleration of the intruder. The threshold force and
the dynamics of the failure event are experimentally
investigated for different filling heights and column
diameters, using Ottawa sand and glass beads. For the Ottawa
sand, we find that the failure force can be fit by a model
describing the weight of the granular material in a cone
with the vertex at the bottom of the intruder and a vertex
angle of 72°. The agreement between the model and
experiments is good for heights less than the column (tube)
diameter, but measured values deviate from the model for
larger heights. We also report on experiments with glass
beads that reveal unexpected effects for relatively small
ratios of tube diameters to grain size. The dynamics of the
intruder during the failure event is studied using
high-speed video analysis. The granular drag force
monotonically decays during the pullout for sufficiently
large tube diameters. In narrow columns, a monotonic decay
of drag force after failure is observed for low heights,
whereas a secondary peak can be seen in sufficiently deep
and narrow columns, indicating the existence of different
mechanisms of failure. The normalized drag force declines
with intruder displacement closely for all tube diameters
within small displacements.},
Doi = {10.1039/d0sm01914c},
Key = {fds355199}
}
@article{fds361657,
Author = {Zhao, Y and Zhao, Y and Wang, D and Zheng, H and Chakraborty, B and Socolar, JES},
Title = {Ultra-stable shear jammed granular material},
Journal = {Physical Review X},
Volume = {12},
Pages = {031021},
Year = {2021},
Month = {May},
Abstract = {Dry granular materials such as sand, gravel, pills, or
agricultural grains, can become rigid when compressed or
sheared. At low density, one can distort the shape of a
container of granular material without encountering any
resistance. Under isotropic compression, the material will
reach a certain {\it jamming} density and then resist
further compression. {\em Shear jamming} occurs when
resistance to shear emerges in a system at a density lower
than the jamming density, and the elastic properties of such
states have important implications for industrial and
geophysical processes. We report on experimental
observations of changes in the mechanical properties of a
shear-jammed granular material subjected to small-amplitude,
quasi-static cyclic shear. We study a layer of plastic discs
confined to a shear cell, using photoelasticimetry to
measure all inter-particle vector forces. For sufficiently
small cyclic shear amplitudes and large enough initial
shear, the material evolves to an unexpected "ultra-stable"
state in which all the particle positions and inter-particle
contact forces remain unchanged after each complete shear
cycle for thousands of cycles. The stress response of these
states to small imposed shear is nearly elastic, in contrast
to the original shear jammed state.},
Key = {fds361657}
}
@article{fds375851,
Author = {Kozlowski, R and Zheng, H and Daniels, KE and Socolar,
JES},
Title = {Particle dynamics in two-dimensional point-loaded granular
media composed of circular or pentagonal
grains},
Journal = {Powders and Grains 2021 - 9th International Conference on
Micromechanics on Granular Media},
Volume = {249},
Series = {Powders & Grains 2021 – 9th International Conference on
Micromechanics on Granular Media},
Pages = {06010},
Year = {2021},
Month = {June},
url = {https://www.epj-conferences.org/articles/epjconf/abs/2021/03/epjconf_pg2021_06010/epjconf_pg2021_06010.html},
Abstract = {Granular packings exhibit significant changes in rheological
and structural properties when the rotational symmetry of
spherical or circular particles is broken. Here, we report
on experiments exploring the differences in dynamics of a
grain-scale intruder driven through a packing of either
disks or pentagons, where the presence of edges and vertices
on grains introduces the possibility of rotational
constraints at edge-edge contacts. We observe that the
intruder’s stick-slip dynamics are comparable between the
disk packing near the frictional jamming fraction and the
pentagonal packing at significantly lower packing fractions.
