Parallel three-dimensional simulations of quasi-static elastoplastic solids

Hypo-elastoplasticity is a flexible framework for modeling the mechanics of many hard materials under small elastic deformation and large plastic deformation. Under typical loading rates, most laboratory tests of these materials happen in the quasi-static limit, but there are few existing numerical methods tailor-made for this physical regime. In this work, we extend to three dimensions a recent projection method for simulating quasi-static hypo-elastoplastic materials. The method is based on a mathematical correspondence to the incompressible Navier-Stokes equations, where the projection method of Chorin (1968) is an established numerical technique. We develop and utilize a three-dimensional parallel geometric multigrid solver employed to solve a linear system for the quasi-static projection. Our method is tested through simulation of three-dimensional shear band nucleation and growth, a precursor to failure in many materials. As an example system, we employ a physical model of a bulk metallic glass based on the shear transformation zone theory, but the method can be applied to any elastoplasticity model. We consider several examples of three-dimensional shear banding, and examine shear band formation in physically realistic materials with heterogeneous initial conditions under both simple shear deformation and boundary conditions inspired by friction welding.Comment: Final version. Accepted for publication in Computer Physics Communication

Secular change in TTG compositions: Implications for the evolution of Archaean geodynamics

It is estimated that around three quarters of Earth's first generation continental crust had been produced by the end of the Archaean Eon, 2.5 billion years ago. This ancient continental crust is mostly composed of variably deformed and metamorphosed magmatic rocks of the tonalite–trondhjemite–granodiorite (TTG) suite that formed by partial melting of hydrated mafic rocks. However, the geodynamic regime under which TTG magmas formed is a matter of ongoing debate. Using a filtered global geochemical dataset of 563 samples with ages ranging from the Eoarchaean to Neoarchaean (4.0–2.5 Ga), we interrogate the bulk rock major oxide and trace element composition of TTGs to assess evidence for secular change. Despite a high degree of scatter in the data, the concentrations or ratios of several key major oxides and trace elements show statistically significant trends that indicate maxima, minima and/or transitions in the interval 3.3–3.0 Ga. Importantly, a change point analysis of K2O/Na2O, Sr/Y and LaN/YbN demonstrates a statistically significant (>99% confidence) change during this 300 Ma period. These shifts may be linked to a fundamental change in geodynamic regime around the peak in upper mantle temperatures from one dominated by non-uniformitarian, deformable stagnant lid processes to another dominated by the emergence of global mobile lid or plate tectonic processes by the end of the Archaean. A notable change is also evident at 2.8–2.7 Ga that coincides with a major jump in the rate of survival of metamorphic rocks with contrasting thermal gradients, which may relate to the emergence of more potassic continental arc magmas and an increased preservation potential during collisional orogenesis. In many cases, the chemical composition of TTGs shows an increasing spread through the Archaean, reflecting the irreversible differentiation of the lithosphere

Ecological Characteristics of Streams in the Barrenlands near Lac de Gras, N.W.T., Canada

