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At least 1,243 records · Page 69

Structural models and functional annotations for the Sphagnum divinum proteome

This dataset contains the structural models for the primary transcripts of the Sphagnum divinum proteome. Additionally, for a subset of these proteins, sequence and structural alignment results are provided. This dataset represents the most thorough structural study of a Sphagnum species, also known as peat mosses, by providing three-dimensional atomic resolution structures of the majority of the encoded proteins as well as structural alignment results used in the application of annotating the proteome. References (DOI) AlphaFold v2 Monomer: https://doi.org/10.1038/s41586-021-03819-2. References (DOI) US-align2: https://doi.org/10.1038/s41592-022-01585-1

59 BASIC BIOLOGICAL SCIENCES↗

Structural Models and Sequence Alignment Results of the Desulfovibrio vulgaris Proteome

This dataset contains the structural models for the primary transcripts of the Desulfovibrio vulgaris proteome as well as sequence alignment results for a subset of the encoded proteins. For each protein, the five models inferred from AlphaFold 2 are provided. The largest pTM-scoring model for each protein was energy minimized; this minimized structure as well as its AlphaFold pickle output file are also provided. This set of structures represent an alternate source of models for the D. vulgaris proteome to those available in the AlphaFold Protein Structure Database (AFDB). This is a bit more complicated since the proteins reporting in the AFDB originate from an outdated form of the D. vulgaris sequence. The different versions of the D. vulgaris gene annotation are collected in the Chronology subdirectory; further consideration of these changes on the structural space of the proteome are currently underway. For proteins that have been annotated as hypothetical, sequence alignment results from the HHblits and SAdLSA alignment methods are provided. These methods are often more capable to resolve sequence homology than other methods. Therefore, the results from both HHblits and SAdLSA are provided to identify possible homologs for these challenging proteins. Numerous sequence databases are utilized for these alignments. References AlphaFold v2 Multimer: https://doi.org/10.1101/2021.10.04.463034. References HHblits: hhtps://doi.org/10.1186/s12859-019-3019-7. References SAdLSA: hhtps://doi.org/10.3389/fbinf.2021.689960.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate

Lymphatic filariasis is a debilitating illness with an estimated 50 million cases as of 2018. The majority of cases are caused by the parasitic worm W. bancrofti and additional cases by the worms B. malayi and B. timori. Dihydrofolate reductase (DHFR) is an established target in the treatment of cancer, bacterial, and protozoal infections and may be a potential target for drugs targeting parasitic worm infections, including filariasis. Recent studies have shown that known antifolate compounds, including methotrexate, inhibit the activity of W. bancrofti DHFR (WbDHFR). However, the absence of structural information for filarial DHFRs has limited the study of more in-depth structure-function relationships. We report the structure of WbDHFR complexed with NADPH and folate using X-ray diffraction data measured to 2.47 Å resolution. The structure of WbDHFR reveals the usual DHFR fold and is currently only the second nematode DHFR structure in the Protein Data Bank. The equilibrium dissociation constants for NADPH (90 ± 29 nM) and folate (23 ± 4 nM) were determined by equilibrium titrations. The interactions of known antifolates with WbDHFR were analyzed using molecular docking programs and molecular dynamics simulations. Antifolates with a hydrophobic core and extended linker formed favorable interactions with WbDHFR. These combined data should now facilitate the rational design of filarial DHFR inhibitors, which in turn can be used to determine whether DHFR is a viable drug target for filariasis and whether existing antifolates may be repurposed for its treatment.

