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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 415 records · Page 23

Chemical Modeling of the Capture of Radioiodine Species

Iodine is a common fission product resulting from the transmutation of uranium fuel in nuclear power reactors. The short-lived radioactive isotope, 131 I, with a half-life of around eight days, would be a particular health concern if released into the environment. Capture materials, such as activated carbon, are used routinely in nuclear power plants and medical isotope production facilities to remove this hazard during normal operations to reduce emissions to acceptable levels. Iodine, unlike other common fission products such as noble gases, is challenging because of the wide range of molecular forms and oxidation states (from +VII in IF 7 to -I in iodide) that it displays, which can interconvert both in the gas phase and in the solution phase for example. The work in this project is focused on three computational tasks. In the first, we consider the binding of iodine-containing molecules of varying oxidation states to the major component of activated carbon – pristine graphene-like sheets. The second task focused on molecular binding and possible chemical transformations resulting from the reaction of molecular iodine with chemical functional groups on the edge of the graphene sheets or surface defects in the sheet itself. The final task was associated with radiolytic breakdown of 131 I to 131 Xe in iodine containing molecules and investigated the resulting molecular fragmentation process both in the gas phase and on the graphene-like surface. For each of the tasks, the intent was to learn about the thermodynamics and kinetics of the chemical transformations and use the calculations to provide parameters for input into kinetic models describing these processes for interpretation of experimental data in future work.

07 ISOTOPE AND RADIATION SOURCES↗

Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å

HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

59 BASIC BIOLOGICAL SCIENCES↗

Early Career: Mesoscale Fragments of Crystalline Silicon by Chemical Synthesis (Final Technical Report)

Silicon has transformed the modern era, with applications in computing, solar cells, energy storage, and beyond. The traditional approach to making silicon is a high-temperature “top-down” process that affords only the most stable form of silicon, leaving hidden vast swathes of structure-function space. The goal of this program was to establish new approaches to making silicon-based materials from the bottom-up, allowing structural precision from the atomic level up to the bulk, and to understand how structure influences function. Key results included the development of the cyclosilane building blocks and low-temperature methods for their polymerization, as well as new tools for spectroscopic characterization. In addition to revealing new materials chemistry insights, in the five-year period covered by this award, this work resulted in 11 publications and three graduate student theses.

36 MATERIALS SCIENCE↗

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

59 BASIC BIOLOGICAL SCIENCES↗

A deep learning-guided automated workflow in LipidOz for detailed characterization of fungal fatty acid unsaturation by ozonolysis

Understanding fungal lipid biology and metabolism is critical for antifungal target discovery as lipids play central roles in cellular processes. Nuances in lipid structural differences can significantly impact their functions, making it necessary to characterize lipids in detail to enable and understanding of their roles in these complex systems. In particular, lipid double bond (DB) locations are an important component of lipid structure that can only be determined using a few specialized analytical techniques. Ozone-induced dissociation mass spectrometry (OzID-MS) is one such technique that uses ozone to break lipid DBs, producing pairs of characteristic fragments that allow the determination of DB positions. In this work we apply OzID-MS and LipidOz software to analyze the complex lipids of Saccharomyces cerevisiae yeast strains transfected with different fatty acid desaturases from Histoplasma capsulatum to determine the specific unsaturated lipids produce. The automated data analysis in LipidOz made the determination of DB positions from this large dataset more practical, but manual verification for all targets was still time-consuming. The DL model reduces manual involvement in data analysis, but since it was trained using mammalian lipid extracts, the prediction accuracy on yeast-derived data was reduced. We addressed both shortcomings by retraining the DL model to act as a pre-filter to prioritize targets for automated analysis, providing confident manually verified results but requiring less computational time and manual effort. Our workflow resulted in the determination of novel DB positions and enzymatic specificity.

mass spectrometry, deep learning, Lipidomics, doub↗

Numerical and Analytical Modeling of Flow Partitioning in Partially Saturated Fracture Networks

Infiltration processes in fractured-porous media remain a crucial, yet not very well understood component of recharge and vulnerability assessment. Under partially-saturated conditions flows in fractures, percolating fracture networks, and fault zones contribute to the fastest spectrum of infiltration velocities via preferential pathways. Specifically, the partitioning dynamics at fracture intersections determine the magnitude of flow fragmentation into vertical and horizontal components and hence the bulk flow velocity and dispersion of fracture networks. In this work, we derive an approximate analytical solution for the partitioning process and validate it using smoothed particle hydrodynamics simulations. The developed transfer function is conceptually based on simulation results and laboratory experiments carried out in previous works. It allows to efficiently simulate flow through fracture networks with simple cubic structure and arbitrary number of fractures and aperture sizes via linear response theory and convolution of a given input signal. We derive a non-dimensional bulk flow velocity ($\widetilde{v}$) and dispersion coefficient ($\widetilde{D}$) to characterize fracture networks in terms of dimensionless horizontal and vertical time scales $\tau_m$ and $\tau_0$. The dispersion coefficient is shown to strongly depend on the horizontal time scale and converges towards a constant value of $0.08$ within reasonable fluid and geometrical parameter ranges, while the non-dimensional velocity exhibits a characteristic $\widetilde{v} \sim \tau_m^{-1/2}$ scaling. Given that hydraulic information is often only available at limited places within (fractured-porous) aquifer system, such as boreholes or springs, our study intends to provide a rudimentary analytical concept to potentially reconstruct internal fracture network geometries from external boundary information, e.g., the dispersive properties of discharge (groundwater level fluctuations).

