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The classic paradigms for learning and memory recall focus on strengths of synaptic couplings and how these can be modulated to encode memories. In a previous paper [A. K. Behera, M. Rao, S. Sastry, and S. Vaikuntanathan, Physical Review X 13, 041043 (2023)], we demonstrated how a specific non-equilibrium modification of the dynamics of an associative memory system can lead to increase in storage capacity. In this work, using analytical theory and computational inference schemes, we show that the dynamical steady state accessed is in fact similar to those accessed after the operation of a classic unsupervised scheme for improving memory recall, Hebbian unlearning or ``dreaming". Together, our work suggests how nonequilibrium dynamics can provide an alternative route for controlling the memory encoding and recall properties of a variety of synthetic (neuromorphic) and biological systems., Comment: 15 pages, 13 figures

Solids subjected to repeated cycles of stress or deformation can fail after several cycles, a phenomenon termed fatigue failure. Although intensely investigated for a wide range of materials owing to its obvious practical importance, a microscopic understanding of the initiation of fatigue failure continues to be actively pursued, in particular for soft and amorphous materials. We investigate fatigue failure for glasses subjected to cyclic shear deformation through computer simulations. We show that, approaching the so-called fatigue limit, failure times display a power law divergence, at variance with commonly used functional forms, and exhibit strong dependence on the degree of annealing of the glasses. We explore several measures of damage, based on quantification of plastic rearrangements and on dissipated energy. Strikingly, the fraction of particles that undergo plastic rearrangements, and a percolation transition they undergo, are predictive of failure. We also find a robust power law relationship between accumulated damage, quantified by dissipated energy or non-affine displacements, and the failure times, which permits prediction of failure times based on behavior in the initial cycles. These observations reveal salient new microscopic features of fatigue failure and suggest approaches for developing a full microscopic picture of fatigue failure in amorphous solids.

Vitrimers are polymer networks that can undergo bond exchange reactions. They dynamically rearrange their structures while maintaining their overall integrity, thus resulting in unique properties such as self-healing, reprocessability, shape memory and adaptability. Here, we show that the introduction of dynamic bonds directly impacts the polymer density. For a limiting case, where the dynamic bonds are the same size as the polymer chain bonds, simulations and theory show an enhancement in the density, because these bonds induce an increased cohesive force in the liquid, which is entropic in origin. The crosslinks are well mixed in the bulk but are depleted from the air and polymer interface. These findings implicate density as a key variable in polymers with dynamic crosslinkers, one that can be used to facilely tune their properties.

The investigation of collective behaviour in dense assemblies of self-propelled active particles has been motivated by a wide range of biological phenomena. Of particular interest are dynamical transitions of cellular and sub-cellular biological assemblies, including the cytoskeleton and the cell nucleus. Motivated by observations of mechanically induced changes in the dynamics of such systems, and the apparent role of confinement geometry, we study the transition between jammed and fluidized states of active particles assemblies, as a function of the strength and temporal persistence of active forces, and in different confinement geometries. Our results show that the fluidization transition broadly resembles yielding in amorphous solids, consistently with recent suggestions. More specifically, however, we find that a detailed analogy holds with the yielding transition under cyclic shear deformation, for finite persistence times. The fluidization transition is accompanied by driving induced annealing, strong dependence on the initial state of the system, a divergence of time scales to reach steady states, and a discontinuous onset of diffusive motion. We also observe a striking dependence of the transition on persistence times and on the nature of the confinement. Collectively, our results have implications in epigenetic cell state transitions induced by alterations in confinement geometry., Comment: 7 pages, 4 figures and 10 pages of supp. matt

Optimization of atomic structures presents a challenging problem, due to their highly rough and non-convex energy landscape, with wide applications in the fields of drug design, materials discovery, and mechanics. Here, we present a graph reinforcement learning approach, StriderNET, that learns a policy to displace the atoms towards low energy configurations. We evaluate the performance of StriderNET on three complex atomic systems, namely, binary Lennard-Jones particles, calcium silicate hydrates gel, and disordered silicon. We show that StriderNET outperforms all classical optimization algorithms and enables the discovery of a lower energy minimum. In addition, StriderNET exhibits a higher rate of reaching minima with energies, as confirmed by the average over multiple realizations. Finally, we show that StriderNET exhibits inductivity to unseen system sizes that are an order of magnitude different from the training system.

A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used, especially in the presence of large free energy barriers, to estimate free energies using biasing protocols and sampling of transition paths. Kinetic reconstructions of free energy barriers of intermediate height have been performed, with respect to a single order parameter, employing the steady state properties of unconstrained simulation trajectories when barrier crossing is achievable with reasonable computational effort. Considering such cases, we describe a method to estimate free energy surfaces with respect to multiple order parameters from a steady state ensemble of trajectories. The approach applies to cases where the transition rates between pairs of order parameter values considered is not affected by the presence of an absorbing boundary, whereas the macroscopic fluxes and sampling probabilities are. We demonstrate the applicability of our prescription on different test cases of random walkers executing Brownian motion in order parameter space with an underlying (free) energy landscape and discuss strategies to improve numerical estimates of the fluxes and sampling. We next use this approach to reconstruct the free energy surface for supercooled liquid silicon with respect to the degree of crystallinity and density, from unconstrained molecular dynamics simulations, and obtain results quantitatively consistent with earlier results from umbrella sampling.

