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DOE OSTI2023

nautilus : boosting Bayesian importance nested sampling with deep learning

ABSTRACT We introduce a novel approach to boost the efficiency of the importance nested sampling (INS) technique for Bayesian posterior and evidence estimation using deep learning. Unlike rejection-based sampling methods such as vanilla nested sampling (NS) or Markov chain Monte Carlo (MCMC) algorithms, importance sampling techniques can use all likelihood evaluations for posterior and evidence estimation. However, for efficient importance sampling, one needs proposal distributions that closely mimic the posterior distributions. We show how to combine INS with deep learning via neural network regression to accomplish this task. We also introduce nautilus, a reference open-source python implementation of this technique for Bayesian posterior and evidence estimation. We compare nautilus against popular NS and MCMC packages, including emcee, dynesty, ultranest, and pocomc, on a variety of challenging synthetic problems and real-world applications in exoplanet detection, galaxy SED fitting and cosmology. In all applications, the sampling efficiency of nautilus is substantially higher than that of all other samplers, often by more than an order of magnitude. Simultaneously, nautilus delivers highly accurate results and needs fewer likelihood evaluations than all other samplers tested. We also show that nautilus has good scaling with the dimensionality of the likelihood and is easily parallelizable to many CPUs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Boson sampling with Gaussian input states: Toward efficient scaling and certification

A universal quantum computer of large scale is not available yet, however, intermediate models of quantum computation would still permit demonstrations of a quantum computational advantage over classical computing and could challenge the Extended Church-Turing Thesis. One of these models based on single photons interacting via linear optics is called Boson Sampling. Although Boson Sampling was demonstrated and the threshold to claim quantum computational advantage was achieved, the question of how to scale up Boson Sampling experiments remains. To make progress with this problem, here we present a practically achievable pathway to scale Boson Sampling experiments by combining continuous-variable quantum information and temporal encoding. Here, we propose the combination of switchable dual-homodyne and single-photon detections, the temporal loop technique, and scattershot-based Boson Sampling. We detail the required assumptions for concluding computational hardness for this configuration. Furthermore, this particular combination of techniques moves towards an efficient scaling and certification of Boson Sampling, all in a single experimental setup.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Dark Energy Survey Year 3 results: Optimizing the lens sample in a combined galaxy clustering and galaxy-galaxy lensing analysis

We investigate potential gains in cosmological constraints from the combination of galaxy clustering and galaxy-galaxy lensing by optimizing the lens galaxy sample selection using information from Dark Energy Survey (DES) Year 3 data and assuming the DES Year 1 metacalibration sample for the sources. We explore easily reproducible selections based on magnitude cuts in i-band as a function of (photometric) redshift, zphot, and benchmark the potential gains against those using the well-established redMaGiC [E. Rozo et al., Mon. Not. R. Astron. Soc. 461, 1431 (2016)MNRAA40035-871110.1093/mnras/stw1281] sample. We focus on the balance between density and photometric redshift accuracy, while marginalizing over a realistic set of cosmological and systematic parameters. Our optimal selection, the MagLim sample, satisfies i<4zphot+18 and has ∼30% wider redshift distributions but ∼3.5 times more galaxies than redMaGiC. Assuming a wCDM model (i.e. with a free parameter for the dark energy equation of state) and equivalent scale cuts to mitigate nonlinear effects, this leads to 40% increase in the figure of merit for the pair combinations of Ωm, w, and σ8, and gains of 16% in σ8, 10% in Ωm, and 12% in w. Similarly, in ΛCDM, we find an improvement of 19% and 27% on σ8 and Ωm, respectively. We also explore flux-limited samples with a flat magnitude cut finding that the optimal selection, i<22.2, has ∼7 times more galaxies and ∼20% wider redshift distributions compared to MagLim, but slightly worse constraints. We show that our results are robust with respect to the assumed galaxy bias and photometric redshift uncertainties with only moderate further gains from increased number of tomographic bins or the inclusion of bin cross-correlations, except in the case of the flux-limited sample, for which these gains are more significant.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A high-temperature sample changer for parallelized in situ X-ray studies to efficiently explore reaction space

A sample environment for high-throughput X-ray scattering studies in transmission geometry to probe the mechanism and kinetics of moderate-temperature reactions in solution, molten fluxes and solids is described. This high-temperature sample changer enables efficient studies of reactions that are slow relative to the timescale of the X-ray scattering measurements by allowing up to 18 samples to be probed at the same temperature in parallel. This significantly enhances the throughput ofin situX-ray scattering studies as the sample changer effectively facilitates systematic studies that compare different reaction parameters (e.g.concentration, precursor, composition, additives), reference samples (e.g.background, pure precursors) and replicates (to demonstrate reproducibility) with enhanced consistency afforded by the quasi-simultaneous nature of the measurements. The large sample volumes, compared with those typically used for X-ray scattering measurements, are on a similar scale to those in the laboratory, making the results more directly comparable.

