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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

R Coronae Borealis Star Evolution: Simulating 3D Merger Events to 1D Stellar Evolution Including Large-scale Nucleosynthesis

R Coronae Borealis (RCB) stars are rare hydrogen-deficient carbon-rich variable supergiants thought to be the result of dynamically unstable white dwarf mergers. In this article, we attempt to model RCB stars through all the relevant timescales by simulating a merger event in Octo-tiger, a 3D adaptive mesh refinement (AMR) hydrodynamics code, and mapping the post-merger object into MESA, a 1D stellar evolution code. We then post-process the nucleosynthesis on a much larger nuclear reaction network to study the enhancement of s-process elements. We present models that match observations or previous studies in most surface abundances, isotopic ratios, early evolution, and lifetimes. We also observe similar mixing behavior to previous modeling attempts that result in the partial He-burning products visible on the surface in observations. However, we do note that our subsolar models lack any enhancement in s-process elements, which we attribute to a lack of hydrogen in the envelope. We also find that the 16 O/ 18 O isotopic ratio is very sensitive to initial hydrogen abundance and increases outside of the acceptable range with a hydrogen mass fraction greater than 10 -4 .

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Uncertainty Quantification of Calculated Temperatures for the AGR 5/6/7 Experiment

This report documents the quantification of uncertainty of the calculated temperature data for the Advanced Gas Reactor (AGR) 5/6/7 fuel irradiation experiment conducted in the Advanced Test Reactor at Idaho National Laboratory in support of the Advanced Reactor Technologies? research and development program. Recognizing uncertainties inherent in physics and thermal simulations of the AGR 5/6/7 capsules, the results of the numerical simulations are used in combination with statistical analysis methods to improve qualification of measured data. The calculated fuel temperatures for AGR tests are also used for validation of the fission product transport and fuel performance simulation models. These crucial roles of the calculated fuel temperatures in ensuring achievement of the AGR experimental program objectives require accurate determination of the model temperature uncertainties. This report covers temperature uncertainty results for each of the five AGR 5/6/7 capsules. To quantify the uncertainty of calculated temperatures determined using the ABAQUS finite element heat transfer code, this study identifies and analyzes model parameters of potential importance to the calculated temperatures of fuel compacts and thermocouples. The selection of input parameters for uncertainty quantification is based on the ranking of their influences upon temperature predictions. Thus, selected input parameters include those with high sensitivity and those with the largest uncertainty. Propagation of model parameter uncertainty and sensitivity is then used to quantify the overall uncertainty of calculated temperatures. Measurement uncertainty, analysis of modeling assumptions, and expert judgment are used as the basis to quantify the uncertainty range for selected input parameters. The input uncertainties are dynamic, accounting for the effect of unplanned events and changes in thermal properties of capsule components over extended exposure to high temperatures and fast neutron irradiation. The sensitivity analysis performed in this work went beyond the traditional local sensitivity. Using experimental design, analysis of pairwise interactions of model parameters was performed to establish sufficiency of the time dependent first order (linear) expansion terms in constructing the temperature response surface. To achieve completeness, uncertainty propagation made use of pairwise noise correlations of model parameters. Furthermore, using an interpolation scheme over the input parameter domain, the analysis obtains time dependent sensitivity over the test campaign duration. This allows computation of uncertainty for the calculated fuel temperatures and the calculated graphite temperatures at thermocouple locations during the entire irradiation period.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Zero Energy Ready Out of the Box

In this conference paper for the ASHRAE Buildings XV conference, December 2022, PNNL staff share key metrics for companies who are combining off site construction with certification to the U.S. Department of Energy’s Zero Energy Ready Home program to create homes that are both cost effective to construct and high performance to live in. Key performance metrics and measures for modular, panelized, and SIP homes are compared against all homes in the DOE Zero Energy Ready Home program and against new homes built to code. These metrics show that off-site construction homes got similar or better energy performance to site-built homes, and in the case of modular and panelized, at considerably lower average cost than site-built homes. The paper also highlights the experiences of two DOE Zero Energy Ready Home builders who employ offsite construction methods. One builder constructs production homes using pre-assembled panels. The other builder designs and ships kit homes all over the United States. The paper will focus on the optimum value engineering aspects of the panelized construction processes used by each builder to identify management and production practices employed by the builders to operate profitably while meeting high energy performance goals, despite a year marked by skyrocketing materials costs and supply chain and labor shortages. Cost and labor savings methods will be discussed in the context of these two unique business models.

