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DOE OSTI2024

Using Parameter Sweep in WaterTAP to Analyze New Water Treatment Technologies

We describe a powerful and generalized parameter sweep tool in this report that was originally developed to analyze the performance of existing and novel water treatment models being developed in WaterTAP. Since WaterTAP is built upon IDAES and Pyomo, the parameter sweep tool can be used to systematically explore and debug the behavior of most Pyomo and IDAES numerical models. In order to enable meaningful analyses, the parameter sweep tool has been designed with the following features: 1) Model flexibility: The parameter sweep tool does not enforce any restrictions on the types of models that can be used with it. As long as a Pyomo model can be solved and the parameter is active and mutable, the tool only needs functions that describe how to run the model, the sweep parameters, and the output quantities of interest. 2) Flexible sampling: The parameter sweep tool has inbuilt functions to generate samples from a random distribution or a multidimensional Euclidean space. Furthermore, the users have to ability to supply samples generated from a tool of their choice. 3) Multiple sweep types: A user can choose from one of 3 types of parameter sweeps depending on their needs. 4) Detailed outputs: Outputs generated by the parameter sweep tool can be stored in detailed H5 file or user-friendly CSV files for post processing. 5) Parallel computing: The parameter sweep supports shared and distributed memory parallel computing to enable the use of high performance computers (HPC) for large-scale analyses. 6) Modular: The parameter sweep tool is self-contained and can easily be integrated within an outer-loop analysis or as desired by the user. 7) Ease of use: The tool is well documented and a simple sweep can be easily executed by following the online documentation in a few lines of code. We demonstrate the use of the parameter sweep tool on a simple water treatment system from the WaterTAP repository and show its parallel scaling performance on an Apple laptop and NREL's Eagle HPC. The parameter sweep tool is actively being used with models currently being developed within WaterTAP and we expect its use to grow beyond it to other IDAES and Pyomo models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Sharing leaky-integrate-and-fire neurons for memory-efficient spiking neural networks

Spiking Neural Networks (SNNs) have gained increasing attention as energy-efficient neural networks owing to their binary and asynchronous computation. However, their non-linear activation, that is Leaky-Integrate-and-Fire (LIF) neuron, requires additional memory to store a membrane voltage to capture the temporal dynamics of spikes. Although the required memory cost for LIF neurons significantly increases as the input dimension goes larger, a technique to reduce memory for LIF neurons has not been explored so far. To address this, we propose a simple and effective solution, EfficientLIF-Net, which shares the LIF neurons across different layers and channels. Our EfficientLIF-Net achieves comparable accuracy with the standard SNNs while bringing up to ~4.3× forward memory efficiency and ~21.9× backward memory efficiency for LIF neurons. We conduct experiments on various datasets including CIFAR10, CIFAR100, TinyImageNet, ImageNet-100, and N-Caltech101. Furthermore, we show that our approach also offers advantages on Human Activity Recognition (HAR) datasets, which heavily rely on temporal information. The code has been released at https://github.com/Intelligent-Computing-Lab-Yale/EfficientLIF-Net.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

“SLIMPLECTIC” INTEGRATORS: VARIATIONAL INTEGRATORS FOR GENERAL NONCONSERVATIVE SYSTEMS

Symplectic integrators are widely used for long-term integration of conservative astrophysical problems due to their ability to preserve the constants of motion; however, they cannot in general be applied in the presence of nonconservative interactions. In this Letter, we develop the “slimplectic” integrator, a new type of numerical integrator that shares many of the benefits of traditional symplectic integrators yet is applicable to general nonconservative systems. We utilize a fixed-time-step variational integrator formalism applied to the principle of stationary nonconservative action developed in Galley et al. As a result, the generalized momenta and energy (Noether current) evolutions are well-tracked. We discuss several example systems, including damped harmonic oscillators, Poynting–Robertson drag, and gravitational radiation reaction, by utilizing our new publicly available code to demonstrate the slimplectic integrator algorithm. Slimplectic integrators are well-suited for integrations of systems where nonconservative effects play an important role in the long-term dynamical evolution. As such they are particularly appropriate for cosmological or celestial N-body dynamics problems where nonconservative interactions, e.g., gas interactions or dissipative tides, can play an important role.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae)

Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales), is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales), and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb), compact (~40% of the genome is protein coding) and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two “red” RuBisCO activases that are shared across many algal lineages. In conclusion, the Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

kokkos-fft: A shared-memory FFT for the Kokkos ecosystem

kokkos-fft provides a unified, performance-portable interface for Fast Fourier Transforms (FFTs) within the Kokkos ecosystem (C. Trott et al., 2021). It seamlessly integrates with leading local FFT libraries including FFTW, cuFFT, rocFFT, and oneMKL. Designed for simplicity and efficiency, kokkos-fft offers a user experience akin to numpy.fft for in-place and out-of-place transforms, while leveraging the raw speed of vendor-optimized libraries. A demonstration solving 2D Hasegawa-Wakatani turbulence with the Fourier spectral method illustrates how kokkos-fft can deliver significant speedups over Python-based alternatives without drastically increasing code complexity, empowering researchers to perform high-performance FFTs simply and effectively.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles

G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world’s most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Status Report on Activities of the Systems Assessment Task Force, OECD-NEA Expert Group on Accident Tolerant Fuels for LWRs

The Organization for Economic Cooperation and Development /Nuclear Energy Agency (OECD/NEA) Nuclear Science Committee approved the formation of an Expert Group on Accident Tolerant Fuel (ATF) for LWRs (EGATFL) in 2014. Chaired by Kemal Pasamehmetoglu, INL Associate Laboratory Director for Nuclear Science and Technology, the mandate for the EGATFL defines work under three task forces: (1) Systems Assessment, (2) Cladding and Core Materials, and (3) Fuel Concepts. Scope for the Systems Assessment task force (TF1) includes definition of evaluation metrics for ATF, technology readiness level definition, definition of illustrative scenarios for ATF evaluation, and identification of fuel performance and system codes applicable to ATF evaluation. The Cladding and Core Materials (TF2) and Fuel Concepts (TF3) task forces will identify gaps and needs for modeling and experimental demonstration; define key properties of interest; identify the data necessary to perform concept evaluation under normal conditions and illustrative scenarios; identify available infrastructure (internationally) to support experimental needs; and make recommendations on priorities. Where possible, considering proprietary and other export restrictions (e.g., International Traffic in Arms Regulations), the Expert Group will facilitate the sharing of data and lessons learned across the international group membership. The Systems Assessment task force is chaired by Shannon Bragg-Sitton (Idaho National Laboratory [INL], U.S.), the Cladding Task Force is chaired by Marie Moatti (Electricite de France [EdF], France), and the Fuels Task Force is chaired by a Masaki Kurata (Japan Atomic Energy Agency [JAEA], Japan). The original Expert Group mandate was established for June 2014 to June 2016. In April 2016 the Expert Group voted to extend the mandate one additional year to June 2017 in order to complete the task force deliverables; this request was subsequently approved by the Nuclear Science Committee. This report provides an update on the status Systems Assessment Task Force activities.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

DYNAMIC PRA OF A MULTI-UNIT PLANT

Dynamic Probabilistic Risk Analysis (PRA) methods couple stochastic methods (e.g., RAVEN, ADAPT, ADS, MCDET) with safety analysis codes (RELAP5-3D, MELCOR, MAAP) to determine risk associated to complex systems such as nuclear plants. Compared to classical PRA methods, which are based on static logic structures (e.g., Event-Trees, Fault-Trees), they can evaluate with higher resolution the safety impact of timing and sequencing of events on the accident progression. Recently, special attention has been given to nuclear plants which consist of multiple units and, in particular, on the safety impact of system dependencies, shared systems and common resources on core damage frequencies. In the literature, while classical PRA methods have been employed to model multi-unit plants, Dynamic PRA methods have never been applied to analyze a full multi-unit model. This paper presents a PRA analysis of a multi-unit plant using Dynamic PRA methods. We employ RAVEN as stochastic method coupled with RELAP5-3D. The plant under consideration consists of the three units and their associated spent fuel pools (SFPs). The studied initiating event is a seismic induced station blackout event. We will describe in detail how the multi-unit plant has been constructed and, in particular, how unit dependencies and shared resources are modeled.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

