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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Proteomics-Based Tools for Evaluation of Cell-Free Protein Synthesis

Cell-free protein synthesis (CFPS) has the potential to produce enzymes, therapeutic agents, and other proteins, while circumventing difficulties associated with in vivo heterologous expression. However, the contents of the cell-free extracts used to carry out synthesis are generally not characterized, which hampers progress toward enhancing yield or functional activity of the target protein. Here we explored the utility of mass spectrometry (MS)-based proteomics for characterizing the bacterial extracts used for transcribing and translating gene sequences into proteins as well as the products of CFPS reactions. Full proteome experiments identified over 1000 proteins per reaction. The complete set of proteins necessary for transcription and translation were found, demonstrating the ability to define potential metabolic capabilities of the extract. Further, MS-based techniques allowed characterization of the CFPS product and provided insight into the synthesis reaction and potential functional activity of the product. These capabilities were demonstrated using two different CFPS products, the commonly used standard green fluorescent protein (GFP, 27 kDa) and the polyketide synthase DEBS1 (394 kDa). For the large, multidomain DEBS1, substantial premature termination of protein translation was observed. Additionally, MS/MS analysis, as part of a conventional full proteomics workflow, identified post-translational modifications, including the chromophore in GFP, as well as the three phosphopantetheinylation sites in DEBS1. A hypothesis-driven approach focused on these three sites identified that all were correctly modified for DEBS1 expressed in vivo but with less complete coverage for protein expressed in CFPS reactions. These post-translational modifications are essential for functional activity, and the ability to identify them with mass spectrometry is valuable for judging the success of the CFPS reaction. Collectively, the use of MS-based proteomics will prove advantageous for advancing the application of CFPS and related techniques.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Solving the Trivial Crossing Problem While Preserving the Nodal Symmetry of the Wave Function

In an adiabatic mixed quantum-classical simulation, the avoided crossing of weakly coupled eigenstates can lead to unphysical discontinuities in wave function dynamics, otherwise known as the trivial crossing problem. A standard solution to the trivial crossing problem eliminates spatial discontinuities in wave function dynamics by imposing changes to the eigenstate of the wave function. In this paper, we show that this solution has the side effect of introducing transient discontinuities in the nodal symmetry of the wave function. We present an alternative solution to the trivial crossing problem that preserves both the spatial and nodal structure of the adiabatic wave function. By considering a model of exciton dynamics on conjugated polymer systems, we show that failure to preserve wave function symmetry yields exciton dynamics that depends unphysically on polymer system size. We demonstrate that our symmetry-preserving solution to the trivial crossing problem yields more realistic dynamics and can thus improve the accuracy of simulations of larger systems that are prone to the trivial crossing problem.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Baseflow Identification via Explainable AI With Kolmogorov‐Arnold Networks

Abstract Hydrological models often involve constitutive laws that may not be optimal in every application. We propose to replace such laws with the Kolmogorov‐Arnold networks (KANs), a class of neural networks designed to identify symbolic expressions. We demonstrate KAN's potential on the problem of baseflow identification, a notoriously challenging task plagued by significant uncertainty. KAN‐derived functional dependencies of the baseflow components on the aridity index outperform their original counterparts; they demonstrate that water availability, rather than potential evapotranspiration, drives baseflow by constraining actual evapotranspiration under arid conditions. On a test set, they increase the Nash‐Sutcliffe efficiency (NSE) by 65%, decrease the root mean squared error by 29%, and increase the Kling‐Gupta efficiency by 34%. This superior performance is achieved while reducing the number of fitting parameters from three to two. Next, we use data from 378 catchments across the continental United States to refine the water‐balance equation at the mean‐annual scale. The KAN‐derived equations based on the refined water balance outperform both the current aridity index model, with up to a 105% increase in NSE, and the KAN‐derived equations based on the original water balance. While the performance of our model and tree‐based machine learning methods is similar, KANs offer the advantage of simplicity and transparency and require no specific software or computational tools. This case study focuses on the aridity index formulation, but the approach is flexible and transferable to other hydrological processes. Plain Language Summary Equations used in hydrologic model are often suboptimal, resulting in reduced prediction accuracy and efficiency. We implemented Kolmogorov‐Arnold networks (KAN), a machine learning algorithm for deriving symbolic formulations, to estimate groundwater recharge and showed that it outperforms an existing state‐of‐the‐art semi‐empirical formulation. In hydrology, Nash‐Sutcliffe efficiency (NSE), root mean squared error (RMSE), and Kling‐Gupta efficiency (KGE) are commonly used to evaluate model performance. Higher NSE and KGE values indicate better performance, while lower RMSE values are preferable. Our results show that NSE increased by 71%, RMSE decreased by 32%, and KGE improved by 25%. In addition, KAN identifies an optimal functional form and can be used to derive new analytical formulas using the prior knowledge. The KAN‐inspired equation outperformed the original formulation and reduced the fitting parameters. Furthermore, we refined the water‐balance equation at the mean‐annual scale and showed that, based on the new water‐balance equation, KAN can derive new formulations that are superior to the original aridity index formulations (up to 105% increase in NSE) and KAN‐derived equations based on the original water balance. These findings highlight the significant potential of KAN to advance the scientific understanding of a wide range of hydrologic processes. Key Points Kolmogorov‐Arnold networks (KANs) enhance interpretability of machine‐learned hydrological models KAN‐derived symbolic formulations outperform state‐of‐the‐art semi‐empirical aridity indices KAN‐identified functional form yields an analytical index with fewer fitting parameters and improved performance

