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At least 91 records · Page 5

Multidimensional scaling informed by F -statistic: Visualizing grouped microbiome data with inference

Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. Here, in this study, we introduce a new MDS-based ordination method, “F-informed MDS,” which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community’s response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.

Biological and medical sciences↗

Lectures on Lie Group Analysis: Solving Differential Equations Using Symmetries

These notes are meant to be a supplemental reference for the beginner Lie Group Analyst. It is assumed that the reader has a basic concept of the fundamentals of Lie Group Theory (LGT), e.g. has seen the derivation of the infinitesimal generator and understands the mathematical meaning behind invariance. An excellent reference is Albright et al., “Symmetry Analysis of Differential Equations: A Primer,”. The reader is urged to read at least the first three chapters of that document to be able to follow the outset of Chapter 2 of this document. The reader should also have a general understanding of calculus, ordinary differential equations, and partial differential equations.

97 MATHEMATICS AND COMPUTING↗

Jurassic deserts and CO2 sequestration: the Glen Canyon Group in Utah, western USA

The Early Jurassic in the Western Interior of USA consisted of an extensive desert environment, including one of the largest ergs in geologic history. The Navajo erg has been estimated to extend as much as 2.2 million square kilometers, though the preserved extent is somewhat smaller. The Mesozoic was a global greenhouse phase, and during the Jurassic this region experienced fluctuations in climate aridity, reflected in the depositional environment. In addition to extensive dunefields, interdune deposits (lakes and oases) and fluvial systems are also documented within formations of the Glen Canyon Group. The Navajo Sandstone has received much attention as a potential CO2 injection target in recent years. It consists of thick, aeolian sandstones with high porosity and permeability, occurs in both outcrop and subcrop, and has industry data. Mapping of stratigraphic and sedimentologic changes within the Navajo Sandstone has been undertaken in localized areas, however piecing together these studies and developing regional models for CO2 potential has not received as much attention. There is significant industry data across Utah, and utilizing this data to pivot from a focus on hydrocarbon extraction to CO2 injection is an effective way to move forward with green energy, and to meet carbon neutral emission goals. Using legacy well data, we are developing a more comprehensive study of the Navajo Sandstone as a potential CO2 reservoir, in addition to identifying other zones of interest within the Glen Canyon Group, and improving understanding of stratigraphic complexity within one of the most significant aeolian systems in the world.

Mahon, Elizabeth↗

Klaus Mayer's Legacy and Leadership of Nuclear Forensics and the International Technical Working Group

The Nuclear Forensics International Technical Working Group (ITWG), in an evidentiary sense, has Dr. Klaus Mayer’s fingerprints all over it. His contributions to the working group and the broader international nuclear forensics community have been profound. As Klaus retires from the European Commission’s Joint Research Centre in Karlsruhe, Germany (JRC-Karlsruhe), it is only fitting to reflect on his dedication and lasting impact on nuclear forensics—guiding its evolution from its early days to its establishment as a vital tool for competent authorities in preventing and responding to the serious threat of nuclear and other radioactive materials out of regulatory control.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Generation IV International Forum – Knowledge Management and Knowledge Preservation: An initiative from the Education and Training Working Group

Dr. Patricia Paviet is the Chair of the Generation IV International Forum – Education and Training Working Group. As such, she is overseeing and directing several initiative: The GIF webinar series and the Pitch your Gen IV Research competition. This group has launched a new initiative on knowledge management and knowledge preservation of advanced reactor systems and how lessons learned are passed on in an international context. The paper is a summary of the various GIF member countries’ strategies to preserve and transfer the knowledge of advanced reactors.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

RINO: Renormalization Group Invariance with No Labels

A common challenge with supervised machine learning (ML) in high energy physics (HEP) is the reliance on simulations for labeled data, which can often mismodel the underlying collision or detector response. To help mitigate this problem of domain shift, we propose RINO (Renormalization Group Invariance with No Labels), a self-supervised learning approach that can instead pretrain models directly on collision data, learning embeddings invariant to renormalization group flow scales. In this work, we pretrain a transformer-based model on jets originating from quantum chromodynamic (QCD) interactions from the JetClass dataset, emulating real QCD-dominated experimental data, and then finetune on the JetNet dataset -- emulating simulations -- for the task of identifying jets originating from top quark decays. RINO demonstrates improved generalization from the JetNet training data to JetClass data compared to supervised training on JetNet from scratch, demonstrating the potential for RINO pretraining on real collision data followed by fine-tuning on small, high-quality MC datasets, to improve the robustness of ML models in HEP.

