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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Comparative mitogenomics of kingdom Fungi – evolutionary insights and metagenomic applications

Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.

Ahrendt, Steven R. [USDOE Joint Genome Institute (↗
DOE OSTI2024

Assessing Uncertainty in Modeling Stress Corrosion Cracking

This report summarizes the collaboration between Sandia National Laboratories (SNL) and the Nuclear Regulatory Commission (NRC) to improve the state of knowledge on chloride induced stress corrosion cracking (CISCC). The foundation of this work relied on using SNL’s CISCC computer code to assess the current state of knowledge for probabilistically modeling CISCC on stainless steel canisters. This work is presented as three tasks. The first task is exploring and independently comparing crack growth rate (CGR) models typically used in CISCC modeling by the research community. The second task is implementing two of the more conservative CGR models from the first task into SNL’s full CISCC code to understand the impact of the different CGR models on a full probabilistic analysis while studying uncertainty from three key input parameters. The combined work of the first two tasks showed that properly measuring salt deposition rates is impactful to reducing uncertainty when modeling CISCC. The work in Task 2 also showed how probabilistic CGR models can be more appropriate at capturing aleatory uncertainty when modeling SCC. Lastly, appropriate and realistic input parameters relevant for CISCC modeling were documented in the last task as a product of the simulations considered in the first two tasks.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Measurement of directional muon beams generated at the Berkeley Lab Laser Accelerator

We present the detection of directional muon beams produced using a PW laser facility at the Lawrence Berkeley National Laboratory. The muon source is a multi-GeV electron beam generated in a laser-plasma accelerator interacting with a high- converter target. The GeV photons resulting from the interaction are converted into a high-flux, directional muon beam via pair production. By employing scintillators to capture delayed events, we were able to identify the produced muons and characterize the source. Using theoretical knowledge of the muon production process combined with simulations that are in excellent agreement with the experiments, we demonstrate that laser-plasma accelerators have the capability of generating electron beams with characteristics suitable to produce GeV-scale muons that offer unique advantages with respect to the cosmic background. Laser-plasma-accelerator-based muon sources can therefore enhance muon imaging applications thanks to their compactness, directionality, and high yields, which reduce the exposure time by orders of magnitude compared to cosmic ray muons. Using the eant4-based simulation code we developed to gain insight into the experimental results, we can design future experiments and applications based on LPA-generated muons.

Terzani, Davide↗
DOE OSTI2022

Phylogeny and Expression Atlas of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Agave

Agave species are widely cultivated crassulacean acid metabolism (CAM) plants for alcoholic beverages, food and fiber production. Among these, the Agave hybrid H11648 ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for sisal fiber in the tropical areas of Brazil, China, and African countries. The plants of Agave hybrid H11648 have a long life cycle and large leaves, which require a huge amount of nitrogen nutrient. However, the molecular basis of nitrogen transport and allocation has not been well understood in agave. In this study, we identified 19 NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY(NPF) genes (called AhNPFs) with full-length coding sequences in Agave hybrid H11648. Our analysis of gene expression in various types of tissues revealed the tissue-specific expression pattern of AhNPFs. We further examined their expression patterns at different leaf developmental stages, under abiotic/biotic stresses and nutrient deficiency. The results reveal several candidate regulators in the agave NPF family, including AhNPF4.3/5.2/7.1. We first characterized the NPF genes in agave based on published leaf transcriptome datasets and emphasized their potential functions. The study will benefit future studies related to nitrogen nutrient in agave.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Implementation of a Drift Flux Model into SAM with Development of a Verification and Validation Test Suite for Modeling of Noncondensable Gas Mixtures