60 APPLIED LIFE SCIENCES↗

Structural diversity among multinary pnictide oxides: a minireview focused on semiconducting and superconducting heteroanionic materials

Incorporating different anions with varied ionic sizes and charges is a rapidly growing approach to bring out unusual physical properties among various classes of solid-state materials, pnictides and chalcogenides in particular. This minireview is focused on hetero-anionic materials based on the pnictogens, which have been demonstrated to offer an impressive diversity of crystal chemistry and electronic structures. In addition, many pnictide oxides or oxypnictides, over the course of the last decade, have been shown to exhibit a broad spectrum of superconducting, magnetic, and semiconducting properties. However, the structural diversity of the mixed-anion materials is far greater than the several known structure types, or their variants, of the well-known layered superconductive materials. Therefore, with this treatise, we aim to provide a comprehensive overview of the crystal chemistry of pnictide oxides by recounting almost 40 different structures of such ternary and multinary compounds. In addition to the structural aspects, we also highlight some of the challenges associated with the synthesis, and briefly summarize reported, to date, physical properties of this remarkable class of solids.

crystal structure↗

Structural Optimization (Final Technical Report V.2.0)

The overall Project (Project) objective is to materially decrease the leveled cost of energy (LCOE) of the Columbia Power (CPwr) StingRAY utility-scale wave energy converter (WEC). This will be achieved by reducing structural material and manufacturing costs and increasing energy output. In this Project, improving the overall Power-to-Weight ratio (PWR) is accomplished through lowering design margins - allowing for weight reduction and more efficient, cost-effective WEC manufacturing and assembly - and by optimizing mass-related WEC performance parameters, such as center of gravity and system inertia. A mixed materials approach to further structural optimization was developed under this Project and validated with extensive laboratory structural testing. This approach substitutes fiber-reinforced plastic (FRP) for steel where appropriate. The benefits of steel are maintained where most useful, for instance at structural joints where the stiffness of steel is required, and the complex geometry is more readily fabricated with steel. However, there are structural spans whose simple shapes are readily fabricated with mandrel-wound FRP and where significant cost and weight savings can be found. An adhesive, double lap shear joint is used to join the FRP and steel subcomponents.

16 TIDAL AND WAVE POWER↗

Software Verification and Validation Guidelines for Non-Linear Soil-Structure Interaction Analysis

Seismic analysis of structures, systems, and components (SSCs), including the consideration of soil-structure interaction (SSI) effects, is an important and required step in the design and licensing of nuclear power plant SSCs important to safety. Historically, the SSI analysis of nuclear structures has been performed using equivalent linear methods. However, there has been considerable industry investment in alternative seismic design and analysis approaches to reduce the construction cost of new reactors. Toward that goal and in alignment with the Licensing Modernization Project (LMP) framework, the Nuclear Regulatory Commission (US NRC) has proposed a risk-informed, performance-based approach to seismic design that allows inelastic response in those nuclear plant structures not required for confinement. As a complementary effort, reactor designers are exploring nonlinear seismic analysis methods to optimize structural designs and reduce construction costs.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Crystal Structure Prediction of Binary Alloys via Deep Potential

Predicting crystal structure has been a challenging problem in physics and materials science for a long time. A reliable energy calculation engine combined with an efficient global search algorithm, such as particle swarm optimization algorithm or genetic algorithm, is needed to conduct crystal structure prediction. In recent years, machine learning-based interatomic potential energy surface models have been proposed, potentially allowing us to perform crystal structure prediction for systems with the accuracy of density functional theory (DFT) and the speed of empirical force fields. In this paper, we employ a previously developed Deep Potential model to predict the intermetallic compound of the aluminum–magnesium system, and find six meta-stable phases with negative or nearly zero formation energy. In particular, Mg 12 Al 8 shows excellent ductility and Mg 5 Al 27 has a high Young's modulus. Based on our benchmark results, we propose a relatively robust structure screening criterion that selects potentially stable structures from the Deep Potential-based convex hull and performs DFT refinement. By using this criterion, the computational cost needed to construct the convex hull with ab initio accuracy can be dramatically reduced.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiple experimental studies of pore structure and mineral grain sizes of the Woodford shale in southern Oklahoma, USA