Chemistry↗

DOE OSTI2026

Design and Integration of a Compact Mobile Outdoor Soil Sampling Agricultural Robot

The lack of feedback on soil management for crop systems necessitates the collection of soil samples to derive insights into prevailing soil conditions. Achieving an accurate model of these plantations requires a substantial number of soil samples, which is a labor-intensive process that can suffer from inconsistencies in both the methodology of collection and the locations from which samples are gathered. In addition, the close spacing of crop rows constrains the maneuverability of mobile agricultural equipment during sample collection. This article proposes the use of agricultural robotics to facilitate the acquisition of composite soil samples with minimal human intervention, allowing for precise data collection for a Populus plant system. More specifically, this article presents a case study on the design and construction of a compact agricultural robot for soil sample collection. The performance of the robot, including its soil collection efficacy, maneuverability, and positional accuracy, is evaluated.

42 ENGINEERING↗

DOE OSTI2021

Solving the sample size problem for resource selection functions

Abstract Sample size sufficiency is a critical consideration for estimating resource selection functions (RSFs) from GPS‐based animal telemetry. Cited thresholds for sufficiency include a number of captured animals and as many relocations per animal N as possible. These thresholds render many RSF‐based studies misleading if large sample sizes were truly insufficient, or unpublishable if small sample sizes were sufficient but failed to meet reviewer expectations. We provide the first comprehensive solution for RSF sample size by deriving closed‐form mathematical expressions for the number of animals M and the number of relocations per animal N required for model outputs to a given degree of precision. The sample sizes needed depend on just 3 biologically meaningful quantities: habitat selection strength, variation in individual selection and a novel measure of landscape complexity, which we define rigorously. The mathematical expressions are calculable for any environmental dataset at any spatial scale and are applicable to any study involving resource selection (including sessile organisms). We validate our analytical solutions using globally relevant empirical data including 5,678,623 GPS locations from 511 animals from 10 species (omnivores, carnivores and herbivores living in boreal, temperate and tropical forests, montane woodlands, swamps and Arctic tundra). Our analytic expressions show that the required M and N must decline with increasing selection strength and increasing landscape complexity, and this decline is insensitive to the definition of availability used in the analysis. Our results demonstrate that the most biologically relevant effects on the utilization distribution (i.e. those landscape conditions with the greatest absolute magnitude of resource selection) can often be estimated with much fewer than animals. We identify several critical steps in implementing these equations, including (a) a priori selection of expected model coefficients and (b) regular sampling of background (pseudoabsence) data within a given definition of availability. We discuss possible methods to identify a priori expectations for habitat selection coefficients, effects of scale on RSF estimation and caveats for rare species applications. We argue that these equations should be a mandatory component for all future RSF studies.

Street, Garrett M.↗

DOE OSTI2022

A Subspace-Inclusive Sampling Method for the Computational Design of Compositionally Graded Alloys

Abstract Compositionally graded alloys, a subclass of functionally graded materials (FGMs), utilize localized variations in composition with a single metal part to achieve higher performance than traditional single material parts. In previous work [Kirk, T., Galvan, E., Malak, R., and Arroyave, R., 2018, “Computational Design of Gradient Paths in Additively Manufactured Functionally Graded Materials,” J. Mech. Des., 140, p. 111410. 10.1115/1.4040816], the authors presented a computational design methodology that avoids common issues which limit a gradient alloy’s feasibility, such as deleterious phases, and optimizes for performance objectives. However, the previous methodology only samples the interior of a composition space, meaning designed gradients must include all elements in the space throughout the gradient. Because even small amounts of additional alloying elements can introduce new deleterious phases, this characteristic often neglects potentially simpler solutions to otherwise unsolvable problems and, consequently, discourages the addition of new elements to the state space. The present work improves upon the previous methodology by introducing a sampling method that includes subspaces with fewer elements in the design search. The new method samples within an artificially expanded form of the state space and projects samples outside the true region to the nearest true subspace. This method is evaluated first by observing the sample distribution in each subspace of a 3D, 4D, and 5D state space. Next, a parametric study in a synthetic 3D problem compares the performance of the new sampling scheme to the previous methodology. Lastly, the updated methodology is applied to design a gradient from stainless steel to equiatomic NiTi that has practical uses such as embedded shape memory actuation and for which the previous methodology fails to find a feasible path.

