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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Systematic calibration of an integrated x-ray and optical tomography system for preclinical radiation research

Purpose: The cone beam computed tomography (CBCT) guided small animal radiation research platform (SARRP) has been developed for focal tumor irradiation, allowing laboratory researchers to test basic biological hypotheses that can modify radiotherapy outcomes in ways that were not feasible previously. CBCT provides excellent bone to soft tissue contrast, but is incapable of differentiating tumors from surrounding soft tissue. Bioluminescence tomography (BLT), in contrast, allows direct visualization of even subpalpable tumors and quantitative evaluation of tumor response. Integration of BLT with CBCT offers complementary image information, with CBCT delineating anatomic structures and BLT differentiating luminescent tumors. This study is to develop a systematic method to calibrate an integrated CBCT and BLT imaging system which can be adopted onboard the SARRP to guide focal tumor irradiation. Methods: The integrated imaging system consists of CBCT, diffuse optical tomography (DOT), and BLT. The anatomy acquired from CBCT and optical properties acquired from DOT serve as a priori information for the subsequent BLT reconstruction. Phantoms were designed and procedures were developed to calibrate the CBCT, DOT/BLT, and the entire integrated system. Geometrical calibration was performed to calibrate the CBCT system. Flat field correction was performed to correct the nonuniform response of the optical imaging system. Absolute emittance calibration was performed to convert the camera readout to the emittance at the phantom or animal surface, which enabled the direct reconstruction of the bioluminescence source strength. Phantom and mouse imaging were performed to validate the calibration. Results: All calibration procedures were successfully performed. Both CBCT of a thin wire and a euthanized mouse revealed no spatial artifact, validating the accuracy of the CBCT calibration. The absolute emittance calibration was validated with a 650 nm laser source, resulting in a 3.0% difference between simulated and measured signal. The calibration of the entire system was confirmed through the CBCT and BLT reconstruction of a bioluminescence source placed inside a tissue-simulating optical phantom. Using a spatial region constraint, the source position was reconstructed with less than 1 mm error and the source strength reconstructed with less than 24% error. Conclusions: A practical and systematic method has been developed to calibrate an integrated x-ray and optical tomography imaging system, including the respective CBCT and optical tomography system calibration and the geometrical calibration of the entire system. The method can be modified and adopted to calibrate CBCT and optical tomography systems that are operated independently or hybrid x-ray and optical tomography imaging systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Projective Integral Updates for High-Dimensional Variational Inference

Variational inference is an approximation framework for Bayesian inference that seeks to improve quantified uncertainty in predictions by optimizing a simplified distribution over parameters to stand in for the full posterior. Capturing model variations that remain consistent with training data enables more robust predictions by reducing parameter sensitivity. This work introduces a fixed-point optimization for variational inference that is applicable when every feasible log density can be expressed as a linear combination of functions from a given basis. In such cases, the optimizer becomes a fixed-point of projective integral updates. When the basis spans univariate quadratics in each parameter, the feasible distributions are Gaussian mean-fields and the projective integral updates yield quasi-Newton variational Bayes (QNVB). Other bases and updates are also possible. Since these updates require high-dimensional integration, this work begins by proposing an efficient quasirandom sequence of quadratures for mean-field distributions. Each iterate of the sequence contains two evaluation points that combine to correctly integrate all univariate quadratic functions and, if the mean-field factors are symmetric, all univariate cubics. More importantly, averaging results over short subsequences achieves periodic exactness on a much larger space of multivariate polynomials of quadratic total degree. The corresponding variational updates require four loss evaluations with standard (not second-order) backpropagation to eliminate error terms from over half of all multivariate quadratic basis functions. Furthermore, this integration technique is motivated by first proposing stochastic blocked mean-field quadratures, which may be useful in other contexts. A PyTorch implementation of QNVB allows for better control over model uncertainty during training than competing methods. Experiments demonstrate superior generalizability for multiple learning problems and architectures.

