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DOE OSTI2020

Dissolution of poorly soluble uranyl phosphate phases in the Metaautunite Subgroup under uranyl peroxide cage cluster forming conditions

Uranyl phosphate minerals are widespread in uranium deposits and usually exhibit very low solubility in aqueous systems. Uranyl phosphates of the autunite group and metaautunite subgroup impact the mobility of uranium in the environment and have inspired groundwater remediation strategies that emphasize their low solubility. The importance of soluble uranium-bearing macro-anions, including nanoscale uranyl peroxide cage clusters, is largely unexplored relative to solubilization of normally low-solubility uranium minerals. Eight synthetic analogs of metaautunite subgroup minerals have been prepared and placed in various alkaline aqueous solutions containing hydrogen peroxide and tetraethylammonium hydroxide. Each uranyl phosphate studied has a topologically identical anionic sheet of uranyl square bipyramids and phosphate tetrahedra combined with various cations (Li + , Na + , K + , Rb + , Cs + , Mg 2+ , Ca 2+ , Ba 2+ ) and water in the interlayer. Uranyl peroxides formed under many of the experimental conditions examined, including solid studtite [(UO 2 )(O 2 )(H 2 O) 2 ](H 2 O) 2 and soluble uranyl peroxide cage clusters containing as many as 28 uranyl ions. Uranyl phosphate solids in contact with solutions in which uranyl peroxide cage clusters formed dissolved extensively or completely. The greatest dissolution of uranyl phosphates occurred in systems that contained cations with larger hydrated radii, Li + and Na + . The details of the uranium speciation in solution depended on the pH and counter cations provided from the interlayers of the uranyl phosphate solids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Magnetic contributions to corundum-eskolaite and corundum-hematite phase equilibria: A DFT cluster expansion study

Magnetic contributions have the potential to significantly influence predicted phase stability within alloy and mineral mixing phase diagrams, yet have been historically challenging to incorporate due to a significant increase to phase space sampling. Here, in this work, we employ a computational protocol that includes spin orientation as an additional configurational component within multi-component cluster expansions between magnetic and non-magnetic metal oxide alloys [calculated using density functional theory (DFT) and the generalized gradient approximation]. This approach was used to determine the effect of magnetic contributions to corundum-eskolaite and corundum-hematite phase equilibria from first principles. Two-component cluster expansions of the magnetic components of eskolaite and hematite were first performed showing the ability of this method to properly calculate their respective magnetic properties. Two-component cluster expansions were then performed for non-magnetic Al(III) and ferromagnetic Cr(III) and Fe(III), and phase diagrams were calculated for later comparison. Finally, a non-magnetic Al(III) and “up” and “down” magnetic configurations for anti-ferromagnetic Cr(III) and Fe(III) were performed. Magnetic contributions to the calculated phase diagram for the corundumeskolaite system were shown to be inconsequential but are vital for accurate determination of the corundum-hematite solvus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

The Ellipticity of Galaxy Clusters at a Large Radius

Galaxy clusters are the largest known gravitationally bound structures in the universe, consisting of hundreds to thousands of galaxies (Figure 1). Dark matter contributes the majority of mass to galaxy clusters, and therefore has a strong influence on the arrangement of member galaxies. By determining the shape of galaxy clusters, we can figure out the shape of the dark matter, which is important for cosmology and galaxy formation studies.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

VC3: Virtual Clusters for Community Computation (Final Technical Report)

A traditional HPC computing facility provides a large amount of computing power but has a fixed environment designed to satisfy local needs. This makes it very challenging for users to deploy complex applications that span multiple sites and require specific application software, scheduling middleware, or sharing policies. This project addressed many of these challenges by making it possible for researchers to easily aggregate and share resources, install custom software environments, and deploy clustering frameworks across multiple HPC facilities through the concept of “virtual clusters”. We designed and implemented a prototype virtual cluster facility that enabled unprivileged users to create dynamic aggregations of computing power across multiple sites, deployed with custom middleware and complex software dependencies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Detection of Anomalies in Gamma Background Radiation Data with K-Means and Self-Organizing Map Clustering Algorithms (Consortium on Nuclear Security Technologies (CONNECT) Q1 Report)

