Elastic to plastic transition in amorphous solids.

The response of amorphous solids to mechanical loads is accompanied by plasticity that is generically associated with "non-affine" quadrupolar events seen in the resulting displacement field. To develop a continuum theory, one needs to assess when these quadrupolar events have a finite density, allowing the development of a field theory. Is there a transition, as a function of the material parameters and the nature of the loads, from isolated plastic events whose density is zero to a regime governed by a finite density? And if so, what is the nature of this transition? The aim of the paper is to explore this issue. The motivation for the present study stems from recent research in which it was shown that gradients of the quadrupolar fields act as dipole charges that can screen elasticity. Analytically soluble examples of mechanical loading that lead to screening and emergent length scales (that are absent in classical elasticity) have been analyzed and tested. However, "gradients of quadrupolar fields" make sense only when the density of quadrupoles is finite, and hence, the issue is central to this article. The article introduces a notion of polarizability under the strain of Eshelby quadrupoles and concludes that the onset of a density of such quadrupoles with random orientations can only appear when the polarizability is finite.

Creep failure of amorphous solids under tensile stress.

Applying constant tensile stress to a piece of amorphous solid results in a slow extension, followed by an eventual rapid mechanical collapse. This "creep" process is of paramount engineering concern, and as such was the subject of study in a variety of materials, for more than a century. Predictive theories for τ_{w}, the expected time of collapse, are incomplete, mainly due to its dependence on a bewildering variety of parameters, including temperature, system size, tensile force, but also the detailed microscopic interactions between constituents. The complex dependence of the collapse time on all the parameters is discussed below, using simulations of strip of amorphous material. Different scenarios are observed for ductile and brittle materials, resulting in serious difficulties in creating an all-encompassing theory that could offer safety measures for given conditions. A central aim of this paper is to employ scaling concepts, to achieve data collapse for the probability distribution function (pdf) of lnτ_{w}. The scaling ideas result in a universal function which provides a prediction of the pdf of lnτ_{w} for out-of-sample systems, from measurements at other values of these parameters. The predictive power of the scaling theory is demonstrated for both ductile and brittle systems. Finally, we present a derivation of universal scaling function for brittle materials. The ductile case appears to be due to a plastic necking instability and is left for future research.

Scaling theory for Wöhler plots in amorphous solids under cyclic forcing.

In mechanical engineering Wöhler plots serve to measure the average number of load cycles before materials break, as a function of the maximal stress in each cycle. Although such plots have been prevalent in engineering for more than 150 years, their theoretical understanding is lacking. Recently a scaling theory of Wöhler plots in the context of cyclic bending was offered [Bhowmik, arXiv:2103.03040 (2021)]. Here we elaborate further on cyclic bending and extend the considerations to cyclic tensile loads on an amorphous strip of material; the scaling theory applies to both types of cyclic loading equally well. On the basis of atomistic simulations we conclude that the crucial quantities to focus on are the accumulated damage and the average damage per cycle. The dependence of these quantities on the loading determines the statistics of the number of cycles to failure. Finally, we consider the probability distribution functions of the number of cycles to failure and demonstrate that the scaling theory allows prediction of these distributions at one value of the forcing amplitude from measurements and another value.

Aging and Failure of a Polymer Chain under Tension.

The rupture of a polymer chain maintained at temperature T under fixed tension is prototypical to a wide array of systems failing under constant external stress and random perturbations. Past research focused on analytic and numerical studies of the mean rate of collapse of such a chain. Surprisingly, an analytic calculation of the probability distribution function (PDF) of collapse rates appears to be lacking. Since rare events of rapid collapse can be important and even catastrophic, we present here a theory of this distribution, with a stress on its tail of fast rates. We show that the tail of the PDF is a power law with a universal exponent that is theoretically determined. Extensive numerics validate the offered theory. Lessons pertaining to other problems of the same type are drawn.

Diffusion in agitated frictional granular matter near the jamming transition.

We study agitated frictional disks in two dimensions with the aim of developing a scaling theory for their diffusion over time. As a function of the area fraction ϕ and mean-square velocity fluctuations 〈v^{2}〉 the mean-square displacement of the disks 〈d^{2}〉 spans four to five orders of magnitude. The motion evolves from a subdiffusive form to a complex diffusive behavior at long times. The statistics of 〈d^{n}〉 at all times are multiscaling, since the probability distribution function (PDF) of displacements has very broad wings. Even where a diffusion constant can be identified it is a complex function of ϕ and 〈v^{2}〉. By identifying the relevant length and time scales and their interdependence one can rescale the data for the mean-square displacement and the PDF of displacements into collapsed scaling functions for all ϕ and 〈v^{2}〉. These scaling functions provide a predictive tool, allowing one to infer from one set of measurements (at a given ϕ and 〈v^{2}〉) what are the expected results at any value of ϕ and 〈v^{2}〉 within the scaling range.

