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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Inactivation of the glutamine/amino acid transporter ASCT2 by 1,2,3-dithiazoles: proteoliposomes as a tool to gain insights in the molecular mechanism of action and of antitumor activity

The ASCT2 transport system catalyses a sodium-dependent antiport of glutamine and other neutral amino acids which is involved in amino acid metabolism. A library of 1,2,3-dithiazoles was designed, synthesized and evaluated as inhibitors of the glutamine/amino acid ASCT2 transporter in the model system of proteoliposomes reconstituted with the rat liver transporter. Fifteen of the tested compounds at concentration of 20 μM or below, inhibited more than 50% the glutamine/glutamine antiport catalysed by the reconstituted transporter. These good inhibitors bear a phenyl ring with electron withdrawing substituents. The inhibition was reversed by 1,4-dithioerythritol indicating that the effect was likely owed to the formation of mixed sulfides with the protein's Cys residue(s). A dose–response analysis of the most active compounds gave IC{sub 50} values in the range of 3–30 μM. Kinetic inhibition studies indicated a non-competitive inhibition, presumably because of a potential covalent interaction of the dithiazoles with cysteine thiol groups that are not located at the substrate binding site. Indeed, computational studies using a homology structural model of ASCT2 transporter, suggested as possible binding targets, Cys-207 or Cys-210, that belong to the CXXC motif of the protein. -- Highlights: ► Non‐competitive inhibition of ASCT2 by 1,2,3-dithiazoles was studied in proteoliposomes. ► Different 1,2,3-dithiazoles were synthesized and evaluated as transporter inhibitors. ► Many compounds potently inhibited the glutamine/glutamine antiport catalyzed by ASCT2. ► The inhibition was reversed by DTE indicating reaction with protein Cys. ► The most active compounds gave IC{sub 50} in the range of 3–30 μM.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery

Nicotinate mononucleotide adenylyltransferase NadD is an essential enzyme in the biosynthesis of the NAD cofactor, which has been implicated as a target for developing new antimycobacterial therapies. Here we report the crystal structure of Mycobacterium tuberculosis NadD ( Mt NadD) at a resolution of 2.4 Å. A remarkable new feature of the MtNadD structure, compared with other members of this enzyme family, is a 310 helix that locks the active site in an over-closed conformation. As a result, Mt NadD is rendered inactive as it is topologically incompatible with substrate binding and catalysis. Directed mutagenesis was also used to further dissect the structural elements that contribute to the interactions of the two Mt NadD substrates, i.e. ATP and nicotinic acid mononucleotide (NaMN). For inhibitory profiling of partially active mutants and wild type Mt NadD, we used a small molecule inhibitor of MtNadD with moderate affinity ( K i ~ 25 μM) and antimycobacterial activity (MIC 80 ) ~ 40-80 μM). This analysis revealed interferences with some of the residues in the NaMN binding subsite consistent with the competitive inhibition observed for the NaMN substrate (but not ATP). A detailed steady-state kinetic analysis of Mt NadD suggests that ATP must first bind to allow efficient NaMN binding and catalysis. This sequential mechanism is consistent with the requirement of transition to catalytically competent (open) conformation hypothesized from structural modeling. A possible physiological significance of this mechanism is to enable the down-regulation of NAD synthesis under ATP-limiting dormancy conditions. Lastly, these findings point to a possible new strategy for designing inhibitors that lock the enzyme in the inactive over-closed conformation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Evaluating Global Streamflow Simulations by a Physically-based Routing Model Coupled with the Community Land Model