We connect this stark contrast in packing fraction with the
average speed and rotation fields of grains during slip
events, finding that rotation of pentagons is limited and
the flow of pentagonal grains is largely confined in front
of the intruder, whereas disks rotate more on average and
circulate around the intruder to fill the open channel
behind it. Our results indicate that grain-scale rotation
constraints significantly modify collective motion of grains
on mesoscopic scales and correspondingly enhance resistance
to penetration of a local intruder.},
Doi = {10.1051/epjconf/202124906010},
Key = {fds375851}
}
@article{fds360481,
Author = {Kozlowski, R and Zheng, H and Daniels, KE and Socolar,
JES},
Title = {Stress propagation in locally loaded packings of disks and
pentagons.},
Journal = {Soft matter},
Volume = {17},
Number = {44},
Pages = {10120-10127},
Year = {2021},
Month = {November},
url = {http://dx.doi.org/10.1039/d1sm01137e},
Abstract = {The mechanical strength and flow of granular materials can
depend strongly on the shapes of individual grains. We
report quantitative results obtained from photoelasticimetry
experiments on locally loaded, quasi-two-dimensional
granular packings of either disks or pentagons exhibiting
stick-slip dynamics. Packings of pentagons resist the
intruder at significantly lower packing fractions than
packings of disks, transmitting stresses from the intruder
to the boundaries over a smaller spatial extent. Moreover,
packings of pentagons feature significantly fewer
back-bending force chains than packings of disks. Data
obtained on the forward spatial extent of stresses and
back-bending force chains collapse when the packing fraction
is rescaled according to the packing fraction of steady
state open channel formation, though data on intruder forces
and dynamics do not collapse. We comment on the influence of
system size on these findings and highlight connections with
the dynamics of the disks and pentagons during slip
events.},
Doi = {10.1039/d1sm01137e},
Key = {fds360481}
}
@article{fds359292,
Author = {Basak, R and Manuel Carlevaro and C and Kozlowski, R and Cheng, C and Pugnaloni, LA and Kramár, M and Zheng, H and Socolar, JES and Kondic,
L},
Title = {Two Approaches to Quantification of Force Networks in
Particulate Systems},
Journal = {Journal of Engineering Mechanics},
Volume = {147},
Number = {11},
Year = {2021},
Month = {November},
url = {http://dx.doi.org/10.1061/(ASCE)EM.1943-7889.0002003},
Abstract = {The interactions between particles in dense particulate
systems are organized in force networks, mesoscale features
that influence the macroscopic response to applied stresses.
The detailed structure of these networks is, however,
difficult to extract from experiments that cannot resolve
individual contact forces. In this study, we showed that
certain persistent homology (PH) measures extracted from
data accessible to experiment are strongly correlated with
the same features extracted from the full contact force
network. We performed simulations known to accurately model
experiments on an intruder being pushed through a
two-dimensional (2D) granular layer and compared PH
properties of full contact force networks and networks
constructed using only the sum of the normal forces on each
grain. We found that the main features were highly
correlated, suggesting that data commonly available in
experiments are sufficient for quantifying the structure of
force networks in evolving granular systems.},
Doi = {10.1061/(ASCE)EM.1943-7889.0002003},
Key = {fds359292}
}
@article{fds361360,
Author = {Kluge, L and Socolar, JES and Schöll, E},
Title = {Random logic networks: From classical Boolean to quantum
dynamics.},
Journal = {Physical review. E},
Volume = {104},
Number = {6-1},
Pages = {064308},
Year = {2021},
Month = {December},
url = {https://arxiv.org/abs/2108.10813},
Abstract = {We investigate dynamical properties of a quantum
generalization of classical reversible Boolean networks. The
state of each node is encoded as a single qubit, and
classical Boolean logic operations are supplemented by
controlled bit-flip and Hadamard operations. We consider
synchronous updating schemes in which each qubit is updated
at each step based on stored values of the qubits from the
previous step. We investigate the periodic or quasiperiodic
behavior of quantum networks, and we analyze the propagation
of single site perturbations through the quantum networks
with input degree one. A nonclassical mechanism for
perturbation propagation leads to substantially different
evolution of the Hamming distance between the original and
perturbed states.},
Doi = {10.1103/physreve.104.064308},
Key = {fds361360}
}
@article{fds363371,
Author = {Pugnaloni, LA and Carlevaro, CM and Kozlowski, R and Zheng, H and Kondic, L and Socolar, JES},
Title = {Universal features of the stick-slip dynamics of an intruder
moving through a confined granular medium.},
Journal = {Physical review. E},
Volume = {105},
Number = {4},
Pages = {L042902},
Year = {2022},
Month = {April},
url = {http://dx.doi.org/10.1103/physreve.105.l042902},
Abstract = {Experiments and simulations of an intruder dragged by a
spring through a two-dimensional annulus of granular
material exhibit robust force fluctuations. At low packing
fractions (ϕ<ϕ_{0}), the intruder clears an open channel.
