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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Kinetic equilibrium reconstructions of plasmas in the MAST database and preparation for reconstruction of the first plasmas in MAST upgrade

Reconstructions of plasma equilibria using magnetic sensors were routine during operation of the Mega Ampere Spherical Tokamak (MAST) device, but reconstructions using kinetic profiles were not. These are necessary for stability and disruption analysis of the MAST database, as well as for operation in the upgrade to the device, MAST-U. The three-dimensional (3D) code VALEN is used to determine eddy currents in the 3D vessel structures for vacuum coil test shots, which are then mapped to effective resistances in the two-dimensional vessel groupings in the EFIT equilibrium reconstruction code to be used in conjunction with nearby loop voltage measurements for estimated currents in the structures during reconstruction. Kinetic equilibrium reconstructions with EFIT, using all available magnetic sensors as well as Thomson scattering measurements of electron temperature and density, charge exchange recombination spectroscopy measurements of ion temperature, and internal magnetic field pitch angle measurements from a motional Stark effect (MSE) diagnostic are performed for a large database of MAST discharges. Excellent convergence errors are obtained for the portions of the discharges where the stored energy was not too low, and it is found that reconstructions performed with temperature and density measurements but without MSE data usually already match the pitch angle measurements well. A database of 275 kinetic equilibria is used to test the ideal MHD stability calculation capability for MAST. In conclusion, the necessary changes to conducting structure in VALEN, and diagnostic setup in EFIT have been completed for the upgrade from MAST to MAST-U, enabling kinetic reconstructions to commence from the first plasma discharges of the upgraded device.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2017

Individualized Selection of Beam Angles and Treatment Isocenter in Tangential Breast Intensity Modulated Radiation Therapy

Purpose and Objective: Propose a novel method for individualized selection of beam angles and treatment isocenter in tangential breast intensity modulated radiation therapy (IMRT). Methods and Materials: For each patient, beam and isocenter selection starts with the fully automatic generation of a large database of IMRT plans (up to 847 in this study); each of these plans belongs to a unique combination of isocenter position, lateral beam angle, and medial beam angle. The imposed hard planning constraint on patient maximum dose may result in plans with unacceptable target dose delivery. Such plans are excluded from further analyses. Owing to differences in beam setup, database plans differ in mean doses to organs at risk (OARs). These mean doses are used to construct 2-dimensional graphs, showing relationships between: (1) contralateral breast dose and ipsilateral lung dose; and (2) contralateral breast dose and heart dose (analyzed only for left-sided). The graphs can be used for selection of the isocenter and beam angles with the optimal, patient-specific tradeoffs between the mean OAR doses. For 30 previously treated patients (15 left-sided and 15 right-sided tumors), graphs were generated considering only the clinically applied isocenter with 121 tangential beam angle pairs. For 20 of the 30 patients, 6 alternative isocenters were also investigated. Results: Computation time for automatic generation of 121 IMRT plans took on average 30 minutes. The generated graphs demonstrated large variations in tradeoffs between conflicting OAR objectives, depending on beam angles and patient anatomy. For patients with isocenter optimization, 847 IMRT plans were considered. Adding isocenter position optimization next to beam angle optimization had a small impact on the final plan quality. Conclusion: A method is proposed for individualized selection of beam angles in tangential breast IMRT. This may be especially important for patients with cardiac risk factors or an enhanced risk for the development of contralateral breast cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
NASA NTRS1996

Incorporating Oracle on-line space management with long-term archival technology

The storage requirements of today's organizations are exploding. As computers continue to escalate in processing power, applications grow in complexity and data files grow in size and in number. As a result, organizations are forced to procure more and more megabytes of storage space. This paper focuses on how to expand the storage capacity of a Very Large Database (VLDB) cost-effectively within a Oracle7 data warehouse system by integrating long term archival storage sub-systems with traditional magnetic media. The Oracle architecture described in this paper was based on an actual proof of concept for a customer looking to store archived data on optical disks yet still have access to this data without user intervention. The customer had a requirement to maintain 10 years worth of data on-line. Data less than a year old still had the potential to be updated thus will reside on conventional magnetic disks. Data older than a year will be considered archived and will be placed on optical disks. The ability to archive data to optical disk and still have access to that data provides the system a means to retain large amounts of data that is readily accessible yet significantly reduces the cost of total system storage. Therefore, the cost benefits of archival storage devices can be incorporated into the Oracle storage medium and I/O subsystem without loosing any of the functionality of transaction processing, yet at the same time providing an organization access to all their data.

