Mapping out the glassy landscape of a mesoscopic elastoplastic model.

We develop a mesoscopic model to study the plastic behavior of an amorphous material under cyclic loading. The model is depinning-like and driven by a disordered thresholds dynamics that is coupled by long-range elastic interactions. We propose a simple protocol of "glass preparation" that allows us to mimic thermalization at high temperatures as well as aging at vanishing temperature.

A mechano-sensing mechanism for waving in plant roots.

Arabidopsis roots grown on inclined agar surfaces exhibit unusual sinusoidal patterns known as root-waving. The origin of these patterns has been ascribed to both genetic and environmental factors. Here we propose a mechano-sensing model for root-waving, based on a combination of friction induced by gravitropism, the elasticity of the root and the anchoring of the root to the agar by thin hairs, and demonstrate its relevance to previously obtained experimental results.

Cooperative effects driving the multi-periodic dynamics of cyclically sheared amorphous solids.

When subject to cyclic forcing, amorphous solids can reach periodic, repetitive states, where the system behaves plastically, but the particles return to their initial positions after one or more forcing cycles, where the latter response is called multi-periodic. It is known that plasticity in amorphous materials is mediated by local rearrangements called "soft spots" or "shear transformation zones." Experiments and simulations indicate that soft spots can be modeled as hysteretic two-state entities interacting via quadrupolar displacement fields generated when they switch states and that these interactions can give rise to multi-periodic behavior.

Rectified random cell motility as a mechanism for embryo elongation.

The body of vertebrate embryos forms by posterior elongation from a terminal growth zone called the tail bud. The tail bud is a source of highly motile cells that eventually constitute the presomitic mesoderm (PSM), a tissue that plays an important role in elongation movements. PSM cells establish an anterior-posterior cell motility gradient that parallels a gradient associated with the degradation of a specific cellular signal (FGF) known to be implicated in cell motility.

Topology of the energy landscape of sheared amorphous solids and the irreversibility transition.

Recent experiments and simulations of amorphous solids plastically deformed by an oscillatory drive have found a surprising 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. It was also found that 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.

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.

Secondary school canteens in Australia: analysis of canteen menus from a repeated cross-sectional national survey.

Objective: The current study aimed to assess the nutritional quality of Australian secondary school canteen menus.

Design: Stratified national samples of schools provided canteen menus in 2012-2013 and 2018, which were systematically assessed against a 'traffic light' classification system according to the National Healthy School Canteen Guidelines. Items were classified as green (healthiest and recommended to dominate canteen menus), amber (select carefully) or red (low nutritional quality, should not appear on canteen menus), and pricing and promotional strategies were recorded.

Forced deterministic dynamics on a random energy landscape: Implications for the physics of amorphous solids.

The dynamics of supercooled liquids and plastically deformed amorphous solids is known to be dominated by the structure of their rough energy landscapes. Recent experiments and simulations on amorphous solids subjected to oscillatory shear at athermal conditions have shown that for small strain amplitudes these systems reach limit cycles of different periodicities after a transient. However, for larger strain amplitudes the transients become longer and for strain amplitudes exceeding a critical value the system reaches a diffusive steady state.

Annealing and rejuvenation in a two-dimensional model amorphous solid under oscillatory shear.

We study the annealing and rejuvenation behavior of a two-dimensional amorphous solid model under oscillatory shear. We show that, depending on the cooling protocol used to create the initial configuration, the mean potential energy can either decrease or increase under subyield oscillatory shear. For post-yield oscillatory shear, the mean potential energy increases and is independent on the initial conditions.

Networks and Hierarchies: How Amorphous Materials Learn to Remember.

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 subcycles.

Critical diffusivity in the reversibility-irreversibility transition of amorphous solids under oscillatory shear.

Recently it was shown that under oscillatory shear at zero temperature an amorphous solid transitions from asymptotically periodic to asymptotically diffusive steady-state at a critical maximal strain amplitude. Current understanding of the physics behind this transition is lacking. Here we show, using computer simulations, evidence that the diffusivity of the vector of coordinates of the particles comprising an amorphous solid, when subject to oscillatory shear, undergoes a second order phase transition at the reversibility-irreversibility transition point.

Revealing the cellular degradome by mass spectrometry analysis of proteasome-cleaved peptides.

Cellular function is critically regulated through degradation of substrates by the proteasome. To enable direct analysis of naturally cleaved proteasomal peptides under physiological conditions, we developed mass spectrometry analysis of proteolytic peptides (MAPP), a method for proteasomal footprinting that allows for capture, isolation and analysis of proteasome-cleaved peptides. Application of MAPP to cancer cell lines as well as primary immune cells revealed dynamic modulation of the cellular degradome in response to various stimuli, such as proinflammatory signals.

Excitable Dynamics and Yap-Dependent Mechanical Cues Drive the Segmentation Clock.