Accurately simulating hydrological processes such as streamflow is important in land surface modeling because they can influence other land surface processes, such as carbon cycle dynamics, through various interaction pathways. This study aims to evaluate the global application of a recently developed Model for Scale Adaptive River Transport (MOSART)coupled with theCommunity Land Model, version 4 (CLM4). To support the global implementation of MOSART, a comprehensive global hydrography dataset has been derived at multiple resolutions from different sources. The simulated runoff fields are first evaluated against the composite runoff map from theGlobal RunoffData Centre (GRDC). The simulated streamflow is then shown to reproduce reasonably well the observed daily andmonthly streamflow at over 1600 of the world’smajor river stations in terms of annual, seasonal, and daily flow statistics. The impacts of model structure complexity are evaluated, and results show that the spatial and temporal variability of river velocity simulated byMOSART is necessary for capturing streamflow seasonality and annual maximum flood. Other sources of the simulation bias include uncertainties in the atmospheric forcing, as revealed by simulations driven by four different climate datasets, and human influences, based on a classification framework that quantifies the impact levels of large dams on the streamflow worldwide.

global evaluation, routing model, community land m↗
DOE OSTI2015

Analysis of the interaction between host factor Sam68 and viral elements during foot-and-mouth disease virus infections

Background: The nuclear protein Src-associated protein of 68 kDa in mitosis (Sam68) is known to bind RNA and be involved in cellular processes triggered in response to environmental stresses, including virus infection. Interestingly, Sam68 is a multi-functional protein implicated in the life cycle of retroviruses and picornaviruses and is also considered a marker of virus-induced stress granules (SGs). Recently, we demonstrated the partial redistribution of Sam68 to the cytoplasm in FMDV infected cells, its interaction with viral protease 3C pro , and found a significant reduction in viral titers as consequence of Sam68-specific siRNA knockdowns. Despite of that, details of how it benefits FMDV remains to be elucidated. Methods: Sam68 cytoplasmic localization was examined by immunofluorescent microscopy, counterstaining with antibodies against Sam68, a viral capsid protein and markers of SGs. The relevance of RAAA motifs in the IRES was investigated using electromobility shift assays with Sam68 protein and parental and mutant FMDV RNAs. In addition, full genome WT and mutant or G-luc replicon RNAs were tested following transfection in mammalian cells. The impact of Sam68 depletion to virus protein and RNA synthesis was investigated in a cell-free system. Lastly, through co-immunoprecipitation, structural modeling, and subcellular fractionation, viral protein interactions with Sam68 were explored. Results: FMDV-induced cytoplasmic redistribution of Sam68 resulted in it temporarily co-localizing with SG marker: TIA-1. Mutations that disrupted FMDV IRES RAAA motifs, with putative affinity to Sam68 in domain 3 and 4 cause a reduction on the formation of ribonucleoprotein complexes with this protein and resulted in non-viable progeny viruses and replication-impaired replicons. Furthermore, depletion of Sam68 in cell-free extracts greatly diminished FMDV RNA replication, which was restored by addition of recombinant Sam68. The results here demonstrated that Sam68 specifically co-precipitates with both FMDV 3D pol and 3C pro consistent with early observations of FMDV 3C pro -induced cleavage of Sam68. Conclusion: We have found that Sam68 is a specific binding partner for FMDV non-structural proteins 3C pro and 3D pol and showed that mutations at RAAA motifs in IRES domains 3 and 4 cause a decrease in Sam68 affinity to these RNA elements and rendered the mutant RNA non-viable. Interestingly, in FMDV infected cells re-localized Sam68 was transiently detected along with SG markers in the cytoplasm. These results support the importance of Sam68 as a host factor co-opted by FMDV during infection and demonstrate that Sam68 interact with both, FMDV RNA motifs in the IRES and viral non-structural proteins 3C pro and 3D pol .

