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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Structural, biophysical, and biochemical insights into C–S bond cleavage by dimethylsulfone monooxygenase

Sulfur is an essential element for life. Bacteria can obtain sulfur from inorganic sulfate; but in the sulfur starvation–induced response,Pseudomonadsemploy two-component flavin-dependent monooxygenases (TC-FMOs) from themsuandsfnoperons to assimilate sulfur from environmental compounds including alkanesulfonates and dialkylsulfones. Here, we report binding studies of oxidized FMN to enzymes involved within theP. fluorescensenzymatic pathway responsible for converting dimethylsulfone (DMSO 2 ) to sulfite. In this catabolic pathway, SfnG serves as the initial TC-FMO for sulfur assimilation, which is investigated in detail by solving the 2.6-Å resolution crystal structure of unliganded SfnG and the 1.75-Å resolution crystal structure of the SfnG ternary complex containing FMN and DMSO 2 . We find that SfnG adopts a (β/α) 8 barrel fold with a distinct quaternary configuration from other tetrameric class C TC-FMOs. To probe the unexpected tetramer arrangement, structural heterogeneity is assessed by chromatography and light scattering to confirm ligand binding correlates with a tetramer. Binding of FMN and DMSO 2 accompanies ordering of the active site, with DMSO 2 bound on thesi-face of the flavin. A previously unobserved protein backbone conformation is found within the oxygen-binding site on there-face of the flavin. Functional assays and the positioning of ligands with respect to the oxygen-binding site are consistent with use of an N5-(hydro)peroxyflavin pathway. Biochemical endpoint assays and docking studies reveal SfnG breaks the C–S bond of a range of dialkylsulfones.

