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At least 1,567 records · Page 87

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DOE OSTI2023

Variable energy X-ray fluorescence source

Here we detail the design of a variable energy, x-ray fluorescence source using a low activity (1.8×10 6 dpm) 99 Tc β source that irradiates thin foils. By rotating the source among foils of Ti, Zn, Nb, Ag, and Au, the device produces x rays between 4 and 70 keV at a rate near 1 Hz. When the source is placed in a storage position, the external radiation is non-detectable. The design of the shielding and rotation mechanism permits use in vacuum and at liquid nitrogen temperature. The design is intended for the study of the low energy response to radiation impinging upon Ge detector surfaces. The source will be useful for understanding the detector response in large-scale Ge arrays such as MAJORANA and LEGEND.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Detection efficiency measurement and operational tests of the X-Arapuca for the first module of DUNE far detector

The Deep Underground Neutrino Experiment (DUNE) is a dual-site experiment for long-baseline neutrino oscillation studies, able to resolve the neutrino mass hierarchy and measure δ$_{CP}$. DUNE will also have sensitivity to supernova neutrinos and to processes beyond the Standard Model, such as nucleon decay searches. The Far Detector (FD) will consist of four liquid argon TPC (17.5 kt total mass) with systems for the detection of charge and scintillation light produced by an ionization event. The charge detection system permits both calorimetry and position determination. In addition, the photon-detection system (PDS) enhances the detector capabilities for all DUNE physics drivers. The PDS of the first FD module consists of light collector modules placed in the inactive space between the innermost wire planes of the TPC anode. The light collectors, the so-called X-ARAPUCAS, are functionally a light trap that captures wavelength-shifted photons inside boxes with highly reflective internal surfaces where they are guided to Silicon Photo-multipliers (SiPM) by wavelength-shifting (WLS) bars. Functionality and operational tests of the X-ARAPUCAS to be installed in ProtoDUNE-SP phase II (FD DUNE prototype at the scale 1:20), as well as the measurement of their absolute detection efficiency is reported in this publication.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Radiation tolerance studies of the HV-mux GaNFETs for the HL-LHC ATLAS ITk Strip detector

For the High-Luminosity upgrade of the LHC, the current ATLAS inner detector will be replaced with a new silicon charged-particle tracker, the ITk, which consists of the ITk Pixel and the ITk Strip subdetector. The high voltage multiplexing (HV-Mux) GaNFETs are radiation-tolerant transistors that permit switching off high voltage to malfunctioning sensors on the ITk Strip modules. To ensure the reliability of the GaNFETs in the high radiation environment expected at the HL-LHC, a sample of the production batch was exposed to gamma radiation. Finally, the GaNFETs were characterized pre-irradiation and post-irradiation, and monitored during irradiation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Rapid curing dynamics of PEG-thiol-ene resins allow facile 3D bioprinting and in-air cell-laden microgel fabrication

Thiol-norbornene photoclick hydrogels are highly efficient in tissue engineering applications due to their fast gelation, cytocompatibility, and tunability. In this work, we utilized the advantageous features of polyethylene glycol (PEG)-thiol-ene resins to enable fabrication of complex and heterogeneous tissue scaffolds using 3D bioprinting and in-air drop encapsulation techniques. We demonstrated that photoclickable PEG-thiol-ene resins could be tuned by varying the ratio of PEG-dithiol to PEG norbornene to generate a wide range of mechanical stiffness (0.5–12 kPa) and swelling ratios. Importantly, all formulations maintained a constant, rapid gelation time (<0.5 s). We used this resin in biological projection microstereolithography (BioPµSL) to print complex structures with geometric fidelity and demonstrated biocompatibility by printing cell-laden microgrids. Moreover, the rapid gelling kinetics of this resin permitted high-throughput fabrication of tunable, cell-laden microgels in air using a biological in-air drop encapsulation apparatus (BioIDEA). We demonstrated that these microgels could support cell viability and be assembled into a gradient structure. This PEG-thiol-ene resin, along with BioPµSL and BioIDEA technology, will allow rapid fabrication of complex and heterogeneous tissues that mimic native tissues with cellular and mechanical gradients. The engineered tissue scaffolds with a controlled microscale porosity could be utilized in applications including gradient tissue engineering, biosensing, and in vitro tissue models.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Cyclone Fani: the tug-of-war between regional warming and anthropogenic aerosol effects

