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At least 289 records · Page 16

A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina

The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.

59 BASIC BIOLOGICAL SCIENCES↗

Death at watersheds: Galaxy quenching in low-density environments

The evolution of galaxies is influenced by their local and global environment in the cosmic web. Galaxies with very old stellar populations (VO galaxies with D n (4000) index ≥1.75) mostly lie in the centres of galaxy clusters, where they evolve under the influence of processes characteristic of high-density cluster environments. However, VO galaxies have also been found in poor groups in global low-density environments between superclusters, which we call watershed regions. Our aim is to analyse the properties of galaxies in various cosmic environments with a focus on VO galaxies in the watershed regions to understand their evolution, and the origin of the large-scale morphology–density relation. We employ the Sloan Digital Sky Survey DR10 MAIN spectroscopic galaxy sample in the redshift range 0.009 ≤ z ≤ 0.200 to calculate the luminosity–density field of galaxies, to determine groups and filaments in the galaxy distribution, and to obtain data on galaxy properties. The luminosity–density field with smoothing length 8 h -1 Mpc, D8, characterises the global environment of galaxies. We analyse the group and galaxy contents of regions with various D8 thresholds. We divide groups into low- and high-luminosity groups based on the highest luminosity of groups in the watershed region, L gr ≤ 15 × 10 12 h -2 L ⊙ . We compare the stellar masses, the concentration index, and the stellar velocity dispersions of quenched and star-forming galaxies among single galaxies, satellite galaxies, and the brightest group galaxies (BGGs) in various environments. We show that the global density is most strongly related to the richness of galaxy groups. Its influence on the overall star formation quenching in galaxies is less strong. Correlations between the morphological properties of galaxies and the global density field are the weakest. The watershed regions with D8 < 1 are populated mostly by single galaxies, constituting 70% of all galaxies there, and by low-luminosity groups. Still, approximately one-third of all galaxies in the watershed regions are VO galaxies. They have lower stellar masses, smaller stellar velocity dispersions, and stellar populations that are up to 2 Gyr younger than those of VO galaxies in other global environments. In higher density global environments (D8 > 1), the morphological properties of galaxies are very similar. Differences in galaxy properties are the largest between satellites and BGGs in groups. Our results suggest that galaxy evolution is determined by the birthplace of galaxies in the cosmic web, and mainly by internal processes which lead to the present-day properties of galaxies. This may explain the similarity of (VO) galaxies in extremely different environments.

79 ASTRONOMY AND ASTROPHYSICS↗

OpenCGRA: An Open-Source Unified Framework for Modeling,Testing, and Evaluating CGRAs

Coarse-grained reconfigurable arrays (CGRAs),loosely defined as arrays of functional units (e.g, adder, sub-tractor, multiplier, divider, or larger multi-operation units, butsmaller than a general-purpose core) interconnected through aNetwork-on-Chip, provide higher flexibility than domain-specificASIC accelerators while offering increased hardware efficiencywith respect to fine-grained reconfigurable devices, such as FieldProgrammable Gate Arrays (FPGAs). The fast evolving fieldsof machine learning and edge computing, which are seeing acontinuous flow of novel algorithms and larger models, makeCGRAs ideal target architectures to allow domain specializationwithout loosing too much generality. They also generally offerquicker and more effective reconfigurability than FPGAs, po-tentially allowing adaptation during actual algorithm execution,and implement a dataflow programming paradigm that adaptswell to these emerging workloads. Designing and generating aCGRA, however, still requires to define the type and number ofthe specific functional units, implement their interconnect andthe network topology, and perform its simulation and validation,given a variety of workloads of interest.In this paper, we propose OpenCGRA, a Python-based unifiedframework that integrates generation, modeling, testing and eval-uation for CGRAs. OpenCGRA is the first open-source integratedframework able to support the full top-to-bottom design flow forspecializing and implementing CGRAs: modeling at different ab-straction levels (functional level, cycle level, register-transfer level),generation, simulation, testing at different granularities (unit test-ing, integration testing, property-based testing), and characteriza-tion (area, power, and timing). OpenCGRAs will be made availableon GitHub.

CGRA, synthesis↗

High Fidelity CFD Simulations Supporting the KP-FHR

Kairos Power, LLC, is developing its version of the Fluoride-cooled High-temperature Reactor, the KP-FHR. The design uses a pebble bed core with fluoride salt as a coolant. The pebbles used in the KP-FHR have a diameter of 4 cm, with a shell fuel region where TRISO particles are embedded. A Pebble bed core design is adopted by several Gen IV reactors, They boast many benefits, such as fuel integrity, highly efficient heat transfer, and passive safety. However, it is challenging to accurately predict temperature and flow inside a pebble bed. Traditional approaches use the porous media model, which regards the pebble bed as a continuous medium, but with different temperature fields representing different levels, such as the fluid temperature, pebble surface temperature, and pebble center temperature. Empirical heat transfer correlations are adopted to calculate the heat transfer coefficient between different phases. However, empirical correlations are usually validated with experimental data, which usually lacks detail inside the pebble bed. The available experimental data is also generally at a high Reynolds number, which falls outside of the conditions of KP-FHR. Explicit computational fluid dynamics (CFD) simulations of randomly packed pebble beds have only become feasible recently. This is thanks to the rapid development of computational power and scalable algorithms. In this work, we used the Spectral Element Method (SEM) CFD code NekRS to simulate the randomly packed pebble bed in a cylindrical container. NekRS, which is the GPU variant of Nek5000, but refactored to utilize the computational power of GPUs using the OCCA library to run on hybrid architecture high performance computing systems. It was initially developed with the libParamunal library, but truncated and tuned for large-scale turbulence simulation. As a result, the SEM reaches higher precision with the same degrees of freedom by using a high-order Lagrange polynomial basis distributed on Gauss-Lobatto-Legendre quadrature inside each element, compared to lower-order methods, such the Finite Volume Method and Finite Element Method. The report is divided into five parts. We start with a general discussion of the pebble bed reactor, along with a specific investigation into the KP-FHR. The second part presents the numerical methodology. In the third part, we study a modular pebble bed with 1741 pebbles in a container of 7 pebble-diameter radius. Beyond LES simulations done by NekRS, we also leveraged the thermal radiation model in OpenFOAM to study heat transfer under no-forced-flow scenarios. Then, in the fourth part we simulated a pebble bed similar to the size of the Hermes Test Reactor. The total number of pebbles is in these simulations is 34,374. The container radius is 14 pebble-diameters. Finally, the report concludes in part five, with a discussion of future work.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DESI 2024 III: baryon acoustic oscillations from galaxies and quasars

