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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Fully Homomorphic Encryption

This code implements a Fully Homomorphic Encryption (FHE) system, enabling secure computation on encrypted data without requiring decryption. It supports encryption, decryption, and homomorphic operations like matrix multiplication and addition. This code is adaptable for integrating FHE into linear-time invariant (LTI) systems, including digital control and filtering. With proper configuration from subject matter expertise, encrypted system parameters and signals can be manipulated to perform tasks like state updates, output calculations, and convolution in the encrypted domain. By preserving the structure of LTI systems while ensuring privacy, the framework facilitates secure applications in areas such as autonomous systems, signal processing, and industrial automation. The code initializes the encryption system using parameters provided in the env dictionary. These parameters include the ciphertext modulus, key dimension, plaintext fixed-point scaling factor, and noise bound. During initialization, a secret key is generated, which is essential for encrypting and decrypting data securely. The modular design allows users to tailor these parameters to specific use cases or security requirements. The code implements multiple cryptographic schemes. The learning with errors (LWE) encryption method encodes cleartext message to their plaintext fixed-point representation then encrypted into ciphertext space with additive noise. This noise ensures the security of the scheme, relying on the computational hardness of the LWE problem. The code also includes the Gentry-Sahai-Waters (GSW) scheme based off the LWE problem. Homomorphic matrix multiplication is performed between the LWE and GSW to encrypted data. This is achieved using a decomposition function on the LWE ciphertext during the multiplication operation. For higher-dimensional data, the code includes a method to encrypt entire matrices (GSWMat) using GSW encryption. These encrypted matrices can then be used for homomorphic matrix multiplications (MatMult). The decryption function uses the secret key to recover the original plaintext, removing the added noise and scaling that was originally applied during encryption.

Lois, Roberts [Idaho National Laboratory (INL), Id↗
DOE OSTI2023

MILK : a Python scripting interface to MAUD for automation of Rietveld analysis

Modern diffraction experiments ( e.g. in situ parametric studies) present scientists with many diffraction patterns to analyze. Interactive analyses via graphical user interfaces tend to slow down obtaining quantitative results such as lattice parameters and phase fractions. Furthermore, Rietveld refinement strategies ( i.e. the parameter turn-on-off sequences) tend to be instrument specific or even specific to a given dataset, such that selection of strategies can become a bottleneck for efficient data analysis. Managing multi-histogram datasets such as from multi-bank neutron diffractometers or caked 2D synchrotron data presents additional challenges due to the large number of histogram-specific parameters. To overcome these challenges in the Rietveld software Material Analysis Using Diffraction ( MAUD ), the MAUD Interface Language Kit ( MILK ) is developed along with an updated text batch interface for MAUD . The open-source software MILK is computer-platform independent and is packaged as a Python library that interfaces with MAUD . Using MILK , model selection ( e.g. various texture or peak-broadening models), Rietveld parameter manipulation and distributed parallel batch computing can be performed through a high-level Python interface. A high-level interface enables analysis workflows to be easily programmed, shared and applied to large datasets, and external tools to be integrated with MAUD . Through modification to the MAUD batch interface, plot and data exports have been improved. The resulting hierarchical folders from Rietveld refinements with MILK are compatible with Cinema: Debye–Scherrer , a tool for visualizing and inspecting the results of multi-parameter analyses of large quantities of diffraction data. In this manuscript, the combined Python scripting and visualization capability of MILK is demonstrated with a quantitative texture and phase analysis of data collected at the HIPPO neutron diffractometer.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Tracking C–H activation with orbital resolution

Transition metal reactivity toward carbon–hydrogen (C–H) bonds hinges on the interplay of electron donation and withdrawal at the metal center. Manipulating this reactivity in a controlled way is difficult because the hypothesized metal-alkane charge-transfer interactions are challenging to access experimentally. Using time-resolved x-ray spectroscopy, we track the charge-transfer interactions during C–H activation of octane by a cyclopentadienyl rhodium carbonyl complex. Changes in oxidation state as well as valence-orbital energies and character emerge in the data on a femtosecond to nanosecond timescale. The x-ray spectroscopic signatures reflect how alkane-to-metal donation determines metal-alkane complex stability and how metal-to-alkane back-donation facilitates C–H bond cleavage by oxidative addition. Furthermore, the ability to dissect charge-transfer interactions on an orbital level provides opportunities for manipulating C–H reactivity at transition metals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A machine learning approach for clinker quality prediction and nonlinear model predictive control design for a rotary cement kiln

