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DOE OSTI2022

Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair

Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

SMEFT ATLAS: The landscape beyond the Standard Model

The Standard Model Effective Field Theory (SMEFT) based on the unbroken gauge group SU(3) 𝐶 ⊗SU(2) 𝐿 ⊗U(1) 𝑌 and containing only particles of the Standard Model (SM) has developed in the last decade to a mature field. It is the framework to be used in the energy gap from scales sufficiently higher than the electroweak scale up to the lowest energy scale at which new particles show up. We summarize the present status of this theory with a particular emphasize on its role in the indirect search for new physics (NP). While flavour physics of both quarks and leptons is the main topic of our review, we also discuss electric dipole moments, anomalous magnetic moments (𝑔−2) 𝜇,𝑒 , 𝑍-pole observables, Higgs observables and high-𝑝𝑇 scattering processes within the SMEFT. We group the observables into ten classes and list for each class the most relevant operators and the corresponding renormalization group equations (RGEs). We exhibit the correlations between different classes implied both by the operator mixing and the SU(2) 𝐿 gauge symmetry. Our main goal is to provide an insight into the complicated operator structure of this framework which hopefully will facilitate the identification of valid ultraviolet completions behind possible anomalies observed in future data. Numerous colourful charts, and 85 tables, while representing rather complicated RG evolution from the NP scale down to the electroweak scale, beautify the involved SMEFT landscape. Over 1000 references to the literature underline the importance and the popularity of this field. We discuss both top-down and bottom-up approaches as well as their interplay. This allows us eventually to present an atlas of different landscapes beyond the SM that includes heavy gauge bosons and scalars, vector-like quarks and leptons and leptoquarks.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRS2005

New Directions in Space Operations Services in Support of Interplanetary Exploration

To gain access to the necessary operational processes and data in support of NASA's Lunar/Mars Exploration Initiative, new services, adequate levels of computing cycles and access to myriad forms of data must be provided to onboard spacecraft and ground based personnel/systems (earth, lunar and Martian) to enable interplanetary exploration by humans. These systems, cycles and access to vast amounts of development, test and operational data will be required to provide a new level of services not currently available to existing spacecraft, on board crews and other operational personnel. Although current voice, video and data systems in support of current space based operations has been adequate, new highly reliable and autonomous processes and services will be necessary for future space exploration activities. These services will range from the more mundane voice in LEO to voice in interplanetary travel which because of the high latencies will require new voice processes and standards. New services, like component failure predictions based on data mining of significant quantities of data, located at disparate locations, will be required. 3D or holographic representation of onboard components, systems or family members will greatly improve maintenance, operations and service restoration not to mention crew morale. Current operational systems and standards, like the Internet Protocol, will not able to provide the level of service required end to end from an end point on the Martian surface like a scientific instrument to a researcher at a university. Ground operations whether earth, lunar or Martian and in flight operations to the moon and especially to Mars will require significant autonomy that will require access to highly reliable processing capabilities, data storage based on network storage technologies. Significant processing cycles will be needed onboard but could be borrowed from other locations either ground based or onboard other spacecraft. Reliability will be a key factor with onboard and distributed backup processing an absolutely necessary requirement. Current cluster processing/Grid technologies may provide the basis for providing these services. An overview of existing services, future services that will be required and the technologies and standards required to be developed will be presented. The purpose of this paper will be to initiate a technological roadmap, albeit at a high level, of current voice, video, data and network technologies and standards (which show promise for adaptation or evolution) to what technologies and standards need to be redefined, adjusted or areas where new ones require development. The roadmap should begin the differentiation between non manned and manned processes/services where applicable. The paper will be based in part on the activities of the CCSDS Monitor and Control working group which is beginning the process of standardization of the these processes. Another element of the paper will be based on an analysis of current technologies supporting space flight processes and services at JSC, MSFC, GSFC and to a lesser extent at KSC. Work being accomplished in areas such as Grid computing, data mining and network storage at ARC, IBM and the University of Alabama at Huntsville will be researched and analyzed.

