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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry

The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product’s primary structure reliably and reproducibly. The major objective of the present study was to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up approaches, such as confirming protein integrity, sequencing variable domains, ruling out artefacts, and revealing modifications and their locations. A panel of three mAbs was selected and centrally provided to twenty laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). A variety of different MS instrument platforms and ion dissociation techniques were employed. Overall, the present study confirms that MD/TD MS strategies are valuable and readily available tools in laboratories worldwide. They provide complementary information to the bottom-up approach and can add unique information, which may be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. One of the limitations revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS, but the number of TD/MD MS experts is still very low.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry

Top-down proteomics by mass spectrometry (MS) involves the mass measurement of an intact protein followed by subsequent activation of the protein to generate product ions. Electron-based fragmentation methods like electron capture dissociation and electron transfer dissociation are widely used for these types of analyses. Recently, electron ionization dissociation (EID), which utilizes higher energy electrons (>20 eV) has been suggested to be more efficient for top-down protein fragmentation compared to other electron-based dissociation methods. In this paper, we demonstrate that the use of EID enhances protein fragmentation and subsequent detection of protein fragments. Protein product ions can form by either single cleavage events, resulting in terminal fragments containing the C-terminus or N-terminus of the protein, or by multiple cleavage events to give rise to internal fragments that include neither the C-terminus nor the N-terminus of the protein. Conventionally, internal fragments have been disregarded, as reliable assignments of these fragments were limited. Here, we demonstrate that internal fragments generated by EID can account for ~20–40% of the mass spectral signals detected by top-down EID-MS experiments. By including internal fragments, the extent of the protein sequence that can be explained from a single tandem mass spectrum increases from ~50 to ~99% for 29 kDa carbonic anhydrase II and 8.6 kDa ubiquitin. When searching for internal fragments during data analysis, previously unassigned peaks can be readily and accurately assigned to confirm a given protein sequence and to enhance the utility of top-down protein sequencing experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Natural Abundance Isotope Ratio Measurements of Organic Molecules Using 21 T FTICR MS

Subtle variations in stable isotope ratios at natural abundance are challenging to measure but can yield critical insights into biological, physical, and geochemical processes. Well established methods, particularly multi-collector, gas-source or plasma isotope ratio mass spectrometry (IRMS) are the gold standard for stable isotope measurement but inherent limitations in these approaches make them ill-suited to determining site-specific and multiply substituted isotopic abundances of all but a few compounds, or to characterizing mixtures or larger intact molecules. Additionally, Fourier transform mass spectrometry (FTMS), namely Orbitrap mass spectrometry, has recently demonstrated the ability to measure natural abundance isotope ratios with chemically informative accuracy and precision. Here, we report the first use of Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for the accurate (<1‰) and precise (<1‰ standard error) simultaneous determination of $δ$ 13 C and $δ$ 15 N in caffeine isotopologues and provide a discussion of the critical instrumental parameters necessary to make such measurements. Finally, we report the ability to make these measurements with online liquid chromatography, expanding the ability of this technique to explore mixtures in the future.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2024

A Field-Deployable Magnetic Resonance Imaging Rhizotron for Modeling and Enhancing Root Growth and Biogeochemical Function

A collaborative team from Texas A&M AgriLife Research, ABQMR Inc., the Soil Health Institute, the Athinoula A. Martinos Center for Biomedical Imaging, and NIST developed low-field magnetic resonance imaging (LF-MRI) instrumentation capable of imaging intact soil-root systems. The system measured root biomass, architecture, 3D mass distribution, and growth rates, providing a non-destructive means to evaluate ideal plant characteristics based on root metrics. It also successfully generated three-dimensional images of soil water content, a key property influencing root growth and exploration. Operating much like an MRI used in a medical setting, the system functioned in field conditions without damaging plants, overcoming the limitations of traditional methods such as trenching, soil coring, and root excavation. Over the course of the project, the team designed and built three functional prototype systems. These prototypes provided new insights into root–water–soil interactions that drive processes such as nutrient uptake, water use, and carbon management. This information contributed to efforts to optimize plants for carbon sequestration without sacrificing economic yield. The project also supported the identification of desirable traits for energy sorghum, including high root growth rates, more vertical root angles, and enhanced drought resilience under water-limiting conditions.