We investigate the rigidity transition associated with shear jamming in frictionless, as well as frictional, disk packings in the quasi-static regime and at low shear rates. For frictionless disks, the transition is under quasistatic shear is discontinuous, with an instantaneous emergence of a system spanning rigid cluster at the jamming transition. For frictional systems, the transition appears continuous for finite shear rates, but becomes sharper for lower shear rates. In the quasi-static limit, it is discontinuous as in the frictionless case. Thus, our results show that the rigidity transition associated with shear jamming is discontinuous, as demonstrated in a past for isotropic jamming of frictionless particles, and therefore a unifying feature of the jamming transition in general.

The existence of a phase transition between two distinct liquid phases in single-component network-forming liquids (e.g., water, silica, silicon) has elicited considerable scientific interest. The challenge, both for experiments and simulations, is that the liquid-liquid phase transition occurs under deeply supercooled conditions, where crystallization occurs very rapidly. Thus, early evidence from numerical equation of state studies was challenged, with the argument that slow spontaneous crystallization had been misinterpreted as evidence of a second liquid state. Rigorous free energy calculations have subsequently confirmed the existence of a liquid-liquid phase transition in some models of water, and exciting new experimental evidence has since supported these computational results. Similar results have so far not been found for silicon. Here, we present results from free energy calculations performed for silicon modelled with the classical, empirical Stillinger-Weber potential. Through a careful study employing state-of-the-art constrained simulation protocols and numerous checks for thermodynamic consistency, we find that there are two distinct metastable liquid states and a phase transition. Our results resolve a long-standing debate concerning the existence of a liquid-liquid transition in supercooled liquid silicon and address key questions regarding the nature of the phase transition and the associated critical point.

Glass-forming liquids are broadly classified as being fragile or strong, depending on the deviation from Arrhenius behavior of their relaxation times. A fragile to strong crossover is observed or inferred in liquids like water and silica, and more recently also in metallic glasses and phase change alloys, leading to the expectation that such a crossover is more widely realised among glass formers. We investigate computationally the well-studied Kob-Andersen model, accessing temperatures well below the mode coupling temperature $T_{MCT}$. We find that relaxation times exhibit a crossover in dynamics around $T_{MCT}$, and discuss whether it bears characteristics of the fragile to strong crossover. Several aspects of dynamical heterogeneity exhibit behavior mirroring the dynamical crossover, whereas thermodynamic quantities do not. In particular, the Adam-Gibbs relation describing the relation between relaxation times and configurational entropy continues to hold below the dynamical crossover, when anharmonic corrections to the vibrational entropy are included.

We investigate the dynamics of soft sphere liquids through computer simulations for spatial dimensions from $d =3$ to $8$, over a wide range of temperatures and densities. Employing a scaling of density-temperature dependent relaxation times, we precisely identify the density $\phi_0$ which marks the ideal glass transition in the hard sphere limit, and a crossover from sub- to super-Arrhenius temperature dependence. The difference between $\phi_0$ and the athermal jamming density $\phi_J$, small in 3 and 4 dimensions, increases with dimension, with $\phi_0 > \phi_J$ for $d > 4$. We compare our results with recent theoretical calculations., Comment: Supplemental Material included as ancillary file

Associative memory, a form of content-addressable memory, facilitates information storage and retrieval in many biological and physical systems. In statistical mechanics models, associative memory at equilibrium is represented through attractor basins in the free energy landscape. Here, we use the Hopfield model, a paradigmatic model to describe associate memory, to investigate the effect of non-equilibrium activity on memory retention and recall. We introduce activity into the system as gaussian-colored noise which breaks detailed balance and forces the system out of equilibrium. We observe that, under these non-equilibrium conditions, the Hopfield network has a higher storage capacity than that allowed at equilibrium. Using analytical and numerical techniques, we show that the rate of entropy production modifies the energy landscape and helps the system to access memory regions which were previously inaccessible., Comment: 19 pages, 4 figures

We study numerically the critical behavior and marginal stability of the shear jamming transition for frictionless soft spheres, observed to occur over a finite range of densities, associated with isotropic jamming for densities above the minimum jamming (J-point) density. Several quantities are shown to scale near the shear jamming point in the same way as the isotropic jamming point. We compute the exponents associated with the small force distribution and the interparticle gap distribution,and show that the corresponding exponents are consistent with the marginal stability condition observed for isotropic jamming, and with predictions of the mean field theory of jamming in hard spheres., Comment: 6 pages, 2 figures and supplemental material as ancillary file

We consider the yielding behaviour of a model glass subjected to asymmetric cyclic shear deformation, wherein the applied strain varies between 0 and a maximum value $\gamma_{\rm max}$, and study its dependence on the degree of annealing of the glass and system size. The yielding behaviour of well annealed glasses (unlike poorly annealed glasses) display striking differences from the symmetric case, with the emergence of an intermediate strain regime with substantial plasticity but no yielding. The observed behaviour is satisfactorily captured by a recently proposed model. For larger system sizes, the intermediate strain regime narrows, leading to a remarkable reversal of yield strain with annealing., Comment: 6 pages, 4 figure, SM as ancillary file

We study a mean field elastoplastic model, embedded within a disordered landscape of local yield barriers, to shed light on the behaviour of athermal amorphous solids subject to oscillatory shear. We show that the model presents a genuine dynamical transition between an elastic and a yielded state, and qualitatively reproduces the dependence on the initial degree of annealing found in particle simulations. For initial conditions prepared below the analytically derived threshold energy, we observe a non-trivial, non-monotonic approach to the yielded state. The timescale diverges as one approaches the yielding point from above, which we identify with the fatigue limit. We finally discuss the connections to brittle yielding under uniform shear., Comment: 23 pages, 21 figures (version accepted for publication in Phys. Rev. Lett.)

