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DOE OSTI2016

Use of regularized principal component analysis to model anatomical changes during head and neck radiation therapy for treatment adaptation and response assessment

Purpose: To develop standard (SPCA) and regularized (RPCA) principal component analysis models of anatomical changes from daily cone beam CTs (CBCTs) of head and neck (H&N) patients and assess their potential use in adaptive radiation therapy, and for extracting quantitative information for treatment response assessment. Methods: Planning CT images of ten H&N patients were artificially deformed to create “digital phantom” images, which modeled systematic anatomical changes during radiation therapy. Artificial deformations closely mirrored patients’ actual deformations and were interpolated to generate 35 synthetic CBCTs, representing evolving anatomy over 35 fractions. Deformation vector fields (DVFs) were acquired between pCT and synthetic CBCTs (i.e., digital phantoms) and between pCT and clinical CBCTs. Patient-specific SPCA and RPCA models were built from these synthetic and clinical DVF sets. EigenDVFs (EDVFs) having the largest eigenvalues were hypothesized to capture the major anatomical deformations during treatment. Results: Principal component analysis (PCA) models achieve variable results, depending on the size and location of anatomical change. Random changes prevent or degrade PCA’s ability to detect underlying systematic change. RPCA is able to detect smaller systematic changes against the background of random fraction-to-fraction changes and is therefore more successful than SPCA at capturing systematic changes early in treatment. SPCA models were less successful at modeling systematic changes in clinical patient images, which contain a wider range of random motion than synthetic CBCTs, while the regularized approach was able to extract major modes of motion. Conclusions: Leading EDVFs from the both PCA approaches have the potential to capture systematic anatomical change during H&N radiotherapy when systematic changes are large enough with respect to random fraction-to-fraction changes. In all cases the RPCA approach appears to be more reliable at capturing systematic changes, enabling dosimetric consequences to be projected once trends are established early in a treatment course, or based on population models.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Accurate design of megadalton-scale two-component icosahedral protein complexes

Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB

ABSTRACT RcsB is a highly conserved transcription regulator of the Rcs phosphorelay system, a complex two-component signal transduction system (N. Majdalani and S. Gottesman, Annu Rev Microbiol 59:379–405, 2005; A. J. Wolfe, Curr Opin Microbiol 13:204–209, 2010, https://doi.org/10.1016/j.mib.2010.01.002 ; D. J. Clarke, Future Microbiol 5:1173–1184, 2010, https://doi.org/10.2217/fmb.10.83 ). RcsB plays an important role in virulence and pathogenicity in human hosts by regulating biofilm formation. RcsB can regulate transcription alone or together with its auxiliary transcription regulators by forming heterodimers. This complexity allows RcsB to regulate transcription of more than 600 bacterial genes in response to different stresses (D. Wang et al., Mol Plant Microbe Interact 25:6–17, 2012, https://doi.org/10.1094/MPMI-08-11-0207 ). Despite increasing knowledge of RcsB importance, molecular mechanisms that drive the ability of RcsB to control transcription of a large number of genes remain unclear. Here, we present crystal structures of unphosphorylated RcsB in complex with the consensus DNA-binding sequence of 22-mer (DNA22) and 18-mer (DNA18) of the flhDC operon from Escherichia coli determined at 3.15- and 3.37-Å resolution, respectively. The results of our structural analysis combined with the results of in vitro binding assays provide valuable insights to the protein regulatory mechanism, demonstrate how RcsB recognizes target DNA sequences, and reveal a unique oligomeric state that allows RcsB to form homo- and heterodimers. This information will help us understand the complex mechanisms of transcriptional regulation by RcsB in bacteria. IMPORTANCE RcsB is a well-studied two-component response regulator of the Rcs phosphorelay system, conserved within the family Enterobacteriaceae , which includes many pathogens. It is a global regulator, controlling more than 5% of bacterial genes associated with capsule biosynthesis, flagellar biogenesis, cell wall biosynthesis, antibiotic resistance, biofilm formation, and virulence in pathogens. Knowledge of RcsB structure represents a unique opportunity to explore mechanisms that regulate the Rcs phosphorelay system and its role in the family Enterobacteriaceae .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes

It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Josephson junction with two superconducting current components

The properties of a Josephson junction with the 2π- and 4π-periodic superconducting current component have been analyzed. In the range of low voltages, such a junction exhibits the 4π periodicity of the phase difference for the Majorana current amplitude much smaller than the Josephson current, which makes it possible to observe Josephson current oscillations with a fractional period for small dissipation β < 1 in the hysteresis region. The effect the 4π-periodic Majorana current component is also manifested in a change in the sequence of steps in the ladder structure emerging on the current–voltage (I–V) characteristic of the junction. We have determined the interval of external electromagnetic radiation amplitudes, in which the manifestation of the fractional Josephson effect on the I–V characteristic is most significant.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2018

