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EJ/SJ Dynamic Datasets for CCS Systems and the Energy Transition Atlas Web Tool
For presentation at the 2023 FECM / NETL Carbon Management Research Project Review Meeting, Pittsburgh, PA, August 30-September 1, 2023.
Containerization in the ATLAS Offline Code Management System
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Cloud Atlas: An Interactive Apparatus for Air Quality Awareness
This paper introduces a research project of a kinetic apparatus that translates collected air quality data to users. The kinetic mechanical skeleton is embedded with processors and electronics, and constantly changes its form according to air quality data collected online via a web crawler. By translating invisible environmental conditions, such as air quality data into morphological, colorful, and acoustic changes for the device, the participants can be aware of the phenomenon of air pollution in real time. The interac- tions between participants' movements and the changes of the device imply how human behaviors can affect the state of the atmosphere. As a result, the device evokes public awareness and participation in environmental issues through tangible experiences. This research aims to explore a new kind of responsive architecture that acts as a medium between invisible environments and inhabitants.
Evolution of the ATLAS event data model for the HL-LHC
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Physics Division Strategic Plan Fiscal Years 2020-2024
The vision of the Physics Division (PHY) at Argonne National Laboratory is to continue enhancing its role as a world-leading institution in basic nuclear physics research and its applications. Key to this vision is for PHY to continue to safely and effectively operate and evolve the capabilities of the Argonne Tandem Linac Accelerator System (ATLAS) facility to best serve its users. ATLAS is the Department of Energy (DOE) accelerator facility for low-energy nuclear physics research. The research carried out by PHY covers many themes in contemporary science but can be distilled into five areas of focus. These themes are interconnected, with continuously evolving synergies between the various groups and facilities in PHY and the broader Laboratory. This five-year strategic plan serves to illustrate our current capabilities and new directions related to these five areas of focus (ATLAS also develops an independent strategic plan): Accelerator research and design. The goal of this theme is to design, fabricate, test, and implement novel accelerator systems, with a focus on high-intensity ion and electron systems. These R&D activities have led to enhancements in the ATLAS accelerator system. Among others, the division’s accelerator systems are in use or planned for use at Fermilab, the Advanced Photon Source, and in a broad variety of applications at the Facility for Rare Isotope Beams (FRIB). Atom trapping and fundamental symmetries. The goal of this theme is to explore and exploit the uses of advanced laser cooling and trapping techniques to manipulate atoms. There are three main areas of focus. First is in the application of the atom trap trace analysis (ATTA) technique for age determination of groundwater and ice by using radio-krypton dating. The next two trapping-based programs involve tests of fundamental symmetries in nature: the cooling and trapping of radium-225 with the aim of determining limits on an observation of its electric dipole moment and precision measurements of the beta decay properties of helium-6 to set limits on the tensor coupling constant. This is complemented by measurements of similar properties in lithium-8 and boron-8. Nuclear astrophysics. The goal of this theme is to enhance our understanding of how elements are created in the universe via explosive nucleosynthesis and how stars evolve. To meet the challenges of this theme, many of the capabilities of ATLAS are being enhanced, including the development of new beams through a new in-flight separator (RAISOR) and the anticipated neutron-generator upgrade of the Californium Rare Isotope Breeder Upgrade facility (nuCARIBU). These are coupled to state-of-the-art instruments such as the Canadian Penning Trap, Helical Orbit Spectrometer, Gammasphere, GRETINA, Multi-Sampling Ionization Chamber, the Fragment Mass Analyzer, and Argonne Gas-filled Fragment Analyzer, and a new low-background experimental area for decay studies. Nuclear structure. The goal of this theme is to understand the structure of nuclei, both stable and radioactive, in terms of single-particle properties, their shapes, and the dynamics governing reactions between them. These include questions such as what are the limits of nuclear stability and what are the properties of super heavy nuclei. As with the nuclear astrophysics theme, the capabilities of ATLAS, guided by the ATLAS user community, are continuously being enhanced to this end. The Division has strategic initiatives to play a leading role in the development of instrumentation and research programs at the FRIB. Quantum chromodynamics (QCD) and hadron physics. The goal of this theme is to lead major research programs focused on revealing the quark and gluon structure of protons, neutrons, nuclei, and short-lived mesons and baryons. These involve major programs at Jefferson Lab, Fermilab, and smaller facilities. They are complemented by theoretical endeavors centered on the question of how hadrons and their properties emerge from QCD. Out of these activities arise strategic initiatives to play a major role in the forthcoming Electron-Ion Collider (EIC).