baseflow↗
DOE OSTI2021

SuFExable polymers with helical structures derived from thionyl tetrafluoride

Sulfur(VI) fluoride exchange (SuFEx) is a category of click chemistry that enables covalent linking of modular units through sulfur(VI) connective hubs. The efficiency of SuFEx and the stability of the resulting bonds have led to polymer chemistry applications. Now, we report the SuFEx click chemistry synthesis of several structurally diverse SOF 4 -derived copolymers based on the polymerization of bis(iminosulfur oxydifluorides) and bis(aryl silyl ethers). This polymer class presents two key characteristics. First, the [-N=S(=O)F-O-] polymer backbone linkages are themselves SuFExable and undergo precise SuFEx-based post-modification with phenols or amines to yield branched functional polymers. Second, studies of individual polymer chains of several of these new materials indicate helical polymer structures. The robust nature of SuFEx click chemistry offers the potential for post-polymerization modification, enabling the synthesis of materials with control over composition and conformation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Mechanism of NMDA receptor channel block by MK-801 and memantine

The NMDA (N-methyl-d-aspartate) receptor transduces the binding of glutamate and glycine, coupling it to the opening of a calcium-permeable ion channel. Owing to the lack of high-resolution structural studies of the NMDA receptor, the mechanism by which ion-channel blockers occlude ion permeation is not well understood. Here we show that removal of the amino-terminal domains from the GluN1–GluN2B NMDA receptor yields a functional receptor and crystals with good diffraction properties, allowing us to map the binding site of the NMDA receptor blocker, MK-801. Here, this crystal structure, together with long-timescale molecular dynamics simulations, shows how MK-801 and memantine (a drug approved for the treatment of Alzheimer’s disease) bind within the vestibule of the ion channel, promote closure of the ion channel gate and lodge between the M3-helix-bundle crossing and the M2-pore loops, physically blocking ion permeation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Targeting colorectal cancer with small-molecule inhibitors of ALDH1B1

Aldehyde dehydrogenases (ALDHs) are promising cancer drug targets, as certain isoforms are required for the survival of stem-like tumor cells. We have discovered selective inhibitors of ALDH1B1, a mitochondrial enzyme that promotes colorectal and pancreatic cancer. We describe bicyclic imidazoliums and guanidines that target the ALDH1B1 active site with comparable molecular interactions and potencies. Both pharmacophores abrogate ALDH1B1 function in cells; however, the guanidines circumvent an off-target mitochondrial toxicity exhibited by the imidazoliums. Our lead isoform-selective guanidinyl antagonists of ALDHs exhibit proteome-wide target specificity, and they selectively block the growth of colon cancer spheroids and organoids. Finally, we have used genetic and chemical perturbations to elucidate the ALDH1B1-dependent transcriptome, which includes genes that regulate mitochondrial metabolism and ribosomal function. Our findings support an essential role for ALDH1B1 in colorectal cancer, provide molecular probes for studying ALDH1B1 functions and yield leads for developing ALDH1B1-targeting therapies.