Engineering↗

DOE OSTI2023

Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format

Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes ( e . g ., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5–2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

G-LiHT Campaign Leaf Sample details & photos, March 2017: Puerto Rico

This data package includes details of leaves sampled for leaf spectra and chemistry from 5 sites in Puerto Rico, in March of 2017. Sunlit canopy and shaded leaves of 66 species were collected. Data for each sample includes species, leaf age, type of analysis (spectroscopy, gas exchange, chemistry), sample number and sample photographs. The data package includes a spreadsheet with sample information and a zip file of photographs (1.6 GB). This data was collected as part of the 2017 BNL–G-LiHT leaf spectra campaign. See related datasets for leaf spectral reflectance and transmittance, leaf mass area (LMA), and leaf chemistry. Note that leaf sample details are also included in related datasets.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Characterization and CST Batch Contact Equilibrium Testing of Modified Tank 9H Process Supernate Samples in Support of TCCR

The Tank Closure Cesium Removal (TCCR) system uses ion exchange columns filled with crystalline silicotitanate (CST) media to process radioactive waste solutions for the removal of ¹³⁷Cs. TCCR currently focuses on dissolving Savannah River Site (SRS) radioactive tank waste (primarily sodium saltcake solids) within Tank 10H followed by at-tank ion exchange column treatment. Two supernate batches from Tank 10H have been processed through the TCCR unit and processing of a third batch is expected soon. After processing of this supernate batch, plans are to replace the CST columns and process dissolved salt solution from Tank 9H through Tank 10H and then through the new CST columns installed in the TCCR unit. The new columns are expected to contain either a media similar to an archived CST batch (IE-911) or the R9120-B CST media used in the current TCCR columns (the two materials are fundamentally the same; just different specifications, product names, and preconditioning steps). Samples of Tank 9H dissolved saltcake were received at the Savannah River National Laboratory (SRNL) and characterized. The Tank 9H supernate contained a high sodium concentration (~9.6 M Na⁺) and will require dilution to near 6 M [Na⁺] prior to processing through the TCCR unit. The cesium concentration in Tank 9H is currently significantly higher than was observed with Tank 10H. Three dilutions of the Tank 9H supernate were conducted to mimic possible dilutions that could be conducted in the tank farm prior to TCCR processing using inhibited water, sodium hydroxide, and sodium nitrate solutions. Dilution #1 was prepared by diluting the Tank 9H supernate by a factor of 1.6 with inhibited water, Dilution #2 was prepared by diluting the Tank 9H supernate by a factor of 3.7 with a mixed sodium hydroxide/sodium nitrate diluent, and Dilution #3 was prepared by also diluting by a factor of 3.7 but with sodium hydroxide only. All three dilutions have similar Na⁺ concentrations (~6 M), but Dilutions #2 and #3 contain significantly less cesium. Major and key minor components of the diluted Tank 9H supernate samples are provided in Table ES-1. Batch contact equilibrium tests were conducted with the Tank 9H dilutions and the two different CST media batches being considered for use in the new TCCR columns. Results are summarized in Table ES-2 and compared to ZAM model predictions. The highest cesium distribution coefficient and percent removal were observed with Dilution #3. IE-911 CST (an archived CST media batch) was more effective at removing cesium than the more recently prepared R9120-B CST media, though both media samples removed >88% of the cesium and the differences may not be statistically different considering the overall uncertainty. Based on the results, maximum cesium loadings were calculated for each CST media type and Tank 9H dilution. In general, maximum cesium loadings from dilutions of this supernate batch are quite high (approaching 0.1 mmol total Cs⁺/g CST for Dilution #1). The highest calculated maximum ¹³⁷Cs loading for the Tank 9H dilutions using the ZAM model with input of the tank compositions and batch contact results was 207 Ci/kg CST (Dilution #1 with IE-911 CST). In all cases, higher maximum cesium loading values were predicted for IE-911 CST versus R9120-B, although the differences varied considerably between the dilutions. The maximum loading value for IE-911 CST with Tank 9H Dilution #1 was only 7% higher than the maximum loading for R9120-B. The maximum loading value for IE-911 CST with Dilution #3 was 24% higher than the maximum loading for R9120-B. Dilution #2 was intermediate between these values. Note that these maximum loading values are the theoretical calculated values, and actual operating conditions will cause differences. A CST binder dilution (correction) factor near 0.7 (relative to pure powder CST) was required for each batch contact test with IE-911 engineered CST using the three Tank 9H dilutions. Correction factors calculated for R9120-B CST ranged from 0.56 to 0.66 for the three dilutions. Following the batch contact tests, the CST samples were isolated from the Tank 9H solution, washed, dried, and digested in acid following established procedures. The analysis results are provided in Table ES-3. Total cesium loading values determined by CST digestion were similar to the calculated loading values based on solution analysis (Table ES-2) for all samples. In addition, the CST was observed to load calcium (R9120-B sample only), iron, strontium, lead, uranium, and plutonium after contact with the waste supernate, as has been observed previously.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Analysis of Tank 38H (HTF-38-20-103, -104) and Tank 43H (HTF-43-20-105, -106) Samples for Support of the Enrichment Control and Corrosion Control Programs