Above ϕ_{0}, stick-slip dynamics develop, with an average
energy release that is independent of the particle-particle
and particle-base friction coefficients but does depend on
the width W of the annulus and the diameter D of the
intruder. A simple model predicts the dependence of ϕ_{0}
on W and D, allowing for a data collapse for the average
energy release as a function of ϕ/ϕ_{0}. These results
pose challenges for theories of mechanical failure in
amorphous materials.},
Doi = {10.1103/physreve.105.l042902},
Key = {fds363371}
}
@article{fds365314,
Author = {Zhao, Y and Wang, D and Zheng, H and Chakraborty, B and Socolar,
JES},
Title = {Ultrastable Shear-Jammed Granular Material},
Journal = {Physical Review X},
Volume = {12},
Number = {3},
Publisher = {American Physical Society (APS)},
Year = {2022},
Month = {July},
url = {http://dx.doi.org/10.1103/PhysRevX.12.031021},
Abstract = {Dry granular materials, such as sand, gravel, pills, or
agricultural grains, can become rigid when compressed or
sheared. Under isotropic compression, the material reaches a
certain jamming density and then resists further
compression. Shear jamming occurs when resistance to shear
emerges in a system at a density lower than the jamming
density. Although shear jamming is prevalent in frictional
granular materials, their stability properties are not well
described by standard elasticity theory and thus call for
experimental characterization. We report on experimental
observations of changes in the mechanical properties of a
shear-jammed granular material subjected to small-amplitude,
quasistatic cyclic shear. We study a layer of plastic disks
confined to a shear cell, using photoelasticimetry to
measure all interparticle vector forces. For sufficiently
small cyclic shear amplitudes and large enough initial
shear, the material evolves to an unexpected
"ultrastable"state in which all the particle positions and
interparticle contact forces remain unchanged after each
complete shear cycle for thousands of cycles. The stress
response of these states to small imposed shear is nearly
elastic, in contrast to the original shear-jammed
state.},
Doi = {10.1103/PhysRevX.12.031021},
Key = {fds365314}
}
@article{fds365180,
Author = {Kozlowski, R and Zheng, H and Daniels, KE and Socolar,
JES},
Title = {Stick-Slip Dynamics in a Granular Material With Varying
Grain Angularity},
Journal = {Frontiers in Physics},
Volume = {10},
Year = {2022},
Month = {July},
url = {http://dx.doi.org/10.3389/fphy.2022.916190},
Abstract = {Experiments, simulations, and theoretical treatments of
granular materials typically feature circular or elliptical
grains. However, grains found in natural systems often have
flat faces that introduce local rotational constraints;
these rotational constraints have been shown to affect, for
example, the jamming transition, discontinuous shear
thickening, and ordered states in colloids and thermalized
grains. In this work, we experimentally investigate the
effects of grain angularity on stick-slip dynamics. A
weighted slider is pulled by a spring over a gravity-packed
granular bed composed of polygonal grains with varying
angularity. We find that packings of triangular or square
grains have higher shear strengths than packings of
pentagons, hexagons, heptagons, or disks. Additionally, as
the number of sides increases, sticking periods, during
which the slider remains motionless while the spring force
on it increases, become shorter on average, with the
material yielding at smaller applied stresses. Lastly, we
find that dilation of the medium during sticking periods
tends to be larger for grains with higher angularity, in
part because of the presence of stilt-like columnar
structures that prop the slider up. We report on
measurements of the pulling force on the slider, particle
dynamics during slip events, and properties of force-bearing
contact networks identified via photoelasticity. Our
findings indicate that high angularity of grains (pentagons,