Moran, Steven M.↗
DOE OSTI2020

Exhaustive Product Analysis of Three Benzene Discharges by Microwave Spectroscopy

Using chirped and cavity microwave spectroscopies, automated double resonance, new high-speed fitting and deep learning algorithms, and large databases of computed structures, the discharge products of benzene alone, or in combination with molecular oxygen or nitrogen, have been exhaustively characterized between 6.5 and 26 GHz. In total, more than 3300 spectral features were observed; 89% of these, accounting for 97% of the total intensity, have now been assigned to 152 distinct chemical species and 60 of their variants (i.e., isotopic species and vibrationally excited states). Roughly 50 of the products are entirely new or poorly characterized at high resolution, including many heavier by mass than the precursor benzene. These findings provide direct evidence for a rich architecture of two- and three-dimensional carbon and indicate that benzene growth, particularly the formation of ring–chain molecules, occurs facilely under our experimental conditions. The present analysis also illustrates the utility of microwave spectroscopy as a precision tool for complex mixture analysis, irrespective of whether the rotational spectrum of a product species is known a priori or not. From this large quantity of data, for example, it is possible to determine with confidence the relative abundances of different product masses, but more importantly the relative abundances of different isomers with the same mass. We review the complementary nature of this type of analysis to traditional mass spectrometry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Atlas of putative minima and low-lying energy networks of water clusters n = 3 - 25

We report a database consisting of the putative minima and ~3.2 million local minima lying within 5 kcal/mol from the putative minima for water clusters of sizes n = 3 – 25 using an improved version of the Monte Carlo Temperature Basin Paving (MCTBP) global optimization procedure in conjunction with the ab-initio based, flexible, polarizable Thole-Type Model (TTM2.1-F, version 2.1) interaction potential for water. Several of the low-lying structures, as well as lowlying penta-coordinated water networks obtained with the TTM2.1-F potential, were further refined at the Møller-Plesset second order perturbation MP2/aug-cc-pVTZ level of theory. In total, we have identified 3,138,303 networks corresponding to local minima of the clusters n = 3 – 25, whose Cartesian coordinates and relative energies can be obtained from the webpage https://sites.uw.edu/wdbase/. Networks containing penta-coordinated water molecules start to appear at n = 11 and, quite surprisingly, are energetically close (within 1 – 3 kcal/mol) to the putative minima, a fact that has been confirmed from the MP2 calculations. This large database of water cluster minima spanning quite dissimilar hydrogen bonding networks is expected to influence the development and assessment of the accuracy of interaction potentials for water as well as lower scaling electronic structure methods (such as different density functionals). Furthermore, it can also be used in conjunction with data science approaches (including but no limited to neural networks, machine and deep learning) to understand the properties of water, nature’s most important substance.

Rakshit, Avijit↗
DOE OSTI2014

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C—H⋯O hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Large Ensemble Analytic Framework for Consequence-Driven Discovery of Climate Change Scenarios

An analytic scenario generation framework is developed based on the idea that the same climate outcome can result from very different socioeconomic and policy drivers. The framework builds on the Scenario Matrix Framework’s abstraction of “challenges to mitigation” and “challenges to adaptation” to facilitate the flexible discovery of diverse and consequential scenarios. We combine visual and statistical techniques for interrogating a large factorial data set of 33,750 scenarios generated using the Global Change Assessment Model. We demonstrate how the analytic framework can aid in identifying which scenario assumptions are most tied to user-specified measures for policy relevant outcomes of interest, specifically for our example high or low mitigation costs. We show that the current approach for selecting reference scenarios can miss policy relevant scenario narratives that often emerge as hybrids of optimistic and pessimistic scenario assumptions. We also show that the same scenario assumption can be associated with both high and low mitigation costs depending on the climate outcome of interest and the mitigation policy context. In the illustrative example, we show how agricultural productivity, population growth, and economic growth are most predictive of the level of mitigation costs. Formulating policy relevant scenarios of deeply and broadly uncertain futures benefits from large ensemble-based exploration of quantitative measures of consequences. To this end, we have contributed a large database of climate change futures that can support “bottom-up” scenario generation techniques that capture a broader array of consequences than those that emerge from limited sampling of a few reference scenarios.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2014