3C protease↗
DOE OSTI2023

The local ordering of polar solvents around crystalline carbon nitride nanosheets in solution

The crystalline graphitic carbon nitride, poly-triazine imide (PTI) is highly unusual among layered materials since it is spontaneously soluble in aprotic, polar solvents including dimethylformamide (DMF). The PTI material consists of layers of carbon nitride intercalated with LiBr. When dissolved, the resulting solutions consist of dissolved, luminescent single to multilayer nanosheets of around 60–125 nm in diameter and Li+ and Br- ions originating from the intercalating salt. To understand this unique solubility, the structure of these solutions has been investigated by high-energy X-ray and neutron diffraction. Although the diffraction patterns are dominated by inter-solvent correlations there are clear differences between the X-ray diffraction data of the PTI solution and the solvent in the 4–6 Å -1 range, with real space differences persisting to at least 10 Å. Structural modelling using both neutron and X-ray datasets as a constraint reveal the formation of distinct, dense solvation shells surrounding the nanoparticles with a layer of Br - close to the PTI-solvent interface. This solvent ordering provides a configuration that is energetically favourable underpinning thermodynamically driven PTI dissolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Gate-based quantum computing for protein design

Protein design is a technique to engineer proteins by permuting amino acids in the sequence to obtain novel functionalities. However, exploring all possible combinations of amino acids is generally impossible due to the exponential growth of possibilities with the number of designable sites. The present work introduces circuits implementing a pure quantum approach, Grover’s algorithm, to solve protein design problems. Our algorithms can adjust to implement any custom pair-wise energy tables and protein structure models. Moreover, the algorithm’s oracle is designed to consist of only adder functions. Quantum computer simulators validate the practicality of our circuits, containing up to 234 qubits. However, a smaller circuit is implemented on real quantum devices. Our results show that using iterations, the circuits find the correct results among all N possibilities, providing the expected quadratic speed up of Grover’s algorithm over classical methods (i.e.,).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

INTERPLAY OF NEUTRINO OPACITIES IN CORE-COLLAPSE SUPERNOVA SIMULATIONS

We have conducted a series of numerical experiments using spherically symmetric, general relativistic, neutrino radiation hydrodynamics with the code Agile-BOLTZTRAN to examine the effects of modern neutrino opacities on the development of supernova simulations. We test the effects of opacities by removing opacities or by undoing opacity improvements for individual opacities and groups of opacities. We find that improvements to electron capture (EC) on nuclei, namely EC on an ensemble of nuclei using modern nuclear structure models rather than the simpler independent-particle approximation (IPA) for EC on a mean nucleus, plays the most important role during core collapse of all tested neutrino opacities. Low-energy neutrinos emitted by modern nuclear EC preferentially escape during collapse without the energy downscattering on electrons required to enhance neutrino escape and deleptonization for the models with IPA nuclear EC. During shock breakout the primary influence on the emergent neutrinos arises from non-isoenergetic scattering (NIS) on electrons. For the accretion phase, NIS on free nucleons and pair emission by e {sup +} e {sup -} annihilation have the largest impact on the neutrino emission and shock evolution. Other opacities evaluated, including nucleon-nucleon bremsstrahlung and especially neutrino-positron scattering, have little measurable impact on neutrino emission or shock dynamics. Modern treatments of nuclear EC, e {sup +} e {sup -}-annihilation pair emission, and NIS on electrons and free nucleons are critical elements of core-collapse simulations of all dimensionality.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Numerical study of the effect of propped surface area and fracture conductivity on shale gas production: Application for multi-size proppant pumping schedule design

Hydraulic fracturing is a technique extensively used in the oil and gas industry, where water, proppant (sand) and additives are injected into unconventional reservoirs to enhance the recovery of shale hydrocarbon. Although some previous studies have developed pumping schedules that maximize gas production for a single-size proppant, there are very few studies that consider the effect of varying proppant diameters across pumping stages on shale gas production. Motivated by this, we carried out an extensive sensitivity analysis to determine the effect of different proppant diameters on the average fracture conductivity (FC), average propped surface area (PSA) and cumulative shale gas production volume. We found out that the cumulative shale gas production volume depends on both the average PSA and average FC. We also found out that small-diameter proppant resulted in higher average PSA and lower average FC, whereas large-diameter proppant resulted in lower average PSA and higher average FC. Hence, we designed a multi-size proppant pumping schedule considering both of these parameters into account for simultaneously propagating multiple fractures to maximize shale gas production from unconventional reservoirs. Since the size of injected proppant particles determines the average PSA and average FC for the propped hydraulic fractures, we developed a novel framework called Sequentially Interlinked Modeling Structure (SIMS) to predict the average PSA, average FC and cumulative shale gas production volume at the end of 10 years for a given pumping schedule. Then, we used this SIMS framework to obtain a multi-size proppant pumping schedule that maximizes shale gas production. In closing, we demonstrated that the obtained pumping schedule gives a cumulative shale gas production volume greater than the values obtained from the existing pumping schedules.