Science & Technology - Other Topics↗
DOE OSTI2022

NRAP-Open-IAM: NRAP Open Source Integrated Assessment Model

Note: This is the last version (a2.6.1) of NRAP-Open-IAM released during NRAP Phase II in 2022. The latest version of NRAP-Open-IAM is available here: https://edx.netl.doe.gov/dataset/phase-iii-nrap-open-iam NRAP-Open-IAM is an open-source software product that enables quantification of containment effectiveness and leakage risk at storage sites in the context of system uncertainties and variability. NRAP-Open-IAM represents the next-generation in a line of systems-based computational models developed for quantitative geological carbon storage (GCS) risk assessment. The model comprises a set of reduced-order and analytical models of various components of the GCS system, potential leakage pathways, receptors of concern including impact to groundwater resources and the atmosphere, a framework to support stochastic simulation, time stepping, uncertainty quantification, other analytical functionality for scenario and risk-performance evaluation, and a basic graphical user interface to support scenario development, data input simulation definition, and basic post-processing and results display. As the NRAP Open-IAM functionality continues to evolve, we continue to add to its capability to develop quantitative, probabilistic, and time-dependent profiles of the evolution of risk at a GCS site and evaluate the influence of uncertain parameters on uncertainty in predicted risk. It can be used to quantify the dynamics of reservoir saturation plume and pressure-affected area, for evaluation of the area of potential groundwater impact (i.e., Area of Review) and monitoring requirements to support cost and regulatory analysis, and for consideration of different post-injection site care and closure scenarios. This submission contains the current version of NRAP-Open-IAM available for evaluation and testing. To use the NRAP-Open-IAM, download the source code (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/4c24a3da-3b40-4ffe-9892-c807ae9f8760) then open the NRAP-Open-IAM user's guide (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669) to read more about the tool. Installation instructions for Windows, Mac, and Linux can be found in the "installers" folder of the extracted NRAP-Open-IAM folder and describe setup of environment (e.g., Python libraries) needed for proper work of the tool. Test of installation can be done by running "python openiam_setup_tests.py" in the "setup" folder. The installation test also runs a test suite to see if the NRAP-Open-IAM has been installed correctly. To run the test suite separately, run "python iam_test.py" in the "test" folder. User's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669 Developer's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/3bc6ee7d-609d-4eb6-80ba-fa6130ee0313 Reservoir simulation data used in some examples distributed with NRAP-Open-IAM: - Kimberlina: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/eb62cece-61b2-4037-9b6d-32407dde2ab8 - Kimberlina (compartmentalized): https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/366f9530-3b32-4b84-affe-ab2df1d9a8b5 - FutureGen 2.0: https://edx.netl.doe.gov/dataset/futuregen-2-0-1008-simulation-reservoir-lookup-table NRAP-Open-IAM GitLab repository: https://gitlab.com/NRAP/OpenIAM Related publications: - Bacon, D., Yonkofski, C., Brown, C., Demirkanli, D. and Whiting, J., 2019. Risk-based post injection site care and monitoring for commercial-scale carbon storage: Reevaluation of the FutureGen 2.0 site using NRAP-Open-IAM and DREAM. International Journal of Greenhouse Gas Control 90: 102784. - Bacon, D. Demirkanli, D., and White, S., 2020. Probabilistic risk-based Area of Review (AoR) determination for a deep-saline carbon storage site. International Journal of Greenhouse Gas Control 102: 103153. - Harp, D., Oldenburg, C., and Pawar, R., 2019. A metric for evaluating conformance robustness during geologic CO2 sequestration operations. International Journal of Greenhouse Gas Control 85: 100-108. - Lackey, G., Vasylkivska, V., Huerta, N., King, S., and Dilmore, R., 2019. Managing well leakage risks at a geologic carbon storage site with many wells, International Journal of Greenhouse Gas Control, 88 :182-194. - Vasylkivska, V., Dilmore, R., Lackey, G., Zhang, Y., King, S., Bacon, D., Chen, B., Mansoor, K., and Harp, D., 2021. NRAP-Open-IAM: A flexible open-source integrated assessment model for geologic carbon storage risk assessment and management, Environmental Modelling & Software, 143: 105114. Presentations: - Chen, B., Harp, D., and Pawar, R., A data assimilation approach (ES-MDA) coupling with NRAP-Open-IAM for quantifying uncertainty reduction in geological CO2 sequestration. AGUFM 2019: T44A-02. - Chen, B., and Harp, D., Improving risk analysis precision for geologic CO2 sequestration by quantifying the uncertainty reduction before and after acquiring monitoring data. 14th Greenhouse Gas Control Technologies Conference, Melbourne, Australia, 2018, pp. 21-26. - Harp, D., National Risk Assessment Partnership Task 2: Containment Assurance. No. LA-UR-19-28654, Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2019. - Vasylkivska, V., King, S., Bacon, D., Harp, D., Chen, B., Mansoor, K., Onishi, T., Yang, Y., Zhang, Y., and Keating, E., NRAP-Open-IAM: An open-source integrated assessment model, poster, Mastering the Subsurface Through Technology Innovation, Partnerships and Collaboration: Carbon Storage and Oil and Natural Gas Technologies Review Meeting, Pittsburgh, PA, August 13-16, 2018. - Vasylkivska, V., Lackey, G., King, S., Wentworth, A., Huerta, N., Creason, C., DiGiulio, J., Yang, Y., and Dilmore, R., Long-term risk analysis of a geologic CO2 storage project during the post-injection period, SIAM Conference on Computational Science and Engineering, Spokane, WA, February 25-March 1, 2019. - Vasylkivska, V., Overview of the NRAP-Open-IAM tool for carbon storage (beta release), 2019 Annual NRAP Tool Users Meeting, Pittsburgh, PA, August 27, 2019. - Vasylkivska, V., Bacon, D., Chen, B., Dilmore, R., Harp, D., King, S., Lackey, G., Lindner, E., Liu, G., Mansoor, K. and Zhang, Y., NRAP-Open-IAM: A new, open-source code for integrated assessment of geologic carbon storage containment effectiveness and leakage risk, poster, American Geophysical Union Fall Meeting 2020 (virtual meeting), December 2020. - Vasylkivska, V., NRAP open-source integrated assessment model and relevant application, oral presentation, NRAP workshop "NRAP Tools for Geologic Carbon Storage Risk-Based Decision Making" held in conjunction with Groundwater Protection Council (GWPC) 2021 Annual Forum (virtual meeting), Salt Lake City, UT, September 2021. - Vasylkivska, V., NRAP-Open-IAM: open-source integrated assessment model, digital poster/demonstration, software demonstration session, 2022 Carbon Management Project Review Meeting, August 16, 2022

AoR↗
DOE OSTI2025

Evaluation of probability density function descriptions for three-component Rayleigh–Taylor mixing