We examined spatiotemporal variation in the physical, chemical, and biological characteristics of pristine streams that represent a range of conditions near Lac de Gras in the Barrenlands region of the Northwest Territories, Canada. Principal component analysis organized streams into four groups on the basis of seven physical characteristics. Despite broad differences among groups in physical characteristics, variation in chemical and biological characteristics was generally not large, with only pH and coarse particulate organic matter differing among the four groups. Nevertheless, several chemical and biological variables were correlated with physical characteristics, particularly measures of stream size (bankfull width and depth, drainage area, and stream discharge). Annual variability in climate affected stream temperature and discharge and influenced several biotic characteristics, particularly the growth of young-of-the-year arctic grayling (Thymallus arcticus). Barrenland streams share basic characteristics of Alaskan tundra streams, as a result of similar climatic regimes. Key differences between the two areas, however, appear related to the lake-outlet nature of the Barrenland streams, which may contribute to higher growth of young-of-the-year arctic grayling than would be expected from regional climate.On a étudié la variation spatio-temporelle dans les caractéristiques physiques, chimiques et biologiques de cours d'eau vierges qui témoignent d'une gamme de conditions près du lac de Gras dans la région des Barrenlands, dans les Territoires du Nord-Ouest, au Canada. L'analyse des composantes principales a divisé les cours d'eau en quatre groupes, d'après sept caractéristiques physiques. En dépit de différences marquées dans ces dernières entre les groupes, la variation dans les attributs chimiques et biologiques n'était généralement pas très grande, avec seulement le pH et les grosses particules organiques qui montraient des différences entre les quatre groupes. Plusieurs variables chimiques et biologiques étaient néanmoins corrélées avec les attributs physiques, en particulier les mesures de la taille des cours d'eau (largeur et profondeur du débordement, aire de drainage et débit). La variabilité annuelle du climat avait une incidence sur la température et le débit des cours d'eau et elle influençait plusieurs caractéristiques biotiques, en particulier la croissance des jeunes de l'année chez l'ombre arctique. Les cours d'eau des Barrenlands ont en commun les caractéristiques fondamentales des cours d'eau de la toundra alaskienne, vu qu'ils sont soumis à des régimes climatiques similaires. Les différences majeures entre les deux régions semblent cependant liées au fait que la décharge des cours d'eau des Barrenlands se fait dans un lac, ce qui pourrait contribuer à une croissance des jeunes de l'année chez l'ombre arctique plus forte que le climat régional ne le laisserait croire

An accurate calculation of the nucleon axial charge with lattice QCD

We report on a lattice QCD calculation of the nucleon axial charge, $g_A$, using M\"{o}bius Domain-Wall fermions solved on the dynamical $N_f=2+1+1$ HISQ ensembles after they are smeared using the gradient-flow algorithm. The calculation is performed with three pion masses, $m_\pi\sim\{310,220,130\}$ MeV. Three lattice spacings ($a\sim\{0.15,0.12,0.09\}$ fm) are used with the heaviest pion mass, while the coarsest two spacings are used on the middle pion mass and only the coarsest spacing is used with the near physical pion mass. On the $m_\pi\sim220$ MeV, $a\sim0.12$ fm point, a dedicated volume study is performed with $m_\pi L \sim \{3.22,4.29,5.36\}$. Using a new strategy motivated by the Feynman-Hellmann Theorem, we achieve a precise determination of $g_A$ with relatively low statistics, and demonstrable control over the excited state, continuum, infinite volume and chiral extrapolation systematic uncertainties, the latter of which remains the dominant uncertainty. Our final determination at 2.6\% total uncertainty is $g_A = 1.278(21)(26)$, with the first uncertainty including statistical and systematic uncertainties from fitting and the second including model selection systematics related to the chiral and continuum extrapolation. The largest reduction of the second uncertainty will come from a greater number of pion mass points as well as more precise lattice QCD results near the physical pion mass.Comment: 17 pages + 11 pages of references and appendices. 15 figures. Interested readers can download the Python analysis scripts and an hdf5 data file at https://github.com/callat-qcd/project_gA_v

Ask For It: Development of a Health Advocacy Intervention for Adults with Intellectual Disability and Their General Practitioners

Two per cent of people in Australia have intellectual disability and the adults in this population often have poor health status. This poor health can be partly attributed to communication difficulties encountered by people with intellectual disability and also health professionals in consultation settings. The design and development processes of an educational intervention to improve communication between patients, general practitioners (GPs) and also advocates in a population of adults with intellectual disability are described. The design process was collaborative and involved adults with intellectual disability, GPs, parents, support workers and other professionals. It was a nine-step development process and led to the final communication tool package, the ask (advocacy skills kit) 5-year health diary and educational session. As a result of the collaborative design and development processes, this diary included qualities not found in most other medical record keeping systems: visual appeal, advice on how to be a health advocate, utility for a range of users, privacy, portability and sufficient capacity to record personal patient information which enhanced communication between doctor, patient and advocate. It is proving to be very popular. Clear implications were found for applying established criteria and incorporating the needs of users in the design of educational interventions in the intellectually disabled population. Health promotion tools aiming to improve the current poor health status of adults with intellectual disability should be developed further

Lack of functional and expression homology between human and mouse aldo-keto reductase 1C enzymes: implications for modelling human cancers