We present the DESI 2024 galaxy and quasar baryon acoustic oscillations (BAO) measurements using over 5.7 million unique galaxy and quasar redshifts in the range 0.1 < z < 2.1. Divided by tracer type, we utilize 300,017 galaxies from the magnitude-limited Bright Galaxy Survey with 0.1 < z < 0.4, 2,138,600 Luminous Red Galaxies with 0.4 < z < 1.1, 2,432,022 Emission Line Galaxies with 0.8 < z < 1.6, and 856,652 quasars with 0.8 < z < 2.1, over a ∼ 7,500 square degree footprint. The analysis was blinded at the catalog-level to avoid confirmation bias. All fiducial choices of the BAO fitting and reconstruction methodology, as well as the size of the systematic errors, were determined on the basis of the tests with mock catalogs and the blinded data catalogs. We present several improvements to the BAO analysis pipeline, including enhancing the BAO fitting and reconstruction methods in a more physically-motivated direction, and also present results using combinations of tracers. We employ a unified BAO analysis method across all tracers. We present a re-analysis of SDSS BOSS and eBOSS results applying the improved DESI methodology and find scatter consistent with the level of the quoted SDSS theoretical systematic uncertainties. With the total effective survey volume of ∼ 18 Gpc3, the combined precision of the BAO measurements across the six different redshift bins is ∼0.52%, marking a 1.2-fold improvement over the previous state-of-the-art results using only first-year data. We detect the BAO in all of these six redshift bins. The highest significance of BAO detection is 9.1σ at the effective redshift of 0.93, with a constraint of 0.86% placed on the BAO scale. We find that our observed BAO scales are systematically larger than the prediction of the Planck 2018-ΛCDM at z < 0.8. We translate the results into transverse comoving distance and radial Hubble distance measurements, which are used to constrain cosmological models in our companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗

Persistent mysteries of jet engines, formation, propagation, and particle acceleration: Have they been addressed experimentally?

Here, the physics of astrophysical jets can be divided into three regimes: (i) engine and launch (ii) propagation and collimation, (iii) dissipation and particle acceleration. Since astrophysical jets comprise a huge range of scales and phenomena, practicality dictates that most studies of jets intentionally or inadvertently focus on one of these regimes, and even therein, one body of work may be simply boundary condition for another. We first discuss long standing persistent mysteries that pertain the physics of each of these regimes, independent of the method used to study them. This discussion makes contact with frontiers of plasma astrophysics more generally. While observations theory, and simulations, and have long been the main tools of the trade, what about laboratory experiments? Jet related experiments have offered controlled studies of specific principles, physical processes, and benchmarks for numerical and theoretical calculations. We discuss what has been accomplished on these fronts. Although experiments have indeed helped us to understand certain processes, proof of principle concepts, and benchmarked codes, they have yet to solved an astrophysical jet mystery on their own. A challenge is that experimental tools used for jet-related experiments so far, are typically not machines originally designed for that purpose, or designed with specific astrophysical mysteries in mind. This presents an opportunity for a different way of thinking about the development of future platforms: start with the astrophysical mystery and build an experiment to address it.

79 ASTRONOMY AND ASTROPHYSICS↗

Cancer genomics predicts disease relapse and therapeutic response to neoadjuvant chemotherapy of hormone sensitive breast cancers

Several studies provide insight into the landscape of breast cancer genomics with the genomic characterization of tumors offering exceptional opportunities in defining therapies tailored to the patient’s specific need. However, translating genomic data into personalized treatment regimens has been hampered partly due to uncertainties in deviating from guideline based clinical protocols. Here we report a genomic approach to predict favorable outcome to treatment responses thus enabling personalized medicine in the selection of specific treatment regimens. The genomic data were divided into a training set of N = 835 cases and a validation set consisting of 1315 hormone sensitive, 634 triple negative breast cancer (TNBC) and 1365 breast cancer patients with information on neoadjuvant chemotherapy responses. Patients were selected by the following criteria: estrogen receptor (ER) status, lymph node invasion, recurrence free survival. The k-means classification algorithm delineated clusters with low- and high- expression of genes related to recurrence of disease; a multivariate Cox’s proportional hazard model defined recurrence risk for disease. Classifier genes were validated by Immunohistochemistry (IHC) using tissue microarray sections containing both normal and cancerous tissues and by evaluating findings deposited in the human protein atlas repository. Based on the leave-on-out cross validation procedure of 4 independent data sets we identified 51-genes associated with disease relapse and selected 10, i.e. TOP2A, AURKA, CKS2, CCNB2, CDK1 SLC19A1, E2F8, E2F1, PRC1, KIF11 for in depth validation. Expression of the mechanistically linked disease regulated genes significantly correlated with recurrence free survival among ER-positive and triple negative breast cancer patients and was independent of age, tumor size, histological grade and node status. Importantly, the classifier genes predicted pathological complete responses to neoadjuvant chemotherapy (P < 0.001) with high expression of these genes being associated with an improved therapeutic response toward two different anthracycline-taxane regimens; thus, highlighting the prospective for precision medicine. Our study demonstrates the potential of classifier genes to predict risk for disease relapse and treatment response to chemotherapies. The classifier genes enable rational selection of patients who benefit best from a given chemotherapy thus providing the best possible care. The findings encourage independent clinical validation.

