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PAVplotR

PAVplotR is an R package that accepts as input a haploid VCF and, for a user-specified bin size, calculates proportional presence-absence variation (PAV). First, all variants in the file are considered to calculate an expanded coordinate system that accounts for insertions relative to the reference sequence. Next, for each sample in the VCF, proportional PAV is summarized per bin in the expanded coordinate system and finally, PAV is plotted such that rows are samples and columns are bins with the x-axis (chromosome position) labeled according to the reference haplotype's original coordinate system.

Harder, Avril↗

Predicting September Arctic Sea Ice: A Multimodel Seasonal Skill Comparison

This study quantifies the state of the art in the rapidly growing field of seasonal Arctic sea ice prediction. A novel multimodel dataset of retrospective seasonal predictions of September Arctic sea ice is created and analyzed, consisting of community contributions from 17 statistical models and 17 dynamical models. Prediction skill is compared over the period 2001–20 for predictions of pan-Arctic sea ice extent (SIE), regional SIE, and local sea ice concentration (SIC) initialized on 1 June, 1 July, 1 August, and 1 September. This diverse set of statistical and dynamical models can individually predict linearly detrended pan-Arctic SIE anomalies with skill, and a multimodel median prediction has correlation coefficients of 0.79, 0.86, 0.92, and 0.99 at these respective initialization times. Regional SIE predictions have similar skill to pan-Arctic predictions in the Alaskan and Siberian regions, whereas regional skill is lower in the Canadian, Atlantic, and central Arctic sectors. The skill of dynamical and statistical models is generally comparable for pan-Arctic SIE, whereas dynamical models outperform their statistical counterparts for regional and local predictions. The prediction systems are found to provide the most value added relative to basic reference forecasts in the extreme SIE years of 1996, 2007, and 2012. SIE prediction errors do not show clear trends over time, suggesting that there has been minimal change in inherent sea ice predictability over the satellite era. Overall, this study demonstrates that there are bright prospects for skillful operational predictions of September sea ice at least 3 months in advance.

54 ENVIRONMENTAL SCIENCES↗

Criticality in the Shallow-to-Deep Transition of Simulated Tropical Marine Convection

Idealized simulations of tropical, marine convection depict shallow, nonprecipitating cumuli located beneath the 0°C level transitioning into cumulonimbi that reach up to 12 km and higher. The timing of the transition was only weakly related to environmental stability, and 13 of the 15 simulations run with 5 different lapse-rate profiles had rain develop at nearly the same time after model start. The key quantity that apparently controlled deep convective formation was vertical acceleration inside cloudy updrafts between cloud base and the 0°C level. Below a critical value of updraft vertical acceleration, little rainfall occurred. Just as the domain-mean updraft acceleration reached the critical value, the first convection quickly grew to past 12 km altitude. Then, as acceleration increased above the critical value, rain rate averaged in the model domain increased quickly over about a 3-h-long period. The specific value of the critical updraft acceleration depended on how updrafts were defined and in what layer the acceleration was averaged; however, regardless of how criticality was defined, a robust relationship between domain-mean updraft vertical acceleration and rain rate occurred. Positive acceleration of updrafts below the 0°C level was present below 2.75 km and was largest in the 500 m above cloud base. However, the maximum difference between updraft and environmental temperatures occurred between 2 and 3 km. The domain-mean Archimedean buoyancy of updrafts relative to some reference state was a poor predictor for domain-mean rain rate. In conclusion, the exact value of the critical updraft acceleration likely depends on numerous other factors that were not investigated.

54 ENVIRONMENTAL SCIENCES↗

Introduction to special section: Induced seismicity

Induced seismicity refers to earthquakes related to anthropogenic activities such as wastewater disposal, hydraulic fracturing, and geothermal energy production. In Oklahoma, wastewater disposal is considered to have caused more than 100 earthquakes of magnitude 4 and above (M4+) since 2010. Similarly, over 50 such events have been recorded in the Permian Basin of Texas and New Mexico. Additionally, some of these earthquakes have magnitudes exceeding 5.0, including a magnitude 5.8 event in Pawnee, Oklahoma, in a magnitude 5.6 event in the Peace River Oil Sands Area in Alberta, and a magnitude 5.4 event in the Delaware Basin of Texas.