Electric-Field Behavior of the Resonance Features of the Tunneling Photocurrent Component in InAs(QD)/GaAs Heterostructures

The electric-field behavior of resonance features of the photoelectric characteristics of InAs/GaAs heterostructures is investigated. The emission of carriers excited by light from InAs quantum dots into the GaAs matrix is discussed. It is shown that at the temperature of liquid nitrogen the photocurrent in a strong transverse electric field is only determined by the effect of electron tunneling through a barrier formed at the quantum-dot interfaces. Comparison of the experimental curves with the results obtained using a quasiclassical expression for the tunneling-current component and subsequent analysis of the potential structure made it possible to refine the parameters of the heterostructure under study. The contribution of the resonance component caused by possible electron tunneling through the barrier with the participation of the local defect states to the total tunneling current is analyzed. The influence of the level of excitation of the system on the photocurrent flowing through the InAs/GaAs heterojunction is theoretically studied.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Studies on the thermal breakdown of common Li-ion battery electrolyte components

While much attention is paid to the impact of the active materials on the catastrophic failure of lithium ion batteries, much of the severity of a battery failure is also governed by the electrolytes used, which are typically flammable themselves and can decompose during battery failure. The use of LiPF 6 salt can be problematic as well, not only catalyzing electrolyte decomposition, but also providing a mechanism for HF production. This work evaluates the safety performance of the common components ethylene carbonate (EC), diethyl carbonate (DEC), dimethyl carbonate (DMC), and ethyl methyl carbonate (EMC) in the context of the gasses produced during thermal decomposition, looking at both the quantity and composition of the vapor produced. EC and DEC were found to be the largest contributors to gas production, both producing upwards of 1.5 moles of gas/mole of electrolyte. DMC was found to be relatively stable, producing very little gas regardless of the presence of LiPF 6 . EMC was stable on its own, but the addition of LiPF 6 catalyzed decomposition of the solvent. As a result, while gas analysis did not show evidence of significant quantities of any acutely toxic materials, the gasses themselves all contained enough flammable components to potentially ignite in air.

25 ENERGY STORAGE↗

DOE OSTI2021

(Invited) Understanding Multi-Component Transport and Reaction Phenomena in Bipolar Membranes Used for Electrosynthesis

Bipolar membranes (BPMs), which have long seen usage in electrodialysis reactors for the generation of acid and base, have recently demonstrated potential to become critical components in electrochemical synthesis devices. Because they can operate under large pH gradients, BPMs enable favorable environments for electrocatalysis at the individual electrodes. Critical to the implementation of BPMs in these devices is understanding the kinetics of water dissociation that occurs within the BPM junction as well as the co- and counter-ion crossover through the BPM, which both present significant obstacles to developing efficient and stable BPM-devices for electrosynthesis applications. Prior work has modeled ion transport in bipolar membranes in neutral salt solutions for electrodialysis. However, no model exists for the BPM under the harsh applied pH gradients that would be present in electrosynthesis, and there is significant need to explore the effects of the internal hydration on the lifetime and performance of BPMs in such environments. Additionally, a mechanistic understanding of water dissociation catalysis will be required to develop interfacial catalysts that enable the high current density operation required for scalable electrosynthesis of fuels. In this talk, we discuss modeling methodologies and physics inherent in BPMs and present our recent model of ion transport and water dissociation catalysis in BPMs across the pH scale. Specifically, we simulate multi-ion transport for a BPM with various electrolyte combinations on each side of the membrane, demonstrating the significance of co- and counter-ion crossover in BPMs operating under harsh pH gradients. We then investigate effects caused by hydration gradients that occur due to internal ion-exchange and examine potential methods for improving performance and mitigating crossover. Finally, we examine the impact of the interfacial water dissociation catalyst and perform sensitivity analysis on the key properties (catalyst point of zero charge and pKa) that dictate catalyst performance. These results provide information that is critical to developing a comprehensive understanding of multi-component phenomena in BPMs and to informing the design and implementation of BPMs in next-generation devices for the numerous electrosynthesis chemistries that benefit from operation under an applied pH gradient.