Before Cyclone Amphan took place in 2020, Cyclone Fani (May 2019) is the strongest pre-monsoon cyclone in the Bay of Bengal (BOB) since 1991, killing 90 people in eastern India and Bangladesh while causing US$1.81 billion of damages. Fani developed during a period of high concentration of anthropogenic aerosols in the BOB with abnormally high sea surface temperature (SST), thereby presenting an opportunity to understand the compound effects of atmospheric aerosols and regional climate warming on a tropical cyclone. A quantitative attribution analysis was conducted using the Weather Research and Forecasting model with chemistry (WRF-Chem) run at the convection-permitting (4 km) grid spacing, accompanied by an ensemble of coarser-resolution simulations to quantify the uncertainty. The removal of post-1990 trends in the tropospheric variables and SST from WRF-Chem's initial conditions (IC) and boundary conditions (BC, including the lateral and lower boundary conditions) resulted in a reduction of cyclone precipitation by about 51% during the 5 d of April 28-May 2. The removal of tropospheric warming shows approximately twice as strong an effect on Fani (39% reduction in precipitation) as that of SST warming (22% reduction). When aerosol's direct and indirect effects were removed from the simulations, i.e., no aerosol influence on radiation and cloud microphysics, Fani initially strengthened but later weakened, as measured by geopotential height and precipitation amounts. These results suggest that aerosol and its interaction with the atmosphere acted to mitigate the strengthening effect of anthropogenic warming on Fani, but was not strong enough to entirely counteract it. Although the ensemble of coarser simulations appears to overestimate Cyclone Fani in terms of precipitation, the direction of the effects is in agreement with that obtained from the 4 km simulations. Given the increasing anthropogenic aerosols in the BOB, future attribution studies using more sophisticated dynamical aerosol models on BOB tropical cyclones are urged.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

River systems under peaked stress

The change in the global energy production mix towards variable renewable energy sources requires efficient utilization of regulated rivers to optimise hydropower operations meet the needs of a changing energy market. However, the flexible operation of hydropower plants causes non-natural, sub-daily fluctuating flows in the receiving water bodies, often referred to as ‘hydropeaking’. Drastic changes in sub-daily flow regimes undermine attempts to improve river system health. Environmental decision makers, including permitting authorities and river basin managers facing the intense and increasing pressure on river environments, should consider ecosystem services and biodiversity issues more thoroughly. The need for research innovations in hydropeaking operation design to fulfil both the water and energy security responsibilities of hydropower is highlighted. Our paper outlines optimized hydropeaking design as a future research direction to help researchers, managers, and decision-makers prioritize actions that could enable better integration of river science and energy system planning. The goal of this is to find a balanced hydropower operation strategy.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

A statistical mechanism for operator growth

It was recently conjectured that in generic quantum many-body systems, the spectral density of local operators has the slowest high-frequency decay as permitted by locality. We show that the infinite-temperature version of this ‘universal operator growth hypothesis’ holds for the quantum Ising spin model in d ≥ 2 dimensions, and for the chaotic Ising chain (with longitudinal and transverse fields) in one dimension. Moreover, the disordered chaotic Ising chain that exhibits many-body localization can have the same high-frequency spectral density asymptotics as thermalizing models. Our argument is statistical in nature, and is based on the observation that the moments of the spectral density can be written as a sign-problem-free sum over paths of Pauli string operators.

Physics↗

DOE OSTI2025

On infinite tensor networks, complementary recovery and type II factors

We initiate a study of local operator algebras at the boundary of infinite tensor networks, using the mathematical theory of inductive limits. In particular, we consider tensor networks in which each layer acts as a quantum code with complementary recovery, a property that features prominently in the bulk-to-boundary maps intrinsic to holographic quantum error-correcting codes. In this case, we decompose the limiting Hilbert space and the algebras of observables in a way that keeps track of the entanglement in the network. As a specific example, we describe this inductive limit for the holographic Harlow-Pastawski-Preskill-Yoshida code model and relate its algebraic and error-correction features. We find that the local algebras in this model are given by the hyperfinite type II$_\infty$ factor. Next, we discuss other networks that build upon this framework and comment on a connection between type II factors and stabilizer circuits. We conclude with a discussion of multiscale entanglement renormalization ansatz networks in which complementary recovery is broken. We argue that this breaking possibly permits a limiting type III von Neumann algebra, making them more suitable ansätze for approximating subregions of quantum field theories.