The correlation between local structure and the propensity for structural rearrangements has been widely investigated in glass forming liquids and glasses. In this paper we use the excess two-body entropy $S_2$ and tetrahedrality $\n_{tet}$ as the per-particle local structural order parameters to explore such correlations in a three-dimensional model glass subjected to cyclic shear deformation. We first show that for both liquid configurations and the corresponding inherent structures, local ordering increases upon lowering temperature, signaled by a decrease in the two-body entropy and an increase in tetrahedrality. When the inherent structures, or glasses, are periodically sheared athermally, they eventually reach absorbing states for small shear amplitudes, which do not change from one cycle to the next. Large strain amplitudes result in the formation of shear bands, within which particle motion is diffusive. We show that in the steady state, there is a clear difference in the local structural environment of particles that will be part of plastic rearrangements during the next shear cycle and that of particles that are immobile. In particular, particles with higher $S_2$ and lower $n_{tet}$ are more likely to go through rearrangements irrespective of the average energies of the configurations and strain amplitude. For high shear, we find very distinctive local order outside the mobile shear band region, where almost $30\%$ of the particles are involved in icosahedral clusters, contrasting strongly with the fraction of $<5\%$ found inside the shear band., Comment: 11 pages, 9 figures

Multi-component self-assembly mixtures offer the possibility of encoding multiple target structures with the same set of interacting components. Selective retrieval of one of the stored structures has been attempted by preparing an initial state that favours the assembly of the required target, through seeding, concentration patterning or specific choices of interaction strengths. This may not be possible in an experiment where on-the-fly reconfiguration of the building blocks to switch functionality may be required. In this paper, we explore principles of inverse design of a multi-component self-assembly mixture capable of encoding two competing structures that can be selected through simple temperature protocols. We design the target structures to realise the generic situation in which one of targets has the lower nucleation barrier while the other is globally more stable. We observe that to avoid the formation of spurious or chimeric aggregates, the number of neighbouring component pairs that occur in both structures should be minimal. Our design also requires the inclusion of components that are part only of one of the target structures, but we observe that to maximize the selectivity of retrieval, the component library itself should be maximally shared by the two targets. We demonstrate that temperature protocols can be designed which lead to the formation of either one of the target structures with high selectivity. We discuss the important role played by secondary aggregation products, which we term vestigial aggregates.

We study the kinetics of crystallization in deeply supercooled liquid silicon employing computer simulations and the Stillinger-Weber three body potential. The free energy barriers to crystallisation are computed using umbrella sampling Monte Carlo simulations, and for selected low temperature and zero pressure state points, using unconstrained molecular dynamics simulations to reconstruct the free energy from a mean first passage time formulation. We focus on state points that have been described in earlier work [Sastry and Angell, Nature Mater., 2, 739, 2003] as straddling a first order liquid-liquid phase transition (LLPT) between two metastable liquid states. It was argued subsequently [Ricci et al., Mol. Phys., 117, 3254, 2019] that the apparent phase transition is in fact due the loss of metastability of the liquid state with respect to the globally stable crystalline state. The presence or absence of a barrier to crystallization for these state points is therefore of importance to ascertain, with due attention to ambiguities that may arise from the choice of order parameters. We discuss our choice of order parameters and also our choice of methods to calculate the free energy at deep supercooling. We find a well-defined free energy barrier to crystallisation and demonstrate that both umbrella sampling and mean first passage time methods yield results that agree quantitatively. Our results thus provide strong evidence against the possibility that the liquids at state points close to the reported LLPT exhibit slow, spontaneous crystallisation, but they do not address the existence of a LLPT (or lack thereof). We also compute the free energy barriers to crystallisation at other state points over a broad range of temperatures and pressures, and discuss the effect of changes in the microscopic structure of the metastable liquid on the free energy barrier heights.

We present a review on the study of metastable silicon, primarily focusing mainly on the aspects of liquid-liquid transition, critical point and phase behaviour, structural and dynamic properties of liquid phase as well as crystal nucleation. We begin with an extensive survey of the investigations of liquid silicon pursued over three decades, with salient experimental, theoretical and simulation results. Following which we present various scenarios put forward to rationalize the density and related anomalies often observed in water and other network forming liquids. After which we present the more recent investigations (both simulation and experimental works) of the phase behavior of Silicon. Since a significant part of metastable silicon work is on a classical empirical potential an important question to address is the reliability of this potential in describing the behavior of silicon. To provide a critical assessment of the applicability of classical simulation results to real silicon we present a comparison of the structural, dynamical, and thermodynamic quantities obtained from the SW potential with those from ab initio simulations and with available experimental data. We also discuss the sensitivity of the thermodynamic properties to model parameters.

