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A design of an enduring Pu critical assembly has been produced. This is very important to DOE/NNSA missions. This assembly would result in advances/improvements in nuclear data validation, analytical methods validation, dosimetry, reactor kinetics, materials, and more.
The raw bulk metagenomic data were trimmed and de-novo assembled. The assemblies were screened for viral contigs (by virsorter2, Deepvirfinder, VIBRANT, checkV) and binned to generate MAGs that were further refined by Hi-C read links.
Over the years of commercial nuclear power plant operations in the United States (U.S.), many fuel assemblies have lost the capability to perform all of their desired functions. These assemblies have lost the capability to be handled, stored, or transported to meet regulations resulting in them being classified as damaged fuel. The causes of these failed assemblies are diverse and plant-specific. The majority of these failed assemblies are contained in a damaged fuel can that will be used in conjunction with a storage and/or transportation system. The storage and transportation systems have a limit on how many slots can be filled with damaged fuel cans. A damaged fuel can is generally a stainless steel container that confines damaged SNF and is closed on its end by screened openings. These screened openings allow gaseous and liquid media to escape but minimize the dispersal of gross particulate material. Out of an abundance of caution a few reactors have loaded high burnup fuel into damaged fuel cans. Damaged fuel is not licensed for storage or transport in the U.S., because the regulations for storage and transport do not specify exactly how to classify damaged fuel. Instead the regulations license/certify packages that specify approved contents. Damaged fuel must be included in the approved contents to be a viable option. In many cases damaged SNF is encapsulated in a damaged fuel can to ensure it can confine gross fuel particles, debris, and or damaged assemblies to a known volume within a loaded cask. This damaged fuel can may then be utilized in the same way as an assembly in a storage and transportation design system. Some storage cask systems utilize top and bottom plugs to confine debris in damaged fuel. The most recent domestic documentation on damaged SNF was performed by the U.S. Energy Information Administration (EIA) and used data from U.S. reactors concluding in June 30th 2013 to produce Form GC-859, “Nuclear Fuel Data Survey”. Based on this form there were 136,821 boiling water reactor (BWR) spent nuclear fuel (SNF) assemblies and 104,647 pressurized water reactor (PWR) SNF assemblies for a total of 241,468 SNF assemblies in the U.S. Out of these 241,468 SNF assemblies, 4,521 assemblies were classified as failed. Some assemblies were also disassembled and the fuel rods or pieces of fuel rods were combined together to make a consolidated assembly. A consolidated assembly may include damaged fuel, or it could have been consolidated as part of a demonstration project. The GC-859 data includes 2,550 consolidated assemblies containing between 0 and 264 whole fuel rods. These consolidated assemblies could be placed in single assembly canisters and stored in the spent fuel pool. For dry storage and transportation, a single assembly canister is generally placed in a damaged fuel can. In addition to the consolidated assemblies, 2,391 uncanistered fuel rod pieces exist, which were removed from 494 assemblies.
The Department of Energy invests tens of millions of dollars each year to develop the next generation of nuclear engineering modeling & simulation (M&S) tools. These tools are used to analyze advanced reactor designs and the safety of current nuclear operations. As computers become more powerful, we are able to enhance resolution in our calculations. This improved resolution is taking us to a point where the limitations of simulation capability are in the quality of data, including our ability to quantify the uncertainty and sensitivity of the data. In order to model systems of interest with increasing accuracy, the industry must improve key nuclear data measurements. Thus, M&S tools need evaluated and quality-assured experimental data for validation purposes. The International Criticality Safety Benchmark Evaluation Project (ICSBEP) compiles and evaluates experiment data in a handbook that can be used by criticality safety engineers and others to validate computer codes and cross-section libraries at nuclear facilities. Both critical and subcritical experiments are included in the handbook. Figure 1 organizes all the benchmark evaluations that have been performed by the isotope of interest, in this case Pb, and the average neutron energy the system. Compared to other isotopes of interest for nuclear applications, there are few benchmark evaluations for Pb systems. The lack of integral measurements to determine errors in Pb cross-section data has caused the latest nuclear cross-section libraries to over/underestimate k eff compared to experimental results. Therefore, this evaluation fills an important knowledge gap in benchmark evaluations.
