Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.

Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.

Permanent shear localization in dense disordered materials due to microscopic inertia.

In this work using computer simulations of 3D model of dense disordered solids we show, for the first time, the appearance of shear localization in the stationary flow under homogeneous driving conditions. To rationalize our simulation results we develop a continuum model, that couples the dynamics of the local flow to the evolution of a kinetic temperature field related to the local inertial dynamics. Our model predicts that the coupling of the flow field to this additional destabilizing field appears only as a necessary condition for shear localization, a minimum system size is necessary to accommodate the flow instability. Moreover we show that this size criterion resulting from our continuum description is in quantitative agreement with our particle-based simulation results.

Residual stress in athermal soft disordered solids: insights from microscopic and mesoscale models.

In soft amorphous materials, shear cessation after large shear deformation leads to configurations having residual shear stress. The origin of these states and the distribution of the local shear stresses within the material is not well understood, despite its importance for the change in material properties and consequent applications. In this work, we use molecular dynamics simulations of a model dense non-Brownian soft amorphous material to probe the non-trivial relaxation process towards a residual stress state. We find that, similar to thermal glasses, an increase in shear rate prior to the shear cessation leads to lower residual stress states. We rationalise our findings using a mesoscopic elasto-plastic description that explicitly includes a long range elastic response to local shear transformations. We find that after flow cessation the initial stress relaxation indeed depends on the pre-sheared stress state, but the final residual stress is majorly determined by newly activated plastic events occurring during the relaxation process, a scenario consistent with the phenomenology of avalanche dynamics in the low shear rate limit of steadily sheared amorphous solids. Our simplified coarse grained description not only allows capturing the phenomenology of residual stress states but also rationalising the altered material properties that are probed using small and large deformation protocols applied to the relaxed material.

The fate of shear-oscillated amorphous solids.

The behavior of shear-oscillated amorphous materials is studied using a coarse-grained model. Samples are prepared at different degrees of annealing and then subjected to athermal and quasi-static oscillatory deformations at various fixed amplitudes. The steady-state reached after several oscillations is fully determined by the initial preparation and the oscillation amplitude, as seen from stroboscopic stress and energy measurements. Under small oscillations, poorly annealed materials display shear-annealing, while ultra-stabilized materials are insensitive to them. Yet, beyond a critical oscillation amplitude, both kinds of materials display a discontinuous transition to the same mixed state composed of a fluid shear-band embedded in a marginal solid. Quantitative relations between uniform shear and the steady-state reached with this protocol are established. The transient regime characterizing the growth and the motion of the shear band is also studied.

Elastoplastic Approach Based on Microscopic Insights for the Steady State and Transient Dynamics of Sheared Disordered Solids.

We develop a framework to study the mechanical response of athermal amorphous solids via a coupling of mesoscale and microscopic models. Using measurements of coarse-grained quantities from simulations of dense disordered particulate systems, we present a coherent elastoplastic model approach for deformation and flow of yield stress materials. For a given set of parameters, this model allows us to match consistently transient and steady state features of driven disordered systems with diverse preparation histories under both applied shear-rate and creep protocols.

Microscopic precursors of failure in soft matter.

The mechanical properties of soft matter are of great importance in countless applications, in addition of being an active field of academic research. Given the relative ease with which soft materials can be deformed, their non-linear behavior is of particular relevance. Large loads eventually result in material failure. In this Perspective article, we discuss recent work aiming at detecting precursors of failure by scrutinizing the microscopic structure and dynamics of soft systems under various conditions of loading. In particular, we show that the microscopic dynamics is a powerful indicator of the ultimate fate of soft materials, capable of unveiling precursors of failure up to thousands of seconds before any macroscopic sign of weakening.

Criticality at a Finite Strain Rate in Fluidized Soft Glassy Materials.

We study the emergence of critical dynamics in the steady shear rheology of fluidized soft glassy materials. Within a mesoscale elastoplastic model accounting for a shear band instability, we show how additional noise can induce a transition from a phase separated to homogeneous flow, accompanied by critical-like fluctuations of the macroscopic shear rate. Both macroscopic quantities and fluctuations exhibit power law behaviors in the vicinity of this transition, consistent with previous experimental findings on vibrated granular media. Altogether, our results suggest a generic scenario for the emergence of criticality when shear weakening mechanisms compete with a fluidizing noise.

Confinement-Induced Transition between Wavelike Collective Cell Migration Modes.