Pore structure study is an important part of unconventional shale reservoir characterization, since the pore system provides the primary petroleum storage space and fluid flow pathways. Previous studies have suggested that the pore structure is related to the total organic carbon (TOC) content, mineral compositions, and the maturity of the organic matter (OM). However, few studies have focused on the mineral grains, the primary grains being deposited but before cementation, which are the building blocks of shale. Eight Woodford Shale outcrop samples from southern Oklahoma were chosen to study the effects of mineral grain size on the pore structure characterization, using multiple and complementary experimental approaches, including laser diffraction, mineralogy, TOC, pyrolysis, liquid immersion porosimetry, mercury intrusion porosimetry, gas physisorption, (ultra) small angle X-ray scattering, scanning electron microscopy, and spontaneous imbibition. The results from different experiments of eight samples show that the Woodford Shale has the mean mineral grain diameters at 3–6 μm, a wide range of porosity at 3–40% and pore diameters at 50–1,000 nm, and various pore connectivity. Grain size variation was probably caused by the sea-level fluctuation during its deposition, which affect the porosity, pore size distribution, and pore connectivity. With decreasing mineral grain sizes, the porosity tends to increase while the pore connectivity worsens. The results also indicate that OM and carbonates in this low-maturity Woodford Shale could block the pores and decrease the porosity. Coupling with the grain size analyses, the control of depositional environment on grain sizes and subsequent effects on pore structure is identified. The pore structure characteristics over a wide pore-diameter range provided by multiple experiments could improve the understanding of storage space and fluid flow in the Woodford Shale to further increase its petroleum production.

54 ENVIRONMENTAL SCIENCES↗

Simple Scattering: Lipid nanoparticle structural data repository

Lipid nanoparticles (LNPs) are being intensively researched and developed to leverage their ability to safely and effectively deliver therapeutics. To achieve optimal therapeutic delivery, a comprehensive understanding of the relationship between formulation, structure, and efficacy is critical. However, the vast chemical space involved in the production of LNPs and the resulting structural complexity make the structure to function relationship challenging to assess and predict. New components and formulation procedures, which provide new opportunities for the use of LNPs, would be best identified and optimized using high-throughput characterization methods. Recently, a high-throughput workflow, consisting of automated mixing, small-angle X-ray scattering (SAXS), and cellular assays, demonstrated a link between formulation, internal structure, and efficacy for a library of LNPs. As SAXS data can be rapidly collected, the stage is set for the collection of thousands of SAXS profiles from a myriad of LNP formulations. In addition, correlated LNP small-angle neutron scattering (SANS) datasets, where components are systematically deuterated for additional contrast inside, provide complementary structural information. The centralization of SAXS and SANS datasets from LNPs, with appropriate, standardized metadata describing formulation parameters, into a data repository will provide valuable guidance for the formulation of LNPs with desired properties. To this end, we introduce Simple Scattering, an easy-to-use, open data repository for storing and sharing groups of correlated scattering profiles obtained from LNP screening experiments. Here, we discuss the current state of the repository, including limitations and upcoming changes, and our vision towards future usage in developing our collective knowledge base of LNPs.

59 BASIC BIOLOGICAL SCIENCES↗

Synthesis and Crystal Structure of the Zintl Phases NaSrSb, NaBaSb and NaEuSb

This work details the synthesis and the crystal structures of the ternary compounds NaSrSb, NaBaSb and NaEuSb. They are isostructural and adopt the hexagonal ZrNiAl-type structure (space group P6¯2m; Pearson code hP9). The structure determination in all three cases was performed using single-crystal X-ray diffraction methods. The structure features isolated Sb3– anions arranged in layers stacked along the crystallographic c-axis. In the interstices, alkali and alkaline-earth metal cations are found in tetrahedral and square pyramidal coordination environments, respectively. The formal partitioning of the valence electrons adheres to the valence rules, i.e., Na+Sr2+Sb3–, Na+Ba2+Sb3– and Na+Eu2+Sb3– can be considered as Zintl phases with intrinsic semiconductor behavior. Electronic band structure calculations conducted for NaBaSb are consistent with this notion and show a direct gap of approx. 0.9 eV. Additionally, the calculations hint at possible inverted Dirac cones, a feature that is reminiscent of topological quantum materials.