Results from simulations of a three-component Rayleigh–Taylor (RT) mixing problem are presented. These simulations are conducted in heavy–light–heavy and heavy–intermediate–light configurations, and each of these configurations are further considered in high- and low-Reynolds-number regimes. This results in RT-unstable flow with one or both interfaces initially unstable, permitting the influence of problem configuration on the statistical description of three-component RT-driven mixing to be considered. Mass fraction covariances are observed to undergo a sign change through the mixing layer in all four configurations considered. This appears to be unique to the multi-component case and represents another way in which multi-component RT mixing differs from the two-component case. Qualitative and quantitative comparisons of joint and marginal probability density function (PDF) descriptions of species concentration are made. Three-, five-, and six-parameter model PDFs are compared against simulation data to assess how accurately they describe the mixing, and it is found that three-component mixing requires at least a five-parameter model PDF to accurately describe the mixing. Notably, the marginal distributions of three-component mixing do not appear to conform to a beta distribution, representing a departure from the classical two-component RT case. In conclusion, statistical neutrality also appears to influence the optimal choice of model PDF, which is found to be a function of problem configuration.

Large-eddy simulation↗
NASA NTRS2015

The Rapid Response Radiation Survey (R3S) Mission Using the HISat Conformal Satellite Architecture

The Rapid Response Radiation Survey (R3S) experiment, designed as a quick turnaround mission to make radiation measurements in LEO, will fly as a hosted payload in partnership with NovaWurks using their Hyper-integrated Satlet (HiSat) architecture. The need for the mission arises as the Nowcast of Atmospheric Ionization Radiation for Aviation Safety (NAIRAS) model moves from a research effort into an operational radiation assessment tool. The data collected by R3S, in addition to the complementary data from a NASA Langley Research Center (LaRC) atmospheric balloon mission entitled Radiation Dosimetry Experiment (RaDX), will validate exposure prediction capabilities of NAIRAS. This paper discusses the development of the R3S experiment as made possible by use of the HiSat architecture. The system design and operational modes of the experiment are described, as well as the experiment interfaces to the HiSat satellite via the user defined adapter (UDA) provided by NovaWurks. This paper outlines the steps taken by the project to execute the R3S mission in the 4 months of design, build, and test. Finally, description of the engineering process is provided, including the use of facilitated rapid/concurrent engineering sessions, the associated documentation, and the review process employed.

Miller, Nathanael↗
DOE OSTI2025

3D Printing of Highly Porous Polypropylene Separators for Lithium‐Ion Batteries Using Fused Deposition Modeling and Thermally Induced Phase Separation

Appearing as one of the key-components of lithium-ion batteries (LIBs), this work specifically focuses on the additive manufacturing (AM) of custom-shape separators, facilitated by the filament material extrusion process, also called fused deposition modeling (FDM). The development and optimization of composite thermoplastic filament feedstocks combining polypropylene and paraffin wax, followed by the 3D printing of the separator membranes is shown. A post-processing step, based on thermal induced phase separation (TIPS), is introduced to promote porosity formation through removal of the paraffin wax sacrificial phase within the 3D printed items. Separators with different polypropylene/paraffin wax ratios are developed and the impact on printability, mechanical strength, porosity, and electrochemical performances, is thoroughly discussed. X-ray micro-computed tomography is employed to assess the geometric fidelity and to detect printing defects in a complex 3D lattice structure. The performance of the 3D printed porous separators is also compared to a commercial separator. This pioneering research establishes a foundation for the creation of porous separators that can adapt to and conform into 3D printed battery architectures with novel form factors, and also creates opportunities for the use of FDM and TIPS for a wide range of applications that employ porous structures beyond the energy storage field.