Hao, Zichun [Caltech] (ORCID:0000000256244907)↗

Facies Analysis of the Prairie Du Chien Group in the Illinois Basin and Analogous Rocks in Missouri and Kentucky

Funded in 2023 by the U.S. Department of Energy’s Phase II Carbon Storage Assurance Facility Enterprise (CarbonSAFE) initiative, a Heidelberg Materials cement plant in Mitchell, Indiana, is currently being evaluated as a potential Carbon Capture and Storage (CCS) subsurface injection site. The Heidelberg CCS project targets the middle to upper Prairie du Chien Group (Early Ordovician) in southwestern Indiana. Assessment of reservoir feasibility requires collection of field data, seismic surveys, well-log correlation, geologic modeling, characterization well drilling, well testing, and reservoir simulation. However, the proposed Heidelberg CCS site is in a data-limited region, lacking both outcrop analogs and deep wells penetrating the target interval, which makes geologic modelling difficult prior to drilling a characterization well. To directly address this problem, the present study was undertaken to understand the sedimentologic composition and stratigraphic architecture of the Prairie du Chien Group from analogous outcrops and cores in the Illinois Basin and adjacent regions.

Ali, Shah Bilawal [Univ. of Illinois at Urbana-Cha↗

Engineered Solutions Group's SMR Containment Cable and Electrical Penetration Assembly System

GAIN Project CRADA Number NFE-21-08839, entitled “SMR Containment Cable and EPA System” was initiated by the partnership of Oak Ridge National Laboratory (ORNL) and Engineered Solutions Group (ESG) to test an ESG-designed Electrical Penetration Assembly and Containment Cabling System Qualified for not only legacy LWR designs, but also Small Modular Reactors designs currently being designed by several different suppliers. This project was undertaken to fill the equipment gap of EPA and Cabling Systems that require much more severe environmental requirements than legacy plant applications present due to their smaller containment volumes that result in high energy densities compared to legacy designs. This high energy density results in severe accident environments and more severe normal operating conditions as well. We developed two approaches to qualify Electrical Penetration Assembly (EPA) and Containment Cabling Systems for SMRs and Advanced Reactors. We take into consideration the more severe environmental parameters found with SMR designs. The system will need to meet a qualification test program addressing wear/cyclic aging, potential radiation exposure, thermal aging, vibration aging, thermal cycling, seismic qualification, electrical fault testing (per IEEE 317) and accident simulation. The equipment must meet the requirements of 10CFR50.49, GDC 50 in 10CFR50 Appendix A, and 10CFR50 Appendix J. NRC Regulatory Guides (RGs) identify an acceptable way of meeting regulatory requirements. RGs frequently endorse a standard for meeting these requirements. Specific to this review, equipment would be qualified in accordance with the following IEEE Standards. • IEEE 317-2013 (Electrical Penetration Assemblies), which is endorsed by RG 1.63, Rev. 3, • IEEE 323-2003 and the more current IEC/IEEE 60780-323 (Environmental Qualification of 1E Equipment) which is endorsed by RG 1.89. IEEE 323-2003 is endorsed by RG 1.209, • IEEE 344-2020 (Seismic Qualification. The 2013 version endorsed by RG 1.100, Rev. 4, with exceptions), • IEEE 383-2015 (Electrical Cables) (which is endorsed by RG 1.189 Rev. 4 and the -2003 version endorsed by RG 1.211 rev. 0), • IEEE 572-2019 (Electrical Connectors and Assemblies), which is endorsed by 1.156 Rev 1, and • [IEEE 1202 (endorsed by RG 1.189) would normally be applicable but the advanced cable designs are impervious to this cable flame test.] The primary goal of such a program is to provide an EPA design that can meet the qualification requirements for all legacy light water reactor plants currently operating as well as new plant designs including light water Small Modular Reactors. Thus, these requirements are applicable to plants licensed under 10CFR50 and 10CFR52. Other reactor designs may be evaluated, and this test system and qualification method applied to those applications if the requirements would satisfy the requirements of the intended plant. A secondary benefit of this work is to document some of the history and background in these requirements as there have been recent delays in an SMR licensing process due to NRC Requests for Additional Information in this subject matter area.

