Scalable, Data-Driven, and High-Resolution Building Models for Control Optimization
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32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
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Data for "RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides"
For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ ( R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides , providing a streamlined method for addressing genetic engineering challenges in the yeast.
gene editing↗
Data from A Mass Spectrometry-Based High-Throughput Screening Method for Engineering Fatty Acid Synthases with Improved Production of Medium Chain Fatty Acids
Microbial cell factories have been extensively engineered to produce free fatty acids (FFAs) as key components of crucial nutrients, soaps, industrial chemicals, and fuels. However, our ability to control the composition of microbially synthesized FFAs is still limited, particularly, for producing medium‐chain fatty acids (MCFAs). This is mainly due to the lack of high‐throughput approaches for FFA analysis to engineer enzymes with desirable product specificity. Here we report a mass spectrometry (MS)‐based method for rapid profiling of MCFAs in Saccharomyces cerevisiae by using membrane lipids as a proxy. In particular, matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐ToF) MS was used to detect shorter acyl chain phosphatidylcholines from membrane lipids and a higher m/z peak ratio at 730 and 758 was used as an indication for improved MCFA production. This colony‐based method can be performed at a rate of ~2 s per sample, representing a substantial improvement over gas chromatography‐MS (typically >30 min per sample) as the gold standard method for FFA detection. To demonstrate the power of this method, we performed site‐saturation mutagenesis of the yeast fatty acid synthase and identified nine missense mutations that resulted in improved MCFA production relative to the wild‐type strain. Colony‐based MALDI‐ToF MS screening provides an effective approach for engineering microbial fatty acid compositions in a high‐throughput manner.
Conversion↗
Historic American engineering record. Nevada national security site, Bren Tower Complex. Written historical and descriptive data and field records
The BREN (Bare Reactor Experiment, Nevada) Tower Complex is significant for its role in the history of nuclear testing, radiation dosimetry studies, and early field testing of the Strategic Missile Defense System designs. At the time it was built in 1962, the 1,527 ft (465 m) BREN Tower was the tallest structure west of the Mississippi River and exceeded the height of the Empire State Building by 55 ft (17 m). It remains the tallest ever erected specifically for scientific purposes and was designed and built to facilitate the experimental dosimetry studies necessary for the development of accurate radiation dose rates for the survivors of Hiroshima and Nagasaki. The tower was a key component of the Atomic Bomb Casualty Commission’s (ABCC) mission to predict the health effects of radiation exposure. Moved to its current location in 1966, the crucial dosimetry studies continued with Operation HENRE (High Energy Neutron Reactions Experiment). These experiments and the data they generated became the basis for a dosimetry system called the Tentative 1965 Dose or more commonly the T65D model. Used to estimate radiation doses received by individuals, the T65D model was applied until the mid-1980s when it was replaced by a new dosimetry system known as DS86 based on the Monte Carlo method of dose rate calculation. However, the BREN Tower data are still used for verification of the validity of the DS86 model. In addition to its importance in radiation heath effects research, the BREN Tower Complex is also significant for its role in the Brilliant Pebbles research project, a major component of the Strategic Defense Initiative popularly known as the “Star Wars” Initiative. Instigated under the Reagan Administration, the program’s purpose was to develop a system to shield the United States and allies from a ballistic missile attack. The centerpiece of the Strategic Defense System was space-based, kinetic-kill vehicles. In 1991, BREN Tower was used for the tether tests of the Brilliant Pebbles prototype vehicle at the earth’s surface prior to the more costly space testing program. The success of these tests established the Brilliant Pebbles program as an essential component of America’s space-based missile defense system even after the dismantling of the Soviet Union. Data from the Brilliant Pebbles research program continues to inspire current missile defense system research (Independent Working Group 2009).