Abstract Cement manufacturing is energy‐intensive (5Gj/t) and comprises a significant portion of the energy footprint of concrete systems. Incorporating modern monitoring, simulation and control systems will allow lower energy use, lower environmental impact, and lower costs of this widely used construction material. One of the goals of the CESMII roadmap project on the Smart Manufacturing of Cement included developing an analytical process model for clinker quality that includes the chemistry of the kiln feed and accounts for critical process variables. This predictive model will be used in nonlinear model predictive control system designed to significantly reduce process energy use while maintaining or improving product quality. In the cement manufacturing plant used in this study, the kiln feed (meal) is tested every 12 h and used to estimate the mineral composition of the cement kiln output (clinker) using the stoichiometry‐based Bogue's model and the expertise of the plant operators. During kiln operation, kiln output (clinker) is sampled and tested every 2 h to measure its chemical and mineral composition. The predicted and measured values of the clinker composition are used by the plant operators to adjust the kiln input stream and the production process characteristics to maintain stable operation and uniform product quality. However, the time delay between prediction and testing, along with inaccuracies inherent in the Bogue's model have made any process changes designed to minimize energy use problematic, especially in‐light of potential clinker quality issues that process changes often pose. A new analytical model that integrates quality information and process operation information has been developed from data collected from 2 years of production from an operating cement facility. To make the model fuel‐type‐independent, consumed heat energy was computed in the model instead of fuel type and amount. A Feedforward Network was trained and tailored from collected data. Many data‐based simulations were conducted to quantitatively evaluate the proposed model and the 5‐fold cross‐validation procedure was used to test the models. The resulting predictive model was shown to have a low root mean square error (MSE) with respect to the estimated clinker mineral composition compared to that using the industry standard “Bogue’ model”. The end goal of this work was to develop a single machine learning tool that allows the use of quality control data and process control variables to improve energy efficiency of the process in a continuous fashion. The proposed nonlinear model predictive control system (NMPC) can generate predicted kiln production characteristics based on manipulated variables in manner that accurately follows the target product quality values. Simulation results also show that the proposed model produced accurate predictions of kiln outputs that fell within the required constraints, while manipulating control variables within typical operational ranges.

Ali, Asem M.↗
DOE OSTI2022

Beyond carbon flux partitioning: Carbon allocation and nonstructural carbon dynamics inferred from continuous fluxes

Carbon (C) allocation and nonstructural carbon (NSC) dynamics play essential roles in plant growth and survival under stress and disturbance. However, quantitative understanding of these processes remains limited. Here, in this work, we propose a framework where we connect commonly measured carbon cycle components (eddy covariance fluxes of canopy CO 2 exchange, soil CO 2 efflux, and allometry-based biomass and net primary production) by a simple mass balance model to derive ecosystem-level NSC dynamics (NSC i ), C translocation (dC i ), and the biomass production efficiency (BPE i ) in above- and belowground plant (i = agp and bgp) compartments. We applied this framework to two long-term monitored loblolly pine (Pinus taeda) plantations of different ages in North Carolina and characterized the variations of NSC and allocation in years under normal and drought conditions. The results indicated that the young stand did not have net NSC flux at the annual scale, whereas the mature stand stored a near-constant proportion of new assimilates as NSC every year under normal conditions, which was comparable in magnitude to new structural growth. Roots consumed NSC in drought and stored a significant amount of NSC post drought. The above- and belowground dC i and BPE i varied more from year to year in the young stand and approached a relatively stable pattern in the mature stand. The belowground BPE bgp differed the most between the young and mature stands and was most responsive to drought. With the internal C dynamics quantified, this framework may also improve biomass production estimation, which reveals the variations resulting from droughts. Overall, these quantified ecosystem-scale dynamics were consistent with existing evidence from tree-based manipulative experiments and measurements and demonstrated that combining the continuous fluxes as proposed here can provide additional information about plant internal C dynamics. Given that it is based on broadly available flux data, the proposed framework is promising to improve the allocation algorithms in ecosystem C cycle models and offers new insights into observed variability in soil–plant–climate interactions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Complete resolution across the neodymium/samarium isotopic envelope with a liquid sampling‐atmospheric pressure glow discharge — Orbitrap mass spectrometer

