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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) employed a pair of reference xenograft proteomes for initial platform validation and ongoing quality control of its data collection for The Cancer Genome Atlas (TCGA) tumors. These two xenografts, representing basal and luminal-B human breast cancer, were fractionated and analyzed on six mass spectrometers in a total of 46 replicates divided between iTRAQ and label-free technologies, spanning a total of 1095 LC-MS/MS experiments. These data represent a unique opportunity to evaluate the stability of proteomic differentiation by mass spectrometry over many months of time for individual instruments or across instruments running dissimilar workflows. We evaluated iTRAQ reporter ions, label-free spectral counts, and label-free extracted ion chromatograms as strategies for data interpretation. From these assessments we found that differential genes from a single replicate were confirmed by other replicates on the same instrument from 61-93% of the time. When comparing across different instruments and quantitative technologies, differential genes were reproduced by other data sets from 67-99% of the time. Projecting gene differences to biological pathways and networks increased the similarities. These overlaps send an encouraging message about the maturity of technologies for proteomic differentiation.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2019

P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data

The use of mass-spectrometry-based techniques for global protein profiling of biomedical or environmental experiments has become a major focus in research centered on biomarker discovery; however, one of the most important issues recently highlighted in the new era of omics data generation is the ability to perform analyses in a robust and reproducible manner. This has been hypothesized to be one of the issues hindering the ability of clinical proteomics to successfully identify clinical diagnostic and prognostic biomarkers of disease. P-Mart (https://pmart.labworks.org) is an interactive web-based software environment that enables domain scientists to perform quality-control processing, statistics, and exploration of large-complex proteomics data sets without requiring statistical programming. P-Mart is developed in a manner that allows researchers to perform analyses via a series of modules, explore the results using interactive visualization, and finalize the analyses with a collection of output files documenting all stages of the analysis and a report to allow reproduction of the analysis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multinuclear Solid-State NMR and NMR Crystallography of Solid Forms of Creatine and Creatinine

Creatine is a performance-enhancing supplement with two widely available commercial solid forms, namely, creatine monohydrate (creatine·H 2 O) and creatine HCl, the latter of which does not have a reported crystal structure. Moreover, commercial formulations of creatine may contain creatinine, an undesired impurity phase resulting from the self-cyclization of creatine during manufacturing. Therefore, reliable methods for characterizing the different solid forms of creatine and detecting the presence of creatinine are essential. Herein, we address these challenges using 13 C, 15 N, and 35 Cl solid-state NMR (SSNMR) spectroscopy to obtain distinct spectral fingerprints for creatine·H 2 O and creatine HCl, along with creatinine and creatinine HCl. The acquisition of these SSNMR spectra offers a robust approach for both the rapid characterization of each solid form and the detection of the impurity phases. Additionally, quadrupolar NMR crystallography-guided crystal structure prediction (QNMRX-CSP) was applied for the de novo crystal structure determination of creatine HCl, which was validated by the subsequently determined single-crystal X-ray diffraction (SCXRD) structure. Finally, to investigate the relationship between NMR parameters and structural features, 13 C and 15 N chemical shifts and 35 Cl electric field gradient (EFG) tensors were computed from geometry-optimized structures of the four solid forms by using dispersion-corrected DFT-D2* methods. Finally, this integrative approach offers a powerful framework for advancing the structural understanding and quality control of creatine-based supplements and next-generation formulations, as well as a wide range of other solid pharmaceuticals and nutraceuticals.

NMR↗
DOE OSTI2025

Multiphoton and Harmonic Imaging of Microarchitected Materials

Microadditive manufacturing has revolutionized the production of complex, nano- to microscale components across various fields. This work investigates two-photon (2P) and three-photon (3P) fluorescence imaging, as well as third-harmonic generation (THG) microscopy, to examine periodic microarchitected lattice structures fabricated using multiphoton lithography (MPL). By immersing the structures in refractive index matching fluids, we demonstrate high-fidelity 3D reconstructions of both fluorescent structures using 2P and 3P microscopy as well as low-fluorescence structures using THG microscopy. These results show that multiphoton fluorescence (MPF) imaging offers reduced signal decay with respect to depth compared to single-photon techniques in the examined structures. We further demonstrate the ability to nondestructively identify intentional internal modifications of the structure that are not immediately visible with scanning electron microscope (SEM) images and compression-induced fractures, highlighting the potential of these techniques for quality control and defect detection in microadditively manufactured components.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Forecasting Battery Electrode Performance via Electrochemical Fluorescence Microscopy and Machine-Learning

