Static and dynamic features of granular material failure due to upward pulling of a buried sphere by a slowly increasing force.

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.

Stress propagation in locally loaded packings of disks and pentagons.

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.

Shear-Jammed, Fragile, and Steady States in Homogeneously Strained Granular Materials.

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.

Hard sphere packings within cylinders.

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.

Delayed transition to new cell fates during cellular reprogramming.

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.

Phase transformations in binary colloidal monolayers.

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.

Graph fission in an evolving voter model.

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.

Regulatory logic and pattern formation in the early sea urchin embryo.

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).

Global control of cell-cycle transcription by coupled CDK and network oscillators.

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.

Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors.

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.

Evolution of force networks during stick-slip motion of an intruder in a granular material: Topological measures extracted from experimental data.

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.

Hierarchical freezing in a lattice model.

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.

Universal features of the stick-slip dynamics of an intruder moving through a confined granular medium.

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.

Reliability of transcriptional cycles and the yeast cell-cycle oscillator.

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.

Random logic networks: From classical Boolean to quantum dynamics.

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.

Yielding, rigidity, and tensile stress in sheared columns of hexapod granules.

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.

Dispersion tuning and route reconfiguration of acoustic waves in valley topological phononic crystals.

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 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 acoustic devices.

Intruder in a two-dimensional granular system: Effects of dynamic and static basal friction on stick-slip and clogging dynamics.

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.

Boolean modeling of collective effects in complex networks.

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.

Seismicity in sheared granular matter.

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.