A Collaboration Website for Muon Catalyzed Fusion and Muon Beam Production

This research initiative establishes a dynamic online platform geared towards supporting the burgeoning Muon Catalyzed Fusion collaboration, focusing on the concurrent development of particle accelerators and transport beamlines for muon beams. The central feature of this endeavor is the creation of a multifaceted website comprising both public facing and private sections to cater to diverse user needs. The public segment is meticulously designed to serve as an educational hub, featuring information pages targeted at the general public alongside private pages exclusively accessible to collaboration members. These pages will host an array of multimedia elements, ranging from images and text animations to video lectures, covering an extensive spectrum of topics integral to the science of Muon Catalyzed Fusion. Encompassing areas such as Acceleration, Applications, Instrumentation, Beamline Design, and beam dynamics design codes, the educational content aims to make complex scientific concepts more accessible to a broader audience. Ensuring seamless accessibility across various devices and operating systems, the website incorporates integration with collaborative tools such as Google Docs for document collaboration, GitHub for code repository management, and WordPress for blogging with interactive commenting features. The bifurcation between public and private sections is a strategic approach to maintaining transparency while safeguarding proprietary research and works in progress. The public pages are strategically crafted to disseminate information, showcasing the latest endeavors and achievements within the NK Labs collaboration, including lectures, published papers, and regular blog posts open to public comments. On the other hand, the private section provides collaboration members with a secure space to share unpublished or nonpublic research, fostering collaborative efforts through integrated Google Docs and Python Plotty for shared graphing work. In essence, this ambitious project endeavors to bridge the gap between complex scientific knowledge and public understanding, enhance collaboration among researchers, and serve as a dynamic and inclusive platform for sharing and advancing the state-of-the-art in Muon Catalyzed Fusion and Accelerators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

POLARIS: Agent-based modeling framework development and implementation for integrated travel demand and network and operations simulations

Here, we discuss the development of an agent-based modelling software development kit, and the implementation and validation of a model using it that integrates dynamic simulation of travel demand, network supply and network operations. A description is given of the core utilities in the kit: a parallel discrete event engine, interprocess exchange engine, and memory allocator, as well as a number of ancillary utilities: visualization library, database IO library, and scenario manager. The overall framework emphasizes the design goals of: generality, code agility, and high performance. This framework allows the modeling of several aspects of transportation system that are typically done with separate stand-alone software applications, in a high-performance and extensible manner. The issue of integrating such models as dynamic traffic assignment and disaggregate demand models has been a long standing issue for transportation modelers. The integrated approach shows a possible way to resolve this difficulty. The simulation model built from the POLARIS framework is a single, shared-memory process for handling all aspects of the integrated urban simulation. The resulting gains in computational efficiency and performance allow planning models to be extended to include previously separate aspects of the urban system, enhancing the utility of such models from the planning perspective. Lastly, initial tests with case studies involving traffic management center impacts on various network events such as accidents, congestion and weather events, show the potential of the system.

42 ENGINEERING↗

DOE OSTI2020

Distributed quantum sensing enhanced by continuous-variable error correction

Abstract A distributed sensing protocol uses a network of local sensing nodes to estimate a global feature of the network, such as a weighted average of locally detectable parameters. In the noiseless case, continuous-variable (CV) multipartite entanglement shared by the nodes can improve the precision of parameter estimation relative to the precision attainable by a network without shared entanglement; for an entangled protocol, the root mean square estimation error scales like 1/ M with the number M of sensing nodes, the so-called Heisenberg scaling, while for protocols without entanglement, the error scales like 1 / M . However, in the presence of loss and other noise sources, although multipartite entanglement still has some advantages for sensing displacements and phases, the scaling of the precision with M is less favorable. In this paper, we show that using CV error correction codes can enhance the robustness of sensing protocols against imperfections and reinstate Heisenberg scaling up to moderate values of M . Furthermore, while previous distributed sensing protocols could measure only a single quadrature, we construct a protocol in which both quadratures can be sensed simultaneously. Our work demonstrates the value of CV error correction codes in realistic sensing scenarios.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

IBEX: An open infrastructure software platform to facilitate collaborative work in radiomics

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The IBEX software package was developed using the MATLAB and C/C++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and C/C++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX’s functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX’s source code can be downloaded. Conclusions: The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Assessment and validation of NEAMS tools for high-fidelity multiphysics transient modeling of microreactors: Application of NEAMS codes to perform multiphysics modeling analyses of micro-reactor concepts