Predicting lithium-ion battery performance is hindered by microscale electrode heterogeneities invisible to conventional diagnostics. Here, we combine electrochemical fluorescence microscopy (EFM), which maps electronic connectivity by visualizing an electrofluorophore reaction distribution, with a multitask ElasticNet regression to forecast discharge capacity from spatial heterogeneity. Analyzing 196 images from six pilot-scale LiNi 0.5 Mn 0.3 Co 0.2 O 2 cathodes with varying carbon loadings, we extract 62 descriptors that capture morphology and texture. A compact five-feature model predicts capacity across eight discharge rates, achieving a per-target R 2 of up to 0.63 and an overall R 2 of 0.92, with a mean absolute percentage error of less than 2%. This performance rivals impedance-based approaches while avoiding their reliance on postformation data and incomplete electronic network information. Our facile and rapid, image-driven method may enable electrode quality control upstream of costly cell assembly to offer a transformative tool for data-driven battery research and manufacturing.

battery electrodes↗
DOE OSTI2025

Raman Digital Twin of Monolayer Janus Transition Metal Dichalcogenides

Monolayer transition metal dichalcogenides (TMDs) are a key class of two-dimensional (2D) materials with broad technological potential. Their Janus counterparts exhibit unique properties due to broken out-of-plane symmetry and further enrich the functionalities of TMDs. However, experimental synthesis and identification of Janus TMDs remain challenging. It is thus highly desirable to have a rapid, simple, and in situ characterization technique to monitor, in real time, the conversion process from the parent to Janus structure. Raman spectroscopy stands out for such a task as it is a powerful, nondestructive, and very commonly used tool to characterize 2D materials both in situ and ex situ. To realize the full potential of Raman spectroscopy on rapid characterization of Janus TMDs, we present a computational “Raman digital twin” library for various monolayer Janus TMDs in both 2H and Td phases. We focus on group-6 TMDs: MoS 2 , WS 2 , MoSe 2 , WSe 2 , MoTe 2 , WTe 2 and their Janus variants: MoSSe, MoSTe, MoSeTe, WSSe, WSTe, and WSeTe. Using first-principles density functional theory (DFT), we calculate their vibrational properties and predict distinct Raman fingerprints. These phonon and Raman signatures reflect each material’s structural symmetry and atomic composition, enabling clear identification via Raman spectroscopy. Our theoretical work supports experimental efforts by providing benchmarks for material identification, structural analysis, and quality control. In conclusion, the computational library expedites the discovery and development of Janus 2D materials, facilitating tighter integration between theoretical predictions and experimental validation.

Chalcogenides↗
DOE OSTI2015

Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism

A new class of antimicrobial benzoxaborole compounds was identified as a potent inhibitor of leucyl-tRNA synthetase (LeuRS) and therefore of protein synthesis. In a novel mechanism, AN2690 (5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole) blocks fungal cytoplasmic LeuRS by covalently trapping tRNA Leu in the editing site of the enzyme’s CP1 domain. However, some resistant mutation sites are located outside of the CP1 hydrolytic editing active site. Thus, their mode of action that undermines drug inhibition was not understood. A combination of X-ray crystallography, molecular dynamics, metadynamics, biochemical experiments, and mutational analysis of a distal benzoxaborole-resistant mutant uncovered a eukaryote-specific tyrosine “switch” that is critical to tRNA-dependent post-transfer editing. The tyrosine “switch” has three states that shift between interactions with a lysine and the 3’-hydroxyl of the tRNA terminus, to inhibit or promote post-transfer editing. The oxaborole’s mechanism of action capitalizes upon one of these editing active site states. This tunable editing mechanism in eukaryotic and archaeal LeuRSs is proposed to facilitate precise quality control of aminoacylation fidelity. These mechanistic distinctions could also be capitalized upon for development of the benzoxaboroles as a broad spectrum antibacterial.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Synthesis and Purification of Homogeneous Lipid-Based Peptide Nanocarriers by Overcoming Phospholipid Ester Hydrolysis