42 ENGINEERING↗

Zirconium‐Based Metal–Organic Frameworks with Free Hydroxy Groups for Enhanced Perfluorooctanoic Acid Uptake in Water

Perfluorooctanoic acid (PFOA) is a highly recalcitrant organic pollutant, and its bioaccumulation severely endangers human health. While various methods are developed for PFOA removal, the targeted design of adsorbents with high efficiency and reusability remains largely unexplored. Here, in this work, the rational design and synthesis of two novel zirconium‐based metal‒organic frameworks (MOFs) bearing free ortho ‐hydroxy sites, namely noninterpenetrated PCN‐1001 and twofold interpenetrated PCN‐1002, are presented. Single crystal analysis of the pure ligand reveals that intramolecular hydrogen bonding plays a pivotal role in directing the formation of MOFs with free hydroxy groups. Furthermore, the transformation from PCN‐1001 to PCN‐1002 is realized. Compared to PCN‐1001, PCN‐1002 displays higher chemical stability due to interpenetration, thereby demonstrating an exceptional PFOA adsorption capacity of up to 632 mg g −1 (1.53 mmol g −1 ), which is comparable to the reported record values. Moreover, PCN‐1002 shows rapid kinetics, high selectivity, and long‐life cycles in PFOA removal tests. Solid‐state nuclear magnetic resonance results and density functional theory calculations reveal that multiple hydrogen bonds between the free ortho ‐hydroxy sites and PFOA, along with Lewis acid‐base interaction, work collaboratively to enhance PFOA adsorption.

36 MATERIALS SCIENCE↗

Effect of cellulose reducing ends and primary hydroxyl groups modifications on cellulose-cellulase interactions and cellulose hydrolysis

Cellulose reducing ends are believed to play a vital role in the cellulose recalcitrance to enzymatic conversion. However, their role in insoluble cellulose accessibility and hydrolysis is not clear. Thus, in this study, reducing ends of insoluble cellulose derived from various sources were modified by applying reducing and/or oxidizing agents. Here, the effects of cellulose reducing ends modification on cellulose reducing ends, cellulose structure, and cellulose accessibility to cellulase were evaluated along with the impact on cellulose hydrolysis with complete as well purified cellulase components. Sodium borohydride (NaBH 4 ) reduction and sodium chlorite-acetic acid (SC/AA) oxidation were able to modify more than 90% and 60% of the reducing ends, respectively, while the bicinchoninic acid (BCA) reagent applied for various cycles oxidized cellulose reducing ends to various extents. X-ray diffractograms of the treated solids showed that these treatments did not change the cellulose crystalline structure and the change in crystallinity index was insignificant. Surprisingly, it was found that the cellulose reducing ends modification, either through selective NaBH 4 reduction or BCA oxidation, had a negligible impact on cellulose accessibility as well on cellulose hydrolysis rates or final conversions with complete cellulase at loadings as low as 0.5 mg protein/g cellulose. In fact, in contrast to what is traditionally believed, modifications of cellulose reducing ends by these two methods had no apparent impact on cellulose conversion with purified cellulase components and their synergy. However, SC/AA oxidation resulted in significant drop in cellulose conversion (10%–50%) with complete as well purified cellulase components. Nonetheless, further research revealed that the cause for drop in cellulose conversion for the SC/AA oxidation case was due to primary hydroxyl groups (PHGs) oxidation and not the oxidation of reducing ends. Furthermore, it was found that the PHGs modification affects cellulose accessibility and slows the cellulase uptake as well resulting in significant drop in cellulose conversions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geochemical Assessment for Carbon Sequestration in the Conasauga Group, Northwest Georgia, USA