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data

Cancer is driven by the acquisition of somatic DNA lesions. Distinguishing the early driver mutations from subsequent passenger mutations is key to molecular sub-typing of cancers, and the discovery of novel biomarkers. The availability of genomics technologies (mainly wholegenome and exome sequencing, and transcript sampling via RNA-seq, collectively referred to as NGS) have fueled recent studies on somatic mutation discovery. However, the vision is challenged by the complexity, redundancy, and errors in genomic data, and the difficulty of investigating the proteome using only genomic approaches. Recently, combination of proteomic and genomic technologies are increasingly employed. However, the complexity and redundancy of NGS data remains a challenge for proteogenomics, and various trade-offs must be made to allow for the searches to take place. This paperprovides a discussion of two such trade-offs, relating to large database search, and FDR calculations, and their implication to cancer proteogenomics. Moreover, it extends and develops the idea of a unified genomic variant database that can be searched by any mass spectrometry sample. A total of 879 BAM files downloaded from TCGA repository were used to create a 4.34 GB unified FASTA database which contained 2,787,062 novel splice junctions, 38,464 deletions, 1105 insertions, and 182,302 substitutions. Proteomic data from a single ovarian carcinoma sample (439,858 spectra) was searched against the database. By applying the most conservative FDR measure, we have identified 524 novel peptides and 65,578 known peptides at 1% FDR threshold. The novel peptides include interesting examples of doubly mutated peptides, frame-shifts, and non-sample-recruited mutations, which emphasize the strength of our approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ca X ML: Chemistry‐informed machine learning explains mutual changes between protein conformations and calcium ions in calcium‐binding proteins using structural and topological features

Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes. However, it is unclear whether the limited experimental data available can be effectively used to train models to accurately predict the charges of calcium-binding protein variants. Here, we developed a chemistry-informed, machine-learning algorithm that implements a game theoretic approach to explain the output of a machine-learning model without the prerequisite of an excessively large database for high-performance prediction of atomic charges. We used the ab initio electronic structure data representing calcium ions and the structures of the disordered segments of calcium-binding peptides with surrounding water molecules to train several explainable models. Network theory was used to extract the topological features of atomic interactions in the structurally complex data dictated by the coordination chemistry of a calcium ion, a potent indicator of its charge state in protein. Our design created a computational tool of Ca X ML, which provided a framework of explainable machine learning model to annotate ionic charges of calcium ions in calcium-binding proteins in response to the chemical changes in an environment. Our framework will provide new insights into protein design for engineering functionality based on the limited size of scientific data in a genome space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Trajectory analysis via a geometric feature space approach

This study aimed to organize a body of trajectories in order to identify, search for and classify both common and uncommon behaviors among objects such as aircraft and ships. Existing comparison functions such as the Fréchet distance are computationally expensive and yield counterintuitive results in some cases. We propose an approach using feature vectors whose components represent succinctly the salient information in trajectories. These features incorporate basic information such as the total distance traveled and the distance between start/stop points as well as geometric features related to the properties of the convex hull, trajectory curvature and general distance geometry. Additionally, these features can generally be mapped easily to behaviors of interest to humans who are searching large databases. Most of these geometric features are invariant under rigid transformation. Furthermore, we demonstrate the use of different subsets of these features to identify trajectories similar to an exemplar, cluster a database of several hundred thousand trajectories and identify outliers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Drugging the entire human proteome: Are we there yet?

