On the existence of thermodynamically stable rigid solids

Thawed matrix method for computing local mechanical properties of amorphous solids

We present a method for computing locally varying nonlinear mechanical properties in particle simulations of amorphous solids. Plastic rearrangements outside a probed region are suppressed by introducing an external field that directly penalizes large nonaffine displacements. With increasing strength of the field, plastic deformation can be localized. We characterize the distribution of local plastic yield stresses (residual local stresses to instability) with our approach and assess the correlation of their spatial maps with plastic activity in a model two-dimensional amorphous solid. Our approach reduces artifacts inherent in a previous method known as the "frozen matrix" approach that enforces fully affine deformation and improves the prediction of plastic rearrangements from structural information.

Continuum mechanics of nonideal crystals: Microscopic approach based on projection-operator formalism

We present a microscopic derivation of the laws of continuum mechanics of nonideal ordered solids including dissipation, defect diffusion, and heat transport. The starting point is the classical many-body Hamiltonian. The approach relies on the Zwanzig-Mori projection operator formalism to connect microscopic fluctuations to thermodynamic derivatives and transport coefficients. Conservation laws and spontaneous symmetry breaking, implemented via Bogoliubov's inequality, determine the selection of the slow variables. Density fluctuations in reciprocal space encode the displacement field and the defect concentration. Isothermal and adiabatic elastic constants are obtained from equilibrium correlations, while transport coefficients are given as Green-Kubo formulas, providing the basis for their measurement in atomistic simulations or colloidal experiments. The approach to the linearized continuum mechanics and results are compared to others from the literature.

Brittle yielding in supercooled liquids below the critical temperature of mode coupling theory

Molecular dynamics computer simulations of a polydisperse soft-sphere model under shear are presented. The starting point for these simulations are deeply supercooled samples far below the critical temperature, T c, of mode coupling theory. These samples are fully equilibrated with the aid of the swap Monte Carlo technique. For states below T c, we identify a lifetime τlt that measures the time scale on which the system can be considered as an amorphous solid. The temperature dependence of τlt can be well described by an Arrhenius law. The existence of transient amorphous solid states below T c is associated with the possibility of brittle yielding, as manifested by a sharp stress drop in the stress–strain relation and shear banding. We show that brittle yielding requires, on the one hand, low shear rates and, on the other hand, the time scale corresponding to the inverse shear rate has to be smaller or of the order of τlt. Both conditions can only be met for a large lifetime τlt, i.e., for states far below T c.

Pattern stabilization in swarms of programmable active matter: A probe for turbulence at large length scales

We propose an algorithm for creating stable, ordered, swarms of active robotic agents arranged in any given pattern. The strategy involves suppressing a class of fluctuations known as "nonaffine" displacements, viz., those involving nonlinear deformations of a reference pattern, while all (or most) affine deformations are allowed. We show that this can be achieved using precisely calculated, fluctuating, thrust forces associated with a vanishing average power input. A surprising outcome of our study is that once the structure of the swarm is maintained at steady state, the statistics of the underlying flow field is determined solely from the statistics of the forces needed to stabilize the swarm.

On the yielding of a point-defect-rich model crystal under shear: insights from molecular dynamics simulations

In real crystals and at finite temperatures point defects are inevitable. Under shear their dynamics severely influence the mechanical properties of these crystals, giving rise to non-linear effects, such as ductility. In an effort to elucidate the complex behavior of crystals under plastic deformation it is crucial to explore and to understand the interplay between the timescale related to the equilibrium point-defect diffusion and the shear-induced timescale. Based on extensive non-equilibrium molecular dynamics simulations we present a detailed investigation on the yielding behavior of cluster crystals, an archetypical model for a defect-rich crystal: in such a system clusters of overlapping particles occupy the lattice sites of a regular (FCC) structure. In equilibrium particles diffuse via site-to-site hopping while maintaining the crystalline structure intact. We investigate these cluster crystals at a fixed density and at different temperatures where the system remains in the FCC structure: temperature allows us to vary the diffusion timescale appropriately. We then expose the crystal to shear, thereby choosing shear rates which cover timescales that are both higher and lower than the equilibrium diffusion timescales. We investigate the macroscopic and microscopic response of our cluster crystal to shear and find that the yielding scenario of such a system does not rely on the diffusion of the particles - it is rather related to the plastic deformation of the underlying crystalline structure. The local bond order parameters and the measurement of local angles between neighboring clusters confirm the cooperative movement of the clusters close to the yield point. Performing complementary, related simulations for an FCC crystal formed by harshly repulsive particles reveals similarities in the yielding behavior between both systems. Still we find that the diffusion of particles does influence characteristic features in the cluster crystal, such as a less prominent increase of order parameters close to the yield point. Our simulations provide for the first time an insight into the role of the diffusion of defects in the yielding behavior of a defect-rich crystal under shear. These observations will thus be helpful in the development of theories for the plastic deformation of defect-rich crystals.