We investigate the heterogeneity of dynamics, the breakdown of the Stokes-Einstein relation and fragility in a model glass forming liquid, a binary mixture of soft spheres with a harmonic interaction potential, for spatial dimensions from 3 to 8. Dynamical heterogeneity is quantified through the dynamical susceptibility $\chi_4$, and the non-Gaussian parameter $\alpha_2$. We find that the fragility, the degree of breakdown of the Stokes-Einstein relation, as well as heterogeneity of dynamics, decrease with increasing spatial dimensionality. We briefly describe the dependence of fragility on density, and use it to resolve an apparent inconsistency with previous results.

A wide range of materials can exist in microscopically disordered solid forms, referred to as amorphous solids or glasses. Such materials -- oxide glasses and metallic glasses, to polymer glasses, and soft solids such as colloidal glasses, emulsions and granular packings -- are useful as structural materials in a variety of contexts. Their deformation and flow behaviour is relevant for many others. Apart from fundamental questions associated with the formation of these solids, comprehending their mechanical behaviour is thus of interest, and of significance for their use as materials. In particular, the nature of plasticity and yielding behaviour in amorphous solids has been actively investigated. Different amorphous solids exhibit behaviour that is apparently diverse and qualitatively different from those of crystalline materials. A goal of recent investigations has been to comprehend the unifying characteristics of amorphous plasticity and to understand the apparent differences among them. We summarise some of the recent progress in this direction. We focus on insights obtained from computer simulation studies, and in particular those employing oscillatory shear deformation of model glasses.

We study numerically the yielding transition of a two dimensional model glass subjected to athermal quasi-static cyclic shear deformation, with the aim of investigating the effect on the yielding behaviour of the degree of annealing, which in turn depends on the preparation protocol. We find two distinct regimes of annealing separated by a threshold energy. Poorly annealed glasses progressively evolve towards the threshold energy as the strain amplitude is increased towards the yielding value. Well annealed glasses with initial energies below the threshold energy exhibit stable behaviour, with negligible change in energy with increasing strain amplitude, till they yield. Discontinuities in energy and stress at yielding increase with the degree of annealing, consistently with recent results found in three dimensions. We observe significant structural change with strain amplitude that closely mirrors the changes in energy and stresses. We investigate groups of particles that are involved in plastic rearrangements. We analyse the distributions of avalanche sizes, of clusters of connected rearranging particles, and related quantities, employing finite size scaling analysis. We verify previously investigated relations between exponents characterising these distributions, and a newly proposed relation between exponents describing avalanche and cluster size distributions.

We investigate avalanches associated with plastic rearrangements and the nature of structural change in the prototypical strong glass, silica, computationally. Although qualitative aspects of yielding in silica are similar to other glasses, we find that the statistics of avalanches exhibits non-trivial behaviour. Investigating the statistics of avalanches and clusters in detail, we propose and verify a new relation between exponents characterizing the size distribution of avalanches and clusters. Across the yielding transition, anomalous structural change and densification, associated with a suppression of tetrahedral order, is observed to accompany strain localisation., Comment: Manuscript + Supplementary Material as Ancillary file

We consider the yielding behavior of amorphous solids under cyclic shear deformation and show that it can be mapped into a random walk in a confining potential with an absorbing boundary. The resulting dynamics is governed by the first passage time into the absorbing state and suffices to capture the essential qualitative features recently observed in atomistic simulations of amorphous solids. Our results provide insight into the mechanism underlying yielding and its robustness. When the possibility of activated escape from absorbing states is added, it leads to a unique determination of a threshold energy and yield strain, suggesting thereby an appealing approach to understanding fatigue failure., Comment: Revised version, 6 pages, 2 figures and Supplemental Material as ancillary file

Recent experiments and simulations of amorphous solids plastically deformed by oscillatory drive have foundsurprising behavior - for small strain amplitudes the dynamics can be reversible, which is contrary to the usual notion of plasticity as an irreversible form of deformation. This reversibility allows the system to reach limit-cycles in which plastic events repeat indefinitely under the oscillatory drive. Reaching reversible limit-cycles, can take a large number of driving cycles and it was surmised that the plastic events encountered during the transient period are not encountered again and are thus irreversible. Using a graph representation of the stable configurations of the system and the plastic events connecting them, we show that the notion of reversibility is more subtle. We find that reversible plastic events are abundant, and that a large portion of the plastic events encountered during the transient period are actually reversible, in the sense that they can be part of a reversible deformation path. We observe that the transition graph can be decomposed into clusters of configurations that are connected by reversible transitions. These clusters are the strongly connected components of the graph and their sizes turn out to be power-law distributed. The largest of these are grouped in regions of reversibility, which in turn are confined by regions of irreversibility whose number proliferates at larger strains. Our results provide an explanation for the irreversibility transition - the divergence of the transient period at a critical forcing amplitude. Long transients result from transition between clusters of reversibility in a search for a cluster large enough to contain a limit-cycle of a specific amplitude. For large enough amplitudes, the search time becomes very large, since sizes of the limit cycles become incompatible with the sizes of the regions of reversibility., Comment: 14 pages, 7 figures. Revised version with figures regrouped and two figures added

Understanding the mechanical response and failure of solids is of obvious importance in their use as structural materials. The nature of plastic deformation leading to yielding of amorphous solids has been vigorously pursued in recent years. Investigations employing both unidirectional and cyclic deformation protocols reveal a strong dependence of yielding behaviour on the degree of annealing. Below a threshold degree of annealing, the nature of yielding changes qualitatively, to progressively more discontinuous yielding. Theoretical investigations of yielding in amorphous solids have almost exclusively focused on yielding under unidirectional deformation, but cyclic deformation reveals several interesting features that remain largely un-investigated. Focusing on athermal cyclic deformation, I investigate a family of models based on an energy landscape description. These models reproduce key interesting features observed in simulations, and provide an interpretation for the intriguing presence of a threshold energy.

