Dynamic screening by plasticity in amorphous solids.

In recent work it was shown that elasticity theory can break down in amorphous solids subjected to nonuniform static loads. The elastic fields are screened by geometric dipoles; these stem from gradients of the quadrupole field associated with plastic responses. Here we study the dynamical responses induced by oscillatory loads. The required modification to classical elasticity is described. Exact solutions for the displacement field in circular geometry are presented, demonstrating that dipole screening results in essential departures from the expected predictions of classical elasticity theory. Numerical simulations are conducted to validate the theoretical predictions and to delineate their range of validity.

Precise spatial memory in local random networks.

Self-sustained, elevated neuronal activity persisting on timescales of 10 s or longer is thought to be vital for aspects of working memory, including brain representations of real space. Continuous-attractor neural networks, one of the most well-known modeling frameworks for persistent activity, have been able to model crucial aspects of such spatial memory. These models tend to require highly structured or regular synaptic architectures. In contrast, we study numerical simulations of a geometrically embedded model with a local, but otherwise random, connectivity profile; imposing a global regulation of our system's mean firing rate produces localized, finely spaced discrete attractors that effectively span a two-dimensional manifold. We demonstrate how the set of attracting states can reliably encode a representation of the spatial locations at which the system receives external input, thereby accomplishing spatial memory via attractor dynamics without synaptic fine-tuning or regular structure. We then measure the network's storage capacity numerically and find that the statistics of retrievable positions are also equivalent to a full tiling of the plane, something hitherto achievable only with (approximately) translationally invariant synapses, and which may be of interest in modeling such biological phenomena as visuospatial working memory in two dimensions.

Plastic instabilities in charged granular systems: Competition between elasticity and electrostatics.

Electrostatic theory preserves charges, but allows dipolar excitations. Elasticity theory preserves dipoles, but allows quadrupolar (Eshelby-like) plastic events. Charged amorphous granular systems are interesting in their own right; here we focus on their plastic instabilities and examine their mechanical response to external strain and to an external electric field, to expose the competition between elasticity and electrostatics. In this paper a generic model is offered, its mechanical instabilities are examined, and a theoretical analysis is presented. Plastic instabilities are discussed as saddle-node bifurcations that can be fully understood in terms of eigenvalues and eigenfunctions of the relevant Hessian matrix. This system exhibits moduli that describe how electric polarization and stress are influenced by strain and the electric field. Theoretical expression for these moduli are offered and compared to the measurements in numerical simulations.

Scaling theory of shear-induced inhomogeneous dilation in granular matter.

Shearing with a finite shear rate a compressed granular system results in a region of grains flowing over a compact, static assembly. Perforce this region is dilated to a degree that depends on the shear rate, the loading pressure, gravity, various material parameters, and the preparation protocol. In spite of numerous studies of granular flows a predictive theory of the amount of dilation is still lacking. Here, we offer a scaling theory that is focused on such a prediction as a function of shear rate and the dissipative parameters of the granular assembly. The resulting scaling laws are universal with respect to changing the interparticle force laws.

Force distributions in frictional granular media.

We report a joint experimental and theoretical investigation of the probability distribution functions (PDFs) of the normal and tangential (frictional) forces in amorphous frictional media. We consider both the joint PDF of normal and tangential forces together, and the marginal PDFs of normal forces separately and tangential forces separately. A maximum entropy formalism is utilized for all these cases after identifying the appropriate constraints. Excellent agreements with both experimental and simulation data are reported. The proposed joint PDF predicts giant slip events at low pressures, again in agreement with observations.

The sandpile revisited: computer assisted determination of constitutive relations and the breaking of scaling.

We revisit the problem of the stress distribution in a frictional sandpile with both normal and tangential (frictional) inter-granular forces, under gravity, equipped with a new numerical method of generating such assemblies. Numerical simulations allow a determination of the spatial dependence of all the components of the stress field, principle stress axis, angle of repose, as a function of systems size, the coefficient of static friction and the frictional interaction with the bottom surface. We compare these results with the predictions of a theory based on continuum equilibrium mechanics. Basic to the theory of sandpiles are assumptions about the form of scaling solutions and constitutive relations for cohesive-less hard grains for which no typical scale is available. We find that these constitutive relations must be modified; moreover for smaller friction coefficients and smaller piles these scaling assumptions break down in the bulk of the sandpile due to the presence of length scales that must be carefully identified. Fortunately, for larger friction coefficient and for larger piles the breaking of scaling is weak in the bulk, allowing an approximate analytic theory which agrees well with the observations. After identifying the crucial scale, triggering the breaking of scaling, we provide a predictive theory to when scaling solutions are expected to break down. At the bottom of the pile the scaling assumption breaks always, due to the different interactions with the bottom surface. The consequences for measurable quantities like the pressure distribution and shear stress at the bottom of the pile are discussed. For example one can have a transition from no dip in the base-pressure to a dip at the center of the pile as friction increases.