59 BASIC BIOLOGICAL SCIENCES↗

Parsed synthesis of pyocyanin via co-culture enables context-dependent intercellular redox communication

Abstract Background Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication. Results We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture’s phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture. Conclusions Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems.

Chun, Kayla↗

The Design and Evaluation of Zero Trust Architecture for Electric Vehicle Charging Infrastructure: EVs @ Scale Series on EV Charging Station Cybersecurity

Implementing a zero trust architecture can significantly bolster the security of electric vehicle (EV) charging infrastructure. EV charging infrastructure includes numerous networked interfaces, each of which can present potential vulnerabilities. When these vulnerabilities are exploited, they can compromise the entire system, leading to severe operational and security risks. Zero trust is a security model that operates on the principle of "never trust, always verify," which helps manage the attack surface and limit the scope of any potential compromises. Fundamentally, this model ensures that no entity, whether inside or outside the network, is trusted by default. The design principles of zero trust include continuous verification, strict deny-by-default access controls, and micro-segmentation. Continuous verification ensures that every request is thoroughly checked, regardless of its origin. Strict access controls enforce the principle of least privilege, allowing users and devices only the minimum necessary access to perform their functions. Micro-segmentation involves dividing the network into smaller, isolated segments to prevent lateral movement in case of a breach. In the context of EV charging infrastructure, zero trust can be implemented through various strategies. For example, multi-factor authentication (MFA) can be required for engineers to access the management interfaces and control systems of charging stations. Real-time monitoring and analysis of network traffic can help detect and respond to anomalies. Systems that do not need to communicate with each other can be micro-segmented to enhance security. All communications should adhere to predefined policies to be permitted. Additionally, encrypting communications can protect sensitive information exchanged between chargers and management systems. This paper presents a zero trust architecture specifically designed for EV charging infrastructure. Implementing zero trust not only mitigates risks but also builds a resilient infrastructure capable of withstanding and quickly recovering from cyber threats. The architecture addresses six defined security objectives. A comprehensive test plan is developed to assess the architecture against these objectives, and the results of the evaluation are reported. This approach is essential for maintaining the reliability and integrity of EV charging services in an increasingly interconnected and vulnerable digital landscape. This is the first in a planned series of papers exploring the implementation of zero trust in EV charging infrastructure. Each paper will delve into different aspects and applications of zero trust, highlighting how various work processes and requirements can lead to distinct architectural designs. These architectures will be tailored to address specific security challenges and operational needs within the EV charging ecosystem, ensuring a robust and adaptable security framework.

33 ADVANCED PROPULSION SYSTEMS↗

A consistent, Bayesian, approach to the cross section probability distribution in the unresolved resonance region

The cross sections of neutron-induced reactions can be divided into three energy ranges: the resolved resonance region (RRR), the unresolved resonance region (URR), and the fast region. In general, the cross sections in the URR show significant fluctuations that cannot be predicted and cannot be experimentally resolved, thus, it is commonly assumed that the cross section at a specific energy is given by a probability distribution function (PDF) over a range of values that can span several orders of magnitude. The current methodology used to describe such behavior is to construct the PDF by stochastically generating resonance ladders and numerically measuring the PDF. The resonance ladders are sampled using known resonance statistical properties and average resonance widths and spacings extrapolated from the RRR. Although this is a standard and widely used technique, it is computationally very expensive, therefore, an alternative, analytical, approach would be preferable due to the considerable speed up of the computational time in real life applications. Moreover, the current methodology does not take into account existing experimental data, such for total and capture cross sections, that are available for many nuclei. Finally, this approach was developed to be used in reactor-scale applications and it is not suited for use in single-event applications. In this work we will rethink the entire approach to the PDF construction using a Bayesian mindset. This will allow us to provide a different definition of the PDF that allows a much faster calculation of the higher-temperature PDFs and a proper combination of theoretical and experimental PDFs following the probability theory. We will also show that our definition is well suited for single-event applications and we will make an explicit connection between our method and the standard approach. We do this by showing that the central limit theorem applies and our method leads to the same PDF obtained with the standard methodology, for a large number of events per history.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Geometry versus growth: Internal consistency of the flat ΛCDM model with KiDS-1000

Here, we carry out a multi-probe self-consistency test of the flat Lambda Cold Dark Matter (ΛCDM) model with the aim of exploring potential causes of the reported tensions between high- and low-redshift cosmological observations. We divide the model into two theory regimes determined by the smooth background (geometry) and the evolution of matter density fluctuations (growth), each governed by an independent set of ΛCDM cosmological parameters. This extended model is constrained by a combination of weak gravitational lensing measurements from the Kilo-Degree Survey, galaxy clustering signatures extracted from Sloan Digital Sky Survey campaigns and the Six-Degree Field Galaxy Survey, and the angular baryon acoustic scale and the primordial scalar fluctuation power spectrum measured in Planck cosmic microwave background (CMB) data. For both the weak lensing data set individually and the combined probes, we find strong consistency between the geometry and growth parameters, as well as with the posterior of standard ΛCDM analysis. In the non-split analysis, for which one single set of parameters was used, tension in the amplitude of matter density fluctuations as measured by the parameter S 8 persists at around 3σ, with a 1.5% constraint of S 8 = 0.776$_{–0.008}^{+0.016}$ for the combined probes. We also observe a less significant preference (at least 2σ) for higher values of the Hubble constant, H 0 = 70.5$_{–1.5}^{+0.7}$ km s –1 Mpc –1 , as well as for lower values of the total matter density parameter Ω m = 0.289$_{–0.005}^{+0.007}$ compared to the full Planck analysis. Including the subset of the CMB information in the probe combination enhances these differences rather than alleviate them, which we link to the discrepancy between low and high multipoles in Planck data. Our geometry versus growth analysis does not yet yield clear signs regarding whether the origin of the discrepancies lies in ΛCDM structure growth or expansion history but holds promise as an insightful test for forthcoming, more powerful data.

