A hierarchical reduced-order model applied to nuclear reactors

Modelling the neutron transport of a nuclear reactor is a very computationally demanding task that requires a large number of degrees of freedom to accurately capture all of the physics. For a complete reactor picture, other physics must be incorporated, through coupling, further exacerbating the computational demand. Computational modelling has many benefits: optimisation, real-time analysis, and safety analysis are some of the more important ones. However, nuclear modelling has yet to capitalise on these, and existing approaches are too computationally demanding. Machine Learning has seen incredible growth over the last decade, but it has yet to be utilised within the nuclear modelling community to the same extent. The frameworks available represent incredibly efficient and optimised code, having been written to run on GPUs and AI computers. Presented here is a physics-driven neural network that solves neutron transport, first for the diffusion approximation and then extended to the whole transport problem. One method that can potentially reduce the computational complexity is Reduced-Order Modelling (ROM), which is a way to define a low-dimensional space in which a high-dimensional system can be approximated. These established methods can be used with machine learning methods, potentially reducing computational costs further than either method individually. A method to utilise autoencoders with a projection-based framework is also presented here. The structure of a reactor can be broken down, forming a hierarchy which starts with the reactor core, which is populated by fuel assemblies, which are then populated by fuel rods. This hierarchy means that materials are repeated within a solution, and many existing methods do not capitalise on this and instead resolve the entire global domain. This research presents two ways to utilise this structure with ROM. The first involves combining it with domain decomposition, producing ROMs for the sub-structures. The second presents a hierarchical interpolating method, reducing the number of sub-domains within the solution that need to be resolved.Open Acces

An autoencoder-based reduced-order model for eigenvalue problems with application to neutron diffusion

Using an autoencoder for dimensionality reduction, this paper presents a novel projection-based reduced-order model for eigenvalue problems. Reduced-order modelling relies on finding suitable basis functions which define a low-dimensional space in which a high-dimensional system is approximated. Proper orthogonal decomposition (POD) and singular value decomposition (SVD) are often used for this purpose and yield an optimal linear subspace. Autoencoders provide a nonlinear alternative to POD/SVD, that may capture, more efficiently, features or patterns in the high-fidelity model results. Reduced-order models based on an autoencoder and a novel hybrid SVD-autoencoder are developed. These methods are compared with the standard POD-Galerkin approach and are applied to two test cases taken from the field of nuclear reactor physics.Comment: 35 pages, 33 figure

The importance of extracellular vesicle purification for downstream analysis:A comparison of differential centrifugation and size exclusion chromatography for helminth pathogens

BackgroundRobust protocols for the isolation of extracellular vesicles (EVs) from the rest of their excretory-secretory products are necessary for downstream studies and application development. The most widely used purification method of EVs for helminth pathogens is currently differential centrifugation (DC). In contrast, size exclusion chromatography (SEC) has been included in the purification pipeline for EVs from other pathogens, highlighting there is not an agreed research community ‘gold standard’ for EV isolation. In this case study, Fasciola hepatica from natural populations were cultured in order to collect EVs from culture media and evaluate a SEC or DC approach to pathogen helminth EV purification.Methodology/Principal findingsTransmission electron and atomic force microscopy demonstrated that EVs prepared by SEC were both smaller in size and less diverse than EV resolved by DC. Protein quantification and Western blotting further demonstrated that SEC purification realised a higher EV purity to free excretory-secretory protein (ESP) yield ratio compared to DC approaches as evident by the reduction of soluble free cathepsin L proteases in SEC EV preparations. Proteomic analysis further highlighted DC contamination from ESP as shown by an increased diversity of protein identifications and unique peptide hits in DC EVs as compared to SEC EVs. In addition, SEC purified EVs contained less tegumental based proteins than DC purified EVs.Conclusions/SignificanceThe data suggests that DC and SEC purification methods do not isolate equivalent EV population profiles and caution should be taken in the choice of EV purification utilised, with certain protocols for DC preparations including more free ES proteins and tegumental artefacts. We propose that SEC methods should be used for EV purification prior to downstream studies.</div

Major Shifts in Pelagic Micronekton and Macrozooplankton Community Structure in an Upwelling Ecosystem Related to an Unprecedented Marine Heatwave