Collider Physics (Final Technical Report)
The UNM members of the ATLAS Collaboration published a comprehensive study of ATLAS Pixel leakage current recorded from the beginning of Run 1 through the end of Run 2. This study depended upon a hardware system that was designed and built by UNM and installed by us in the ATLAS cavern. The study compared ATLAS data to predictions by the Hamburg Model, thereby leveraging ATLAS data to improve a widely used simulation that has application to other LHC experiments as well as silicon systems in radiation environments outside HEP applications. Having validated the model in this way, we then used it to make predictions for ATLAS tracker design and operational conditions in Run 3 and beyond.
Production of C-14 and Stable Ion Beams at the Argonne Tandem Linac Accelerator System with the ECR3 Ion Source
The Argonne Tandem Linac Accelerator System (ATLAS) at Argonne National Laboratory (ANL) paused production of carbon-14 ion beams with the removal of the Tandem Van de Graaff in 2013. Installation of ECR3, an Electron Cyclotron Resonance Ion Source, returned that production capability to ATLAS, with the first C-14 beam delivered in December 2020. Information is presented on C-14 beam current, gas consumption and N-14 filtering techniques using stripping foils at different sections of ATLAS. ECR3 also fulfilled the operational goal of adding flexibility to ATLAS stable beam production capabilities. Beneficial impacts to ATLAS operation, beam development and experimental programs are discussed.
Automated Calibration for Rapid Optical Spectroscopy Sensor Development for Online Monitoring
An automated platform has been developed to assist researchers in the rapid development of optical spectroscopy sensors to quantify species from spectral data. This platform performs calibration and validation measurements simultaneously. Real-time, in situ monitoring of complex systems through optical spectroscopy has been shown to be a useful tool; however, building calibration models requires development time, which can be a limiting factor in the case of radiological or otherwise hazardous systems. While calibration time can be reduced through optimized design of experiments, this study approached the challenge differently through automation. The ATLAS (Automated Transient Learning for Applied Sensors) platform used pneumatic control of stock solutions to cycle flow profiles through desired calibration concentrations for multivariate model construction. Additionally, the transients between desired concentrations based on flow calculations were used as validation measurements to understand model predictive capabilities. This automated approach yielded an incredible 76% reduction in model development time and a 60% reduction in sample volume versus estimated manual sample preparation and static measurements. The ATLAS system was demonstrated on two systems: a three-lanthanide system with Pr/Nd/Ho representing a use case with significant overlap or interference between analyte signatures and an alternate system containing Pr/Nd/Ni to demonstrate a use case in which broad-band corrosion species signatures interfered with more distinct lanthanide absorbance profiles. Both systems resulted in strong model prediction performance (RMSEP < 9%). Lastly, ATLAS was demonstrated as a tool to simulate process monitoring scenarios (e.g., column separation) in which models can be further optimized to account for day-to-day changes as necessary (e.g., baseline correction). Ultimately, ATLAS offers a vital tool to rapidly screen monitoring methods, investigate sensor fusion, and explore more complex systems (i.e., larger numbers of species).
