Probability distribution of inherent states in models of granular media and glasses

The present paper develops a Statistical Mechanics approach to the inherent states of glassy systems and granular materials by following the original ideas proposed by Edwards for granular media. We consider three lattice models (a diluted spin glass, a system of hard spheres under gravity and a hard-spheres binary mixture under gravity) introduced to describe glassy and granular systems. They are evolved using a “tap dynamics” analogous to that of experiments on granular media. We show that the asymptotic states reached in such a dynamics are not dependent on the particular sample history and are characterized by a few thermodynamical parameters. We assume that under stationarity these systems are distributed in their inherent states satisfying the principle of maximum entropy. This leads to a generalized Gibbs distribution characterized by new “thermodynamical” parameters, called “configurational temperatures” (related to Edwards compactivity for granular materials). Finally, we show by Monte Carlo calculations that the average of macroscopic quantities over the tap dynamics and over such distribution indeed coincide. In particular, in the diluted spin glass and in the system of hard spheres under gravity, the asymptotic states reached by the system are found to be described by a single “configurational temperature”. Whereas in the hard-spheres binary mixture under gravity the asymptotic states reached by the system are found to be described by two thermodynamic parameters, coinciding with the two configurational temperatures which characterize the distribution among the inherent states when the principle of maximum entropy is satisfied under the constraint that the energies of the two species are independently fixed. Received 19 March 2002 and Received in final form 14 June 2002     

Jamming: A simple introduction

Amorphous materials as diverse as foams, emulsions, colloidal suspensions and granular media can jam into a rigid, disordered state where they withstand finite shear stresses before yielding. Here we give a simple introduction to the surprising physics displayed by a very simple model system for the jamming transition: frictionless, soft spheres at zero temperature and zero shear that act through purely repulsive contact forces. This system starts to become rigid, i.e. goes through the jamming transition, whenever the confining pressure becomes positive. We highlight some of the remarkable geometrical features of the zero pressure jamming point and discuss the peculiar mechanical properties of these systems for small pressures.     

Self-organization of the critical state in granular superconductors

The critical state in granular superconductors is studied using two mathematical models: systems of differential equations for the gauge-invariant phase difference and a simplified model that is described by a system of coupled mappings and in many cases is equivalent to the standard models used for studying self-organized criticality. It is shown that the critical state of granular superconductors is self-organized in all cases studied. In addition, it is shown that the models employed are essentially equivalent, i.e., they demonstrate not only the same critical behavior, but they also lead to the same noncritical phenomena. The first demonstration of the existence of self-organized criticality in a system of nonlinear differential equations and its equivalence to self-organized criticality in standard models is given in this paper.     

Microstructure characterization and bulk properties of disordered two-phase media

A general formalism is developed to statistically characterize the microstructure of porous and other composite media composed of inclusions (particles) distributed throughout a matrix phase (which, in the case of porous media, is the void phase). This is accomplished by introducing a new and generaln-point distribution functionH _n and by deriving two series representations of it in terms of the probability density functions that characterize the configuration of particles; quantities that, in principle, are known for the ensemble under consideration. In the special case of an equilibrium ensemble, these two equivalent but topologically different series for theH _n are generalizations of the Kirkwood-Salsburg and Mayer hierarchies of liquid-state theory for a special mixture of particles described in the text. This methodology provides a means of calculating any class of correlation functions that have arisen in rigorous bounds on transport properties (e.g., conductivity and fluid permeability) and mechanical properties (e.g., elastic moduli) for nontrivial models of two-phase disordered media. Asymptotic and bounding properties of the general functionH _n are described. To illustrate the use of the formalism, some new results are presented for theH _n and it is shown how such information is employed to compute bounds on bulk properties for models of fully penetrable (i.e., randomly centered) spheres, totally impenetrable spheres, and spheres distributed with arbitrary degree of impenetrability. Among other results, bounds are computed on the fluid permeability, for assemblages of impenetrable as well as penetrable spheres, with heretofore unattained accuracy.     