Bui, Justin C↗

DOE OSTI2018

Protective Ceramic Coatings for Solid Oxide Fuel Cell (SOFC) Balance‐of‐Plant Components

Solid oxide fuel cells (SOFCs) have the potential to meet the growing need for electrical power generation if the cost per megawatt can be further reduced. Currently, SOFC stacks are replaced too frequently to be cost competitive. SOFC service life can be extended by preventing chromium‐ (Cr‐) bearing species from evaporating from the interior surfaces of balance of plant (BOP) components and poisoning the cathode to increase the lifetime. We have developed yttria‐stabilized zirconia (YSZ) and aluminum oxide‐ (Al 2 O 3 ‐) modified sol‐gel paints or inks for coating BOP components. 430 stainless steel (430SS) substrates with three surface conditions were coated with the 0.8–1.5 µ m thick YSZ and Al 2 O 3 paints. The coated 430SS samples were tested for thermal cycling resistance, thermal soak, and Cr evaporation. Thermal soak and thermal cycling test results show promise for the YSZ‐coated 430SS substrates. The Cr evaporation test of a coated substrate showed a 51% reduction in Cr generation, when compared with a bare substrate.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Study on Closely Related Citrus CMMs based on Chemometrics and Prediction of Components-Targets-Diseases Network by Ingenuity Pathway Analysis

As the representatives of closely related Chinese medicinal materials (CMMs) originated from Rutaceae family, Aurantii fructus immaturus (AFI), Aurantii fructus (AF), Citri reticulatae pericarpium viride (CRPV), and Citri reticulatae pericarpium (CRP) have better functions in regulating qi and promoting gastrointestinal motility. However, differences in the quality of closely related Citrus CMMs have not yet been revealed until now. Herein, this study focused on the systematic differentiation and in-depth understanding of closely related Citrus CMMs by a strategy integrating chemometrics and network pharmacology. Determined by ultra performance liquid chromatography, the content of nine flavonoids showed obvious fluctuations in the decoction pieces from different species (Citrus aurantium Linnaeus and Citrus reticulate Blanco) with decreasing levels in the samples of ripe fruits. Decoction pieces from the different species and ripening stages were well distinguished by orthogonal projection to latent structure-discriminate analysis (OPLS-DA) and cluster analysis. As a result, four active components including narirutin, naringenin, hesperidin, and 3,5,6,7,8,3′,4′-heptemthoxyflavone were filtered out by variable importance for the projection (VIP) value (VIP > 1.0), which were regarded as chemotaxonomic markers. Furthermore, a components-targets-diseases network was constructed via ingenuity pathway analysis (IPA), and the correlations were predicted between four chemotaxonomic markers, 223 targets, and three diseases including colitis, breast cancer, and colorectal cancer. The obtained results will be of great significance for identifying closely related Citrus CMMs and conduce to improving the resource utilization of CMMs.

Mu, Qixuan↗

DOE OSTI2021

Dynamical Components Analysis (DCA) v1.0.0

Dynamical Components Analysis is a Python implementation of the method described in "Unsupervised discovery of temporal structure in noisy data with dynamical components analysis". It implements the method as well as related data analysis functions.

Livezey, Jesse↗

DOE OSTI2021

Dynamical Components Analysis (DCA) v1.0.0

Livezey, Jesse↗

DOE OSTI2019

TOGA: A TOUGH code for modeling three-phase, multi-component, and non-isothermal processes involved in CO2-based Enhanced Oil Recovery (TOGA) v1.0

TOGA (TOUGH Oil, Gas, Aqueous) is a numerical reservoir simulator for modeling non-isothermal flow and transport of water, CO2, multicomponent oil, and related gas components for applications including CO2-enhanced oil recovery (CO2-EOR) and geologic carbon sequestration in depleted oil and gas reservoirs. TOGA uses an approach based on the Peng-Robinson equation of state (PR-EOS) to calculate the thermophysical properties of the gas and oil phases including the gas/oil components dissolved in the aqueous phase, and uses a mixing model to estimate the thermophysical properties of the aqueous phase.

Oldenburg, CurtisM↗

DOE OSTI2026

Forced Component Estimation Statistical Method Intercomparison Project (ForceSMIP)

Anthropogenic climate change is unfolding rapidly, yet its regional manifestation can be obscured by internal variability. A primary goal of climate science is to identify the externally forced climate response from among the noise of internal variability. Separating the forced response from internal variability can be addressed in climate models by using a large ensemble to average over different possible realizations of internal variability. However, with only one realization of the real world, it is a major challenge to isolate the forced response directly in observations. In the Forced Component Estimation Statistical Method Intercomparison Project (ForceSMIP), contributors used existing and newly developed statistical and machine learning methods to estimate the forced response over 1950–2022 within individual realizations of the climate system. Participants used neural networks, linear inverse models, fingerprinting methods, and low-frequency component analysis, among other approaches. These methods were trained using large ensembles from multiple climate models and then applied to observations. Here, we evaluate method performance within large ensembles and investigate the estimates of the forced response in observations. Our results show that many different types of methods are skillful for estimating the forced response in climate models, though the relative skill of individual methods varies depending on the variable and evaluation metric. Methods with comparable skill in models can give a wide range of estimates of the forced response pattern in observations, illustrating the epistemic uncertainty in forced response estimates. ForceSMIP gives new insights into the forced response in observations, its uncertainty, and methods for its estimation.

