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At least 1,081 records · Page 60
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Topological Characterization and Uncertainty Visualization of Atmospheric Rivers

Atmospheric rivers (ARs) are long, narrow regions of water vapor in the Earth's atmosphere that transport heat and moisture from the tropics to the mid-latitudes. ARs are often associated with extreme weather events in North America and contribute significantly to water supply and flood risk. However, characterizing ARs has been a major challenge due to the lack of a universal definition and their structural variations. Existing AR detection tools (ARDTs) produce distinct AR boundaries for the same event, making the risk assessment of ARs a difficult task. Understanding these uncertainties is crucial to improving the predictability of AR impacts, including their landfall areas and associated precipitation, which could cause catastrophic flooding and landslides over the coastal regions. In this work, we develop an uncertainty visualization framework that captures boundary and interior uncertainties, i.e., structural variations, of an ensemble of ARs that arise from a set of ARDTs. We first provide a statistical overview of the AR boundaries using the contour boxplots of Whitaker et al. that highlight the structural variations of AR boundaries based on their nesting relationships. We then introduce the topological skeletons of ARs based on Morse complexes that characterize the interior variation of an ensemble of ARs. We propose an uncertainty visualization of these topological skeletons, inspired by MetroSets of Jacobson et al. that emphasizes the agreements and disagreements across the ensemble members. Through case studies and expert feedback, we demonstrate that the two approaches complement each other, and together they could facilitate an effective comparative analysis process and provide a more confident outlook on an AR's shape, area, and onshore impact.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query language (MassQL) aims to make this process accessible and applicable across multiple analysis platforms. While advanced computational methods are capable of predicting compound structures from fragmentation data, AI/ML approaches often rely on complex, opaque criteria that are difficult to interpret or modify. As a result, their predictive patterns cannot be readily translated into human-readable rules, such as those used in MassQL. Here, in this study, we introduce ChemEcho, a machine learning embedding method that converts tandem mass spectrometry data into sparse feature vectors containing peak and neutral mass subformulae to enhance explainable AI/ML-based methods. An advantage of this approach is that decision trees trained using these feature vectors can be directly translated to MassQL. Using a battery of decision trees trained using ChemEcho embeddings to predict molecular attributes, we generated over 1500 MassQL queries for 765 molecular features and evaluated their precision and recall. From these queries, the 50 highest-performing queries were integrated into the MassQL compendium. This set of generated MassQL queries included environmentally and biologically relevant classes such as PFAS and molecules containing phosphate or sulfate substructures. To illustrate the impact these queries would have on a typical metabolomics experiment, these MassQL queries were applied to a public metabolomics data set─resulting in a marked increase in the structural information derived from tandem mass spectra. Access and reuse of these queries is expected to enhance structural annotation in untargeted experiments, leading to more specific claims and advancing many applications in metabolomics.

Harwood, Thomas V. [USDOE Joint Genome Institute (↗
NASA NTRS1982

Structure of the Saint Francois Mountains and surrounding lead belt, S.E. Missouri: Inference from thermal IR and other data sets

Progress in the preparation of manuscripts on the discovery of a Precambrian rift running NW-SE through Missouri as seen in free air and Bouguer gravity anomalies and in HCMM data, and on digital image processing of potential field and topographic data on the rift is reported. Copies of the papers are attached. Contrast-enhanced HCMM images that have been transformed to Mercator projections are presented. Shaded relief map overlays of thermal and apparent thermal inertia images used as part of a masers thesis examining correlations between HCMM data products, linears, and geologic units are presented. Progress in examination of the difference in information content of daytime infrared, night time infrared, albedo, and thermal inertia images and their application to he identification of linears not directly controlled by topography is reported. Thermal infrared and albedo data were coded as hue, saturation and brightness values to generate a color display, which is included.