Environmental screening of gamma radiation consists of detecting weak nuisance and anomaly signal in the presence of strong and highly varying background. In a typical scenario, a mobile detector-spectrometer continuously measures gamma radiation spectra in short, e.g., one-second, signal acquisition intervals. The measurement data is a 2D matrix, where one dimension is gamma ray energy, and the other dimension is the number of measurements or total time. In principle, gamma radiation sources can be detected and identified from the measured data by their unique spectral lines. Detecting sources from data measured in a search scenario is difficult due to the highly varying background because of naturally occurring radioactive material (NORM), and low signal-to-noise ratio (S/N) of spectral signal measured during one-second acquisition intervals. The objective of this work is to explore unsupervised machine learning (ML) algorithms for detection and identification of weak nuisances and anomalies events in the presence of highly fluctuating background. The challenge is that spectral lines of isotopes are difficult to observe in one-second measurements. Averaging over the entire measurement campaign data set reveals spectral lines of most common background isotopes. Spectral lines of orphan sources, which might appear only in a few measurements during the campaign, will be washed out if averaging is performed over the entire measurement data set. The approach we have explored consists of extracting one-second measurements containing weak spectral features through data clustering. Averaging one-second spectra in a cluster should reveal the presence of anomaly sources. We created two ML models using K-means clustering and Neural Network Self-organizing Map (SOM). Performance of these ML models was benchmarked using search data. One data set contained 137 Cs source, and another dataset contained 131 I source.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2022

VC3: Virtual Clusters for Community Computation

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

A Look At Topics and Topic Clusters for DOE Laboratories, 1996 - 2021 [Slides]

Beginning in 2018, Elsevier through its Scopus database introduced topics to further refine its classification of publications: Previous classification schemes used concepts such as subject areas, e.g., physics and astronomy, chemistry, computer science, etc.; Topics, in contrast, are much more granular. There are over 96,000 and their titles/contents are very specific, e.g., “Multilayers; Interfaces (materials); Individual layer." Elsevier topic clusters or Clarivate citation topics represent good approaches to examining an institution’s scientific productivity areas. These approaches have the granularity that is not present in the previous categorization approaches used by these databases. The Elsevier topic clusters for the DOE Laboratories do not appear to vary that much over the 1996 – 2021 period. In some cases (ANL, LBNL, LANL, ORNL, and PNNL), there were over 1000 topic clusters at these Laboratories, but a consistent set formed the core of the publication activity. Diversity is viewed as a desirable property of a research portfolio. Examining the balance component of the DOE laboratories, the spread is uneven or not diverse. This may be due to the missions of these laboratories. The balance of a single university was unequal too.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2024

Containers on Switches: A Cluster School Experience

Network switches, such as those from Arista and Mellanox, often have underutilized computational resources in the form of built-in processors and memory. By leveraging these untapped resources, we can optimize functionality and efficiency of computational cluster networks. Our research focuses on deploying containers directly onto these switches to execute various auxiliary tasks ranging from metric logging to system-wide management via post-boot configuration. By doing so, we can significantly enchance the capabilities of the cluster without the need for additional dedicated hardware. Our research involved five distinct scenarios where switch utilization could have a profound impact on HPC Clusters: run cloud-init services via link-local connection; configuring a Telegraf container to export metrics; deploying a caching proxy; creating a reconfigurable IPv6 DHCP/DNS provider for VLAN; and implementing a client detection with Magellan discovery. These scenarios were containerized with podman and docker, and tested both physically on the switch virtually on a QEMU VM both running SONiC OS. Testing and findings indicate that network switches can indeed be used for these scenarios. They offer a wide range of possibilities beyond these applications. They run as expected as containers on the switches, and although there were some minor issues, work-arounds were implemented. Overall, this is a positive result that can be further explored with more scenarios.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Enhancing Superionic Conductivity in Cluster-Based Sodium-Rich Antiperovskites

Sodium (Na) superionic conductors are the key to developing next-generation solid-state batteries with safety and low cost. However, most of the known Na-conductors exhibit limited ionic conductivities at room temperature (RT), hindering their practical applications. To meet the challenge, a series of Li- and Na-rich antiperovskite superionic conductors based on cluster ions (e.g. BH4- and BCl4-) have been theoretically developed [e.g. Fang et al. PNAS 114, 11046, 2017; ACS App. Mat. Inter. 11, 963, 2018]. These materials exhibit superior properties as solid electrolytes with greatly enhanced ionic conductivities at RT. One cluster-based solid electrolyte of such, Na3O(BH)4, has been successfully synthesized for the first time most recently and its measured RT ionic conductivity is well above 10-3 S/cm which is four orders of magnitude higher than that of its halogen counterparts Na3OX (X = Cl, Br, I) [Sun et al. J. Am. Chem. Soc. 141, 5640, 2019]. In this work, we aim to further enhance the ionic conductivity of the Na-superionic conductor by using chemical mixing according to the size effect. The study further shows the advantage of utilizing cluster ions as building blocks, introducing additional degrees of freedom into tuning the properties of superionic conductors.