Gaussian mean-field↗
DOE OSTI2019

Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration

Background: The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. In addition to providing a robust means of identifier conversion, BRM also incorporates a suite of miRNA-target databases upon which to query target genes or to perform reverse target lookups using gene identifiers. Results: BRM has the capability to perform cross-species identifier lookups across common identifier types, directly integrate datasets across platform or species by performing identifier retrievals in the background, and retrieve miRNA targets from multiple databases simultaneously and integrate the resulting gene targets with experimental mRNA data. Here we use workflows provided in BRM to integrate RNAseq data across species to identify common biomarkers of exposure after treatment of human lung cells and zebrafish to benzo[a]pyrene (BAP). We further use the miRNA Target workflow to experimentally determine the role of miRNAs as regulators of BAP toxicity and identify the predicted functional consequences of miRNA-target regulation in our system. The output from BRM can easily and directly be uploaded to freely available visualization tools for further analysis. From these examples, we were able to identify an important role for several miRNAs as potential regulators of BAP toxicity in human lung cells associated with cell migration, cell communication, cell junction assembly and regulation of cell death. Conclusions: Overall, BRM provides bioinformatics tools to assist biologists having minimal programming skills with analysis and integration of high-content omics’ data from various transcriptomic and proteomic platforms. BRM workflows were developed in Java and other open-source technologies and are served publicly using Apache Tomcat at https://cbb.pnnl.gov/brm/.

bioinformatics, MicroRNA, systems biology, Genomic↗
DOE OSTI2023

Technical Challenges and Gaps in Integration of Advanced Sensors, Instrumentation, and Communication Technologies with Digital Twins for Nuclear Application

This paper explores integrating advanced sensor, instrumentation, and communication technologies with digital twin technologies for nuclear energy application. Digital twins and digital-twin-enabling technologies are expected to integrate with future nuclear reactor designs and have the potential to impact currently operating nuclear power plants. Greater digital integration, advanced instrumentation and control systems, and advanced operations and maintenance practices are all associated with digital-twin-enabling technologies. Advanced sensors, instrumentation, and communication technology are expected to comprise important elements of the infrastructure required to develop and operate a nuclear digital twin system. This paper identifies and discusses challenges and gaps in developing and implementing advanced sensors and instrumentation and communication technology to be integrated with a digital twin in current and advanced reactor applications. It is important to address some challenge and gap to enable a successful near-term deploying advanced sensors, instrumentation, and communication technologies integrated with digital twins.

Yadav, Vaibhav↗
DOE OSTI2021

Integrated photonics on thin-film lithium niobate

Lithium niobate (LN), an outstanding and versatile material, has influenced our daily life for decades—from enabling high-speed optical communications that form the backbone of the Internet to realizing radio-frequency filtering used in our cell phones. This half-century-old material is currently embracing a revolution in thin-film LN integrated photonics. The successes of manufacturing wafer-scale, high-quality thin films of LN-on-insulator (LNOI) and breakthroughs in nanofabrication techniques have made high-performance integrated nanophotonic components possible. With rapid development in the past few years, some of these thin-film LN devices, such as optical modulators and nonlinear wavelength converters, have already outperformed their legacy counterparts realized in bulk LN crystals. Furthermore, the nanophotonic integration has enabled ultra-low-loss resonators in LN, which has unlocked many novel applications such as optical frequency combs and quantum transducers. In this review, we cover—from basic principles to the state of the art—the diverse aspects of integrated thin-film LN photonics, including the materials, basic passive components, and various active devices based on electro-optics, all-optical nonlinearities, and acousto-optics. We also identify challenges that this platform is currently facing and point out future opportunities. The field of integrated LNOI photonics is advancing rapidly and poised to make critical impacts on a broad range of applications in communication, signal processing, and quantum information.

Zhu, Di (ORCID:0000000302101860)↗
DOE OSTI2020

A heterogeneously integrated silicon photonic/lithium niobate travelling wave electro-optic modulator

Silicon photonics is a platform that enables densely integrated photonic components and systems and integration with electronic circuits. Depletion mode modulators designed on this platform suffer from a fundamental frequency response limit due to the mobility of carriers in silicon. Lithium niobate-based modulators have demonstrated high performance, but the material is difficult to process and cannot be easily integrated with other photonic components and electronics. In this manuscript, we simultaneously take advantage of the benefits of silicon photonics and the Pockels effect in lithium niobate by heterogeneously integrating silicon photonic-integrated circuits with thin-film lithium niobate samples. We demonstrate the most CMOS-compatible thin-film lithium niobate modulator to date, which has electro-optic 3 dB bandwidths of 30.6 GHz and half-wave voltages of 6.7 V×cm. These modulators are fabricated entirely in CMOS facilities, with the exception of the bonding of a thin-film lithium niobate sample post fabrication, and require no etching of lithium niobate.