Emergence of the self-similar property in gene expression dynamics

Many theoretical models have recently been proposed to understand the structure of cellular systems composed of various types of elements (e.g., proteins, metabolites and genes) and their interactions. However, the cell is a highly dynamic system with thousands of functional elements fluctuating across temporal states. Therefore, structural analysis alone is not sufficient to reproduce the cell's observed behavior.In this article, we analyze the gene expression dynamics (i.e., how the amount of mRNA molecules in cell fluctuate in time) by using a new constructive approach, which reveals a symmetry embedded in gene expression fluctuations and characterizes the dynamical equation of gene expression (i.e., a specific stochastic differential equation). First, by using experimental data of human and yeast gene expression time series, we found a symmetry in short-time transition probability from time t to time t+1. We call it self-similarity symmetry (i.e., the gene expression short-time fluctuations contain a repeating pattern of smaller and smaller parts that are like the whole, but different in size). Secondly, we reconstruct the global behavior of the observed distribution of gene expression (i.e., scaling-law) and the local behavior of the power-law tail of this distribution. This approach may represent a step forward toward an integrated image of the basic elements of the whole cell.     

Dynamics of chain molecules in disordered materials

The dynamic behavior of hard chains in disordered materials composed of fixed hard spheres is studied using discontinuous molecular dynamics simulations. The matrix induces entanglements in the chain fluid, i.e., for high matrix densities the diffusion coefficient D scales with the chain length N as D is approximately N(-2). At high matrix densities the rotational relaxation time becomes very large but the translational diffusion is not affected significantly; i.e., the chains display a dynamic heterogeneity reminiscent of probe diffusion in supercooled liquids and glasses. We show that this is because some chains are trapped, and move via a hopping mechanism. There are no signatures of this dynamic heterogeneity in the matrix static structure, however, which is identical to that of a hard-sphere liquid.     

Open problems in active chaotic flows: Competition between chaos and order in granular materials

There are many systems where interaction among the elementary building blocks-no matter how well understood-does not even give a glimpse of the behavior of the global system itself. Characteristic for these systems is the ability to display structure without any external organizing principle being applied. They self-organize as a consequence of synthesis and collective phenomena and the behavior cannot be understood in terms of the systems' constitutive elements alone. A simple example is flowing granular materials, i.e., systems composed of particles or grains. How the grains interact with each other is reasonably well understood; as to how particles move, the governing law is Newton's second law. There are no surprises at this level. However, when the particles are many and the material is vibrated or tumbled, surprising behavior emerges. Systems self-organize in complex patterns that cannot be deduced from the behavior of the particles alone. Self-organization is often the result of competing effects; flowing granular matter displays both mixing and segregation. Small differences in either size or density lead to flow-induced segregation and order; similar to fluids, noncohesive granular materials can display chaotic mixing and disorder. Competition gives rise to a wealth of experimental outcomes. Equilibrium structures, obtained experimentally in quasi-two-dimensional systems, display organization in the presence of disorder, and are captured by a continuum flow model incorporating collisional diffusion and density-driven segregation. Several open issues remain to be addressed. These include analysis of segregating chaotic systems from a dynamical systems viewpoint, and understanding three-dimensional systems and wet granular systems (slurries). General aspects of the competition between chaos-enhanced mixing and properties-induced de-mixing go beyond granular materials and may offer a paradigm for other kinds of physical systems. (c) 2002 American Institute of Physics.     

Janssen's law and stress fluctuations in confined dry granular materials

In order to clarify the mechanisms which determine the Janssen's law for the pressure distribution at the bottom of a silo we reconsider the so-called q-model describing an assembly of granular particles on a lattice, confined between vertical walls. We find that the expected macroscopic behavior with the correct scaling is obtained whenever a mechanism able to transfer the weight from the interior of the silo to the walls in an efficient way is present, i.e., in mean field regime. Deviations from the Janssen law's found in lattice models are due to the absence of this efficient mechanism. We investigate the scaling properties of a stick-slip model recently introduced, and find that relative fluctuations do not disappear for large systems and are of the order of average values. Finally we observe that an exponential local weight distribution at the bottom of the silo is independent of the model considered.     

Two scenarios for avalanche dynamics in inclined granular layers

We report experimental measurements of avalanche behavior of thin granular layers on an inclined plane for low volume flow rate. The dynamical properties of avalanches were quantitatively and qualitatively different for smooth glass beads compared to irregular granular materials such as sand. Two scenarios for granular avalanches on an incline are identified, and a theoretical explanation for these different scenarios is developed based on a depth-averaged approach that takes into account the differing rheologies of the granular materials.     