54 ENVIRONMENTAL SCIENCES↗
The AmeriFlux Data Activity and Data System: An Evolving Collection of Data Management Techniques, Tools, Products and Services
The Carbon Dioxide Information Analysis Center (CDIAC) at Oak Ridge National Laboratory (ORNL), USA has provided scientific data management support for the U.S. Department of Energy and international climate change science since 1982. Over this period, climate change science has expanded from research focusing on basic understanding of geochemical cycles, particularly the carbon cycle, to integrated research addressing climate change impacts, vulnerability, adaptation, and mitigation. Interests in climate change data and information worldwide have grown remarkably and, as a result, so have demands and expectations for CDIAC’s data systems. To meet the growing demands, CDIAC’s strategy has been to design flexible data systems using proven technologies blended with new, evolving technologies and standards. CDIAC development teams are multidisciplinary and include computer science and information technology expertise, but also scientific expertise necessary to address data quality and documentation issues and to identify data products and system capabilities needed by climate change scientists. CDIAC has learned there is rarely a single commercial tool or product readily available to satisfy long-term scientific data system requirements (i.e., one size does not fit all and the breadth and diversity of environmental data are often too complex for easy use with commercial products) and typically deploys a variety of tools and data products in an effort to provide credible data freely to users worldwide. Like many scientific data management applications, CDIAC’s data systems are highly customized to satisfy specific scientific usage requirements (e.g., developing data products specific for model use) but are also designed to be flexible and interoperable to take advantage of new software engineering techniques, standards (e.g., metadata standards) and tools and to support future Earth system data efforts (e.g., ocean acidification). CDIAC has provided data management support for numerous long-term measurement projects crucial to climate change science. One current example is the AmeriFlux measurement network. AmeriFlux provides continuous measurements from forests, grasslands, wetlands, and croplands in North, Central, and South America and offers important insight about carbon cycling in terrestrial ecosystems. We share our approaches in satisfying the challenges of delivering AmeriFlux data worldwide to benefit others with similar challenges handling climate change data, further heighten awareness and use of an outstanding ecological data resource, and highlight expanded software engineering applications being used for climate change measurement data.
Boden, Thomas A.↗
Experimental evaluation of a flexible I/O architecture for accelerating workflow engines in ultrascale environments
The increasing volume of scientific data and the limited scalability and performance of storage systems are currently presenting a significant limitation for the productivity of the scientific workflows running on both high-performance computing (HPC) and cloud platforms. Clearly needed is better integration of storage systems and workflow engines to address this problem. This paper presents and evaluates a novel solution that leverages codesign principles for integrating Hercules—an in-memory data store—with a workflow management system. We consider four main aspects: workflow representation, task scheduling, task placement, and task termination. As a result, the experimental evaluation on both cloud and HPC systems demonstrates significant performance and scalability improvements over existing state-of-the-art approaches.
97 MATHEMATICS AND COMPUTING↗
Editorial: Data-driven machine learning for advancing hydrological and hydraulic predictability
The growing influence of machine learning (ML) in every aspect of our lives has led to revolutionary advancements in our understanding, prediction, and decision-making capabilities. One field that stands to benefit greatly from applying these techniques includes hydrology and hydraulics. The ability to predict hydrological and hydraulic phenomena with greater accuracy and reliability is of utmost importance, given the increasing threats posed by climate change and extreme weather/climate events. In this editorial, we explore the significant contributions made by four recent studies that aim to advance hydrological and hydraulic predictability through data-driven ML.