42 ENGINEERING↗
DOE OSTI2021

Hybrid integrated photonic platforms: opinion

While photonic integration has made remarkable progress in recent years, there is no one integrated photonic platform that offers all desired functionalities and manufacturability on the same platform. GaAs and InP-based optoelectronic integrated circuits (OEICs) were very popular in the past decades; however, silicon photonics has recently emerged as a preferred platform due to its high-density and high-yield manufacturability leveraging the CMOS ecosystem, although it lacks optical gain, the Pockels effect, and other characteristics. On the other hand, hybrid photonic integration adds new and diverse functionalities to the host materials like silicon. This opinion paper investigates hybrid integrated photonic platforms, and discusses the new functionalities added to the silicon CMOS photonic platform.

42 ENGINEERING↗
DOE OSTI2018

Development of a landscape integrity model framework to support regional conservation planning

Land managers increasingly rely upon landscape assessments to understand the status of natural resources and identify conservation priorities. Many of these landscape planning efforts rely on geospatial models that characterize the ecological integrity of the landscape. These general models utilize measures of habitat disturbance and human activity to map indices of ecological integrity. Here, we built upon these modeling frameworks by developing a Landscape Integrity Index (LII) model using geospatial datasets of the human footprint, as well as incorporation of other indicators of ecological integrity such as biodiversity and vegetation departure. Our LII model serves as a general indicator of ecological integrity in a regional context of human activity, biodiversity, and change in habitat composition. Finally, we also discuss the application of the LII framework in two related coarse-filter landscape conservation approaches to expand the size and connectedness of protected areas as regional mitigation for anticipated land-use changes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration

The kinetics of HIV-1 decay under treatment depends on the class of antiretrovirals used. Mathematical models are useful to interpret the different profiles, providing quantitative information about the kinetics of virus replication and the cell populations contributing to viral decay. We modeled proviral integration in short- and long-lived infected cells to compare viral kinetics under treatment with and without the integrase inhibitor raltegravir (RAL). We fitted the model to data obtained from participants treated with RAL-containing regimes or with a four-drug regimen of protease and reverse transcriptase inhibitors. Our model explains the existence and quantifies the three phases of HIV-1 RNA decay in RAL-based regimens vs. the two phases observed in therapies without RAL. Our findings indicate that HIV-1 infection is mostly sustained by short-lived infected cells with fast integration and a short viral production period, and by long-lived infected cells with slow integration but an equally short viral production period. We propose that these cells represent activated and resting infected CD4+ T-cells, respectively, and estimate that infection of resting cells represent ~4% of productive reverse transcription events in chronic infection. RAL reveals the kinetics of proviral integration, showing that in short-lived cells the pre-integration population has a half-life of ~7 hours, whereas in long-lived cells this half-life is ~6 weeks. We also show that the efficacy of RAL can be estimated by the difference in viral load at the start of the second phase in protocols with and without RAL. Altogether, we provide a mechanistic model of viral infection that parsimoniously explains the kinetics of viral load decline under multiple classes of antiretrovirals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