58 GEOSCIENCES↗

Leaf sample detail, Feb2016-May2016, PA-SLZ, PA-PNM, PA-BCI: Panama

This data package contains details of the date, location, species and photographs of leaf samples collected on a monthly basis from Feb to May 2016 from Parque Natural Metropolitano (PA-PNM), Barro Colorado Island (PA-BCI) and Bosque Protector San Lorenzo (PA-SLZ) in Panama. Data from BCI only available for March. This data was collected as part of the 2016 El Niño-Southern Oscillation (ENSO) campaign. Included in this data package are an Excel file with data (2016ENSO_Panama_LeafSamples) and two Excel files with associated metadata. Sample photos are included in five zip files, organized by month and site. Also included is a Word document (Metadata_description_2016_ENSO_Panama) with details such as data collection methods, equipment used, and site information. Data to be used as a reference to linking related datasets including leaf water potential, leaf spectra, LMA, gas exchange and leaf chemistry (CHN, NSC). Most leaves were sampled from sunlit canopy trees. VERSION 2 update. The identification of a species from the PNM site has been corrected as follows: the identification of the tree initially identified as Pseudosamanea guachapele (ALBIED) has been revised to Albizia adinocephala (ALBIAD). The updated data package includes revised data, metadata and protocol documents updated to reflect this change.

54 ENVIRONMENTAL SCIENCES↗

Effects of Shallow-Velocity Reductions on 3D Propagation of Seismic Waves

Abstract We perform 3D simulations of seismic wavefields to clarify effects of strong reductions of shallow velocities on long-period seismic waves. The simulations use a reference Community Velocity Model of southern California and a modified version with strong velocity reductions in the top 500 m of the Los Angeles basin. Differences between wavefields generated by 10 earthquakes in the reference and perturbed models are analyzed. Velocity changes are estimated by measuring relative time shifts between reference and perturbed seismograms using wavelet cross-correlation spectra. The results indicate that strong localized temporal velocity drops near the surface, such as those observed during strong ground motions, may generate regional perturbations of wavefields at periods up to 20 s. These perturbations may be misinterpreted as generated by temporal changes at seismogenic depths. The results also have important implications for waveform tomography studies.

Geochemistry & Geophysics↗

Heterogeneous mantle effects on the behavior of SmKS waves and outermost core imaging

Seismic traveltime anomalies of waves that traverse the uppermost 100–200 km of the outer core have been interpreted as evidence of reduced seismic velocities (relative to radial reference models) just below the core–mantle boundary (CMB). These studies typically investigate differential traveltimes of SmKS waves, which propagate as P waves through the shallowest outer core and reflect from the underside of the CMB m times. The use of SmKS and S(m- 1)KS differential traveltimes for core imaging are often assumed to suppress contributions from earthquake location errors and unknown and unmodelled seismic velocity heterogeneity in the mantle. The goal of this study is to understand the extent to which differential SmKS traveltimes are, in fact, affected by anomalous mantle structure, potentially including both velocity heterogeneity and anisotropy. Velocity variations affect not only a wave’s traveltime, but also the path of a wave, which can be observed in deviations of the wave’s incoming direction. Since radial velocity variations in the outer core will only minimally affect the wave path, in contrast to other potential effects, measuring the incoming direction of SmKS waves provides an additional diagnostic as to the origin of traveltime anomalies. Here we use arrays of seismometers to measure traveltime and direction anomalies of SmKS waves that sample the uppermost outer core. We form subarrays of EarthScope’s regional Transportable Array stations, thus measuring local variations in traveltime and direction. We observe systematic lateral variations in both traveltime and incoming wave direction, which cannot be explained by changes to the radial seismic velocity profile of the outer core. Moreover, we find a correlation between incoming wave direction and traveltime anomaly, suggesting that observed traveltime anomalies may be caused, at least in part, by changes to the wave path and not solely by perturbations in outer core velocity. Modelling of 1-D ray and 3-D wave propagation in global 3-D tomographic models of mantle velocity anomalies match the trend of the observed traveltime anomalies. Overall, we demonstrate that observed SmKS traveltime anomalies may have a significant contribution from 3-D mantle structure, and not solely from outer core structure.

58 GEOSCIENCES↗

Methodology for Digital Image Correlation and Infrared Measurement of Melting Aluminum Bars

Ultimately, our experiment measures two quantities on an aluminum bar: motion (which modeling must predict) and temperature (which sets thermal boundary conditions). For motion, stereo DIC is a technique to use imaging data to provide displacements relative to a reference image down to 1/100th of a pixel. We use a calibrated infrared imaging method for accurate temperature measurements. We will be capturing simultaneous data and then registering temperature data in space to the same coordinate system as the displacement data. While we will later show that our experiments are repeatable, indicating that separate experiments for motion and temperature would provide similar data, the simultaneous and registered data removes test to test variability as a source of uncertainty for model calibration and reduces the number of time-consuming tests that must be performed.