Bradford, Robert N.↗

NASA NTRS1976

Space processing payload experiment requirements

An overview is given of the definition of research requirements and derivation of engineering design requirements for a group of 77 representative applications of space processing. Representative requirements are documented for applied research in space on biological processes, chemical/fluid phenomena, solidification processes, and glass/ceramics processes. Design requirements for payload equipment to accommodate these research requirements are presented in engineering terms, such as power requirements, schematic diagrams, etc. In addition, a summary of the 77 applied research topics is included.

Taylor, K. R.↗

DOE OSTI2016

Theoretical insights into the selective oxidation of methane to methanol in copper-exchanged mordenite

Selective oxidation of methane to methanol is one of the most difficult chemical processes to perform. A potential group of catalysts to achieve CH 4 partial oxidation are Cu-exchanged zeolites mimicking the active structure of the enzyme methane monooxygenase. However, the details of this conversion, including the structure of the active site, are still under debate. In this contribution, periodic density functional theory (DFT) methods were employed to explore the molecular features of the selective oxidation of methane to methanol catalyzed by Cu-exchanged mordenite (Cu-MOR). We focused on two types of previously suggested active species, CuOCu and CuOOCu. Our calculations indicate that the formation of CuOCu is more feasible than that of CuOOCu. In addition, a much lower C–H dissociation barrier is located on the former active site, indicating that C–H bond activation is easily achieved with CuOCu. We calculated the energy barriers of all elementary steps for the entire process, including catalyst activation, CH 4 activation, and CH 3 OH desorption. Finally, our calculations are in agreement with experimental observations and present the first theoretical study examining the entire process of selective oxidation of methane to methanol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Investigation of Coupled Processes in Argillite Rock: FY18 Progress

The report presents the current status of the TOUGH-FLAC and TOUGH-RBSN simulators for modeling of coupled THM processes in argillite, including fracturing, and verification of the TOUGH-FLAC model against major in situ heater experiments at the Mont Terri Underground Research Laboratory (URL) in Switzerland and at the URL in Bure, France. The heater experiments modeled are the Mont Terri FE (Full-scale Emplacement) Experiment, conducted as part of the Mont Terri Project, and the TED and ALC experiments conducted in Callovo-Oxfordian claystone (COx) at the Meuse/Haute-Marne (MHM) URL in Bure, France. The modeling of the TED and ALC heater experiments is part of a modeling task (Task E) of the international DECOVALEX-2019 project. DECOVALEX, which stands for DEvelopment of COupled Models and their VALidation against EXperiments, is an international collaborative activity, in which DOE and LBNL gain access to unique laboratory and field data defined as modeling test cases. DECOVALEX tasks are studied collectively among several international groups to better understand the processes and to improve numerical models that could eventually be applied in the performance assessment for nuclear waste disposal in clay host rocks and bentonite backfill. The report also includes a description of LBNL’s activities for modeling gas migration in bentonite related to Task A of the international DECOVALEX project, and presents new FY2018 work related to monitoring and characterization of faults using a unique borehole tool.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2016

Research, Development and Demonstration (RD&D) Needs for Light Water Reactor (LWR) Technologies A Report to the Reactor Technology Subcommittee of the Nuclear Energy Advisory Committee (NEAC) Office of Nuclear Energy U.S. Department of Energy

The LWR RD&D Working Group developed a detailed list of RD&D suggestions and recommendations, which are provided in Appendix D. The Working Group then undertook a systematic ranking process, described in Appendix E. The results of the ranking process are not meant to be a strict set of priorities, but rather should provide insight into how the items generally ranked within the Working Group. Future discussions and investigation into these items could provide information that would support a change in these priorities or in their emphasis. The results of this prioritization are provided below. Note that in general, many RD&D ideas are applicable to both new Advanced Light Water Reactor (ALWR) plants and currently operating plants.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

Arrangements for communicating data in a computing system using multiple processors

Systems and methods for reducing data movement in a computer system. The systems and methods use information or knowledge about the structure of an algorithm, operations to be executed at a receiving processing unit, variables or subsets or groups of variables in a distributed algorithm, or other forms of contextual information, for reducing the number of bits transmitted from at least one transmitting processing unit to at least one receiving processing unit or storage device.