U.S. Department of Energy Building Technologies Pr↗
DOE OSTI2020

Accelerating Hanford Site Cleanup through Operations Research Modeling - 20238

The Hanford Site cleanup effort will require the integration of dozens of unique facilities and processes, many of which will be first-of-a-kind in implementation and design. Each facility will be governed by its own set of operating logic, configured with a unique array of unit operations, and subject to a set of constraints that will affect its behavior. The collection of facilities have multiple points of interface, making the operations of any one facility potentially significant to the operations of other up- or downstream processes. It is therefore highly desirable to accurately predict these operations, as it allows for Site officials to identify and preempt bottlenecks and vulnerabilities before they unexpectedly inhibit the cleanup mission. With the quantity and complexity of the processes that will be on Site, building a pen-and-paper or even a spreadsheet-assisted model of the cleanup mission quickly becomes overwhelming in scope and inaccurate in execution. The Engineering organization for the Site's Tank Operations Contract (TOC) has therefore implemented the use of operations research (OR) modeling to simulate and predict future operations of Site facilities. These models are created using a discrete event simulation tool that allows for the development of detailed, versatile, and robust models. Not only can these models account for complex logical behaviors, but they can also simulate process details down to the level of vessel sizing, labor utilization, equipment reliability, and resource availability. To date, the TOC has developed OR models for several facilities on Site, including for single-shell tank (SST) farms, double-shell tank (DST) farms, the Effluent Treatment Facility (ETF), and the waste transfer system. These models have focused on identifying bottlenecks and operational constraints, and have been used to quantify the effects of implementing process changes. This latter point is particularly valuable, as it allows for several alternatives to be studied in a virtual setting before committing resources to making a change in the field. The decision to develop OR models has gained tremendous support from the Site's stakeholders and the U.S. Department of Energy (DOE) management, and has prompted the use of the tool to support additional internal and external initiatives. Recently, an initiative was proposed to use the models to help identify and provide quantitative backing for risks and opportunities for the TOC. This application of OR could not only help inform how the TOC manages its risks (e.g. quantities and types of spare parts), but could also help drive process improvements whose benefits might otherwise be hard to quantify. The models have also been used to drive the TOC's cloud computing, artificial intelligence (AI), and machine learning (ML) initiatives. These initiatives will not only improve the ability of the TOC to more rapidly respond to the needs of its customers, but it will also aid in the ability of the TOC to analyze and improve the processes it studies. Partnership with two external software development and consulting companies (Lanner and Ynformed) has furthered not only the application of AI and ML within the TOC, but has also spurred the development of new/improved software tools and platforms used by the companies. These partnerships have proven to be mutually beneficial and productive, and have set a precedent for the types of gains that can be made by exploring such options. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Excitation functions and isomeric cross-section ratios of (d,xn) reactions on 86 Sr

Excitation functions of the 86 Sr(d,n) 87m,87g Y, 86 Sr(d,2n) 86m,86g Y and 86 Sr(d,3n) 85m,85g Y reactions on enriched 86 Sr target were measured by the activation technique up to deuteron energies of 49 MeV. The isomeric cross-section ratios as a function of projectile energy were deduced from the measured data for 87m Y, 87g Y(cum), 86m Y, 86g Y(cum), 85m Y and 85g Y pairs for the same energy range. All measurements are reported for the first time. The experimental data were compared with the data from the TENDL library which is based on TALYS calculation with default parameters. No satisfactory agreement was observed. Nuclear model calculations were then performed using the codes TALYS and EMPIRE with some parameter adjustments, and compared with the experimental data. The quality of the agreement between experimental data and model calculations was numerically quantified. In general, the data as well as the isomeric cross-section ratios are partially reproduced by the model calculations, provided the input model parameters are properly chosen and the level structure of the product nucleus is thoughtfully considered.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Error-Bounded Learned Scientific Data Compression with Preservation of Derived Quantities

