The effects of forcing and dissipation on phase transitions in thin granular layers

Recent experimental and computational studies of vibrated thin layers of identical spheres have shown transitions to ordered phases similar to those seen in equilibrium systems. Motivated by these results, we carry out simulations of hard inelastic spheres forced by homogenous white noise. We find a transition to an ordered state of the same symmetry as that seen in the experiments, but the clear phase separation observed in the vibrated system is absent. Simulations of purely elastic spheres also show no evidence for phase separation. We show that the energy injection in the vibrated system is dramatically different in the different phases, and suggest that this creates an effective surface tension not present in the equilibrium or randomly forced systems. We do find, however, that inelasticity suppresses the onset of the ordered phase with random forcing, as is observed in the vibrating system, and that the amount of the suppression is proportional to the degree of inelasticity. The suppression depends on the details of the energy injection mechanism, but is completely eliminated when inelastic collisions are replaced by uniform system-wide energy dissipation.Comment: 10 pages, 5 figure

Geometry of Valley Growth

Although amphitheater-shaped valley heads can be cut by groundwater flows emerging from springs, recent geological evidence suggests that other processes may also produce similar features, thus confounding the interpretations of such valley heads on Earth and Mars. To better understand the origin of this topographic form we combine field observations, laboratory experiments, analysis of a high-resolution topographic map, and mathematical theory to quantitatively characterize a class of physical phenomena that produce amphitheater-shaped heads. The resulting geometric growth equation accurately predicts the shape of decimeter-wide channels in laboratory experiments, 100-meter wide valleys in Florida and Idaho, and kilometer wide valleys on Mars. We find that whenever the processes shaping a landscape favor the growth of sharply protruding features, channels develop amphitheater-shaped heads with an aspect ratio of pi

Unsteady Crack Motion and Branching in a Phase-Field Model of Brittle Fracture

Crack propagation is studied numerically using a continuum phase-field approach to mode III brittle fracture. The results shed light on the physics that controls the speed of accelerating cracks and the characteristic branching instability at a fraction of the wave speed.Comment: 11 pages, 4 figure

Phase field model of premelting of grain boundaries

We present a phase field model of solidification which includes the effects of the crystalline orientation in the solid phase. This model describes grain boundaries as well as solid-liquid boundaries within a unified framework. With an appropriate choice of coupling of the phase field variable to the gradient of the crystalline orientation variable in the free energy, we find that high angle boundaries undergo a premelting transition. As the melting temperature is approached from below, low angle grain boundaries remain narrow. The width of the liquid layer at high angle grain boundaries diverges logarithmically. In addition, for some choices of model coupling, there may be a discontinuous jump in the width of the fluid layer as function of temperature.Comment: 6 pages, 9 figures, RevTeX

Estimation of prokaryotic supergenome size and composition from gene frequency distributions

BACKGROUND: Because prokaryotic genomes experience a rapid flux of genes, selection may act at a higher level than an individual genome. We explore a quantitative model of the distributed genome whereby groups of genomes evolve by acquiring genes from a fixed reservoir which we denote as supergenome. Previous attempts to understand the nature of the supergenome treated genomes as random, independent collections of genes and assumed that the supergenome consists of a small number of homogeneous sub-reservoirs. Here we explore the consequences of relaxing both assumptions. RESULTS: We surveyed several methods for estimating the size and composition of the supergenome. The methods assumed that genomes were either random, independent samples of the supergenome or that they evolved from a common ancestor along a known tree via stochastic sampling from the reservoir. The reservoir was assumed to be either a collection of homogeneous sub-reservoirs or alternatively composed of genes with Gamma distributed gain probabilities. Empirical gene frequencies were used to either compute the likelihood of the data directly or first to reconstruct the history of gene gains and then compute the likelihood of the reconstructed numbers of gains. CONCLUSIONS: Supergenome size estimates using the empirical gene frequencies directly are not robust with respect to the choice of the model. By contrast, using the gene frequencies and the phylogenetic tree to reconstruct multiple gene gains produces reliable estimates of the supergenome size and indicates that a homogeneous supergenome is more consistent with the data than a supergenome with Gamma distributed gain probabilities

Properties of Ridges in Elastic Membranes

When a thin elastic sheet is confined to a region much smaller than its size the morphology of the resulting crumpled membrane is a network of straight ridges or folds that meet at sharp vertices. A virial theorem predicts the ratio of the total bending and stretching energies of a ridge. Small strains and curvatures persist far away from the ridge. We discuss several kinds of perturbations that distinguish a ridge in a crumpled sheet from an isolated ridge studied earlier (A. E. Lobkovsky, Phys. Rev. E. 53 3750 (1996)). Linear response as well as buckling properties are investigated. We find that quite generally, the energy of a ridge can change by no more than a finite fraction before it buckles.Comment: 13 pages, RevTeX, acknowledgement adde