36 MATERIALS SCIENCE↗

Engineering Atomic-to-Nano Scale Structural Homogeneity towards High Corrosion Resistance of Amorphous Magnesium-Based Alloys

Magnesium-based amorphous alloys have aroused broad interest in being applied in marine use due to their merits of lightweight and high strength. Yet, the poor corrosion resistance to chloride-containing seawater has hindered their practical applications. Herein, we propose a new strategy to improve the chloride corrosion resistance of amorphous Mg 65 Cu 15 Ag 10 Gd 10 alloys by engineering atomic-to-nano scale structural homogeneity, which is implemented by heating the material to the critical temperature of the liquid–liquid transition. By using various electrochemical, microscopic, and spectroscopic characterization methods, we reveal that the liquid–liquid transition can rearrange the local structural units in the amorphous structure, slightly decreasing the alloy structure’s homogeneity, accelerate the formation of protective passivation film, and, therefore, increase the corrosion resistance. Our study has demonstrated the strong coupling between an amorphous structure and corrosion behavior, which is available for optimizing corrosion-resistant alloys.

36 MATERIALS SCIENCE↗

Improved Predictive Tools for Structural Properties of Metal–Organic Frameworks

The accurate determination of structural parameters is necessary to understand the electronic and magnetic properties of metal–organic frameworks (MOFs) and is a first step toward accurate calculations of electronic structure and function for separations and catalysis. Theoretical structural determination of metal-organic frameworks is particularly challenging because they involve ionic, covalent, and noncovalent interactions, which must be treated in a balanced fashion. Here, we apply a diverse group of local exchange-correlation functionals (PBE, PBEsol, PBE-D2, PBE-D3, vdW-DF2, SOGGA, MN15-L, revM06-L, SCAN, and revTPSS) to a broad test set of MOFs to seek the most accurate functionals to study various structural aspects of porous solids, in particular to study lattice constants, unit cell volume, two types of pore size characteristics, bond lengths, bond angles, and torsional angles). The recently developed meta functionals revM06-L and SCAN, without adding any molecular mechanics terms, are able to predict more accurate structures than previously recommended functionals, both those without molecular mechanics terms (PBE, PBEsol, vdW-DF2, and revTPSS) and those with them (PBE-D2 and PBE-D3). To provide a broader test, these two functionals are also tested for lattice constants and band gaps of unary, binary, and ternary semiconductors.

36 MATERIALS SCIENCE↗

The Synthesis and Structure of a Scandium Nitrate Hydroxy-Bridged Dimeric Complex Supported by Bipyridyl Ligands

The current discussion on whether scandium, yttrium and lanthanum should represent Group 3 in the Periodic Table or whether lutetium should replace lanthanum in the group has prompted us to further explore the structural chemistry of the Group 3 elements and compare the coordination numbers and coordination geometries adopted. The steric and electronic properties of the coordinated ligands have a major influence on the structures adopted. We report the synthesis and crystal structure determination of an unusual dinuclear scandium complex [(bipy)(NO 3 ) 2 Sc(µ-OH) 2 Sc(NO 3 ) 2 (bipy)] obtained by the reaction of hydrated scandium nitrate with 2,2'-bipyridyl (bipy) in either ethanol or nitromethane. The crystal structure of the complex shows that the scandium centers are eight coordinate, and the structure obtained contrasts with related complexes found in the lanthanide series [Ln(bipy) 2 (NO 3 ) 3 ] and [Ln(phen) 2 (NO 3 ) 3 ] (phen = phenanthroline) and in [M(terpy)(NO 3 ) 3 ] (M = Sc, Er–Lu), where these complexes are all mononuclear.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Atacama Cosmology Telescope: A Measurement of the DR6 CMB Lensing Power Spectrum and Its Implications for Structure Growth