09 BIOMASS FUELS↗
DOE OSTI2021

Accelerating strain phenotyping with desorption electrospray ionization-imaging mass spectrometry and untargeted analysis of intact microbial colonies

Significance Synthetic biology has entered an era in which reading and writing DNA sequences are no longer rate-limiting steps in microbial strain engineering. Indeed, analytical methods measuring the resulting metabolic outcomes of specific gene edits have lagged behind the ability to generate new recombinant strains. Herein, we report a mass spectrometry strategy to accelerate these analytical workflows by directly analyzing metabolites and molecules produced from engineered microorganisms in a multiplexed process. Using untargeted acquisitions and unsupervised analytics, we assess the molecular features that change across discrete strains including primary target species, secondary products, and species outside the engineered fatty acid biosynthesis pathway.

09 BIOMASS FUELS↗
DOE OSTI2023

Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry

Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO 2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments.

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

Intact mass spectrometry screening to optimize hydroxyl radical dose for protein footprinting

Hydroxyl radical protein footprinting (HRPF) using synchrotron radiation is a well-validated method to assess protein structure in the native solution state. In this method, X-ray radiolysis of water generates hydroxyl radicals that can react with solvent accessible side chains of proteins, with mass spectrometry used to detect the resulting labeled products. An ideal footprinting dose provides sufficient labeling to measure the structure but not so much as to influence the results. The optimization of hydroxyl radical dose is typically performed using an indirect Alexa488 fluorescence assay sensitive to hydroxyl radical concentration, but full evaluation of the experiment's outcome relies upon bottom-up liquid chromatography mass spectrometry (LC-MS) measurements to directly determine sites and extent of oxidative labeling at the peptide and protein level. A direct evaluation of the extent of labeling to provide direct and absolute measurements of dose and “safe” dose ranges in terms of, for example, average numbers of labels per protein, would provide immediate feedback on experimental outcomes prior to embarking on detailed LC-MS analyses. To this end, we describe an approach to integrate intact MS screening of labeled samples immediately following exposure, along with metrics to quantify the extent of observed labeling from the intact mass spectra. Intact MS results on the model protein lysozyme were evaluated in the context of Alexa488 assay results and a bottom-up LC-MS analysis of the same samples. In conclusion, this approach provides a basis for placing delivered hydroxyl radical dose metrics on firmer technical grounds for synchrotron X-ray footprinting of proteins, with explicit parameters to increase the likelihood of a productive experimental outcome. Further, the method directs approaches to provide absolute and direct dosimetry for all types of labeling for protein footprinting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of fire on chemical properties and respiration of boreal forest soils

We collected both organic-rich and sandy soil cores from 12 sites (site_location_and_texture.csv) within Wood Buffalo National Park, Alberta, Canada. Laboratory burns were conducted by exposing intact soil cores to 60 kW m^-2 in a mass loss calorimeter to simulate boreal forest crown fires in order to measure the effects of burning (temp_data.csv) on soil properties including pH, total C, and total nitrogen (N) (metadata.csv). We used 70-day soil incubations and two-pool exponential decay models to characterize the impacts of burning and burn-induced changes in soil properties on soil respiration (soil_moisture_at_end_of_incubation.csv; soil_mass_at_end_of_incubation.csv; respiration_data.csv). Laboratory burns successfully captured a range of soil temperatures that were realistic for natural wildfire events.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Isolating the Contributions of Specific Network Sites to the Diffuse Vibrational Spectrum of Interfacial Water with Isotopomer-Selective Spectroscopy of Cold Clusters