The NEAMS Multiphysics Applications team aims at providing assessment of code useability and functionality for microreactor design and analyses, together with demonstration of their capabilities to properly capture the steady-state and time-dependent behavior of different microreactor concepts. In FY-24, significant progress was achieved in improving multi-physics models of several microreactors systems: HP-MR, GC-MR and KRUSTY. These efforts focused on solving more complex multiphysics problems enabled by enhanced tools capability, verifying and validating results obtained, providing feedback to developers for suggested improvements, and sharing these models to facilitate user training. A series of new multiphysics transients were completed on the HP-MR (using Griffin/BISON/Sockeye) with core startup transient, control drum inadvertent rotation accident, and hydrogen leakage from hydride moderator (also including SWIFT). On the GC-MR, a new full-core model was developed and analyzed through a series of new multiphysics (Griffin/BISON/SAM) transients to simulate moderator leakage (also including SWIFT), flow blockage and coolant depressurization. Additional and updated TRISO failure analyses were completed on the HP-MR unit-cell and GC-MR assembly models leveraging improved TRISO modeling capabilities. The amount of SiC failure following accidental transients at end-of-life was null. However, GC-MR assembly TRISO analysis highlighted Pd penetration rate can be problematic and may require design changes on the studied microreactor concept. The neutronics discrepancies observed on the KRUSTY model in previous years were resolved using hybrid set of Monte Carlo/Deterministic cross-sections. The multiphysics (Griffin neutronics / BISON thermal-mechanics) 15₵ insertion transient simulation displayed good agreement when comparing with experimental data. Initial modeling of the 30 ₵ reactivity insertion also displays promising results. Such close agreement provides important validation data that can be leveraged by the NEAMS program and by microreactor vendors to support licensing of their technology. Finally, important experience was gathered with the NEAMS tools leading to several user feedback shared with tools developers, especially with regards to MOOSE mesh generator and Griffin. This project led to many publications demonstrating modeling capabilities, and to three models shared on the Virtual Test Bed.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Projections of Hourly Meteorology by Balancing Authority Based on the IM3/HyperFACETS Thermodynamic Global Warming (TGW) Simulations

This dataset contains 40 years (1980-2019) of historical hourly meteorology and 80 years (2020-2099) of projected hourly meteorology for 54 Balancing Authorities (BAs) in the conterminous United States. Details about the scenarios and variables included in this dataset are in the readme.pdf file. This dataset is derived from the IM3/HyperFACETS Thermodynamic Global Warming (TGW) simulations (https://doi.org/10.57931/1885756). More details on the TGW approach can be found at: https://tgw-data.msdlive.org/. If you use this dataset please also cite the raw TGW dataset (Jones, A. D., Rastogi, D., Vahmani, P., Stansfield, A., Reed, K., Thurber, T., Ullrich, P., & Rice, J. S. (2022). IM3/HyperFACETS Thermodynamic Global Warming (TGW) Simulation Datasets (v1.0.0) [Data set]. MSD-LIVE Data Repository. https://doi.org/10.57931/1885756). To go from the TGW data to these BA-level aggregated data we first averaged the raw gridded data by county in the United States. That intermediate data step is also stored in MSD-LIVE (https://doi.org/10.57931/1960548). We then population-weight the county-level hourly data in order to create population-weighted meteorology time series for each BA. Historical populations are from the United States Census Bureau and the evolving future populations are based on Shared Socioeconomic Pathways (SSPs) 3 and 5. The four climate scenarios crossed with the two SSPs yield eight different future projections for each BA: rcp45cooler_ssp3, rcp45cooler_ssp5, rcp45hotter_ssp3, rcp45hotter_ssp5, rcp85cooler_ssp3, rcp85cooler_ssp5, rcp85hotterssp3, rcp85hotterssp5. For the historical period and each of the eight future scenarios the dataset has hourly estimates of the population-weighted average of five meteorological variables: Temperature, specific humidity, shortwave radiation, longwave radiation, and wind speed. All times are in Coordinated Universal Time (UTC). The code to go from the raw TGW data to county-level and then BA-level projections is available at: https://github.com/IMMM-SFA/im3components/tree/main/im3components/wrf_to_tell.