NRAP-Open-IAM: NRAP Open Source Integrated Assessment Model

Note: This is the last version (a2.6.1) of NRAP-Open-IAM released during NRAP Phase II in 2022. The latest version of NRAP-Open-IAM is available here: https://edx.netl.doe.gov/dataset/phase-iii-nrap-open-iam NRAP-Open-IAM is an open-source software product that enables quantification of containment effectiveness and leakage risk at storage sites in the context of system uncertainties and variability. NRAP-Open-IAM represents the next-generation in a line of systems-based computational models developed for quantitative geological carbon storage (GCS) risk assessment. The model comprises a set of reduced-order and analytical models of various components of the GCS system, potential leakage pathways, receptors of concern including impact to groundwater resources and the atmosphere, a framework to support stochastic simulation, time stepping, uncertainty quantification, other analytical functionality for scenario and risk-performance evaluation, and a basic graphical user interface to support scenario development, data input simulation definition, and basic post-processing and results display. As the NRAP Open-IAM functionality continues to evolve, we continue to add to its capability to develop quantitative, probabilistic, and time-dependent profiles of the evolution of risk at a GCS site and evaluate the influence of uncertain parameters on uncertainty in predicted risk. It can be used to quantify the dynamics of reservoir saturation plume and pressure-affected area, for evaluation of the area of potential groundwater impact (i.e., Area of Review) and monitoring requirements to support cost and regulatory analysis, and for consideration of different post-injection site care and closure scenarios. This submission contains the current version of NRAP-Open-IAM available for evaluation and testing. To use the NRAP-Open-IAM, download the source code (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/4c24a3da-3b40-4ffe-9892-c807ae9f8760) then open the NRAP-Open-IAM user's guide (https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669) to read more about the tool. Installation instructions for Windows, Mac, and Linux can be found in the "installers" folder of the extracted NRAP-Open-IAM folder and describe setup of environment (e.g., Python libraries) needed for proper work of the tool. Test of installation can be done by running "python openiam_setup_tests.py" in the "setup" folder. The installation test also runs a test suite to see if the NRAP-Open-IAM has been installed correctly. To run the test suite separately, run "python iam_test.py" in the "test" folder. User's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/8b27335a-343c-4836-b8a3-3ad0bdc9e669 Developer's guide: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/3bc6ee7d-609d-4eb6-80ba-fa6130ee0313 Reservoir simulation data used in some examples distributed with NRAP-Open-IAM: - Kimberlina: https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/eb62cece-61b2-4037-9b6d-32407dde2ab8 - Kimberlina (compartmentalized): https://edx.netl.doe.gov/dataset/08f396c8-bc5f-44ad-a028-6e98a6ea6d70/resource/366f9530-3b32-4b84-affe-ab2df1d9a8b5 - FutureGen 2.0: https://edx.netl.doe.gov/dataset/futuregen-2-0-1008-simulation-reservoir-lookup-table NRAP-Open-IAM GitLab repository: https://gitlab.com/NRAP/OpenIAM Related publications: - Bacon, D., Yonkofski, C., Brown, C., Demirkanli, D. and Whiting, J., 2019. Risk-based post injection site care and monitoring for commercial-scale carbon storage: Reevaluation of the FutureGen 2.0 site using NRAP-Open-IAM and DREAM. International Journal of Greenhouse Gas Control 90: 102784. - Bacon, D. Demirkanli, D., and White, S., 2020. Probabilistic risk-based Area of Review (AoR) determination for a deep-saline carbon storage site. International Journal of Greenhouse Gas Control 102: 103153. - Harp, D., Oldenburg, C., and Pawar, R., 2019. A metric for evaluating conformance robustness during geologic CO2 sequestration operations. International Journal of Greenhouse Gas Control 85: 100-108. - Lackey, G., Vasylkivska, V., Huerta, N., King, S., and Dilmore, R., 2019. Managing well leakage risks at a geologic carbon storage site with many wells, International Journal of Greenhouse Gas Control, 88 :182-194. - Vasylkivska, V., Dilmore, R., Lackey, G., Zhang, Y., King, S., Bacon, D., Chen, B., Mansoor, K., and Harp, D., 2021. NRAP-Open-IAM: A flexible open-source integrated assessment model for geologic carbon storage risk assessment and management, Environmental Modelling & Software, 143: 105114. Presentations: - Chen, B., Harp, D., and Pawar, R., A data assimilation approach (ES-MDA) coupling with NRAP-Open-IAM for quantifying uncertainty reduction in geological CO2 sequestration. AGUFM 2019: T44A-02. - Chen, B., and Harp, D., Improving risk analysis precision for geologic CO2 sequestration by quantifying the uncertainty reduction before and after acquiring monitoring data. 14th Greenhouse Gas Control Technologies Conference, Melbourne, Australia, 2018, pp. 21-26. - Harp, D., National Risk Assessment Partnership Task 2: Containment Assurance. No. LA-UR-19-28654, Los Alamos National Laboratory (LANL), Los Alamos, NM (United States), 2019. - Vasylkivska, V., King, S., Bacon, D., Harp, D., Chen, B., Mansoor, K., Onishi, T., Yang, Y., Zhang, Y., and Keating, E., NRAP-Open-IAM: An open-source integrated assessment model, poster, Mastering the Subsurface Through Technology Innovation, Partnerships and Collaboration: Carbon Storage and Oil and Natural Gas Technologies Review Meeting, Pittsburgh, PA, August 13-16, 2018. - Vasylkivska, V., Lackey, G., King, S., Wentworth, A., Huerta, N., Creason, C., DiGiulio, J., Yang, Y., and Dilmore, R., Long-term risk analysis of a geologic CO2 storage project during the post-injection period, SIAM Conference on Computational Science and Engineering, Spokane, WA, February 25-March 1, 2019. - Vasylkivska, V., Overview of the NRAP-Open-IAM tool for carbon storage (beta release), 2019 Annual NRAP Tool Users Meeting, Pittsburgh, PA, August 27, 2019. - Vasylkivska, V., Bacon, D., Chen, B., Dilmore, R., Harp, D., King, S., Lackey, G., Lindner, E., Liu, G., Mansoor, K. and Zhang, Y., NRAP-Open-IAM: A new, open-source code for integrated assessment of geologic carbon storage containment effectiveness and leakage risk, poster, American Geophysical Union Fall Meeting 2020 (virtual meeting), December 2020. - Vasylkivska, V., NRAP open-source integrated assessment model and relevant application, oral presentation, NRAP workshop "NRAP Tools for Geologic Carbon Storage Risk-Based Decision Making" held in conjunction with Groundwater Protection Council (GWPC) 2021 Annual Forum (virtual meeting), Salt Lake City, UT, September 2021. - Vasylkivska, V., NRAP-Open-IAM: open-source integrated assessment model, digital poster/demonstration, software demonstration session, 2022 Carbon Management Project Review Meeting, August 16, 2022