We present new measurements of cosmic microwave background (CMB) lensing over 9400 deg of the sky. These lensing measurements are derived from the Atacama Cosmology Telescope (ACT) Data Release 6 (DR6) CMB data set, which consists of five seasons of ACT CMB temperature and polarization observations. We determine the amplitude of the CMB lensing power spectrum at 2.3% precision (43σ significance) using a novel pipeline that minimizes sensitivity to foregrounds and to noise properties. To ensure that our results are robust, we analyze an extensive set of null tests, consistency tests, and systematic error estimates and employ a blinded analysis framework. Our CMB lensing power spectrum measurement provides constraints on the amplitude of cosmic structure that do not depend on Planck or galaxy survey data, thus giving independent information about large-scale structure growth and potential tensions in structure measurements. The baseline spectrum is well fit by a lensing amplitude of A lens = 1.013 ± 0.023 relative to the Planck 2018 CMB power spectra best-fit ΛCDM model and A lens = 1.005 ± 0.023 relative to the ACT DR4 + WMAP best-fit model. From our lensing power spectrum measurement, we derive constraints on the parameter combination $S^{CMBL}_{8}$ ≡ σ 8 (Ω m /0.3) 0.25 of $S^{CMBL}_{8}$ = 0.818 ± 0.022 from ACT DR6 CMB lensing alone and $S^{CMBL}_{8}$ = 0.813 ± 0.018 when combining ACT DR6 and Planck NPIPE CMB lensing power spectra. These results are in excellent agreement with ΛCDM model constraints from Planck or ACT DR4 + WMAP CMB power spectrum measurements. Our lensing measurements from redshifts z ~ 0.5–5 are thus fully consistent with ΛCDM structure growth predictions based on CMB anisotropies probing primarily z ~ 1100. We find no evidence for a suppression of the amplitude of cosmic structure at low redshifts.

79 ASTRONOMY AND ASTROPHYSICS↗

Deep Green Unannotated Protein Structures

The Deep Green list is based on the identification and curation of conserved unannotated proteins in three green lineage (Viridiplantae) model organisms; Arabidopsis thaliana, Chlamydomonas reinhardtii, and Setaria viridis. Preliminary characterization of Deep Green proteins and genes was done using various informatics tools and published data sets and is presented in Knoshaug, Sun, et al., 2023, submitted. The structures of these unannotated proteins were also predicted using AlphaFold (Jumper et al., 2021). The data deposited here are the AlphaFold structural predictions having the highest pLDDT score and thus identified as the best folded structure (ranked_0). These data enable others to do in-depth structural characterizations to aid in functional characterization leading to deeper understanding of plant biology. References: Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. and Hassabis, D. (2021) Highly accurate protein structure prediction with AlphaFold. Nature, 596:583-589. Knoshaug, E. P., Sun, P., Nag, A., Nguyen, H., Mattoon, E. M., Zhang, N., Liu, J., Chen, C., Cheng, J., Zhang, R., St. John, P., and Umen, J. (submitted) Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii, Arabidopsis thaliana, and Setaria viridis.

09 BIOMASS FUELS↗

Structural, Criticality, and Radiation Dose Calculations to Support SNF Loading into a DOE Standard Canister