Extended three-dimensional impedance map methods for identifying ultrasonic scattering sites

The frequency-dependent ultrasound backscatter from tissues contains information about the microstructure that can be quantified. In many cases, the anatomic microstructure details responsible for ultrasonic scattering remain unidentified. However, their identification would lead to potentially improved methodologies for characterizing tissue and diagnosing disease from ultrasonic backscatter measurements. Recently, three-dimensional (3D) acoustic models of tissue microstructure, termed 3D impedance maps (3DZMs), were introduced to help to identify scattering sources [J. Mamou, M. L. Oelze, W. D. O'Brien, Jr., and J. F. Zachary, "Identifying ultrasonic scattering sites from 3D impedance maps," J. Acoust. Soc. Am. 117, 413-423 (2005)]. In the current study, new 3DZM methodologies are used to model and identify scattering structures. New processing procedures (e.g., registration, interpolations) are presented that allow more accurate 3DZMs to be constructed from histology. New strategies are proposed to construct scattering models [i.e., form factor (FF)] from 3DZMs. These new methods are tested on simulated 3DZMs, and then used to evaluate 3DZMs from three different rodent tumor models. Simulation results demonstrate the ability of the extended strategies to accurately predict FFs and estimate scatterer properties. Using the 3DZM methods, distinct FFs and scatterer properties were obtained for each tumor examined.     

Subdiffusion and cage effect in a sheared granular material

We investigate experimentally the diffusion properties of a bidimensional bidisperse dry granular material under quasistatic cyclic shear. The comparison of these properties with results obtained both in computer simulations of hard spheres systems and Lennard-Jones liquids and experiments on colloidal systems near the glass transition demonstrates a strong analogy between the statistical behavior of granular matter and these systems, despite their intrinsic microscopic differences (thermal vs athermal). More specifically, we study in detail the cage dynamics responsible for the subdiffusion in the slow relaxation regime, and obtain the values of relevant time and length scales.     

High-Resolution Single-Grain Diffraction of Polycrystalline Materials

Polycrystalline bulk materials are ubiquitous in everyday life, including biological, geological, and engineered structural and functional materials. Their fundamental units are individual grains, which are characterized by their microstructure; i.e., the arrangement of lattice defects. The microstructure usually influences the materials properties critically.     

Coarsening in granular systems

We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular media. Thereafter, dilute systems, the so-called “granular gases”, are discussed: idealized kinetic models, such as the gas of inelastic hard spheres in the cooling regime, are the optimal playground to study the slow growth of correlated structures, e.g., shear patterns, vortices, and clusters. In fluidized experiments, liquid–gas or solid–gas separations have been observed. In the case of monolayers of particles, phase coexistence and coarsening appear in several different setups, with mechanical or electrostatic energy input. Phenomenological models describe, even quantitatively, several experimental measures, both for the coarsening dynamics and for the dynamic transition between different granular phases. The origin of the underlying bistability is in general related to negative compressibility from granular hydrodynamics computations, even if the understanding of the mechanism is far from complete. A relevant problem, with important industrial applications, is related to the demixing or segregation of mixtures, for instance in rotating tumblers or on horizontally vibrated plates. Finally, the problem of compaction of highly dense granular materials, which is relevant in many practical situations, is usually described in terms of coarsening dynamics: there, bubbles of misaligned grains evaporate, allowing the coalescence of optimally arranged islands and a progressive reduction of the total occupied volume.     

Variational approach to hard sphere segregation under gravity

It is demonstrated that the minimization of the free energy functional for hard spheres and hard disks yields the result that excited granular materials under gravity segregate not only in the widely known "Brazil nut" fashion, i.e., with the larger particles rising to the top, but also in reverse "Brazil nut" fashion. Specifically, the local density approximation is used to investigate the crossover between the two types of segregation occurring in the liquid state, and the results are found to agree qualitatively with previously published results of simulation and of a simple model based on condensation.     

Preavalanche instabilities in a granular pile

We investigate numerically the transition between static equilibrium and dynamic surface flow of a 2D cohesionless granular system driven by a continuous gravity loading. This transition is characterized by intermittent local dynamic rearrangements and can be described by an order parameter defined as the density of critical contacts, i.e., contacts where the friction is fully mobilized. Analysis of the spatial correlations of critical contacts shows the occurrence of "fluidized" clusters which exhibit a power-law divergence in size at the approach of the stability limit. The results are compatible with recent models that describe the granular system during the static/dynamic transition as a multiphase system.     