Despite the therapeutic promise of phospholipid-based nanocarriers, a major obstacle to their widespread clinical translation is a susceptibility to fatty acid ester hydrolysis, leading to lack of quality control and inconsistencies in self-assembly formulations. Using electrospray ionization mass spectrometry fragmentation in combination with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, we have demonstrated a method to detect hydrolysis of one or both of the fatty acid esters in a PEGylated phospholipid, DSPE-PEG, in conditions commonly applied during nanocarrier production. Because such carriers are increasingly being used to deliver peptide-based therapeutics, we further investigated the hydrolysis of phospholipid esters in conditions used for solid-phase peptide synthesis and high-performance liquid chromatography of peptides. We ultimately detail a synthetic strategy to reliably produce pure phospholipid–peptide bioconjugates (peptide amphiphiles), while avoiding unintended or unnoticed hydrolyzed byproducts that could lead to polymorphic nanotherapeutics with dampened therapeutic efficacy. We believe that such an approach could help standardize phospholipid–peptide-based therapeutic development, testing, and clinical translation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Lateral Heterogeneous Integration of Quantum Cascade Lasers

Broadband terahertz radiation potentially has extensive applications, ranging from personal health care to industrial quality control and security screening. While traditional methods for broadband terahertz generation rely on bulky and expensive mode-locked lasers, frequency combs based on quantum cascade lasers (QCLs) can provide an alternative compact, high power, wideband terahertz source. QCL frequency combs incorporating a heterogeneous gain medium design can obtain even greater spectral range by having multiple lasing transitions at different frequencies. However, despite their greater spectral coverage, the comparatively low gain from such gain media lowers the maximum operating temperature and power. Lateral heterogeneous integration offers the ability to cover an extensive spectral range while maintaining the competitive performance offered from each homogeneous gain media. In this paper, we present the first lateral heterogeneous design for broadband terahertz generation: by combining two different homogeneous gain media, we have achieved a two-color frequency comb spaced by 1.5 THz.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning

Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq’s ability to accurately detect variants under various experimental conditions. Lastly, we show LevSeq’s utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Large-Scale Interlaboratory DI-FT-ICR MS Comparability Study Employing Various Systems

We report ultra-high resolution mass spectrometry (UHR-MS) coupled with direct infusion (DI) electrospray ionization offers a fast solution for accurate untargeted profiling. Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers have been shown to produce a wealth of insights into complex chemical systems because they enable unambiguous molecular formula assignment even if the vast majority of signals is of unknown identity. Inter-laboratory comparisons are required to apply this type of instrumentation in quality control (for food industry or pharmaceutics), large-scale environmental studies or clinical diagnostics. Extended comparisons employing different FT-ICR MS instruments with qualitative direct infusion analysis are scarce since the majority of detected compounds cannot be quantified. The extent to which observations can be reproduced by different laboratories remains unknown. We set up a preliminary study which encompassed a set of seventeen laboratories around the globe, diverse in instrumental characteristics and applications, to analyze the same sets of extracts from commercially available standard human blood plasma and Standard Reference Material (SRM) for blood plasma (SRM1950), which were delivered at different dilutions or spiked with different concentrations of pesticides. The aim of this study was to assess the extent to which the outputs of differently tuned FTICR mass spectrometers, with different technical specifications, are comparable for setting the frames of a future DI-FT-ICR MS ring trial. We concluded that a cluster of five laboratories, with diverse instrumental characteristics showed comparable and representative performance across all experiments, setting a reference to be used in a future ring trial on blood plasma.