79 ASTRONOMY AND ASTROPHYSICS↗

Evaluation of Zero-Net-Rate Pumping Tests

Accurately estimating the distribution of aquifer properties is key to understanding contaminant movement in the subsurface. The distribution of aquifer properties is typically addressed using slug or constant-rate well tests, and the pros and cons of these tests are well known. Slug tests are appealing because they avoid removing contaminated water, but their results are affected by well skin and the small volume of displaced water limits the volume of aquifer that can be evaluated. Constant-rate well tests have the disadvantage of requiring disposal of potentially contaminated water, but they can generate properties that are more representative than slug tests, and they can be used to estimate well efficiency and storativity, which are difficult to characterize using slug tests. Periodic pumping tests are appealing because they have many of the advantages and few of the disadvantages of slug and constant-rate well tests. Periodic pumping tests involve cycling the pumping rate with a regular period and measuring the resulting response in monitoring wells. Some of these tests involve imposing a periodic rate on a constant mean rate. However, other tests involve moving water out and back into the well at rates that are balanced so the net rate after each period is zero. Some zero-net-rate (ZNR) well tests use rates that follow a sinusoidal pattern, whereas others use a square wave pattern that switches between a constant rate of pumping and a constant rate of injection to achieve a zero-net rate. ZNR well tests appear to be a useful compromise between slug and constant rate tests, but methods for conducting and analyzing the results from these tests have received limited evaluation. Periodic pumping tests are typically evaluated through recorded pressure responses to a disturbance source. Recent work has demonstrated that the strain field in the vadose zone shows a response to disturbances in the underlying aquifer. Various instrument designs are available that can record vertical and horizontal strain to very precise resolutions (10-9 ε). Measuring the strain in the vadose zone can present lower costs than measuring pressure in a monitoring well, so using strain could improve the resolution of ZNR tests, as well as make these tests potentially cheaper. A ZNR periodic pumping system was constructed and used to perform tests in the Clemson, South Carolina area. The system was designed to pump and inject with a periodic square-wave, so pumping occurs at a constant rate for half the period and is followed by injection at the same rate for half the period resulting in no net gain or loss of water from the aquifer. The system is designed to generate flow rates from 1 to 3.5 gallons per minute (gpm) with a capacity of 875-gallon per half period. Pressure and strain monitoring points are located in the vicinity of the pumping well. A series of 10 ZNR periodic pumping tests were conducted at the field site, with periods ranging from 2 to 540 minutes. Pressure data were collected and recorded in four monitoring wells in various locations around the pumping well. In addition, vertical and horizontal strain and tilt data were recorded in various locations around the pumping well. Traditional aquifer tests, including slug tests and constant-rate pumping tests were conducted at the field site to provide a baseline of aquifer parameter estimates that are compared the results of ZNR tests. Pressure data measured at monitoring wells during ZNR tests were analyzed utilizing an analytical solution (Streltsova, 1988) that assumes a confined aquifer and estimates hydraulic diffusivity and transmissivity using the time lag and amplitude of the pressure signal. The storativity can be separated out from the hydraulic diffusivity using the transmissivity estimate. The time-lag and amplitude of the pressure signals were estimated using a Fourier transform. The time-lag of the primary period of the pressure increases as a linear function of distance from the pumping well, and it increases as the square root of the period of the ZNR test over a range of periods spanning two orders of magnitudes. The first few harmonics follow similar trends, but the higher frequency harmonics diverge from this trend. Strain and tilt data from various instruments in the vadose and saturated zones are periodic during ZNR tests. The time lags of the strain components increase roughly linearly with distance from the well. Many of the time lags of the strain data from the vadose zone are similar to the time lags observed in the pressure data from a similar distance and pumping period. Theoretical experiments were performed to understand how pressure and strain responds to ZNR periodic pumping. The time-lags of the simulated pressure responses match the field data trends. The results were used to validate the Streltsova (1988) solution for periodic pumping to estimate hydraulic diffusivity. Hydraulic diffusivity was estimated to be 1.8 x 10-2 m2s-1 < Dh < 9.0 x 10-2 m2s-1 using pressure data from all the wells during ZNR tests. Transmissivity was estimated to be 0.8 x 10-4 m2s-1 < T < 4.3 x 10-4 m2s-1. Assuming Storativity = T/Dh gives 1.1 x 10-3 < S < 19 x10-3. Transmissivity is used to estimate the hydraulic conductivity, K, by dividing by the assumed aquifer thickness. Two constant-rate pumping tests were conducted and analyzed using two conceptual models: The Hantush (1961) solution was used to analyze data assuming confined conditions and the Neuman (1974) solution was used to analyze data assuming unconfined conditions. The Hantush (1961) solution estimated transmissivity to be 1.6 x 10-4 m2s-1 < T < 1.8 x 10-4 m2s-1 when using data from all the wells. Storativity was estimated to be 4.4 x 10-3 < S < 8.2 x 10-3. Assuming Dh = T/S gives 0.22 x 10-2 m2s-1 < Dh < 3.6 x 10-2 m2s-1. The Neuman (1974) solution estimated transmissivity to be 0.80 x 10-4 m2s-1 < T < 0.84 x 10-4 m2s-1. Total storativity (S + Sy) was estimated to be 22 x 10-3 < S < 110 x 10-3. Storativity excluding the Sy term was estimated to be 2.2 x 10-3 < S < 2.5 x 10-3. Assuming Dh = T/S gives 0.073 x 10-2 m2s-1 < S < 0.36 x 10-2 m2s-1. Two slug tests were performed on the pumping well, PW-2. The Bouwer and Rice (1976) solution for slug tests was used to analyze the data. This solution works for both confined and unconfined conditions, so both conceptual models were covered through the analysis. Hydraulic conductivity was estimated to be 1.95 x 10-6 ms-1 < K < 2.49 x 10-6 ms-1. Statistical comparison show generally no significant difference in the estimates of Dh, K, or S made using ZNR and conventional pumping tests.. However, the total storage estimated by the Neuman (1974) solution for unconfined settings is larger than that estimate using the Streltsove analysis applied to the ZNR tests. This is likely because the Neuman solution considers delayed yield from storage that the water table, whereas the Streltsova (1988) solution assumes confined conditions. The analysis also indicates that there is a statistically significant difference between parameters estimated with conventional slug tests and those measured with either constant-rate pumping tests or ZNR tests. Hydraulic diffusivity is estimated from the time-lag and the distance from the well. The time-lags of the strain data from the vadose zone are similar to the lags of the pressure data from a similar distance. This indicates that hydraulic diffusivities estimated from the strain data measured in the vadose zone would be similar to the estimates from the pressure data measured in the aquifer. There appear to be sign reversals in some of the strain data that were corrected to estimate the time lag. The dissolved oxygen (CO) concentration was measured during several ZNR tests to evaluate the feasibility of using the procedure to increase contaminant degradation kinetics that are related to DO. The results indicate that DO can be increased during the cycling of ZNR tests in some cases.