The periodic segmentation of the vertebrate body axis into somites, and later vertebrae, relies on a genetic oscillator (the segmentation clock) driving the rhythmic activity of signaling pathways in the presomitic mesoderm (PSM). To understand whether oscillations are an intrinsic property of individual cells or represent a population-level phenomenon, we established culture conditions for stable oscillations at the cellular level. This system was used to demonstrate that oscillations are a collective property of PSM cells that can be actively triggered in vitro by a dynamical quorum sensing signal involving Yap and Notch signaling.

Spontaneous exfoliation of a drying gel.

Wet starch cracks when it dries inhomogeneously, while hot glass cracks when it cools non-uniformly. In both cases, differential shrinkage induced by drying/cooling from the surface causes superficial cracks to grow perpendicular to the surface in different patterns. In contrast with these observations of bulk cracking in brittle materials, when a soft and homogeneously swollen polymer gel dries, differential strains lead to the peeling of a thin layer that spontaneously tears away from the bulk.

Living in a continuous traumatic reality: Impact on elderly persons residing in urban and rural communities.

This study is an exploration of the contribution of exposure to the continuous threat of Qassam rocket attacks to PTSD among elderly residents of urban and rural communities. Specifically, we examined the contribution of sociodemographic variables, psychological resources, and perceived social support to PTSD, and whether this relationship is mediated by cognitive appraisals. The sample consisted of 298 residents of 2 different communities: urban (n = 190), and rural (n = 108).

Core promoter sequence in yeast is a major determinant of expression level.

The core promoter is the regulatory sequence to which RNA polymerase is recruited and where it acts to initiate transcription. Here, we present the first comprehensive study of yeast core promoters, providing massively parallel measurements of core promoter activity and of TSS locations and relative usage for thousands of native and designed sequences. We found core promoter activity to be highly correlated to the activity of the entire promoter and that sequence variation in different core promoter regions substantially tunes its activity in a predictable way.

Systematic dissection of the sequence determinants of gene 3' end mediated expression control.

The 3'end genomic region encodes a wide range of regulatory process including mRNA stability, 3' end processing and translation. Here, we systematically investigate the sequence determinants of 3' end mediated expression control by measuring the effect of 13,000 designed 3' end sequence variants on constitutive expression levels in yeast. By including a high resolution scanning mutagenesis of more than 200 native 3' end sequences in this designed set, we found that most mutations had only a mild effect on expression, and that the vast majority (~90%) of strongly effecting mutations localized to a single positive TA-rich element, similar to a previously described 3' end processing efficiency element, and resulted in up to ten-fold decrease in expression.

Continuous exposure to life threats among different age groups in different types of communities.

The current study compared levels of posttraumatic symptoms (PTS) resulting from continuous exposure to missile attacks among residents of 2 types of communities (urban vs. rural) in 2 different age groups (elderly persons vs. young adults).

Onset of irreversibility and chaos in amorphous solids under periodic shear.

A fundamental problem in the physics of amorphous materials is understanding the transition from reversible to irreversible plastic behavior and its connection to yield. Currently, continuum material modeling relies on phenomenological yield thresholds, however in many cases the transition from elastic to plastic behavior is gradual, which makes it difficult to identify an exact yield criterion. Here we show that under periodic shear, amorphous solids undergo a transition from repetitive, predictable behavior to chaotic, irregular behavior as a function of the strain amplitude.

Rheology and shear band suppression in particle and chain mixtures.

Using numerical simulations we consider an amorphous particle mixture which exhibits shear localization, and find that the addition of even a small fraction of chains strongly enhances the material strength, creating pronounced overshoot features in the stress-strain curves. The strengthening occurs in the case where the chains are initially perpendicular to the shear direction, leading to a suppression of the shear band. This also leads to stiffening effects that are typical of polymeric systems.

Quantitative theory of a time-correlation function in a one-component glass-forming liquid with anisotropic potential.

The Shintani-Tanaka model is a glass-forming system whose constituents interact via an anisotropic potential depending on the angle of a unit vector carried by each particle. The decay of time-correlation functions of the unit vectors exhibits the characteristics of generic relaxation functions during glass transitions. In particular it exhibits a stretched exponential form, with the stretching index beta depending strongly on the temperature.

Aging and relaxation in glass-forming systems.

We propose that there exists a generic class of glass-forming systems that have competing states (of crystalline order or not) which are locally close in energy to the ground state (which is typically unique). Upon cooling, such systems exhibit patches (or clusters) of these competing states which become locally stable in the sense of having a relatively high local shear modulus. It is in between these clusters where aging, relaxation, and plasticity under strain can take place.

Elasticity with arbitrarily shaped inhomogeneity.

A classical problem in elasticity theory involves an inhomogeneity embedded in a material of given stress and shear moduli. The inhomogeneity is a region of arbitrary shape whose stress and shear moduli differ from those of the surrounding medium. In this paper we present a semianalytic method for finding the stress tensor for an infinite plate with such an inhomogeneity.