Stochastic approach to plasticity and yield in amorphous solids.

We focus on the probability distribution function (PDF) P(Δγ;γ) where Δγ are the measured strain intervals between plastic events in a athermal strained amorphous solids, and γ measures the accumulated strain. The tail of this distribution as Δγ→0 (in the thermodynamic limit) scales like Δγ(η). The exponent η is related via scaling relations to the tail of the PDF of the eigenvalues of the plastic modes of the Hessian matrix P(λ) which scales like λ(θ), η=(θ-1)/2. The numerical values of η or θ can be determined easily in the unstrained material and in the yielded state of plastic flow. Special care is called for in the determination of these exponents between these states as γ increases. Determining the γ dependence of the PDF P(Δγ;γ) can shed important light on plasticity and yield. We conclude that the PDF's of both Δγ and λ are not continuous functions of γ. In slowly quenched amorphous solids they undergo two discontinuous transitions, first at γ=0(+) and then at the yield point γ=γ(Y) to plastic flow. In quickly quenched amorphous solids the second transition is smeared out due to the nonexisting stress peak before yield. The nature of these transitions and scaling relations with the system size dependence of 〈Δγ〉 are discussed.

Local elastic response measured near the colloidal glass transition.

We examine the response of a dense colloidal suspension to a local force applied by a small magnetic bead. For small forces, we find a linear relationship between the force and the displacement, suggesting the medium is elastic, even though our colloidal samples macroscopically behave as fluids. We interpret this as a measure of the strength of colloidal caging, reflecting the proximity of the samples' volume fractions to the colloidal glass transition. The strain field of the colloidal particles surrounding the magnetic probe appears similar to that of an isotropic homogeneous elastic medium. When the applied force is removed, the strain relaxes as a stretched exponential in time. We introduce a model that suggests this behavior is due to the diffusive relaxation of strain in the colloidal sample.

Statistical mechanics of glass formation in molecular liquids with OTP as an example.

We extend our statistical mechanical theory of the glass transition from examples consisting of point particles to molecular liquids with internal degrees of freedom. As before, the fundamental assertion is that supercooled liquids are ergodic, although becoming very viscous at lower temperatures, and are therefore describable in principle by statistical mechanics. The theory is based on analyzing the local neighborhoods of each molecule, and a statistical mechanical weight is assigned to every possible local organization. This results in an approximate theory that is in very good agreement with simulations regarding both thermodynamical and dynamical properties.

Do athermal amorphous solids exist?

We study the elastic theory of amorphous solids made of particles with finite range interactions in the thermodynamic limit. For the elastic theory to exist, one requires all the elastic coefficients, linear and nonlinear, to attain a finite thermodynamic limit. We show that for such systems the existence of nonaffine mechanical responses results in anomalous fluctuations of all the nonlinear coefficients of the elastic theory. While the shear modulus exists, the first nonlinear coefficient B(2) has anomalous fluctuations and the second nonlinear coefficient B(3) and all the higher order coefficients (which are nonzero by symmetry) diverge in the thermodynamic limit. These results call into question the existence of elasticity (or solidity) of amorphous solids at finite strains, even at zero temperature. We discuss the physical meaning of these results and propose that in these systems elasticity can never be decoupled from plasticity: the nonlinear response must be very substantially plastic.

Size of plastic events in strained amorphous solids at finite temperatures.

We address the system-size dependence of plastic flow events when an amorphous solid is put under a fixed external strain rate at a finite temperature. For small system sizes at low strain rates and low temperatures the magnitude of plastic events grows with the system size. We explain, however, that this must be a finite-size effect; for larger systems there exist two crossover length scales xi{1} and xi{2}, the first determined by the elastic time scale and the second by the thermal energy scale. For systems of size L>>xi there must exist (L/xi){d} uncorrelated plastic events which occur simultaneously. We present a scaling theory that culminates with the dependence of the crossover scales on temperature and strain rate. Finally, we relate these findings to the temperature and size dependence of the stress fluctuations. We comment on the importance of these considerations for theories of elastoplasticity.

Nonuniversality of the specific heat in glass forming systems.

We present new simulation results for the specific heat in a classical model of a binary mixture glass former in two dimensions. We show that in addition to the formerly observed specific heat peak, there is a second peak at lower temperatures which was not observable in earlier simulations. This is a surprise, as most texts on the glass transition expect a single specific heat peak. We explain the physics of the two specific heat peaks by the micromelting of two types of clusters. While this physics is easily accessible, the consequences are that one should not expect any universality in the temperature dependence of the specific heat in glass formers.

