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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Highly efficient libraries design for saturation mutagenesis

Abstract Saturation mutagenesis is a semi-rational approach for protein engineering where sites are saturated either entirely or partially to include amino acids of interest. We previously reported on a codon compression algorithm, where a set of minimal degenerate codons are selected according to user-defined parameters such as the target organism, type of saturation and usage levels. Here, we communicate an addition to our web tool that considers the distance between the wild-type codon and the library, depending on its purpose. These forms of restricted collections further reduce library size, lowering downstream screening efforts or, in turn, allowing more comprehensive saturation of multiple sites. The library design tool can be accessed via http://www.dynamcc.com/dynamcc_d/. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Combinatorial library design for improving isobutanol production in Saccharomyces cerevisiae

Saccharomyces cerevisiae is the dominant fermentative producer of ethanol in industry and a preferred host for production of other biofuels. That said, rewiring the metabolism of S. cerevisiae to produce other fermentation products, such as isobutanol, remains an academic challenge. Many studies report aerobic production of isobutanol, but ethanol remains a substantial by-product under these conditions due to the Crabtree effect. These studies indicate that the native isobutanol pathway is incapable of carrying sufficient flux to displace ethanol. In this report, we screened a combinatorial library of pathway enzymes to identify an isobutanol pathway cassette capable of supporting the growth of a non-ethanol producing S. cerevisiae . We began by identifying a diverse set of isobutanol pathway enzyme homologs and combined each open reading frame with varied-strength promoters in a combinatorial, pooled fashion. We applied a growth-coupled screen where a functional isobutanol pathway restored NAD + regeneration during glucose catabolism that is otherwise repressed via the Crabtree effect. Using this screen, we isolated a cassette consisting of a mosaic of bacterial and cytosol-localized fungal enzymes that conferred under aerobic conditions the ability to produce 364 mg/L isobutanol (8.8% of the theoretical maximum yield). We next shifted the cofactor usage of the isolated ketol-acid reductoisomerase enzyme in the cassette from NADPH to NADH-preferring to improve redox balance. The approach used herein isolated isobutanol producing strains that approach the best in the literature without producing substantial ethanol titers. Still, the best isolated cassette was insufficient to support anaerobic growth in the absence of ethanol fermentation - indicating the presence of further fundamental gaps in our understanding of yeast fermentation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ginkgo - A math library designed to accelerate Exascale Computing Project science applications

Large-scale simulations require efficient computation across the entire computing hierarchy. A challenge of the Exascale Computing Project (ECP) was to reconcile highly heterogeneous hardware with the myriad of applications that were required to run on these supercomputers. Mathematical software forms the backbone of almost all scientific applications, providing efficient abstractions and operations that are crucial to harness the performance of computing systems. Ginkgo is one such mathematical software library, nurtured by ECP, providing high-performance, user-friendly, and performance portable interfaces for applications in ECP and beyond. In this paper, we elaborate on Ginkgo’s philosophy of high-performance software that is sustainable, reproducible, and easy to use. We showcase the wide feature set of solvers and preconditioners available in Ginkgo and the central concepts involved in their design. We elaborate on four different ECP software integrations: MFEM, PeleLM + SUNDIALS, XGC, and ExaSGD that use Ginkgo to accelerate their science runs. Performance studies of different problems from these applications highlight the effectiveness of Ginkgo and the benefits incurred by these ECP applications.

Cojean, Terry↗
NASA NTRS1990

Discrete event simulation tool for analysis of qualitative models of continuous processing systems

An artificial intelligence design and qualitative modeling tool is disclosed for creating computer models and simulating continuous activities, functions, and/or behavior using developed discrete event techniques. Conveniently, the tool is organized in four modules: library design module, model construction module, simulation module, and experimentation and analysis. The library design module supports the building of library knowledge including component classes and elements pertinent to a particular domain of continuous activities, functions, and behavior being modeled. The continuous behavior is defined discretely with respect to invocation statements, effect statements, and time delays. The functionality of the components is defined in terms of variable cluster instances, independent processes, and modes, further defined in terms of mode transition processes and mode dependent processes. Model construction utilizes the hierarchy of libraries and connects them with appropriate relations. The simulation executes a specialized initialization routine and executes events in a manner that includes selective inherency of characteristics through a time and event schema until the event queue in the simulator is emptied. The experimentation and analysis module supports analysis through the generation of appropriate log files and graphics developments and includes the ability of log file comparisons.