Gulf of Mexico Miocene CO2 Site Characterization Mega Transect
The project Gulf of Mexico Miocene CO2 Site Characterization Mega Transect is one of 9 site characterization projects that were implemented as part of ARRA (American Recovery and Reinvestment Act). Data from this project was used to improve resolution of data in NATCARB in the area of study. Data related to this study has already been incorporated in NATCARB Atlas. The University of Texas at Austin study focused on (1) collecting high-resolution, 3-D (HR3D) seismic datasets of the shallow geologic section to evaluate the capacity of potential reservoirs and the sealing capacity of the confining system, and (2) producing a regional CO2 atlas of Miocene age units of the upper Texas coast submerged lands (southeast Texas). The goal of the study was to evaluate the capability of the Miocene age geologic section of Texas submerged lands to permanently store large volumes of anthropogenic CO2. The geographic locations of three HR3D, “P-Cable” seismic surveys collected in the near-shore waters of southeast Texas offers a vertical and horizontal view (data “cube”) example from the second survey. The dataset's high quality allowed for defining recognizable geologic morphologies (shapes) and possible fluid content, which are important for determining an area’s prospects for geologic storage. The regional CO2 atlas of Miocene age units highlights several topics, including: (1) a regional analyses of petroleum systems as analogs for CO2 storage; (2) petrography, petrology, and extent of confining systems of the Miocene section; (3) static capacity estimate; and (4) examples of characterization methodologies of prospect areas. The HR3D datasets and regional analyses within the CO2 atlas of the offshore Texas Miocene provide a sound basis for a future generation of specific CO2 prospects in the study area.
The Southern Stellar Stream Spectroscopic Survey (S{sup 5}): Chemical Abundances of Seven Stellar Streams
We present high-resolution Magellan/MIKE spectroscopy of 42 red giant stars in seven stellar streams confirmed by the Southern Stellar Stream Spectroscopic Survey (S {sup 5}): ATLAS, Aliqa Uma, Chenab, Elqui, Indus, Jhelum, and Phoenix. Abundances of 30 elements have been derived from over 10,000 individual line measurements or upper limits using photometric stellar parameters and a standard LTE analysis. This is currently the most extensive set of element abundances for stars in stellar streams. Three streams (ATLAS, Aliqa Uma, and Phoenix) are disrupted metal-poor globular clusters, although only weak evidence is seen for the light-element anticorrelations commonly observed in globular clusters. Four streams (Chenab, Elqui, Indus, and Jhelum) are disrupted dwarf galaxies, and their stars display abundance signatures that suggest progenitors with stellar masses ranging from 10{sup 6} to 10{sup 7} M {sub ⊙}. Extensive description is provided for the analysis methods, including the derivation of a new method for including the effect of stellar parameter correlations on each star’s abundance and uncertainty. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.
LungMAP Portal Ecosystem: Systems-level Exploration of the Lung
An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular, imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multi-omics data and a diverse collection of image data that span mammalian lung development, and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, mouse), to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, re-analysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). Finally, as this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP and external research efforts.
Connectivity‐based parcellation of normal and anatomically distorted human cerebral cortex
Abstract For over a century, neuroscientists have been working toward parcellating the human cortex into distinct neurobiological regions. Modern technologies offer many parcellation methods for healthy cortices acquired through magnetic resonance imaging. However, these methods are suboptimal for personalized neurosurgical application given that pathology and resection distort the cerebrum. We sought to overcome this problem by developing a novel connectivity‐based parcellation approach that can be applied at the single‐subject level. Utilizing normative diffusion data, we first developed a machine‐learning (ML) classifier to learn the typical structural connectivity patterns of healthy subjects. Specifically, the Glasser HCP atlas was utilized as a prior to calculate the streamline connectivity between each voxel and each parcel of the atlas. Using the resultant feature vector, we determined the parcel identity of each voxel in neurosurgical patients ( n = 40) and thereby iteratively adjusted the prior. This approach enabled us to create patient‐specific maps independent of brain shape and pathological distortion. The supervised ML classifier re‐parcellated an average of 2.65% of cortical voxels across a healthy dataset ( n = 178) and an average of 5.5% in neurosurgical patients. Our patient dataset consisted of subjects with supratentorial infiltrating gliomas operated on by the senior author who then assessed the validity and practical utility of the re‐parcellated diffusion data. We demonstrate a rapid and effective ML parcellation approach to parcellation of the human cortex during anatomical distortion. Our approach overcomes limitations of indiscriminately applying atlas‐based registration from healthy subjects by employing a voxel‐wise connectivity approach based on individual data.