36 MATERIALS SCIENCE↗
DOE OSTI2023

An analytic and complete equation of state for condensed phase materials

Analytic equations of state (EOS) are intended to reproduce theoretical and experimental data in a single phase portion of the thermodynamic space. We devise a complete and thermodynamically consistent model with four distinct features: (1) a reference isotherm that remains thermodynamically stable, (2) a flexible specific heat model based on a fourth-order rational polynomial, (3) a Grüneisen parameter that depends on specific volume and temperature, and (4) pressure and internal energy functions that can be inverted analytically in temperature. The model aims to improve the accuracy of existing equations of state while remaining computationally efficient. To demonstrate its features, we include calibrations for single-crystal pentaerythritol tetranitrate (PETN), liquid nitromethane (NM), and hexagonal close-packed beryllium (Be) metal. The parameter optimization uses the specific heat capacity, Grüneisen parameter, and static compression curves obtained from density functional theory for the crystalline solids and molecular dynamics simulations for liquid NM. We also present a velocity autocorrelation function that yields accurate phonon densities of states for the EOS calibration from the molecular dynamics trajectories. Each of the three calibrations is constrained to enforce the ambient state from experimental measurements and validated against experimental Hugoniot data from multiple sources. We also include one-dimensional hydrodynamic simulations of the isentropic compression experiments for beryllium conducted at the Z facility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Formation of the oxyl’s potential energy surface by the spectral kinetics of a vibrational mode

One of the most reactive intermediates for oxidative reactions is the oxyl radical, an electron-deficient oxygen atom. The discovery of a new vibration upon photoexcitation of the oxygen evolution catalysis detected the oxyl radical at the SrTiO3 surface. The vibration was assigned to a motion of the sub-surface oxygen underneath the titanium oxyl (Ti–O●−) created upon hole transfer to (or electron extraction from) a hydroxylated surface site. Evidence for such an interfacial mode is derived from its spectral shape, which exhibited a Fano resonance—a coupling of a sharp normal mode to continuum excitations. Here, this Fano resonance is utilized to derive precise formation kinetics of the oxyl radical and its associated potential energy surface (PES). From the Fano lineshape, the formation kinetics are obtained from the anti-resonance (the kinetics of the coupling factor), the resonance (the kinetics of the coupled continuum excitations), and the frequency integrated spectrum (the kinetics of the normal mode’s cross-section). All three perspectives yield logistic function growth with a half-rise of 2.3 ± 0.3 ps and a time constant of 0.48 ± 0.09 ps. A non-equilibrium transient associated with photoexcitation is separated from the rise of the equilibrated PES. The logistic function characterizes the oxyl coverage at the very initial stages (t ∼ 0) to have an exponential growth rate that quickly decreases toward zero as a limiting coverage is reached. Such time-dependent reaction kinetics identify a dynamic activation barrier associated with the formation of a PES and quantify it for oxyl radical coverage.

Chemistry↗
DOE OSTI2025

Asymptotic scaling laws for the stagnation conditions of Z-pinch implosions

Implosions of magnetically driven annular shells (Z pinches) are studied in the laboratory to produce high-energy-density plasmas. Such plasmas have a wide-range of applications including x-ray generation, controlled thermonuclear fusion, and astrophysics studies. In this work, we theoretically investigate the in-flight dynamics of a magnetically driven, imploding cylindrical shell that stagnates onto itself upon collision on axis. The converging flow of the Z-pinch is analyzed by considering the implosion trajectory in the (A, M) parametric plane, where A is the in-flight aspect ratio and M is the implosion Mach number. For an ideal implosion in the absence of instabilities and in the limit of A ≫ 1, we derive asymptotic scaling laws for hydrodynamic quantities evaluated at stagnation (e.g., density, temperature, and pressure) and for performance metrics (e.g., soft x-ray emission, K-shell x-ray emission, and neutron yield) as functions of target-design parameters.

Ruiz, D. E. [Sandia National Laboratories (SNL-NM)↗
DOE OSTI2026

Fast baryonic field painting for Sunyaev-Zel’dovich analyses: Transfer function vs hybrid effective field theory

Here, we present two approaches for “painting” baryonic properties relevant to the Sunyaev-Zel’dovich (SZ) effect—optical depth and Compton-y—onto three-dimensional N-body simulations, using the MillenniumTNG suite as a benchmark. The goal of these methods is to produce fast and accurate reconstruction methods to aid future analyses of baryonic feedback using the SZ effect. The first approach employs a Gaussian process emulator to model the SZ quantities via a transfer function, while the second utilizes hybrid effective field theory (HEFT) to reproduce these quantities within the simulation. Our analysis involves comparing both methods to the true MillenniumTNG optical depth and Compton-y fields using several metrics, including the cross-correlation coefficient, power spectrum, and power spectrum error. Additionally, we assess how well the reconstructed fields correlate with dark matter haloes across various mass thresholds. The results indicate that the transfer function method yields more accurate reconstructions for fields with initially high correlations (r ≈ 1), such as between the optical depth and dark matter fields. Conversely, the HEFT-based approach proves more effective in enhancing correlations for fields with weaker initial correlations (r ∼ 0.5), such as between the Compton-y and dark matter fields. Lastly, we discuss extensions of our methods to improve the reconstruction performance at the field level.