The structural and functional organization of biological tissues relies on the intricate interplay between chemical and mechanical signaling. Whereas the role of constant and transient mechanical perturbations is generally accepted, several studies recently highlighted the existence of long-range mechanical excitations (i.e., waves) at the supracellular level. Here, we confine epithelial cell monolayers to quasi-one-dimensional geometries, to force the establishment of tissue-level waves of well-defined wavelength and period. Numerical simulations based on a self-propelled Voronoi model reproduce the observed waves and exhibit a phase transition between a global and a multinodal wave, controlled by the confinement size. We confirm experimentally the existence of such a phase transition, and show that wavelength and period are independent of the confinement length. Together, these results demonstrate the intrinsic origin of tissue oscillations, which could provide cells with a mechanism to accurately measure distances at the supracellular level.

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.

Mean-Field Scenario for the Athermal Creep Dynamics of Yield-Stress Fluids.

We develop a theoretical description based on an existent mean-field model for the transient dynamics prior to the steady flow of yielding materials. The mean-field model not only reproduces the experimentally observed nonlinear time dependence of the shear-rate response to an external stress, but also allows for the determination of the different physical processes involved in the onset of the reacceleration phase after the initial slowing down and a distinct fluidization phase. The fluidization time displays a power-law dependence on the distance of the applied stress to an age-dependent yield stress, which is not universal but strongly dependent on initial conditions.

Creep dynamics of athermal amorphous materials: a mesoscopic approach.

Yield stress fluids display complex dynamics, in particular when driven into the transient regime between the solid and the flowing state. Inspired by creep experiments on dense amorphous materials, we implement mesoscale elasto-plastic descriptions to analyze such transient dynamics in athermal systems. Both our mean-field and space-dependent approaches consistently reproduce the typical experimental strain rate responses to different applied steps in stress. Moreover, they allow us to understand basic processes involved in the strain rate slowing down (creep) and the strain rate acceleration (fluidization) phases. The fluidization time increases in a power-law fashion as the applied external stress approaches a static yield stress. This stress value is related to the stress over-shoot in shear start-up experiments, and it is known to depend on sample preparation and age. By calculating correlations of the accumulated plasticity in the spatially resolved model, we reveal different modes of cooperative motion during the creep dynamics.

Nonlinear Rheology in a Model Biological Tissue.

The rheological response of dense active matter is a topic of fundamental importance for many processes in nature such as the mechanics of biological tissues. One prominent way to probe mechanical properties of tissues is to study their response to externally applied forces. Using a particle-based model featuring random apoptosis and environment-dependent division rates, we evidence a crossover from linear flow to a shear-thinning regime with an increasing shear rate. To rationalize this nonlinear flow we derive a theoretical mean-field scenario that accounts for the interplay of mechanical and active noise in local stresses. These noises are, respectively, generated by the elastic response of the cell matrix to cell rearrangements and by the internal activity.

Non-trivial rheological exponents in sheared yield stress fluids.

In this work we discuss possible physical origins of non-trivial exponents in the athermal rheology of soft materials at low but finite driving rates. A key ingredient in our scenario is the presence of a self-consistent mechanical noise that stems from the spatial superposition of long-range elastic responses to localized plastically deforming regions. We study analytically a mean-field model, in which this mechanical noise is accounted for by a stress diffusion term coupled to the plastic activity. Within this description we show how a dependence of the shear modulus and/or the local relaxation time on the shear rate introduces corrections to the usual mean-field prediction, concerning the Herschel-Bulkley-type rheological response of exponent 1/2. This feature of the mean-field picture is then shown to be robust with respect to structural disorder and partial relaxation of the local stress. We test this prediction numerically on a mesoscopic lattice model that implements explicitly the long-range elastic response to localized shear transformations, and we conclude on how our scenario might be tested in rheological experiments.

Cell division and death inhibit glassy behaviour of confluent tissues.

We investigate the effects of cell division and apoptosis on collective dynamics in two-dimensional epithelial tissues. Our model includes three key ingredients observed across many epithelia, namely cell-cell adhesion, cell death and a cell division process that depends on the surrounding environment. We show a rich non-equilibrium phase diagram depending on the ratio of cell death to cell division and on the adhesion strength. For large apoptosis rates, cells die out and the tissue disintegrates. As the death rate decreases, however, we show, consecutively, the existence of a gas-like phase, a gel-like phase, and a dense confluent (tissue) phase. Most striking is the observation that the tissue is self-melting through its own internal activity, ruling out the existence of any glassy phase.