Converting genetic network oscillations into somite spatial patterns.

The segmentation of vertebrate embryos, a process known as somitogenesis, depends on a complex genetic network that generates highly dynamic gene expression in an oscillatory manner. A recent proposal for the mechanism underlying these oscillations involves negative-feedback regulation at transcriptional translational levels, also known as the "delay model" [J. Lewis Curr. Biol. 13, 1398 (2003)]. In addition, in the zebrafish a longitudinal positional information signal in the form of an Fgf8 gradient constitutes a determination front that could be used to transform these coupled intracellular temporal oscillations into the observed spatial periodicity of somites. Here we consider an extension of the delay model by taking into account the interaction of the oscillation clock with the determination front. Comparison is made with the known properties of somite formation in the zebrafish embryo. We also show that the model can mimic the anomalies formed when progression of the determination wave front is perturbed and make an experimental prediction that can be used to test the model.

Theory of relaxation dynamics in glass-forming hydrogen-bonded liquids.

We address the relaxation dynamics in hydrogen-bonded supercooled liquids near (but above) the glass transition, measured via broadband dielectric spectroscopy (BDS). We propose a theory based on decomposing the relaxation of the macroscopic dipole moment into contributions from hydrogen-bonded clusters of s molecules, with s(min) < or = s < or = s(max) . The existence of s(max) is translated into a sum rule on the concentrations of clusters of size s . We construct the statistical mechanics of the supercooled liquid subject to this sum rule as a constraint, to estimate the temperature-dependent density of clusters of size s . With a theoretical estimate of the relaxation time of each cluster, we provide predictions for the real and imaginary parts of the frequency-dependent dielectric response. The predicted spectra and their temperature dependence are in accord with measurements, explaining a host of phenomenological fits like the Vogel-Fulcher fit and the stretched exponential fit. Using glycerol as a particular example, we demonstrate quantitative correspondence between theory and experiments. The theory also demonstrates that the alpha peak and the "excess wing" stem from the same physics in this material. The theory also shows that in other hydrogen-bonded glass formers the excess wing can develop into a beta peak, depending on the molecular material parameters (predominantly the surface energy of the clusters). We thus argue that alpha and beta peaks can stem from the same physics. We address the BDS in constrained geometries (pores) and explain why recent experiments on glycerol did not show a deviation from bulk spectra. Finally, we discuss the dc part of the BDS spectrum and argue why it scales with the frequency of the alpha peak, providing an explanation for the remarkable data collapse observed in experiments.

Theory of specific heat in glass-forming systems.

Experimental measurements of the specific heat in glass-forming systems are obtained from the linear response to either slow cooling (or heating) or to oscillatory perturbations with a given frequency about a constant temperature. The latter method gives rise to a complex specific heat with the constraint that the zero frequency limit of the real part should be identified with thermodynamic measurements. Such measurements reveal anomalies in the temperature dependence of the specific heat, including the so called "specific heat peak" in the vicinity of the glass transition. The aim of this paper is to provide theoretical explanations of these anomalies in general and a quantitative theory in the case of a simple model of glass formation. We first present interesting simulation results for the specific heat in a classical model of a binary mixture glass former. We show that in addition to the formerly observed specific heat peak there is a second peak at lower temperatures which was not observable in earlier simulations. Second, we present a general relation between the specific heat, a caloric quantity, and the bulk modulus of the material, a mechanical quantity, and thus offer a smooth connection between the liquid and amorphous solid states. The central result of this paper is a connection between the micromelting of clusters in the system and the appearance of specific heat peaks; we explain the appearance of two peaks by the micromelting of two types of clusters. We relate the two peaks to changes in the bulk and shear moduli. We propose that the phenomenon of glass formation is accompanied by a fast change in the bulk and the shear moduli, but these fast changes occur in different ranges of the temperature. Last, we demonstrate how to construct a theory of the frequency dependent complex specific heat, expected from heterogeneous clustering in the liquid state of glass formers. A specific example is provided in the context of our model for the dynamics of glycerol. We show that the frequency dependence is determined by the same alpha -relaxation mechanism that operates when measuring the viscosity or the dielectric relaxation spectrum. The theoretical frequency dependent specific heat agrees well with experimental measurements on glycerol. We conclude the paper by stating that there is nothing universal about the temperature dependence of the specific heat in glass formers-unfortunately, one needs to understand each case by itself.

The morphostatic limit for a model of skeletal pattern formation in the vertebrate limb.