Sedimentary geological formations are known to be great candidates for geological carbon sequestration. Published studies suggest the southeast of the United States contains many formations suitable for carbon storage. The Cassville 1 Stratigraphic Borehole well could act as a potential carbon reservoir for nearby energy resource facilities in Georgia, United States. Although studies have shown that porous formations are adequate for geological carbon sequestration, it is important to understand possible geochemical reactions between CO 2 and the targeted geological formation before injecting any fluids. In this study, a sandstone sample from the Cassville 1 well is being considered for geological carbon sequestration in the Conasauga Group in Northwest Georgia. Here, the collected sandstone sample, consisting of quartz, K-feldspar, micas, kaolinite, and carbonate minerals such as calcite and dolomite, has a 6% porosity. Leveraging the formation composition and porosity, a one-dimensional continuum reactive transport model was built using CrunchFlow to assess possible geochemical reactions between injected CO 2 and the geological formation. Simulation results show that the carbonate minerals, calcite and dolomite, dissolve during the injection period of 10,000 days, increasing formation porosity from 6% to as much as 30%. The rate and extent of carbonate mineral dissolution and resulting porosity increase are highly sensitive to mineral reactive surface area values. No evidence of mineral precipitation was observed, suggesting that dissolution reactions will control porosity evolution during the CO 2 injection period.

42 ENGINEERING↗

Understanding parton evolution in matter from renormalization group analysis

We perform a renormalization group (RG) analysis of collinear hadron production in deep inelastic scattering on nuclei. We consider the limit where the parent parton energy E is large, while the medium opacity remains small. We identify the fixed order and leading enhanced medium contributions to the semi-inclusive cross sections and derive RG equations that resum multiple emissions near the endpoints of the splitting functions at first order in opacity. These evolution equations treat the same type of radiation enhancement in matter as the modified Dokshitzer-Gribov-Lipatov-Altarelli-Parisi approach, but differ in the way one regulates the collinear divergences. They provide a unique analytic insight into the problem of resummation and a faster and more efficient path to phenomenology. The new RG evolution framework is applied to study fragmentation in eA reactions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

New chronological constraints on the history of the Kalahari Group from the Upper Ugab Valley, Namibia

The sedimentary fill of the Kalahari Basin, which extends across several countries in southern and central Africa, records landscape evolution processes and holds archeological evidence of early hominid occupation. Recent studies have demonstrated that the majority of the Kalahari Group sediments were deposited between the Pliocene and the recent present. However, due to limited access to natural outcrops in the flat Kalahari topography, the chronology of the sequence, mostly its earlier part, is not well constrained.

Cosmogenic nuclides burial dating↗

Group-Additivity–Embedded Multiscale Modeling for Electric Field-Enhanced Nanocatalysis

Elucidating structure-performance relationships remains a central challenge in field-enhanced catalysis, where nanoparticles exhibit nonuniform surface sites with site-dependent responses to electric fields. Low-coordination sites (edges, corners, and tips) are particularly electric field-sensitive (EF), leading to nonuniform charge distribution, adsorption energies, and catalytic activity. Here, using ammonia decomposition on a ruthenium cluster as a model system, we develop a transferable multiscale framework integrating density functional theory, group additivity (GA), Brønsted-Evans-Polanyi scaling, and microkinetic modeling to predict EF-dependent activity across nonuniform cluster sites. Across sites and fields, the nitrogen adsorption energy (E N ) emerges as the governing descriptor, yielding robust volcano relationships whose optimum shifts systematically with field: negative fields strengthen N binding via electron accumulation, while positive fields weaken N binding via charge depletion, moving the optimal E N toward weaker binding. Microkinetic analysis shows that N≡N bond formation remains the key kinetic bottleneck over most conditions; positive fields lower the effective barrier and, critically, increase the fraction of near-optimal active sites, leading to a net enhancement in overall activity relative to zero-field and negative-field cases. By capturing EF- and site-dependent energetics with high accuracy and low computational cost, this GA-embedded multi-scale simulation workflow provides a physically interpretable route to predict and design field-enhanced nanocatalysis.

ammonia decomposition↗

Electronic structure theory with molecular point group symmetries on quantum annealers