Scientific applications continue to grow and produce extremely large amounts of data, which require efficient compression algorithms for long-term storage. Compression errors in scientific applications can have a deleterious impact on downstream processing. Thus, it is crucial to preserve all the “known” Quantities of Interest (QoI) during compression. To address this issue, most existing approaches guarantee the reconstruction error of the original data or primary data (PD), but cannot directly control the problem of preserving the QoI. In this work, we propose a physics-informed compression technique that is composed of two parts: (i) reduction of the PD with bounded errors and (ii) preservation of the QoI. In the first step, we combine tensor decompositions, autoencoders, product quantizers, and error-bounded lossy compressors to bound the reconstruction error at high levels of compression. In the second step, we use constraint satisfaction post-processing followed by quantization to preserve the QoI. To illustrate the challenges of reducing the reconstruction errors of the PD and QoI, we focus on simulation data generated by a large-scale fusion code, XGC, which can produce tens of petabytes in a single day. The results show that our approach can achieve a high compression amount while accurately preserving the QoI within scientifically acceptable bounds.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Nuclide inventory validation: radiochemical assay data quality and modeling challenges in benchmark models development

Oak Ridge National Laboratory is conducting radiochemical assay experiments, using high-precision analytical protocols validated with a comprehensive quality assurance plan, to expand the nuclide inventory validation basis for high burnup spent nuclear fuel. Preliminary measurement data for key actinides and fission products in two pressurized water reactor spent fuel samples are being used to investigate the impact of measurement data uncertainty on the sample burnup estimation. These measurement data are also being used to examine the impact of assumptions applied when developing best-estimate computational models to simulate fuel irradiation history. The simulations are being performed using depletion capabilities in the SCALE code system. Comparison of calculated and measured nuclide concentrations shows good agreement for the considered nuclides. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

A Collaboration Website for Muon Catalyzed Fusion and Muon Beam Production

This project sets up a website to support the nascent Muon Catalyzed Fusion collaboration including development of particle accelerators and transport beamlines for muon beams. The website is envisioned as having the general public information pages and private pages for collaboration members. Multimedia elements like images, text animations, and video lectures, covering a broad spectrum of topics will populate the educational site, covering muon facilities, to comprehensive explorations and seminal documents that define the science of Muon Catalyzed Fusion, Acceleration, Applications, Instrumentation, Beamline Design, and beam dynamics design codes. Ensuring compatibility across devices and operating systems, it also features integration with Google Docs for collaboration, a code repository (GitHub), a blog platform with comments (WordPress), the potential for ChatGPT integration and interactive graph plotting with Python Plotty to enhance data visualization. This project will maintain public and protected private pages, due to the proprietary nature of the work or research in progress. The public sections will be built to foster dissemination of information and highlight recent work within the NK Labs collaboration, including lectures, published papers, and regular blog posts with open commenting. The private section will support unpublished or nonpublic research, by facilitating collaborative efforts through integrated Google Docs and Python Plotty for shared graphing work. Ultimately, this project strives to make complex scientific knowledge more accessible to the public, foster enhanced collaboration, and serve as a platform for sharing cutting-edge research in Muon Catalyzed Fusion and Accelerators.

43 PARTICLE ACCELERATORS↗
DOE OSTI2022

Development of Integrated Thermal Fluids Modeling Capability for MSRs

The DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program supports a full range of computational thermal fluids analysis capabilities and code developments for a broad class of light-water and advanced reactor concepts. The research and development approach under thermal fluids technical area synergistically combines three length and time scales in a hierarchal multi-scale approach. To demonstrate the feasibility and capabilities of a multi-scale thermal fluids capability using these codes, a key joint effort has been pursued to develop an integrated system-and engineering-scale thermal fluids analysis capability with the MOOSE-based codes, through integration of SAM and Pronghorn, both based on the MOOSE framework. This report summarizes the progress in developing an integrated system- and engineering-scale thermal fluids analysis capability based on SAM and Pronghorn for molten salt reactors (MSRs), which gained significant interest in recently years. Two coupling approaches were studied, i.e. separate domain or domain-segregated coupling approach and the domain-overlapping approach. A series of coupled multi-physics models have been developed for a common reference molten salt fast reactor (MSFR) concept, ranging from standalone SAM system model to integrated SAM-Pronghorn-Griffin models. Both the steady state and the transient simulations are performed to the state-of-the-art simulation capabilities of NEAMS software suite in MSFR system applications. This report also covers further development and testing of the gas transport model in SAM for MSR modeling support. The presence of noncondensable gas in MSR systems would have strong impacts on fission gas removal and transport of noble metals throughout the system. Fission products removed through the off-gas system can also impact reactivity and can act as an additional point of heat removal. To ensure that the gas transport model is adequately tested, the supported modeling capabilities and features of SAM were identified, and a suite of tests were developed to test the model for each identified feature. Validation and UQ testing were also performed for the model and demonstrated that the buoyancy term, which was originally developed using non-salt/helium gas experimental data, can capture the experimental gas bubble velocity and diameter to within experimental and code uncertainty. An existing MSRE model was also modified in this work to include the gas transport model and to demonstrate the gas model behavior for realistic conditions of interest.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2023