Driving Rate Dependence of Avalanche Statistics and Shapes at the Yielding Transition.

We study stress time series caused by plastic avalanches in athermally sheared disordered materials. Using particle-based simulations and a mesoscopic elastoplastic model, we analyze system size and shear-rate dependence of the stress-drop duration and size distributions together with their average temporal shape. We find critical exponents different from mean-field predictions, and a clear asymmetry for individual avalanches. We probe scaling relations for the rate dependency of the dynamics and we report a crossover towards mean-field results for strong driving.

Probing relevant ingredients in mean-field approaches for the athermal rheology of yield stress materials.

Although the notion of mechanical noise is expected to play a key role in the non-linear rheology of athermally sheared amorphous systems, its characterization has so far remained elusive. Here, we show using molecular dynamic simulations that in spite of the presence of strong spatio-temporal correlations in the system, the local stress exhibits normal diffusion under the effect of the mechanical noise in the finite driving regime. The diffusion constant appears to be proportional to the mean plastic activity. Our data suggests that the corresponding proportionality constant is density independent, and can be directly related to the specific form of the rheological flow curve, pointing the way to a generic way of modeling mechanical noise in mean-field equations.

On the relevance of disorder in athermal amorphous materials under shear.

We show that, at least at a mean-field level, the effect of structural disorder in sheared amorphous media is very dissimilar depending on the thermal or athermal nature of their underlying dynamics. We first introduce a toy model, including explicitly two types of noise (thermal versus athermal). Within this interpretation framework, we argue that mean-field athermal dynamics can be accounted for by the so-called Hébraud-Lequeux (HL) model, in which the mechanical noise stems explicitly from the plastic activity in the sheared medium. Then, we show that the inclusion of structural disorder, by means of a distribution of yield energy barriers, has no qualitative effect in the HL model, while such a disorder is known to be one of the key ingredients leading kinematically to a finite macroscopic yield stress in other mean-field descriptions, such as the Soft-Glassy-Rheology model. We conclude that the statistical mechanisms at play in the emergence of a macroscopic yield stress, and a complex stationary dynamics at low shear rate, are different in thermal and athermal amorphous systems.

Relaxation in yield stress systems through elastically interacting activated events.

We study consequences of long-range elasticity in thermally assisted dynamics of yield stress materials. Within a two-dimensional mesoscopic model we calculate the mean-square displacement and the dynamical structure factor for tracer particle trajectories. The ballistic regime at short time scales is associated with a compressed exponential decay in the dynamical structure factor, followed by a subdiffusive crossover prior to the onset of diffusion. We relate this crossover to spatiotemporal correlations and thus go beyond established mean field predictions.

Universal and non-universal features in coarse-grained models of flow in disordered solids.

We study the two-dimensional (2D) shear flow of amorphous solids within variants of an elastoplastic model, paying particular attention to spatial correlations and time fluctuations of, e.g., local stresses. The model is based on the local alternation between an elastic regime and plastic events during which the local stress is redistributed. The importance of a fully tensorial description of the stress and of the inclusion of (coarse-grained) convection in the model is investigated; scalar and tensorial models yield similar results, while convection enhances fluctuations and breaks the spurious symmetry between the flow and velocity gradient directions, for instance when shear localisation is observed. Besides, correlation lengths measured with diverse protocols are discussed. One class of such correlation lengths simply scale with the spacing between homogeneously distributed, simultaneous plastic events. This leads to a scaling of the correlation length with the shear rate as γ̇(-1/2) in 2D in the athermal regime, regardless of the details of the model. The radius of the cooperative disk, defined as the near-field region in which plastic events induce a stress redistribution that is not amenable to a mean-field treatment, notably follows this scaling. On the other hand, the cooperative volume measured from the four-point stress susceptibility and its dependence on the system size and the shear rate are model-dependent.

Nonlinear wavelength selection in surface faceting under electromigration.

We report on the control of the faceting of crystal surfaces by means of surface electromigration. When electromigration reinforces the faceting instability, we find perpetual coarsening with a wavelength increasing as t(1/2). For strongly stabilizing electromigration, the surface is stable. For weakly stabilizing electromigration, a cellular pattern is obtained, with a nonlinearly selected wavelength. The selection mechanism is not caused by an instability of steady states, as suggested by previous works in the literature. Instead, the dynamics is found to exhibit coarsening before reaching a continuous family of stable nonequilibrium steady states.