squares, triangles) leads to differences in grain-scale flow
and macroscopic stick-slip dynamics of bulk granular
materials. Our experiments also indicate a continuous change
in dynamics with decreasing angularity as the circular grain
limit is approached.},
Doi = {10.3389/fphy.2022.916190},
Key = {fds365180}
}
@article{fds368344,
Author = {Zhao, Y and Wang, D and Zheng, H and Chakraborty, B and Socolar,
JES},
Title = {Microscopic reversibility and emergent elasticity in
ultrastable granular systems},
Journal = {Frontiers in Physics},
Volume = {10},
Year = {2022},
Month = {November},
url = {http://dx.doi.org/10.3389/fphy.2022.1048683},
Abstract = {In a recent paper (Zhao et al., Phys Rev X, 2022, 12:
031,021), we reported experimental observations of
“ultrastable” states in a shear-jammed granular system
subjected to small-amplitude cyclic shear. In such states,
all the particle positions and contact forces are reproduced
after each shear cycle so that a strobed image of the
stresses and particle positions appears static. In the
present work, we report further analyses of data from those
experiments to characterize both global and local responses
of ultrastable states within a shear cycle, not just the
strobed dynamics. We find that ultrastable states follow a
power-law relation between shear modulus and pressure with
an exponent β ≈ 0.5, reminiscent of critical scaling laws
near jamming. We also examine the evolution of contact
forces measured using photoelasticimetry. We find that there
are two types of contacts: non-persistent contacts that
reversibly open and close; and persistent contacts that
never open and display no measurable sliding. We show that
the non-persistent contacts make a non-negligible
contribution to the emergent shear modulus. We also analyze
the spatial correlations of the stress tensor and compare
them to the predictions of a recent theory of the emergent
elasticity of granular solids, the Vector Charge Theory of
Granular mechanics and dynamics (VCTG) (Nampoothiri et al.,
Phys Rev Lett, 2020, 125: 118,002). We show that our
experimental results can be fit well by VCTG, assuming
uniaxial symmetry of the contact networks. The fits reveal
that the response of the ultrastable states to additional
applied stress is substantially more isotropic than that of
the original shear-jammed states. Our results provide
important insight into the mechanical properties of
frictional granular solids created by shear.},
Doi = {10.3389/fphy.2022.1048683},
Key = {fds368344}
}
@article{fds374258,
Author = {Basak, R and Kozlowski, R and Pugnaloni, LA and Kramar, M and Socolar,
JES and Carlevaro, CM and Kondic, L},
Title = {Evolution of force networks during stick-slip motion of an
intruder in a granular material: Topological measures
extracted from experimental data.},
Journal = {Physical review. E},
Volume = {108},
Number = {5-1},
Pages = {054903},
Year = {2023},
Month = {November},
url = {http://dx.doi.org/10.1103/physreve.108.054903},
Abstract = {In quasi-two-dimensional experiments with photoelastic
particles confined to an annular region, an intruder
constrained to move in a circular path halfway between the
annular walls experiences stick-slip dynamics. We discuss
the response of the granular medium to the driven intruder,
focusing on the evolution of the force network during
sticking periods. Because the available experimental data do
not include precise information about individual contact
forces, we use an approach developed in our previous work
[Basak et al., J. Eng. Mech. 147, 04021100
(2021)0733-939910.1061/(ASCE)EM.1943-7889.0002003] based on
networks constructed from measurements of the integrated
strain magnitude on each particle. These networks are
analyzed using topological measures based on persistence
diagrams, revealing that force networks evolve smoothly but
in a nontrivial manner throughout each sticking period, even
though the intruder and granular particles are stationary.