Biochemical basis for the formation of organ-specific volatile blends in mint

Above-ground material of members of the mint family is commercially distilled to extract essential oils, which are then formulated into a myriad of consumer products. Most of the research aimed at characterizing the processes involved in the formation of terpenoid oil constituents has focused on leaves. We now demonstrate, by investigating three mint species, peppermint ( Mentha ˣ piperita L.), spearmint ( Mentha spicata L.) and horsemint ( Mentha longifolia (L.) Huds.; accessions CMEN 585 and CMEN 584), that other organs – namely stems, rhizomes and roots – also emit volatiles and that the terpenoid volatile composition of these organs can vary substantially from that of leaves, supporting the notion that substantial, currently underappreciated, chemical diversity exists. Differences in volatile quantities released by plants whose roots had been dipped in a Verticillium dahliae -spore suspension (experimental) or dipped in water (controls) were evident: increases of some volatiles in the root headspace of mint species that are susceptible to Verticillium wilt disease (peppermint and M. longifolia CMEN 584) were detected, while the quantities of certain volatiles decreased in rhizomes of species that show resistance to the disease (spearmint and M. longifolia CMEN 585). To address the genetic and biochemical basis underlying chemical diversity, we took advantage of the newly sequenced M. longifolia CMEN 585 genome to identify candidate genes putatively coding for monoterpene synthases (MTSs), the enzymes that catalyze the first committed step in the biosynthesis of monoterpenoid volatiles. The functions of these genes were established by heterologous expression in Escherichia coli , purification of the corresponding recombinant proteins, and enzyme assays, thereby establishing the existence of MTSs with activities to convert a common substrate, geranyl diphosphate, to (+)-α-terpineol, 1,8-cineole, γ-terpinene, and (–)-bornyl diphosphate, but were not active with other potential substrates. In conjunction with previously described MTSs that catalyze the formation of (–)-β-pinene and (–)-limonene, the product profiles of the MTSs identified here can explain the generation of all major monoterpene skeletons represented in the volatiles released by different mint organs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The diphoton $$q_T$$ spectrum at N$$^3$$LL$$^\prime $$ + NNLO

Abstract We present a $$q_T$$ q T -resummed calculation of diphoton production at order N $$^3$$ 3 LL $$^\prime $$ ′ + NNLO. To reach the primed level of accuracy we have implemented the recently published three-loop $${\mathcal {O}}(\alpha _s^3)$$ O ( α s 3 ) virtual corrections in the $$q\bar{q}$$ q q ¯ channel and the three-loop transverse momentum dependent beam functions and combined them with the existing infrastructure of , a code performing resummation at order N $${}^3$$ 3 LL. While the primed predictions are parametrically not more accurate, one typically observes from lower orders and other processes that they are the dominant effect of the next order. We include in both the $$q\bar{q}$$ q q ¯ and loop-induced gg channel the hard contributions consistently together at order $$\alpha _s^3$$ α s 3 and find that the resummed $$q\bar{q}$$ q q ¯ channel without matching stabilizes indeed. Due to large matching corrections and large contributions and uncertainties from the gg channel, the overall improvements are small though. We furthermore study the effect of hybrid-cone photon isolation and hard-scale choice on our fully matched results to describe the ATLAS $$\text {8}$$ 8 TeV data and find that the hybrid-cone isolation worsens agreement at small $$q_T$$ q T compared to smooth-cone isolation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