03 NATURAL GAS↗
DOE OSTI2022

3D Printed Parahydrophobic Surfaces as Multireaction Platforms

We report Parahydrophobic surfaces (PHSs) composed of arrays of cubic μ-pillars with a double scale of roughness and variable wettability were systematically obtained in one step and a widely accessible stereolithographic Formlabs 3D printer. The wettability control was achieved by combining the geometrical parameters (H = height and P = pitch) and the surface modification with fluoroalkyl silane compounds. Homogeneous distribution of F and Si atoms onto the pillars was observed by XPS and SEM-EDAX. A nano-roughness on the heads of the pillars was achieved without any post-treatment. The smallest P values lead to surfaces with static contact angles (CAs) >150° regardless of the H utilized. Interestingly, the relationship 0.6 ≤ H/P ≤ 2.6 obtained here was in good agreement with the H/P values reported for nano- and submicron pillars. Furthermore, experimental CAs, advancing and receding CAs, were consistent with the theoretical prediction from the Cassie–Baxter model. Structures covered with perfluorodecyltriethoxysilane with high H and short P lead to PHSs. Conversely, structures covered with perfluorodecyltrimethoxysilane exhibited a superhydrophobic behavior. Finally, several aqueous reactions, such as precipitation, coordination complex, and nanoparticle synthesis, were carried out by placing the reactive agents as microdroplets on the parahydrophobic pillars, demonstrating the potential application as chemical multi-reaction array platforms for a large variety of relevant fields in microdroplet manipulation, microfluidics systems, and health monitoring, among others.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Comparative study of local atomic structures in Zr{sub 2}Cu{sub x}Ni{sub 1−x} (x = 0, 0.5, 1) metallic glasses

Extensive analysis has been performed to understand the key structural motifs accounting for the difference in glass forming ability in the Zr-Cu and Zr-Ni binary alloy systems. Here, the reliable atomic structure models of Zr{sub 2}Cu{sub x}Ni{sub 1−x} (x = 0, 0.5, 1) are constructed using the combination of X-ray diffraction experiments, ab initio molecular dynamics simulations and a constrained reverse Monte Carlo method. We observe a systematic variation of the interatomic distance of different atomic pairs with respect to the alloy composition. The ideal icosahedral content in all samples is limited, despite the high content of five-fold symmetry motifs. We also demonstrate that the population of Z-clusters in Zr{sub 2}Cu glass is much higher than that in the Zr{sub 2}Ni and Zr{sub 2}Cu{sub 0.5}Ni{sub 0.5} samples. And Z12 〈0, 0, 12, 0〉 Voronoi polyhedra clusters prefer to form around Cu atoms, while Ni-centered clusters are more like Z11 〈0, 2, 8, 1〉 clusters, which is less energetically stable compared to Z12 clusters. These two different structural properties may account for the higher glass forming ability of Zr{sub 2}Cu alloy than that of Zr{sub 2}Ni alloy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis

We investigated Brucella melitensis methionyl-tRNA-synthetase (BmMetRS) with molecular, structural and phenotypic methods to learn if BmMetRS is a promising target for brucellosis drug development. Recombinant BmMetRS was expressed, purified from wild type Brucella melitensis biovar Abortus 2308 strain ATCC/CRP #DD-156 and screened by a thermal melt assay against a focused library of one hundred previously classified methionyl-tRNA-synthetase inhibitors of the blood stage form of Trypanosoma brucei. Three compounds showed appreciable shift of denaturation temperature and were selected for further studies on inhibition of the recombinant enzyme activity and cell viability against wild type B. melitensis strain 16M. BmMetRS protein complexed with these three inhibitors resolved into three-dimensional crystal structures and was analyzed. All three selected methionyl-tRNA-synthetase compounds inhibit recombinant BmMetRS enzymatic functions in an aminoacylation assay at varying concentrations. Furthermore, growth inhibition of B. melitensis strain 16M by the compounds was shown. Inhibitor-BmMetRS crystal structure models were used to illustrate the molecular basis of the enzyme inhibition. Our current data suggests that BmMetRS is a promising target for brucellosis drug development. However, further studies are needed to optimize lead compound potency, efficacy and safety as well as determine the pharmacokinetics, optimal dosage, and duration for effective treatment.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase

S-acylation, also known as palmitoylation, is the most abundant form of protein lipidation in humans. This reversible posttranslational modification, which targets thousands of proteins, is catalyzed by 23 members of the DHHC family of integral membrane enzymes. DHHC enzymes use fatty acyl-CoA as the ubiquitous fatty acyl donor and become autoacylated at a catalytic cysteine; this intermediate subsequently transfers the fatty acyl group to a cysteine in the target protein. Protein S-acylation intersects with almost all areas of human physiology, and several DHHC enzymes are considered as possible therapeutic targets against diseases such as cancer. These efforts would greatly benefit from a detailed understanding of the molecular basis for this crucial enzymatic reaction. Here, in this study, we combine X-ray crystallography with all-atom molecular dynamics simulations to elucidate the structure of the precatalytic complex of human DHHC20 in complex with palmitoyl CoA. The resulting structure reveals that the fatty acyl chain inserts into a hydrophobic pocket within the transmembrane spanning region of the protein, whereas the CoA headgroup is recognized by the cytosolic domain through polar and ionic interactions. Biochemical experiments corroborate the predictions from our structural model. We show, using both computational and experimental analyses, that palmitoyl CoA acts as a bivalent ligand where the interaction of the DHHC enzyme with both the fatty acyl chain and the CoA headgroup is important for catalytic chemistry to proceed. This bivalency explains how, in the presence of high concentrations of free CoA under physiological conditions, DHHC enzymes can efficiently use palmitoyl CoA as a substrate for autoacylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The cataract-associated V41M mutant of human γS-crystallin shows specific structural changes that directly enhance local surface hydrophobicity

Highlights: •We present NMR analysis of V41M, a cataract-causing mutant of human γS-crystallin. •Mutation alters strand–strand interactions throughout the N-terminal domain. •Mutation directly affects Trp46 due to key Met41-S–Trp46-pi interactions. •We identify the basis of the surface hydrophobicity increase and residues involved. -- Abstract: The major crystallins expressed in the human lens are γS-, γC- and γD-crystallins. Several mutations in γS-crystallin are associated with hereditary cataracts, one of which involves the substitution of a highly conserved Valine at position 41 to Methionine. According to a recent report, the mutant protein, V41M, shows lower stability and increased surface hydrophobicity compared to the wild-type, and a propensity for self-aggregation. Here we address the structural differences between the two proteins, with residue-level specificity using NMR spectroscopy. Based on the structural model of the mutant protein, our results clearly show that the mutation creates a major local perturbation almost at the junction of the first and second “Greek-key” motifs in the N-terminal domain. A larger section of the second motif (residues 44–86) appears to be mainly affected. Based on the sizeable chemical shift of the imino proton of the indole side-chain of Trp46 in V41M, we suggest that the sulphur atom of Met41 is involved in an S–π interaction with Trp46. This interaction would bring the last β-strand of the first “Greek-key” motif closer to the first β-strand of the second motif. This appears to lead to a domino effect, towards both the N- and C-terminal ends, even as it decays off substantially beyond the domain interface. During this process discreet hydrophobic surface patches are created, as revealed by ANS-binding. Such changes would not affect the secondary structure or cause a major change in the tertiary structure, but can lead to self-aggregation or aberrant binding interactions of the mutant protein in vivo, and lead to lens opacity or cataract.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