The BEAVRS (Benchmark for Evaluation and Validation of Reactor Simulation) benchmark is solved by PRAGMA, the GPU-based continuous energy Monte Carlo code. The resulting solutions are comprised of the detailed simulation results of two cycles, each of which consists of the zero power physics test (ZPPT) and the core depletion calculations. The ZPPT consists of characteristic parameters, such as critical boron concentration (CBC), control rod bank worth, isothermal temperature coefficients, and assembly-wise detector signal, which are compared with measured data provided by the benchmark administration. The core depletion calculations were performed for both the hot full power and the load follow modes, and the comparison was made with the measured or deduced CBCs and assembly-wise detector signals. In the load follow calculations, the operating power history was approximately applied to simulate the real operation as closely as possible. PRAGMA performed the various calculations with a tremendous number of histories ranging up to hundreds of millions per cycle, exploiting GPUs' massively parallel performance. The load follow run time was shorter than 16 hours on a single rack of computing nodes mounded with 24 gaming GPUs with a remarkable agreement with the measurements for most comparisons. (authors)
Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.
The CMS High Granularity Calorimeter (HGCAL) is the Phase-2 endcap calorimeter upgrade for the High-Luminosity Large Hadron Collider, designed to provide precise spatial, energy, and timing measurements in a high-radiation, high-pileup environment. This work presents an overview of the HGCAL assembly process, detector architecture, and end-to-end data flow. The data flow goes from signal generation in silicon sensors and scintillator tiles through front-end electronics, optical transmission, and back-end data acquisition. The study highlights how the integrated detector, electronics, and readout systems enable efficient event reconstruction and support the physics objectives of the HL-LHC.
Cleanliness validation of printed circuit assemblies has become increasingly important as electronic assemblies become smaller, denser, and more challenging to clean, prompting an increase in reliance in custom solutions. With increasingly fast paced development cycles, long lead times and costs of quality custom surrogate test boards become prohibitive in obtaining cleanliness data that is a true representative of the final product. In this study, aerosol jet printing, an additive manufacturing technology for electronics, was used to manufacture surface insulation resistance (SIR) test structures that were evaluated on their ability to detect cleanliness defects and remain stable when clean, as well as their survivability to standard electronics wash processes. Additionally, in an effort to further increase the agility of true product testing, SIR test structures were printed directly onto ball-grid-arrays (BGAs) and tested the survivability of conformally printed leads for data acquisition. SIR test structures displayed good wash survivability on standard FR4 and BGAs, including wraparounds for on-component prints, and high sensitivity to cleanliness defects. The presented results demonstrate the feasibility of printed SIR structures as a quick-turn, highly customizable solution for wash validation with potential for increased fidelity cleanliness testing.
In 2021 May the Dark Energy Spectroscopic Instrument (DESI) collaboration began a 5 yr spectroscopic redshift survey to produce a detailed map of the evolving three-dimensional structure of the Universe between z = 0 and z ≈ 4. DESI’s principal scientific objectives are to place precise constraints on the equation of state of dark energy, the gravitationally driven growth of large-scale structure, and the sum of the neutrino masses, and to explore the observational signatures of primordial inflation. We present DESI DR1, which consists of all data acquired during the first 13 months of the DESI main survey, as well as a uniform reprocessing of the DESI Survey Validation data, which were previously made public in the DESI Early Data Release. The DR1 main survey includes high-confidence redshifts for 18.7M objects, of which 13.1M are spectroscopically classified as galaxies, 1.6M as quasars, and 4M as stars, making DR1 the largest sample of extragalactic redshifts ever assembled. We summarize the DR1 observations, the spectroscopic data-reduction pipeline and data products, large-scale structure catalogs, value-added catalogs, and describe how to access and interact with the data. In addition to fulfilling its core cosmological objectives with unprecedented precision, we expect DR1 to enable a wide range of transformational astrophysical studies and discoveries.