42 ENGINEERING↗

In crystallo organometallic chemistry

X-ray crystallography is an invaluable tool in design and development of organometallic catalysis, but application typically requires species to display sufficiently high solution concentrations and lifetimes for single crystalline samples to be obtained. In crystallo organometallic chemistry relies on chemical reactions that proceed within the single-crystal environment to access crystalline samples of reactive organometallic fragments that are unavailable by alternate means. Furthermore, this highlight describes approaches to in crystallo organometallic chemistry including (a) solid–gas reactions between transition metal complexes in molecular crystals and diffusing small molecules, (b) reactions of organometallic complexes within the extended lattices of metal–organic frameworks (MOFs), and (c) intracrystalline photochemical transformations to generate reactive organometallic fragments. Application of these methods has enabled characterization of catalytically important transient species, including σ-alkane adducts of transition metals, metal alkyl intermediates implicated in metal-catalyzed carbonylations, and reactive M–L multiply bonded species involved in C–H functionalization chemistry. Opportunities and challenges for in crystallo organometallic chemistry are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, for this work, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

59 BASIC BIOLOGICAL SCIENCES↗

Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer

Heterozygous truncating variants in the sarcomere protein titin (TTN) are the most common genetic cause of heart failure. To understand mechanisms that regulate abundant cardiomyocyte (CM) TTN expression, we characterized highly conserved intron 1 sequences that exhibited dynamic changes in chromatin accessibility during differentiation of human CMs from induced pluripotent stem cells (hiPSC-CMs). Homozygous deletion of these sequences in mice caused embryonic lethality, whereas heterozygous mice showed an allele-specific reduction in Ttn expression. A 296 bp fragment of this element, denoted E1, was sufficient to drive expression of a reporter gene in hiPSC-CMs. Deletion of E1 downregulated TTN expression, impaired sarcomerogenesis, and decreased contractility in hiPSC-CMs. Site-directed mutagenesis of predicted binding sites of NK2 homeobox 5 (NKX2-5) and myocyte enhancer factor 2 (MEF2) within E1 abolished its transcriptional activity. In embryonic mice expressing E1 reporter gene constructs, we validated in vivo cardiac-specific activity of E1 and the requirement for NKX2-5- and MEF2-binding sequences. Moreover, isogenic hiPSC-CMs containing a rare E1 variant in the predicted MEF2-binding motif that was identified in a patient with unexplained dilated cardiomyopathy (DCM) showed reduced TTN expression. Together, these discoveries define an essential, functional enhancer that regulates TTN expression. Manipulation of this element may advance therapeutic strategies to treat DCM caused by TTN haploinsufficiency.

Kim, Yuri↗

Light-Driven C(sp 3 )–C(sp 3 ) Bond Functionalizations Enabled by the PCET Activation of Alcohol O–H Bonds

Methods that enable the selective functionalization of C–C bonds offer unique opportunities for the skeletal diversification of complex molecules and provide access to unique structures without the need for de novo synthesis. While considerable advances have been made in transition-metal-based approaches, much recent work has focused on alternative strategies for C–C bond cleavage enabled by transient free radicals. In particular, alkoxy radicals derived from simple alcohols are known to significantly destabilize adjacent C–C bonds, enabling spontaneous cleavage to eject a carbon-centered radical and afford carbonyl products via β-fragmentation. Here, while this reactivity has long been recognized, its applications in synthesis have been limited, in part, by the challenges associated with generating the key alkoxy radical intermediates.