AoR↗
DOE OSTI2021

IOTA Run 2 Beam Dynamics Studies in Nonlinear Integrable Systems

Nonlinear integrable optics is a promising design approach for suppressing fast collective instabilities. To study it experimentally, a new storage ring, the Integrable Optics Test Accelerator (IOTA), was built at Fermilab. IOTA has recently completed its second scientific run, incorporating many hardware and instrumentation improvements. This report presents the results of the two integrable optics experiments - the quasi-integrable Henon-Heiles octupole system and the fully integrable Danilov-Nagaitsev system. We demonstrate tune spread and dynamic aperture in agreement with tracking simulations, and a stable crossing of the integer resonance. Based on recovered single-particle phase space dynamics, we show improved invariant jitter consistent with intended effective Hamiltonian. We conclude by outlining future plans and efforts towards proton studies and larger designs.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

Coupled Geomechanical Modeling to Assess Cap Rock Integrity and Mechanical Fault Stability: Application to Farnsworth Field Unit Project

Abstract The SWP project is located in a mature waterflood undergoing conversion to CO2-WAG operations in the Farnsworth, Texas, USA. Anthropogenic CO2 is sourced from a fertilizer and an ethanol plant. This work utilizes Farnsworth’s full-field, history-matched, compositional hydrodynamic coupled geomechanical model for assessing the impact of stress changes observed through the history matched field life. Production and injection induced stress changes, fault stability and caprock integrity investigations are performed to project the potential for fault reactivation and the loss of caprock integrity under shear failure. A static mechanical earth model (MEM) was constructed for use in transient coupled geomechanical model based on the existing Southwest Regional Partnership (SWP) geological model. The static MEM inherits the stratigraphic and structural features of the geologic model and incorporates additional overburden, underburden, and sideburden formations required to impose mechanical boundary conditions. Mechanical properties were distributed in the 3D MEM through integration of geophysical logs and 3-dimensional seismic elastic inversion properties using a combination of Bayesian and stochastic interpolation methods. These data are further enhanced by lab derived strength and failure criteria for the caprock interval. Additionally, interpreted faults and other geological features were included as part of the static structural framework to fully represent subsurface hydraulic and mechanical systems and appropriately integrate heterogeneity. Two-way coupling of hydrodynamic flow and geomechanical simulations incorporates the Kozeny-Carman relationship for updating permeability and is history matched through primary, secondary (waterflooding) and tertiary (CO2 WAG) recovery periods before performing a twenty year forecast. Two-way simulations are performed to understand the effective stress perturbations imposed by field operations: water injection and the more recent implementation of WAG. Evaluation of Mohr circles with liquid production and field pressure charts as well as slip tendency and distance to failure metrics indicate that neither our faults or cap rock are critically stressed. This paper presents the results of the Farnsworth initial attempts to integrate the seismic driven 3D MEM into coupled hydrodynamic geomechanical history match simulation workflow.