Gonzalez, Juan Guillermo↗

DOE OSTI2023

Arrangements for communicating and processing data in a computing system

Gonzalez, Juan Guillermo↗

DOE OSTI2021

Prediction of low-Z collinear and noncollinear antiferromagnetic compounds having momentum-dependent spin splitting even without spin-orbit coupling

The over 60 years old Rashba-Dresselhaus effect predicts spin-orbit coupling (SOC) induced momentum-dependent spin splitting and spin polarization in materials with noncentrosymmetric structures. Strong SOC induced effects usually require high-atomic number (Z) elements such as rare-earth elements. It has recently been pointed out that antiferromagnets could hold SOC-independent spin splitting and spin polarization. In the present work we develop the spatial and magnetic symmetry conditions enabling such antiferromagnet (AFM)-induced spin splitting, dividing the 1651 magnetic space groups into seven different spin splitting prototypes (SST-1 to SST-7). This analysis places the physics of AFM spin splitting (SST-4) within the broader context of symmetry conditions that enable the more familiar forms of spin splitting, such as ferromagnetic Zeeman effect (SST-5), nonmagnetic no spin splitting (SST-6), and the nonmagnetic Rashba and Dresselhaus effects (SST-7). The AFM-induced spin splitting and spin polarization do not necessarily require breaking of inversion symmetry or the presence of SOC, hence can exist even in centrosymmetric, low-Z light element compounds, considerably broadening the material base for spin manipulations. We use the “inverse design” approach of first formulating the target property (here, spin splitting in low-Z compounds not restricted to low symmetry structures), then derive the enabling physical design principles—the magnetic symmetry conditions—to search realizable compounds that satisfy these a priori design principles. This process uncovers 422 magnetic space groups (160 centrosymmetric and 262 noncentrosymmetric) that could hold AFM-induced, SOC-independent spin splitting and spin polarization. We then search for stable compounds following such enabling symmetries. We investigate the electronic and spin structures of some selected prototype compounds by density functional theory (DFT) and find spin textures that are different than the traditional Rashba-Dresselhaus patterns and exist even in the absence of SOC effect. We provide the DFT results for all antiferromagnetic spin splitting prototypes (SST-1, SST-2, SST-3, SST-4), and concentrate on two limits of SST-4 that are particularly unusual: When spin splitting is momentum dependent (just like the Rashba effect) but is enabled in antiferromagnets even in the absence of SOC in the Hamiltonian. This includes examples of (a) centrosymmetric SST-4A compounds (e.g., orthorhombic LaMnO 3 illustrating collinear AFM, as well as cubic NiS 2 illustrating noncollinear AFM) and (b) noncentrosymmetric SST-4B compounds (e.g., rhombohedral MnTiO 3 illustrating collinear AFM and hexagonal ScMnO 3 illustrating noncollinear AFM). The symmetry design principles outlined here, along with their transformation into an inverse design material search approach and DFT verification, could open the way to their experimental examination.

36 MATERIALS SCIENCE↗

NASA NTRS1979

The nature of asteroidal differentiation processes - Implications for primordial heat sources

A review of the geochemical data on basaltic achondrite group meteorites, here defined as diogenites, eucrites, howardites, mesosiderites, main-group pallasites and IIIAB irons, suggests that the following processes and properties were important in determining the compositions of igneous materials on asteroidal sized bodies: (1) inhomogeneities in source rock compositions, (2) variable degrees of partial melting from 5-100%, (3) multiple melt genesis from a single source region, (4) fractional crystallization, and (5) remelting of earlier formed igneous rocks. All of this activity started during or shortly after the major asteroidal accretion phase as suggested by the numerous 4.6 Gyr ages for eucrites and may have lasted for at least 200 m.y. The above properties imply an early, intense heat source that was both spatially and temporally variable. A review of asteroid thermal modeling for various heat sources shows that heating by short-lived Al-26 alone appears to be incapable of supplying the observed geochemical variations.