In this work, we demonstrate how machine learning (ML) techniques can be used as an auxiliary tool for nuclear data validation analysis. The output of the ML analysis can inform evaluators and validators on the quality, or lack thereof, of specific nuclear data and benchmark experiments with respect to simulating these experimental benchmark values. To this end, measured and simulated effective neutron multiplication factors, k eff , of 875 selected ICSBEP critical assemblies and the latter's sensitivities with respect to nuclear data as well as benchmarks' features (e.g., material nuclide, core geometry) are used as input for a random forest (RF) regression model. The RF is used to encode the complex inter-dependencies between thousands of nuclear data features (i.e., sensitivity profiles and aspects describing the measurements) and 875 simulated and experimental k eff values in order to understand what nuclear data features are most informative for predicting bias. The complexity of relationships and high-dimensional space is difficult-to-impossible to search fully using simply expert judgment. As a first proof-of-concept—step, it is demonstrated that this technique is able to correctly trace large discrepancies between simulated and experimental k eff back to fabricated shortcomings in nuclear data that were perturbed to simulated k eff values. In a second, real-case scenario, step, the RF algorithm is used to validate the ENDF/B-VIII.0 library in comparison to ENDF/B-VII.1 nuclear data. One case is showcased where the chosen ML algorithms highlighted nuclear data (the 19 F(n,inl) cross section from 0.4–0.9 MeV) that are shown to be problematic by comparing them to associated differential experimental data and nuclear data from other libraries. In addition to that, it is shown that the RF results point towards poor benchmark experiments and associated underestimated uncertainties (e.g., the PU-SOL-THERM-028 series). However, using the RF algorithm for validating nuclear data with respect to k eff is currently limited to pinpointing groups of questionable nuclear data due to the inherent correlations between features introduced by the nuclear data themselves and how k eff is simulated. Due to this, we recommend that the ML methods presented be used to augment—rather than replace—the expert knowledge of evaluators and validators.
Criticality safety analyses are conducted to show compliance with regulatory standards and to demonstrate safe operational conditions during the storage and transportation of spent nuclear fuel. Given the increased interest in the industry in low-enriched uranium plus (LEU+) and higher-burnup fuel, it is important to study the impact of such fuels’ use on criticality safety analyses and the resulting nuclear data–induced uncertainties. Here, in this work, nominal pressurized water reactor assemblies with LEU+ fuel enrichments up to 8 wt% 235 U and high burnups up to 80 GWd/tonne U were studied. The assemblies were placed in a generic burnup credit cask GBC-32. As a result of the different covariance libraries, using the ENDF/B-VII.1 nuclear data library consistently resulted in lower nuclear data uncertainties than did the use of the ENDF/B-VIII.0 data library. The highest contribution in the nuclear data–induced uncertainties resulted from the major actinides, and their contribution increased with increasing burnup and enrichment.
The COVID-19 pandemic highlights the need for computational tools to automate and accelerate drug design for novel protein targets. We leverage deep learning language models to generate and score drug candidates based on predicted protein binding affinity. We pre-trained a deep learning language model (BERT) on ∼9.6 billion molecules and achieved peak performance of 603 petaflops in mixed precision. Our work reduces pre-training time from days to hours, compared to previous efforts with this architecture, while also increasing the dataset size by nearly an order of magnitude. For scoring, we fine-tuned the language model using an assembled set of thousands of protein targets with binding affinity data and searched for inhibitors of specific protein targets, SARS-CoV-2 Mpro and PLpro. We utilized a genetic algorithm approach for finding optimal candidates using the generation and scoring capabilities of the language model. Our generalizable models accelerate the identification of inhibitors for emerging therapeutic targets.
Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.