Characteristic features of persistence diagrams show
identifiable slip precursors. In particular, the number of
generators describing the structure and complexity of force
networks increases consistently before slips. Key features
of the dynamics are similar for granular materials composed
of disks or pentagons, but some details are consistently
different. In particular, we find significantly larger
fluctuations of the measures computed based on persistence
diagrams and, therefore, of the underlying networks, for
systems of pentagonal particles.},
Doi = {10.1103/physreve.108.054903},
Key = {fds374258}
}
@article{fds374512,
Author = {Socolar, JES},
Title = {Quasicrystalline structure of the hat monotile
tilings},
Journal = {Physical Review B},
Volume = {108},
Number = {22},
Publisher = {American Physical Society (APS)},
Year = {2023},
Month = {December},
url = {http://dx.doi.org/10.1103/PhysRevB.108.224109},
Abstract = {Tiling models can reveal unexpected ways in which local
constraints give rise to exotic long-range spatial
structure. The recently discovered hat monotile (and its
mirror image) has been shown to be aperiodic [Smith,
arXiv:2303.10798]; it can tile the plane with no holes or
overlaps, but cannot do so periodically. We show that the
structure enforced by the local space-filling constraints is
quasiperiodic with hexagonal (C6) rotational symmetry.
Although this symmetry is compatible with periodicity, the
incommensurate ratio characterizing the quasiperiodicity
stays locked to the golden mean as the tile parameters are
continuously varied. We analyze a modification of the
metatiles introduced by Smith et al. that yields a set of
key tiles that can be constructed as projections of a subset
of six-dimensional hypercubic lattice points onto the
two-dimensional tiling plane. We analytically compute the
diffraction pattern of a set of unit masses placed at the
tiling vertices, establishing the quasiperiodic nature of
the tiling. We point out several unusual features of the
family of key tilings and associated hat tilings, including
the tile rearrangements associated with the phason degree of
freedom associated with incommensurate density waves, which
exhibit novel features that may influence the elastic
properties of a material in which atoms or larger particles
spontaneously exhibit the symmetries of the hat
tiling.},
Doi = {10.1103/PhysRevB.108.224109},
Key = {fds374512}
}
%% Papers Accepted
@article{fds347761,
Author = {Zhenhua Tian and Chen Shen and Junfei Li and Eric Reit and Hunter
Bachman, Joshua Socolar and Steven A. Cummer and Tony Jun
Huang},
Title = {Dispersion Tuning and Route Reconfiguration of Acoustic
Waves in Valley Topological Phononic Crystals},
Journal = {Nature Communications},
Year = {2019},
Month = {December},
Abstract = {The valley degree of freedom (DOF) in crystals offers great
potential for manipulating classical waves; however, few
studies have investigated dispersion tuning for valley
states, valley states with complex wavenumbers, or valley
states in functionally gradient systems. Here, we present
tunable valley phononic crystals (PCs), which are composed
of 3-DOF hybrid channel-cavity cells. The PCs can realize
multiple novel functionalities, including tuning dispersion
relations, robustly routing surface acoustic waves (SAWs),
controlling wave attenuation, and modulating group
velocities. Moreover, they support valley states and Dirac
cones in the complex wavenumber – frequency domain.
Furthermore, they can be configured to chirped valley PCs,
in which edge modes are slowed down to zero group velocity
states with the energy at different frequencies accumulated
at different designated locations along an interface. This
work may spark future investigations of topological states
with complex wavenumbers in other classical systems, or
topological states in functionally gradient
materials.},
Key = {fds347761}
}
@article{fds347762,
Author = {C. Manuel Carlevaro and Ryan Kozlowski and Luis A. Pugnaloni and Hu
Zheng, Joshua E. S. Socolar and Lou Kondic},
Title = {Intruder in a two-dimensional granular system: Effects of
dynamic and static basal friction on stick-slip and clogging
dynamics},
Journal = {Physical Review E},
Year = {2019},
Month = {December},
Abstract = {We present simulation results for an intruder pulled through
a two-dimensional granular system by a spring using a model
designed to mimic the experiments described by Kozlowski et
al. [Phys. Rev. E 100, 032905 (2019)]. In that previous
study the presence of basal friction between the grains and
the base was observed to change the intruder dynamics from
clogging to stick--slip. Here we first show that our
simulation results are in excellent agreement with the
experimental data for a variety of experimentally accessible
friction coefficients governing interactions of particles
with each other and with boundaries. We then use simulations
to explore a broader range of parameter space, focusing on
the friction between the particles and the base. We consider
both static and dynamic basal friction coefficients, which
are difficult to vary smoothly in experiments. The
simulations show that dynamic friction strongly affects the
stick--slip behaviour when the coefficient is decreased
below 0.1, while static friction plays only a marginal
role.},
Key = {fds347762}
}
%% Papers Submitted
@article{fds225655,
Author = {Y. Yang and L. Fu and C. Marcoux and J. E. S. Socolar and P.