The DOE Standard Canister Demonstration Project includes the development of an internal support structure (ISS) for the 4.6-m-long and 45.7-cm-diameter canister. This study presents structural evaluations, criticality safety assessments, and dose rate calculations conducted within the scope of the ISS design process to support smooth canister loading operations and to ensure safe storage, transportation, and disposal of Peach Bottom 1 Core II (PB2) and Fort St. Vrain (FSV) SNF, currently stored at INL’s CPP-603 facility. The ISS includes a 316L stainless-steel basket that holds 12 PB2 SNF rods. The PB2 basket rests on top of six individual, 78.7-cm-long, 316L stainless-steel columns that are equally spaced and welded to the inner canister wall at the lower end of the shell. These columns represent the FSV basket and can hold one FSV SNF element. An A92014 T6 aluminum spacer disc is bolted to the bottom plate of the PB2 basket to vertically restrain the FSV SNF element after the PB2 basket is placed inside the canister above the FSV basket. The structural evaluations of the ISS followed applicable ASME BPVC.III.3 guidelines and included finite element (FE) analyses of the PB2 basket structure; analyses of welds and bolds; buckling analyses of selected components, and acceptability assessments of the expected basket deformations under loading operations. The criticality safety assessments used the Monte Carlo N-Particle (MCNP) software architecture Version 6.2, including ENDF/B-V continuous-energy cross-section libraries, considering intact SNF in a single storage overpack or two multistorage overpack configurations and intact or failed SNF configured for disposal. The dose rate computations are based on source terms taken from the DOE Spent Fuel Database. The isotopic composition was decay corrected for the year 2022 using the ORIGEN module in the SCALE suite. A 19-group photon spectrum and a 27-group neutron-source spectrum were generated and used in MCNP to calculate estimated dose-equivalent rates, both on DOE Standard Canister contact and at a radial distance of 1 m from the canister surface. The results of this study indicate a structurally sound system that can uphold its criticality safety functions throughout its intended operational phases. Furthermore, this study provides confidence that sufficient radiological protection is technically achievable.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Structural, Criticality, and Radiation Dose Calculations to support SNF Loading into a DOE Standard Canister

The DOE Standard Canister Demonstration Project includes the development of an internal support structure (ISS) for the 4.6-m long and 45.7-cm diameter canister. This study presents structural evaluations, criticality safety assessments, and dose rate calculations conducted within the scope of the ISS design process to support smooth canister loading operations and to ensure safe storage, transportation, and disposal of Peach Bottom 1 Core II (PB2) and Fort St. Vrain (FSV) SNF, currently stored at the CPP-603 facility of the INL. The ISS includes a 316L stainless steel basket that holds twelve PB2 SNF rods. Further, six individual, 78.7-cm long, 316L stainless steel columns are equally spaced and welded to the inner canister wall at the lower end of the shell. These columns represent the FSV basket and can hold one FSV SNF element. An A92014 T6 aluminum spacer disc is bolted to the bottom plate of the PB2 basket to vertically restrain the FSV SNF element after the PB2 basket is placed inside the canister on top of the FSV basket. The structural evaluations of the ISS followed applicable ASME BPVC.III.3 guidelines and included finite element (FE) analyses of the PB2 basket structure; analyses of welds and bolds; buckling analyses of selected components, and acceptability assessments of the expected basket deformations under loading operations. The criticality safety assessments used the Monte Carlo N-Particle (MCNP) software architecture version 6.2 including ENDF/B-V continuous energy cross-section libraries, considering intact SNF in a single storage overpack or two multi-storage overpack configurations, and intact or failed SNF configured for disposal. The dose rate computations are based on source terms taken from the DOE Spent Fuel Database. The isotopic composition was decay corrected for the year 2022 using the ORIGEN module in the SCALE suite. A 19-group photon spectrum and 27-group neutron-source spectra were generated and used in MCNP to calculate estimated dose-equivalent rates, both on DOE Standard Canister contact and at a radial distance of from the canister surface. The results of this study indicate a structurally sound system that can uphold its criticality safety functions throughout its intended operational phases. Further, they increase confidence that sufficient radiological protection is technically achievable.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

ECAR-6576 Rev 0 MARVEL Secondary Support Structure Analysis

The Microreactor Applications Research Validation and Evaluation (MARVEL) microreactor generates electricity using four Stirling cycle engines. Each Stirling engine, along with its mounting system, is called a Secondary Support Structure (SSS). An individual SSS consists of a Secondary Output Structure (SOS), a Secondary Support Structure Base, an insulation block, and assorted hardware. The SOS consists of the Stirling engine, the Secondary Output Structure Ring, a vibration isolator, and hardware. The purpose of this analysis is to show that the SSS is appropriately designed to meet structural, mechanical, and maintenance requirements for specified operating conditions.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