The community structure of pelagic zooplankton and micronekton may be a sensitive indicator of changes in environmental conditions within the California Current ecosystem. Substantial oceanographic changes in 2015 and 2016, due to the anomalously warm ocean conditions associated with a large-scale marine heatwave perturbation, resulted in onshore and northward advection of warmer and more stratified surface waters resulting in reduced upwelling. Here we quantify changes in the macrozooplankton and micronekton community composition and structure based on five highly contrasting ocean conditions. Data from fine-mesh pelagic trawl surveys conducted off Oregon and Washington during early summer of 2011 and 2013–2016 were examined for interannual changes in spatial distribution and abundance of fish and invertebrate taxa. Overall species diversity was highest in 2015 and lowest in 2011, but 2016 was similar to the other years, although the evenness was somewhat lower. The community of taxa in both 2015 and 2016 was significantly different from the previously sampled years. Crustacean plankton densities (especially Euphausiidae) were extremely low in both of these years, and the invertebrate composition became dominated mostly by gelatinous zooplankton. Fishes and cephalopods showed mixed trends overall, but some species such as age-0 Pacific hake were found in relatively high abundances mainly along the shelf break in 2015 and 2016. These results suggest dramatically different pelagic communities were present during the recent warm years with a greater contribution from offshore taxa, especially gelatinous taxa, during 2015 and 2016. The substantial reorganization of the pelagic community has the potential to lead to major alterations in trophic functioning in this normally productive ecosystem

Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species

Aim: To examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia. Location: Neotropics. Methods: Plastid DNA (trnH-psbA; 410 individuals from 54 populations) and nuclear ribosomal internal transcribed spacer (ITS; 85 individuals from 27 populations) sequences were sampled from Mexico to Bolivia, representing the full extent of the taxon's distribution. Divergence of plastid lineages was dated using a Bayesian coalescent approach. Genetic diversity was assessed with indices of haplotype and nucleotide diversities, and genetic structure was examined using spatial analysis of molecular variance (SAMOVA) and haplotype networks. Population expansion within Amazonia was tested using neutrality and mismatch distribution tests. Results: trnH-psbA sequences yielded 19 haplotypes restricted to either Mesoamerica or Amazonia; six haplotypes were found among ITS sequences. Diversification of the plastid DNA haplotypes began c. 14.6 Ma. Haplotype diversity for trnH-psbA was higher in Amazonia. Seven genetically differentiated SAMOVA groups were described for trnH-psbA, of which two were also supported by the presence of unique ITS sequences. Population expansion was suggested for both markers for the SAMOVA group that contains most Amazonian populations. Main conclusions: Our results show marked population genetic structure in F. insipida between Mesoamerica and Amazonia, implying that the Andes and seasonally dry areas of northern South America are eco-climatic barriers to its migration. This pattern is shared with other widespread pioneer species affiliated to wet habitats, indicating that the ecological characteristics of species may impact upon large-scale phylogeography. Ficus insipida also shows genetic structure in north-western Amazonia potentially related to pre-Pleistocene historical events. In contrast, evident population expansion elsewhere in Amazonia, in particular the presence of genetically uniform populations across the south-west, indicate recent colonization. Our findings are consistent with palaeoecological data that suggest recent post-glacial expansion of Amazonian forests in the south

Swimming Against the Flow: Environmental DNA Can Detect Bull Sharks (\u3ci\u3eCarcharhinus leucas\u3c/i\u3e) Across a Dynamic Deltaic Interface

© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd Human activities in coastal areas are accelerating ecosystem changes at an unprecedented pace, resulting in habitat loss, hydrological modifications, and predatory species declines. Understanding how these changes potentially cascade across marine and freshwater ecosystems requires knowing how mobile euryhaline species link these seemingly disparate systems. As upper trophic level predators, bull sharks (Carcharhinus leucas) play a crucial role in marine and freshwater ecosystem health. Telemetry studies in Mobile Bay, Alabama, suggest that bull sharks extensively use the northern portions of the bay, an estuarine–freshwater interface known as the Mobile-Tensaw Delta. To assess whether bull sharks use freshwater habitats in this region, environmental DNA surveys were conducted during the dry summer and wet winter seasons in 2018. In each season, 5 × 1 L water samples were collected at each of 21 sites: five sites in Mobile Bay, six sites in the Mobile-Tensaw Delta, and ten sites throughout the Mobile-Tombigbee and Tensaw-Alabama Rivers. Water samples were vacuum-filtered, DNA extractions were performed on the particulate, and DNA extracts were analyzed with Droplet Digital™ Polymerase Chain Reaction using species-specific primers and an internal probe to amplify a 237-base pair fragment of the mitochondrial NADH dehydrogenase subunit 2 gene in bull sharks. One water sample collected during the summer in the Alabama River met the criteria for a positive detection, thereby confirming the presence of bull shark DNA. While preliminary, this finding suggests that bull sharks use less-urbanized, riverine habitats up to 120 km upriver during Alabama\u27s dry summer season