Rationale Nd and Sm isotope ratios play an important role in geological dating and as nuclear forensic signatures; however, the overlap of the respective 144, 148, 150 Nd/Sm isobars requires prior separations to be performed before analysis on typical MS platforms. The work presented here overcomes these isobaric interferences using ultrahigh‐mass resolution to alleviate interference without prior chemical separations. Methods A liquid sampling‐atmospheric pressure glow discharge ion source was coupled to a standard, QExactive Focus Orbitrap mass spectrometer, providing a mass resolution of ~80 k. A Spectroswiss FTMS booster X2 data acquisition package was used to collect extended transients, providing much higher mass resolution; ~230 k and ~600 k are employed here for Nd and Sm isotopes. Results While the standard Orbitrap resolution is far greater than typical “atomic” MS platforms, it was insufficient to alleviate all isobars. The use of a resolution of ~230 k resulted in baseline separation across the entire isotopic envelope for both Nd and Sm. Isotope ratios obtained from Nd:Sm mixtures using high‐resolution were equivalent to those found for individual‐element solutions, while isotope ratios obtained at a resolution of ~80 k (standard for the OEM data system) showed large deviations. Conclusions Use of ultrahigh‐resolution is an attractive alternative to extensive chemical separations to alleviate severe isobaric interferences. Sufficient mass resolution greatly reduces/eliminates the need for sample manipulations (separations) before analysis while reducing costs and total analysis times.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-Based High-Resolution Ion Mobility Spectrometry–Mass Spectrometry

Ion mobility spectrometry (IMS) is a gas-phase analytical technique that separates ions with different sizes and shapes and is compatible with mass spectrometry (MS) to provide an additional separation dimension. The rapid nature of the IMS separation combined with the high sensitivity of MS-based detection and the ability to derive structural information on analytes in the form of the property collision cross section (CCS) makes IMS particularly well-suited for characterizing complex samples in -omics applications. In such applications, the quality of CCS from IMS measurements is critical to confident annotation of the detected components in the complex -omics samples. However, most IMS instrumentation in mainstream use requires calibration to calculate CCS from measured arrival times, with the most notable exception being drift tube IMS measurements using multifield methods. The strategy for calibrating CCS values, particularly selection of appropriate calibrants, has important implications for CCS accuracy, reproducibility, and transferability between laboratories. The conventional approach to CCS calibration involves explicitly defining calibrants ahead of data acquisition and crucially relies upon availability of reference CCS values. In this work, we present a novel reference-free approach to CCS calibration which leverages trends among putatively identified features and computational CCS prediction to conduct calibrations post-data acquisition and without relying on explicitly defined calibrants. We demonstrated the utility of this reference-free CCS calibration strategy for proteomics application using high-resolution structures for lossless ion manipulations (SLIM)-based IMS-MS. In conclusion, we first validated the accuracy of CCS values using a set of synthetic peptides and then demonstrated using a complex peptide sample from cell lysate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Binary pseudo-random array (BPRA) for inspection and calibration for cylindrical wavefront interferometry

High-accuracy metrology is vitally important in manufacturing ultra-high-quality free-form mirrors designed to manipulate X-ray light with nanometer-scale wavelengths. However, surface topography measurements are instrument dependent, and without the knowledge of how the instrument performs under the practical usage conditions, the measured data contain some degree of uncertainty. Binary Pseudo Random Array (BPRA) “white noise” artifact are effective and useful for characterizing the Instrument Transfer Function (ITF) of surface topography metrology tools and wavefront measurement instrument. BPRA artifact contains features with all spatial frequencies in the instrument bandpass with equal weight. As a result, power spectral density of the patterns has a deterministic white-noise-like character that allows direct determination of the ITF with uniform sensitivity over the entire spatial frequency range. The application examples include electron microscopes, x-ray microscopes, interferometric microscopes, and large field-of-view Fizeau Interferometers. Furthermore, we will introduce the application of BPRA method to characterizing the ITF of Cylindrical Wavefront Interferometry (CWI), by developing the BPRA artifact which matches the radius of curvature of the cylindrical wavefront. The data acquisition and analysis procedures for different applications of the ITF calibration technique developed are also discussed.