Anatomy of plastic events in magnetic amorphous solids.

Plastic events in amorphous solids can be much more than just "shear transformation zones" when the positional degrees of freedom are coupled nontrivially to other degrees of freedom. Here we consider magnetic amorphous solids where mechanical and magnetic degrees of freedom interact, leading to rather complex plastic events whose nature must be disentangled. In this paper we uncover the anatomy of the various contributions to some typical plastic events. These plastic events are seen as Barkhausen noise or other "serrated noises." Using theoretical considerations we explain the observed statistics of the various contributions to the considered plastic events. The richness of contributions and their different characteristics imply that in general the statistics of these serrated noises cannot be universal, but rather highly dependent on the state of the system and on its microscopic interactions.

Elasticity and plasticity in stiff and flexible oligomeric glasses.

In this paper we focus on the mechanical properties of oligomeric glasses (waxes), employing a microscopic model that provides, via numerical simulations, information about the shear modulus of such materials, the failure mechanism via plastic instabilities, and the geometric responses of the oligomers themselves to a mechanical load. We present a microscopic theory that explains the numerically observed phenomena, including an exact theory of the shear modulus and of the plastic instabilities, both local and system spanning. In addition we present a model to explain the geometric changes in the oligomeric chains under increasing strains.

Yield strain in shear banding amorphous solids.

In recent research it was found that the fundamental shear-localizing instability of amorphous solids under external strain, which eventually results in a shear band and failure, consists of a highly correlated array of Eshelby quadrupoles all having the same orientation and some density ρ. In this paper we calculate analytically the energy E(ρ,γ) associated with such highly correlated structures as a function of the density ρ and the external strain γ. We show that for strains smaller than a characteristic strain γ(Y) the total strain energy initially increases as the quadrupole density increases, but that for strains larger than γ(Y) the energy monotonically decreases with quadrupole density. We identify γ(Y) as the yield strain. Its value, derived from values of the qudrupole strength based on the atomistic model, agrees with that from the computed stress-strain curves and broadly with experimental results.

Relaxation mechanisms in glassy dynamics: the Arrhenius and fragile regimes.

Generic glass formers exhibit at least two characteristic changes in their relaxation behavior, first to an Arrhenius-type relaxation at some characteristic temperature and then at a lower characteristic temperature to a super-Arrhenius (fragile) behavior. We address these transitions by studying the statistics of free energy barriers for different systems at different temperatures and space dimensions. We present a clear evidence for changes in the dynamical behavior at the transition to Arrhenius and then to a super-Arrhenius behavior. A simple model is presented, based on the idea of competition between single-particle and cooperative dynamics. We argue that Arrhenius behavior can take place as long as there is enough free volume for the completion of a simple T1 relaxation process. Once free volume is absent one needs a cooperative mechanism to "collect" enough free volume. We show that this model captures all the qualitative behavior observed in simulations throughout the considered temperature range.

Microscopic mechanism of shear bands in amorphous solids.

The fundamental instability responsible for the shear localization which results in shear bands in amorphous solids remains unknown despite an enormous amount of research, both experimental and theoretical. As this is the main mechanism for the failure of metallic glasses, understanding the instability is invaluable in finding how to stabilize such materials against the tendency to shear localize. In this Letter we explain the mechanism for shear localization under shear, which is the appearance of highly correlated lines of Eshelby-like quadrupolar singularities which organize the nonaffine plastic flow of the amorphous solid into a shear band. We prove analytically that such highly correlated solutions in which N quadrupoles are aligned with equal orientations are minimum energy states when the strain is high enough. The line lies at 45 degrees to the compressive stress.

From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development.