02 PETROLEUM↗
DOE OSTI2015

Technology solutions for wind integration in ERCOT

Texas has for more than a decade led all other states in the U.S. with the most wind generation capacity on the U.S. electric grid. The State recognized the value that wind energy could provide, and committed early on to build out the transmission system necessary to move power from the windy regions in West Texas to the major population centers across the state. It also signaled support for renewables on the grid by adopting an aggressive renewable portfolio standard (RPS). The joining of these conditions with favorable Federal tax credits has driven the rapid growth in Texas wind capacity since its small beginning in 2000. In addition to the major transmission grid upgrades, there have been a number of technology and policy improvements that have kept the grid reliable while adding more and more intermittent wind generation. Technology advancements such as better wind forecasting and deployment of a nodal market system have improved the grid efficiency of wind. Successful large scale wind integration into the electric grid, however, continues to pose challenges. The continuing rapid growth in wind energy calls for a number of technology additions that will be needed to reliably accommodate an expected 65% increase in future wind resources. The Center for the Commercialization of Electric Technologies (CCET) recognized this technology challenge in 2009 when it submitted an application for funding of a regional demonstration project under the Recovery Act program administered by the U.S. Department of Energy1. Under that program the administration announced the largest energy grid modernization investment in U.S. history, making available some $3.4 billion in grants to fund development of a broad range of technologies for a more efficient and reliable electric system, including the growth of renewable energy sources like wind and solar. At that time, Texas was (and still is) the nation’s leader in the integration of wind into the grid, and was investing heavily in the infrastructure needed to increase the viability of this important resource. To help Texas and the rest of the nation address the challenges associated with the integration of large amounts of renewables, CCET seized on the federal opportunity to undertake a multi-faceted project aimed at demonstrating the viability of new “smart grid” technologies to facilitate larger amounts of wind energy through better system monitoring capabilities, enhanced operator visualization, and improved load management. In early 2010, CCET was awarded a $27 million grant, half funded by the Department of Energy and half-funded by project participants. With this funding, CCET undertook the project named Discovery Across Texas which has demonstrated how existing and new technologies can better integrate wind power into the state’s grid. The following pages summarize the results of seven technology demonstrations that will help Texas and the nation meet this wind integration challenge.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2015

Tools and Models for Integrating Multiple Cellular Networks

In this grant, we have systematically investigated the integrated networks, which are responsible for the coordination of activity between metabolic pathways in prokaryotes. We have developed several computational tools to analyze the topology of the integrated networks consisting of metabolic, regulatory, and physical interaction networks. The tools are all open-source, and they are available to download from Github, and can be incorporated in the Knowledgebase. Here, we summarize our work as follow. Understanding the topology of the integrated networks is the first step toward understanding its dynamics and evolution. For Aim 1 of this grant, we have developed a novel algorithm to determine and measure the hierarchical structure of transcriptional regulatory networks [1]. The hierarchy captures the direction of information flow in the network. The algorithm is generally applicable to regulatory networks in prokaryotes, yeast and higher organisms. Integrated datasets are extremely beneficial in understanding the biology of a system in a compact manner due to the conflation of multiple layers of information. Therefore for Aim 2 of this grant, we have developed several tools and carried out analysis for integrating system-wide genomic information. To make use of the structural data, we have developed DynaSIN for protein-protein interactions networks with various dynamical interfaces [2]. We then examined the association between network topology with phenotypic effects such as gene essentiality. In particular, we have organized E. coli and S. cerevisiae transcriptional regulatory networks into hierarchies. We then correlated gene phenotypic effects by tinkering with different layers to elucidate which layers were more tolerant to perturbations [3]. In the context of evolution, we also developed a workflow to guide the comparison between different types of biological networks across various species using the concept of rewiring [4], and Furthermore, we have developed CRIT for correlation analysis in systems biology [5]. For Aim 3, we have further investigated the scaling relationship that the number of Transcription Factors (TFs) in a genome is proportional to the square of the total number of genes. We have extended the analysis from transcription factors to various classes of functional categories, and from individual categories to joint distribution [6]. By introducing a new analytical framework, we have generalized the original toolbox model to take into account of metabolic network with arbitrary network topology [7].