Decoding the structural information contained in the interfacial vibrational spectrum of water requires understanding how the spectral signatures of individual water molecules respond to their local hydrogen bonding environments. In this study, we isolated the contributions for the five classes of sites that differ according to the number of donor (D) and acceptor (A) hydrogen bonds that characterize each site. These patterns were measured by exploiting the unique properties of the water cluster cage structures formed in the gas phase upon hydration of a series of cations M+·(H2O)n (M = Li, Na, Cs, NH4, CH3NH3, H3O, and n = 5, 20-22). This selection of ions was chosen to systematically express the A, AD, AAD, ADD, and AADD hydrogen bonding motifs. The spectral signatures of each site were measured using two-color, IR-IR isotopomer-selective photofragmentation vibrational spectroscopy of the cryogenically cooled, mass selected cluster ions in which a single intact H2O is introduced without isotopic scrambling, an important advantage afforded by the cluster regime. The resulting patterns provide an unprecedented picture of the intrinsic line shapes and spectral complexities associated with excitation of the individual OH groups, as well as the correlation between the frequencies of the two OH groups on the same water molecule, as a function of network site. The properties of the surrounding water network that govern this frequency map are evaluated by dissecting electronic structure calculations that explore how changes in the nearby network structures, both within and beyond the first hydration shell, affect the local frequency of an OH oscillator. The qualitative trends are recovered with a simple model that correlates the OH frequency with the network-modulated local electron density in the center of the OH bond.

Yang, Nan↗
DOE OSTI2026

Measurement of 𝐷 0 Meson Photoproduction in Ultraperipheral Heavy Ion Collisions

This Letter reports the first measurement of photonuclear 𝐷 0 meson production in ultraperipheral heavy ion collisions. The study is performed using lead-lead collision data, with an integrated luminosity of 1.34 nb −1 , collected by the CMS experiment at a nucleon-nucleon center-of-mass energy of 5.36 TeV. Photonuclear events, where one of the colliding nuclei breaks up and the other remains intact, are selected based on breakup neutron emissions and by requiring no particle activity in a large rapidity interval in the direction of the photon-emitting nucleus. The 𝐷 0 mesons are reconstructed via the 𝐷 0 → 𝐾 −⁢ 𝜋 + decay channel, with the cross section measured as a function of 𝐷 0 meson transverse momentum and rapidity. The results are compared with next-to-leading-order perturbative QCD calculations that employ recent parametrizations of the lead nuclear parton distribution functions, as well as with predictions based on the color glass condensate framework. This measurement is the first photonuclear collision study characterizing parton distribution functions of lead nuclei for parton fractional momenta 𝑥 (relative to the nucleon) ranging approximately from a few 10 −4 to 10 −2 for different hard energy scale 𝑄 2 selections.

charm quark↗
DOE OSTI2022

Study of interface reaction in a B 4 C/Cr mirror at elevated temperature using soft X-ray reflectivity

Boron carbide is a prominent material for high-brilliance synchrotron optics as it remains stable up to very high temperatures. The present study shows a significant change taking place at 550°C in the buried interface region formed between the Cr adhesive layer and the native oxide layer present on the silicon substrate. An in situ annealing study is carried out at the Indus-1 Reflectivity beamline from room temperature to 550°C (100°C steps). The studied sample is a mirror-like boron carbide thin film of 400 Å thickness deposited with an adhesive layer of 20 Å Cr on a silicon substrate. The corresponding changes in the film structure are recorded using angle-dependent soft X-ray reflectivity measurements carried out in the region of the boron K-edge after each annealing temperature. Analyses performed using the Parratt recursive formalism reveal that the top boron carbide layer remains intact but interface reactions take place in the buried Cr–SiO2 region. After 300°C the Cr layer diffuses towards the substrate. At higher temperatures of 500°C and 550°C the Cr reacts with the native oxide layer and tends to form a low-density compound of chromium oxysilicide (CrSiOx). Depth profiling of Si and Cr distributions obtained from secondary ion mass spectroscopy measurements corroborate the layer model obtained from the soft X-ray reflectivity analyses. Details of the interface reaction taking place near the substrate region of boron carbide/Cr sample are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2026