Critical examination of cohesive-zone models in the theory of dynamic fracture

We have examined a class of cohesive-zone models of dynamic mode-I fracture, looking both at steady-state crack propagation and its stability against out-of-plane perturbations. Our work is an extension of that of Ching, Langer, and Nakanishi (CLN) (Phys. Rev. E, vol. 53, no. 3, p. 2864 (1996)), who studied a non-dissipative version of this model and reported strong instability at all non-zero crack speeds. We have reformulated the CLN theory and have discovered, surprisingly, that their model is mathematically ill-posed. In an attempt to correct this difficulty and to construct models that might exhibit realistic behavior, we have extended the CLN analysis to include dissipative mechanisms within the cohesive zone. We have succeeded to some extent in finding mathematically well posed systems; and we even have found a class of models for which a transition from stability to instability may occur at a nonzero crack speed via a Hopf bifurcation at a finite wavelength of the applied perturbation. However, our general conclusion is that these cohesive-zone models are inherently unsatisfactory for use in dynamical studies. They are extremely difficult mathematically, and they seem to be highly sensitive to details that ought to be physically unimportant.Comment: 19 pages, REVTeX 3.1, epsf.sty, also available at http://itp.ucsb.edu/~lobkovs

Low temperature dynamics of kinks on Ising interfaces

The anisotropic motion of an interface driven by its intrinsic curvature or by an external field is investigated in the context of the kinetic Ising model in both two and three dimensions. We derive in two dimensions (2d) a continuum evolution equation for the density of kinks by a time-dependent and nonlocal mapping to the asymmetric exclusion process. Whereas kinks execute random walks biased by the external field and pile up vertically on the physical 2d lattice, then execute hard-core biased random walks on a transformed 1d lattice. Their density obeys a nonlinear diffusion equation which can be transformed into the standard expression for the interface velocity v = M[(gamma + gamma'')kappa + H]$, where M, gamma + gamma'', and kappa are the interface mobility, stiffness, and curvature, respectively. In 3d, we obtain the velocity of a curved interface near the orientation from an analysis of the self-similar evolution of 2d shrinking terraces. We show that this velocity is consistent with the one predicted from the 3d tensorial generalization of the law for anisotropic curvature-driven motion. In this generalization, both the interface stiffness tensor and the curvature tensor are singular at the orientation. However, their product, which determines the interface velocity, is smooth. In addition, we illustrate how this kink-based kinetic description provides a useful framework for studying more complex situations by modeling the effect of immobile dilute impurities.Comment: 11 pages, 10 figure

Viral Diversity Threshold for Adaptive Immunity in Prokaryotes

Bacteria and archaea face continual onslaughts of rapidly diversifying viruses and plasmids. Many prokaryotes maintain adaptive immune systems known as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas). CRISPR-Cas systems are genomic sensors that serially acquire viral and plasmid DNA fragments (spacers) that are utilized to target and cleave matching viral and plasmid DNA in subsequent genomic invasions, offering critical immunological memory. Only 50% of sequenced bacteria possess CRISPR-Cas immunity, in contrast to over 90% of sequenced archaea. To probe why half of bacteria lack CRISPR-Cas immunity, we combined comparative genomics and mathematical modeling. Analysis of hundreds of diverse prokaryotic genomes shows that CRISPR-Cas systems are substantially more prevalent in thermophiles than in mesophiles. With sequenced bacteria disproportionately mesophilic and sequenced archaea mostly thermophilic, the presence of CRISPR-Cas appears to depend more on environmental temperature than on bacterial-archaeal taxonomy. Mutation rates are typically severalfold higher in mesophilic prokaryotes than in thermophilic prokaryotes. To quantitatively test whether accelerated viral mutation leads microbes to lose CRISPR-Cas systems, we developed a stochastic model of virus-CRISPR coevolution. The model competes CRISPR-Cas-positive (CRISPR-Cas+) prokaryotes against CRISPR-Cas-negative (CRISPR-Cas−) prokaryotes, continually weighing the antiviral benefits conferred by CRISPR-Cas immunity against its fitness costs. Tracking this cost-benefit analysis across parameter space reveals viral mutation rate thresholds beyond which CRISPR-Cas cannot provide sufficient immunity and is purged from host populations. These results offer a simple, testable viral diversity hypothesis to explain why mesophilic bacteria disproportionately lack CRISPR-Cas immunity. More generally, fundamental limits on the adaptability of biological sensors (Lamarckian evolution) are predicted

Erosion of a granular bed driven by laminar fluid flow

Motivated by examples of erosive incision of channels in sand, we investigate the motion of individual grains in a granular bed driven by a laminar fluid to give us new insights into the relationship between hydrodynamic stress and surface granular flow. A closed cell of rectangular cross-section is partially filled with glass beads and a constant fluid flux $Q$ flows through the cell. The refractive indices of the fluid and the glass beads are matched and the cell is illuminated with a laser sheet, allowing us to image individual beads. The bed erodes to a rest height $h_r$ which depends on $Q$. The Shields threshold criterion assumes that the non-dimensional ratio $\theta$ of the viscous stress on the bed to the hydrostatic pressure difference across a grain is sufficient to predict the granular flux. Furthermore, the Shields criterion states that the granular flux is non-zero only for $\theta >\theta_c$. We find that the Shields criterion describes the observed relationship $h_r \propto Q^{1/2}$ when the bed height is offset by approximately half a grain diameter. Introducing this offset in the estimation of $\theta$ yields a collapse of the measured Einstein number $q^*$ to a power-law function of $\theta - \theta_c$ with exponent $1.75 \pm 0.25$. The dynamics of the bed height relaxation are well described by the power law relationship between the granular flux and the bed stress.Comment: 12 pages, 5 figure