TIGER, A thermodynamics Equilibrium Tool for Explosives Update: Improved Solver

The thermodynamic equilibrium code known as TIGER has been in use since the 1970s and is designed to calculate the performance of energetic materials during detonation at high temperatures and pressures. The original TIGER code utilized a limited database consisting of 12 gaseous and 3 condensed constituents, which were composed of the elements carbon (C), hydrogen (H), nitrogen (N), oxygen (O), and aluminum (Al). In contrast, the more modern JCZS3 database features a significantly larger dataset, including 756 gaseous species, 189 positive and negative ions, and 496 condensed constituents derived from 62 different elements. While this expanded product species database allows for the exploration of a broader range of problems relevant to our laboratory, it also introduces challenges related to convergence, particularly when both liquid and solid species coexist under a vapor dome. In this work, we present an improved TIGER solution technique aimed at accurately determining the equilibrium state for systems that can produce a diverse array of products, including both solid and liquid condensed species. This report presents the status of the TIGER solver as of the end of FY25. Ongoing efforts are focused on enhancing the solver, and the report outlines several planned improvements. We anticipate that further developments will require additional documentation in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Evaluation of LLVM Flang for Production HPC Applications and Modern Fortran Features

In 2025, LLVM released its first Flang Fortran compiler version considered ready for widespread evaluation. We know of no published assessment of Flang compiling a workload- derived portfolio of high-performance computing (HPC) applications. We address this gap using workload data from the National Energy Research Scientific Computing Center (NERSC), which supports more than 10,000 scientists on approximately 1,000 projects. The NERSC workload analyses identify many Fortran components in heavily used applications. We selected 10 such packages with available source code. We compiled them with Flang 22.1.3 on NERSC’s Perlmutter system. Six compiled without code modifications, though some required build-system changes. Three compiled after minor source edits, mostly to address Fortran standard violations. One built only without OpenMP enabled. We evaluated seven additional packages selected for their use of, or enablement of, standard Fortran parallel features: multi-image execution and do concurrent. Six such codes compiled with most or all unit tests passing.

Rasmussen, Katherine↗
DOE OSTI2024

An introduction to Spent Nuclear Fuel decay heat for Light Water Reactors: a review from the NEA WPNCS

This paper summarized the efforts performed to understand decay heat estimation from existing spent nuclear fuel (SNF), under the auspices of the Working Party on Nuclear Criticality Safety (WPNCS) of the OECD Nuclear Energy Agency. Needs for precise estimations are related to safety, cost, and optimization of SNF handling, storage, and repository. The physical origins of decay heat (a more correct denomination would be decay power) are then introduced, to identify its main contributors (fission products and actinides) and time-dependent evolution. Due to limited absolute prediction capabilities, experimental information is crucial; measurement facilities and methods are then presented, highlighting both their relevance and our need for maintaining the unique current full-scale facility and developing new ones. The third part of this report is dedicated to the computational aspect of the decay heat estimation: calculation methods, codes, and validation. Different approaches and implementations currently exist for these three aspects, directly impacting our capabilities to predict decay heat and to inform decision-makers. Finally, recommendations from the expert community are proposed, potentially guiding future experimental and computational developments. One of the most important outcomes of this work is the consensus among participants on the need to reduce biases and uncertainties for the estimated SNF decay heat. If it is agreed that uncertainties (being one standard deviation) are on average small (less than a few percent), they still substantially impact various applications when one needs to consider up to three standard deviations, thus covering more than 95% of cases. The second main finding is the need of new decay heat measurements and validation for cases corresponding to more modern fuel characteristics: higher initial enrichment, higher average burnup, as well as shorter and longer cooling time. Similar needs exist for fuel types without public experimental data, such as MOX, VVER, or CANDU fuels. A third outcome is related to SNF assemblies for which no direct validation can be performed, representing the vast majority of cases (due to the large number of SNF assemblies currently stored, or too short or too long cooling periods of interest). A few solutions are possible, depending on the application. For the final repository, systematic measurements of quantities related to decay heat can be performed, such as neutron or gamma emission. This would provide indications of the SNF decay heat at the time of encapsulation. For other applications (short- or long-term cooling), the community would benefit from applying consistent and accepted recommendations on calculation methods, for both decay heat and uncertainties. This would improve the understanding of the results and make comparisons easier.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