holographic dualities↗

DOE OSTI2024

Machine learning materials properties with accurate predictions, uncertainty estimates, domain guidance, and persistent online accessibility

One compelling vision of the future of materials discovery and design involves the use of machine learning (ML) models to predict materials properties and then rapidly find materials tailored for specific applications. However, realizing this vision requires both providing detailed uncertainty quantification (model prediction errors and domain of applicability) and making models readily usable. At present, it is common practice in the community to assess ML model performance only in terms of prediction accuracy (e.g. mean absolute error), while neglecting detailed uncertainty quantification and robust model accessibility and usability. Here, we demonstrate a practical method for realizing both uncertainty and accessibility features with a large set of models. We develop random forest ML models for 33 materials properties spanning an array of data sources (computational and experimental) and property types (electrical, mechanical, thermodynamic, etc). All models have calibrated ensemble error bars to quantify prediction uncertainty and domain of applicability guidance enabled by kernel-density-estimate-based feature distance measures. All data and models are publicly hosted on the Garden-AI infrastructure, which provides an easy-to-use, persistent interface for model dissemination that permits models to be invoked with only a few lines of Python code. We demonstrate the power of this approach by using our models to conduct a fully ML-based materials discovery exercise to search for new stable, highly active perovskite oxide catalyst materials.

domain of applicability↗

DOE OSTI2022

Deep structural clustering for single-cell RNA-seq data jointly through autoencoder and graph neural network

Abstract Single-cell RNA sequencing (scRNA-seq) permits researchers to study the complex mechanisms of cell heterogeneity and diversity. Unsupervised clustering is of central importance for the analysis of the scRNA-seq data, as it can be used to identify putative cell types. However, due to noise impacts, high dimensionality and pervasive dropout events, clustering analysis of scRNA-seq data remains a computational challenge. Here, we propose a new deep structural clustering method for scRNA-seq data, named scDSC, which integrate the structural information into deep clustering of single cells. The proposed scDSC consists of a Zero-Inflated Negative Binomial (ZINB) model-based autoencoder, a graph neural network (GNN) module and a mutual-supervised module. To learn the data representation from the sparse and zero-inflated scRNA-seq data, we add a ZINB model to the basic autoencoder. The GNN module is introduced to capture the structural information among cells. By joining the ZINB-based autoencoder with the GNN module, the model transfers the data representation learned by autoencoder to the corresponding GNN layer. Furthermore, we adopt a mutual supervised strategy to unify these two different deep neural architectures and to guide the clustering task. Extensive experimental results on six real scRNA-seq datasets demonstrate that scDSC outperforms state-of-the-art methods in terms of clustering accuracy and scalability. Our method scDSC is implemented in Python using the Pytorch machine-learning library, and it is freely available at https://github.com/DHUDBlab/scDSC.

Gan, Yanglan↗

DOE OSTI2026

wavess 1.2: presenting an HLA-aware within-host virus sequence simulation framework

Motivation Understanding how virus sequences are shaped by selection can inform vaccine design and transmission inference. Modeling within-host evolution to interrogate these questions requires a detailed mechanistic framework that accurately captures sequence diversification. The CD8 + cytotoxic T-lymphocyte (CTL) response plays an important role in immune-mediated selection and can leave strong signatures in virus sequences; however, existing sequence-based within-host virus modeling frameworks do not explicitly include a human leukocyte antigen (HLA)-aware CTL response. Results We extended our previously published within-host sequence evolution simulator, wavess, to include an explicit CTL response, and share a method for identifying HLA-specific CTL epitopes given a founder virus sequence. We also updated the model to permit a variable recombination rate, which allows for modeling non-adjacent genes, segmented genomes, and recombination hotspots. These extensions to wavess allow for more accurate simulation of viruses and virus genes, particularly in regions of the genome where the immune response is dominated by CTLs (rather than antibodies). It also provides the foundation for investigations of how these newly-added biological mechanisms influence within-host evolution. Availability and implementation The core of wavess is written in Python 3, with helper functions written in R. It is available at https://github.com/MolEvolEpid/wavess.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Rapid Shifts in the Temperature Dependence of Locomotor Performance in an Invasive Frog, Xenopus laevis , Implications for Conservation