Smith-Jones, Austin↗

Implementation of an Orificing Optimization Algorithm in the DASSH Subchannel Analysis Code

The Ducted Assembly Steady-State Heat transfer code (DASSH) performs full-core subchannel thermal hydraulics calculations in liquid metal fast reactors. One of the applications of subchannel codes is to optimize coolant flow orificing. As a design activity, the primary task is to determine the best way to divide assemblies into groups and distribute coolant flow rates among them. This report documents an algorithm implemented in DASSH to automatically optimize coolant orificing. Over the course of multiple iterations, DASSH determines the orifice grouping and flow distribution that minimizes peak coolant, clad, or fuel temperatures across all timesteps for a user-specified number of assembly groups. The total coolant flow rate in the reactor is constrained to achieve the specified core-average outlet temperature. The flow rate to each orifice group may also be constrained by the allowable pressure drop. The distribution of coolant flow among groups is accelerated using a predictor-corrector algorithm based on interpolated results from single-assembly parametric calculations. The assembly orificing grouping is initially predicted based on assembly power but can be refined if results demonstrate that an assembly would fit better in another group. The algorithm is demonstrated with two case studies. The first is a simple model for a reactor core consisting of just fuel assemblies; the pin power distributions are specified to create a situation where the initial assembly grouping prediction is suboptimal. This example is used to describe the initial grouping, demonstrate convergence over multiple iterations, and highlight the impact of regrouping. Then, the algorithm is applied to minimize peak clad and fuel temperatures in an example sodium-cooled fast reactor, the Versatile Test Reactor. The multicycle optimization confirms prior calculations for the reference core design. The example highlights how optimizing for different peak temperatures affects the results and demonstrates the use of the pressure drop constraint to limit the maximum flow rate.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Dark Energy Survey Year 6 Results: Cosmological Constraints from Cosmic Shear

We present legacy cosmic shear measurements and cosmological constraints using six years of Dark Energy Survey imaging data. From these data, we study ~140 million galaxies (8.29 galaxies/arcmin$^2$) that are 50% complete at i=24.0 and extend beyond z=1.2. We divide the galaxies into four redshift bins, and obtain cosmic shear measurement with a signal-to-noise of 83, a factor of 2 higher than the Year 3 analysis. We model the uncertainties due to shear and redshift calibrations, and discard measurements on small angular scales to mitigate baryon feedback and other small-scale uncertainties. We consider two fiducial models to account for the intrinsic alignment (IA) of the galaxies. We conduct a blind analysis in the context of the $Λ$CDM model and find $S_8 \equiv σ_8(Ω_m/0.3)^{0.5}=0.798^{+0.014}_{-0.015}$ (marginalized mean with 68% CL) when using the non-linear alignment model (NLA) and $S_{8} = 0.783^{+0.019}_{-0.015}$ with the tidal alignment and tidal torque model (TATT), providing 1.8% and 2.5% uncertainty on $S_8$. Compared to constraints from the cosmic microwave background from Planck 2018, ACT DR6 and SPT-3G DR1, we find consistency in the full parameter space at 1.1$σ$ (1.7$σ$) and in $S_8$ at 2.0$σ$ (2.3$σ$) for NLA (TATT). The result using the NLA model is preferred according to the Bayesian evidence. We find that the model choice for IA and baryon feedback can impact the value of our $S_8$ constraint up to $1σ$. For our fiducial model choices, the resultant uncertainties in $S_8$ are primarily degraded by the removal of scales, as well as the marginalization over the IA parameters. We demonstrate that our result is internally consistent and robust to different choices in calibrating the data, owing to methodological improvements in shear and redshift measurement, laying the foundation for next-generation cosmic shear programs.