A New CIERRA Gridded Product Climatology for LIS/OTD

The GLM-CIERRA processing generates two products: A level-2 cluster feature dataset that merges flashes that should have been a single flash following the clustering algorithm flash definition (for GLM, this is due to the LCFA thresholds); A set of level-3 gridded products including Flash Extent Density, Convective Probability, etc. The CIERRA Level-3 products are generated on a 0.1 degree grid. This is suboptimal given the spatial variations in GLM pixel size AND the size of gridpoints in the output grid. As a stepping-stone towards developing improved GLM-CIERRA grids, I am testing pixel matching techniques on the LIS/OTD data. The goal is to maintain accuracy while vastly improving computational efficiency. The CIERRA reclustering codes are also being applied to LIS / OTD to merge flashes split by the “first fit” clustering technique. The end result will be standardized grids at the nominal resolution of each instrument (5 km for LIS, 10 km for OTD) that take into account the pixel geometry for each event that comprises a given reclustered flash.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets

MOTIVATION: Metabolic engineering is rapidly evolving as a result of new advances in synthetic biology tools and automation platforms that enable high throughput strain construction, as well as the development of machine learning tools (ML) for biology. However, selecting genetic engineering targets that effectively guide the metabolic engineering process is still challenging. ML can provide predictive power for synthetic biology, but current technical limitations prevent the independent use of ML approaches without previous biological knowledge. RESULTS: Here, we present FluxRETAP, a simple and computationally inexpensive method that leverages the prior mechanistic knowledge embedded in genome-scale models for suggesting targets for genetic overexpression, downregulation or deletion, with the final goal of increasing the production of a desired metabolite. This method can provide a list of desirable engineering targets that can be combined with current ML pipelines. FluxRETAP captured 100% of reaction targets experimentally verified to improve Escherichia coli isoprenol production, 50% of targets that experimentally improved taxadiene production in E. coli and ∼60% of genetic targets from a verified minimal constrained cut-set in Pseudomonas putida, while providing additional high priority targets that could be tested. Overall, FluxRETAP is an efficient algorithm for identifying a prioritized list of testable genetic and reaction targets. AVAILABILITY AND IMPLEMENTATION: FluxRETAP is implemented in python and released under the creative commons license. The implementation and code are freely available at: https://github.com/JBEI/FluxRETAP.

Czajka, Jeffrey J↗
DOE OSTI2020

A chromosome-scale reference genome of trifoliate orange ( Poncirus trifoliata ) provides insights into disease resistance, cold tolerance and genome evolution in Citrus

Trifoliate orange (Poncirus trifoliata), a deciduous close relative of evergreen Citrus, has important traits for citrus production, including tolerance/resistance to citrus greening disease (Huanglongbing, HLB) and other major diseases, and cold tolerance. It has been one of the most important rootstocks, and one of the most valuable sources of resistance and tolerance genes for citrus. Here we present a high-quality, chromosomescale genome assembly of P. trifoliata. The 264.9-Mb assembly contains nine chromosomal pseudomolecules with 25 538 protein-coding genes, covering 97.2% of the estimated gene space. Comparative analyses of P. trifoliata and nine Citrus genomes revealed 605 species-specific genes and six rapidly evolving gene families in the P. trifoliata genome. Poncirus trifoliata has evolved specific adaptation in the C-repeat/ DREB binding factor (CBF)-dependent and CBF-independent cold signaling pathways to tolerate cold. We identified candidate genes within quantitative trait loci for HLB tolerance, and at the loci for resistance to citrus tristeza virus and citrus nematode. Genetic diversity analysis of Poncirus accessions and Poncirus/ Citrus hybrids shows a narrow genetic base in the US germplasm collection, and points to the importance of collecting and preserving more natural genetic variation. Two phenotypically divergent Poncirus accessions are found to be clonally related, supporting a previous conjecture that dwarf Flying Dragon originated as a mutant of a non-dwarfing type. The high-quality genome reveals features and evolutionary insights of Poncirus, and it will serve as a valuable resource for genetic, genomic and molecular research and manipulation in citrus.

54 ENVIRONMENTAL SCIENCES↗