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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 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

CFM-ID 4.0: More Accurate ESI MS/MS Spectral Prediction and Compound Identification

In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for identifying and annotating metabolites. As this typically involves matching a given MS spectrum against an experimentally acquired reference spectral library, this approach is limited by the coverage and size of such libraries (which typically number in the thousands). These experimental libraries can be greatly extended by predicting the MS spectra of known chemical structures (which number in the millions) to create computational reference spectral libraries. To facilitate the generation of predicted spectral reference libraries we developed CFM-ID, a computer program that can accurately predict ESI-MS/MS spectrum for a given compound structure. CFM-ID is one of the best-performing methods for compound-to-mass-spectrum prediction, and also one of the top tools for in silico mass-spectrum-to-compound identification. This work improves CFM-ID’s ability to predict ESI-MS/MS spectra from compounds by: (1) learning parameters from features based on the molecular topology, (2) adding a new approach to ring cleavage that models such cleavage as a sequence of simple chemical bond dissociations and (3) expanding its hand-written rule-based predictor to cover more chemical classes, including acylcarnitines, acylcholines, flavonols, flavones, flavanones, and flavonoid glycosides. We demonstrate that this new version of CFM-ID (version 4.0) is significantly more accurate than previous CFM-ID versions, in terms of both EI-MS/MS spectral prediction and compound identification. CFM-ID 4.0 is available at http://cfmid4.wishartlab.com/ as a webservice and docker images can be downloaded at https://hub.docker.com/r/wishartlab/cfmid

Wang, Fei↗
DOE OSTI2025

Pd–Methyl Bond Energy─Property Correlations, Noncorrelations, Machine Learning Models, and Application to Polymerization Catalysis

Metal–carbon bonds are a key intermediate in a variety of homogeneous organometallic transformations and often determine the critical thermodynamics and kinetics of catalytic processes. Surprisingly, the influence of different ligands on metal–carbon bond strengths has been largely overlooked. Here, in this study, we evaluated nearly 700 experimental Pd–methyl complexes by calculating their bond dissociation energies using density functional theory (DFT) and compared these bond strengths to several fundamental molecular properties, and this revealed several surprising correlations and noncorrelations. Most surprising was that several fundamental properties, such as the bond length, bond force constant, and bond electron density, have no correlation with bond strength, despite these correlations often holding for main-group compounds. We were indeed able to identify key ligand-dependent chemical features/descriptors that provided a highly accurate machine learning model and provided insight into the general factors that control the Pd–carbon bond strength, such as radical delocalization and nucleophilicity. Insights gained from the Pd–Me bond energy analysis were then applied to CO migratory insertion steps that are part of copolymerization reactions.

binding energy↗
DOE OSTI2024

Negative components in the representation $\frac{𝑑^{2}⁡(𝜎⁢𝐸)}{𝑑⁡𝐸^2}$ of heavy-ion fusion cross sections

Negative components are observed in the representation $\frac{𝑑^{2}⁡(𝜎⁢𝐸)}{𝑑⁡𝐸^2}$ in heavy-ion fusions related to recent studies of noticeable oscillations in the high-energy region of the fusion excitation functions. A modified multiGaussian model has been developed, which includes contributions for both positive and negative components in the $\frac{𝑑^{2}⁡(𝜎⁢𝐸)}{𝑑⁡𝐸^2}$ representation. The model reproduces the heavy-ion fusion excitation functions very well, including oscillations. The property of these negative components in the $\frac{𝑑^{2}⁡(𝜎⁢𝐸)}{𝑑⁡𝐸^2}$ spectrum and the reaction mechanism of fusion at energies above the Coulomb barrier are investigated. Finally, the model also reproduces well light heavy-ion fusion reactions between 12 C and 16 O at high energy; results imply that the compound nucleus channel effect may have an important contribution at the high energy region for all fusion systems.

