991 research outputs found
50 Years Later: Women, Work & the Work Ahead (Infographic)
How have things changed for women in the labor force over the last 50 years
Achieving Efficient Strong Scaling with PETSc using Hybrid MPI/OpenMP Optimisation
The increasing number of processing elements and decreas- ing memory to core
ratio in modern high-performance platforms makes efficient strong scaling a key
requirement for numerical algorithms. In order to achieve efficient scalability
on massively parallel systems scientific software must evolve across the entire
stack to exploit the multiple levels of parallelism exposed in modern
architectures. In this paper we demonstrate the use of hybrid MPI/OpenMP
parallelisation to optimise parallel sparse matrix-vector multiplication in
PETSc, a widely used scientific library for the scalable solution of partial
differential equations. Using large matrices generated by Fluidity, an open
source CFD application code which uses PETSc as its linear solver engine, we
evaluate the effect of explicit communication overlap using task-based
parallelism and show how to further improve performance by explicitly load
balancing threads within MPI processes. We demonstrate a significant speedup
over the pure-MPI mode and efficient strong scaling of sparse matrix-vector
multiplication on Fujitsu PRIMEHPC FX10 and Cray XE6 systems
Direct seeding trees on farmland in the Western Australian wheatbelt
Field and nursery experiments were conducted to determine suitable species, weed control methods, sowing times and seeding techniques. Sowing time was the most significant variable evident in the field experiments. Trees sown in the winter months of June and July out-performed later sowing times. Early sowing of trees in areas of low seasonal rainfall appears to offer considerable advantages for successful establishment over late sowing
EXAFS of the type-1 copper site of rusticyanin
AbstractExtended X-ray absorption fine structure (EXAFS) spectra at the Cu K-edge have been recorded of the oxidized and reduced form at pH 3.5 of rusticyanin, the type-1 or ‘blue’-copper protein from Thiobacillus ferrooxidans. The EXAFS of oxidized rusticyanin is well simulated with models assuming a ligand set of 2 N(His) and 1 S(Cys) at 1.99 and 2.16 Å, respectively. Upon reduction, the average Cu-N ligand distance increases by approx. 0.08Å. For both redox states studied, the fit by the simulation is significantly improved by including a contribution of an additional sulfur ligand at approx. 2.8 Å. From comparison with structural data of other blue-copper proteins, it is concluded that the copper coordination environment is relatively rigid, which may be a clue to its high redox potential
Natriuretic Peptides and Nitric Oxide Stimulate cGMP Synthesis in Different Cellular Compartments
Cyclic nucleotide-gated (CNG) channels are a family of ion channels activated by the binding of cyclic nucleotides. Endogenous channels have been used to measure cyclic nucleotide signals in photoreceptor outer segments and olfactory cilia for decades. Here we have investigated the subcellular localization of cGMP signals by monitoring CNG channel activity in response to agonists that activate either particulate or soluble guanylyl cyclase. CNG channels were heterologously expressed in either human embryonic kidney (HEK)-293 cells that stably overexpress a particulate guanylyl cyclase (HEK-NPRA cells), or cultured vascular smooth muscle cells (VSMCs). Atrial natriuretic peptide (ANP) was used to activate the particulate guanylyl cyclase and the nitric oxide donor S-nitroso-n-acetylpenicillamine (SNAP) was used to activate the soluble guanylyl cyclase. CNG channel activity was monitored by measuring Ca2+ or Mn2+ influx through the channels using the fluorescent dye, fura-2. We found that in HEK-NPRA cells, ANP-induced increases in cGMP levels activated CNG channels in a dose-dependent manner (0.05–10 nM), whereas SNAP (0.01–100 μM) induced increases in cGMP levels triggered little or no activation of CNG channels (P < 0.01). After pretreatment with 100 μM 3-isobutyl-1-methylxanthine (IBMX), a nonspecific phosphodiesterase inhibitor, ANP-induced Mn2+ influx through CNG channels was significantly enhanced, while SNAP-induced Mn2+ influx remained small. In contrast, we found that in the presence of IBMX, both 1 nM ANP and 100 μM SNAP triggered similar increases in total cGMP levels. We next sought to determine if cGMP signals are compartmentalized in VSMCs, which endogenously express particulate and soluble guanylyl cyclase. We found that 10 nM ANP induced activation of CNG channels more readily than 100 μM SNAP; whereas 100 μM SNAP triggered higher levels of total cellular cGMP accumulation. These results suggest that cGMP signals are spatially segregated within cells, and that the functional compartmentalization of cGMP signals may underlie the unique actions of ANP and nitric oxide
Modelling the impact of liner shipping network perturbations on container cargo routing: Southeast Asia to Europe application
Understanding how container routing stands to be impacted by different scenarios of liner shipping network perturbations such as natural disasters or new major infrastructure developments is of key importance for decision-making in the liner shipping industry. The variety of actors and processes within modern supply chains and the complexity of their relationships have previously led to the development of simulation-based models, whose application has been largely compromised by their dependency on extensive and often confidential sets of data. This study proposes the application of optimisation techniques less dependent on complex data sets in order to develop a quantitative framework to assess the impacts of disruptive events on liner shipping networks. We provide a categorization of liner network perturbations, differentiating between systemic and external and formulate a container assignment model that minimises routing costs extending previous implementations to allow feasible solutions when routing capacity is reduced below transport demand. We develop a base case network for the Southeast Asia to Europe liner shipping trade and review of accidents related to port disruptions for two scenarios of seismic and political conflict hazards. Numerical results identify alternative routing paths and costs in the aftermath of port disruptions scenarios and suggest higher vulnerability of intra-regional connectivity
Reduced Order Modeling of an Adaptive Mesh Ocean Model
Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv
Direct numerical simulations of particle-laden density currents with adaptive, discontinuous finite elements
High-resolution direct numerical simulations (DNSs) are an important tool for
the detailed analysis of turbidity current dynamics. Models that resolve the
vertical structure and turbulence of the flow are typically based upon the
Navier–Stokes equations. Two-dimensional simulations are known to produce
unrealistic cohesive vortices that are not representative of the real
three-dimensional physics. The effect of this phenomena is particularly
apparent in the later stages of flow propagation. The ideal solution to this
problem is to run the simulation in three dimensions but this is
computationally expensive.
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This paper presents a novel finite-element (FE) DNS turbidity current model
that has been built within Fluidity, an open source, general purpose,
computational fluid dynamics code. The model is validated through re-creation
of a lock release density current at a Grashof number of 5 × 10<sup>6</sup> in
two and three dimensions. Validation of the model considers the flow energy
budget, sedimentation rate, head speed, wall normal velocity profiles and the
final deposit. Conservation of energy in particular is found to be a good
metric for measuring model performance in capturing the range of dynamics on a
range of meshes. FE models scale well over many thousands of processors and do
not impose restrictions on domain shape, but they are computationally
expensive. The use of adaptive mesh optimisation is shown to reduce the
required element count by approximately two orders of magnitude in comparison
with fixed, uniform mesh simulations. This leads to a substantial reduction in
computational cost. The computational savings and flexibility afforded by
adaptivity along with the flexibility of FE methods make this model well
suited to simulating turbidity currents in complex domains
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