Abbott, T. M.C. [Cerro-Tololo InterAmerican Obs.]↗

Evaluating the Effectiveness of an Ultrasonic Acoustic Deterrent in Reducing Bat Fatalities at Wind Energy Facilities

This project was designed to use thermal video cameras and fatality monitoring to evaluate the effectiveness of an ultrasonic acoustic deterrent (UAD) on bat activity and mortality, respectively. Our goals were to redesign the UAD device and installation infrastructure, determine the placement on wind turbines to optimize safety, compatibility and functionality, and to compare the mortality among the following conditions: Control (deterrents off and turbines feathered up to the manufacturer’s cut-in speed of 3.5 m/s), Deterrent (deterrents on and turbines feathered up to the manufacturer’s cut-in speed of 3.5 m/s), Curtailment (deterrents off and turbines feathered up to 5/ m/s), and combination (deterrents on and turbines feathered up to 5 m/s). The project was divided into a Feasibility Study and Comparative Study. The objectives for the Feasibility Study were to develop an installation strategy, redesign a previous iteration of a UAD to improve performance and weatherization, and test the effectiveness of the deterrents on bat activity. The Feasibility Study was intended to work out potential issues using a relatively small number of devices prior to manufacturing and installing numerous devices for a larger-scale comparative study. The division of the project into these separate studies was based on previous experience and the challenges of assessing the capabilities of an untested UAD. During the initial development and manufacturing of the UAD, NRG Systems decided to use a piezoelectric transducer rather than an electrostatic transducer, which was used by a previous device (i.e. Deaton UAD). NRG Systems conducted lab testing (i.e., IP67 or Ingress Protection) to ensure no water or dust ingress. In addition, shock/drop trials and variations in temperature exposure were conducted as part of the reliability testing. NRG Systems also developed a communications system to allow for continuous performance monitoring of the UADs. For the Feasibility Study, we installed 6 UADs on each of 2 Gamesa G90 2-MW wind turbines (Turbine 14 and 8) at the South Chestnut Wind Energy Facility, Pennsylvania and monitored activity under control and treatment (i.e. Deterrent) conditions using thermal video monitoring. There are two major sources of variation in bat activity (beyond the anticipated treatment effect): 1) environment around the turbines might inherently favor more activity at one than the other; 2) weather conditions on any given night or within season difference (e.g., migration later during the study period) might favor more activity on some nights than on other nights. Because we could only monitor two turbines on any night, we sought to control the potential influences of these two sources by alternating the turbine on which deterrents were activated each night. If there were no loss of data due to technical failures, this design would result in an equal number of deterrent and control nights at each turbine through the monitoring period, balancing the effects of both sources of variation. We compared the time bats spent and the number of events that occurred in overlapping cameras FOV as an indicator of risk, since 80% of the overlapping FOV of the cameras was in the RSA. Equipment failures, majority due to lightning, resulted in only 17 nights with useable data, with unbalanced treatment assignment within turbines and uneven distribution of treatment assignment throughout the observational period. This resulted in a confounding of treatment assignment and seasonal change. Deterrent treatment was measured at Turbine 14 on only 2 of the first 8 usable nights (spanning the period from 8/18-9/17), whereas 6 times on Turbine 8. From 9/18-927, deterrent was on at Turbine 14 on 6 of the remaining 10 nights, and 4 on Turbine 8. We recorded a total of 1,057 bats and observed a reduction in number of events and duration of events at the UAD-activated turbine when it was Turbine 14. When Turbine 8 had the UAD activated, we observed no difference in number or duration of events. Variation between turbines is not unusual and can cause issues when study designs have no true replication, i.e., multiple turbines per treatment. Within-turbine differences suggested a trend for reduced activity when UADs were activated, particularly for Turbine 14. These results may be caused by the overall higher bat activity at Turbine 8 and confounding of treatment assignment and seasonal trends. We mapped 58 bat events in 3-dimensional space (3D), 30 and 28 events during control and treatment conditions, respectively. We observed bats crossing the rotor plane under both control and treatment conditions and observed a total of 40 confirmed or near-collisions (i.e., target close to blade but no visual confirmation of a strike) out of a total of 1,491 medium and high confidence bat observations (880 control, 611 at treatment). Twice as many collisions/possible collisions were observed during control conditions. Given the challenges with the equipment and potential confounding of the data (i.e., different activity levels at the two wind turbines), we were unable to determine whether this initial turbine placement and orientation was optimal. Given no new information on how best to install the devices, we elected to use the same placement and orientation for the comparative study. For the Comparative Study, the objectives were to investigate the relative mortality rates among 4 treatments. We searched the area within 90 m of each turbine daily to recover the highest number of fresh fatalities possible. We were unable to detect a clear reduction in mortality from deterrents alone for any individual species. Surprisingly, mortality rate of the eastern red bat (Lasiurus borealis) was estimated to be 1.3–4.2 times as much when turbines were operating normally and UADs were on than when UADs were off. Reduction in mortality of all bat species combined due to curtailment of turbines was estimated to be between 0%–38%. This effect was nullified when, in addition to curtailment, UADs were on, with 95% confidence interval ranging from a 45% reduction to a 36% increase in mortality. This was likely due to the large proportion of eastern red bats in the total carcass population. Mortality of all low-frequency echolocating bats combined (i.e. hoary bat [L. cinereus], big brown bat [Eptesicus fuscus], silver-haired bat [Lasionycteris noctivagans]) relative to control was lower when curtailed (95% CI: 0%–74%), but the addition of UADs had no detectable effect (95%CI: 13%–79%). The combined treatment reduced mortality in silver-haired bats relative to control by 11%–99%, compared to curtailment (81% reduction–67% increase) or deterrent (82% reduction–67% increase) alone. Because silver-haired bats comprised a large proportion of low-frequency calling bats found during this study, a similar effect was seen for that group. The higher mortality observed for eastern red bats at UAD compared to control could have been caused by several factors, such as the effective range of the UAD, particularly at higher frequencies, behavior, positioning of the devices on the nacelle, or a combination of these. We used 3D thermal videography to compare control and UAD bat behavior from two turbines using a total of 203 3D bat-tracks across 34 nights. We recorded a similar number of bat-tracks between treatment groups, with 51% and 49% for control and UAD, respectively. Due to potential differences in bat behavior around spinning vs stationary turbine blades, we examined UAD effectiveness separately for non-operating turbines (feathered below cut-in speed of 3.5 m/s) and operating (normal operation above wind speed of 3.5 m/s). We found a higher proportion of bat-tracks at operating turbines (82%) compared to non-operating turbines (18%), although this does not account for overall time turbines were operating versus not. At non-operating turbines the UAD appears to be effective at reducing the amount of time, flight length, and number of passes through the rotor plane, compared to control. In addition, we found bats approached turbines similarly between control and treatment turbines, with 61% of control and 63% of UAD bat-tracks originating leeward of the hub. In contrast, at operating turbines, we saw little change in bat behavior in response to UADs. For example, we found an increase in the average duration of bat-tracks between non-operating and operating turbines for UAD but at control turbines we found average duration decreased once turbines became operational. Both control and UAD had a high proportion of bat-tracks that crossed the rotor plane (i.e., collision risk) originate from the windward side when turbines were operational 65% to 92%, respectively. Given that the UAD devices closest to the blades were orientated parallel to the blades, its possible bats were not exposed to the signal until they were close to the turbine blades, as suggested by the slightly higher mean duration within 5 meters of the blades for UAD turbines. Future research should consider concentrating UAD intensity on the areas of risk (i.e. blades) with enough buffer to allow bats to react to the sound before entering the rotor-swept area (RSA). In addition, investigating the potential of installing UAD units windward of the turbine blades (e.g. a hub-mounted UAD), particularly since even under control conditions, a relatively high proportion (65%) of crosses through the blade plane originated windward. 3D thermal videography provided valuable information on future testing strategies (e.g. device placement, UAD orientation) to improve UAD effectiveness when bats are at risk (i.e., operating wind turbines). Across the entire project we experienced issues with the operation and communication with the UADs. Most of the issues occurred during the Feasibility Study and were resolved prior to the Comparability Study. Additional challenges surfaced during the Comparability Study but were remedied immediately and are thought to have little impact on the results. We had logistical constraints at the project that limited our ability use traditional methods in our camera calibration. Several calibrations showed inaccurate scales, which may have been related to inadequate spatial coverage of “points” in the camera calibration volume. Because we were using actual video recordings of bats at a wind turbine, the behavior of bats could have concentrated “points” in specific areas of the turbine (i.e. leeward of nacelle), and limited “points” in other areas, resulting in camera calibration issues. We have plans to address these inconsistencies and improving the software and related methodologies by early 2020.