Each of the ~20 000 proteins in the human proteome is a potential target for compounds that bind to it and modify its function. The 3D structures of most of these proteins are now available. Here, we discuss the prospects for using these structures to perform proteome-wide virtual HTS (VHTS). Furthermore, we compare physics-based (docking) and AI VHTS approaches, some of which are now being applied with large databases of compounds to thousands of targets. Although preliminary proteome-wide screens are now within our grasp, further methodological developments are expected to improve the accuracy of the results.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Recent aspects of uranium toxicology in medical geology

Uranium (U) is a chemo-toxic, radiotoxic and even a carcinogenic element. Due to its radioactivity, the effects of U on humans health have been extensively investigated. Prolonged U exposure may cause kidney disease and cancer. The geological distribution of U radionuclides is still a great concern for human health. Uranium in groundwater, frequently used as drinking water, and general environmental pollution with U raise concerns about the potential public health problem in several areas of Asia. The particular paleo-geological hallmark of India and other Southern Asiatic regions enhances the risk of U pollution in rural and urban communities. This paper highlights different health and environmental aspects of U as well as uptake and intake. It discusses levels of U in soil and water and the related health issues. Also described are different issues of U pollution, such as U and fertilizers, occupational exposure in miners, use and hazards of U in weapons (depleted U), U and plutonium as catalysts in the reaction between DNA and H{sub 2}O{sub 2,} and recycling of U from groundwater to surface soils in irrigation. For use in medical geology and U research, large databases and data warehouses are currently available in Europe and the United States. - Highlights: • Uranium (U) is a chemo-toxic, radiotoxic and even a carcinogenic element. • Effects of U on humans health have been extensively studied in recent years. • Prolonged U exposure may cause kidney disease and cancer. • Drinking water is a source of U exposure in some parts of the world.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Machine learning surrogates for ion energy–angle distributions in thermal and RF plasma sheaths

Ion energy–angle distributions (IEADs) at material surfaces are a critical input for plasma–material interaction (PMI) studies in fusion devices, yet they are computationally expensive to obtain using particle-in-cell (PIC) simulations. In this work, we develop a machine learning surrogate based on a deep deconvolutional neural network (DDeCNN) trained on large databases generated with the hPIC2 code. The surrogate is capable of reconstructing IEADs from sheath parameters for both thermal and radio-frequency (RF) plasmas, including cases with multiple ion species. Across thousands of test cases, the model achieves high accuracy, with over 97 % of predictions classified as good or average based on standard error metrics (MAE, MSE, L2). Even in the more challenging RF and multi-species regimes, the surrogate reliably captures the multi-peak structure of PIC results. Once trained, the surrogate produces IEADs in milliseconds on a common workstation, yielding speedups of six to seven orders of magnitude compared with running a full PIC simulation. This computational gain enables dense parameter scans and direct coupling of IEAD predictions with PMI and erosion models on whole-device scales in fusion-relevant conditions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Thermochemical Data Fusion Using Graph Representation Learning

Large databases are required for “Big Data” applications in catalysis and materials science. Thermochemical databases can be created by combining data from various sources and by correcting low-fidelity datasets to higher accuracy with minimal computation. To achieve this “data fusion”, thermochemical quantities of interest, calculated at various levels of density functional theory (DFT), need to be mapped to the same, high levels of theory. In this work, a graph theoretical, statistical framework is proposed for such tasks. Subgraph frequencies are shown to provide a natural representation for learning these fusion maps. The maps are linear and are learnt with automated descriptor selection. Using a dataset of as few as ~1% from the QM9 database of 133,885 molecules, these models can predict multiple thermochemical quantities at a higher level of theory with an accuracy of 1 kcal/mol. Here, the method is explainable, generalizable, and provides a diagnostic tool for outlier identification

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

Accurate calculation of many-body energies in water clusters using a classical geometry-dependent induction model

We incorporate geometry-dependent distributed multipole and polarizability surfaces into an induction model that is used to describe the 3- and 4-body terms of the interaction between water molecules. The expansion is carried out up to hexadecapole with the multipoles distributed on the atom sites. Dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole distributed polarizabilities are used to represent the response of the multipoles to an electric field. We compare the model against two large databases consisting of 43,844 3-body terms and 3,603 4-body terms obtained from high level ab initio calculations previously used to fit the MB-pol and q-AQUA interaction potentials. The classical induction model with no adjustable parameters reproduces the ab-initio 3- and 4-body terms contained in these teo Databases with a Root-Mean-Square-Error (RMSE) of 0.104/0.058 and a Mean-Absolute-Error (MAE) of 0.054/0.026 kcal/mol, respectively, results that are on a par with those obtained 1 by fitting the same data using tens of thousands of Permutationally Invariant Polynomials (PIPs). This demonstrates the accuracy of this physically motivated model in describing the 3- and 4-body terms in the interactions between water molecules with no adjustable parameters. The triple-dipole-dispersion energy was included in the 3-body energy and was found to be small but not quite negligible. The model represents a practical, efficient and transferable approach for obtaining accurate non-additive interactions for multi-component systems without the need of performing tens of thousands of high level electronic structure calculations and fitting them with tens of thousands of PIPs.