Arvidson, R. E.↗
DOE OSTI2025

CASM Monte Carlo: Calculations of the thermodynamic and kinetic properties of complex multicomponent crystals

Monte Carlo techniques play a central role in statistical mechanics approaches that connect macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo techniques for the study of multicomponent crystalline materials within the Clusters Approach to Statistical Mechanics (CASM) software suite, and demonstrates their use in model systems to calculate free energies and kinetic coefficients, study phase transitions, and construct phase diagrams from first principles. Many crystal structures are complex, with multiple sublattices occupied by differing sets of chemical species, along with the presence of vacancies or interstitial species. This imposes constraints on concentration variables, the form of thermodynamic potentials, and the values of kinetic transport coefficients. The framework used by CASM to formulate thermodynamic potentials and kinetic transport coefficients accounting for arbitrarily complex crystal structures is presented and demonstrated with examples of increasing complexity. Additionally, an overview of the capabilities of the CASM software specific to Monte Carlo methods is given, and a new CASM software package is introduced, casm-flow, which helps automate the setup, submission, management, and analysis of Monte Carlo simulations.

Cluster expansion↗
DOE OSTI2023

Entropic control of the free-energy landscape of an archetypal biomolecular machine

Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here, we dissect the free-energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free-energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free-energy landscape). Here, we propose that such ligand-dependent entropic control of free-energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.

Science & Technology - Other Topics↗
NASA NTRS1989

Classical geometries defined by exterior differential systems on higher frame bundles

Exterior differential ideals are discussed, and sets of invariant generators presented, for Reimannian, conformal and projective geometries, and for specializations such as Ricci-flat, self-dual and Einstein-Maxwell theories. The Cartan characteristic integers are explicitly calculated, and involutory basis forms found, for each of these (specialized to four dimensions), exposing their algebraic structure and showing how they generate well-posed sets of partial differential equations.

Estabrook, Frank B.↗
DOE OSTI2020

Assessing Collision Cross Section Calibration Strategies for Traveling Wave-Based Ion Mobility Separations in Structures for Lossless Ion Manipulations

The collision cross section (CCS) is an important property that aids in the structural characterization of molecules. Here, we investigated the CCS calibration accuracy with traveling waves ion mobility spectrometry (TWIMS) separations in structures for lossless ion manipulations (SLIM) using three sets of calibrants. A series of singly negatively-charged phospholipids and bile acids were calibrated in nitrogen buffer gas using two different TW waveform profiles (square and sine) and amplitudes (20 V0-p, 25 V0-p, and 30 V 0-p ). The calibration errors for the three calibrant sets Agilent tuning mixture and polyalanine, and one assembled in-house showed negligible differences using a sine-shaped TW waveform. Furthermore, calibration errors were all within 1-2 % of the DTIMS measurements, with lower errors for sine waveforms, presumably due to the lower average and maximum fields experienced by ions. Finally, ultrahigh resolution multi-pass (long path length) SLIM TWIMS demonstrated improved CCS calibration for phospholipid and bile acid isomers.

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

Protein N -Glycans in Healthy and Sclerotic Glomeruli in Diabetic Kidney Disease

Diabetes is expected to directly affect renal glycosylation; yet to date, there has not been a comprehensive evaluation of alterations in N-glycan composition in the glomeruli of patients with diabetic kidney disease (DKD). Here, we used untargeted mass spectrometry imaging to identify N-glycan structures in healthy and sclerotic glomeruli in formalin-fixed paraffin-embedded sections from needle biopsies of five patients with DKD and three healthy kidney samples. Regional proteomics was performed on glomeruli from additional biopsies from the same patients to compare the abundances of enzymes involved in glycosylation. Secondary analysis of single-nucleus RNA sequencing (snRNAseq) data were used to inform on transcript levels of glycosylation machinery in different cell types and states. We detected 120 N-glycans, and among them, we identified 12 of these protein post-translated modifications that were significantly increased in glomeruli. All glomeruli-specific N-glycans contained an N-acetyllactosamine epitope. Five N-glycan structures were highly discriminant between sclerotic and healthy glomeruli. Sclerotic glomeruli had an additional set of glycans lacking fucose linked to their core, and they did not show tetra-antennary structures that were common in healthy glomeruli. Orthogonal omics analyses revealed lower protein abundance and lower gene expression involved in synthesizing fucosylated and branched N-glycans in sclerotic podocytes. In snRNAseq and regional proteomics analyses, we observed that genes and/or proteins involved in sialylation and N-acetyllactosamine synthesis were also downregulated in DKD glomeruli, but this alteration remained undetectable by our spatial N-glycomics assay. Integrative spatial glycomics, proteomics, and transcriptomics revealed protein N-glycosylation characteristic of sclerotic glomeruli in DKD.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2003