Munechika, K↗
DOE OSTI2024

The endocannabinoid system in bovine tissues: characterization of transcript abundance in the growing Holstein steer

Abstract Background The endocannabinoid system (ECS) is highly integrated with seemingly all physiological and pathophysiological processes in the body. There is increasing interest in utilizing bioactive plant compounds, for promoting health and improving production in livestock. Given the established interaction between phytochemicals and the ECS, there are many opportunities for identification and development of therapies to address a range of diseases and disorders. However, the ECS has not been thoroughly characterized in cattle, especially in the gastrointestinal tract. The objective of this study was to characterize the distribution and transcriptional abundance of genes associated with the endocannabinoid system in bovine tissues. Methods Tissues including brain, spleen, thyroid, lung, liver, kidney, mesenteric vein, tongue, sublingual mucosa, rumen, omasum, duodenum, jejunum, ileum and colon were collected from 10-mo old Holstein steers (n = 6). Total RNA was extracted and gene expression was measured using absolute quantification real time qPCR. Gene expression of endocannabinoid receptorsCNR1andCNR2, synthesis enzymesDAGLA,DAGLBandNAPEPLD, degradation enzymesMGLLandFAAH, and transient receptor potential vanilloidsTRPV3andTRPV6was measured. Data were analyzed in R using a Kruskal-Wallis followed by a Wilcoxon rank-sum test. Results are reported as the median copy number/20 ng of equivalent cDNA (CN) with interquartile range (IQR). Results The greatest expression ofCNR1andCNR2was in the brain and spleen, respectively. Expression of either receptor was not detected in any gastrointestinal tissues, however there was a tendency (P = 0.095) forCNR2to be expressed above background in rumen. Expression of endocannabinoid synthesis and degradation enzymes varied greatly across tissues. Brain tissue had the greatestDAGLAexpression at 641 CN (IQR 52;P ≤ 0.05).DAGLBwas detected in all tissues, with brain and spleen having the greatest expression (P ≤ 0.05). Expression ofNAPEPLDin the gastrointestinal tract was lowest in tongue and sublingual mucosal. There was no difference in expression ofNAPEPLDbetween hindgut tissues, however these tissues collectively had 592% greater expression than rumen and omasum (P ≤ 0.05). WhileMGLLwas found to be expressed in all tissues, expression ofFAAHwas only above the limit of detection in brain, liver, kidney, jejunum and ileum.TRPV3was expressed above background in tongue, rumen, omasum and colon. Although not different from each other, thyroid and duodenum had the greatest expression ofTRPV6, with 285 (IQR 164) and 563 (IQR 467) CN compared to all other tissues (P < 0.05). Conclusions These data demonstrate the complex distribution and variation of the ECS in bovine tissues. Expression patterns suggest that regulatory functions of this system are tissue dependent, providing initial insight into potential target tissues for manipulation of the ECS.

Veterinary Sciences↗
DOE OSTI2025

Verification of the PERSENT Software

Ongoing commercial design activities require a thorough verification of the Argonne Reactor Computation codes be performed. DIF3D is central to this system and substantial work has been done to verify its accuracy on several identified commercial needs. This manuscript details the verification work done on PERSENT which relies upon the DIF3D code for its forward and adjoint flux solution. Previous work identified the PERSENT features required to be verified to support commercial design activities, features of which are generally applicable to hexagonal-Z fast reactor designs. The scope of this verification effort includes verifying PERSENT’s ability to correctly calculate four key quantities: perturbation worth distributions, kinetics parameters, sensitivity coefficients, and cross section uncertainty quantification. This manuscript provides the verification tasks and their results with respect to these quantities needed for commercial design activities. For the perturbation worth distributions, hand calculations are deployed to verify the PERSENT calculated results. Similarly, hand calculation of the PERSENT computed kinetics parameters is also used to verify the PERSENT results. In both of these, the input to PERSENT is manipulated to ensure the hand calculation exactly matches the equations PERSENT is calculating. The sensitivity coefficients involve calculating the derivatives of a parameter (such as reactivity worth), with respect to the cross section data. Direct finite difference calculations with DIF3D are used to verify the PERSENT calculated results. For the uncertainty quantification, manufactured input to PERSENT is used to allow an exact hand calculation to reproduce the PERSENT calculated results. The work detailed in this report verified that significant issues were identified for earlier versions of PERSENT for sensitivity coefficients which were corrected in this work and thus version 12.1.0 of PERSENT must be used to reproduce all of the verified work in this report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter

Signal digitization is a commonly overlooked part of ion mobility-mass spectrometry (IMS-MS) workflows, yet it is a significant contributor for determining signal-to-noise ratios and MS resolution. Here we report on the integration of a 2 GS/s, 14-bit ADC with a structures for lossless ion manipulations (SLIM)-IMS-MS and compare the performance to a commonly used 8-bit ADC. The 14-bit ADC provided an effective reduction in digitized noise by factor of ~6, owing largely to the use of smaller bit sizes. The low baseline allowed the threshold voltage levels to be set very close to the MCP baseline voltage, allowing for as much signal to be acquired as possible without causing overloading or excessive digitization of MCP baseline noise. Analyses of Agilent tuning mixture ions and a complex mixture of heavy labeled phosphopeptides showed that the 14-bit ADC (compared to the 8-bit ADC) provided a modest signal-to-noise increase (~1.5 to 2-fold) for high intensity ions, such as the Agilent tuning mixture ions and the 2+ and 3+ charge states of many phosphopeptide constituents. However, signal enhancements were as much as 10-fold for low intensity ions, and the 14-bit ADC enabled discernable signal intensities otherwise lost using an 8-bit digitizer. Additionally, the 14-bit ADC required ~14-fold fewer mass spectra to be averaged to produce a mass spectrum with similar S/N as the 8-bit ADC under identical conditions, potentially providing an order of magnitude higher measurement throughput. The high resolution, low baseline, and fast speed of the new 14-bit ADC enables high performance digitization of MS, IMS-MS, and SLIM-IMS-MS spectra, and allows a much fuller picture of analyte profiles in complex mixtures to be acquired.

data acquisition, digitization, ion mobility spect↗
DOE OSTI2024

A versatile high-speed x-ray microscope for sub-10 nm imaging

We have developed a next-generation scanning x-ray microscope RASMI (RApid Scanning Microscopy Instrument) for high-throughput tomographic imaging. RASMI is installed at the hard x-ray nanoprobe beamline at NSLS-II and is capable of manipulating 1D multilayer Laue lenses (MLLs) and 2D optics (both zone plates and monolithically assembled 2D MLLs). The sample scanning stage utilizes line-focusing interferometry as an encoder while performing fly-scanning data acquisition. The system can be configured for both position- and time-triggering modes during fly-scanning. The microscope demonstrated a detector-limited data acquisition rate of 1.25 kHz during ptychography measurements. The initial x-ray results yielded a sample-limited resolution of ∼6 nm in 2D. RASMI can be adopted for in-vacuum applications and is a foundation for the next-generation scanning microscopy systems to be developed and commissioned at NSLS-II.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Data from A Genetic Toolbox for Metabolic Engineering of Issatchenkia orientalis

The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis , which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis .

Conversion↗
DOE OSTI2026

Coarse-grained fixed-point tensor networks and holographic reflected entropy in 3D gravity

We use the framework of fixed-point BCFT tensor networks to present a microscopic CFT derivation of the correspondence between reflected entropy (RE) and entanglement wedge cross section (EW) in AdS 3 /CFT 2 , for both bipartite and multipartite settings. These fixed-point tensor networks, obtained by triangulating Euclidean CFT path integrals, allow us to explicitly construct the canonical purification via cutting-and-gluing CFT path integrals. Employing modular flow in the large-c limit, we demonstrate that these intrinsic CFT manipulations reproduce bulk geometric prescriptions, without assuming the AdS/CFT dictionary. The emergence of bulk geometry is traced to coarse-graining over heavy states in the large-c limit. Universal coarse-grained BCFT data for compact 2D CFTs, through the relation to Liouville theory with ZZ boundary conditions, yields hyperbolic geometry on the Cauchy slice. The corresponding averaged replica partition functions reproduce all candidate EWs, arising from different averaging patterns, with the dominant one providing the correct RE and EW. In this way, many heuristic tensor-network intuitions in toy models are made precise and established directly from intrinsic CFT data.

AdS-CFT correspondence↗
DOE OSTI2023

Machine learning-based ethylene and carbon monoxide estimation, real-time optimization, and multivariable feedback control of an experimental electrochemical reactor