AGR-5/6/7 Irradiation Experiment Fission Product Mass Balance

This report presents the fission product mass balance for the AGR-5/6/7 TRISO fuel irradiation experiment. The fission product inventories deposited on capsule components outside of the fuel (e.g., stainless-steel shells, graphite holders, Grafoil disks, and associated hardware) were quantified as part of the post-irradiation examination (PIE) to assess the performance of this fuel. Comparisons were made between these inventories and depletion calculations, non-destructive measurements of fuel fission product inventories in the intact fuel compacts, prior AGR experiments, and results from among each of the five distinct AGR-5/6/7 capsules. The data served as estimates of the condensable fission products released from the fuel during irradiation. Excluding Capsule 1 (which experienced accidental damage during irradiation) and Capsule 3 (which was tested at very high irradiation temperatures of >1300°C), the results indicate that the AGR-5/6/7 fuel performed comparably to fuel from earlier AGR experiments. The mass balance results were also used to estimate the number of particles with in-pile SiC failures. Subject to the assumptions made in these estimates, and excluding Capsules 1 and 3, the in-pile SiC failure rates for AGR-5/6/7 are comparable to those observed in AGR-2.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Soil porous microstructure control over soil organic matter mobility: A multimethod workflow for understanding chemistry-dependent organic matter binding in soil

Soil organic matter (SOM) has attracted a great deal of interest; particularly for its potential to mitigate human derived CO 2 emissions. Studies have demonstrated that SOM plays a critical role in carbon storage and CO 2 sequestration. However, the sorption properties of SOM, which influence its transport in pore water and stabilization within the soil, remain poorly understood. This study develops a workflow to: (1) examine compound-specific advective and diffusive transport and desorption behaviors, (2) quantify desorption rates through stop-flow and continuous-flow column experiments, and (3) evaluate the impact of soil microporosity on SOM mobility using high-resolution imaging and extractions. Intact core column experiments were conducted on Uncultivated (Natural) and Cultivated soil samples, both were arid soils, collected in Washington State. X-ray computed tomography was employed to measure porosity and pore connectivity, while Fourier-transform ion cyclotron resonance mass spectrometry was used to analyze SOM composition. The findings revealed that cultivation increased total carbon and nitrogen levels due to irrigation and fertilization, enhancing carbon capture potential in arid soils. In contrast, the Natural soil, characterized by higher porosity and connectivity, contained more oxidized carbon. Pore network analysis indicated that soil compaction in the Cultivated soil may lead to longer diffusion pathways, significantly influencing SOM transport and stability.

Hydraulic Properties↗
DOE OSTI2020

Nanometer-scale structure differences in the myofilament lattice spacing of two cockroach leg muscles correspond to their different functions

ABSTRACT Muscle is highly organized across multiple length scales. Consequently, small changes in the arrangement of myofilaments can influence macroscopic mechanical function. Two leg muscles of a cockroach have identical innervation, mass, twitch responses, length–tension curves and force–velocity relationships. However, during running, one muscle is dissipative (a ‘brake’), while the other dissipates and produces significant positive mechanical work (bifunctional). Using time-resolved X-ray diffraction in intact, contracting muscle, we simultaneously measured the myofilament lattice spacing, packing structure and macroscopic force production of these muscles to test whether structural differences in the myofilament lattice might correspond to the muscles' different mechanical functions. While the packing patterns are the same, one muscle has 1 nm smaller lattice spacing at rest. Under isometric stimulation, the difference in lattice spacing disappeared, consistent with the two muscles' identical steady-state behavior. During periodic contractions, one muscle undergoes a 1 nm greater change in lattice spacing, which correlates with force. This is the first identified structural feature in the myofilament lattice of these two muscles that shares their whole-muscle dynamic differences and quasi-static similarities.

Tune, Travis Carver↗
DOE OSTI2025

Measurement of photonuclear jet production in ultraperipheral Pb + Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV with the ATLAS detector