Fang, Hong↗

DOE OSTI2025

Measuring Nuclear Clusters in the Short-Baseline Near Detector

The Short-Baseline Near Detector (SBND) is the first Liquid Argon Time Projection Chamber (LArTPC) with high enough resolution and large enough neutrino flux to measure the cross-section for production of heavier-than-proton fragments in neutrino interactions. SBND is an 112-ton LArTPC, and lies 110 m downstream from the Booster Neutrino Beam target, where it is collecting more than two million neutrino interactions per year. As a result of both the intranuclear cascade and nuclear de-excitation, neutrino interactions with argon can produce nuclear clusters such as deuterons, tritons, helions and alpha particles, which have so far only been seen as vertex activity or mis-reconstructed as protons. With LArTPC technology's excellent reconstruction capabilities and SBND's unprecedented neutrino statistics, a measurement of these nuclear clusters could distinguish between nuclear models and improve neutrino energy reconstruction. This poster presents the status of simulation and reconstruction of nuclear clusters in SBND.

Beever, Anna L. [Unlisted, US] (ORCID:000900069339↗

DOE OSTI2025

Ligated Cluster Building Blocks as Chemical Donors and Acceptors for Two-Dimensional Metal Chalcogenides and Phosphorene Nanoribbons

Final report for studies on ligated transition metal chalcogenide clusters building blocks for serving as dopants in two dimensional semiconductors. The primary result is extending the superatom concept to transition metal chalcogenide clusters including a similarity with the perioidic electronic structures that are found in the periodic table. These results have found both new magic numbers, and new magic clusters with large spin magnetic moments.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Unitary Selective Coupled-Cluster Method

Simulating molecules using the Variational Quantum Eigensolver method is one of the promising applications for NISQ-era quantum computers. Designing an efficient ansatz to represent the electronic wave function is crucial in such simulations. Standard unitary coupled-cluster with singles and doubles (UCCSD) ansatz tends to have a large number of insignificant terms that do not lower the energy of the system. In this work, we present a unitary selective coupled-cluster method, a way to construct a unitary coupled-cluster ansatz iteratively using a selection procedure with excitations up to fourth order. This approach uses the electronic Hamiltonian matrix elements and the amplitudes for excitations already present in the ansatz to find the important excitations of higher order and to add them to the ansatz. The important feature of the method is that it systematically reduces the energy error with increasing ansatz size for a set of test molecules. {The main advantage of the proposed method is that the effort to increase the ansatz does not require any additional measurements on a quantum computer.}

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Modeling Clustered DNA Damage by Ionizing Radiation Using Multinomial Damage Probabilities and Energy Imparted Spectra

Simple and complex clustered DNA damage represent the critical initial damage caused by radiation. In this paper, a multinomial probability model of clustered damage is developed with probabilities dependent on the energy imparted to DNA and surrounding water molecules. The model consists of four probabilities: (A) direct damage of sugar-phosphate moieties leading to SSB, (B) OH− radical formation with subsequent SSB and BD formation, (C) direct damage to DNA bases, and (D) energy imparted to histone proteins and other molecules in a volume not leading to SSB or BD. These probabilities are augmented by introducing probabilities for the relative location of SSB using a ≤10 bp criteria for a double-strand break (DSB) and for the possible success of a radical attack that leads to SSB or BD. Model predictions for electrons, 4He, and 12C ions are compared to the experimental data and show good agreement. Thus, the developed model allows an accurate and rapid computational method to predict simple and complex clustered DNA damage as a function of radiation quality and to explore the resulting challenges to DNA repair.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study

Molecular HIV surveillance is a promising public health strategy for curbing the HIV epidemic. Clustering technologies used by health departments to date are limited in their ability to infer/forecast cluster growth trajectories. Resolution of the spatiotemporal dynamics of clusters, through phylodynamic and phylogeographic modelling, is one potential strategy to develop a forecasting tool; however, the projected utility of this approach needs assessment. Prior to incorporating novel phylodynamic-based molecular surveillance tools, we sought to identify possible issues related to their feasibility, acceptability, interpretation, and utility. Qualitative data were collected via focus groups among field experts (n = 17, 52.9% female) using semi-structured, open-ended questions. Data were coded using an iterative process, first through the development of provisional themes and subthemes, followed by independent line-by-line coding by two coders. Most participants routinely used molecular methods for HIV surveillance. All agreed that linking molecular sequences to epidemiological data is important for improving HIV surveillance. We found that, in addition to methodological challenges, a variety of implementation barriers are expected in relation to the uptake of phylodynamic methods for HIV surveillance. The participants identified several opportunities to enhance current methods, as well as increase the usability and utility of promising works-in-progress.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Oxygen Reduction Reaction Catalyzed by Carbon-Supported Platinum Few-Atom Clusters: Significant Enhancement by Doping of Atomic Cobalt