A recently proposed mathematical model of a "core" set of cellular and molecular interactions present in the developing vertebrate limb was shown to exhibit pattern-forming instabilities and limb skeleton-like patterns under certain restrictive conditions, suggesting that it may authentically represent the underlying embryonic process (Hentschel et al., Proc. R. Soc. B 271, 1713-1722, 2004). The model, an eight-equation system of partial differential equations, incorporates the behavior of mesenchymal cells as "reactors," both participating in the generation of morphogen patterns and changing their state and position in response to them. The full system, which has smooth solutions that exist globally in time, is nonetheless highly complex and difficult to handle analytically or numerically. According to a recent classification of developmental mechanisms (Salazar-Ciudad et al., Development 130, 2027-2037, 2003), the limb model of Hentschel et al. is "morphodynamic," since differentiation of new cell types occurs simultaneously with cell rearrangement. This contrasts with "morphostatic" mechanisms, in which cell identity becomes established independently of cell rearrangement. Under the hypothesis that development of some vertebrate limbs employs the core mechanism in a morphostatic fashion, we derive in an analytically rigorous fashion a pair of equations representing the spatiotemporal evolution of the morphogen fields under the assumption that cell differentiation relaxes faster than the evolution of the overall cell density (i.e., the morphostatic limit of the full system). This simple reaction-diffusion system is unique in having been derived analytically from a substantially more complex system involving multiple morphogens, extracellular matrix deposition, haptotaxis, and cell translocation. We identify regions in the parameter space of the reduced system where Turing-type pattern formation is possible, which we refer to as its "Turing space." Obtained values of the parameters are used in numerical simulations of the reduced system, using a new Galerkin finite element method, in tissue domains with nonstandard geometry. The reduced system exhibits patterns of spots and stripes like those seen in developing limbs, indicating its potential utility in hybrid continuum-discrete stochastic modeling of limb development. Lastly, we discuss the possible role in limb evolution of selection for increasingly morphostatic developmental mechanisms.

Multiscale models for vertebrate limb development.

Dynamical systems in which geometrically extended model cells produce and interact with diffusible (morphogen) and nondiffusible (extracellular matrix) chemical fields have proved very useful as models for developmental processes. The embryonic vertebrate limb is an apt system for such mathematical and computational modeling since it has been the subject of hundreds of experimental studies, and its normal and variant morphologies and spatiotemporal organization of expressed genes are well known. Because of its stereotypical proximodistally generated increase in the number of parallel skeletal elements, the limb lends itself to being modeled by Turing-type systems which are capable of producing periodic, or quasiperiodic, arrangements of spot- and stripe-like elements. This chapter describes several such models, including, (i) a system of partial differential equations in which changing cell density enters into the dynamics explicitly, (ii) a model for morphogen dynamics alone, derived from the latter system in the "morphostatic limit" where cell movement relaxes on a much slower time-scale than cell differentiation, (iii) a discrete stochastic model for the simplified pattern formation that occurs when limb cells are placed in planar culture, and (iv) several hybrid models in which continuum morphogen systems interact with cells represented as energy-minimizing mesoscopic entities. Progress in devising computational methods for handling 3D, multiscale, multimodel simulations of organogenesis is discussed, as well as for simulating reaction-diffusion dynamics in domains of irregular shape.

Statistical mechanics of the glass transition as revealed by a Voronoi tesselation.

The statistical mechanics of simple glass forming systems in two dimensions is worked out. The glass disorder is encoded via a Voronoi tesselation, and the statistical mechanics is performed directly in this encoding. The theory provides, without free parameters, an explanation of the glass transition phenomenology, including the identification of two different temperatures, T(g) and T(c) , the first associated with jamming and the second associated with crystallization at very low temperatures.

A finite element method for growth in biological development.

We describe finite element simulations of limb growth based on Stokes flow models with a nonzero divergence representing growth due to nutrients in the early stages of limb bud development. We introduce a "tissue pressure" whose spatial derivatives yield the growth velocity in the limb and our explicit time advancing algorithm for such tissue flows is described in de tail. The limb boundary is approached by spline functions to compute the curvature and the unit outward normal vector. At each time step, a mixed hybrid finite element problem is solved, where the condition that the velocity is strictly normal to the limb boundary is treated by a Lagrange multiplier technique. Numerical results are presented.

Synchronization is enhanced in weighted complex networks.

The propensity for synchronization of complex networks with directed and weighted links is considered. We show that a weighting procedure based upon the global structure of network pathways enhances complete synchronization of identical dynamical units in scale-free networks. Furthermore, we numerically show that very similar conditions hold also for phase synchronization of nonidentical chaotic oscillators.

On multiscale approaches to three-dimensional modelling of morphogenesis.

In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion model and a state automaton with well-defined conditions for cell differentiation transitions to model genetic regulation. This environment allows us to rapidly and compactly create computational models of a class of complex-developmental phenomena. To illustrate model development, we simulate a simplified version of the formation of the skeletal pattern in a growing embryonic vertebrate limb.