Balancing Authority↗

DOE OSTI2015

Water Governance Process Assessment: Evaluating the Link between Decision Making Processes and Outcomes in the Columbia River Basin

Academics and practitioners agree that in water governance, the quality of a decision making process should influence the quality of the outcome and the degree to which it is accepted by interested parties. However, finding a feasible way to evaluate and then improve the quality of a decision making process has proven elusive. Systematically collecting evidence of a link between process and outcome is also challenging. In my dissertation, I developed a synthesis framework for evaluating and improving water governance decision making to address these two challenges. The synthesis framework, which I call the Water Governance Process Assessment (Water GPA), draws upon 22 existing frameworks rooted in resilience, adaptive governance, and good governance. From these frameworks, I identified and provided a way to evaluate four characteristics critical to good water governance decision making processes: 1) accountability, 2) inclusivity, and 3) information, and 4) context. I applied the Water GPA framework to the recent reviews of the Columbia River Treaty by the United States and Canada. I collected data for the case studies through semi-structured interviews and surveys of process participants from the federal agencies, Tribal and First Nations, state/provincial governments, local governments, stakeholder interests, and citizens. I coded and analyzed the interviews using the qualitative analysis software QSR NVivo and the characteristics identified in the Water GPA framework. I used the two case study applications to demonstrate how to use the framework. I identified what aspects of the four process categories served as barriers and building blocks for good water governance in each water governance process. I also gleaned lessons learned and recommendations including some for determining process leadership, ensuring meaningful engagement and inclusivity, addressing sovereignty issues, setting decision criteria, sharing decision authority, allocating resources in future processes in the US and BC portions of the Columbia River Basin and similar basins. In my case studies, I also investigated which characteristics of the water governance decision making process influenced the direct outcomes of those processes (the decisions) as well as other non-target outcomes (such as trust, co-produced science, new coalitions, etc.). All four characteristics outlined in the Water Governance Process Assessment (Water GPA), played some role in the development of the content and/or support of the two case study decision documents (US Regional Recommendation and BC Provincial Decision). Generally, when the characteristic of the process was done well, it improved the legitimacy and acceptance of the decision. At the same time performing poorly in one area did not necessarily torpedo the process or decision. In both case studies, it appears that the interplay between the process characteristics (that is where two or more characteristics converge) had a greater influence over the decision. Further work is needed to clearly identify what characteristics of a process are most influential in different situations. The Water GPA is one useful tool for this effort.

13 HYDRO ENERGY↗

DOE OSTI2017

Kip, Version 1.0

This high-performance ray tracing library provides very fast rendering, compact code, type flexibility via C++ 'generic programming' techniques, and ease of use through an application programming interface (API) that functions independently of any GUI, on-screen display, or other enclosing application. Kip supports constructive solid geometry models based on any of several built-in shapes and operators and allows for new, user-defined shapes and operators. Additional features include basic texturing, input/output of models using a simple human-readable file format with full error checking and detailed diagnostics, and support for shared data parallelism. Kip is written in pure, ANSI Standard C++, is entirely platform independent, and is very easy to use, as it requires no build system, configuration or installation scripts, wizards, special preprocessing, makefiles, or external libraries.

Staley, Martin↗

DOE OSTI2023

The Genetics of Aerotolerant Growth in Zymomonas mobilis

Reduced genome bacteria are genetically simplified systems that facilitate biological study and industrial use. The free-living Alphaproteobacterium, Zymomonas mobilis, has a naturally reduced genome containing fewer than 2000 protein coding genes. Despite its small genome, Z. mobilis thrives in diverse conditions including the presence or absence of atmospheric oxygen. However, insufficient characterization of essential and conditionally essential genes has limited broader adoption of Z. mobilis as a model Alphaproteobacterium. Here, we use genome-scale CRISPRi-seq to systematically identify and characterize Z. mobilis genes that are conditionally essential for aerotolerant or anaerobic growth, or are generally essential across both conditions. Comparative genomics revealed that the essentiality of most "generally essential" genes was shared between Z. mobilis and other Alphaproteobacteria, validating Z. mobilis as reduced genome model. Among conditionally essential genes, we found that the DNA repair gene, recJ, was critical only for aerobic growth but reduced the mutation rate under both conditions. Further, we show that genes encoding the F1FO ATP synthase and Rnf respiratory complex are required for anaerobic growth of Z. mobilis. Combining CRISPRi partial knockdowns with metabolomics and membrane potential measurements, we determined that the ATP synthase generates membrane potential that is consumed by Rnf to power downstream processes. Rnf knockdown strains accumulated isoprenoid biosynthesis intermediates, suggesting a key role for Rnf in powering essential biosynthetic reactions. Our work establishes Z. mobilis as a streamlined model for alphaproteobacterial genetics, has broad implications in bacterial energy coupling, and informs Z. mobilis genome manipulation for optimized production of valuable isoprenoid-based bioproducts

Alphaproteobacteria↗