$t\overline{t}t\overline{t}$ signatures through the lens of color-octet scalars
We reinterpret two recent LHC searches for events containing four top quarks ($t\overline{t}t\overline{t}$) in the context of supersymmetric models with Dirac gauginos and color-octet scalars (sgluons). We explore whether sgluon contributions to the four-top production cross section σ ($pp$ → $t\overline{t}t\overline{t}$) can accommodate an excess of four-top events recently reported by the ATLAS collaboration. We also study constraints on these models from an ATLAS search for new phenomena with high jet multiplicity and significant missing transverse energy ($E^{miss}_{T}$) sensitive to signals with four top quarks. We find that these two analyses provide complementary constraints, with the jets + $E^{miss}_{T}$ search exceeding the four-top cross section measurement in sensitivity for sgluons heavier than about 800 GeV. We ultimately find that either a scalar or a pseudoscalar sgluon can currently fit the ATLAS excess in a range of reasonable benchmark scenarios, though a pseudoscalar in minimal Dirac gaugino models is ruled out. We finally offer sensitivity projections for these analyses at the HL-LHC, mapping the 5σ discovery potential in sgluon parameter space and computing exclusion limits at 95% CL in scenarios where no excess is found.
A global metagenomic map of urban microbiomes and antimicrobial resistance
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
The New Small Wheel electronics
The increase in luminosity, and consequent higher backgrounds, of the LHC upgrades require improved rejection of fake tracks in the forward region of the ATLAS Muon Spectrometer. The New Small Wheel upgrade of the Muon Spectrometer aims to reduce the large background of fake triggers from track segments that don't originate from the interaction point. The New Small Wheel employs two detector technologies, the resistive strip Micromegas detectors and the “small” Thin Gap Chambers, with a total of 2.45 million electrodes to be sensed. The two technologies require the design of a complex electronics system given that it consists of two different detector technologies and is required to provide both precision readout and a fast trigger. It will operate in a high background radiation region up to about 20 kHz/cm 2 at the expected HL-LHC luminosity of $\mathcal{L}$= 7.5 × 10 34 cm -2 s -1 . The architecture of the system is strongly defined by the GBTx data aggregation ASIC, the newly-introduced FELIX data router and the software based data handler of the ATLAS detector. The electronics complex of this new detector was designed and developed in the last ten years and consists of multiple radiation tolerant Application Specific Integrated Circuits, multiple front-end boards, dense boards with FPGA's and purpose-built Trigger Processor boards within the ATCA standard. The New Small Wheel has been installed in 2021 and is undergoing integration within ATLAS for LHC Run 3. It should operate through the end of Run 4 (December 2032). In this manuscript, the overall design of the New Small Wheel electronics is presented.
Photometric calibration in u -band using blue halo stars
ABSTRACT We develop a method to calibrate u-band photometry based on the observed colour of blue Galactic halo stars. The Galactic halo stars belong to an old stellar population of the Milky Way and have relatively low metallicity. The ‘blue tip’ of the halo population – the main sequence turn-off (MSTO) stars – is known to have a relatively uniform intrinsic edge u-g colour with only slow spatial variation. In SDSS data, the observed variation is correlated with Galactic Latitude, which we attribute to contamination by higher metallicity disc stars and fit with an empirical curve. This curve can then be used to calibrate u-band imaging if g-band imaging of matching depth is available. Our approach can be applied to single-field observations at |b| > 30°, and removes the need for standard star observations or overlap with calibrated u-band imaging. We include in our method the calibration of g-band data with ATLAS-Refcat2. We test our approach on stars in KiDS DR 4, ATLAS DR 4, and DECam imaging from the NOIRLab Source Catalog (NSC DR2), and compare our calibration with SDSS. For this process, we use synthetic magnitudes to derive the colour equations between these data sets, in order to improve zero-point accuracy. We find an improvement for all data sets, reaching a zero-point precision of 0.016 mag for KiDS (compared to the original 0.033 mag), 0.020 mag for ATLAS (originally 0.027 mag), and 0.016 mag for DECam (originally 0.041 mag). Thus, this method alone reaches the goal of 0.02 mag photometric precision in u-band for the Rubin Observatory’s Legacy Survey of Space and Time (LSST).