molecular analysis water, aqueous↗
DOE OSTI2024

Critical Assessment of Electronic Structure Descriptors for Predicting Perovskite Catalytic Properties

The discovery and design of materials which can efficiently catalyze the oxygen reduction and evolution reactions at reduced temperatures is important for facilitating the widespread adoption of fuel cell and electrolyzer technologies. Numerous studies have produced correlations between catalytic properties, such as oxygen surface exchange or electrode area specific resistance (ASR), and properties of the catalyst material. However, correlations have historically been limited in scope (e.g., using only a few materials or at a single temperature) and it has been difficult to provide detailed assessments of their robustness. Here, in this study, we assess the ability of the O p-band center electronic structure descriptor, obtained from density functional theory (DFT) calculations, to correlate with oxygen surface exchange rates, diffusivities, and area specific resistances for a large database of perovskite oxide catalytic properties. By data mining the literature, we obtain 747 catalytic property value data points spanning 299 unique perovskite compositions from 313 studies. We assess linear correlations of each property with the O p-band center and find generally modest correlations that are qualitatively useful (prediction mean absolute errors of about 0.5 log units are typical), where the correlations are improved at higher temperatures (e.g., 800 °C vs. 500 °C) and significantly improve when considering fits to the subset of materials which have multiple independent measurements. These findings suggest that the spread of property data is significantly influenced by experimental uncertainty, and subsequent measurements of additional materials will likely improve the O p-band center correlations.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2013

Large-Scale Screening of Zeolite Structures for CO2 Membrane Separations

We have conducted large-scale screening of zeolite materials for CO2/CH4 and CO2/N-2 membrane separation applications using the free energy landscape of the guest molecules inside these porous materials. We show how advanced molecular simulations can be integrated with the design of a simple separation process to arrive at a metric to rank performance of over 87 000 different zeolite structures, including the known IZA zeolite structures. Our novel, efficient algorithm using graphics processing units can accurately characterize both the adsorption and diffusion properties of a given structure in just a few seconds and accordingly find a set of optimal structures for different desired purity of separated gases from a large database of porous materials in reasonable wall time. Our analysis reveals that the optimal structures for separations usually consist of channels with adsorption sites spread relatively uniformly across the entire channel such that they feature well-balanced CO2 adsorption and diffusion properties. Our screening also shows that the top structures in the predicted zeolite database outperform the best known zeolite by a factor of 4-7. Finally, we have identified a completely different optimal set of zeolite structures that are suitable for an inverse process, in which the CO2 is retained while CH4 or N-2 is passed through a membrane.

Kim, JH↗
DOE OSTI2016

Metal–organic framework with optimally selective xenon adsorption and separation

Nuclear energy is considered among the most viable alternatives to our current fossil fuel based energy economy.1 The mass-deployment of nuclear energy as an emissions-free source requires the reprocessing of used nuclear fuel to mitigate the waste.2 One of the major concerns with reprocessing used nuclear fuel is the release of volatile radionuclides such as Xe and Kr. The most mature process for removing these radionuclides is energy- and capital-intensive cryogenic distillation. Alternatively, porous materials such as metal-organic frameworks (MOFs) have demonstrated the ability to selectively adsorb Xe and Kr at ambient conditions.3-8 High-throughput computational screening of large databases of porous materials has identified a calcium-based nanoporous MOF, SBMOF-1, as the most selective for Xe over Kr.9,10 Here, we affirm this prediction and report that SBMOF-1 exhibits by far the highest Xe adsorption capacity and a remarkable Xe/Kr selectivity under relevant nuclear reprocessing conditions. The exceptional selectivity of SBMOF-1 is attributed to its pore size tailored to Xe and its dense wall of atoms that constructs a binding site with a high affinity for Xe, as evident by single crystal X-ray diffraction and molecular simulation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