The advanced thermal-hydraulic system code, System Analysis Module (SAM), was originally developed for the modeling of single-phase flow in advanced reactors. It has since been expanded to include a four-equation drift flux model for the modeling of two-phase flows containing a noncondensable gas. The model was expanded to support the modeling of molten salt reactor (MSR) designs in which the fuel is directly dissolved in the circulating coolant. These designs have shown that circulating gas bubbles can play an important role in the management of fission products and the operational behavior of the reactor. A drift flux model was implemented to more accurately capture the localized behavior of the void in the core and its impact on the mass transfer of fission products. A thorough assessment of the new model was performed by developing a verification and validation test suite. Verification problems were designed to test all major terms in the new governing equations. The new model converged to the correct solution at the expected order of accuracy for all verification cases. The validation cases included a wide range of flow and void conditions in different pipe geometries. Although higher void experiments show a slight underprediction of void by the drift flux model, experiments that aim to reproduce Molten Salt Reactor Experiment (MSRE) experimental conditions show good agreement with the model. The gas transport model was activated for a SAM model of the MSRE to demonstrate that it can be used in a more complex model. Finally, this gas transport model will be used along with an interfacial area transport equation being implemented in SAM for the prediction of mass transport behavior in MSR conditions.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

Aeroelastic Modeling for Distributed Wind Turbines: March 11, 2021 - November 10, 2021

Aeroelastic modeling (AM) is the primary methodology for structural and performance assessment of any wind turbine whereby providing an understanding of the impact of design parameters on its loading and power response before witnessing it in the field. Despite these advantages, the use of AM in the Distributed Wind Technology (DWT) sector is limited, especially within the less established manufacturers. This project represents an in-depth assessment of the status of AM and its role within the Standards for the DWT industry. The study gathered input and feedback from a large number of national and international stakeholders, reviewed technical strengths and weaknesses of the current edition of the design standards, analyzed recent industry workshops' and meetings' minutes, collected publicly available AM templates, and provided an evaluation of the existing AM codes. The study achieved several goals including providing strategies for the load assessment categorization of turbines based on rotor swept area and archetype, and guidance for AM verification and validation (V&V), which includes discussions of measurement requirements and a sample test-plan useful for future V&V campaigns and design standard development. This document summarizes the different tasks conducted in the course of the project and highlights the steps required to improve the AM adoption based on a multifaceted approach that encompasses: 1) augmenting AM software capabilities, 2) publishing AM best-practices and design-basis, 3) creating new model templates, 4) providing guidance for V&V of codes and specific turbine models leveraging field testing best-practice, and 5) addressing weaknesses in the current standards. Many of the future objectives identified in this study could leverage NREL's upcoming testing campaigns of three modern distributed wind turbines. Recommendations within this study will advance the value and the ease-of-use of AM, thereby allowing the industry to better capitalize this underutilized tool resulting in a more efficient design process, an easier path to certification, and overall better and more distributed reliable wind turbine products.

17 WIND ENERGY↗
DOE OSTI2022

Cryogenic tracer irradiation facility at the university of Texas at Austin

We report on a cryogenic gas irradiation facility in the 1.1 MW TRIGA reactor at The University of Texas at Austin. The system was designed to produce radioactive xenon and argon for environmental studies, and it can be applied to produce other gaseous radiotracers. The system design includes modeling accident scenarios to ensure operation does not risk damage to the reactor and minimizes risk of release of radioactive material. In conclusion, the SCALE code was used to model a 30-day irradiation of one liter of Xe-126 and the predicted activity is 0.9 Ci of Xe-127 at irradiation end.

Ar-37↗
DOE OSTI2021

Dark Energy Survey Year 3 Results: Deep Field optical + near-infrared images and catalogue

ABSTRACT We describe the Dark Energy Survey (DES) Deep Fields, a set of images and associated multiwavelength catalogue (ugrizJHKs) built from Dark Energy Camera (DECam) and Visible and Infrared Survey Telescope for Astronomy (VISTA) data. The DES Deep Fields comprise 11 fields (10 DES supernova fields plus COSMOS), with a total area of ∼30 sq. deg. in ugriz bands and reaching a maximum i-band depth of 26.75 (AB, 10σ, 2 arcsec). We present a catalogue for the DES 3-yr cosmology analysis of those four fields with full 8-band coverage, totalling 5.88 sq. deg. after masking. Numbering 2.8 million objects (1.6 million post-masking), our catalogue is drawn from images coadded to consistent depths of r = 25.7, i = 25, and z = 24.3 mag. We use a new model-fitting code, built upon established methods, to deblend sources and ensure consistent colours across the u-band to Ks-band wavelength range. We further detail the tight control we maintain over the point-spread function modelling required for the model fitting, astrometry and consistency of photometry between the four fields. The catalogue allows us to perform a careful star–galaxy separation and produces excellent photometric redshift performance (NMAD = 0.023 at i < 23). The Deep-Fields catalogue will be made available as part of the cosmology data products release, following the completion of the DES 3-yr weak lensing and galaxy clustering cosmology work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