3D printing↗
DOE OSTI2020

Assessment of the 3420 Building Filtered Exhaust Stack Sampling Probe Location: Stack Verification Following Fan and Air Blender Additions

The Pacific Northwest National Laboratory (PNNL) 3420 Building, which is part of the Physical Sciences Facility (PSF), houses radiological capabilities that results in the requirement that emissions monitoring must be conducted for potential radionuclides in the exhaust air discharge of this building. The air monitoring system is required to conform to Title 40 of the Code of Federal Regulations part 61 (40 CFR 61) Subpart H, which in turns requires a sampling probe in the exhaust stream to conform to the criteria of American National Standards Institute / Health Physics Society (ANSI/HPS) N13.1-2011, Sampling and Monitoring Releases of Airborne Radioactive Substances from the Stack and Ducts of Nuclear Facilities. To support the air emissions permit for the 3420 Building on the PNNL campus, stack testing that used computational fluid dynamics (CFD) modeling as a surrogate stack and verification tests of velocity uniformity and flow angle on the retrofitted facility stack was performed. The ANSI/HPS N13.1-2011 criteria for the air monitoring probe location are that velocity uniformity, gaseous tracer uniformity, and particulate tracer uniformity must be less than or equal to 20%COV. Furthermore, no point in the sampling location may have a gaseous tracer concentration that varies from the mean concentration by more than 30%. Additionally, the flow angle at the sampling location must not be more than 20°. The CFD modeling of the stack, as reported by Recknagle et al. (2018) demonstrated that the stack meets the criteria at the probe location. The velocity uniformity and flow angle results from the 3420 stack verification tests, performed in October 2020, demonstrated that the CFD model results may be used to support the qualification of the stack sampling location. The measured velocity uniformity verification test result was 1.4%COV. This value is well within the uniformity criterion, which is that the velocity uniformity be =20%COV. Additionally, this value is well within the criterion that the actual stack measurement must be within 5% of the surrogate stack result of 2.1%COV when all four fans were operating. Additionally, the measured average flow angle at the 3420 stack monitor location was 15.5 degrees. Although this is higher than expected based on the CFD model, the result is =20 degrees, so the criterion is met. Based on these stack verification test results, the reconfigured 3420 Building filtered exhaust stack meets the qualification criteria given in the ANSI/HPS N13.1-2011 standard. Further changes to the system configuration or operating conditions that are outside the bounds described in this and the CFD report (Recknagle et al., 2018) may require additional tests and additional analysis to determine compliance with the standard.

3420 Building↗
DOE OSTI2021

Closing the Loop on Automotive Carbon Fiber Prepreg Manufacturing Scrap

The project demonstrated how to “close the loop” on carbon fiber by integrating industrial carbon fiber scrap into new functional components in an automotive lightweighting application. The project serves as a validation of discontinuous recycled carbon fiber in a commercial context, while generating comprehensive material data throughout the production chain. To this end, the project exhibited increasing complexity as material evaluation progressed from benchtop to commercial scale through full-scale part production, with key material properties thoroughly characterized throughout the process. Of particular focus was the form of the fiber that was fed into compounding, as recycled fiber has historically been problematic to feed at commercial-scale. Carbon fiber is energy-intensive to manufacture, so reuse of existing fiber material can reduce costs and increase sustainability. Additionally, by integrating recovered short fiber into a thermoplastic, regrind processes can be used to provide feedstock for later generations of product. While regrind plastics are not “infinitely recyclable”, reusing the manufacturing scrap over several generations of products can greatly increase material sustainability and lower the fractional embodied energy of each successive product. As such, this project supports the IACMI technical goals of (1) 25% lower carbon fiber-reinforced polymer (CFRP) cost, (2) 50% reduction in CFRP embodied energy, and (3) 80% composite recyclability into useful products. The initial stage of the project involved down selecting surface treatment (sizing) chemistries. Sizing evaluations were performed on Vartega’s chemically recycled intermediate modulus fiber along with standard modulus dry scrap which was oversized with sizing provided by Michelman. More dramatic improvements from sizing were found on the standard rather than the intermediate modulus fibers. The strength of the chemically recycled individual fibers were evaluated by Michelman and ORNL through single fiber testing and found to be comparable to similarly evaluated virgin fibers. UDRI’s mechanical testing on injection molded test specimens identified similar mechanical properties and fiber distribution relative to benchmark specimens. Additional surface chemistry tests and visualizations were performed by the Colorado School of Mines to confirm close conformance between the benchmark and recycled-fiber specimens. As the mechanical test results exceeded the 80% threshold established as the go/no-go(GNG), the project scale was increased to use commercial-scale equipment that would both better characterize the manufacturing utility of the target product format and allow qualitative assessment of a complex commercial part. An upscaled compounding evaluation was performed with a 27 mm twin-screw compounding extruding using oversized standard modulus fibers that were formatted to improve bulk solids transfer. The project team anticipated that milestone mechanical benchmarks could be achieved given the favorable performance of the sized standard modulus material identified in the initial micro-compounding trials. While the mechanical performance did meet the milestone target for that phase of the project, mechanical properties for this standard modulus-based compound were still less than those of the Ford specification. To compare the performance, the project team oversized intermediate modulus dry fibers and compounded them with the project resin at BASF using a 40 mm compounder. Test specimen mechanical performance exceeded the targets laid out in both the project milestone and the Ford specification. A series of prototype parts were successfully molded, albeit with instances of short shot components due to the high thermal conductivity of the carbon fiber compared to glass fiber for which the prototype tool was designed for. The project demonstrated that recycled carbon fiber is a viable option in fiber reinforced compound, providing greatly increased strength and modulus for applications that require them. The “agglomerated” format that facilitated effective bulk solids transfer of recovered fiber showed promise for industrial application.