17 WIND ENERGY↗

Measuring Thread Timing to Assess the Feasibility of Early-Bird Message Delivery Across Systems and Scales

Early-bird communication is a communication/computation overlap technique that leverages fine-grained communication to improve application run-time. Communication is divided such that each individual thread can initiate transmission of its portion of the data upon completion rather than waiting for a dedicated communication phase. The benefit of early-bird communication depends on the completion timing of the individual threads: On the one hand, if all threads are complete at nearly the same time, the overheads of sending multiple messages will accumulate, leading to performance that is worse than if a single message had been sent. On the other hand, if thread completions are spread out in time, those that complete earlier can send data while others continue working, leading to performance that is better than if a single message had been sent. The challenge is that the completion times are currently unknown and can vary based on application, problem size, system software, and underlying hardware. In this paper, we address this lacuna by measuring and evaluating the potential overlap afforded by early-bird communication for a selection of proxy applications. These measurements help us understand whether a given application could benefit from early-bird communication. Here, we present our technique for gathering this data and evaluate data collected from three proxy applications: MiniFE, MiniMD, and MiniQMC. Each application is run on three systems with distinct CPU architectures and strong scales across three run sizes. To characterize the behavior of these workloads, we study the trends of thread timings at both a macro level, across all threads across all runs of an application, and a micro level, that is, within a single process of a single run. We observe that our tested applications exhibit significantly different thread arrival distributions. The machine used had a significant impact, with the window of potential overlap varying by as much as an order of magnitude.