low & intermediate energy heavy-ion reactions↗
DOE OSTI2020

Photolysis Controls Atmospheric Budgets of Biogenic Secondary Organic Aerosol

Secondary organic aerosol (SOA) accounts for a large fraction of tropospheric particulate matter. While SOA production rates and mechanisms have been extensively investigated, loss pathways remain uncertain. Most large-scale chemistry and transport models account for mechanical deposition of SOA, but not chemical losses, such as photolysis. There is also a paucity of laboratory measurements of SOA photolysis, which limits how well photolytic losses can be modeled. Here we show, through a combined experimental and modeling approach, that photolytic loss of SOA mass significantly alters SOA budget predictions. Using environmental chamber experiments, we find that SOA produced from several biogenic volatile organic compounds (VOCs) undergoes photolysis-induced mass loss at rates between 0 and 2.2% ± 0.4% of nitrogen dioxide (NO 2 ) photolysis, equivalent to average atmospheric lifetimes as short as 10 hours. We incorporate our photolysis rates into a regional chemical transport model to test the sensitivity of predicted SOA mass concentrations to photolytic losses. The addition of photolysis at rates consistent with our experimental conditions causes a ~50% reduction in biogenic SOA loadings over the Amazon, indicating that photolysis exerts a substantial control over the atmospheric SOA lifetime, with a likely dependence upon SOA molecular composition and thus production mechanisms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Tensor network investigation of the double layer Kagome compound Ca 10 Cr 7 O 28

Quantum spin liquids are exotic quantum phases of matter that do not order even at zero temperature. While there are several toy models and simple Hamiltonians that could host a quantum spin liquid as their ground state, it is very rare to find actual, realistic materials that exhibit their properties. At the same time, the classical simulation of such instances of strongly correlated systems is intricate and reliable methods are scarce. Here, in this work, we investigate the quantum magnet Ca 10 Cr 7 O 28 that has recently been discovered to exhibit properties of a quantum spin liquid in inelastic neutron scattering experiments. This compound has a distorted bilayer Kagome lattice crystal structure consisting of Cr 5+ ions with spin- moments. Coincidentally, the lattice structure renders a tensor network algorithm in 2D applicable that can be seen as a new variant of a projected entangled simplex state algorithm in the thermodynamic limit. In this first numerical investigation of this material that takes into account genuine quantum correlations, good agreement with the experimental findings is found. Our study contributes to uplifting tensor networks from conceptual tools to methods to describe real two-dimensional quantum materials.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Octofitter: Fast, Flexible, and Accurate Orbit Modeling to Detect Exoplanets

As next-generation imaging instruments and interferometers search for planets closer to their stars, they must contend with increasing orbital motion and longer integration times. These compounding effects make it difficult to detect faint planets but also present an opportunity. Increased orbital motion makes it possible to move the search for planets into the orbital domain, where direct images can be freely combined with the radial velocity and proper motion anomaly, even without a confirmed detection in any single epoch. In this paper, we present a fast and differentiable multimethod orbit-modeling and planet detection code called Octofitter. This code is designed to be highly modular and allows users to easily adjust priors, change parameterizations, and specify arbitrary function relations between the parameters of one or more planets. Octofitter further supplies tools for examining model outputs including prior and posterior predictive checks and simulation-based calibration. We demonstrate the capabilities of Octofitter on real and simulated data from different instruments and methods, including HD 91312, simulated JWST/NIRISS aperture masking interferometry observations, radial velocity curves, and grids of images from the Gemini Planet Imager. We show that Octofitter can reliably recover faint planets in long sequences of images with arbitrary orbital motion. This publicly available tool will enable the broad application of multiepoch and multimethod exoplanet detection, which could improve how future targeted ground- and space-based surveys are performed. Finally, its rapid convergence makes it a useful addition to the existing ecosystem of tools for modeling the orbits of directly imaged planets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Modeling fission dynamics at the barrier in a discrete-basis formalism

A configuration-interaction model is presented for the barrier region of induced fission. The configuration space is composed of seniority-zero configurations constructed from self-consistent mean-field wave functions. The Hamiltonian matrix elements between configurations include diabatic and pairing interactions between particles. Other aspects of the Hamiltonian are treated statistically, guided by phenomenological input of compound-nucleus transmission coefficients. In this exploratory study the configuration space is restricted to neutron excitations only. A key observable calculated in the model is the fission-to-capture branching ratio. We find that both pairing and diabatic interactions are important for achieving large branching to the fission channels. In accordance with the transition-state theory of fission, the calculated branching ratio is found to be quite insensitive to the fission decay widths of the pre-scission configurations. Furthermore, the barrier-top dynamics appear to be quite different from transition-state theory in that the transport is distributed over many excited configurations at the barrier top.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Functional promiscuity of small multidrug resistance transporters from Staphylococcus aureus , Pseudomonas aeruginosa , and Francisella tularensis