Charbonneau, B. B. Yellen},
Title = {Martensitic transformations in binary colloidal
monolayers},
Journal = {PNAS},
Year = {2014},
Month = {October},
Key = {fds225655}
}
@article{fds353923,
Author = {R. Kozlowski and H. Zheng and K. E. Daniels and J. E. S.
Socolar},
Title = {Particle dynamics in point-loaded granular media composed of
circular or polygonal grains},
Journal = {Powders and Grains 2021 Proceedings},
Year = {2020},
Abstract = {Granular packings exhibit significant changes in rheological
and structural properties when the rotational symmetry of
spherical or circular particles is broken. Here, we report
on experiments exploring the differences in dynamics of a
grain-scale intruder driven through a packing of either
disks or pentagons, where the presence of edges and vertices
on grains introduces the possibility of rotational
constraints at edge-edge contacts. We observe that the
intruder's stick-slip dynamics are comparable between the
disk packing near the frictional jamming fraction and the
pentagonal packing at significantly lower packing fractions.
We connect this stark contrast in packing fraction with the
average speed and rotation fields of grains during slip
events, finding that rotation of pentagons is limited and
the flow of pentagonal grains is largely confined in front
of the intruder, whereas disks rotate more on average and
circulate around the intruder to fill the open channel
behind it. Our results indicate that grain-scale rotation
constraints significantly modify collective motion of grains
on mesoscopic scales and correspondingly enhance resistance
to penetration of a local intruder.},
Key = {fds353923}
}
@article{fds360486,
Author = {Yiqiu Zhao and Yuchen Zhao and Dong Wang and Hu Zheng and Bulbul
Chakraborty, Joshua E. S. Socolar},
Title = {Stability of shear-jammed granular materials: yielding and
stabilization under small-amplitude cyclic
shear},
Journal = {Physical Review X},
Year = {2021},
url = {https://arxiv.org/pdf/2105.00313.pdf},
Abstract = {We report on experiments that probe the stability of a
two-dimensional jammed granular system formed by imposing a
quasistatic simple shear strain γI on an initially stress
free packing. We subject the shear jammed system to
quasistatic cyclic shear with strain amplitude δγ. We
observe two distinct outcomes after thousands of shear
cycles. For small γI or large δγ, the system reaches a
stress-free, yielding state exhibiting diffusive strobed
particle displacements with a diffusion co- efficient
proportional to δγ. For large γI and small δγ, the
system evolves to a stable state in which both particle
positions and contact forces are unchanged after each cycle
and the response to small strain reversals is highly
elastic. Compared to the original shear jammed state, a
stable state reached after many cycles has a smaller stress
anisotropy, a much higher shear stiffness, and less tendency
to dilate when sheared. Remarkably, we find that stable
states show a power-law relation between shear modulus and
pressure with an exponent β ≈ 0.5, independent of δγ.
Based on our measurements, we construct a phase diagram in
the (γI,δγ) plane showing where our shear-jammed granular
materials either stabilize or yield in the long-time
limit.},
Key = {fds360486}
}
%% Preprints
@article{fds370616,
Author = {Socolar, JES},
Title = {Quasicrystalline structure of the Smith monotile
tilings},
Year = {2023},
Month = {May},
Key = {fds370616}
}
%% Book Reviews
@article{fds353927,
Author = {J. E. S. Socolar},
Title = {From Conception to Kamchatka},
Journal = {Inference},
Volume = {5},
Number = {2},
Year = {2020},
url = {https://inference-review.com/article/from-conception-to-kamchatka},
Abstract = {Review of "The Second Kind of Impossible," by Paul
Steinhardt.},
Key = {fds353927}
}
|