09 BIOMASS FUELS↗
DOE OSTI2016

High-Voltage LED Light Engine with Integrated Driver

LED luminaires have seen dramatic changes in cost breakdown over the past few years. The LED component cost, which until recently was the dominant portion of luminaire cost, has fallen to a level of the same order as the other luminaire components, such as the driver, housing, optics etc. With the current state of the technology, further luminaire performance improvement and cost reduction is realized most effectively by optimization of the whole system, rather than a single component. This project focuses on improving the integration between LEDs and drivers. Lumileds has developed a light engine platform based on low-cost high-power LEDs and driver topologies optimized for integration with these LEDs on a single substrate. The integration of driver and LEDs enables an estimated luminaire cost reduction of about 25% for targeted applications, mostly due to significant reductions in driver and housing cost. The high-power LEDs are based on Lumileds’ patterned sapphire substrate flip-chip (PSS-FC) technology, affording reduced die fabrication and packaging cost compared to existing technology. Two general versions of PSS-FC die were developed in order to create the desired voltage and flux increments for driver integration: (i) small single-junction die (0.5 mm 2 ), optimal for distributed lighting applications, and (ii) larger multi-junction die (2 mm 2 and 4 mm 2 ) for high-power directional applications. Two driver topologies were developed: a tapped linear driver topology and a single-stage switch-mode topology, taking advantage of the flexible voltage configurations of the new PSS-FC die and the simplification opportunities enabled by integration of LEDs and driver on the same board. A prototype light engine was developed for an outdoor “core module” application based on the multi-junction PSS-FC die and the single-stage switch-mode driver. The light engine meets the project efficacy target of 128 lm/W at a luminous flux greater than 4100 lm, a correlated color temperature (CCT) of 4000K and a color rendering index (CRI) greater than 70.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2016

Integrated Surface/subsurface flow modeling in PFLOTRAN

Understanding soil water, groundwater, and shallow surface water dynamics as an integrated hydrological system is critical for understanding the Earth’s critical zone, the thin outer layer at our planet’s surface where vegetation, soil, rock, and gases interact to regulate the environment. Computational tools that take this view of soil moisture and shallow surface flows as a single integrated system are typically referred to as integrated surface/subsurface hydrology models. We extend the open-source, highly parallel, subsurface flow and reactive transport simulator PFLOTRAN to accommodate surface flows. In contrast to most previous implementations, we do not represent a distinct surface system. Instead, the vertical gradient in hydraulic head at the land surface is neglected, which allows the surface flow system to be eliminated and incorporated directly into the subsurface system. This tight coupling approach leads to a robust capability and also greatly simplifies implementation in existing subsurface simulators such as PFLOTRAN. Successful comparisons to independent numerical solutions build confidence in the approximation and implementation. Example simulations of the Walker Branch and East Fork Poplar Creek watersheds near Oak Ridge, Tennessee demonstrate the robustness of the approach in geometrically complex applications. The lack of a robust integrated surface/subsurface hydrology capability had been a barrier to PFLOTRAN’s use in critical zone studies. This work addresses that capability gap, thus enabling PFLOTRAN as a community platform for building integrated models of the critical zone.