42 ENGINEERING↗
Contrastive Machine Learning with Gamma Spectroscopy Data Augmentations for Detecting Shielded Radiological Material Transfers
Data analysis techniques can be powerful tools for rapidly analyzing data and extracting information that can be used in a latent space for categorizing observations between classes of data. Machine learning models that exploit learned data relationships can address a variety of nuclear nonproliferation challenges like the detection and tracking of shielded radiological material transfers. The high resource cost of manually labeling radiation spectra is a hindrance to the rapid analysis of data collected from persistent monitoring and to the adoption of supervised machine learning methods that require large volumes of curated training data. Instead, contrastive self-supervised learning on unlabeled spectra can enhance models that are built on limited labeled radiation datasets. This work demonstrates that contrastive machine learning is an effective technique for leveraging unlabeled data in detecting and characterizing nuclear material transfers demonstrated on radiation measurements collected at an Oak Ridge National Laboratory testbed, where sodium iodide detectors measure gamma radiation emitted by material transfers between the High Flux Isotope Reactor and the Radiochemical Engineering Development Center. Label-invariant data augmentations tailored for gamma radiation detection physics are used on unlabeled spectra to contrastively train an encoder, learning a complex, embedded state space with self-supervision. A linear classifier is then trained on a limited set of labeled data to distinguish transfer spectra between byproducts and tracked nuclear material using representations from the contrastively trained encoder. The optimized hyperparameter model achieves a balanced accuracy score of 80.30%. Any given model—that is, a trained encoder and classifier—shows preferential treatment for specific subclasses of transfer types. Regardless of the classifier complexity, a supervised classifier using contrastively trained representations achieves higher accuracy than using spectra when trained and tested on limited labeled data.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Reynolds-Averaged Turbulence Modeling Using Deep Learning with Local Flow Features: An Empirical Approach
Reynolds-Averaged Navier-Stoke (RANS) models offer an alternative avenue in predicting flow characteristics when the corresponding experiments are difficult to achieve due to geometry complexity, limited budget, or knowledge. RANS models require the knowledge of subgrid scale physics to solve conservation equations for mass, energy, and momentum. Mechanistic turbulence models, such as k-epsilon, are generally evaluated and calibrated for specific flow conditions with various degrees of uncertainty. These models have limited capability to assimilate a substantial amount of data due to model form constraints. Meanwhile, deep learning (DL) has been proven to be universal approximators with the potential to assimilate available, relevant, and adequately evaluated data. Moreover, deep neural networks (DNNs) can create surrogate models without knowing function forms. Such a data-driven approach can be used in updating fluid models based on observations as opposed to hard-wiring models with precalibrated correlations. The paper presents progress in applying DNNs to model Reynolds stress using two machine learning (ML) frameworks. A novel flow feature coverage mapping is proposed to quantify the physics coverage of DL-based closures. It can be used to examine the sufficiency of training data and input flow features for data-driven turbulence models. The case of a backward-facing step is formulated to demonstrate that not only can DNNs discover underlying correlation behind fluid data but also they can be implemented in RANS to predict flow characteristics without numerical stability issues. Finally, the presented research is a crucial stepping-stone toward the data-driven turbulence modeling, which potentially benefits the design of data-driven experiments that can be used to validate fluid models with ML-based fluid closures.
42 ENGINEERING↗
Advanced Combustion and Fuels; NREL (National Renewable Energy Laboratory)
Presented at the U.S. Department of Energy Vehicle Technologies Office 2015 Annual Merit Review and Peer Evaluation Meeting, held June 8-12, 2015, in Arlington, Virginia. It addresses technical barriers of inadequate data and predictive tools for fuel and lubricant effects on advanced combustion engines, with the strategy being through collaboration, develop techniques, tools, and data to quantify critical fuel physico-chemical effects to enable development of advanced combustion engines that use alternative fuels.
33 ADVANCED PROPULSION SYSTEMS↗
An Experimental Study of Uncertainty Considerations Associated with Predicting Auto-ignition Timing using Livengood-Wu Integral Method
The application of the Livengood-Wu (LW) integral method as a tool to estimate knock onset in spark ignited (SI) engines and combustion phasing in advanced compression ignition (ACI) engines has been demonstrated through simulations several times. In this study, the effect of uncertainties associated with parameters required for the LW integral method, when used as a tool for model based control of ignition timing in an ACI engine, were experimentally studied using five full boiling range gasoline fuels. As a first step, the method was applied to experimental data from a rapid compression machine and it was found that the ability of the LW integral method to predict ignition timing was very sensitive to the performance of the chemical kinetic model of each fuel. The method was subsequently applied to experimental data from a single-cylinder gasoline engine with simple approximations for the LW integral input parameters, and it was found that the predicted time of ignition was significantly different from the actual start of combustion. Systematic evaluation of various parametric uncertainties conducted thereafter showed that the uncertainty in cylinder charge temperature has the greatest influence. Improved methods of estimating cylinder charge temperature are proposed to account for the previously determined corrections, to enable the use of the LW integral method for model based control of ignition timing.