Piezoelectric Actuator Modeling Using MSC/NASTRAN and MATLAB

This paper presents a procedure for modeling structures containing piezoelectric actuators using MSCMASTRAN and MATLAB. The paper describes the utility and functionality of one set of validated modeling tools. The tools described herein use MSCMASTRAN to model the structure with piezoelectric actuators and a thermally induced strain to model straining of the actuators due to an applied voltage field. MATLAB scripts are used to assemble the dynamic equations and to generate frequency response functions. The application of these tools is discussed using a cantilever aluminum beam with a surface mounted piezoelectric actuator as a sample problem. Software in the form of MSCINASTRAN DMAP input commands, MATLAB scripts, and a step-by-step procedure to solve the example problem are provided. Analysis results are generated in terms of frequency response functions from deflection and strain data as a function of input voltage to the actuator.

Reaves, Mercedes C.↗
DOE OSTI2025

Electronic Structure Tuning of Lanthanidocene Photocatalysts for C–F Bond Cleavage

A set of nine new robust, tunable cerium complexes supported by an ansa-bis(cyclopentadienyl) ligand, [Me 2 Si(η 5 -Cp R ) 2 ]CeX ( an Cp R )CeX, are excellent homogeneous visible-light photocatalysts for the monodefluoroalkylation of trifluorotoluene with Mg(CH 2 C 6 H 5 ) 2 THF 2 (R = Me 4 , SiMe 3 , X = N(SiMe 3 ) 2 (N″), X = CH(SiMe 3 ) 2 (R''), Cl, OC 6 H 2 t Bu 2 -2,6,Me-4 (OAr)). The trends in photocatalytic activity within the series are explained by photophysical spectroscopic analyses. The aryloxide complex [Me 2 Si(Cp SiMe3 ) 2 ]CeOAr, which has the highest activity (95% substrate conversion in 27 h), shows the most negative (most reducing) excited-state reduction potential (-2.71 V vs Fc). The precatalyst excited-state lifetimes are also exceptionally long. Detailed photoluminescence, NMR spectroscopic, and kinetic studies on chloride [Me 2 Si(Cp Me4 ) 2 ]CeCl suggest that the "ate" complex [{Me 2 Si(Cp Me4 ) 2 } 2 Ce III ClBn][MgBn] is the active catalyst in the alkylation reaction to form PhCF 2 CH 2 Ph with high selectivity over PhCF 2 H. Finally, the reaction rates are up to 30 times higher than previously reported for organometallic rare-earth photocatalysts for these Ce complexes and comparable to established Ir-based photoredox systems.

catalysts↗
DOE OSTI2022

VERDI: VERsatile DIffractometer with wide-angle polarization analysis for magnetic structure studies in powders and single crystals

The VERsatile DIffractometer will set a new standard for a world-class magnetic diffractometer with versatility for both powder and single crystal samples and capability for wide-angle polarization analysis. The instrument will utilize a large single-frame bandwidth and will offer high-resolution at low momentum transfers and excellent signal-to-noise ratio. A horizontal elliptical mirror concept with interchangeable guide pieces will provide high flexibility in beam divergence to allow for a high-resolution powder mode, a high-intensity single crystal mode, and a polarized beam option. A major science focus will be quantum materials that exhibit emergent properties arising from collective effects in condensed matter. The unique use of polarized neutrons to isolate the magnetic signature will provide optimal experimental input to state-of-the-art modeling approaches to access detailed insight into local magnetic ordering.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Pipeline Structural Stability Under Nuclear Blast Pressure Loading

This report documents a set of simplified models to predict pipeline collapse under nuclear pressure loading. After a review of pipeline design literature, a set of simple expressions have been selected to represent an approximation of the threshold pressure for failure from cross- sectional yielding, cross-section buckling, and longitudinal buckling. These expressions provide a first-order approximation on load levels needed to achieve collapse. As a demonstration, the collapse pressure for a set of representative pipelines are calculated. Estimated pressure fields are also computed for a set of nuclear detonations, providing estimates of the ground range limit for pipeline collapse.