Climate attribution↗

DOE OSTI2023

Diffuse Reflectance Spectroscopy and Principal Component Analysis to Retrospectively Determine Production History of Plutonium Dioxide

Diffuse reflectance spectroscopy measurements in the shortwave infrared (930–1600 nm) spectral region were acquired for Pu 2 (C 2 O 4 ) 3 •9H 2 O and its thermal decomposition product, PuO 2 . We analyzed a total of eight PuO 2 samples that were produced at different calcination temperatures (300, 350, 450, 525, 600, 675, 750, and 900 °C). Our goal was to identify spectroscopic fingerprints that could be used to gain retrospective information regarding the production parameters of these important nuclear compounds. The diffuse reflectance spectrum of Pu 2 (C 2 O 4 ) 3 •9H 2 O features several broad bands that currently preclude detailed analysis. However, all PuO 2 samples produced relatively sharp spectral features that got sharper and more intense for samples that were produced at higher calcination temperatures. The electronic band observed at 1433 nm in the diffuse reflectance spectra of PuO 2 was found to be a sensitive indicator of crystallinity; a result that is corroborated by ancillary Raman spectroscopy measurements. Principal component analysis of diffuse reflectance spectra was able to clearly rank and categorize PuO 2 samples based on the calcination temperature that was employed during their production. Thus, we show herein that important retrospective information pertaining to the process history of PuO 2 can be gained through the relatively simplistic combination of diffuse reflectance spectroscopy and principal component analysis. This discovery presents a new method for determining the provenance and process history of PuO 2 and should have an impact in the fields of nuclear forensics and nuclear nonproliferation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Data for Genome-Wide Association and Genomic Prediction for Yield and Component Traits of Miscanthus sacchariflorus

Accelerating biomass improvement is a major goal of miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of miscanthus breeding. The present study conducted genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single-nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus .

Biomass Analytics↗

DOE OSTI2022

Long Term Per-Component Power and Thermal Measurements of the OLCF Summit System

As we move into the exascale era, the power and energy footprints of high-performance computing (HPC) systems have grown significantly larger. Due to the harsh power and thermal conditions the system, components are exposed to extreme operating conditions. Operation of such modern HPC systems requires deep insights into long term system behavior to maintain its efficiency as well as its longevity. To help the HPC community to gain such insights, we provide a dataset that records the long-term power and thermal behavior of the 200PF pre-exascale supercomputer at the Oak Ridge Leadership Computing Facility (OLCF), Summit. This system is an IBM AC922 based system that has 9,252 IBM Power9 CPUs and 27,756 Nvidia V100 GPUs and can consume up to 13MW power at peak. Heat removal is performed using medium temperature direct liquid cooling and rear-door heat exchanger based secondary cooling loop. Originally extracted from a high-resolution (1Hz) per-component (GPUs, CPUs) measurements from the system, we primarily provide a dataset that has 10-second and 1-minute mean power and thermal measurements selected from five month-long segments over the course of 2020 (January and August), 2021 (February and August), and 2022 (January). For convenience, we also provide various sub datasets randomly sampled from the time and space (hosts) of the cluster. Further details and example code for analysis can be found in the following GitHub repository: https://github.com/at-aaims/summit_power_and_thermal_data

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Update on Benchmark Analysis of Component Critical Configurations of KRUSTY

Kilowatt Reactor Using Stirling Technology (KRUSTY) is prototype designed as a proof of concept for NASA’s Kilo power program, which was funded in order to create a small reactor for various space applications such as providing power for a colony on Mars or the moon and eventually as a possible option for powering rockets on deep space missions. Before the final prototype design was tested in March 2018, the component critical configuration, which had less external equipment than the prototype design, was created in November 2017. Both of these designs had less external equipment than the final version will have. This component critical con figuration was used to determine the worth of the beryllium oxide (BeO) reflector and of the boron carbide (B4C) control rod as well as creating necessary benchmark configurations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