Oxygen reduction reaction (ORR) plays an important role in dictating the performance of various electrochemical energy technologies. As platinum nanoparticles have served as the catalysts of choice towards ORR, minimizing the cost of the catalysts by diminishing the platinum nanoparticle size has become a critical route to advancing the technological development. Herein, first-principle calculations show that carbon-supported Pt 9 clusters represent the threshold domain size, and the ORR activity can be significantly improved by doping of adjacent cobalt atoms. This is confirmed experimentally, where platinum and cobalt are dispersed in nitrogen-doped carbon nanowires in varied forms, single atoms, few-atom clusters, and nanoparticles, depending on the initial feeds. The sample consisting primarily of Pt 2~7 clusters doped with atomic Co species exhibits the best mass activity among the series, with a current density of 4.16 A mg Pt − 1 at +0.85 V vs. RHE that is almost 50 times higher than that of commercial Pt/C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Near-infrared Census of RR Lyrae Variables in the Messier 3 Globular Cluster and the Period–Luminosity Relations

We present new near-infrared (NIR), JHK {sub s}, time-series observations of RR Lyrae variables in the Messier 3 (NGC 5272) globular cluster using the WIRCam instrument at the 3.6 m Canada–France–Hawaii Telescope. Our observations cover a sky area of ∼21′ × 21′ around the cluster center and provide an average of 20 epochs of homogeneous JHK {sub s}-band photometry. New homogeneous photometry is used to estimate robust mean magnitudes for 175 fundamental-mode (RRab), 47 overtone-mode (RRc), and 11 mixed-mode (RRd) variables. Our sample of 233 RR Lyrae variables is the largest thus far obtained in a single cluster with time-resolved, multiband NIR photometry. NIR-to-optical amplitude ratios for RR Lyrae in Messier 3 exhibit a systematic increase moving from RRc to short-period (P < 0.6 day) and long-period (P ≳ 0.6 day) RRab variables. We derive JHK {sub s}-band period–luminosity relations for RRab, RRc, and the combined sample of variables. Absolute calibrations based on the theoretically predicted period–luminosity–metallicity relations for RR Lyrae stars yield a distance modulus, μ=15.041±0.017 (statistical)±0.036 (systematic) mag, to Messier 3. When anchored to trigonometric parallaxes for nearby RR Lyrae stars from the Hubble Space Telescope and the Gaia mission, our distance estimates are consistent with those resulting from the theoretical calibrations, albeit with relatively larger systematic uncertainties.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Radial Segregation between Red Giant Populations in the Globular Cluster NGC 3201: Tentative Role of Varying Mass among the Progenitors

In the globular cluster NGC 3201, we study subpopulations (SPs) of red giants (RGs) distinguished by their characteristics. In its central part, we make use of multicolor Hubble Space Telescope (HST) photometry coupled with spectroscopy of RGs spread out over a larger cluster face. In the color index CI = (m{sub F275W}−m{sub F336W}) −(m{sub F336W}−m{sub F439W}), RGs commonly referred to as first generation, SPI, are separated from the counterparts of the second generation, SPII. The latter are more concentrated than the former at a confidence level of P = 93%, within the field covered by the HST photometry. Their minor portion (∼28%, SPIIm) located in the middle of the δCI range spanned across the split RG branch relative to the splitting edge is more centrally concentrated at a higher confidence level of 96%. We found, from the [Na/Fe]−δCI plot for RGs in common between the photometry and spectroscopy, that SPI and SPII are mostly overlapped within 0.0 < [Na/Fe] < 0.3. RGs with [Na/Fe] < 0.0 (mostly SPI) keep their lower concentration to the cluster center over larger radial distance as compared to SPII RGs with [Na/Fe] > 0.3 at a confidence level of P = 88%. It is increased up to 95% if a restriction on [O/Fe] is imposed. The obtained result, particularly in the central part, is a clue that SPIIm RGs are the descendants of more massive progenitors. Of these RGs approximately one-third probably originate from recent (within the past 1.5 Gyr) blue stragglers with M {sub BS} > 1.1M {sub ☉}, and the other two-thirds could be accounted for by older collision products of primordial MS stars.

47 OTHER INSTRUMENTATION↗