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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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At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A FAIR-compliant parts catalogue for genome engineering and expression control in Saccharomyces cerevisiae

The synthetic biology toolkit for baker's yeast, Saccharomyces cerevisiae, includes extensive genome engineering toolkits and parts repositories. However, with the increasing complexity of engineering tasks and versatile applications of this model eukaryote, there is a continued interest to expand and diversify the rational engineering capabilities in this chassis by FAIR (findable, accessible, interoperable, and reproducible) compliance. In this study, we designed and characterised 41 synthetic guide RNA sequences to expand the CRISPR-based genome engineering capabilities for easy and efficient replacement of genomically encoded elements. Moreover, we characterize in high temporal resolution 20 native promoters and 18 terminators using fluorescein and LUDOX CL-X as references for GFP expression and OD600 measurements, respectively. Additionally, all data and reported analysis is provided in a publicly accessible jupyter notebook providing a tool for researchers with low-coding skills to further explore the generated data as well as a template for researchers to write their own scripts. We expect the data, parts, and databases associated with this study to support a FAIR-compliant resource for further advancing the engineering of yeasts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Hands-On Computer Science: The Array of Things Experimental Urban Instrument

Chicago's Array of Things (AoT) project is aptly described as a technology experiment or a "smart city" prototype. The concept of such an extensible "instrument" arose within a larger translational research vision applying computer science and engineering research for the multidimensional benefit of people and communities in cities. The AoT project hypothesized that wireless intelligent sensor networks could enable both quantitative social science and urban monitoring while also stimulating youth interest in science and technology. Successful deployment of such sensor networks could provide open data from urban measurements not only in support of diverse research questions-in environmental dynamics, urban architecture, engineering, and social sciences-but also informing community groups and city planners. Further, the AoT project and its successor SAGE project are a computer science and engineering experiment, but its success is inextricably tied to community engagement and experiential education. Simply put, community acceptance is a prerequisite to installing and testing the instrument.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Quantum-Inspired Bayesian Sampling for Uncertainty Quantification and Machine Learning (Final Technical Report)

With increasing simulation and measurement data, machine learning and artificial intelligence have been widely used in computational decision-making of complex engineering systems. The resulting tools, such as uncertainty quantification solvers, reinforcement learning, and physics-informed machine learning, have achieved great success in critical DOE tasks such as material discovery and design, energy system modeling and control, and numerical weather and climate prediction. A core topic in scientific machine learning and artificial intelligence is Bayesian inference: given an observed data set, people want to estimate the posterior distribution of a (possibly large) number of hidden parameters. Due to the flexibility and weak assumptions, Bayesian sampling has been the mainstream Bayesian inference solvers despite the rapid progress of approximate Bayesian inference. Classical Bayesian sampling methods such as Markov-chain Monte Carlo suffer from a low-acceptance rate due to the random walk nature, therefore state-of-the-art techniques use Hamiltonian Monte Carlo and its variants to efficiently draw posterior samples in a high dimension. The key idea of Hamiltonian Monte Carlo and its variants is to simulate the Hamiltonian dynamics of a classical particle with a fixed mass, and their performance significantly degrades when the posterior distribution is highly spiky or has multiple modes. Leveraging the idea of quantum physics, this project has investigated new theory, algorithms and applications of Bayesian inference (especially Bayesian sampling). The main results include: (1) novel quantum-inspired Bayesian sampling methods that can lead to better accuracy for challenging multi-modal or spiky distributions, (2) more scalable machine learning framework leveraging tensor-compressed Bayesian inference, and (3) Bayesian and sampling approaches for verifying the robustness of continuous and binary neural networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

WATTS: Workflow and template toolkit for simulation

Modeling and simulation in many science and engineering domains often involves the execution and/or iteration of a sequence of applications, with data transfer between applications typically required. These applications often do not have a formal application programming interface (API). Instead, executing an application requires first writing a text-based input file, the format of which is typically defined in a user’s manual. While text-based input files are suitable for simple one-off calculations, they can become cumbersome if a user wants to execute the applications multiple times and systematically vary input parameters, especially when a complex workflow is involved. In this case, they must resort to either manually making changes in the input file or developing their own script that modifies the input file and executes the application. Depending on the format of the input file, writing such a script can be a non-trivial and error-prone task.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Surrogate Modeling of Nonlinear Dynamic Systems: A Comparative Study