Abstract Small multidrug resistance transporters efflux toxic compounds from bacteria and are a minimal system to understand multidrug transport. Most previous studies have focused on EmrE, the model SMR from Escherichia coli , finding that EmrE has a broader substrate profile than previously thought and that EmrE may perform multiple types of transport, resulting in substrate‐dependent resistance or susceptibility . Here, we performed a broad screen to identify potential substrates of three other SMRs: PAsmr from Pseudomonas aeruginosa ; FTsmr from Francisella tularensis ; and SAsmr from Staphylococcus aureus . This screen tested metabolic differences in E. coli expressing each transporter versus an inactive mutant, for a clean comparison of sequence and substrate‐specific differences in transporter function, and identified many substrates for each transporter. In general, resistance compounds were charged, and susceptibility substrates were uncharged, but hydrophobicity was not correlated with phenotype. Two resistance hits and two susceptibility hits were validated via growth assays and IC50 calculations. Susceptibility is proposed to occur via substrate‐gated proton leak, and the addition of bicarbonate antagonizes the susceptibility phenotype, consistent with this hypothesis.

Biochemistry & Molecular Biology↗
DOE OSTI2020

ATOMIC Simulations and Experimental Data for Basalt-like Compounds

This data consists of simulations and experimental measurements of laser-induced breakdown spectroscopy (LIBS). The simulations are produced by ATOMIC, a general purpose plasma modeling and kinetics code that has been designed to compute emission (or absorption) spectra from plasmas [2]. The makeup of the plasma was considered to be divided into some proportion water, some proportion Martian atmosphere (CO2), and some proportion target (from the rock or object impacted by the laser), where these proportions add to 1. Based on expert knowledge, the proportion of water was kept in the range [0.0,0.5] and the proportion of atmosphere was kept in the range [0.02, 0.9]. Our overall suite of simulations contains six sets of simulations that differ in which elements were considered to make up the target. Within each set, we used uniformly drawn temperatures and log mass densities within pre-specified ranges. The temperature range was [0.5,1.5] eV and the log (base 10) mass density range was [-7,-4]. The proportion of water, atmosphere, and target were drawn from a symmetric Dirichlet distribution, but draws in which the propor- tion of water or atmosphere exceeded the pre-specified limits were rejected from the design. Up to eleven constituent elements (Si, Al, Fe, Mg, Ca, O, Ti, Mn, Na, K, P) were considered for the target, as they are the most common elements found in basalt compounds and were used in [1]. For each run, the proportions of the constituent elements making up the target were drawn from a symmetric Dirichlet distribution. We ran 1,350 simulations that included nonzero proportions of all eleven elements. We also ran simulations which excluded some of these elements. In particular, we ran 1,000 simulations that only included nonzero proportions for the six most common elements (Si, Al, Fe, Mg, Ca, O). We also ran five sets, each with 500 simulations, that only included nonzero proportions for five of the six most common elements (but where all sets included O). Thus, we generated a total of 4,850 spectra representing basalt-like compounds in which the target was comprised of oxygen and between four and ten other elements. The ATOMIC code produced spectra over a range of 240nm - 880nm that roughly mimics the range collected by the ChemCam instrument on the Mars rover Curiosity. Each spectra had 32,000 wavelengths split across three spectrometer ranges (to mimic ChemCam). The experimental data, described in [1], measures a prepared basalt sample. All files are kept in directories whose names indicate the set of elements considered for the target with file names numbered to indicate the line in the design files used to produce the simulation. The designs are provided as text files with names indicating their purpose. The experimental data is provided as a CSV file which contains a header with measurement information, followed by a collection of 50 shots across a collection of wavelengths, along with the computed median and mean across shots.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Preparation and Characterization of Inclusion Complexes of β-Cyclodextrin and Phenolics from Wheat Bran by Combination of Experimental and Computational Techniques

Bitterness often associated with whole wheat products may be related to phenolics in the bran. Cyclodextrins (CDs) are known to form inclusion complexes. The objective was to form inclusion complexes between β-CD and wheat phenolics. Pure phenolic acids (trans-ferulic acid (FA), caffeic acid (CA), and p-coumaric acid (CO)) and phenolic acids from wheat bran were used to investigate complex formation potential. Complexes were characterized by spectroscopy techniques, and a computational and molecular modeling study was carried out. The relative amount of complex formation between β-CD and wheat bran extract was CA > CO > FA. The phenolic compounds formed inclusion complexes with β-CDs by non-covalent bonds. The quantum-mechanical calculations supported the experimental results. The most stable complex was CO/β-CD complex. The ΔH value for CO/β-CD complex was -11.72 kcal/mol and was about 3 kcal/mol more stable than the other complexes. The QSPR model showed good correlation between binding energy and 1H NMR shift for the H5 signal. This research shows that phenolics and β-CD inclusion complexes could be utilized to improve the perception of whole meal food products since inclusion complexes have the potential to mask the bitter flavor and enhance the stability of the phenolics in wheat bran.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Lignin-Derived Phenolic Compounds and Water Are Effective Cosolvents for Reductive Catalytic Fractionation