We present a numerical investigation of the density fluctuations in a model glass under cyclic shear deformation. At low amplitude of shear, below yielding, the system reaches a steady absorbing state in which density fluctuations are suppressed revealing a clear fingerprint of hyperuniformity up to a finite length scale. The opposite scenario is observed above yielding, where the density fluctuations are strongly enhanced. We demonstrate that the transition to this state is accompanied by a spatial phase separation into two distinct hyperuniform regions, as a consequence of shear band formation above the yield amplitude., Comment: 5 pages, 4 figures

Granular packings display the remarkable phenomenon of dilatancy [1], wherein their volume increases upon shear deformation. Conventional wisdom and previous results suggest that dilatancy, as also the related phenomenon of shear-induced jamming, requires frictional interactions [2, 3]. Here, we investigate the occurrence of dilatancy and shear jamming in frictionless packings. We show that the existence of isotropic jamming densities {\phi}j above the minimal density, the J-point density {\phi}J [4, 5], leads both to the emergence of shear-induced jamming and dilatancy. Packings at {\phi}J form a significant threshold state into which systems evolve in the limit of vanishing pressure under constant pressure shear, irrespective of the initial jamming density {\phi}j. While packings for different {\phi}j display equivalent scaling properties under compression [6], they exhibit striking differences in rheological behaviour under shear. The yield stress under constant volume shear increases discontinuously with density when {\phi}j > {\phi}J, contrary to the continuous behavior in generic packings that jam at {\phi}J [4, 7].

Cell neighbor exchanges are integral to tissue rearrangements in biology, including development and repair. Often these processes occur via topological T1 transitions analogous to those observed in foams, grains and colloids. However, in contrast to in non-living materials the T1 transitions in biological tissues are rate-limited and cannot occur instantaneously due to the finite time required to remodel complex structures at cell-cell junctions. Here we study how this rate-limiting process affects the mechanics and collective behavior of cells in a tissue by introducing this important biological constraint in a theoretical vertex-based model as an intrinsic single-cell property. We report in the absence of this time constraint, the tissue undergoes a motility-driven glass transition characterized by a sharp increase in the intermittency of cell-cell rearrangements. Remarkably, this glass transition disappears as T1 transitions are temporally limited. As a unique consequence of limited rearrangements, we also find that the tissue develops spatially correlated streams of fast and slow cells, in which the fast cells organize into stream-like patterns with leader-follower interactions, and maintain optimally stable cell-cell contacts. The predictions of this work is compared with existing in-vivo experiments in Drosophila pupal development.

During a spontaneous change, a macroscopic physical system will evolve towards a macro-state with more realizations. This observation is at the basis of the Statistical Mechanical version of the Second Law of Thermodynamics, and it provides an interpretation of entropy in terms of probabilities. However, we cannot rely on the statistical-mechanical expressions for entropy in systems that are far from equilibrium. In this paper, we compare various extensions of the definition of entropy, which have been proposed for non-equilibrium systems. It has recently been proposed that measures of information density may serve to quantify entropy in both equilibrium and nonequilibrium systems. We propose a new "bit-wise" method to measure the information density for off lattice systems. This method does not rely on coarse-graining of the particle coordinates. We then compare different estimates of the system entropy, based on information density and on the structural properties of the system, and check if the various entropies are mutually consistent and, importantly, whether they can detect non-trivial ordering phenomena. We find that, except for simple (one-dimensional) cases, the different methods yield answers that are at best qualitatively similar, and often not even that, although in several cases, different entropy estimates do detect ordering phenomena qualitatively. Our entropy estimates based on bit-wise data compression contain no adjustable scaling factor, and show large quantitative differences with the thermodynamic entropy obtained from equilibrium simulations. Hence, our results suggest that, at present, there is not yet a single, structure-based entropy definition that has general validity for equilibrium and non equilibrium systems.

Yielding behavior in amorphous solids has been investigated in computer simulations employing uniform and cyclic shear deformation. Recent results characterise yielding as a discontinuous transition, with the degree of annealing of glasses being a significant parameter. Under uniform shear, discontinuous changes in stresses at yielding occur in the high annealing regime, separated from the poor annealing regime in which yielding is gradual. In cyclic shear simulations, relatively poorly annealed glasses become progressively better annealed as the yielding point is approached, with a relatively modest but clear discontinuous change at yielding. To understand better the role of annealing on yielding characteristics, we perform athermal quasistaic cyclic shear simulations of glasses prepared with a wide range of annealing in two qualitatively different systems -- a model of silica (a network glass), and an atomic binary mixture glass. Two strikingly different regimes of behavior emerge: Energies of poorly annealed samples evolve towards a unique threshold energy as the strain amplitude increases, before yielding takes place. Well annealed samples, in contrast, show no significant energy change with strain amplitude till they yield, accompanied by discontinuous energy changes that increase with the degree of annealing. Significantly, the threshold energy for both systems correspond to dynamical crossover temperatures associated with changes in the character of the energy landscape sampled by glass forming liquids. Uniform shear simulations support the recently discussed scenario of a random critical point separating ductile and brittle yielding, which our results now associate with dynamical crossover temperatures in the corresponding liquids.