Liu, R. Henry [University of California, Berkeley,↗
DOE OSTI2026

Nuclear cold QCD: Review and future strategy

This review examines data from hadron-nucleus collisions, primarily focusing on hard processes like Drell-Yan, heavy flavor, and quarkonium production. It highlights observed modifications of particle yields as functions of momentum and rapidity, aiming to clarify the underlying QCD effects on cold nuclear matter. It outlines strategies for future experiments, including the Electron-Ion Collider, to distinguish between these effects. Key questions address the universality of suppression mechanisms and the role of nonperturbative physics, providing a road map for upcoming measurements of hadrons on nuclei.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Longitudinal dynamics and particle production in relativistic nuclear collisions

This work presents a three-dimensional dynamical initialization model for relativistic heavy-ion collisions, implementing local energy-momentum conservation and baryon charge fluctuations at string junctions. Constraining parameters using experimental data from p + p collisions at various collision energies, the model provides a very good description of the charged hadron and net proton rapidity distributions in Au +Au collisions from 7.7 to 200 GeV and Pb + Pb collisions at 8.77 and 17.3 GeV. Here we demonstrate the importance of fluctuations of baryon densities to string junctions for describing net-proton distributions at collision energies of 62.4 and 200 GeV. Including this improved baryon stopping description along with the requirement of strangeness neutrality also yields a good description of identified particle yields as functions of the collision energy above 7.7 GeV. We further study asymmetric p + Al and (p,d, 3 He) + Au collisions at the top RHIC energy and p + Pb, Xe + Xe, and Pb + Pb collisions at LHC energies. We identify the produced particle rapidity distributions in asymmetric collision systems as particularly useful for constraining models of the early-time longitudinal dynamics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Magnetization Process of Atacamite: A Case of Weakly Coupled S = 1/2 Sawtooth Chains

We present a combined experimental and theoretical study of the mineral atacamite Cu 2 Cl(OH) 3 . Density-functional theory yields a Hamiltonian describing anisotropic sawtooth chains with weak 3D connections. Experimentally, we fully characterize the antiferromagnetically ordered state. Here, magnetic order shows a complex evolution with the magnetic field, while, starting at 31.5 T, we observe a plateaulike magnetization at about M sat /2. Based on complementary theoretical approaches, we show that the latter is unrelated to the known magnetization plateau of a sawtooth chain. Instead, we provide evidence that the magnetization process in atacamite is a field-driven canting of a 3D network of weakly coupled sawtooth chains that form giant moments.

1-dimensional spin chains↗
DOE OSTI2020

MassIVE MSV000085948 - Utilization of syringyl lignin-derived compounds and production of 2-pyrone-4,6-dicarboxylic acid by Pseudomonas putida KT2440: Lignin is an abundant aromatic polymer formed in plants by coupling reactions of p-coumaryl, coniferyl, and sinapyl alcohols. Pseudomonas putida KT2440 (P. putida KT2440), a robust soil bacterium, naturally catabolizes many aromatic compounds derived from lignin as carbon and energy sources and has been extensively engineered to valorize guaiacyl (G) and p-hydroxyphenyl (H) lignin-derived aromatic species to valuable chemicals. However, only a few studies report the capacity of Pseudomonads to grow on syringyl (S) lignin-derived compounds. In this work, we demonstrate that P. putida KT2440 catabolizes syringate in the presence of an auxiliary energy source. Overexpression of vanAB, encoding a native Rieske non-heme iron monooxygenase, enabled catabolism of syringate and syringaldehyde without an additional carbon and energy source. In vitro biochemical characterization of VanAB confirmed that this enzyme O-demethylates syringate to 3-O-methylgallate and, subsequently, 3-O-methylgallate to gallate, albeit 4- and 55-fold less efficiently than vanillate, respectively. Transcriptomics and proteomics experiments demonstrate that the galADBC transcripts and enzymes required for gallate catabolism are induced when vanAB is overexpressed during cultivation in syringate. Further, we show that that the endogenous protocatechuate-3,4-dioxygenase PcaHG ring-opens gallate to produce 2-pyrone-4,6-dicarboxylic acid (PDC), a promising bio-based chemical. Constitutive overexpression of vanAB and pcaHG along with galA deletion enabled PDC production from SA at a 70% (mol/mol) yield. Furthermore, leveraging the LigAB dioxygenase from Sphingobium sp. SYK-6 and VanAB O-demethylase from Pseudomonas sp. HR199 enabled simultaneous conversion of monomers with S-, G-, and H-type functionality to PDC at 82% (mol/mol) yield. Overall, this study elucidates a native pathway for catabolism of syringyl lignin-derived compounds in P. putida KT2440 and demonstrates the potential of this robust host for biological funneling of substrates derived from all three canonical monolignols.