Quantum computation has the potential to revolutionize quantum chemistry through major speedups in computation times and an exponential reduction in computational resources. Here, we combine the symmetry-adapted Jordan–Wigner encoding based on the full Boolean symmetry group $\mathbb{Z}$$^{k}_{2}$ with our new implementation of the Xia–Bian–Kais (XBK) method for improving the efficiency of electronic structure theory calculations on quantum annealers, particularly by reducing the number of qubits needed to achieve the same accuracy. By providing a more extensive symmetry-adapted encoding (SAE) than previous work, we are able to simulate molecules larger than those previously reported that have been studied using methods developed for quantum annealers and without using an active space. We calculated the potential energy surfaces of H 2 , LiH, He 2 , H 2 O, O 2 , N 2 , Li 2 , F 2 , CO, BH 3 , NH 3 , and CH 4 , with the largest molecule in the STO-6G basis set requiring 16 qubits with our SAE, and compared them with full configuration interaction results. The application of SAE to the XBK method provides an exponential reduction in the size of the Hilbert space and scales well with the size of the problem. It does not introduce significant additional errors for even or large values of a key variational parameter that determines the number of ancilla qubits used in the XBK method’s Hamiltonian embedding, or for certain molecules such as He 2 and H 2 O. Here, we provide an explanation for this behavior and a recommendation on the usage of our method. In addition, we briefly discuss the potential of extracting electronic excited states from our method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Scaling up the transcorrelated density matrix renormalization group

Explicitly correlated methods, such as the transcorrelated method which shifts a Jastrow or Gutzwiller correlator from the wave function to the Hamiltonian, are designed for high-accuracy calculations of electronic structures, but their application to larger systems has been hampered by the computational cost. We develop improved techniques for the transcorrelated density-matrix renormalization group (DMRG), in which the ground state of the transcorrelated Hamiltonian is represented as a matrix product state (MPS), and demonstrate large-scale calculations of the ground-state energy of the two-dimensional Fermi-Hubbard model. Our developments stem from three technical inventions: (i) constructing matrix product operators (MPOs) of transcorrelated Hamiltonians with low bond dimension and high sparsity, (ii) exploiting the entanglement structure of the ground states to increase the accuracy of the MPS representation, and (iii) optimizing the nonlinear parameter of the Gutzwiller correlator to mitigate the nonvariational nature of the transcorrelated method. Here, we examine systems of size up to 12×12 lattice sites, four times larger than previous transcorrelated DMRG studies, and demonstrate that transcorrelated DMRG yields significant improvements over standard nontranscorrelated DMRG for equivalent computational effort. Transcorrelated DMRG reduces the error of the ground-state energy by 2.4×–14×, with the smallest improvement seen for a small system at half filling and the largest improvement in a dilute closed-shell system.

Density matrix renormalization group↗

Phase diagram of generalized XY model using the tensor renormalization group

We use the higher-order tensor renormalization group method to study the two-dimensional generalized XY model that admits integer and half-integer vortices. This model is the deformation of the classical XY model and has a rich phase structure consisting of nematic, ferromagnetic, and disordered phases and three transition lines belonging to the Berezinskii-Kosterlitz-Thouless and Ising class. We explore the model for a wide range of temperatures, T , and the deformation parameter, Δ , and compute specific heat along with integer and half-integer magnetic susceptibility, finding both Berezinskii-Kosterlitz-Thouless-like and Ising-like transitions and the region where they meet. Published by the American Physical Society 2024

2-dimensional systems↗

Five-point functions and the permutation group 𝑆 5

Five-point functions and five-body wave functions play an important role in many areas of nuclear and particle physics, e.g., in 2 →3 scattering processes, in the five-gluon vertex, or in the study of pentaquarks. In this work we consider the permutation group 𝑆 5 to facilitate the description of such objects. We work out the multiplets transforming under irreducible representations of 𝑆 5 and provide compact formulas allowing one to cast the permutations of an object 𝑓 12345 into combinations with definite permutation symmetry. We also give the explicit expressions for the irreducible multiplet products. We consider several practical applications as examples: We arrange the four-momenta and Lorentz invariants of a five-point function into the multiplet structure, we work out the color tensors of the five-gluon vertex in the multiplet notation, and we discuss applications for five-body wave functions like those of pentaquarks.

Bethe-Salpeter equation↗