Self-organization, and transitions from reversible to irreversible behaviour, of interacting particle assemblies driven by externally imposed stresses or deformation is of interest in comprehending diverse phenomena in soft matter. They have been investigated in a wide range of systems, such as colloidal suspensions, glasses, and granular matter. In different density and driving regimes, such behaviour is related to yielding of amorphous solids, jamming, and memory formation, \emph{etc.} How these phenomena are related to each other has not, however, been much studied. In order to obtain a unified view of the different regimes of behaviour, and transitions between them, we investigate computationally the response of soft sphere assemblies to athermal cyclic shear deformation over a wide range of densities and amplitudes of shear deformation. Cyclic shear deformation induces transitions from reversible to irreversible behaviour in both unjammed and jammed soft sphere packings. Well above isotropic jamming density ($\bf{\phi_J}$), this transition corresponds to yielding. In the vicinity of the jamming point, up to a higher density limit we designate ${\bf \phi_J^{cyc}}$, an unjammed phase emerges between a localised, \emph{absorbing} phase, and a diffusive, {\emph irreversible} phase. The emergence of the unjammed phase signals the shifting of the jamming point to higher densities as a result of annealing, and opens a window where shear jamming becomes possible for frictionless packings. Below $\bf{\phi_J}$, two distinct localised states, termed point and loop reversibile, are observed. We characterise in detail the different regimes and transitions between them, and obtain a unified density-shear amplitude phase diagram.

We study the inverse problem of tuning interaction parameters between charged colloidal particles interacting with a hard-core repulsive Yukawa potential, so that they assemble into specified crystal structures. Here, we target the body-centered-cubic (bcc) structure which is only stable in a small region in the phase diagram of charged colloids and is, therefore, challenging to find. In order to achieve this goal, we use the statistical fluctuations in the bond orientational order parameters to tune the interaction parameters for the bcc structure, while initializing the system in the fluid phase, using the Statistical Physics-inspired Inverse Design (SP-ID) algorithm [1]. We also find that this optimization algorithm correctly senses the fluid-solid phase boundaries for charged colloids. Finally, we repeat the procedure employing the Covariance Matrix Adaptation - Evolution Strategy (CMA-ES), a cutting edge optimization technique, and compare the relative efficacy of the two methods.

We consider the slow and athermal deformations of amorphous solids and show how the ensuing sequence of discrete plastic rearrangements can be mapped onto a directed network. The network topology reveals a set of highly connected regions joined by occasional one-way transitions. The highly connected regions include hierarchically organized hysteresis cycles and sub-cycles. At small to moderate strains this organization leads to near-perfect return point memory. The transitions in the network can be traced back to localized particle rearrangements (soft-spots) that interact via Eshelby-type deformation fields. By linking topology to dynamics, the network representations provides new insights into the mechanisms that lead to reversible and irreversible behavior in amorphous solids., Comment: 5 pages, 4 figures. Minor changes, addition of of ancillary file providing numerical implementation details and supporting evidence

We find that in simulations of quasi-statically sheared frictional disks, the shear jamming transition can be characterized by an abrupt jump in the number of force bearing contacts between particles. This mechanical coordination number increases discontinuously from $Z = 0$ to $Z \gtrsim d +1$ at a critical shear value $\gamma_c$, as opposed to a smooth increase in the number of geometric contacts. This is accompanied by a diverging timescale $\tau^*$ that characterizes the time required by the system to attain force balance when subjected to a perturbation. As the global shear $\gamma$ approaches the critical value $\gamma_c$ from below, one observes the divergence of the time taken to relax to a state where all the inter-particle contacts have uniformly zero force. Above $\gamma_{c}$, the system settles into a state characterized by finite forces between particles, with the timescale also increasing as $\gamma \to \gamma_{c}^{+}$. By using two different protocols to generate force balanced configurations, we show that this timescale divergence is a robust feature that accompanies the shear jamming transition., Comment: 7 pages, 5 figures

Memory formation in matter is a theme of broad intellectual relevance; it sits at the interdisciplinary crossroads of physics, biology, chemistry, and computer science. Memory connotes the ability to encode, access, and erase signatures of past history in the state of a system. Once the system has completely relaxed to thermal equilibrium, it is no longer able to recall aspects of its evolution. Memory of initial conditions or previous training protocols will be lost. Thus many forms of memory are intrinsically tied to far-from-equilibrium behavior and to transient response to a perturbation. This general behavior arises in diverse contexts in condensed matter physics and materials: phase change memory, shape memory, echoes, memory effects in glasses, return-point memory in disordered magnets, as well as related contexts in computer science. Yet, as opposed to the situation in biology, there is currently no common categorization and description of the memory behavior that appears to be prevalent throughout condensed-matter systems. Here we focus on material memories. We will describe the basic phenomenology of a few of the known behaviors that can be understood as constituting a memory. We hope that this will be a guide towards developing the unifying conceptual underpinnings for a broad understanding of memory effects that appear in materials.