42 ENGINEERING↗
NASA NTRS1991

Integrated flow and structural modeling for rocket engine component test facility propellant systems

A set of PC-based computational Dynamic Fluid Flow Simulation models is presented for modeling facility gas and cryogenic systems. Data obtained provide important information regarding performance envelope parameters for the facility using different engine components; time-dependent valve setting for controlling steady-state, quasi-steady state, and transient profiles; optimum facility pipe and pipe component sizes and parameters; momentum transfer loads; and fluid conditions at critical points. A set of COSMIC NASTRAN-based finite element models is also presented to evaluate the loads and stresses on test facility piping systems from fluid and gaseous effects, thermal chill down, and occasional wind loads. The models are based on Apple Macintosh software which makes it possible to change numerous parameters.

Dequay, L.↗
NASA NTRS2003

Velocity Structure and Plasma Properties in Halo CMEs

We have identified a set of 23 Halo CMEs through July 2002 and 21 Partial Halo CMEs from the LASCO Halo CME Mail Archive for which Ultraviolet Coronagraph Spectrometer (UVCS) spectra exist. For each event we have collected basic information such as the event speed, whether or not UVCS caught the bright front, lines detected, Doppler shift and associated flare class. We have also obtained excellent observations of some of the spectacular events in November 2003, and we have made theoretical calculations pertaining to CME expansion at the heights observed by UVCS. We first analyzed the halo CMEs on 21 April and 24 August 2002 and the partial halo on 23 July 2002, because the X-class flares associated with these CMEs were extensively observed by RHESSI and other instruments as part of the MAX MILLENIUM campaign. These very fast CMEs showed extremely violent disruption of the pre-CME streamers, little or no cool prominence material, and the unusual (for UVCS heights) hot emission line [Fe XVIII]. Results, including a discussion of the current sheet interpretation for the [Fe XVIII] emission, are published in Raymond et al. and presented at the Fall 2002 AGU meeting and the solar physics summer school in L'Aquila, Italy. We are currently preparing two papers on the Dec. 28, 2000 partial halo event. This event was chosen to take advantage of the SEP event measured by WIND and ACE, and because a Type II radio burst coincides with the time that broad, blue-shifted O VI emission appeared in the UVCS spectra. One paper deals with a new density and velocity diagnostic for very fast CMEs; pumping of O VI lambda 1032 by Ly beta and pumping of O VI lambda 1038 by O VI lambda 1032. The other discusses physics of the shock wave and association with the SEP event. In the coming year we plan to expand the list of Halo and Partial Halo events observed by UVCS through the end of 2003. We will look at those events as a class to search for correlation between UV spectral characteristics and other CME and flare parameters. We will also choose several events for more detailed study, probably including the November 2003 events. We expect to support extended visits to CfA by S. Mancuso and A. Ciaravella. In the past year the grant covered some salary support for members of the SAO UVCS team and a 1 month visit to CfA by Angela Ciaravella, along with trips to meetings by J. Lin and J. Raymond and page charges for two papers.

Wagner, William↗
NASA NTRS2004

Velocity Structure and Plasma Properties in Halo CMES

We have identified a set of 23 Halo CMEs and 21 Partial Halo CMEs from the LASCO Halo CME Archive for which UVCS spectra exist through July 2002. For each event we have collected basic information such as the event speed, whether or not UVCS caught the bright front, lines detected, Doppler shift and associated flare class. We are currently analyzing the subset for which UVCS caught the CME front. We also obtained excellent observations of some of the spectacular events in November 2003, and we have made theoretical calculations pertaining to CME expansion at the heights observed by UVCS. In one event we were able to analyze the properties of the current sheet in detail.

Raymond, John C.↗
NASA NTRS1989

Effect of structured visual environments on apparent eye level

Each of 12 subjects set a binocularly viewed target to apparent eye level; the target was projected on the rear wall of an open box, the floor of which was horizontal or pitched up and down at angles of 7.5 degrees and 15 degrees. Settings of the target were systematically biased by 60% of the pitch angle when the interior of the box was illuminated, but by only 5% when the interior of the box was darkened. Within-subjects variability of the settings was less under illuminated viewing conditions than in the dark, but was independent of box pitch angle. In a second experiment, 11 subjects were tested with an illuminated pitched box, yielding biases of 53% and 49% for binocular and monocular viewing conditions, respectively. The results are discussed in terms of individual and interactive effects of optical, gravitational, and extraretinal eye-position information in determining judgements of eye level.

NASA Center ARC↗
DOE OSTI2021

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