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Beckham, Gregg↗
DOE OSTI2019

Dark Energy Survey year 1 results: Joint analysis of galaxy clustering, galaxy lensing, and CMB lensing two-point functions

We perform a joint analysis of the auto and cross-correlations between three cosmic fields: the galaxy density field, the galaxy weak lensing shear field, and the cosmic microwave background (CMB) weak lensing convergence field. These three fields are measured using roughly 1300 sq. deg. of overlapping optical imaging data from first year observations of the Dark Energy Survey (DES) and millimeter-wave observations of the CMB from both the South Pole Telescope Sunyaev-Zel’dovich survey and Planck. We present cosmological constraints from the joint analysis of the two-point correlation functions between galaxy density and galaxy shear with CMB lensing. We test for consistency between these measurements and the DES-only two-point function measurements, finding no evidence for inconsistency in the context of flat Λ CDM cosmological models. Performing a joint analysis of five of the possible correlation functions between these fields (excluding only the CMB lensing autospectrum) yields S 8 ≡ σ 8 $\sqrt{Ω_{m}}/0.3$ = 0.782$^{+0.019}_{-0.025}$ and Ω m = 0.260$^{+0.029}_{-0.019}$. We test for consistency between these five correlation function measurements and the Planck -only measurement of the CMB lensing autospectrum, again finding no evidence for inconsistency in the context of flat Λ CDM models. Combining constraints from all six two-point functions yields S 8 = 0.776$^{+0.014}_{-0.021}$ and Ω m = 0.271$^{+0.022}_{-0.016}$. These results provide a powerful test and confirmation of the results from the first year DES joint-probes analysis.

Abbott, T. M. C.↗
DOE OSTI2021

Isolation of a Cyclopentasilane from Magnesium Reduction of a Linear Hexasilane

The reductive cyclization of two linear hexasilanes is contrasted, where a methylated precursor yielded a cyclohexasilane while the tert-butyl-functionalized analog unexpectedly yielded a cyclopentasilane. A comprehensive analysis using X-ray diffraction, IR, HR, HRMS, and multinuclear (1H, 13C and 29Si) 1D and 2D NMR spectroscopy identified the 1,2-dihydrodisilane tBuPhHSi–SiHPhtBu as an additional product, which was interpreted as supportive of a mechanism involving silylene elimination. Here, the results of this study may prove informative about substituent effects in the practice of complex organosilicon molecular synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Enhanced intersystem crossing of boron dipyrromethene by TEMPO radical

Radical enhanced intersystem crossing (EISC) of organic chromophores is an important approach to generate a long-lived triplet state for various electronic and optoelectronic applications. However, structural factors and design rules to promote EISC are not entirely clear. In this work, we report a series of boron dipyrromethene (BODIPY) derivatives covalently linked with a 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) radical with varying distances and topologies. We show that the incorporation of the TEMPO radical to BODIPY results in strong fluorescence quenching by up to 85% as a result of EISC and enhanced internal conversion. In BDP-2AR [2-(4-methyleneamino-TEMPO) BODIPY], a dyad with the shortest BODIPY–TEMPO through-bond distance, we observe the fastest EISC rate (τ isc = 1.4 ns) and the longest triplet excited state lifetime (τ T = 32 μs) compared to other distance and geometry variations. Contrary to previous reports and a general presumption, the BODIPY–TEMPO through-bond distance in this system does not play a significant role on the triplet formation rate and yield. Finally, density functional theory suggests a folding of the TEMPO radical to form a sandwich-like structure with a BODIPY ring that leads to a decrease in the through-space distance, providing a new and an interesting insight for the radical enhanced intersystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