Alcohols↗

Mass spectrometry structural analysis of intrinsically disordered phosphoproteins

Phosphorylation is a ubiquitous protein modification that is known to play important roles in many biological phenomena including cell signaling, the opening and closing of membrane protein channels, and even triggering of amyloid protein aggregation. Despite the effects phosphorylation has on protein function, the impact phosphorylation has on the structure of proteins is not well understood. Here, to determine how phosphorylation affects the structure of proteins, top-down mass spectrometry (TD-MS) and ion mobility-mass spectrometry (IM-MS) were performed on various phosphorylated proteins and their dephosphorylated proteoforms. TD-MS with collision- and electron-based fragmentation techniques was utilized to locate phosphorylation sites on the intrinsically disordered amyloid proteins β-casein and α-synuclein. TD-MS also provided evidence that alkaline phosphatase dephosphorylates β-casein from the N-terminus to the C-terminus. Furthermore, IM-MS of common phosphorylated proteins such as β-casein, α-casein, ovalbumin, and phosvitin indicates that phosphorylation promotes compaction of protein structure in denaturing as well as native conditions. Increases in abundance of more compact conformers are also observed when the disease related amyloid protein α-synuclein is phosphorylated at serine 129. We interpret the increased abundance of more compact conformers when proteins are phosphorylated as evidence that salt bridges form between negatively charged phosphates and positively charged residues, which alters protein structure. Salt bridge formation due to phosphorylation could be a mechanism for regulating protein function and be responsible for many of the phenomena observed in nature.

Amyloid proteins↗

Alpha-decay induced shortening of fission tracks simulated by in situ ion irradiation

The diffusion of defects (e.g., vacancies and interstitials) and elements used for dating (e.g., He and Pb) in a mineral structure is a thermal process: This is the primary assumption used to determine the age and thermal history of minerals. For instance, thermal history reconstruction, through the number and length distribution of tracks produced by spontaneous fission of 238 U, is obtained by assuming a thermal event to be the only energy source for shortening of fission tracks. Here, we report a new, non-thermal energy source that induces additional shortening of fission tracks by the irradiation of alpha-recoils from the alpha-decay of 238 U and 232 Th. We simulate alpha-decay induced track-shortening by combining ion accelerator irradiations with transmission electron microscopy. This allows for the first observation of track-shrinkage during in situ ion irradiation. We show that rather than alpha-particles, alpha-recoils induce a significant shortening of fission tracks by nuclear-collisions. The shortening of track-length can be quantified as a function of alpha-decay event dose. However, apatite is less sensitive than zircon to this non-thermal process. Furthermore, the findings exemplify the interactions among different types of self-irradiation from alpha-particles, alpha-recoils and fission-fragment nuclei in single mineral grains and have important implications for the use of zircon and apatite for radiometric dating and thermochronology.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Small-𝑥 Factorization in the Target Fragmentation Region

We consider the differential cross-section for single-inclusive jet production with transverse momentum 𝑃 ⊥ in deep inelastic scattering at small Bjorken 𝑥 Bj , mediated by a virtual photon with virtuality 𝑄 2 . Unlike most studies at small 𝑥, which focus on particle production in the current fragmentation region, we investigate the kinematic regime where the jet is produced in the target fragmentation hemisphere of the Breit frame, and with 𝑃 ⊥ ≪ 𝑄. For a longitudinally polarized photon, we demonstrate that this cross section is not power suppressed in 𝑃 ⊥ /𝑄 and we derive a factorized expression in terms of extended quark and gluon jet fracture functions. Our formula, valid at next-to-leading order in 𝛼 𝑠 at small 𝑥, is akin to the Altarelli-Martinelli identity for the longitudinal DIS structure function. Numerical estimates show that the extended quark jet fracture function is the most sensitive to saturation effects in large nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

AlphaFold -assisted structure determination of a bacterial protein of unknown function using X-ray and electron crystallography

Macromolecular crystallography generally requires the recovery of missing phase information from diffraction data to reconstruct an electron-density map of the crystallized molecule. Most recent structures have been solved using molecular replacement as a phasing method, requiring an a priori structure that is closely related to the target protein to serve as a search model; when no such search model exists, molecular replacement is not possible. New advances in computational machine-learning methods, however, have resulted in major advances in protein structure predictions from sequence information. Methods that generate predicted structural models of sufficient accuracy provide a powerful approach to molecular replacement. Taking advantage of these advances, AlphaFold predictions were applied to enable structure determination of a bacterial protein of unknown function (UniProtKB Q63NT7, NCBI locus BPSS0212) based on diffraction data that had evaded phasing attempts using MIR and anomalous scattering methods. Using both X-ray and micro-electron (microED) diffraction data, it was possible to solve the structure of the main fragment of the protein using a predicted model of that domain as a starting point. The use of predicted structural models importantly expands the promise of electron diffraction, where structure determination relies critically on molecular replacement.

molecular replacement↗

Measurement of isolated-photon plus two-jet production in p p collisions at s = 13 TeV with the ATLAS detector