INTERIOR STRUCTURE OF WATER PLANETS: IMPLICATIONS FOR THEIR DYNAMO SOURCE REGIONS

Recent discoveries of water-rich, sub-Neptunian- to Neptunian-massed exoplanets with short-period orbits present a new parameter space for the study of exoplanetary dynamos. We explore the geometry of the dynamo source region within this parameter space using 1D interior structure models. We model planets with four chemically distinct layers that consist of (1) an iron core, (2) a silicate layer, (3) an H{sub 2}O layer, and (4) an H/He envelope. By varying the total planetary mass in the range of 1-19 M{sub Circled-Plus }, the mass fraction of the H/He envelope between 0.1% and 5.1%, and the equilibrium temperature between 100 K and 1000 K, a survey of the parameter space for potential dynamo source region geometries is conducted. We find that due to the nature of the phase diagram of water at pressure and temperature conditions of planetary interiors, two different dynamo source region geometries are obtainable. Specifically, we find that smaller planets, and planets with thicker H/He envelopes, are likely to be in the regime of a thick-shelled dynamo. Massive planets, and planets with thin H/He envelopes, are likely to be in the regime of a thin-shelled dynamo. Also, small variations of these parameters can produce large interior structure differences. This implies the potential to constrain these parameters based on observations of a planet's magnetic field signature.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

CO2 response screen in grass Brachypodium reveals the key role of a MAP kinase in CO2-triggered stomatal closure

Abstract Plants respond to increased CO2 concentrations through stomatal closure, which can contribute to increased water use efficiency. Grasses display faster stomatal responses than eudicots due to dumbbell-shaped guard cells flanked by subsidiary cells working in opposition. However, forward genetic screening for stomatal CO2 signal transduction mutants in grasses has yet to be reported. The grass model Brachypodium distachyon is closely related to agronomically important cereal crops, sharing largely collinear genomes. To gain insights into CO2 control mechanisms of stomatal movements in grasses, we developed an unbiased forward genetic screen with an EMS-mutagenized B. distachyon M5 generation population using infrared imaging to identify plants with altered leaf temperatures at elevated CO2. Among isolated mutants, a “chill1” mutant exhibited cooler leaf temperatures than wild-type Bd21-3 parent control plants after exposure to increased CO2. chill1 plants showed strongly impaired high CO2-induced stomatal closure despite retaining a robust abscisic acid-induced stomatal closing response. Through bulked segregant whole-genome sequencing analyses followed by analyses of further backcrossed F4 generation plants and generation and characterization of sodium azide and CRISPR-cas9 mutants, chill1 was mapped to a protein kinase, Mitogen-Activated Protein Kinase 5 (BdMPK5). The chill1 mutation impaired BdMPK5 protein-mediated CO2/HCO3− sensing together with the High Temperature 1 (HT1) Raf-like kinase in vitro. Furthermore, AlphaFold2-directed structural modeling predicted that the identified BdMPK5-D90N chill1 mutant residue is located at the interface of BdMPK5 with the BdHT1 Raf-like kinase. BdMPK5 is a key signaling component that mediates CO2-induced stomatal movements and is proposed to function as a component of the primary CO2 sensor in grasses.

Lopez, Bryn N. K. (ORCID:0009000937288216)↗
DOE OSTI2022

Progress on Demonstration of a MOOSE-Based Coupled Capability for Hot Channel Factors in Fast Reactors