CMM Sequential Analysis Program

This report documents a design agency (DA) method to evaluate coordinate measuring machine (CMM) data by constructing an algorithm that is equivalent to the production agency (PA) algorithm for processing the raw CMM data. Several refinements of the CMM analyses were implemented at both the PA and the DA to process inherent limitations of the raw data, such as the absence of measurements at the exact ends of the connector-adapter assembly (CAA) and the recovery from these limitations through (worst-case) adjustments to the the positional errors. Also, inherent errors of the CMM measurements were accommodated by introducing a guard band, which effectively lowered the tolerance so that the CMM code could not pass bad parts. The DA and the PA showed remarkable agreement in all areas of analysis. The ultimate comparison is shown in Figures 13a and 13b, where the effect of using a guard band and end adjustments to the CMM measurements were clearly shown.

42 ENGINEERING↗
DOE OSTI2022

Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the “microbial dark matter” (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Geothermal Play Fairway Analysis, Part 2: GIS methodology

Play Fairway Analysis (PFA) in geothermal exploration originates from a systematic methodology developed within the petroleum industry and is based on a geologic, geophysical, and hydrologic framework of identified geothermal systems. We tailored this methodology to study the geothermal resource potential of the Snake River Plain and surrounding region, but it can be adapted to other geothermal resource settings. We adapted the PFA approach to geothermal resource exploration by cataloging the critical elements controlling exploitable hydrothermal systems, establishing risk matrices that evaluate these elements in terms of both probability of success and level of knowledge, and building a code-based ‘processing model’ to process results. A geographic information system was used to compile a range of different data types, which we refer to as elements (e.g., faults, vents, heat flow, etc.), with distinct characteristics and measures of confidence. Discontinuous discrete data (points, lines, or polygons) for each element were transformed into continuous interpretive 2D grid surfaces called evidence layers. Because different data types have varying uncertainties, most evidence layers have an accompanying confidence layer which reflects spatial variations in these uncertainties. Risk layers, as defined here, are the product of evidence and confidence layers, and are the building blocks used to construct Common Risk Segment (CRS) maps for heat, permeability, and seal, using a weighted sum for permeability and heat, but a different approach with seal. CRS maps quantify the variable risk associated with each of these critical components. In a final step, the three CRS maps were combined into a Composite Common Risk Segment (CCRS) map, using a modified weighted sum, for results that reveal favorable areas for geothermal exploration. Additional maps are also presented that do not mix contributions from evidence and confidence (to allow an isolated view of evidence and confidence), as well as maps that calculate favorability using the product of components instead of a weighted sum (to highlight where all components are present). Our approach helped to identify areas of high geothermal favorability in the western and central Snake River Plain during the first phase of study and helped identify more precise local drilling targets during the second phase of work. By identifying favorable areas, this methodology can help to reduce uncertainty in geothermal energy exploration and development.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Simplified Approach for Scoping Assessment of Non-LWR Source Terms