36 MATERIALS SCIENCE↗

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M –1 cm –1 ) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Linking Pharmacogenomic Information on Drug Safety and Efficacy with Ethnic Minority Populations

Numerous prescription drugs’ labeling contains pharmacogenomic (PGx) information to aid health providers and patients in the safe and effective use of drugs. However, clinical studies for such PGx biomarkers and related drug doses are generally not conducted in diverse ethnic populations. Thus, it is urgently important to incorporate PGx information with genetic characteristics of racial and ethnic minority populations and utilize it to promote minority health. In this project a bioinformatics approach was developed to enhance the collection of PGx information related to ethnic minorities to pave the way toward understanding the population-wide utility of PGx information. To address this challenge, we first gathered PGx information from drug labels. Second, we extracted data on the allele frequency information of genetic variants in ethnic minority groups from public resources. Then, we collected published research articles on PGx biomarkers and related drugs for reference. Finally, the data were integrated and formatted to build a new PGx database containing information on known drugs and biomarkers for ethnic minority groups. This database provides scientific information needed to evaluate available PGx information to enhance drug dose selection and drug safety for ethnic minority populations.

60 APPLIED LIFE SCIENCES↗

Systematically tracking the hourly progression of large wildfires using GOES satellite observations

Abstract. In the western United States, prolonged drought, a warming climate, and historical fuel buildup have contributed to larger and more intense wildfires as well as to longer fire seasons. As these costly wildfires become more common, new tools and methods are essential for improving our understanding of the evolution of fires and how extreme weather conditions, including heat waves, windstorms, droughts, and varying levels of active-fire suppression, influence fire spread. Here, we develop the Geostationary Operational Environmental Satellites (GOES)-Observed Fire Event Representation (GOFER) algorithm to derive the hourly fire progression of large wildfires and create a product of hourly fire perimeters, active-fire lines, and fire spread rates. Using GOES-East and GOES-West geostationary satellite detections of active fires, we test the GOFER algorithm on 28 large wildfires in California from 2019 to 2021. The GOFER algorithm includes parameter optimizations for defining the burned-to-unburned boundary and correcting for the parallax effect from elevated terrain. We evaluate GOFER perimeters using 12 h data from the Visible Infrared Imaging Radiometer Suite (VIIRS)-derived Fire Event Data Suite (FEDS) and final fire perimeters from the California's Fire and Resource Assessment Program (FRAP). Although the GOES imagery used to derive GOFER has a coarser resolution (2 km at the Equator), the final fire perimeters from GOFER correspond reasonably well to those obtained from FRAP, with a mean Intersection-over-Union (IoU) of 0.77, in comparison to 0.83 between FEDS and FRAP; the IoU indicates the area of overlap over the area of the union relative to the reference perimeters, in which 0 is no agreement and 1 is perfect agreement. GOFER fills a key temporal gap present in other fire tracking products that rely on low-Earth-orbit imagery, where perimeters are available at intervals of 12 h or longer or at ad hoc intervals from aircraft overflights. This is particularly relevant when a fire spreads rapidly, such as at maximum hourly spread rates of over 5 km h−1. Our GOFER algorithm for deriving the hourly fire progression using GOES can be applied to large wildfires across North and South America and reveals considerable variability in the rates of fire spread on diurnal timescales. The resulting GOFER product has a broad set of potential applications, including the development of predictive models for fire spread and the improvement of atmospheric transport models for surface smoke estimates. The resulting GOFER product has a broad set of potential applications, including the development of predictive models for fire spread and the improvement of atmospheric transport models for surface smoke estimates (https://doi.org/10.5281/zenodo.8327264, Liu et al., 2023).