Mittlefehldt, D. W.↗

NASA NTRS2004

Developing the JPL Engineering Processes

This paper briefly recounts the recent history of process reengineering at the NASA Jet Propulsion Laboratory, with a focus on the engineering processes. The JPL process structure is described and the process development activities of the past several years outlined. The main focus of the paper is on the current process structure, the emphasis on the flight project life cycle, the governance approach that lead to Flight Project Practices, and the remaining effort to capture process knowledge at the detail level of the work group.

reengineering↗

NASA NTRS2016

Performance Analysis of a Hardware Implemented Complex Signal Kurtosis Radio-Frequency Interference Detector

Radio-frequency interference (RFI) is a known problem for passive remote sensing as evidenced in the L-band radiometers SMOS, Aquarius and more recently, SMAP. Various algorithms have been developed and implemented on SMAP to improve science measurements. This was achieved by the use of a digital microwave radiometer. RFI mitigation becomes more challenging for microwave radiometers operating at higher frequencies in shared allocations. At higher frequencies larger bandwidths are also desirable for lower measurement noise further adding to processing challenges. This work focuses on finding improved RFI mitigation techniques that will be effective at additional frequencies and at higher bandwidths. To aid the development and testing of applicable detection and mitigation techniques, a wide-band RFI algorithm testing environment has been developed using the Reconfigurable Open Architecture Computing Hardware System (ROACH) built by the Collaboration for Astronomy Signal Processing and Electronics Research (CASPER) Group. The testing environment also consists of various test equipment used to reproduce typical signals that a radiometer may see including those with and without RFI. The testing environment permits quick evaluations of RFI mitigation algorithms as well as show that they are implementable in hardware. The algorithm implemented is a complex signal kurtosis detector which was modeled and simulated. The complex signal kurtosis detector showed improved performance over the real kurtosis detector under certain conditions. The real kurtosis is implemented on SMAP at 24 MHz bandwidth. The complex signal kurtosis algorithm was then implemented in hardware at 200 MHz bandwidth using the ROACH. In this work, performance of the complex signal kurtosis and the real signal kurtosis are compared. Performance evaluations and comparisons in both simulation as well as experimental hardware implementations were done with the use of receiver operating characteristic (ROC) curves. The complex kurtosis algorithm has the potential to reduce data rate due to onboard processing in addition to improving RFI detection performance.

microwaves↗

DOE OSTI2015

MENDF71x. Multigroup Neutron Cross Section Data Tables Based upon ENDF/B-VII.1

A new multi-group neutron cross section library has been released along with the release of NDI version 2.0.20. The library is named MENDF71x and is based upon the evaluations released in ENDF/B-VII.1 which was made publicly available in December 2011. ENDF/B-VII.1 consists of 423 evaluations of which ten are excited states evaluations and 413 are ground state evaluations. MENDF71x was created by processing the 423 evaluations into 618-group, downscatter only NDI data tables. The ENDF/B evaluation files were processed using NJOY version 99.393 with the exception of 35 Cl and 233 U. Those two isotopes had unique properties that required that we process the evaluation using NJOY version 2012. The MENDF71x library was only processed to room temperature, i.e., 293.6 K. In the future, we plan on producing a multi-temperature library based on ENDF/B-VII.1 and compatible with MENDF71x.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS2011