This report describes a structure to aid in evaluation of release mitigation strategies across a range of reactor technologies. The assessment performed for example reactor concepts utilizes previous studies of postulated accident sequences for each reactor concept. This simplified approach classifies release mitigation strategies based on a range of barriers, physical attenuation processes, and system performance. It is not, however, intended to develop quantitative estimates of radiological release magnitudes and compositions to the environment. Rather, this approach is intended to identify the characteristics of a reactor design concepts release mitigation strategies that are most important to different classes of accident scenarios. It uses a scoping methodology to provide an approximate, order-of-magnitude, estimate of the radiological release to the environment and associated off-site consequences. This scoping method is applied to different reactor concepts, considering the performance of barriers to fission product release for these concepts under sample accident scenarios. The accident scenarios and sensitivity evaluations are selected in this report to evaluate the role of different fission product barriers in ameliorating the source term to the environment and associated off-site consequences. This report applies this structure to characterize how release mitigation measures are integrated to define overall release mitigation strategies for High Temperature Gas Reactors (HTGRs), Sodium Fast Reactors (SFRs), and liquid fueled Molten Salt Reactors (MSRs). To support this evaluation framework, factors defining a chain of release attenuation stages, and thus an overall mitigation strategy, must be established through mechanistic source term calculations. This has typically required the application of an integral plant analysis code such as MELCOR. At present, there is insufficient evidence to support a priori evaluation of the effectiveness of a release mitigation strategy for advanced reactor concepts across the spectrum of events that could challenge the radiological containment function. While it is clear that these designs have significant margin to radiological release to the environment for the scenarios comprising the design basis, detailed studies have not yet been performed to assess the risk profile for these plants. Such studies would require extensive evaluation across a reasonably complete spectrum of accident scenarios that could lead to radiological release to the environment.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Transcriptomics (PB-DP3)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Sample data was acquired using a Illumina HiSeq sequencer system and processed for RNA sequencing (RNA-Seq) expression analysis. Transcriptomic differential expression analysis revealed coordinated circadian clock-driven adjustment of the cell cycle and rewiring of energy and carbon metabolism. Processed RNA-Seq datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed RNA-seq results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Increasing Industry Involvement: A Solution from a Student's Perspective

Many engineering employers are finding that graduates are not sufficiently equipped to begin contributing productively when they exit a 4-year institution and enter the workforce. The Intern Professional Development Center (IPDC) is a proposed business model that exposes engineering undergraduates to industry-relevant knowledge, while providing them with working experience during their degree. Using a tri-stage approach, the IPDC engages with students early in their academic careers, provides continuous training and development opportunities, and finally connects the students with potential employers. The two topics most commonly under-represented in engineering programs are: - Familiarity with drafting software - Knowledge of relevant codes and standards. The Intern Professional Development Center (IPDC): A tri-stage solution for recruiting, training, and encouraging the workforce of tomorrow. An IPDC allows students to be active members of industry during their undergraduate careers, leading to: - Improved local talent retention; - Improved graduation and academic performance statistics; - Near-guarantee for post-graduation employment. In March of 2019, the first IPDC prototype began operating in the Tri-Cities, Washington. Since then, 3 undergraduate students have entered the IPDC at Stage 2, beginning with the standard training and professional development. Of those 3 students, 2 have already moved on to Stage 3, with successful ongoing internships with local employers. At a performance review for one of the IPDC's Stage 3 students after 90 days of employment, the direct manager said: 'How soon can we get another one?'.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2024

Air-coupled tsunamis generated from impacts and airbursts: Our understanding before Hunga-Tonga Hunga-Ha'apai