To gain performance, developers often build scientific applications in procedural languages, such as C or Fortran, which unfortunately reduces flexibility. To address this imbalance, the authors present CompuCell3D, a multitiered, flexible, and scalable problem-solving environment for morphogenesis simulations that's written in C++ using object-oriented design patterns.

A framework for three-dimensional simulation of morphogenesis.

We present COMPUCELL3D, a software framework for three-dimensional simulation of morphogenesis in different organisms. COMPUCELL3D employs biologically relevant models for cell clustering, growth, and interaction with chemical fields. COMPUCELL3D uses design patterns for speed, efficient memory management, extensibility, and flexibility to allow an almost unlimited variety of simulations. We have verified COMPUCELL3D by building a model of growth and skeletal pattern formation in the avian (chicken) limb bud. Binaries and source code are available, along with documentation and input files for sample simulations, at http:// compucell.sourceforge.net.

Dynamical instabilities of quasistatic crack propagation under thermal stress.

We address the theory of quasistatic crack propagation in a strip of glass that is pulled from a hot oven towards a cold bath. This problem had been carefully studied in a number of experiments that offer a wealth of data to challenge the theory. We improve upon previous theoretical treatments in a number of ways. First, we offer a technical improvement of the discussion of the instability towards the creation of a straight crack. This improvement consists in employing Padé approximants to solve the relevant Wiener-Hopf factorization problem that is associated with this transition. Next we improve the discussion of the onset of oscillatory instability towards an undulating crack. We offer a way of considering the problem as a sum of solutions of a finite strip without a crack and an infinite medium with a crack. This allows us to present a closed form solution of the stress intensity factors in the vicinity of the oscillatory instability. Most importantly we develop a dynamical description of the actual trajectory in the regime of oscillatory crack. This theory is based on the dynamical law for crack propagation proposed by Hodgdon and Sethna. We show that this dynamical law results in a solution of the actual crack trajectory in post-critical conditions; we can compute from first principles the critical value of the control parameters, and the characteristics of the solution such as the wavelength of the oscillations. We present detailed comparison with experimental measurements without any free parameters. The comparison appears quite excellent. Finally we show that the dynamical law can be translated to an equation for the amplitude of the oscillatory crack; this equation predicts correctly the scaling exponents observed in experiments.

Transition in the fractal properties from diffusion-limited aggregation to Laplacian growth via their generalization.

We study the fractal and multifractal properties (i.e., the generalized dimensions of the harmonic measure) of a two-parameter family of growth patterns that result from a growth model that interpolates between diffusion-limited aggregation (DLA) and Laplacian growth patterns in two dimensions. The two parameters are beta that determines the size of particles accreted to the interface, and C that measures the degree of coverage of the interface by each layer accreted to the growth pattern at every growth step. DLA and Laplacian growth are obtained at beta=0, C=0 and beta=2, C=1, respectively. The main purpose of this paper is to show that there exists a line in the beta-C phase diagram that separates fractal (D<2) from nonfractal (D=2) growth patterns. Moreover, Laplacian growth is argued to lie in the nonfractal part of the phase diagram. Some of our arguments are not rigorous, but together with the numerics they indicate this result rather strongly. We first consider the family of models obtained for beta=0, C>0, and derive for them a scaling relation D=2D(3). We then propose that this family has growth patterns for which D=2 for some C>C(cr), where C(cr) may be zero. Next we consider the whole beta-C phase diagram and define a line that separates two-dimensional growth patterns from fractal patterns with D<2. We explain that Laplacian growth lies in the region belonging to two-dimensional growth patterns, motivating the main conjecture of this paper, i.e., that Laplacian growth patterns are two dimensional. The meaning of this result is that the branches of Laplacian growth patterns have finite (and growing) area on scales much larger than any ultraviolet cutoff length.

Quasistatic fractures in brittle media and iterated conformal maps.

We study the geometrical characteristic of quasistatic fractures in brittle media, using iterated conformal maps to determine the evolution of the fracture pattern. This method allows an efficient and accurate solution of the Lamé equations without resorting to lattice models. Typical fracture patterns exhibit increased ramification due to the increase of the stress at the tips. We find the roughness exponent of the experimentally relevant backbone of the fracture pattern, it crosses over from about 0.5 for small scales to about 0.75 for large scales. We propose that this crossover reflects the increased ramification of the fracture pattern.