Yielding in an amorphous solid subject to constant stress at finite temperatures

Understanding the nature of the yield transition is a long-standing problem in the physics of amorphous solids. Here we use molecular dynamics simulations to study the response of amorphous solids to constant stresses at finite temperatures. We compare amorphous solids that are prepared using fast and slow quenches and show that for thermal systems, the steady-state velocity exhibits a continuous transition from very slow creep to a finite strain rate as a function of the stress. This behavior is observed for both well-annealed and poorly annealed systems. However, the transient dynamics is different in the latter and involves overcoming an energy barrier. Due to the different simulation protocol, the strain rate as a function of stress and temperature follows a scaling relation that is different from the ones that are shown for systems where the strain is controlled. Collapsing the data using this scaling relation allows us to calculate critical exponents for the dynamics close to yield, including an exponent for thermal rounding. We also demonstrate that strain slips due to avalanche events above yield follow standard scaling relations and we extract critical exponents that are comparable to the ones obtained in previous studies that performed simulations of both molecular dynamics and elastoplastic models using strain-rate control.

The role of annealing in determining the yielding behavior of glasses under cyclic shear deformation

Yielding behavior in amorphous solids has been investigated in computer simulations using uniform and cyclic shear deformation. Recent results characterize 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 quasistatic 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 toward 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 until they yield, accompanied by discontinuous energy changes that increase with the degree of annealing. Significantly, the threshold energy for both systems corresponds to dynamical cross-over temperatures associated with changes in the character of the energy landscape sampled by glass-forming liquids.

Flow heterogeneities in supercooled liquids and glasses under shear

Using extensive nonequilibrium molecular dynamics simulations, we investigate a glass-forming binary Lennard-Jones mixture under shear. Both supercooled liquids and glasses are considered. Our focus is on the characterization of inhomogeneous flow patterns such as shear bands that appear as a transient response to the external shear. For the supercooled liquids, we analyze the crossover from Newtonian to non-Newtonian behavior with increasing shear rate γ[over ̇]. Above a critical shear rate γ[over ̇]_{c} where a non-Newtonian response sets in, the transient dynamics are associated with the occurrence of short-lived vertical shear bands, i.e., bands of high mobility that form perpendicular to the flow direction. In the glass states, long-lived horizontal shear bands, i.e., bands of high mobility parallel to the flow direction, are observed in addition to vertical ones. The systems with shear bands are characterized in terms of mobility maps, stress-strain relations, mean-squared displacements, and (local) potential energies. The initial formation of a horizontal shear band provides an efficient stress release, corresponds to a local minimum of the potential energy, and is followed by a slow broadening of the band towards the homogeneously flowing fluid in the steady state. Whether a horizontal or a vertical shear band forms cannot be predicted from the initial undeformed sample. Furthermore, we show that with increasing system size, the probability for the occurrence of horizontal shear bands increases.

Steady state dynamic dependence between local mobility and non-affine fluctuations in two-dimensional aggregates

Motivated by qualitative experimental observations in collective behavior of self-propelled camphor particles at air-water interfaces, we study a generic aggregate forming system in two dimensions using canonical ensemble constant temperature molecular dynamics simulation. The aggregates form due to the competition between short-range attraction and long-range repulsion of pair-wise interactions as a generic proxy for the specific case of short-range capillary attraction competing with long-range Marangoni-assisted repulsion in camphor boat systems. Choosing the appropriate set of interaction parameters, we focus on characterising the local dynamics in two specific limiting morphologies, viz. compact and string-like aggregates. We focus on the temporal evolution of the mobility of an individual particle and the dynamic change in its nearest neighbourhood, measured in terms of the Debye-Waller factor ([Formula: see text]) and the non-affine parameter ([Formula: see text]), respectively (both defined in the text), and their interrelation over several lengths of observation time [Formula: see text]. The distribution for both measures are found to follow the relation: [Formula: see text] for the measured quantity x. The exponent [Formula: see text] is equal to two and one respectively, for the compact and string-like morphologies following the respective ideal fractal dimension of these aggregates. A functional dependence between these two observables is determined from a detailed statistical analysis of their joint and conditional distributions. The results obtained can readily be used and verified by experiments on aggregate forming systems more generic than the specific camphor boat system that motivated us, such as globular proteins, nanoparticle self-assembly etc. Further, the insights gained from this study might be useful to understand the evolution of collective dynamics in diverse glass-forming systems.

Nucleation Theory for Yielding of Nearly Defect-Free Crystals: Understanding Rate Dependent Yield Points

Experiments and simulations show that when an initially defect-free rigid crystal is subjected to deformation at a constant rate, irreversible plastic flow commences at the so-called yield point. The yield point is a weak function of the deformation rate, which is usually expressed as a power law with an extremely small nonuniversal exponent. We reanalyze a representative set of published data on nanometer sized, mostly defect-free Cu, Ni, and Au crystals in light of a recently proposed theory of yielding based on nucleation of stable stress-free regions inside the metastable rigid solid. The single relation derived here, which is not a power law, explains data covering 15 orders of magnitude in timescales.