SRNL analyzed samples from Tank 38H and Tank 43H to support ECP and CCP. The results indicate the concentrations of most species in the Tank 38H surface sample decreased from the previous surface sample. The Tank 38H sub-surface sample shows only minor changes in concentration for soluble species in the solution (e.g., Na, Al, Cs-137) but a large drop in concentrations for species typically associated with sludge solids (e.g., U, Pu, Fe, Si) likely because of a decrease in sludge solids from the previous sample. The large differences in the concentrations of major components between the Tank 38H surface and sub-surface samples indicate significant stratification of solution species within the tank.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Underground Test Area (UGTA) Sampling Plan for Corrective Action Units 101 and 102: Central and Western Pahute Mesa, Nevada National Security Site, Nevada

The purpose of this groundwater sampling plan (referred to herein as “the Plan”) is to describe the approach for collecting and analyzing groundwater samples to meet the objectives of the U.S. Department of Energy (DOE), Environmental Management (EM) Nevada Program’s Underground Test Area (UGTA) Activity. The Plan is focused on the Central and Western Pahute Mesa corrective action units (CAUs 101 and 102). The remaining UGTA CAUs are in the final stage of the UGTA strategy (Closure Report [CR] stage), and monitoring requirements for these CAUs are described in their respective CRs. The Plan supersedes the Nevada National Security Site Integrated Groundwater Sampling Plan and its ensuing Record of Technical Change (ROTC) (DOE/EMNV, 2019b). The Plan is designed to ensure compliance with the UGTA Quality Assurance Plan (QAP) and its ensuing ROTC (DOE/EMNV, 2018), and the Federal Facility Agreement and Consent Order (FFACO) (1996, as amended). The Plan is implemented by the Environmental Program Services (EPS) contractor. Implementation of the Plan provides data to complete corrective actions prescribed by the FFACO to protect the public from groundwater contaminated by historical underground nuclear testing. The Plan’s scope comprises sample collection and analysis requirements for assessing the extent of groundwater contamination from underground nuclear testing. Sampling wells located in the communities surrounding the Nevada National Security Site (NNSS) is performed by other organizations (e.g., management and operating [M&O] contractor) and is therefore not included within the Plan. The results of the community sampling are presented in the annual NNSS environmental reports.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Optimized Microwave Digestion and Quantification Procedure for Boron Carbide samples

A microwave-assisted HNO3-H2SO4-HF digestion system was explored/optimized for the total dissolution of Boron Carbide samples followed by multi-elemental determination using ICP-MS and ICP OES, in order to improve the methods used in a previous try using a microwave-assisted H2O2-HNO3-HF digestion system. The samples were microwave digested to accomplish complete dissolution needed to perform quantitative analysis of their metal content. Two Boron Carbide samples were provided to us: JM10 and JM11. The Boron Carbide samples were completely dissolved at the end of the optimized microwave digestion procedure that was developed. The digested samples were analyzed for metals mostly by ICP MS; few elements were analyzed by ICP-OES. Microwave digestion reactions were performed in a Titan MPS instrument (Perkin Elmer, USA). Titan MPS instrument is equipped with Temperature and Pressure regulations and controlled by software. Each microwave digestion batch contained the samples of interest along with a reagent blank and one certified standard (1632e) in order to (i) compensate for the contaminations present in the reagents, (ii) ensure that the digestion was complete and (iii) that there was a good recovery of all the constituents. The certified standard used (1632e) was provided with USGS certificates of analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Cesium Batch Contact Equilibrium Testing of Crystalline Silicotitanate (CST) Sieve Cuts in SRS Average Simulant and Examination of CST Samples Aged in Caustic and Simulant in Support of Tank Closure Cesium Removal 1A (TCCR-1A)