36 MATERIALS SCIENCE↗
NASA NTRS2001

Durability Characterization of Advanced Polymeric Composites at Cryogenic Temperatures

The next generation of reusable launch vehicles will require technology development in several key areas. Of these key areas, the development of polymeric composite cryogenic fuel tanks promises to present one of the most difficult technical challenges. It is envisioned that a polymer matrix composite (PMC) tank would be a large shell structure capable of containing cryogenic fuels and carrying a range of structural loads. The criteria that will be imposed on such a design include reduced weight, conformal geometry, and impermeability. It is this last criterion, impermeability, that will provide the focus of this paper. The essence of the impermeability criterion is that the tank remains leak free throughout its design lifetime. To address this criterion, one of the first steps is to conduct a complete durability assessment of the PMC materials. At Langley Research Center, a durability assessment of promising new polyimide-based PMCs is underway. This durability program has focused on designing a set of critical laboratory experiments that will determine fundamental material properties under combined thermal-mechanical loading at cryogenic temperatures. The test program provides measurements of lamina and laminate properties, including strength, stiffness, and fracture toughness. The performance of the PMC materials is monitored as a function of exposure conditions and aging time. Residual properties after exposure are measured at cryogenic temperatures and provide quantitative values of residual strength and stiffness. Primary degradation mechanisms and the associated damage modes are measured with both destructive and nondestructive techniques. In addition to mechanical properties, a range of physical properties, such as weight, glass transition, and crack density, are measured and correlated with the test conditions. This paper will report on the progress of this research program and present critical results and illustrative examples of current findings.

Gates, T. S.↗
DOE OSTI2020

The arbitrary‐order virtual element method for linear elastodynamics models: convergence, stability and dispersion‐dissipation analysis

Abstract We design the conforming virtual element method for the numerical approximation of the two‐dimensional elastodynamics problem. We prove stability and convergence of the semidiscrete approximation and derive optimal error estimates under h ‐ and p ‐refinement in both the energy and the L 2 norms. The performance of the proposed virtual element method is assessed on a set of different computational meshes, including nonconvex cells up to order four in the h ‐refinement setting. Exponential convergence is also experimentally observed under p ‐refinement. Finally, we present a dispersion‐dissipation analysis for both the semidiscrete and fully discrete schemes, showing that polygonal meshes behave as classical simplicial/quadrilateral grids in terms of dispersion‐dissipation properties.

Antonietti, Paola F.↗
DOE OSTI2022

Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection

Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences

The ease with which a particular DNA segment adopts the left-handed Z-conformation depends largely on the sequence and on the degree of negative supercoiling to which it is subjected. We describe a computer program (Z-hunt) that is designed to search long sequences of naturally occurring DNA and retrieve those nucleotide combinations of up to 24 bp in length which show a strong propensity for Z-DNA formation. Incorporated into Z-hunt is a statistical mechanical model based on empirically determined energetic parameters for the B to Z transition accumulated to date. The Z-forming potential of a sequence is assessed by ranking its behavior as a function of negative superhelicity relative to the behavior of similar sized randomly generated nucleotide sequences assembled from over 80,000 combinations. The program makes it possible to compare directly the Z-forming potential of sequences with different base compositions and different sequence lengths. Using Z-hunt, we have analyzed the DNA sequences of the bacteriophage phi X174, plasmid pBR322, the animal virus SV40 and the replicative form of the eukaryotic adenovirus-2. The results are compared with those previously obtained by others from experiments designed to locate Z-DNA forming regions in these sequences using probes which show specificity for the left-handed DNA conformation.