Abstract Temperature is a critical abiotic factor impacting all aspects of the biology of organisms, especially in ectotherms. As such, it is an important determinant of the potential invasive ability of organisms and may limit population expansion unless organisms can physiologically respond to changes in temperature either through plasticity or by adapting to their novel environment. Here, we studied the African clawed frog, Xenopus laevis, which has become invasive on a global scale. We compared adults from an invasive population of western France with individuals from two populations in the native range in South Africa. We measured the thermal dependence of locomotor performance in adults given its relevance to dispersal, predator escape, and prey capture. Our results show significant differences in the limits of the 80% performance breadth interval for endurance with the French population showing a left shift in its limits congruent with the colder climate experienced in France. The French invasive population was introduced only about 40 years ago suggesting a rapid shift in the thermal physiology. Given that all individuals were acclimated under laboratory conditions at 23°C for 2 months this suggests that the invasive frogs have adapted to their new environment. These data may allow the refinement of physiologically informed species distribution models permitting better estimates of future ranges at risk of invasion.

Araspin, Laurie↗

DOE OSTI2020

Trends and drivers of marine fish landings in Portugal since its entrance in the European Union

Abstract Marine landings in Portugal have decreased at a higher rate than fishing effort in the last 20 years. Identifying the variables driving the quantity and composition of landings is pivotal to understand the dynamics of the fisheries sector, which entails complex social and environmental aspects. In this study, we investigate the main drivers of marine fish landings in continental Portugal between 1989 and 2014. To identify common trends in time series, and quantify the importance of environmental factors, we applied a dynamic factor analysis considering four regions and three types of gear (trawling, purse-seine, and a multi-gear fishery). Our results show the importance of fishing effort as the most relevant factor driving marine landings in Portugal, both at the long and short terms. In addition, the effect of environmental factors such as the winter river discharge and the spring East Atlantic Teleconnection index should not be neglected, probably through mechanisms affecting coastal productivity. We provide a comprehensive amount of information that permits to improve our understanding of the trends of the most important commercial species in Portugal during the period of study.

Bueno-Pardo, Juan↗

DOE OSTI2022

Nonlinear dimension reduction for surrogate modeling using gradient information

We introduce a method for the nonlinear dimension reduction of a high-dimensional function $u:{\mathbb{R}}^d\rightarrow{\mathbb{R}}$, $d\gg 1$. Our objective is to identify a nonlinear feature map $g:{\mathbb{R}}^d\rightarrow{\mathbb{R}}^m$, with a prescribed intermediate dimension $m\ll d$, so that $u$ can be well approximated by $f\circ g$ for some profile function $f:{\mathbb{R}}^m\rightarrow{\mathbb{R}}$. We propose to build the feature map by aligning the Jacobian $\nabla g$ with the gradient $\nabla u$, and we theoretically analyze the properties of the resulting $g$. Once $g$ is built, we construct $f$ by solving a gradient-enhanced least squares problem. Our practical algorithm uses a sample $\{{\textbf{x}}^{(i)},u({\textbf{x}}^{(i)}),\nabla u({\textbf{x}}^{(i)})\}_{i=1}^N$ and builds both $g$ and $f$ on adaptive downward-closed polynomial spaces, using cross validation to avoid overfitting. We numerically evaluate the performance of our algorithm across different benchmarks, and explore the impact of the intermediate dimension $m$. We show that building a nonlinear feature map $g$ can permit more accurate approximation of $u$ than a linear $g$, for the same input data set.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Language Barriers in Organismal Biology: What Can Journals Do Better?

Synopsis In the field of organismal biology, as in much of academia, there is a strong incentive to publish in internationally recognized, highly regarded, English-language journals to promote career advancement. This expectation has created a linguistic hegemony in scientific publishing, whereby scholars for whom English is an additional language face additional barriers to achieving the same scientific recognition as scholars who speak English as a first language. Here, we surveyed the author guidelines of 230 journals in organismal biology with impact factors of 1.5 or greater for linguistically inclusive and equitable practices and policies. We looked for efforts that reflect first steps toward reducing barriers to publication for authors globally, including the presence of statements that encouraged submissions from authors of diverse nationalities and backgrounds, policies regarding manuscript rejection based on perceived inadequacies of the English language, the existence of bias-conscious reviewer practices, whether translation and editing resources or services are available, allowance for non-English abstracts, summaries, or translations, and whether journals offer license options that would permit authors (or other scholars) to translate their work and publish it elsewhere. We also directly contacted a subset of journals to verify whether the information on their author guidelines page accurately reflects their policies and the accommodations they would make. We reveal that journals and publishers have made little progress toward beginning to recognize or reduce language barriers. Counter to our predictions, journals associated with scientific societies did not appear to have more inclusive policies compared to non-society journals. Many policies lacked transparency and clarity, which can generate uncertainty, result in avoidable manuscript rejections, and necessitate additional time and effort from both prospective authors and journal editors. We highlight examples of equitable policies and summarize actions that journals can take to begin to alleviate barriers to scientific publishing.