Compression Ignition↗
Data Efficiency Assessment of Generative Adversarial Networks for Critical Heat Flux Synthetic Data Generation
This study investigates the application of generative artificial intelligence techniques, particularly conditional generative adversarial networks (cGAN), in real-world engineering contexts, with a specific focus on synthetic data generation for critical heat flux (CHF). Utilizing a dataset comprising more than 20,000 real experimental CHF measurements, we conduct a series of experiments to examine cGAN’s behavior. These experiments encompass varying sizes of the training dataset, training cGAN on data from diverse experimental sources to generate new data on unseen experimental setups, and assessing the impact of excluding various input features on cGAN’s data generation accuracy. Our findings underscore the pronounced data dependency of cGAN for reliable performance, with decreased efficacy observed with smaller training dataset sizes. Notably, cGAN exhibits varying performance when trained on data from different experiments, with superior predictive capabilities observed for certain experiment sources compared to others. For instance, when cGAN was trained on data from Smolin et al.’s experiments or Zenkevich et al., it exhibited relatively good performance in generating the data from Becker et al., Kirillov et al., and Alekseev et al. experiments. In contrast, when trained with Alekseev et al.’s data and tasked with generating other experimental setups, cGAN showed notably poor performance. In both scenarios, cGAN’s performance was inferior compared to training on samples from all experiments concurrently. A feature importance analysis highlights the significant influence of parameters such as mass flux and heated length on accurate CHF generation, while other parameters like diameter and pressure have less impact. Inlet temperature is identified as a moderating factor by cGAN.
22 - GENERAL STUDIES OF NUCLEAR REACTORS↗
Understanding Data Structures by Extracting Memory Access Graphs
Understanding the data structures employed by a program is important for reverse engineering activities and can improve the results of automated software analysis techniques. In a compiled binary, access to data structure fields and array indices defined in the source program are replaced by raw pointer arithmetic. We present a representation for capturing the essential details of how a program accesses memory regions, which we call a Memory Access Graph (MAG), and a static analysis for automatically extracting this information from a program binary. The static analysis to extract the MAGs from the program is straightforward and does not require sophisticated integer or pointer analysis. The MAGs are readily understood by reverse engineers; they are generally able to perceive the data structure definition corresponding to a MAG. We briefly discuss automatic extraction of structure definitions outlining some of the difficulties in doing so.
97 MATHEMATICS AND COMPUTING↗
Dynamic responses of submerged components in advanced reactors: experimental and numerical studies
The seismic design of an advanced nuclear reactor must consider the interaction of vessel internal components with the surrounding coolant: fluid–structure interaction (FSI). Available analytical solutions for FSI of submerged components do not accommodate multiple-component, intense seismic inputs and complex reactor and internal geometries. Physical testing of reactor vessels and internals to inform seismic design is impractical and cost-prohibitive, leaving the use of verified and validated, robust numerical models as the only plausible option for analysis and design. Physical data that could be used for validating such numerical models for multi-component shaking are not available. This article describes an experimental program performed on a 6-degree-of-freedom earthquake simulator to generate data that could support validation of seismic FSI numerical models for submerged components in commercial finite element codes. A scaled model of a base-supported reactor vessel with simplified representations of submerged internals was tested to generate submerged-component response histories for a range of seismic inputs. The generated data were used to validate numerical models in the finite element code LS-DYNA. Numerical models were validated for calculation of hydrodynamic pressure responses on internals, in-water frequencies of internals, and acceleration responses of internals. The generated data and the analysis recommendations could aid engineering analysts designing submerged components and systems for seismic effects.