58 GEOSCIENCES↗
DOE OSTI2016

Well Integrity for Natural Gas Storage in Depleted Reservoirs and Aquifers

Introduction Motivation The 2015-2016 Aliso Canyon/Porter Ranch natural gas well blowout emitted approximately 100,000 tonnes of natural gas (mostly methane, CH 4 ) over four months. The blowout impacted thousands of nearby residents, who were displaced from their homes. The high visibility of the event has led to increased scrutiny of the safety of natural gas storage at the Aliso Canyon facility, as well as broader concern for natural gas storage integrity throughout the country. Federal Review of Well Integrity In April of 2016, the U.S. Department of Energy (DOE), in conjunction with the U.S. Department of Transportation (DOT) through the Pipeline and Hazardous Materials Safety Administration (PHMSA), announced the formation of a new Interagency Task Force on Natural Gas Storage Safety. The Task Force enlisted a group of scientists and engineers at the DOE National Laboratories to review the state of well integrity in natural gas storage in the U.S. The overarching objective of the review is to gather, analyze, catalogue, and disseminate information and findings that can lead to improved natural gas storage safety and security and thus reduce the risk of future events. The “Protecting our Infrastructure of Pipelines and Enhancing Safety Act of 2016’’ or the ‘‘PIPES Act of 2016,’’which was signed into law on June 22, 2016, created an Aliso Canyon Natural Gas Leak Task Force led by the Secretary of Energy and consisting of representatives from the DOT, Environmental Protection Agency (EPA), Department of Health and Human Services, Federal Energy Regulatory Commission (FERC), Department of Commerce and the Department of Interior. The Task Force was asked to perform an analysis of the Aliso Canyon event and make recommendations on preventing similar incidents in the future. The PIPES Act also required that DOT/PHMSA promulgate minimum safety standards for underground storage that would take effect within two years. Background on the DOE National Laboratories Well Integrity Work Group One of the primary areas that the Task Force is studying is integrity of natural gas wells at storage facilities. The DOE Office of Fossil Energy (FE) took the lead in this area and asked scientists and engineers from the National Energy Technology Laboratory (NETL), Lawrence Livermore National Laboratory (LLNL), Sandia National Laboratories (SNL), and Lawrence Berkeley National Laboratory (LBNL)) to form a Work Group to address this area. This Work Group is an expansion of the original “Lab Team” comprising scientists and engineers from SNL, LLNL, and LBNL which was formed to support the State of California’s response to the Aliso Canyon incident and operated under the Governor of California’s Aliso Canyon Emergency Order (1/6/2016). The Lab Team played a key role in advising the State of California’s Department of Conservation (DOC) in its oversight of SoCalGas during and after the incident.

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DOE OSTI2018

DISTINCT: Diversity in Solar Talent Through INnovative Curriculum and Training: An Integrated Research and Education Approach towards Creating Diversity and Advancing Utility-Scale Solar Technology

The DISTINCT project research objective is to develop an innovative N-port power converter for a utility-scale PV system that is modular, compact and cost-effective and that will enable the integration of a high-frequency, high-voltage solid-state transformer. The novelty of the proposed research is the electrical power conversion architecture using an N-port converter system that replaces the output 60Hz transformer with an integrated high-frequency low-weight solid-state transformer reducing power electronics and BOS costs to meet SunShot goals through modularity and direct high-voltage interconnection. A challenge in direct integration with a 13.8kV line is the high voltage handling capacity of the converters combined with high efficiency operation. The front-end converter for each port is a Neutral-Point Clamped (NPC) Multi-Level dc-dc Dual-Active Bridge (ML-DAB) which allows Maximum Power Point Tracking (MPPT). The integrated high frequency transformer provides the galvanic isolation between the PV and grid side and also steps up the low dc voltage from PV source. Following the ML-DAB stage, in each port, is an inverter with H-bridge configuration or NPC configuration. N number of NPC inverters’ outputs are cascaded to attain the per-phase line-to-neutral voltage to connect directly to the distribution grid (i.e. 13.8 kV). The cascaded inverters have the inherent advantage of using lower rated devices, smaller filters and low Total Harmonic Distortion (THD) required for PV grid interconnection. Our analysis and simulation results show improved performance on cost, efficiency, service life with zero downtime and THD. A comprehensive control scheme is presented to ensure the maximum power from each port and each phase are sent to the grid. A functional prototype of a 2-port converter with ML-DAB and cascaded H-bridges has been designed, built, and tested in a laboratory setup to verify the target technical metrics. The N-port converter system due to its modular structure with individual control per port can be easily adapted to integrate functionalities that go well beyond the conventional grid support functions and mitigates impacts of forecasted fast ramp downs or ramp ups and single-fault conditions by automatic reconfiguration of the output.

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