Non-NASA Center↗
DOE OSTI2024

Jackson, L., Johnson, M.B., Latrach, A., Grimes, D., Martinez, C., and Mclaughlin, J.F., 2024, Multidisciplinary geotechnical data collection, curation, and analysis for conformity with the regulatory framework for geologic carbon storage in Wyoming, USA: Geological Society of America Abstracts with Programs. Vol. 56, No. 5, 2024, doi: 10.1130/abs/2024AM-405024

Title: Multidisciplinary Geotechnical Data Collection, Curation, and Analysis for Conformity with the Regulatory Framework for Geologic Carbon Storage in Wyoming, USA. Text: Construction and operation of wells for geologic sequestration of carbon dioxide necessitate that they are permitted under the Environmental Protection Agency’s Underground Injection Control Class VI requirements. Class VI wells conform to stringent requirements to ensure long-term safety and integrity of the storage site and the protection of Underground Sources of Drinking Water. Entities pursuing Class VI permitting must provide comprehensive geologic site characterization, including regional geologic structure and stratigraphy, aquifer information, reservoir and confining unit geomechanical properties, geochemical analyses, assessment of trapping capacity and mechanisms, and a variety of other of multidisciplinary geotechnical data. The Wyoming Class VI Site Characterization Database Project is focused on developing a geologic site characterization database of geotechnical information, which has been compiled and verified from established, public databases/entities and scientific literature to expedite Class VI permitting in Sweetwater County within the Greater Green River Basin of southern Wyoming. The preliminary suite of compiled data from 14,000 wells includes 8,000 wells with logs and 7,250 wells with formation tops, ~70 wells with core data (e.g., X-Ray diffraction, petrographic, and petrophysical data), ~2,500 water analyses, ~740 seismic events data, and ~520 bottom-hole temperature measurements. Future work on—and stemming from—this project will include new core analyses, calculation and interpolation of subsurface temperature gradients, mechanical earth models, geochemical simulations, storage capacity estimation, stratigraphic column generation and correlation, and construction of subsurface maps. Finally, this work will help to inspire and facilitate subsurface data compilation and curation beyond Sweetwater County, Wyoming.

42 ENGINEERING↗
DOE OSTI2024

CRISPR-Cas12a bends DNA to destabilize base pairs during target interrogation

RNA-guided endonucleases are involved in processes ranging from adaptive immunity to site-specific transposition and have revolutionized genome editing. CRISPR-Cas9, -Cas12 and related proteins use guide RNAs to recognize ~20-nucleotide target sites within genomic DNA by mechanisms that are not yet fully understood. We used structural and biochemical methods to assess early steps in DNA recognition by Cas12a protein-guide RNA complexes. We show here that Cas12a initiates DNA target recognition by bending DNA to induce transient nucleotide flipping that exposes nucleobases for DNA-RNA hybridization. Cryo-EM structural analysis of a trapped Cas12a–RNA–DNA surveillance complex and fluorescence-based conformational probing show that Cas12a-induced DNA helix destabilization enables target discovery and engagement. This mechanism of initial DNA interrogation resembles that of CRISPR-Cas9 despite distinct evolutionary origins and different RNA-DNA hybridization directionality of these enzyme families. Our findings support a model in which RNA-mediated DNA interference begins with local helix distortion by transient CRISPR-Cas protein binding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The differing effects of a dual acting regulator on SIRT1