Geology↗

Reverse Osmosis Simulation Data

This dataset consists of computational fluid dynamics (CFD) output for various spacer configurations in a feed-water channel in reverse osmosis (RO) applications. Feed-water channels transport brine solution to the RO membrane surfaces. The spacers embedded in the channels help improve membrane performance by disrupting the concentration boundary layer growth on membrane surfaces. Refer to the "Related Work" resource below for more details. This dataset considers a feed-water channel of length 150mm. The inlet brine velocity and concentration are fixed at 0.1m/s and 100kg/m3 respectively. The diameter of the cylindrical spacers is fixed as 0.3mm and six varying inter-spacer distances of 0.75mm, 1mm, 1.5mm, 2mm, 2.5mm, and 3mm are simulated. The dataset comprising the steady, spatial fields of solute concentration, velocity, and density near each spacer is placed in the folder corresponding to the spacer configuration considered. We run two sets of CFD simulations and include the outputs from both sets for each configuration: (1) with a coarser mesh, producing low-resolution (LR) data of spatial resolution 20x20, and (2) with a finer mesh, producing high-resolution (HR) data of spatial resolution 100x100. These data points can be treated as images with the quantities of interest as their channels and can be used to train machine learning models to learn a mapping from the LR images as inputs to the HR images as outputs.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DarkQuest: A dark sector upgrade to SpinQuest at the 120 GeV Fermilab Main Injector

Expanding the mass range and techniques by which we search for dark matter is an important part of the worldwide particle physics program. Accelerator-based searches for dark matter and dark sector particles are a uniquely compelling part of this program as a way to both create and detect dark matter in the laboratory and explore the dark sector by searching for mediators and excited dark matter particles. This paper focuses on developing the DarkQuest experimental concept and gives an outlook on related enhancements collectively referred to as LongQuest. DarkQuest is a proton fixed-target experiment with leading sensitivity to an array of visible dark sector signatures in the MeV-GeV mass range. Because it builds off of existing accelerator and detector infrastructure, it offers a powerful but modest-cost experimental initiative that can be realized on a short timescale.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Graphical Optimization of Spectral Shift Reconstructions for Optical Backscatter Reflectometry

Optical backscatter reflectometry (OBR) is an interferometric technique that can be used to measure local changes in temperature and mechanical strain based on spectral analyses of backscattered light from a singlemode optical fiber. The technique uses Fourier analyses to resolve spectra resulting from reflections occurring over a discrete region along the fiber. These spectra are cross-correlated with reference spectra to calculate the relative spectral shifts between measurements. The maximum of the cross-correlated spectra—termed quality—is a metric that quantifies the degree of correlation between the two measurements. Recently, this quality metric was incorporated into an adaptive algorithm to (1) selectively vary the reference measurement until the quality exceeds a predefined threshold and (2) calculate incremental spectral shifts that can be summed to determine the spectral shift relative to the initial reference. Using a graphical (network) framework, this effort demonstrated the optimal reconstruction of distributed OBR measurements for all sensing locations using a maximum spanning tree (MST). By allowing the reference to vary as a function of both time and sensing location, the MST and other adaptive algorithms could resolve spectral shifts at some locations, even if others can no longer be resolved.

47 OTHER INSTRUMENTATION↗

Ceramic Composite Inert Matrix Fuel Forms in High-Temperature Gas-Cooled Microreactors

Here, this work optimizes micro-prismatic high-temperature gas reactor (HTGR) designs to reduce the energy-normalized mass of spent nuclear fuel (SNF) and high-level waste (HLW) produced. The optimization was performed for the current graphite moderator and an inert matrix fuel (IMF) concept employing different composite moderators in a prismatic design architecture. The fuel matrix is magnesium oxide (MgO) with entrained tristructural-isotropic (TRISO) fuel. The moderator materials, including beryllium oxide (MgO-BeO) and beryllium (MgO-Be) at 40 vol % loading and yttrium hydride (MgO-YH x=1.9 ) and zirconium hydride (MgO-ZrH x=1.9 ) at 15 vol % loading, were entrained within the MgO host matrix. A generic graphite micro-prismatic HTGR is used as the baseline point design where the external dimensions are held constant. The composite moderator designs use 19.9% enriched uranium nitride TRISO fuel and hexagonal assemblies. For each IMF concept, an optimization study was performed to maximize the discharge burnup of the fuel by varying the TRISO packing fraction and the lattice pitch of the assemblies. The mass of SNF and HLW, other waste metrics, fuel cost, environmental impact metrics, and the activity of the SNF and HLW at 100 years and 100 000 years were calculated for the optimized IMF and graphite reference designs. The IMF results were subsequently compared to those of the graphite reference and the values for a light water reactor (LWR) and a small modular LWR. For the SNF and HLW, all the IMF concepts and the graphite reference produced less waste compared to the traditional LWR designs. However, the IMF concepts outperformed the graphite reference regarding the mass of SNF and HLW. For the other waste metrics, the IMF concepts showed reductions in fuel cost with improved environmental metrics relative to the graphite reference. Overall, the IMF concepts significantly reduced the SNF and HLW produced per unit of energy generated compared to traditional LWR designs.

