A scalable parallel finite element framework for growing geometries. Application to metal additive manufacturing

This work introduces an innovative parallel, fully-distributed finite element framework for growing geometries and its application to metal additive manufacturing. It is well-known that virtual part design and qualification in additive manufacturing requires highly-accurate multiscale and multiphysics analyses. Only high performance computing tools are able to handle such complexity in time frames compatible with time-to-market. However, efficiency, without loss of accuracy, has rarely held the centre stage in the numerical community. Here, in contrast, the framework is designed to adequately exploit the resources of high-end distributed-memory machines. It is grounded on three building blocks: (1) Hierarchical adaptive mesh refinement with octree-based meshes; (2) a parallel strategy to model the growth of the geometry; (3) state-of-the-art parallel iterative linear solvers. Computational experiments consider the heat transfer analysis at the part scale of the printing process by powder-bed technologies. After verification against a 3D benchmark, a strong-scaling analysis assesses performance and identifies major sources of parallel overhead. A third numerical example examines the efficiency and robustness of (2) in a curved 3D shape. Unprecedented parallelism and scalability were achieved in this work. Hence, this framework contributes to take on higher complexity and/or accuracy, not only of part-scale simulations of metal or polymer additive manufacturing, but also in welding, sedimentation, atherosclerosis, or any other physical problem where the physical domain of interest grows in time

Algorithm engineering for optimal alignment of protein structure distance matrices

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model for computing optimal structural alignments based on dense inter-residue distance matrices. We therefore reformulate the problem as a special graph problem and give a tight integer linear programming model. We then present algorithm engineering techniques to handle the huge integer linear programs of real-life distance matrix alignment problems. Applying these techniques, we can compute provably optimal Dali alignments for the very first time

Embracing additive manufacture: implications for foot and ankle orthosis design

<p>Abstract</p> <p>Background</p> <p>The design of foot and ankle orthoses is currently limited by the methods used to fabricate the devices, particularly in terms of geometric freedom and potential to include innovative new features. Additive manufacturing (AM) technologies, where objects are constructed via a series of sub-millimetre layers of a substrate material, may present the opportunity to overcome these limitations and allow novel devices to be produced that are highly personalised for the individual, both in terms of fit and functionality.</p> <p>Two novel devices, a foot orthosis (FO) designed to include adjustable elements to relieve pressure at the metatarsal heads, and an ankle foot orthosis (AFO) designed to have adjustable stiffness levels in the sagittal plane, were developed and fabricated using AM. The devices were then tested on a healthy participant to determine if the intended biomechanical modes of action were achieved.</p> <p>Results</p> <p>The adjustable, pressure relieving FO was found to be able to significantly reduce pressure under the targeted metatarsal heads. The AFO was shown to have distinct effects on ankle kinematics which could be varied by adjusting the stiffness level of the device.</p> <p>Conclusions</p> <p>The results presented here demonstrate the potential design freedom made available by AM, and suggest that it may allow novel personalised orthotic devices to be produced which are beyond the current state of the art.</p

Build-up and decline of organic matter during PeECE III

Increasing atmospheric carbon dioxide (CO2) concentrations due to anthropogenic fossil fuel combustion are currently changing the ocean's chemistry. Increasing oceanic [CO2] and consequently decreasing seawater pH have the potential to significantly impact marine life. Here we describe and analyze the build-up and decline of a natural phytoplankton bloom initiated during the 2005 mesocosm Pelagic Ecosystem CO2 Enrichment study (PeECE III). The draw-down of inorganic nutrients in the upper surface layer of the mesocosms was reflected by a concomitant increase of organic matter until day t11, the peak of the bloom. From then on, biomass standing stocks steadily decreased as more and more particulate organic matter was lost into the deeper layer of the mesocosms. We show that organic carbon export to the deeper layer was significantly enhanced at elevated CO2. This phenomenon might have impacted organic matter remineralization leading to decreased oxygen concentrations in the deeper layer of the high CO2 mesocosms as indicated by deep water ammonium concentrations. This would have important implications for our understanding of pelagic ecosystem functioning and future carbon cycling

Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actnidiae provides insight into the origins of an emergent plant disease

The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries – even millennia – ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease

Evaluating additive manufacturing for the production of custom head supports: A comparison against a commercial head support under static loading conditions

The provision of wheelchair seating accessories, such as head supports, is often limited to the use of commercial products. Additive manufacturing has the potential to produce custom seating components, but there are very few examples of published work. This article reports a method of utilising 3D scanning, computer-aided design and additive manufacturing for the fabrication of a custom head support for a wheelchair. Three custom head supports, of the same shape, were manufactured in nylon using a continuous filament fabrication machine. The custom head supports were tested against an equivalent and widely used commercial head support using ISO 16840-3:2014. The head supports were statically loaded in two configurations, one modelling a posterior force on the inner rear surface and the other modelling a lateral force on the side. The posterior force resulted in failure of the supporting bracketry before the custom head support. A similar magnitude of forces was applied laterally for the custom and commercial head support. When the load was removed, the custom recovered to its original shape while the commercial sustained plastic deformation. The addition of a joint in the head support increased the maximum displacement, 128.6 mm compared to 71.7 mm, and the use of carbon fibre resulted in the head support sustaining a higher force at larger displacements, increase in 30 N. Based on the deformation and recovery characteristics, the results indicate that additive manufacturing could be an appropriate method to produce lighter weight, highly customised, cost-effective and safe head supports for wheelchair users

The response of temperate aquatic ecosystems to global warming: novel insights from a multidisciplinary project

This article serves as an introduction to this special issue of Marine Biology, but also as a review of the key findings of the AQUASHIFT research program which is the source of the articles published in this issue. AQUASHIFT is an interdisciplinary research program targeted to analyze the response of temperate zone aquatic ecosystems (both marine and freshwater) to global warming. The main conclusions of AQUASHIFT relate to (a) shifts in geographic distribution, (b) shifts in seasonality, (c) temporal mismatch in food chains, (d) biomass responses to warming, (e) responses of body size, (f) harmful bloom intensity, (f), changes of biodiversity, and (g) the dependence of shifts to temperature changes during critical seasonal windows