Engineering↗
Local composition activity coefficient model for mixed-gas adsorption equilibria
Taking into consideration the adsorbate–adsorbent interactions, a novel activity coefficient model is derived from the non-random two-liquid theory for mixed-gas adsorption equilibria. In contrast with the conventional activity coefficient models developed for bulk liquids, the new model correctly predicts negative deviations from ideality for adsorbed phase mixtures including azeotropic behavior exhibited by selected gas-adsorbent systems. Here, the requiring a single binary interaction parameter per adsorbate–adsorbate pair, the model successfully correlates wide varieties of binary adsorption isotherm data and it should be a powerful engineering thermodynamic tool in correlating and predicting mixed-gas adsorption equilibria.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Flexible and Scalable Data-Acquisition Using the artdaq Toolkit
The Real-Time Systems Engineering Department of the Scientific Computing Division at Fermilab is developing a flexible, scalable, and powerful data-acquisition (DAQ) toolkit which serves the needs of experiments from bench-top hardware tests to large high-energy physics experiments. The toolkit provides data transport and event building capabilities with the option for experimenters to inject art analysis code at key points in the DAQ for filtering or monitoring. The toolkit also provides configuration management, run control, and low-level hardware communication utilities. Firmware blocks for several commercial data acquisition boards are provided, allowing experimenters to approach the DAQ from a high level. A fully-functional DAQ "solution" of the toolkit is provided in otsdaq, sacrificing some flexibility in favor of being ready-to-use. artdaq is being used for several current and upcoming experiments, and will continue to be refined and expanded for use in the next generation of neutrino and muon experiments.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Toward 3D data visualization using virtual reality tools
Virtual Reality (VR) offers the opportunity to display data, instrumentation, and experimental setups in three dimensions and gives the user the ability to interact with the objects. This technology moves visualization beyond two-dimensional projections on a flat screen with a fixed field of view in which a keyboard or another similar controller is needed to change the view. Advances in both hardware and software for VR make it possible for the non-expert to develop visualization tools for scientific applications both for viewing and for sharing data or diagnostic hardware between users in three dimensions. Furthermore, this manuscript describes application development using two VR software tools, Unity gaming engine and A-frame, for visualizing data and high energy physics targets.
47 OTHER INSTRUMENTATION↗
A comprehensive experimental and kinetic modeling study of di-isobutylene isomers: Part 1
We report di-isobutylene has received significant attention as a promising fuel blendstock, as it can be synthesized via biological routes and is a short-listed molecule from the Co-Optima initiative. Di-isobutylene is also popularly used as an alkene representative in multi-component surrogate models for engine studies of gasoline fuels. However, there is limited experimental data available in the literature for neat di-isobutylene under engine-like conditions. Hence, most existing di-isobutylene models have not been extensively validated, particularly at lower temperatures (< 1000 K). Most gasoline surrogate models include the di-isobutylene sub-mechanism published by Metcalfe et al. with little or no modification. The current study is undertaken to develop a detailed kinetic model for di-isobutylene and validate the model using a wide range of relevant experimental data. Part 1 of this study exclusively focuses on the low- to intermediate temperature kinetics of di-isobutylene. An upcoming part 2 discusses the high-temperature model development and validation of the relevant experimental targets. Ignition delay time measurements for the di-isobutylene isomers were performed at pressures ranging from 15 - 30 bar at equivalence ratios of 0.5, 1.0, and 2.0 diluted in air and in the temperature range 650 - 900 K using two independent rapid compression machine facilities. In addition, measurements of species identified during the oxidation of these isomers were performed in a jet-stirred reactor and in a rapid compression machine. A detailed kinetic model for the di-isobutylene isomers is developed to capture the wide range of new experimental targets. For the first time, a comprehensive low-temperature chemistry submodel is included. The differences in the important reaction pathways for the accurate prediction of the oxidation of the two DIB isomers are compared using reaction path analysis. In conclusion, the most sensitive reactions controlling the ignition delay times of the DIB isomers under the pressure and temperature conditions necessary for autoignition in engines are identified.
09 BIOMASS FUELS↗