We study the yielding behaviour of a model glass under cyclic athermal quastistatic deformation computationally, and show that yielding is characterised by the discontinuous appearance of shear bands, whose width is about ten particle diameters at their initiation, in which the strain gets localised. Strain localisation is accompanied by a corresponding change in the energies, and a decrease in the density in the shear band. We show that the glass remains well annealed outside the shear band whereas the energies correspond to the highest possible energy minima at the given density within the shear band. Diffusive motion of particles characterising the yielded state are confined to the shear bands, whose mean positions display movement over repeated cycles. Outside the shear band, particle motions are sub-diffusive but remain finite. Despite the discontinuous nature of their appearance, shear bands are reversible in the sense that a reduction in the amplitude of cyclic deformation to values below yielding leads to the healing and disappearance of the shear bands.

A major challenge in simulating glassy systems is the ability to generate configurations that may be found in equilibrium at sufficiently low temperatures, in order to probe static and dynamic behaviour close to the glass transition. A variety of approaches have recently explored ways of surmounting this obstacle. Here, we explore the possibility of employing mechanical agitation, in the form of cyclic shear deformation, to generate low energy configurations in a model glass former. We perform shear deformation simulations over a range of temperatures, shear rates and strain amplitudes. We find that shear deformation induces faster relaxation towards low energy configurations, or overaging, in simulations at sufficiently low temperatures, consistently with previous results for athermal shear. However, for temperatures at which simulations can be run till a steady state is reached with or without shear deformation, we find that the inclusion of shear deformation does not result in any speed up of the relaxation towards low energy configurations. Although we find the configurations from shear simulations to have properties indistinguishable from an equilibrium ensemble, the cyclic shear procedure does not guarantee that we generate an equilibrium ensemble at a desired temperature. In order to ensure equilibrium sampling, we develop a hybrid Monte Carlo algorithm that employs cyclic shear as a trial generation step, and has acceptance probabilities that depend not only on the change in internal energy but also on heat dissipated (equivalently, work done). We show that such an algorithm indeed generates an equilibrium ensemble., Comment: Extrapolation of high temperature relaxation times is not valid at lower temperatures because of a crossover in dynamics [see P. Das and S. Sastry, JNCS:X 14 (2022): 100098; arXiv:2204.04411], requiring a reinterpretation of the results. Additional results [Fig. 2 (c), Fig. A6] regarding overaging have been included. The material has been rearranged, with minor changes

We study a model amorphous solid that is subjected to repeated athermal cyclic shear deformation. It has previously been demonstrated that the memory of the amplitudes of shear deformation the system is subjected to (or trained at) is encoded, and can be retrieved by subsequent deformation cycles that serve as read operations. Here we consider different read protocols and measurements and show that single and multiple memories can be robustly retrieved through these different protocols. We also show that shear deformation by a larger amplitude always erases the stored memories. These observations are similar to those in experiments with non-Brownian colloidal suspensions and corresponding models, but differ in the possibility of storing multiple memories non-transiently. Such a possibility has been associated with the presence of cycles of transitions that take place in the model amorphous solids, between local energy minima. Here, we study low density sphere assemblies which serve as models for non-Brownian colloidal suspensions, under athermal deformation, and identify a regime where multiple memories are stored in these systems as well non-transiently. We show that the regime where storing multiple memories non-transiently corresponds to the presence of loop reversibility, rather than point reversibility of configurations under cyclic deformation.

The slow down of dynamics in glass forming liquids as the glass transition is approached has been characterised through the Adam-Gibbs relation, which relates relaxation time scales to the configurational entropy. The Adam-Gibbs relation cannot apply simultaneously to all relaxation times scales unless they are coupled, and exhibit closely related temperature dependences. The breakdown of the Stokes-Einstein relation presents an interesting situation to the contrary, and in analysing it, it has recently been shown that the Adam-Gibbs relation applies to diffusion coefficients rather than to viscosity or structural relaxation times related to the decay of density fluctuations. However, for multi-component liquids -- the typical cases considered in computer simulations, metallic glass formers, etc. -- such a statement raises the question of which diffusion coefficient is described by the Adam-Gibbs relation. All diffusion coefficients can be consistently described by the Adam-Gibbs relation if they bear a power law relationship with each other. Remarkably, we find that for a wide range of glass formers, and for a wide range of temperatures spanning the normal and the slow relaxation regimes, such a relationship holds. We briefly discuss possible rationalisations of the observed behaviour.