Hot channel factors (HCFs) are computed values that account for the impact on predicted peak fuel, cladding, and coolant temperatures due to uncertainties in the as-built reactor’s material properties and geometry as well as uncertainties due to modeling approximations. Reduction in computed HCF values via reduction or elimination of modeling approximations may translate to significant economic savings if the reactor power can be raised due to the extra temperature margin gained. While limited historical datasets exist for sodium-cooled fast reactors (SFRs), there are no available HCF data for lead-cooled fast reactors (LFRs) outside of work generated previously within NEAMS. The computation of HCFs involves insights from reactor physics, thermal fluids and heat conduction calculations to determine how the peak temperatures respond to various uncertainties in the design. Due to the significant advantages for multi-physics coupling offered by the MOOSE framework, Griffin (MOOSE-based reactor physics code), MOOSE Heat Conduction Module, and Cardinal (MOOSE-wrapped multi-physics application which includes the NekRS thermal fluids code) are being coupled together using the MOOSE MultiApp System to develop a highfidelity multi-physics modeling capability for HCF simulations. This high-fidelity coupling workflow may also be beneficial for other fast reactor applications in the future. In previous work, Griffin and NekRS were individually assessed to ensure the necessary capabilities were in place. This work describes initial efforts to couple the codes (including folding in the MOOSE Heat Conduction Module) and determining the workflow for the perturbed calculations which will leverage the Stochastic Tools Module (STM). To our knowledge, this is the first coupling of Griffin and NekRS as well as the first exploratory use of Stochastic Tools Module for Cardinal. In this report, the neutronics code Griffin, the heat conduction solver in MOOSE, and the MOOSE-wrapped application containing NekRS (Cardinal) are linked together to demonstrate the coupled capability. Griffin and Cardinal are linked dynamically by specifying shared libraries. Different coupling hierarchies are tested for selecting the most appropriate coupling strategy. A coupling scheme is selected based on the efficiency of calculation and ease of data communication. Multiple tests are performed to choose suitable mesh structure, model configurations, scheme setup and boundary conditions to avoid loss of energy due to data interpolation between different modules or weak imposition of fluxes in finite element codes. Computational experiments are performed to study the tolerance control of each type of iteration to avoid false convergence. The coupled capability is demonstrated in both single pin and 7-pin models based on LFR materials and geometry. The study finds that the use of too large a time step size in the heat conduction module can lead to temperature oscillation even though the heat conduction equation does not have a time-derivative kernel, but only the time-dependent boundary condition. A 7-pin model without duct region achieved good convergence in the coupled calculation while a 7 pin model with duct region experienced data communication issues which need to be resolved.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2019

Enzymatic basis for C‐lignin monomer biosynthesis in the seed coat of Cleome hassleriana

Summary C‐lignin is a linear polymer of caffeyl alcohol, found in the seed coats of several exotic plant species, with promising properties for generation of carbon fibers and high value chemicals. In the ornamental plant Cleome hassleriana , guaiacyl (G) lignin is deposited in the seed coat for the first 6–12 days after pollination, after which G‐lignin deposition ceases and C‐lignin accumulates, providing an excellent model system to study C‐lignin biosynthesis. We performed RNA sequencing of seed coats harvested at 2‐day intervals throughout development. Bioinformatic analysis identified a complete set of lignin biosynthesis genes for Cleome . Transcript analysis coupled with kinetic analysis of recombinant enzymes in Escherichia coli revealed that the switch to C‐lignin formation was accompanied by down‐regulation of transcripts encoding functional caffeoyl CoA‐ and caffeic acid 3‐ O ‐methyltransferases ( CC o AOMT and COMT ) and a form of cinnamyl alcohol dehydrogenase (Ch CAD 4) with preference for coniferaldehyde as substrate, and up‐regulation of a form of CAD (Ch CAD 5) with preference for caffealdehyde. Based on these analyses, blockage of lignin monomer methylation by down‐regulation of both O ‐methyltransferases ( OMT s) and methionine synthase (for provision of C1 units) appears to be the major factor in diversion of flux to C‐lignin in the Cleome seed coat, although the change in CAD specificity also contributes based on the reduction of C‐lignin levels in transgenic Cleome with down‐regulation of Ch CAD 5. Structure modeling and mutational analysis identified amino acid residues important for the preference of Ch CAD 5 for caffealdehyde.

Zhuo, Chunliu↗