<p>Abstract</p> <p>Background</p> <p>Over recent years, enzymes of the aldo-keto reductase (AKR) 1C subfamily have been implicated in the progression of prostate, breast, endometrial and leukemic cancers. This is due to the ability of AKR1C enzymes to modify androgens, estrogens, progesterone and prostaglandins (PGs) in a tissue-specific manner, regulating the activity of nuclear receptors and other downstream effects. Evidence supporting a role for AKR1C enzymes in cancer derives mostly from studies with isolated primary cells from patients or immortalized cell lines. Mice are ideal organisms for <it>in vivo </it>studies, using knock-out or over-expression strains. However, the functional conservation of AKR1C enzymes between human and mice has yet to be described.</p> <p>Results</p> <p>In this study, we have characterized and compared the four human (AKR1C1,-1C2, -1C3 and -1C4) and the eight murine (AKR1C6, -1C12, -1C13, -1C14, -1C18, -1C19, -1C20 and -1C21) isoforms in their phylogeny, substrate preference and tissue distribution. We have found divergent evolution between human and murine AKR1C enzymes that was reflected by differing substrate preference. Murine enzymes did not perform the 11β-ketoreduction of prostaglandin (PG) D₂, an activity specific to human AKR1C3 and important in promoting leukemic cell survival. Instead, murine AKR1C6 was able to perform the 9-ketoreduction of PGE₂, an activity absent amongst human isoforms. Nevertheless, reduction of the key steroids androstenedione, 5α-dihydrotestosterone, progesterone and estrone was found in murine isoforms. However, unlike humans, no AKR1C isoforms were detected in murine prostate, testes, uterus and haemopoietic progenitors.</p> <p>Conclusions</p> <p>This study exposes significant lack of phylogenetic and functional homology between human and murine AKR1C enzymes. Therefore, we conclude that mice are not suitable to model the role of AKR1C in human cancers and leukemia.</p

Ion Chamber Collection Efficiencies for Proton Spot Scanning Calibration

Charge accumulation was measured under calibration conditions in the spread-out Bragg peak (SOBP) using the calibration bias as well as a range of voltages from 10V to 500V and a Farmer-style ion chamber. Collection efficiency was determined by extrapolating to infinite voltage. Similar measurements were taken in an identical dose distribution with a much shorter spot duration. The impact of each of the three models on calibration was then quantified using the TRS-398 protocol. The collection efficiency for the standard calibration was determined to agree well with the prediction of a continuous beam recombination correction. The standard calibration field was found to persistently agree with a continuous beam recombination correction for much lower operating biases. The collection efficiency result for the short spot duration field did not agree with either the continuous or pulsed-beam correction. Using the incorrect recombination model under the standard calibration conditions resulted in a 0.5% calibration difference. We have determined that our spot scanning system would be most appropriately calibrated using a recombination correction with continuous beam model. Physicists responsible for the calibration of such systems are advised to take measurements described here to correctly identify the applicable recombination model for their clinics.Comment: Submitted December 16, 2015 to Medical Physic

Manifold learning for coarse-graining atomistic simulations: Application to amorphous solids

We introduce a generalized machine learning framework to probabilistically parameterize upper-scale models in the form of nonlinear PDEs consistent with a continuum theory, based on coarse-grained atomistic simulation data of mechanical deformation and flow processes. The proposed framework utilizes a hypothesized coarse-graining methodology with manifold learning and surrogate-based optimization techniques. Coarse-grained high-dimensional data describing quantities of interest of the multiscale models are projected onto a nonlinear manifold whose geometric and topological structure is exploited for measuring behavioral discrepancies in the form of manifold distances. A surrogate model is constructed using Gaussian process regression to identify a mapping between stochastic parameters and distances. Derivative-free optimization is employed to adaptively identify a unique set of parameters of the upper-scale model capable of rapidly reproducing the system's behavior while maintaining consistency with coarse-grained atomic-level simulations. The proposed method is applied to learn the parameters of the shear transformation zone (STZ) theory of plasticity that describes plastic deformation in amorphous solids as well as coarse-graining parameters needed to translate between atomistic and continuum representations. We show that the methodology is able to successfully link coarse-grained microscale simulations to macroscale observables and achieve a high-level of parity between the models across scales.Comment: 34 pages, 12 figures, references added, Section 4 added, Section 2.1 update