47 OTHER INSTRUMENTATION↗
DOE OSTI2019

Observed Spatiotemporal Changes in the Mechanisms of Extreme Water Available for Runoff in the Western United States

We used a quality-controlled Snowpack Telemetry (SNOTEL) data set (1979–2017) combined with the nonparametric regional Kendall test (RKT) to examine changes in annual maximum water available for runoff at the land surface under four hydrometeorological conditions (snowmelt only, rain-on-snow, all melt with or without rainfall, and all melt plus rainfall on snow-free ground) over the mountainous regions of the western U.S. Our RKT analyses indicated significant declining trends at point (SNOTEL) scale under all four conditions. The annual maximum of all melt plus rainfall decreased primarily in the southwestern U.S., while the frequency of rain-on-snow events increased significantly in the northwestern U.S. The rate of annual maximum snowmelt only decreased in 10 of 11 ecological regions across the western U.S. These results suggest that under a warming climate, the four types of annual maximum water available for runoff have been substantially decreasing at local scale across the western U.S.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A Meteorology and Snow Data Set From Adjacent Forested and Meadow Sites at Crested Butte, CO, USA

We present meteorology and snow observation data collected at sites in the southwestern Colorado Rocky Mountains (USA) over three consecutive water years with different amounts of snow water equivalent (SWE) accumulation: A year with above average SWE (2019), a year with average SWE (2020), and a year with below average SWE (2021). This data set is distinguished by its emphasis on paired open-forest sites in a continental snow climate. Approximately once a month during February–May, we collected data from 15 to 20 snow pits and took 8 to 19 snow depth transects. Our sampling sites were in open and adjacent forested areas at 3,100 m and in a lower elevation aspen (3,035 m) and higher elevation conifer stand (3,395 m). In total, we recorded 270 individual snow pit density and temperature profiles and over 4,000 snow depth measurements. These data are complimented by continuous meteorological measurements from two weather stations: One in the open and one in the adjacent forest. Meteorology data—including incoming shortwave and longwave radiation, outgoing shortwave radiation, relative humidity, wind speed, snow depth, and air and infrared surface temperature—were quality controlled and the forcing data were gap-filled. These data are available to download from Bonner, Smyth, et al. at three levels of processing, including a level with downscaled, adjusted precipitation based on data assimilation using observed snow depth and a process-based snow model. We demonstrate the utility of these data with a modeling experiment that explores open-forest differences and identifies opportunities for improvements in model representation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

High-Resolution Near-Surface Imaging at the Basin Scale Using Dark Fiber and Distributed Acoustic Sensing: Toward Site Effect Estimation in Urban Environments

Near-surface seismic structure, particularly the shear wave velocity (V s ), can strongly affect local site response, and should be accurately estimated for ground motion prediction during seismic hazard assessment. The Imperial Valley (California), occupying the southern end of the Salton Trough, is a seismically active basin with thick surficial lacustrine sedimentary deposits. In this study, we utilize ambient noise records and local earthquake events for high-resolution near-surface characterization and site effect estimation with an unlit fiber-optic telecommunication infrastructure (dark fiber) in Imperial Valley by using the distributed acoustic sensing (DAS) technique. We apply ambient noise interferometry to retrieve coherent surface waves from DAS records, and evaluate performances of three different surface wave methods on DAS ambient noise dispersion imaging. We develop a quality control workflow to improve the dispersion measurement of noisy portions of the DAS data set by using a data selection strategy. Using the joint inversion of both the fundamental mode and higher overtones of Rayleigh waves, a high resolution two-dimensional (2D) V s structure down to 70 m depth is obtained. We successfully achieve an improved V s 30 (the time-averaged shear-wave velocity in the top 30 m) model with higher spatial-resolution and reliability compared to the existing community model for the area. We also explore the potential for utilizing DAS earthquake events for site amplification estimation. The preliminary results reveal a clear anti-correlation between the approximated site response and the V s 30 profile. In conclusion, our results indicate the potential utility of DAS deployed on dark fiber for near-surface characterization in appropriate contexts.