Reductive catalytic fractionation (RCF) is an effective lignin-first biorefining method to extract lignin as a stabilized oil from lignocellulosic biomass. To realize RCF at scale, process modeling has shown that minimizing the use of exogenous organic solvents is critical. To this end, here we investigate the ability of lignin-derived monomers to act as either solvents or cosolvents for RCF. We begin by examining the influence of lignin-derived aromatic compounds (4-propylguaiacol, 4-propylphenol, and propylbenzene) on RCF monomer yields and subsequently extend our analysis to mixtures of 4-propylguaiacol and either methanol or water. Here, we demonstrate that 4-propylguaiacol is an effective solvent for lignin extraction and depolymerization during RCF, especially when used in combination with water as a cosolvent. Cosolvent mixtures of 4-propylguaiacol and water enable up to 81% lignin extraction, monomer yields up to 25 wt %, and postreaction phase separation. However, unlike methanol, water as a cosolvent fails to inhibit aromatic ring hydrogenation when conducted over Ru/C as a catalyst, potentially leading to excess hydrogen consumption in a process utilizing this approach. Nonetheless, these results suggest a promising strategy for eliminating external organic solvents from RCF by utilizing mixtures of lignin-derived compounds and water as alternative extraction solvents.

09 BIOMASS FUELS↗
DOE OSTI2026

Tabulated data for Lignin-Derived Phenolic Compounds and Water Are Effective Cosolvents for Reductive Catalytic Fractionation

Reductive catalytic fractionation (RCF) is an effective lignin-first biorefining method to extract lignin as a stabilized oil from lignocellulosic biomass. To realize RCF at scale, process modeling has shown that minimizing the use of exogenous organic solvents is critical. To this end, here we investigate the ability of lignin-derived monomers to act as either solvents or cosolvents for RCF. We begin by examining the influence of lignin-derived aromatic compounds (4-propylguaiacol, 4-propylphenol, and propylbenzene) on RCF monomer yields and subsequently extend our analysis to mixtures of 4-propylguaiacol and either methanol or water. We demonstrate that 4-propylguaiacol is an effective solvent for lignin extraction and depolymerization during RCF, especially when used in combination with water as a cosolvent. Cosolvent mixtures of 4-propylguaiacol and water enable up to 81% lignin extraction, monomer yields up to 25 wt %, and postreaction phase separation. However, unlike methanol, water as a cosolvent fails to inhibit aromatic ring hydrogenation when conducted over Ru/C as a catalyst, potentially leading to excess hydrogen consumption in a process utilizing this approach. Nonetheless, these results suggest a promising strategy for eliminating external organic solvents from RCF by utilizing mixtures of lignin-derived compounds and water as alternative extraction solvents. This is the tabulated data for the paper

biorefining↗
DOE OSTI2026

Lignin-Derived Phenolic Compounds and Water Are Effective Cosolvents for Reductive Catalytic Fractionation

Reductive catalytic fractionation (RCF) is an effective lignin-first biorefining method to extract lignin as a stabilized oil from lignocellulosic biomass. To realize RCF at scale, process modeling has shown that minimizing the use of exogenous organic solvents is critical. To this end, here we investigate the ability of lignin-derived monomers to act as either solvents or cosolvents for RCF. We begin by examining the influence of lignin-derived aromatic compounds (4-propylguaiacol, 4-propylphenol, and propylbenzene) on RCF monomer yields and subsequently extend our analysis to mixtures of 4-propylguaiacol and either methanol or water. We demonstrate that 4-propylguaiacol is an effective solvent for lignin extraction and depolymerization during RCF, especially when used in combination with water as a cosolvent. Cosolvent mixtures of 4-propylguaiacol and water enable up to 81% lignin extraction, monomer yields up to 25 wt %, and postreaction phase separation. However, unlike methanol, water as a cosolvent fails to inhibit aromatic ring hydrogenation when conducted over Ru/C as a catalyst, potentially leading to excess hydrogen consumption in a process utilizing this approach. Nonetheless, these results suggest a promising strategy for eliminating external organic solvents from RCF by utilizing mixtures of lignin-derived compounds and water as alternative extraction solvents.

biorefining↗
DOE OSTI2025

Harnessing the Power of Machine Learning and Omics to Identify Environmental Regulation on Microbial Functional Composition for Soil C, N, and P Cycling