SIRT1 is an NAD + -dependent protein deacetylase that has been shown to play a significant role in many biological pathways, such as insulin secretion, tumor formation, lipid metabolism, and neurodegeneration. There is great interest in understanding the regulation of SIRT1 to better understand SIRT1-related diseases and to better design therapeutic approaches that target SIRT1. There are many known protein and small molecule activators and inhibitors of SIRT1. One well-studied SIRT1 regulator, resveratrol, has historically been regarded as a SIRT1 activator, however, recent studies have shown that it can also act as an inhibitor depending on the identity of the peptide substrate. The inhibitory nature of resveratrol has yet to be studied in detail. Understanding the mechanism behind this dual behavior is crucial for assessing the potential side effects of STAC-based therapeutics. Here, we investigate the detailed mechanism of substrate-dependent SIRT1 regulation by resveratrol. We demonstrate that resveratrol alters the substrate recognition of SIRT1 by affecting the K M values without significantly impacting the catalytic rate k cat ). Furthermore, resveratrol destabilizes SIRT1 and extends its conformation, but the conformational changes differ between the activation and inhibition scenarios. We propose that resveratrol renders SIRT1 more flexible in the activation scenario, leading to increased activity, while in the inhibition scenario, it unravels the SIRT1 structure, compromising substrate recognition. Our findings highlight the importance of substrate identity in resveratrol-mediated SIRT1 regulation and provide insights into the allosteric control of SIRT1. This knowledge can guide the development of targeted therapeutics for diseases associated with dysregulated SIRT1 activity.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1988

Vortex methods for separated flows

The numerical solution of the Euler or Navier-Stokes equations by Lagrangian vortex methods is discussed. The mathematical background is presented in an elementary fashion and includes the relationship with traditional point-vortex studies, the convergence to smooth solutions of the Euler equations, and the essential differences between two- and three-dimensional cases. The difficulties in extending the method to viscous or compressible flows are explained. The overlap with the excellent review articles available is kept to a minimum and more emphasis is placed on the area of expertise, namely two-dimensional flows around bluff bodies. When solid walls are present, complete mathematical models are not available and a more heuristic attitude must be adopted. The imposition of inviscid and viscous boundary conditions without conformal mappings or image vortices and the creation of vorticity along solid walls are examined in detail. Methods for boundary-layer treatment and the question of the Kutta condition are discussed. Practical aspects and tips helpful in creating a method that really works are explained. The topics include the robustness of the method and the assessment of accuracy, vortex-core profiles, timemarching schemes, numerical dissipation, and efficient programming. Calculations of flows past streamlined or bluff bodies are used as examples when appropriate.

Spalart, Philippe R.↗
DOE OSTI2021

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae : Hairpin-Swapped Dimer and Its Conformational Change

VxrA and VxrB are cognate histidine kinase (HK)-response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. Here, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the type six secretion system, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structures of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown; however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A virtual element generalization on polygonal meshes of the Scott-Vogelius finite element method for the 2-D Stokes problem

The Virtual Element Method (VEM) is a Galerkin approximation method that extends the Finite Element Method (FEM) to polytopal meshes. In this paper, we present a conforming formulation that generalizes the Scott-Vogelius finite element method for the numerical approximation of the Stokes problem to polygonal meshes in the framework of the virtual element method. In particular, we consider a straightforward application of the virtual element approximation space for scalar elliptic problems to the vector case and approximate the pressure variable through discontinuous polynomials. We assess the effectiveness of the numerical approximation by investigating the convergence on a manufactured solution problem and a set of representative polygonal meshes. Finally, we numerically show that this formulation is convergent with optimal convergence rates except for the lowest-order case on triangular meshes, where the method coincides with the $\mathbb{P}_1$ – $\mathbb{P}_0$ Scott-Vogelius scheme, and on square meshes, which are situations that are well-known to be unstable.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A virtual element generalization on polygonal meshes of the Scott-Vogelius finite element method for the 2-D Stokes problem

The virtual element method (VEM) is a Galerkin approximation method that extends the finite element method to polytopal meshes. In this paper, we present a conforming formulation that generalizes the Scott-Vogelius finite element method (FEM) for the numerical approximation of the Stokes problem to polygonal meshes in the framework of the virtual element method. In particular, we consider a straightforward application of the virtual element approximation space for scalar elliptic problems to the vector case and approximate the pressure variable through discontinuous polynomials. We assess the effectiveness of the numerical approximation by investigating the convergence on a manufactured solution problem and a set of representative polygonal meshes. We numerically show that this formulation is convergent with optimal convergence rates except for the lowest-order case on triangular and square meshes where the method coincides with the P 1 - P 0 Scott-Vogelius scheme, which is well-known to be unstable.

97 MATHEMATICS AND COMPUTING↗