Batch contact testing to determine cesium equilibrium loading on Crystalline Silicotitanate ion exchange media in Savannah River Site Average Waste Simulant at 25 °C indicated that smaller diameter particles isolated by sieving pretreated CST media may load slightly higher (<10%) amounts of cesium, though the differences are within analytical uncertainty. In addition, ion exchange media sub-samples stored in 2-4 M NaOH and caustic simulant solutions for ~2.5 years were examined by optical microscopy and the 3 M NaOH sample was also analyzed to determine whether changes in the particle size distribution occurred during storage. No visual indications of particle attrition or agglomeration were observed for any sample. Particle size analysis indicated that a slight decrease occurred in the average particle diameter following contact with 3 M NaOH (541 µm average diameter versus 566 µm for the pretreated CST prior to contact). A small increase (from 0 to <0.5 wt. %) in the number of particles ranging from 271 and 322 µm was also observed for the CST sample contacted with 3 M NaOH relative to a sample of the original pretreated material. However, this small change could be due to sub-sampling differences or analytical uncertainty. It does not appear that small particles are formed to a significant degree during CST caustic contact or that small particles which do form (presumably from attrition of larger particles during pretreatment) load significantly more cesium than the bulk material. Minimal other negative consequences were observed associated with CST extended caustic or simulant contact, except for the tendency for more concentrated salt solutions to form some salt crystals which deposit on the media over time.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Results of the Short-Term Analyses of the Salt (Macro) Batch 5 Tank 41H Qualification Sample (Resample)

Savannah River National Laboratory (SRNL) analyzed samples from Tank 41H in November 2021 in support of qualification of Salt Waste Processing Facility (SWPF) Salt Batch 5. This document reports the short-term results of the analyses of samples of Tank 41H. Analysis of the Tank 41H Salt Batch 5 sample indicates that the material does not display any unusual characteristics or observations, such as floating solids, the presence of large amounts of solids, or unusual colors. Further sample results will be reported in a future document. This report satisfies part of Deliverable 3 of the Technical Task Request (TTR). After a data review it was found that the original results reported in the revision 0 of this document were actually from Salt Batch 4 (Tank 21H). A new set of samples was sent for analysis to satisfy deliverable 3 of the TTR. The results from the original analyses have been replaced with the recent analyses of the actual Salt Batch 5 sample.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Results of the Short-Term Analyses of the Salt (Macro) Batch 5 Tank 41H Qualification Sample (Resample)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2023

Optimize electron beam energy toward in-situ imaging of large thick bio-samples with nanometer resolution

To optimize electron energy toward in-situ imaging large bio-samples up to 10-μm thickness with nanoscale resolution, we implemented an analytical model based on elastic and inelastic characteristic angles 1. This model can be used to predict the transverse beam size broadening as a function of electron energy while the probe beam traverses through the sample. As result, the optimal choice of the electron beam energy can be realized. While the sample thickness is less than 10 μm, there exists an optimal electron beam energy below 10 MeV regarding a specific sample thickness. However, for samples thicker than 10 μm, the optimal beam energy is 10 MeV, and the ultimate resolution could become worse with the increase of the sample thickness.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Effect of Sample Thickness on the Tensile Strength of Small Graphite Discs

This report formally documents the completion of the Advanced Reactor Technologies (ART) Level 3 Milestone (M3TG-24OR0501054), “Continue activities related to Split Disc-DIC - complete analysis of effect of sample thickness on one fine grain graphite,” due May 31, 2024. Details within this report outline the status of activities aimed at elucidating the effect of sample thickness on the tensile strength measurement using the small-disc, split-disc testing standard in support of the US Department of Energy’s ART Graphite R&D Program. The ASTM D8289, Standard Test Method for Tensile Strength Estimate by Disc Compression of Manufactured Graphite, was developed to provide an alternative means for testing tensile strength on smaller specimens, which are compatible with available irradiation capsule volumes, and other compatibility measurements. ASTM D8289 specifies that acceptable specimen diameter can range from 6 to 12.7 mm and that the maximum allowed sample thickness should be half of the diameter. However, information is limited with respect to the effect of thickness on the measured splitting tensile strength. This report documents efforts to understand the effect of sample thickness on splitting tensile strength. The work involved testing Ø12.7 mm samples of fine-grain graphites 2114 and IG-110 of different thicknesses (6.35, 5, 4, and 3 mm). The digital image correlation (DIC) method was applied to the samples, along with the ASTM D8289 Standard, to help interpret the measured results.

36 MATERIALS SCIENCE↗