Exploring the link between crystal defects and nonaffine displacement fluctuations

We generalize and then use a recently introduced formalism to study thermal fluctuations of atomic displacements in several two- and three-dimensional crystals. We study both close-packed and open crystals with multiatom bases. Atomic displacement fluctuations in a solid, once coarse grained over some neighborhood, may be decomposed into two mutually orthogonal components. In any dimension d there are always d^{2} affine displacements representing local strains and rotations of the ideal reference configuration. In addition, there exist a number of nonaffine localized displacement modes that cannot be represented as strains or rotations. The number of these modes depends on d and the size of the coarse-graining region. All thermodynamic averages and correlation functions concerning the affine and nonaffine displacements may be computed within harmonic theory. We show that for compact crystals, such as the square and triangular crystals in d=2 and the simple body-centered-cubic and face-centered-cubic crystals in d=3, a single set of d-fold degenerate modes always dominates the nonaffine subspace and is separated from the rest by a large gap. These modes may be identified with specific precursor configurations that lead to lattice defects. In open crystals, such as the honeycomb and kagome lattices, there is no prominent gap, although soft nonaffine modes continue to be associated with known floppy modes representing localized defects. Higher-order coupling between affine and nonaffine components of the displacements quantifies the tendency of the lattice to be destroyed by large homogeneous strains. We show that this coupling is larger by almost an order of magnitude for open lattices as compared to compact ones. Deformation mechanisms such as lattice slips and stacking faults in close-packed crystals can also be understood within this framework. The qualitative features of these conclusions are expected to be independent of the details of the atomic interactions.

Dynamical solid-liquid transition through oscillatory shear

Starting from an ideal crystalline state, we numerically study a nonequilibrium dynamical order-disorder transition promoted by the application of a periodic shearing protocol at low temperatures in model systems in three dimensions. We observe a discontinuous dynamical transition from an ordered to a disordered steady state. Through the analysis of large-scale simulations, we show that the amorphization mechanism around the discontinuous transition is reminiscent of spinodal decomposition.

Precursors of fluidisation in the creep response of a soft glass

Via extensive numerical simulations, we study the fluidisation process of dense amorphous materials subjected to an external shear stress, using a three-dimensional colloidal glass model. In order to disentangle possible boundary effects from finite size effects in the process of fluidisation, we implement a novel geometry-constrained protocol with periodic boundary conditions. We show that this protocol is well controlled and that the longtime fluidisation dynamics is, to a great extent, independent of the details of the protocol parameters. Our protocol, therefore, provides an ideal tool to investigate the bulk dynamics prior to yielding and to study finite size effects regarding the fluidisation process. Our study reveals the existence of precursors to fluidisation observed as a peak in the strain-rate fluctuations, that allows for a robust definition of a fluidisation time. Although the exponents in the power-law creep dynamics seem not to depend significantly on the system size, we reveal strong finite size effects for the onset of fluidisation.

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

Binding of small molecules to proteins often involves large conformational changes in the latter, which open up pathways to the binding site. Observing and pinpointing these rare events in large scale, all-atom, computations of specific protein-ligand complexes, is expensive and to a great extent serendipitous. Further, relevant collective variables which characterise specific binding or un-binding scenarios are still difficult to identify despite the large body of work on the subject. Here, we show that possible primary and secondary binding pathways can be discovered from short simulations of the apo-protein without waiting for an actual binding event to occur. We use a projection formalism, introduced earlier to study deformation in solids, to analyse local atomic displacements into two mutually orthogonal subspaces—those which are “affine” i.e. expressible as a homogeneous deformation of the native structure, and those which are not. The susceptibility to non-affine displacements among the various residues in the apo- protein is then shown to correlate with typical binding pathways and sites crucial for allosteric modifications. We validate our observation with all-atom computations of three proteins, T4-Lysozyme, Src kinase and Cytochrome P450.

Designing drugs which target specific proteins involved in diseases consumes a lot of time and effort in the pharmaceutical industry. In recent times, in silico design of drugs using all-atom molecular modelling has started to provide crucial inputs. Even so, discovery of binding pathways of small molecules both at the primary binding site, as well as sites for allosteric control, is time consuming and often fortuitous. We provide here a framework within which critical conformational changes likely to occur during binding are quantified from statistical analysis of configurations of proteins in their apo, or inactive form, greatly simplifying identification of target residues. We illustrate this idea by analysing ligand binding pathways for three proteins T4- Lysozyme, P450 and Src kinase, which are active respectively in the immune system, metabolism and cancer.