The 2010 AOP Workshop Summary Report

The rationale behind the current workshop, which was hosted by Biospherical Instruments Inc. (BSI), was to update the community and get community input with respect to the following: topics not addressed during the first workshop, specifically the processing of above-water apparent optical property (AOP data) within the Processing of Radiometric Observations of Seawater using Information Technologies (PROSIT) architecture; PROSIT data processing issues that have developed or tasks that have been completed, since the first workshop; and NASA instrumentation developments, both above- and in-water, that are relevant to both workshops and next generation mission planning. The workshop emphasized presentations on new AOP instrumentation, desired and required features for processing above-water measurements of the AOPs of seawater, working group discussions, and a community update for the in-water data processing already present in PROSIT. The six working groups were organized as follows: a) data ingest and data products; b) required and desired features for optically shallow and optically deep waters; c) contamination rejection (clouds), corrections, and data filtering; d) sun photometry and polarimetry; e) instrumentation networks; and f) hyperspectral versus fixed-wavelength sensors. The instrumentation networks working group was intended to provide more detailed information about desired and required features of autonomous sampling systems. Plenary discussions produced a number of recommendations for evolving and documenting PROSIT.

Hooker, Stanford B.↗

DOE OSTI2018

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

A critical step in the biogeochemical cycle of sulfur on Earth is microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Previous studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases (DsrAB) that could confer the capacity for microbial sulfite/sulfate reduction but were not affiliated with known organisms. Thus, the identity of a significant fraction of sulfate/sulfite-reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate/sulfite reduction in the genomes of organisms from 13 bacterial and archaeal phyla, thereby more than doubling the number of microbial phyla associated with this process. Eight of the 13 newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Organisms from Verrucomicrobia and two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota, contain some of the earliest evolved dsrAB genes. The capacity for sulfite reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of modulating sulfur metabolism in associated cells has been acquired by putatively symbiotic bacteria. We conclude that current functional predictions based on phylogeny significantly underestimate the extent of sulfate/sulfite reduction across Earth's ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Scaling Inference Using Triton to Accelerate Particle Physics at the LHC and DUNE

DUNE and the LHC experiments consist of unique and cutting-edge particle detectors that create massive, complex, and rich datasets with billions of events. They require sophisticated algorithms to reconstruct and interpret the data. Modern machine learning algorithms provide a powerful toolset to detect and classify particles, from familiar image processing convolutional neural networks to newer graph neural network architectures. A full reconstruction of these particle collisions requires novel approaches to handle the computing challenge of processing so much raw data. In a series of studies, physicists from Fermilab, CERN, and university groups explored how to accelerate their data processing using the Triton Inference Server.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Assessment of Hydroxyl Radical Reactivity in Sulfur-Containing Amino Acid Models Under Acidic pH

Methionine residues in proteins and peptides are frequently oxidized by losing one electron. The presence of nearby amide groups is crucial for this process, enabling methionine to participate in long-range electron transfer. Hydroxyl radical (HO•) plays an important role being generated in aerobic organisms by cellular metabolisms as well as by exogenous sources such as ionizing radiations. The reaction of HO• with methionine mainly affords the one-electron oxidation of the thioether moiety through two consecutive steps (HO• addition to the sulfur followed by HO− elimination). We recently investigated the reaction of HO• with model peptides mimicking methionine and its cysteine-methylated counterpart, i.e., CH3C(O)NHCHXC(O)NHCH3, where X = CH2CH2SCH3 or CH2SCH3 at pH 7. The reaction mechanism varied depending on the distance between the sulfur atom and the peptide backbone, but, for a better understanding of various suggested equilibria, the analysis of the flux of protons is required. We extended the previous study to the present work at pH 4 using pulse radiolysis techniques with conductivity and optical detection of transient species, as well as analysis of final products by LC-MS and high-resolution MS/MS following γ-radiolysis. Comparing all the data provided a better understanding of how the presence of nearby amide groups influences the one-electron oxidation mechanism.

Biochemistry & Molecular Biology↗