97 MATHEMATICS AND COMPUTING↗

COMPUTATIONAL MODELING OF IGNITION AND PREMIXED FLAME PROPAGATION INITIATED BY A PRE-CHAMBER TURBULENT JET

Addressing the pressing need for reduced carbon emissions, Turbulent Jet Ignition (TJI) emerges as a promising technology for ultra-lean combustion, offering enhanced thermal efficiencies and minimized cyclic variability in spark-ignited engines. To facilitate rapid testing and integration of this technology, a robust computational modeling framework is crucial. This study delves into the predictive capabilities of computational models for main-chamber ignition and premixed flame propagation using a single-cycle TJI rig measured by Biswas et al. (Applied Thermal Engineering, vol 106, 2016). Employing an open-source compressible flow simulation solver with Large Eddy Simulation (LES) for turbulence modeling, the investigation integrates the conventional Laminar Finite Rate Chemistry (LFRC) model alongside the transported Probability Density Method (PDF) for turbulence-chemistry interaction. A fully-consistent Eulerian Monte-Carlo Fields (EMCF) method is utilized to approximate the transported PDF, while Interaction by Exchange with Mean is employed to close micro-mixing terms in stochastic differential equations. A reduced chemical reaction mechanism with 21 species and 84 reactions (DRM-19) is used for solving chemical kinetics, and a double Gaussian energy deposition model is used to approximate the spark ignition in the pre-chamber. An unstructured O-grid mesh with 0.3 million cells in the prechamber and 1 million cells in the main chamber is employed. Results are divided into two phases: pre-chamber initialization and full TJI simulations. Validation of the predicted pre-chamber flame propagation and the lean ignition in the main-chamber is carried out by using available experimental data. Under quiescent conditions, both the LFRC and transported PDF methods largely underestimate the flame speed and subsequent pressure growth in the pre-chamber. A linear momentum forcing technique is applied to investigate the impact of initial turbulence in the pre-chamber, demonstrating a notable influence on flame propagation. Fine-tuning of the forcing coefficient reproduces the sudden pressure growth observed in the experiment. The experimentally validated pre-chamber simulation serves as the initial condition for the full TJI simulations. It is found that the LFRC model fails to predict lean-ignition in the main-chamber, resulting in a misfiring event. Incorporation of turbulence-chemistry interaction using the transported PDF method substantially improves the prediction of the ignition event in the main-chamber, achieving fair qualitative agreement and quantitative validation of combustion parameters within ±10% of the reported experimental data. The rich simulation results consisting of a full set of statistical description of the thermo-chemical states enable us to gain deep insights into the ignition mechanisms in the main chamber, which is limited when done experimentally. A novel dual ignition phenomenon is revealed in the TJI rig for the first time. Initially, a primary ignition kernel is formed at a downstream location which eventually detaches from the main jet. As the jet momentum decreases, a secondary ignition event follows, this time at a more upstream location which eventually combines with the primary ignition kernel to form a single connected flame front. Investigation of these ignition sequences in chemical composition space reveal distinct differences between the two. The primary ignition event in the main-chamber is followed by a large concentration of active radicals from the pre-chamber jet, accelerating the chain-branching steps, characterizing what has been referred to as flame ignition. In contrast, the secondary ignition occurs in the absence of active radicals in the pre-chamber jet, hence characterized as jet ignition. Further analysis of the effect of pre-chamber jet characteristics on lean ignition in the main-chamber is conducted by setting up cases with different initial pressure ratios (por) between the two chambers, a non-dimensional parameter, ranging from 1.2 to 3.2. As the initial pressure ratio increases, jet momentum increases, with dual ignition observed in cases above por= 2.2. Case with por= 3.2 lead to misfiring. The effect of ignition sequence on global combustion characteristics of TJI is analyzed. Dual ignition events lead to non-monotonicity in combustion characteristics such as global reaction progress variable, flame penetration, and global heat release rate. In dual ignition events, although the rate of fuel consumption and global heat release rate is initially lower, the secondary ignition leads to a sudden increase in flame surface area, resulting in a sudden jump and promoting the overall performance of the TJI system.

42 ENGINEERING↗

DECOVALEX-2023: Task E Final Report

This is the Task E final report for DECOVALEX-2023. Task E is focused on understanding thermal, two-phase hydrological, and mechanical (TH2M) processes, especially related to predicting brine migration in the excavation damaged zone around a heated excavation in salt. Salt is attractive as a disposal medium for radioactive waste because it is self-healing and is essentially impermeable and essentially non-porous in the far field (away from excavations). Investigation of the short-term (days to years) near-field (centimeters to tens of meters) behavior of salt is important for radioactive waste disposal because this early period strongly controls the amount of brine in a salt repository. Brine leads to corrosion of waste forms and waste packages, and possible dissolution of radionuclides with brine transport being a potential transport vector to the accessible environment. The main test case used in Task E is the ongoing Brine Availability Test in Salt (BATS) heater test located underground at the Waste Isolation Pilot Plant (WIPP) near Carlsbad, New Mexico, USA. The Task was divided into a series of Steps. Step 0 was an introduction to processes in salt, that included matching historical unheated brine inflow data from boreholes at WIPP and matching temperature observations during BATS heater test 1a. Step 1 included validation of models against a thermo-poroelastic analytical solution relevant to heated boreholes in salt, and two-phase flow around an excavation in salt. Step 2 required all the individual components covered in steps 0 and 1 to come together to match observed brine inflow behavior during the BATS 1a heater test. There were a range of approaches from the teams, from mechanistic to prescriptive. Given the uncertainties in the problem, some teams used one- or two-dimensional models of the processes, while other teams included more geometrical complexity in three-dimensional models. The key learning points from Task E have been: • Heat conduction through salt typically requires non-linear thermal conductivity (as a function of temperature), but most models do a good job matching observations, given appropriate adjustments to the applied power and some thermocouple locations. • Thermal pressurization requires coupled thermal-hydrological-mechanical (THM) responses that consider the thermal expansion of the fluid and solid phases. • Initialization of two-phase flow models around a borehole or excavation in salt are more realistically represented as “wetting up”, rather than “drying down” (i.e., the initial state after excavation is mostly dry, rather than mostly wet). • The BATS 1a heater test includes a significant release of brine after the end of heating, which requires a large increase in permeability to recreate. Task E has been a great learning experience for all the teams involved, and feedback from the modeling teams has led to changes in the design of follow-on BATS experiments, which are now ongoing underground at WIPP. There was a balance throughout the task between freedom to model phenomena how each team saw fit, and prescriptiveness in problem design to bring the modeling teams closer together to allow attribution of smaller differences between models to different modeling choices. The modeling approaches seem to go through two phases: an early phase of discovery or testing, and a later phase of refinement and improvement. In future modeling efforts, different field data could be used (e.g., BATS 2) and more time should be included in the processes for teams to make multiple model refinement or even significant changes to their conceptual model or setup, based on lessons learned from the modeling exercise.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