The dynamics of isolated-photon plus two-jet production in pp collisions at a centre-of-mass energy of 13 TeV are studied with the ATLAS detector at the LHC using a dataset corresponding to an integrated luminosity of 36.1 fb−1. Cross sections are measured as functions of a variety of observables, including angular correlations and invariant masses of the objects in the final state, γ+jet+jet. Measurements are also performed in phase-space regions enriched in each of the two underlying physical mechanisms, namely direct and fragmentation processes. The measurements cover the range of photon (jet) transverse momenta from 150 GeV (100 GeV) to 2 TeV. The tree-level plus parton-shower predictions from SHERPA and PYTHIA as well as the next-to-leading-order QCD predictions from SHERPA are compared with the measurements. The next-to-leading-order QCD predictions describe the data adequately in shape and normalisation except for regions of phase space such as those with high values of the invariant mass or rapidity separation of the two jets, where the predictions overestimate the data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Ambient Mass Spectrometry Rapid Analysis Methods for Trace Inorganics

The ability to rapidly detect and characterize the chemistry of trace quantities of inorganic species has multiple potential applications, including nuclear safeguards, nuclear forensics, and environmental monitoring. Some mass spectrometric methods currently exist, but they are costly and time-intensive, often destroying chemical information in the process of ionization. Ambient mass spectrometry is a relatively new analytical method in which samples are introduced to the mass spectrometer from atmospheric pressure, rather than from high vacuum. Ambient MS can operate with gentler ionization methods such as electrospray ionization (ESI) and paper-spray ionization (PSI), reducing fragmentation and preserving the chemical information of the analyte. This may be useful for determining the intended purpose of material in a sample. Strontium, part of nuclear fallout, is analyzed here to test these new analytical methods for viability. Electrospray ionization mass spectrometry functions by spraying the sample as a solution through a needle charged to a few kV. A nebulizing gas flows out along with the sample to create the spray before droplets enter a drying chamber with heated drying gas to remove the solvent molecules. From there bare analyte ions enter the mass spectrometer. This method has the advantage of relatively fast sample preparation and stable ionization. More stable ionization produces higher-quality data. Paper-spray ionization mass spectrometry operates by applying sample to a paper triangle. The paper triangle is then electrified in a metal clamp to a few kV before spray solvent is applied. The spray solvent transports analyte in the sample to the tip, where it is ionized and enters the mass spectrometer. One advantage of this method is reduced sample preparation - an analyst can even swipe a surface and cut a triangle directly from the swipe. The data analysis serves to rapidly process tens of samples all at once. The mass spectrometer outputs a file containing a few hundred spectra for each sample. The pipeline processes each one to identify peaks of interest. A full palette of data analysis metrics are generated, including plots of the raw data and plots of calculated values such as isotopic ratios. The pipeline filters the raw data to remove noise and background peaks, as well as peaks representing detector saturation. A heat map is generated to show the overall spectrum in mass-time- intensity space. Post-processing, we obtained the desired calibration curves, demonstrating that both ESI-MS and PSI-MS are viable methods for quantifying trace amounts of inorganics while retaining their chemical speciation information. ESI-MS demonstrated a linear response region of 100 ppb to 20 ppm, with a limit-of-detection of around 100 ppb. At top left is an example spectrum with the {sup 88}SrNO{sub 3} peak identified to show the retention of chemical speciation. PSI-MS showed a linear response region of around 1 ppb to 1 ppm, with a limit-of-detection of near 1 ppb. PSI-MS produced more erratic results than ESI-MS, likely due to the variability in ionization resulting from manual positioning of the paper triangle near the MS inlet. Future efforts will focus on improving the repeatability of PSI-MS as well as analyzing other species of interest such as cerium and uranium. Improvements will also be made to create more reliable data extraction and intelligent data filtering.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Reaction Chemistry at Discrete Organometallic Fragments on Black Phosphorus

Abstract Black phosphorus (bP) is a two‐dimensional van der Waals material unique in its potential to serve as a support for single‐site catalysts due to its similarity to molecular phosphines, ligands quintessential in homogeneous catalysis. However, there is a scarcity of synthetic methods to install single metal centers on the bP lattice. Here, we demonstrate the functionalization of bP nanosheets with molecular Re and Mo complexes. A suite of characterization techniques, including infrared, X‐ray photoelectron and X‐ray absorption spectroscopy as well as scanning transmission electron microscopy corroborate that the functionalized nanosheets contain a high density of discrete metal centers directly bound to the bP surface. Moreover, the supported metal centers are chemically accessible and can undergo ligand exchange transformations without detaching from the surface. The steric and electronic properties of bP as a ligand are estimated with respect to molecular phosphines. Sterically, bP resembles tri(tolyl)phosphine when monodentate to a metal center, and bis(diphenylphosphino)propane when bidentate, whereas electronically bP is a σ‐donor as strong as a trialkyl phosphine. This work is foundational in elucidating the nature of black phosphorus as a ligand and underscores the viability of using bP as a basis for single‐site catalysts.

Mitra, Kendahl L. Walz↗