The effort to prevent or mitigate the effects of an impact on Earth is known as planetary defense. A significant component of planetary defense research involves risk assessment. Much of our understanding of the risk from near-Earth objects comes from the geologic record in the form of impact craters, but not all asteroid impacts are crater-forming events. Small asteroids explode before reaching the surface, generating an airburst, and most impacts into the ocean do not penetrate the water to form a crater in the sea floor. The risk from these non-crater-forming ocean impacts and airbursts is difficult to quantify and represents a significant uncertainty in our assessment of the overall threat. We are currently working to better understand impact scenarios that can generate dangerous tsunamis. One of the suggested mechanisms for the production of asteroid–generated tsunamis is by direct coupling of the pressure wave to the water, analogous to the means by which a moving weather front can generate a meteotsunami. To test this hypothesis, we ran a series of airburst simulations and provided time-resolved pressure and wind profiles to use as source functions for tsunami models. We used the CTH hydrocode to model the various airburst scenarios to compare to the results of other simulations and provide time dependent boundary conditions as input to shallow-water wave propagation codes. The strongest and most destructive meteotsunamis are generated by atmospheric pressure oscillations with amplitudes of only a few hPa1 (mbar), corresponding to changes in sea level of a few cm. The resulting wave is strongest when there is a resonance between the ocean and the atmospheric forcing. A Proudman resonance takes place when the atmospheric disturbance’s translational speed (U) equals the longwave phase speed $\sqrt{gh}$ of shallow water wave. Coupling is strongest when the Froude number (Fr=U/c) is unity. A weather front propagates much slower than the speed of sound, so meteotsunamis are most common and dangerous in shallow bodies of water such as the Mediterranean Sea or Lake Michigan. By contrast, the blast wave from an airburst or crater-forming impact propagates at a speed faster than a tsunami in the deepest ocean, and a Proudman resonance cannot be achieved even though the overpressures are orders of magnitude greater. However, blast wave profiles are N-waves in which a sharp shock wave leading to overpressure is followed by a more gradual rarefaction to a much longer-duration underpressure phase. Even though the blast outruns the water wave it is forcing, the tsunami should continue to be driven by the out-of-resonance gradient associated with the suction phase, which may depend strongly on the details of the airburst or impact scenario. The open question is whether there are any conditions under which such an airburst-driven tsunami can be dangerous enough to contribute to the overall impact risk. We have also identified other potential mechanisms for airburst-generated tsunamis: 1) reaction force at the surface from the plume ejected into space, which carries significant momentum, 2) expanding toroidal vortices at the surface, which travel more slowly than the shock wave and can generate a Proudman resonance in relatively shallow ocean (such as continental shelf), and 3) steam explosion from seawater ablation by a “Type II” (Libyan Desert Glass-type) airburst in which the hot vapor jet descends to the surface. On January 15, 2022, the Hunga-Tonga Hunga-Ha’apai volcano, located approximately 60 km north of Tongatapu, the main island of Tonga, violently erupted with a powerful explosion, culminating the period of volcanic activity that started in December of 2021. This event and resulting tsunamis provided an existence proof for the air pressure wave coupling mechanism we proposed. It also suggests that it can be stronger and more significant over much greater distances than we contemplated, leading to global tsunamis associated with impact events on land as well as in the water. Large atmospheric explosions generate global Lamb waves with larger amplitudes, longer periods, and slower speeds than the local and regional blast waves we modeled prior to that event. This paper reviews our analysis and modeling of airburst-driven tsunamis prior to the 2022 Hunga-Tonga Hunga-Ha’apai tsunami, which was the subject of two presentations at the 2023 Planetary Defense Conference and is the subject of another paper currently in preparation.

54 ENVIRONMENTAL SCIENCES↗
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 OSTI2024

Integrating ytopt and libEnsemble to autotune OpenMC

Ytopt is a Python machine-learning-based autotuning software package developed within the ECP PROTEAS-TUNE project. The ytopt software adopts an asynchronous search framework that consists of sampling a small number of input parameter configurations and progressively fitting a surrogate model over the input-output space until exhausting the user-defined maximum number of evaluations or the wall-clock time. libEnsemble is a Python toolkit for coordinating workflows of asynchronous and dynamic ensembles of calculations across massively parallel resources developed within the ECP PETSc/TAO project. libEnsemble helps users take advantage of massively parallel resources to solve design, decision, and inference problems and expands the class of problems that can benefit from increased parallelism. In this paper we present our methodology and framework to integrate ytopt and libEnsemble to take advantage of massively parallel resources to accelerate the autotuning process. Specifically, we focus on using the proposed framework to autotune the ECP ExaSMR application OpenMC, an open source Monte Carlo particle transport code. OpenMC has seven tunable parameters some of which have large ranges such as the number of particles in-flight, which is in the range of 100,000 to 8 million, with its default setting of 1 million. Setting the proper combination of these parameter values to achieve the best performance is extremely time-consuming. Therefore, we apply the proposed framework to autotune the MPI/OpenMP offload version of OpenMC based on a user-defined metric such as the figure of merit (FoM) (particles/s) or energy efficiency energy-delay product (EDP) on Crusher at Oak Ridge Leadership Computing Facility. In conclusion, the experimental results show that we achieve the improvement up to 29.49% in FoM and up to 30.44% in EDP.

Autotuning↗
DOE OSTI2021

Co‑cultivation of the anaerobic fungus Caecomyces churrovis with Methanobacterium bryantii enhances transcription of carbohydrate binding modules, dockerins, and pyruvate formate lyases on specific substrates

Abstract Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal–methanogen physical associations and fungal cell wall development and remodeling.

09 BIOMASS FUELS↗