# Browsing by Author "Socolar, Joshua ES"

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Item Open Access Emergence of limit-periodic order in tiling models.(Phys Rev E Stat Nonlin Soft Matter Phys, 2014-07) Marcoux, Catherine; Byington, Travis W; Qian, Zongjin; Charbonneau, Patrick; Socolar, Joshua ESA 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.Item Open Access Hard sphere packings within cylinders.(Soft Matter, 2016-03-07) Fu, Lin; Steinhardt, William; Zhao, Hao; Socolar, Joshua ES; Charbonneau, PatrickArrangements 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.Item Open Access Phase diagram and aggregation dynamics of a monolayer of paramagnetic colloids(2017-06-01) Pham, An T; Zhuang, Yuan; Detwiler, Paige; Socolar, Joshua ES; Charbonneau, Patrick; Yellen, Benjamin BWe have developed a tunable colloidal system and a corresponding simulation 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 rapidly rotating in-plane component. The sign and strength of the interactions vary with the tilt angle $\theta$ of the rotating magnetic field. For a purely in-plane field, $\theta=90^{\circ}$, 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 $50^{\circ}\lesssim \theta\lesssim 55^{\circ}$, the two-body interaction gives a short-range attractive and long-range repulsive (SALR) 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 thus further characterize the anomalous behavior by measuring the time-dependent cluster size distribution.Item Open Access Phase transformations in binary colloidal monolayers.(Soft Matter, 2015-03-28) Yang, Ye; Fu, Lin; Marcoux, Catherine; Socolar, Joshua ES; Charbonneau, Patrick; Yellen, Benjamin BPhase 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.Item Open Access Random logic networks: From classical Boolean to quantum dynamics(Physical Review E) Kluge, Lucas; Socolar, Joshua ES; Schöll, EckehardWe 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 non-classical mechanism for perturbation propagation leads to substantially different evolution of the Hamming distance between the original and perturbed states.Item Open Access Reliability of transcriptional cycles and the yeast cell-cycle oscillator.(PLoS computational biology, 2010) Sevim, Volkan; Gong, Xinwei; Socolar, Joshua ESA 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.Item Open Access Stress propagation in locally loaded packings of disks and pentagonsKozlowski, Ryan; Zheng, Hu; Daniels, Karen E; Socolar, Joshua ESThe 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.Item Open Access Yielding, rigidity, and tensile stress in sheared columns of hexapod granules(Physical Review E) Zhao, Yuchen; Barés, Jonathan; Socolar, Joshua ESGranular packings of non-convex or elongated particles can form free-standing 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 non-interlocking 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, $\alpha$, of the sphero-cylinders and subject the packings to quasistatic direct shear. For small $\alpha$, we observe a finite yield stress. For large $\alpha$, however, the column becomes rigid when sheared, supporting stresses that increase sharply with increasing strain. Analysis of X-ray micro-computed 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 stabilize the particle cluster.