Surrogate models play a vital role in overcoming the computational challenge in designing and analyzing nonlinear dynamic systems, especially in the presence of uncertainty. This paper presents a comparative study of different surrogate modeling techniques for nonlinear dynamic systems. Four surrogate modeling methods, namely, Gaussian process (GP) regression, a long short-term memory (LSTM) network, a convolutional neural network (CNN) with LSTM (CNN-LSTM), and a CNN with bidirectional LSTM (CNN-BLSTM), are studied and compared. All these model types can predict the future behavior of dynamic systems over long periods based on training data from relatively short periods. The multi-dimensional inputs of surrogate models are organized in a nonlinear autoregressive exogenous model (NARX) scheme to enable recursive prediction over long periods, where current predictions replace inputs from the previous time window. Three numerical examples, including one mathematical example and two nonlinear engineering analysis models, are used to compare the performance of the four surrogate modeling techniques. The results show that the GP-NARX surrogate model tends to have more stable performance than the other three deep learning (DL)-based methods for the three particular examples studied. The tuning effort of GP-NARX is also much lower than its deep learning-based counterparts.

42 ENGINEERING↗
DOE OSTI2021

A Co-design Framework for Online Data Analysis and Reduction

Science applications preparing for the exascale era are increasingly exploring in situ computations comprising of simulation-analysis-reduction pipelines coupled in-memory. Efficient composition and execution of such complex pipelines for a target platform is a codesign process that evaluates the impact and tradeoffs of various application- and system-specific parameters. In this article, we describe a toolset for automating performance studies of composed HPC applications that perform online data reduction and analysis. We describe Cheetah, a new framework for composing parametric studies on coupled applications, and Savanna, a runtime engine for orchestrating and executing campaigns of codesign experiments. Furthermore, this toolset facilitates understanding the impact of various factors such as process placement, synchronicity of algorithms, and storage versus compute requirements for online analysis of large data. Ultimately, we aim to create a catalog of performance results that can help scientists understand tradeoffs when designing next-generation simulations that make use of online processing techniques. We illustrate the design of Cheetah and Savanna, and present application examples that use this framework to conduct codesign studies on small clusters as well as leadership class supercomputers.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

diyepw: A Python package for Do-It-Yourself EnergyPlus weather file generation

diyepw allows for quick and easy generation of a set of EnergyPlus weather (EPW) files for a given location over a given historical period. The user can obtain weather files using an open-source, automated workflow by simply specifying the location of interest using the World Meteorological Organization weather station ID number, and specifying a year or set of years for which to generate EPW files. Building energy modelers can use these auto-generated weather files in building performance simulations to represent the actual observed weather conditions in the location(s) of interest, based on meteorological observations obtained from the National Oceanic and Atmospheric Administration's Integrated Surface Database. Because observed weather data are not available for every meteorological variable specified in the EPW format, diyepw starts with a widely-used set of typical meteorological year (TMY) files, using them as the template to generate new EPW files by substituting in the observed values of selected meteorological variables that are known to affect building energy performance. Its output is a weather file or group of weather files that conform to the data standards associated with the EPW format so they can be used with any building performance simulation software employing EnergyPlus as its simulation engine.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Hypothesis testing via AI: Generating physically interpretable models of scientific data with machine learning (Full Technical Report)

Deep learning has demonstrated an exceptional ability to solve complex tasks (an engineering success); however, it has done so at the expense of the ability to generate new knowledge (a scientific failure). We propose an alternative framework—entitled Deep Symbolic Regression (DSR)—in which artificial neural networks (NNs) rapidly generate hypotheses about physical relationships among inputs. This framework bypasses the need to interpret an NN altogether, while still leveraging the representational power of deep learning. The resulting models are tractable mathematical expressions, which are inherently and readily human interpretable and can provide insights into underlying physical phenomena. Further, we fold this methodology into the scientific process by allowing the scientist to directly integrate a priori knowledge and beliefs to accelerate learning. We demonstrate this methodology on symbolic regression—the problem of rediscovering underlying expressions describing a dataset—and achieve state-of-the-art performance across a wide variety of symbolic regression problems. Further, we generalize our DSR framework to apply to the more general class of symbolic optimization problems, in which one seeks to optimize a sequence of symbols or “tokens” under a black-box reward function. Examples of other symbolic optimization problems include neural architecture search and computational antibody design. Our generalized tool, Deep Symbolic Optimization (DSO), has been demonstrated on the task of learning symbolic control policies for reinforcement learning environments, and has been adopted as an enabling capability for computational antibody design.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Developing Multi-Gene CRISPRa/I Programs to Accelerate DBTL Cycles in ABF Hosts Engineered for Chemical Production (CRADA 468)

