Shear Stress Correlations in Hard and Soft Sphere Fluids

The shear stress autocorrelation function has been studied recently by molecular dynamics simulation using the 1/q^n potential for very large n. The results are analyzed and interpreted here by comparing them to the shear stress response function for hard spheres. It is shown that the hard sphere response function has a singular contribution and that this is reproduced accurately by the simulations for large n. A simple model for the stress autocorrelation function at finite n is proposed, based on the required hard sphere limiting form.Comment: 14 pages, 2 figures; submitted for special issue of Molecular Physic

Elastocaloric response of PbTiO3 predicted from a first-principles effective Hamiltonian

A first-principles based effective Hamiltonian is used within a molecular dynamics simulation to study the elastocaloric effect in PbTiO3. It is found that the transition temperature is a linear function of uniaxial tensile stress. Negative temperature change is calculated, when the uniaxial tensile stress is switched off, as a function of initial temperature Delta-T(T_initial). It is predicted that the formation of domain structures under uniaxial tensile stress degrades the effectiveness of the elastocaloric effect.Comment: 6 pages, 7 figures, published in JPS

Rheology of a Supercooled Polymer Melt

Molecular dynamics simulations are performed for a polymer melt composed of short chains in quiescent and sheared conditions. The stress relaxation function $G(t)$ exhibits a stretched exponential form in a relatively early stage and ultimately follows the Rouse function in quiescent supercooled state. Transient stress evolution after application of shear obeys the linear growth $\int_0^t dt'G(t')$ for strain less than 0.1 and then saturates into a non-Newtonian viscosity. In steady states, strong shear-thinning and elongation of chains into ellipsoidal shapes are found at extremely small shear. A glassy component of the stress is much enhanced in these examples.Comment: 4 pages, 5 figure

From network to phenotype : the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress

Plants have established different mechanisms to cope with environmental fluctuations and accordingly fine-tune their growth and development through the regulation of complex molecular networks. It is largely unknown how the network architectures change and what the key regulators in stress responses and plant growth are. Here, we investigated a complex, highly interconnected network of 20 Arabidopsis transcription factors (TFs) at the basis of leaf growth inhibition upon mild osmotic stress. We tracked the dynamic behavior of the stress-responsive TFs over time, showing the rapid induction following stress treatment, specifically in growing leaves. The connections between the TFs were uncovered using inducible overexpression lines and were validated with transient expression assays. This study resulted in the identification of a core network, composed of ERF6, ERF8, ERF9, ERF59, and ERF98, which is responsible for most transcriptional connections. The analyses highlight the biological function of this core network in environmental adaptation and its redundancy. Finally, a phenotypic analysis of loss-of-function and gain-of-function lines of the transcription factors established multiple connections between the stress-responsive network and leaf growth

DJ-1 interacts with and regulates paraoxonase-2, an enzyme critical for neuronal survival in response to oxidative stress.

Loss-of-function mutations in DJ-1 (PARK7) gene account for about 1% of all familial Parkinson's disease (PD). While its physiological function(s) are not completely clear, DJ-1 protects neurons against oxidative stress in both in vitro and in vivo models of PD. The molecular mechanism(s) through which DJ-1 alleviates oxidative stress-mediated damage remains elusive. In this study, we identified Paraoxonase-2 (PON2) as an interacting target of DJ-1. PON2 activity is elevated in response to oxidative stress and DJ-1 is crucial for this response. Importantly, we showed that PON2 deficiency hypersensitizes neurons to oxidative stress induced by MPP+ (1-methyl-4-phenylpyridinium). Conversely, over-expression of PON2 protects neurons in this death paradigm. Interestingly, PON2 effectively rescues DJ-1 deficiency-mediated hypersensitivity to oxidative stress. Taken together, our data suggest a model by which DJ-1 exerts its antioxidant activities, at least partly through regulation of PON2

Bent surface free energy differences from simulation

We present a calculation of the change of free energy of a solid surface upon bending of the solid. It is based on extracting the surface stress through a molecular dynamics simulation of a bent slab by using a generalized stress theorem formula, and subsequent integration of the stress with respect to strain as a function of bending curvature. The method is exemplified by obtaining and comparing free energy changes with curvature of various reconstructed Au(001) surfaces.Comment: 14 pages, 2 figures, accepted for publication in Surface Science (ECOSS-19

New model for surface fracture induced by dynamical stress

We introduce a model where an isotropic, dynamically-imposed stress induces fracture in a thin film. Using molecular dynamics simulations, we study how the integrated fragment distribution function depends on the rate of change and magnitude of the imposed stress, as well as on temperature. A mean-field argument shows that the system becomes unstable for a critical value of the stress. We find a striking invariance of the distribution of fragments for fixed ratio of temperature and rate of change of the stress; the interval over which this invariance holds is determined by the force fluctuations at the critical value of the stress.Comment: Revtex, 4 pages, 4 figures available upon reques

Activated dynamics and effective temperature in a steady state sheared glass

We conduct nonequilibrium molecular dynamics simulations to measure the shear stress, the average inherent structure energy, and the effective temperature $T_{eff}$ of a sheared model glass as a function of bath temperature $T$ and shear strain rate. For $T$ above the glass transition temperature $T_0$, the rheology approaches a Newtonian limit and $T_{eff}$ approaches $T$ as the strain rate approaches zero, while for $T<T_0$, the shear stress approaches a yield stress and $T_{eff}$ approaches a limiting value near $T_0$. In the shear-dominated regime at high $T$, high strain rate or at low $T$, we find that the shear stress and the average inherent structure energy each collapse onto a single curve as a function of $T_{eff}$. This indicates that $T_{eff}$ is controlling behavior in this regime.Comment: 4 pages, 2 figures. Revised to include additional data. Inherent structure energy results were included, and much of the shear transformation zone discussion was remove