The Advanced Experimental Fuel Counter (AEFC) is a nondestructive assay (NDA) instrument designed to determine the residual fissile mass in irradiated fuel assemblies for safeguards verification purposes. This is done by actively interrogating an assembly with a neutron source and measuring the total (Singles) and correlated (Doubles) neutron count rates resulting from induced fissions in the irradiated nuclear fuel and relating those rates to the residual fissile mass using calibration curves. Comprehensive NDA measurements of the irradiated fuel inventory at Israeli Research Reactor 1 (IRR-1) were taken with the AEFC to validate a set of previously developed calibration curves. During the campaign, measurements were acquired of 32 standard fuel assemblies and three control assemblies in just nine days. This is a significant majority of the research reactor's irradiated fuel inventory and the largest data set gathered by the AEFC to date. Many of the fuel assemblies measured during the campaign had much shorter cooling times than those assemblies previously measured with the instrument. Calibration curves developed from previous AEFC deployments were used to determine the residual 235 U mass in the measured standard fuel assemblies. The results of the campaign demonstrated that the AEFC can be used to estimate the 235 U mass remaining in a large number of irradiated fuel assemblies with 1%–5% uncertainty in a reasonable amount of time despite operating in a high dose environment.
This report summarizes characterization via scanning/transmission electron microscopy of the microstructures of the unirradiated and irradiated piezoelectric ultrasonic sensor/aluminum substrate assemblies using four commercially available inorganic coupling adhesives to bond two types of piezoelectric crystals to the substrates. The sample assemblies were irradiated in the PULSTAR reactor at NC State University and ultrasonic data was collected in-situ. ORNL LAMDA Laboratory capabilities were utilized to perform pre- and post-irradiation examination of the sensor assemblies. This document summarizes the PIE performed at the ORNL LAMDA laboratory. The results of the PIE described in this report are consistent with the ultrasonic data collected during irradiation – in particular, high temperature epoxy adhesive seemed to provide the best coupling as compared to the refractory ceramic adhesives. It was determined that the quality of the sensor-adhesive-substrates governed the ultrasonic performance of the sensors. It was also apparent that irradiation did not significantly affect bond quality, which is also supported by the ultrasonic data collected during irradiation. A more comprehensive DOE NSUF Final Report including details of materials selection, sample fabrication, initial ultrasonic testing, irradiation and in-situ ultrasonic testing, positron annihilation lifetime spectroscopy and doppler broadening spectroscopy performed at EPRI and NC State University will be published at the conclusion of the project.
The EUCLID (Experiments Underpinned by Computational Learning for Improvements in Nuclear Data) project created a library of sensitivities for nine different integral responses with respect to nuclear data. These integral responses were obtained from measurements at LLNL (Lawrence Livermore National Laboratory) pulsed spheres, critical and sub-critical assemblies. At the same time, covariances for ENDF/B-VIII.0 were processed at LANL (Los Alamos National Laboratory). The combination of these data allow us to study the impact of nuclear-data covariances on various integral responses, either by forward-propagating covariances via sensitivities, or by using nuclear data, integral responses, and sensitivities for adjustment. Here, we will present: the impact of 1 H, 9 Be, 12 C, 27 Al, 56 Fe, 235,238 U, and 239,240 Pu ENDF/B-VIII.0 covariances on simulated bounds of the following integral responses: LLNL pulsed-spheres neutron-leakage spectra, the effective neutron multiplication factor, reaction rates, and reactivity coefficients of ICSBEP critical assemblies. Also, adjustment results with the same nuclear-data covariances and responses will be discussed.
We present hipBone, an open-source performance-portable proxy application for the Nek5000 (and NekRS) computational fluid dynamics applications. HipBone is a fully GPU-accelerated C++ implementation of the original NekBone CPU proxy application with several novel algorithmic and implementation improvements which optimize its performance on modern fine-grain parallel GPU accelerators. Our optimizations include a conversion to store the degrees of freedom of the problem in assembled form in order to reduce the amount of data moved during the main iteration and a portable implementation of the main Poisson operator kernel. We demonstrate near-roofline performance of the operator kernel on three different modern GPU accelerators from two different vendors. We present a novel algorithm for splitting the application of the Poisson operator on GPUs which aggressively hides MPI communication required for both halo exchange and assembly. Our implementation of nearest-neighbor MPI communication then leverages several different routing algorithms and GPU-Direct RDMA capabilities, when available, which improves scalability of the benchmark. We demonstrate the performance of hipBone on three different clusters housed at Oak Ridge National Laboratory, namely, the Summit supercomputer and the Frontier early-access clusters, Spock and Crusher. Our tests demonstrate both portability across different clusters and very good scaling efficiency, especially on large problems.
Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.