Microbial enzyme-mediated soil organic matter (SOM) decomposition regulates many key ecosystem functions, such as elemental cycling, soil carbon sequestration, and soil fertility. However, representing microbial processes in Earth system models (ESMs) remains challenging due to a limited understanding of the spatial patterns of diverse microbial functions responsible for soil carbon (C), nitrogen (N), and phosphorus (P) cycling as well as the underlying mechanisms regulating their relative abundances across various environments. We collected published metagenomics data across the continental US (CONUS) to identify hundreds of microbial genes involved in soil C, N, and P cycling and grouped them into eight enzyme functional classes (EFCs). Each EFC represented a group of gene-encoded potential enzymes that decompose similar soil compounds. By integrating the abundances of omics-informed EFCs with the corresponding environmental information, we trained a machine learning (ML) model to identify key edaphic, climate, and vegetation factors regulating the abundances of each EFC. Quantitative analysis of effects of these factors revealed that the spatial distribution of eight EFCs for soil C, N, and P cycling across CONUS reflected potential resource optimization strategies of microbial communities under nutrient limitation, preferential organic-mineral associations, and climatological stresses. This insight, together with the interpreted ML tool and the CONUS-level benchmark for EFCs abundances, paves the way for parameterizing environmental-regulated microbial functional dynamics in biogeochemical models.

machine learning↗
DOE OSTI2024

High‐Order Nonlinear Frequency Conversion in Transparent Conducting Oxide Thin Films

The study of conductive oxides has gained momentum within the photonics community due to their unique linear and nonlinear optical properties. Despite recent experiments reporting on high harmonic generation from thin films, the optical/electronic behavior of these compounds at the nanoscale is still not fully understood due to the lack of a suitable theoretical model. In the present work, aluminum zinc oxide is excited near its epsilon-near-zero crossing point using incident femtosecond pulses having peak power densities in the 1 TW cm −2 range. A relatively efficient frequency up-conversion including even and odd harmonics up to the seventh order is observed. A hydrodynamic-Maxwell theoretical approach is adopted, capable of simultaneously taking into account linear and nonlinear dispersions, nonlocal effects, surface, magnetic, and bulk nonlinearities in a spectral region that spans over two and a half octaves from the UV to the NIR region. The study enables a deeper understanding of the fundamental material parameters regulating optical nonlinearities, providing important insights to engineer this class of materials for applications in sensing, ultra-fast physics, and spectroscopy.

material modeling↗
DOE OSTI2021

Discovery of TAK-981, a First-in-Class Inhibitor of SUMO-Activating Enzyme for the Treatment of Cancer

SUMOylation is a reversible post-translational modification that regulates protein function through covalent attachment of small ubiquitin-like modifier (SUMO) proteins. The process of SUMOylating proteins involves an enzymatic cascade, the first step of which entails the activation of a SUMO protein through an ATP-dependent process catalyzed by SUMO-activating enzyme (SAE). Here, we describe the identification of TAK-981, a mechanism-based inhibitor of SAE which forms a SUMO–TAK-981 adduct as the inhibitory species within the enzyme catalytic site. Optimization of selectivity against related enzymes as well as enhancement of mean residence time of the adduct were critical to the identification of compounds with potent cellular pathway inhibition and ultimately a prolonged pharmacodynamic effect and efficacy in preclinical tumor models, culminating in the identification of the clinical molecule TAK-981.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Future Anthropogenic Land Use Change Impacts on Carbonaceous Aerosol and Implications for Climate and Air Quality

Future anthropogenic land use change (LUC) may alter atmospheric carbonaceous aerosol (black carbon and organic aerosol) burden by perturbing biogenic and fire emissions. However, there has been little investigation of this effect. We examine the global evolution of future carbonaceous aerosol under the Shared Socioeconomic Pathways projected reforestation and deforestation scenarios using the CESM2 model from present‐day to 2100. Compared to present‐day, the change in future biogenic volatile organic compounds emission follows changes in forest coverage, while fire emissions decrease in both projections, driven by trends in deforestation fires. The associated carbonaceous aerosol burden change produces moderate aerosol direct radiative forcing (−0.021 to +0.034 W/m 2 ) and modest mean reduction in PM 2.5 exposure (−0.11 μg/m 3 to −0.23 μg/m 3 ) in both scenarios. We find that future anthropogenic LUC may be more important in determining atmospheric carbonaceous aerosol burden than direct anthropogenic emissions, highlighting the importance of further constraining the impact of LUC.>

anthropogenic land use change↗