58 GEOSCIENCES↗
DOE OSTI2025

Coupling Remote Sensing With a Process Model for the Simulation of Rangeland Carbon Dynamics

Rangelands provide significant environmental benefits through many ecosystem services, which may include soil organic carbon (SOC) sequestration. However, quantifying SOC stocks and monitoring carbon (C) fluxes in rangelands are challenging due to the considerable spatial and temporal variability tied to rangeland C dynamics as well as limited data availability. We developed the Rangeland Carbon Tracking and Management (RCTM) system to track long-term changes in SOC and ecosystem C fluxes by leveraging remote sensing inputs and environmental variable data sets with algorithms representing terrestrial C-cycle processes. Bayesian calibration was conducted using quality-controlled C flux data sets obtained from 61 Ameriflux and NEON flux tower sites from Western and Midwestern US rangelands to parameterize the model according to dominant vegetation classes (perennial and/or annual grass, grass-shrub mixture, and grass-tree mixture). The resulting RCTM system produced higher model accuracy for estimating annual cumulative gross primary productivity (GPP) (R 2 > 0.6, RMSE <390 g C m -2 ) relative to net ecosystem exchange of CO 2 (NEE) (R 2 > 0.4, RMSE <180 g C m -2 ). Model performance in estimating rangeland C fluxes varied by season and vegetation type. The RCTM captured the spatial variability of SOC stocks with R 2 = 0.6 when validated against SOC measurements across 13 NEON sites. Model simulations indicated slightly enhanced SOC stocks for the flux tower sites during the past decade, which is mainly driven by an increase in precipitation. Future efforts to refine the RCTM system will benefit from long-term network-based monitoring of vegetation biomass, C fluxes, and SOC stocks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

ProDeGe: A computational protocol for fully automated decontamination of genomes

Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes—clean and contaminant—using a combination of homology and feature-based methodologies. On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). Lastly, the procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Opto-nanomechanical spectroscopic material characterization

Cellulosic ethanol is a biofuel of considerable potential in the search for sustainable and renewable bioenergy [1,2]. However, while rich in carbohydrates [3], the plant cell walls exhibit a natural resistance to complex phenotype treatments such as enzymatic microbial deconstruction, heat and acid treatments that can remove the lignin polymers from cellulose before hydrolysis [5]. Noninvasive physical and chemical characterization of the cell walls and the effect of such treatments on biomass are challenging but necessary to understand and overcome such resistance [6]. Although lacking chemical recognition in their traditional forms, the various emerging modalities of nano-mechanical [7] and opto-nano-mechanical [8] force microscopies [9,10] provide a superb window into the needed nanoscale material characterization [6]. Infrared absorption spectroscopy is a powerful, non- destructive and ultra-sensitive technique that can provide the needed molecular fingerprinting but the photothermal channel is delocalized and thus lacks spatial resolution. Utilizing the emerging dynamic concepts of mode synthesizing atomic force microscopy (MSAFM) [11] and virtual resonance [12], we introduce a hybrid photonic and nanomechanical force microscopy (hp-MSAFM) with molecular recognition and characterize the extraction, holopulping and acid treatment of biomass. We present spatially and spectrally resolved cell wall images that reveal both the morphological and the compositional alterations of the cell walls. The measured biomolecular traits are in agreement with chemical maps obtained with infrared and confocal Raman micro-spectroscopies of the same samples. The presented findings should prove highly relevant in fields such as cancer research [13], nanotoxicity [14], energy storage and production [15], where morphological, chemical and subsurface studies of nanocomposites [16], nanoparticle uptake by cells [14], and nanoscale quality control [17] are in demand.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Structural basis of impaired disaggregase function in the oxidation-sensitive SKD3 mutant causing 3-methylglutaconic aciduria

Abstract Mitochondria are critical to cellular and organismal health. To prevent damage, mitochondria have evolved protein quality control machines to survey and maintain the mitochondrial proteome. SKD3, also known as CLPB, is a ring-forming, ATP-fueled protein disaggregase essential for preserving mitochondrial integrity and structure. SKD3 deficiency causes 3-methylglutaconic aciduria type VII (MGCA7) and early death in infants, while mutations in the ATPase domain impair protein disaggregation with the observed loss-of-function correlating with disease severity. How mutations in the non-catalytic N-domain cause disease is unknown. Here, we show that the disease-associated N-domain mutation, Y272C, forms an intramolecular disulfide bond with Cys267 and severely impairs SKD3 Y272C function under oxidizing conditions and in living cells. While Cys267 and Tyr272 are found in all SKD3 isoforms, isoform-1 features an additional α-helix that may compete with substrate-binding as suggested by crystal structure analyses and in silico modeling, underscoring the importance of the N-domain to SKD3 function.

59 BASIC BIOLOGICAL SCIENCES↗