3D Particle Tracking on a Two-Photon Microscope

A 3D single-particle-tracking (SPT) system was developed based on two-photon excitation fluorescence microscopy that can track the motion of particles in three dimensions over a range of 100 μm and with a bandwidth up to 30 Hz. We have implemented two different techniques employing feedback control. The first technique scans a small volume around a particle to build up a volumetric image that is then used to determine the particle's position. The second technique scans only a single plane but utilizes optical aberrations that have been introduced into the optical system that break the axial symmetry of the point spread function and serve as an indicator of the particle's axial position. We verified the performance of the instrument by tracking particles in well-characterized models systems. We then studied the 3D viscoelastic mechanical response of 293 kidney cells using the techniques. Force was applied to the cells, by using a magnetic manipulator, onto the paramagnetic spheres attached to the cell via cellular integrin receptors. The deformation of the cytoskeleton was monitored by following the motion of nearby attached fluorescent polystyrene spheres. We showed that planar stress produces strain in all three dimensions, demonstrating that the 3D motion of the cell is required to fully model cellular mechanical responses.     

Insights into linearized rotor dynamics

Over the last 20 years, linearized rotor-bearing models have been used in lateral vibration analyses of numerous rotating machines: i.e., prediction of critical speeds, unbalance response, non-synchronous response, and instability threshold speed. Advances in computers and computing techniques over this period have had their effect by expanding the complexity of rotor-bearing systems which can be comprehensively analyzed. However, certain fundamental physical and mathematical properties of these systems have naturally remained unchanged. Some of these fundamental properties have not been given the attention or clarification they deserve, in contrast to the coverage given computing techniques and results. This paper has been written to relate various physical properties of linearized rotor-bearing systems to certain unique mathematical properties they possess.     

Granular layers on vibrating plates: effective bending stiffness and particle-size effects

Acoustic methods of land mine detection rely on the vibrations of the top plate of the mine in response to sound. For granular soil (e.g., sand), the particle size is expected to influence the mine response. This hypothesis is studied experimentally using a plate loaded with dry sand of various sizes from hundreds of microns to a few millimeters. For low values of sand mass, the plate resonance decreases with added mass and eventually reaches a minimum without particle size dependence. After the minimum, a frequency increase is observed with additional mass that includes a particle-size effect. Analytical nondissipative continuum models for granular media capture the observed particle-size dependence qualitatively but not quantitatively. In addition, a continuum-based finite element model (FEM) of a two-layer plate is used, with the sand layer replaced by an equivalent elastic layer for evaluation of the effective properties of the layer. Given a thickness of sand layer and corresponding experimental resonance, an inverse FEM problem is solved iteratively to give the effective Young's modulus and bending stiffness that matches the experimental frequency. It is shown that a continuum elastic model must employ a thickness-dependent elastic modulus in order to match experimental values.     

Analytical electron microscopy of silver halide photographic systems

Studies of silver halide (AgX) photographic materials and individual microcomponents by TEM/STEM/SEM/EDX, CL, EFTEM/EELS and digital image analysis techniques are reviewed. Electron-beam-AgX interactions are discussed to clarify relationships between the signals analysed in various operating AEM modes. An optimum strategy of structural and analytical diagnosis of complex silver halide photographic systems by a number of AEM methods is considered, using a number of examples (colour and black-and-white films, AgX microcrystals, and colour coupler dispersions). AEM applications to study of the main stages of the photographic process, i.e., chemical ripening, spectral sensitisation, latent image formation and development are also presented. Current trends and future directions in research of AgX-based photographic systems by AEM techniques are outlined.     

Chord length distributions in binary stochastic media in two and three dimensions

Simple models for transport through stochastic media usually assume that the chord lengths of materials are distributed exponentially. Theory predicts that, in a medium consisting of disks/spheres that can interpenetrate, chord lengths in the background material (between the disks/spheres) should exactly follow an exponential. In a medium with impenetrable (non-overlapping) disks/spheres, the distribution is only approximately exponential. This paper demonstrates, through direct numerical simulations, that for randomly distributed disks in 2D and spheres in 3D, with distributions of radii, chord lengths in the background material (between the disks/spheres) are accurately described by exponentials over five orders of magnitude when the material is dilute. The chord lengths inside the disks and spheres are not exponentially distributed, but those distributions can be calculated. A scaling relationship between the mean chord lengths in the two materials is presented for an infinite medium. By knowing the mean properties of the disks/spheres in a medium, this relationship allows one to accurately describe the statistical properties of the background material. The stochastic simulations are validated by this infinite medium relationship. When the fraction of space occupied by the disks or spheres becomes large, the distributions are no longer accurately described by an exponential.