TRISO↗

A deep decarbonization framework for the United States economy – a sector, sub-sector, and end-use based approach

Achieving the United States' target of net-zero greenhouse gas emissions by 2050 will require technological transformations and energy sector mitigation. To understand the role of dynamically evolving technologies, identify synergies and dissonance and the effect of allocating limited low-carbon biomass resources in decarbonizing the U.S. economy, we developed the Decarbonization Scenario Analysis Model. A Life Cycle Assessment based approach is implemented considering the U.S. economy as the functional unit, to estimate greenhouse gas mitigation potential for projected energy demand based on several sector-level and cross-sectoral decarbonization pathways. Direct and supply-chain emissions are accounted, resulting from changes in patterns of energy generation and consumption, technology breakthroughs, and reductions in fugitive emissions over time at the granularity of economic sectors, sub-sectors, and end-use. Decarbonization strategies are implemented over a reference case developed using Energy Information Administration (EIA AEO) projection of economic activities for 2020–2050. Based on the considered scenarios, 80–90% economy-wide decarbonization relative to the 2020 reference case is projected. Electrification, low-carbon fuels, and reduction of fugitive emissions play the most significant role to decarbonization. The majority of the remaining emissions are accounted to the supply-chain and end-use emissions from natural gas and diesel fossil-based fuels in heavy duty transportation and heavy industries, highlighting the need for developing low-carbon and carbon-negative alternatives to mitigate those fossil-based carbon emissions.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Hydrogen Infrastructure Analysis for the Port Applications [Slides]

The International Maritime Organization has committed to 50% reduction in GHG emissions by 2050 worldwide as of 2023. This analysis includes performing an inventory and modeling efforts to understand the energy, equipment and cost requirements to support decarbonization of cargo handling and shore power at U.S. Ports, along with assessment of zero- and near- zero emission fuel supplies at or near U.S. ports focused upon Hydrogen technologies. Initial market assessment for ocean going vessels for harbor support and ocean-going vessels is explored. An energy analysis is performed on the port system using a holistic approach and considering the port as an entire ecosystem that functions as a transportation and energy node. Presently, a comprehensive view is lacking for future analysis efforts, this analysis seeks to address this gap in data by evaluating four representative port types and the potential for utilizing hydrogen for the maritime industry. Every port is different, but broadly they could be bracketed into reference cases with scaling factors for the relative size of the port operations. These reference ports are for future use, potentially as baselines for analysis and development of demonstration programs. An equipment inventory for each reference port type (container, bulk, breakbulk, and inland waterway) is presented. A comparative analysis of fuel cell electric and battery electric equipment is conducted based on the following criteria: technology readiness level, refueling/charging time, operational range, energy consumption, and fuel cost savings compared to baseline internal combustion engine equipment. The tradeoffs and synergies between two alternative powertrains is highlighted. Based on energy and infrastructure analysis, average and high equipment utilization profiles across different port types is identified and quantified baseline fuel and electricity demand for various decarbonization scenarios. Based on the portfolio of equipment converted to fuel cell electric, the estimates of initial capital investment are provided for hydrogen refueling stations across ports. An energy demand model is developed that predicts well the all-electric cargo handling equipment annual energy consumption for ports with annual tonnage under 2 million twenty-foot equivalent units (TEUs). The model is a good rubric to follow for further energy demand models that can create a scalable solution to understand the energy needs of cargo handling equipment, whether they are all-electric, hydrogen fuel cell, or powered by another fuel-type. Zero and near-zero emission fuel supply at ports is evaluated looking into the characteristics of hydrogen, ammonia, and methanol as an alternative fuel, as well as the bunkering status. The readiness of reference ports to produce ammonia or methanol and bunker the fuel is examined based on the framework developed by the Global Maritime Forum and Rocky Mountain Institute.

08 HYDROGEN↗

Solvent independent reference electrodes for use with non-aqueous electrolytes

The present disclosure relates to a method for forming a reference electrode for use in electrochemical testing applications. The method may involve positioning a porous frit against one end of a hollow tube, and securing the frit and the hollow tube to one another to form an assembly. The method may further involve forming a silver sulfide coating on a silver wire to produce a silver sulfide coated silver wire. The method may further involve filling the hollow tube with a non-aqueous solution, and inserting at least a portion of the silver sulfide coated silver wire into the non-aqueous solution in the hollow tube.

Horwood, Corie↗