In ultrarelativistic heavy ion collisions at the LHC, each nucleus acts a sources of high-energy real photons that can scatter off the opposing nucleus in ultraperipheral photonuclear (𝛾 + 𝐴) collisions. Hard scattering processes initiated by the photons in such collisions provide a novel method for probing nuclear parton distributions in a kinematic region not easily accessible to other measurements. ATLAS has measured production of dijet and multijet final states in ultraperipheral Pb + Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV using a dataset recorded in 2018 with an integrated luminosity of 1.72 nb −1 . Photonuclear final states are selected by requiring a rapidity gap in the photon direction; this selects events where one of the outgoing nuclei remains intact. Jets are reconstructed using the anti-𝑘 t algorithm with radius parameter, 𝑅 = 0.4. Triple-differential cross sections, unfolded for detector response, are measured and presented using two sets of kinematic variables. The first set consists of the total transverse momentum (𝐻 T ), rapidity, and mass of the jet system. The second set uses 𝐻 T and particle-level nuclear and photon parton momentum fractions, 𝑥 A and 𝑧 𝛾 , respectively. The results are compared with leading-order perturbative QCD calculations of photonuclear jet production cross sections, where all leading order predictions using existing fits fall below the data in the shadowing region. More detailed theoretical comparisons will allow these results to strongly constrain nuclear parton distributions, and these data provide results from the LHC directly comparable to early physics results at the planned Electron-Ion Collider.

Parton distribution functions↗
DOE OSTI2024

Top-down proteomics

Proteoforms arising from posttranslational modifications, genetic polymorphisms, and RNA splice variants, play a pivotal role as the key drivers in biology. Thus, a comprehensive understanding of proteoforms is essential for unraveling the intricacies of biological systems and bridging the gap between genotype and phenotype. By analyzing whole proteins without digestion, top-down proteomics (TDP) provides a holistic view of the proteome and presents a next-generation approach for deciphering protein function, uncovering disease mechanisms, and advancing precision medicine. This Primer embarks on a journey into the world of TDP by encapsulating its historical context, underlying principles, recent advances, and an outlook on the future of TDP. The experimental section navigates instrumentation, sample preparation, intact protein separation, tandem mass spectrometry techniques, and data collection. Results decipher raw data, visualize intact protein spectra, unravel data analysis, and explain proteoform identification, characterization, and quantitation, as well as statistical analysis. Various applications of TDP spanning the human proteoform project, biomedical, biopharmaceutical, and clinical applications are described. These are complemented by discussions on measurement reproducibility, limitations, and a forward-looking perspective outlining uncharted waters where the field can advance, and potential exciting future applications of TDP.

Roberts, David S.↗
DOE OSTI2020

Assessing impacts of selective logging on water, energy, and carbon budgets and ecosystem dynamics in Amazon forests using the Functionally Assembled Terrestrial Ecosystem Simulator

Abstract. Tropical forest degradation from logging, fire, and fragmentation not only alters carbon stocks and carbon fluxes, but also impacts physical land surface properties such as albedo and roughness length. Such impacts are poorly quantified to date due to difficulties in accessing and maintaining observational infrastructures, as well as the lack of proper modeling tools for capturing the interactions among biophysical properties, ecosystem demography, canopy structure, and biogeochemical cycling in tropical forests. As a first step to address these limitations, we implemented a selective logging module into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) by mimicking the ecological, biophysical, and biogeochemical processes following a logging event. The model can specify the timing and aerial extent of logging events, splitting the logged forest patch into disturbed and intact patches; determine the survivorship of cohorts in the disturbed patch; and modifying the biomass and necromass (total mass of coarse woody debris and litter) pools following logging. We parameterized the logging module to reproduce a selective logging experiment at the Tapajós National Forest in Brazil and benchmarked model outputs against available field measurements. Our results suggest that the model permits the coexistence of early and late successional functional types and realistically characterizes the seasonality of water and carbon fluxes and stocks, the forest structure and composition, and the ecosystem succession following disturbance. However, the current version of FATES overestimates water stress in the dry season and therefore fails to capture seasonal variation in latent and sensible heat fluxes. Moreover, we observed a bias towards low stem density and leaf area when compared to observations, suggesting that improvements are needed in both carbon allocation and establishment of trees. The effects of logging were assessed by different logging scenarios to represent reduced impact and conventional logging practices, both with high and low logging intensities. The model simulations suggest that in comparison to old-growth forests the logged forests rapidly recover water and energy fluxes in 1 to 3 years. In contrast, the recovery times for carbon stocks, forest structure, and composition are more than 30 years depending on logging practices and intensity. This study lays the foundation to simulate land use change and forest degradation in FATES, which will be an effective tool to directly represent forest management practices and regeneration in the context of Earth system models.

54 ENVIRONMENTAL SCIENCES↗