Electrochemical reduction of CO 2 gas is a novel CO 2 utilization technique that has the potential to mitigate the global climate crisis caused by anthropogenic CO 2 emissions, and enable the large-scale storage of energy generated from renewable sources in the form of carbon-based chemicals and fuels. However, due to the complexity of the electrochemical reactions, the explicit first-principles models for CO2 reduction are not available yet, and there has been a limited effort to develop process modeling, optimization and control of CO 2 electrochemical reactors. To this end, a rotating cylinder electrode (RCE) reactor has been constructed at UCLA to understand the mass transfer and reaction kinetics effects separately on the productivity. In the RCE reactor, the applied potential strongly influences the reaction energetics and the electrode rotation speed affects the hydrodynamic boundary layer and modifies the film mass transfer coefficient, which involves convective and diffusive transport. Further, the present work aims to develop a multi-input multi-output (MIMO) control scheme for the RCE reactor that integrates techniques from artificial and recurrent neural network modeling, nonlinear optimization, and process controller design. Specifically, production rates of two products from the experimental reactor, ethylene and carbon monoxide, are controlled by manipulating two inputs, applied potential and catalyst rotation speed. Process dynamics and controllability are analyzed, a feedback control strategy is designed and the controllers are tuned accordingly. The experimental electrochemical cell is employed to gather data for process modeling and implement the multivariable control system. Finally, the experimental results are presented which demonstrate excellent closed-loop performance by the control system and regulation of the outputs at three different set-points including an economically-optimal set-point.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Evaluating the performance of a high resolution SLIM IM module integrated with an Agilent 6560 IM-QTOF MS - CRADA 413 (Final Report)

Developing new technologies that enhance our abilities to identify molecular signatures is important for the health of the public, the environment, and national security. Deploying these novel technologies requires multiple stages of validation and evaluation. This project focused on evaluating a technology developed at PNNL named Structures for Lossless Ion Manipulations (SLIM) in the context of a commercially available ion mobility mass spectrometer instrument from Agilent Technologies. There is a benefit to integrating the recently developed SLIM module into a real-world instrument platform. Data from the combined instrument will provide new standards for characterizing samples using ion mobility. These standards, related to both the drift time of ions and their resulting collisional cross sections (CCS) will be of value in characterizing samples from both humans and environmental samples, such as soil microbiomes. Because no previous instrument has been designed and implemented to simultaneously analyze the same sample in both constant and oscillating drift fields, the project will provide a new research capability that will support research in a wide variety of applications. The evaluation approach included measuring the resolving power, mass range, sensitivity, and accuracy of two SLIM variations (constant and oscillating fields). Although SLIM performed similarly to the commercial instrument in terms of sensitivity, mass range, and accuracy the resolving power of SLIM far exceeded that of the commercially-available instrument. This validation will provide critically useful data to our commercial partners which they can use to reach informed decisions on the advantages of the SLIM technology such as the outstanding performance and the low cost of manufacturing.

42 ENGINEERING↗
DOE OSTI2025

Data for Regier et al. (2025), "Short-term experimental flooding impacts soil biogeochemistry but not aboveground vegetation in a coastal forest"

Rising sea levels and intensifying storms increase flooding pressure on coastal forests, but the mechanisms that drive coastal forest mortality remain unclear. This study used an ecosystem-scale manipulation (TEMPEST, Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments) to simulate hurricane-level flooding of a coastal forest and explore the individual and interactive impacts of inundation and salinity. This dataset comprises the results reported by Regier et al. (2025) in their paper "Short-term experimental flooding impacts soil biogeochemistry but not aboveground vegetation in a coastal forest." It consists of measurements of:- Belowground conductance- Soil dissolved oxygen and redox- Soil and tree greenhouse gas fluxes- Leaf photosynthesis, stomatal conductance, and intercellular carbon dioxide- Sap flux- Soil volumetric water content and electrical conductivityAll files are plain-text CSV (comma separated value) and no special software is required to read them.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

A Preprocessing Tool for Enhanced Ion Mobility–Mass Spectrometry-Based Omics Workflows

The ability to improve the data quality of ion mobility–mass spectrometry (IM-MS) measurements is of great importance for enabling modular and efficient computational workflows and gaining better qualitative and quantitative insights from complex biological and environmental samples. We developed the PNNL PreProcessor, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format. Different experimental approaches are supported for IM-MS based on Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), including liquid chromatography (LC) and infusion analyses. The algorithms extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. Specifically, multidimensional smoothing improves peak shapes of poorly defined low-abundance signals, and saturation repair reconstructs the intensity profile of high-abundance peaks from various analyte types. Further, other functionalities are data compression and interpolation, IM demultiplexing, noise filtering by low intensity threshold and spike removal, and exporting of acquisition metadata. Several advantages of the tool are illustrated, including an increase of 19.4% in lipid annotations and a two-times faster processing of LC-DT IM-MS data-independent acquisition spectra from a complex lipid extract of a standard human plasma sample. The software is freely available at https://omics.pnl.gov/software/pnnl-preprocessor.

59 BASIC BIOLOGICAL SCIENCES↗