Van Hove Exciton-Cageons and High-Tc_c Superconductivity: VIIID Solitons and Nonlinear Dynamics

The low-temperature orthorhombic (LTO) phase transition in La$_{2-x}$Sr$_x$CuO$_4$ can be interpreted as a dynamic Jahn-Teller effect, in which the degenerate electronic states are associated with the large densities of states at the two van Hove singularities. The equations describing this phase are strongly nonlinear. This paper illustrates some consequences of the nonlinearity, by presenting a rich variety of exact nonlinear wave solutions for the model. Of particular interest are soliton lattice solutions: arrays of domain walls separating regions of local low-temperature tetragonal (LTT) symmetry. These arrays have a {\it macroscopic} average symmetry higher than LTT. These lattices can display either orthorhombic (`orthons') or tetragonal (`tetrons') symmetry, and can serve as models for a microscopic description of the dynamic JT LTO and high-temperature tetragonal phases, respectively.Comment: 17 pages plain TeX, 14 figures available upon reques

Mass-flowering crops have a greater impact than semi-natural habitat on crop pollinators and pollen deposition

Context: Maximising insect pollination of mass-flowering crops is a widely-discussed approach to sustainable agriculture. Management actions can target landscape-scale semi-natural habitat, cropping patterns or field-scale features, but little is known about their relative effectiveness. Objective: To test how landscape composition (area of mass-flowering crops and semi-natural habitat) and field-scale habitat (margins and hedges) affect pollinator species richness, abundance, and pollen deposition within crop fields. Methods: We surveyed all flower visitors (Diptera, Coleoptera and Hymenoptera) in oilseed rape fields and related them to landscape composition and field features. Flower visitors were classified as bees, non-bee pollinators and brassica specialists. Total pollen deposition by individual taxa was estimated using single visit pollen deposition on stigmas combined with insect abundance. Results: The area of mass-flowering crop had a negative effect on the species richness and abundance of bees in fields, but not other flower visitors. The area of semi-natural habitat in the surrounding landscape had a positive effect on bees, but was not as important as the area of mass-flowering crop. Taxonomic richness and abundance varied significantly between years for non-bee pollinators. Greater cover of mass-flowering crops surrounding fields had a negative effect on pollen deposition, but only when non-bee pollinator numbers were reduced. Conclusions: Management choices that result in landscape homogenisation, such as large areas of mass-flowering crops, may reduce pollination services by reducing the numbers of bees visiting fields. Non-bee insect pollinators may buffer these landscape effects on pollen deposition, and management to support their populations should be considered

Bias correction of high-resolution regional climate model precipitation output gives the best estimates of precipitation in Himalayan catchments

The need to provide accurate estimates of precipitation over catchments in the Hindu Kush, Karakoram, and Himalaya mountain ranges for hydrological and water resource systems assessments is widely recognised, as is identifying precipitation extremes for assessing hydro‐meteorological hazards. Here, we investigate the ability of bias‐corrected Weather Research and Forecasting model output at 5 km grid spacing to reproduce the spatiotemporal variability of precipitation for the Beas and Sutlej river basins in the Himalaya, measured by 44 stations spread over the period 1980 to 2012. For the Sutlej basin, we find that the raw (uncorrected) model output generally underestimated annual, monthly, and (particularly low‐intensity) daily precipitation amounts. For the Beas basin, the model performance was better, although biases still existed. It is speculated that the cause of the dry bias over the Sutlej basin is a failure of the model to represent an early‐morning maximum in precipitation during the monsoon period, which is related to excessive precipitation falling upwind. However, applying a non‐linear bias‐correction method to the model output resulted in much better results, which were superior to precipitation estimates from reanalysis and two gridded datasets. These findings highlight the difficulty in using current gridded datasets as input for hydrological modelling in Himalayan catchments, suggesting that bias‐corrected high‐resolution regional climate model output is in fact necessary. Moreover, precipitation extremes over the Beas and Sutlej basins were considerably under‐represented in the gridded datasets, suggesting that bias‐corrected regional climate model output is also necessary for hydro‐meteorological risk assessments in Himalayan catchments