Bacterial metabolism is comprised of large and complex gene networks that can produce valuable chemical products. Sophisticated organism engineering efforts are required to optimize production of high-value compounds from these networks. In principle, synthetic multi-gene transcriptional programs could be constructed to reengineer these networks for efficient industrial chemical production. In practice, however, our incomplete ability to understand and model the underlying networks, combined with our limited ability to predictably control the expression of multiple genes makes achieving this goal difficult. To overcome these challenges, we will combine new CRISPR-Cas multi-gene expression programs with computational modeling, machine learning, and multi-omics data to enhance the efficacy of design-build-test-learn (DBTL) cycles. For industrially promising microorganisms in early stages of development, creating technologies for rapidly engineering complex multi-gene programs could be transformative for accelerating data- and model-driven strain design. New CRISPR-Cas tools allow programmable gene activation (CRISPRa) or repression (CRISPRi) at multiple genes simultaneously, using the catalytically inactive Cas9 protein (dCas9) with guide RNAs that recognize DNA targets through predictable Watson-Crick base pairing. To enable accelerated DBTL cycles, we will combine these technologies with advanced Agile BioFoundry (ABF) capabilities for multi-omics data collection and machine learning. We will demonstrate the immediate applicability of these tools by rapidly improving the production of an industrial aromatic in multiple ABF organisms. We recently identified and optimized new transcriptional activators that can be linked to programmable CRISPR-Cas DNA binding domains to activate gene expression in E. coli. We can now use these CRISPRa tools as generalizable trans-acting regulators for combinatorial multi-gene expression tuning that can be easily transferred to new pathways and networks without additional genome engineering. We anticipate these tools will also transfer to new hosts. We have recently found that CRISPRa systems developed in E. coli can be readily ported to Pseudomonas putida, suggesting that multi-gene CRISPRa/i programs for diverse ABF organisms may be within reach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hybrid combustion modeling approach for turbulent jet ignition in natural-gas pre-chamber spark-ignition engines at high EGR

Here, this study presented a hybrid modeling approach for simulating turbulent jet ignition and combustion processes in a natural-gas pre-chamber spark-ignition engine operating under exhaust gas recirculation (EGR) diluted conditions. In-depth analyses of experimental data and simulation results from previous work [Chinnathambi et al., ICEF2021-67836; Kim et al., Fuel 409: 137815, 2026] revealed two key findings: (i) the magnitude of pressure difference between the pre-chamber and main chamber ($∆P_{PC-MC}$) was positively correlated with the combustion duration from the moment of $∆P_{PC-MC}=0$ to the point of 5% mass fraction burned, with larger $∆P_{PC-MC}$ associated with longer duration; and (ii) the turbulent combustion regime in the main chamber transitioned from the broken reaction zone to the corrugated flamelet regime, with the Karlovitz number exceeding 100 immediately after turbulent hot jets were ejected from nozzles, coinciding with observed local extinction events. To accurately simulate the entire combustion process, a hybrid approach was developed under Reynolds-Averaged Navier Stokes framework, combining the G-equation model for pre-chamber combustion with the multi-zone well-stirred reactor approach and a turbulence-chemistry interaction (TCI) submodel for main chamber combustion. The TCI submodel accounted for the attenuation of reaction rates due to turbulent strain and modeled local extinction by suppressing reaction rates under certain flow and flame conditions. When applied to three EGR rate conditions toward the dilution limit, the hybrid modeling approach accurately reproduced experimental data in terms of cylinder pressure, apparent heat release rate, and the observed positive correlation, including the delayed onset of main chamber combustion—a feature not captured by existing combustion models.

computational fluid dynamics simulation↗
DOE OSTI2020

Measuring the effectiveness of high-performance Co-Optima biofuels on suppressing soot formation at high temperature