Nolde-Lopez, B.↗

DOE OSTI2022

An agent-based blackboard system for multi-objective optimization

In the field of multi-objective optimization, there are a multitude of algorithms from which to choose. Each algorithm has strengths and weaknesses associated with the mechanics for finding the Pareto front. Recently, researchers have begun to examine how multi-agent environments can be used to help solve multi-objective optimization problems. In this work, we propose a multi-objective optimization algorithm based on a multi-agent blackboard system (MABS). The MABS framework allows for multiple agents to read and write pertinent optimization problem data to a central blackboard agent. Agents can stochastically search the design space, use previously discovered solutions to explore local optima, or update and prune the Pareto front. A centralized blackboard framework allows the optimization problem to be solved in a cohesive manner and permits stopping, restarting, or updating the optimization problem. The MABS framework is tested against three alternative optimization algorithms across a suite of engineering design problems and typically outperforms the other algorithms in discovering the Pareto front. A parallelizability study is performed where we find that the MABS is able to evaluate a set number of designs, which require an evaluation time ranging from 0 to 300 seconds, quicker than a traditional optimization algorithm: this fact becomes more apparent the longer it takes to evaluate a design. To provide context for the benefits provided by MABS, a real-world nuclear engineering design problem is examined. MABS is used to examine the placement of experiments in a nuclear reactor, where we are able to evaluate hundreds of configurations for experimental placement while maintaining a strict set of safety constraints.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Relaxing Direct Ptychography Sampling Requirements via Parallax Imaging Insights

Direct ptychography enables the retrieval of information encoded in the phase of an electron wave passing through a thin sample by deconvolving the interference effects of a converged probe with known aberrations. Under the weak phase object approximation, this permits the optimal transfer of information using noniterative techniques. However, the achievable resolution of the technique is traditionally limited by the probe step size—setting stringent Nyquist sampling requirements. At the same time, parallax imaging has emerged as a dose-efficient phase technique which relaxes sampling requirements and enables scan-upsampling. Here, we formulate parallax imaging as a quadratic approximation to part of the direct ptychography kernel and use this insight to enable upsampling in direct ptychography. We validate our analytical results numerically using simulated and experimental reconstructions.

direct ptychography, parallax imaging, scan Nyquis↗

DOE OSTI2023

Impact of Blast Overpressure on the Pharmacokinetics of Various Antibiotics in Sprague Dawley Rats

ABSTRACT Introduction Combat injuries are complex and multimodal. Most injuries to the extremities occur because of explosive devices such as improvised explosive devices. Blast exposure dramatically increases the risk of infection in combat wounds, and there is limited available information on the best antibiotic treatments for these injuries. We previously demonstrated that mice exposed to blast displayed a delayed clearance of cefazolin from the plasma and liver; further semi-mechanistic modeling determined that cefazolin concentrations in the skin of these mice were reduced. Our objective was to investigate the effects of blast on the pharmacokinetics of antibiotics of different types used for the treatment of combat wounds in the rat model. Materials and Methods Male Sprague Dawley rats were exposed to blast overpressure followed by injection of a bolus of animal equivalent doses of an antibiotic (cefazolin, cefepime, ertapenem, or clindamycin) into the tail vein at 1-hour post-blast exposure. Blood was collected at predetermined time points via repeated sampling from the tail vein. Animals were also euthanized at predetermined time points, at which time liver, kidney, skin, and blood via cardiac puncture were collected. Antibiotic concentrations were determined by ultra-performance liquid chromatography–tandem mass spectrometry. Results Blast-exposed rats exhibited a similar rate of clearance compared to non-blasted rats in the blood, liver, kidney, and skin, which is inconsistent with the data regarding cefazolin in blast-exposed mice. Conclusions Our results in rats do not recapitulate our previous observation of delayed cefazolin clearance in mice following the blast overpressure exposure. Although using rats permitted us to collect multiple blood samples from the same animals, rats may not be a suitable model for measuring the pharmacokinetics of antibiotics following blast. The interpretation of the results may be challenging because of variation in data among rat subjects in the same sample groups.

General & Internal Medicine↗