We explain the structural origin of the jamming transition in jammed matter as the sudden appearance of k-cores at precise coordination numbers which are related not to the isostatic point, but to the sudden emergence of the 3- and 4-cores as given by k-core percolation theory. At the transition, the k-core variables freeze and the k-core dominates the appearance of rigidity. Surprisingly, the 3-D simulation results can be explained with the result of mean-field k-core percolation in the Erdos-Renyi network. That is, the finite-dimensional transition seems to be explained by the infinite-dimensional k-core, implying that the structure of the jammed pack is compatible with a fully random network., Comment: 5 pages, 3 figures

The formation of self-organised structures that resist shear deformation have been discussed in the context of shear jamming and thickening[1-3], with frictional forces playing a key role. However, shear induces geometric features necessary for jamming even in frictionless packings[4]. We analyse conditions for jamming in such assemblies by solving force and torque balance conditions for their contact geometry. We demonstrate, and validate with frictional simulations, that the isostatic condition for mean contact number Z = D + 1 (for spatial dimension D = 2, 3) holds at jamming for both finite and infinite friction, above the random loose packing density. We show that the shear jamming threshold satisfies the marginal stability condition recently proposed for jamming in frictionless systems[5]. We perform rigidity percolation analysis[6,7] for D = 2 and find that rigidity percolation precedes shear jamming, which however coincides with the percolation of over-constrained regions, leading to the identification of an intermediate phase analogous to that observed in covalent glasses[8].

In this paper we establish a connection between the onset temperature of glassy dynamics with the change in the entropy for a wide range of model systems. We identify the crossing temperature of pair and excess entropies as the onset temperature. Below the onset temperature, the residual multiparticle entropy(RMPE), the difference between excess and pair entropies, becomes positive. The positive entropy can be viewed as equivalent to the larger phase space exploration of the system. The new method of onset temperature prediction from entropy is less ambiguous, as it does not depend on any fitting parameter like the existing methods. Our study also reveals the connection between fragility and the degree of breakdown of the Stokes Einstein (SE) relation., Comment: 8 pages, 4 figures

Fragility, quantifying the rapidity of variation of relaxation times, is analysed for a series of model glass formers, which differ in the softness of their interparticle interactions. In an attempt to rationalize experimental observations in colloidal suspensions that softer interactions lead to stronger (less fragile) glass formers, we study the variation of relaxation dynamics with density, rather than temperature, as a control parameter. We employ density temperature scaling, analyzed in recent studies, to address the question. We find that while employing inverse density in place of temperature leads to the conclusion that softer interactions lead to stronger behaviour, the use of scaled variables involving temperature and density lead to the opposite conclusion, similarly to earlier investigations where temperature variation of relaxation dynamics was analysed for the same systems. We rationalize our results by considering the Adam-Gibbs (AG) fragility, which incorporates the density dependence of the configurational entropy and an activation energy that may arise from other properties of a glass former. Within the framework of the Adam-Gibbs relation, by employing density temperature scaling for the analysis, we find that softer particles make more fragile glasses, as deduced from dynamical quantities, which is found to be consistent with the Adam-Gibbs fragility.

The Adam-Gibbs (AG) relation connects the dynamics of a glass-forming liquid to its the thermodynamics via. the configurational entropy, and is of fundamental importance in descriptions of glassy behaviour. The breakdown of the Stokes-Einstein (SEB) relation between the diffusion coefficient and the viscosity (or structural relaxation times) in glass formers raises the question as to which dynamical quantity the AG relation describes. By performing molecular dynamics simulations, we show that the AG relation is valid over the widest temperature range for the diffusion coefficient and not for the viscosity or relaxation times. Studying relaxation times defined at a given wavelength, we find that SEB and the deviation from the AG relation occur below a temperature at which the correlation length of dynamical heterogeneity equals the wavelength probed.

The origins of rapid dynamical slow down in glass forming liquids in the growth of static length scales, possibly associated with identifiable structural ordering, is a much debated issue. Growth of medium range crystalline order (MRCO) has been observed in various model systems to be associated with glassy behaviour. Such observations raise the question about the eventual state reached by a glass former, if allowed to relax for sufficiently long times. Is a slowly growing crystalline order responsible for slow dynamics? Are the molecular mechanisms for glass transition in liquids with and without MRCO the same? If yes, glass formers with MRCO provide a paradigm for understanding glassy behaviour generically. If not, systems with MRCO form a new class of glass forming materials whose molecular mechanism for slow dynamics may be easier to understand in terms of growing crystalline order, and should be approached in that manner, even while they will not provide generic insights. In this study we perform extensive molecular dynamics simulations of a number of glass forming liquids in two dimensions and show that the static and dynamic properties of glasses with MRCO are different from other glass forming liquids with no predominant local order. We also resolve an important issue regarding the so-called Point-to-set method for determining static length scales, and demonstrate it to be a robust, order agnostic, method for determining static correlation lengths in glass formers.

Amorphous solids are ubiquitous among natural and man-made materials. Often used as structural materials for their attractive mechanical properties, their utility depends critically on their response to applied stresses. Processes underlying such mechanical response, and in particular the yielding behaviour of amorphous solids, are not satisfactorily understood. Although studied extensively[1-14], observed yielding behaviour can be gradual and depend significantly on conditions of study, making it difficult to convincingly validate existing theoretical descriptions of a sharp yielding transition[4, 6, 8, 13, 15]. Here, we employ oscillatory deformation as a reliable probe of the yielding transition. Through extensive computer simulations for a wide range of system sizes, we demonstrate that cyclically deformed model glasses exhibit a sharply defined yielding transition with characteristics that are independent of preparation history. In contrast to prevailing expectations[4, 8, 12], the statistics of avalanches reveals no signature of the impending transition, but exhibit dramatic, qualitative, changes in character across the transition., Comment: Original Submission to Nature Communications (with updated references and acknowledgements)