Soot emissions in combustion are unwanted consequences of burning hydrocarbon fuels. The presence of soot during and following combustion processes is an indication of incomplete combustion and has several negative consequences including the emission of harmful particulates and increased operational costs. Efforts have been made to reduce soot production in combustion engines through utilizing oxygenated biofuels in lieu of traditional nonoxygenated feedstocks. The ongoing Co-Optimization of Fuels and Engines (Co-Optima) initiative from the US Department of Energy (DOE) is focused on accelerating the introduction of affordable, scalable, and sustainable biofuels and high-efficiency, low-emission vehicle engines. The Co-Optima program has identified a handful of biofuel compounds from a list of thousands of potential candidates. In this study, a shock tube was used to evaluate the performance of soot reduction of five high-performance biofuels downselected by the Co-Optima program. Current experiments were performed at test conditions between 1,700 and 2,100 K and 4 and 4.7 atm using shock tube and ultrafast, time-resolve laser absorption diagnostic techniques. The combination of shock heating and nonintrusive laser detection provides a state-of-the-art test platform for high-temperature soot formation under engine conditions. Soot reduction was found in ethanol, cyclopentanone, and methyl acetate; conversely, an α-diisobutylene and methyl furan produced more soot compared to the baseline over longer test times. For each biofuel, several reaction pathways that lead towards soot production were identified. The data collected in these experiments are valuable information for the future of renewable biofuel development and their applicability in engines.

09 BIOMASS FUELS↗
DOE OSTI2020

Joint Genome Institute Analysis Workflow Service (JAWS) v2.7

The U.S. Department of Energy Joint Genome Institute (JGI) has developed the JGI Analysis Workflow Service (JAWS) as a distributed framework to run computational workflows across diverse high-performance computing (HPC) and cloud environments. JAWS enhances the reusability, scalability, and robustness of scientific workflows by orchestrating data movement, code execution, and results retrieval across multiple DOE facilities. At its core, JAWS integrates the Cromwell workflow engine to run workflows expressed in the Workflow Description Language (WDL), ensuring portability and interoperability. To provide consistent runtime environments, JAWS employs container technologies such as Shifter, Apptainer, and Docker. Workflow tasks are managed via HTCondor on HPC backends, while Globus ensures secure and efficient data transfer between sites. JAWS is deployed as a multi-site workflow manager across national laboratory computing facilities, with dedicated instances supporting community projects such as the National Microbiome Data Collaborative (NMDC) and KBase. This distributed, service-oriented architecture enables users to "write once, run anywhere," providing scalable, production-quality workflow execution.

Kirton, Edward↗
DOE OSTI2020

2D Dam-Break Analysis of L Lake and PAR Pond Dams Using HEC-RAS

In 1991 a dam-break study was conducted for the high hazard dams located at L Lake and PAR Pond on the Savannah River Site. Two scenarios were considered, over topping from a Probable Maximum Flood (PMF), and a fair weather dam-break for either or both dams. Unfortunately, no inundation map was developed from the study. The purpose of this project was to redo the original dam-break study with improved data and methodology to generate Inundation maps to assist with emergency response and evacuation plans. The Hydrologic Engineering Center's River Analysis System (HEC-RAS) is a free to download river analysis modeling program developed by the US Army Corps of Engineers capable of 1D and 2D hydraulic calculations. Version 5.0.7 (released March 2019) was used for this project. Digital elevation models for the area were retrieved from the US Geological Survey database and converted to a .hdf file within the program. Then the 2D flood area was identified from the contours. Both L Lake and PAR Pond were inputted as 1D storage areas because DEM data does not contain elevation values under water bodies. An elevation vs volume curve was available for both storage areas. Initial elevations were set for both scenarios. Both dams are earthen dams. The Steel Creek dam at L Lake has 6 ft diameter conduit with an upper and lower sluice gate. PAR pond dam consist of a weir and sluice gate connected to an 8 x 8 ft channel. Both outlets were modeled with a pool elevation vs discharge curve. The steel creek dam sluice gates were assumed to be fully open in all cases. As in the previous study, the dams were set to breach when they were overtopped by 1.5 ft during PMF conditions (Figure 1). A fair weather breach was set to be due to a piping failure (Figure 1). In the dual dam break during fair weather conditions the PAR pond dam fails 3 hours after Steel Creek to achieve maximum flooding in the down stream reaches. Simulation was run 3 days for each case and with a 1 minute computational interval. Maximum flooding occurs under PMF conditions with the failure of both dams. PAR pond dam fails first 16 hours and 32 minutes after the start of the simulation with the Steel creek dam failing 6 minutes later. In all cases, the bridges and roads spanning Steel Creek and Lower Three Runs will be inundated and potentially washed away. The Burtons Ferry Highway south of the storage areas will be partially flooded during PMF failure, dual fair weather failure, and PAR pond failure under fair weather conditions.

54 ENVIRONMENTAL SCIENCES↗