Malin, Jane T.↗
DOE OSTI2025

ORNL Design Engineering Library: Validated Thermoelectric Digital Twins

Radioisotope thermoelectric generators (RTGs) serve a crucial role in supplying thermal and electrical energy for reliable and long-duration power in remote and extreme environments. The thermal energy is provided by the decay of radioisotopes and is converted into electrical energy using the steady-state thermoelectric process by exploiting the Seebeck effect. Maintaining a thermal gradient through the material is necessary to drive current production. Modern predictive multi-physics tools are able to effectively describe the complex and strongly coupled phenomena needed for accurate model-based system engineering efforts needed to develop higher performing RTGs. Experimental validation of model simulations is essential to confirm the accuracy, reliability, and applicability of predictive multiphysics tools. Validation fosters confidence among users, helps meet regulatory requirements, and contributes to the ongoing improvement of simulation techniques, ultimately leading to better, safer, and more efficient designs and processes. Validated models can then be used as digital twins and can be interrogated to understand and quantify the performance gaps between theoretical and physical systems. These insights can be used to build higher performing systems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
NASA NTRS1978

Design principles of the PORT library

The design of PORT stemmed from the basic principles of portability and ease of use. The attributes and mechanisms used in the library to support this philosophy include the use of a portable subset of FORTRAN, and the use of (machine-dependent) functions to supply the necessary environment parameters. Abbreviated calling sequences are mede possible by a simplified error-handling technique, and by the use of a portable stack allocator for temporary workspace. Experiences to date with these approaches, and plans for the future are reviewed.

Fox, P.↗
DOE OSTI2026

Empirical evaluation of all unique Cas9 protospacers in E. coli reveal widespread functionality and rules for gRNA design

The Cas9 nuclease has become central to modern methods and technologies in synthetic biology, largely due to the ease with which it can be targeted to specific DNA loci via guide RNAs (gRNAs). Reports vary widely on the actual specificity of this targeting, with some studies observing 60% of gRNAs possessing no activity against the genome, yet an assumption persists within the E. coli community that inactive gRNAs are rare. To resolve these contradictions, we evaluated the activity of 463 000 unique gRNAs in the E. coli K12 MG1655 genome. We show that the overwhelming majority (at least 93%) of unique gRNAs are functional while only 0.3% are nonfunctional. These nonfunctional gRNAs exhibit strong spacer self-interaction, which can either be excluded using a simple design rule or “repaired” during library design. Finally, this work provides the greater microbial synthetic biology community both a set of nearly half a million empirically evaluated E. coli gRNAs as well as a thoroughly evaluated experimental procedure, complete with appropriate controls for Cas9 activity, for conducting Cas9 assays in E. coli specifically and bacteria more generally. Lastly, we have produced a webapp to allow users to easily browse and extract gRNA sequences from the E. coli genome, which can be accessed at https://grna.ornl.gov.

Kammerdiener, Elise K. [Oak Ridge National Laborat↗
DOE OSTI2023

DeCOIL: Optimization of Degenerate Codon Libraries for Machine Learning-Assisted Protein Engineering

With advances in machine learning (ML)-assisted protein engineering, models based on data, biophysics, and natural evolution are being used to propose informed libraries of protein variants to explore. Synthesizing these libraries for experimental screens is a major bottleneck, as the cost of obtaining large numbers of exact gene sequences is often prohibitive. Degenerate codon (DC) libraries are a cost-effective alternative for generating combinatorial mutagenesis libraries where mutations are targeted to a handful of amino acid sites. However, existing computational methods to optimize DC libraries to include desired protein variants are not well suited to design libraries for ML-assisted protein engineering. To address these drawbacks, we present DEgenerate Codon Optimization for Informed Libraries (DeCOIL), a generalized method which directly optimizes DC libraries to be useful for protein engineering: to sample protein variants that are likely to have both high fitness and high diversity in the sequence search space. Using computational simulations and wet-lab experiments, we demonstrate that DeCOIL is effective across two specific case studies, with potential to be applied to many other use cases. DeCOIL offers several advantages over existing methods, as it is direct, easy-to-use, generalizable, and scalable. With accompanying software, DeCOIL can be readily implemented to generate desired informed libraries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

ORNL/grit

Grit is a software library designed specifically for conducting particle-based Lagrangian simulations with CPU/GPUperformance portability. This library allows researchers and engineers to perform a wide range of simulations, including multiphase flow, and more. Grit employs Message Passing Interface (MPI) for distributed memory parallelism and Kokkos programming model for on-node shared memory parallelism with performance portability across different architectures of GPUs and multi-core/manycore CPUs.

Ge, Wenjun [Oak Ridge National Laboratory (ORNL), ↗
NASA NTRS2003

A NASA Perspective and Validation and Testing of Design Hardening for the Natural Space Radiation Environment (GOMAC Tech 03)

With the dearth of dedicated radiation hardened foundries, new and novel techniques are being developed for hardening designs using non-dedicated foundry services. In this paper, we will discuss the implications of validating these methods for the natural space radiation environment issues: total ionizing dose (TID) and single event effects (SEE). Topics of discussion include: Types of tests that are required, Design coverage (i.e., design libraries: do they need validating for each application?) A new task within NASA to compare existing design. This latter task is a new effort in FY03 utilizing a 8051 microcontroller core from multiple design hardening developers as a test vehicle to evaluate each mitigative technique.

Day, John H.↗
DOE OSTI2021

Sorting for secreted molecule production using a biosensor-in-microdroplet approach

Significance The design–build–test cycle of metabolic engineering is swiftly becoming test limited owing to advances in DNA synthesis and library design. At the same time, improving extracellular production requires high-throughput studies to detect extracellular (not intracellular) content. Traditional approaches that utilize chromatography-based analysis or plate-based fluorescence assays are relatively throughput limited and require a high degree of liquid handling. These limitations are avoided here by creating a generalizable approach for small molecule production screening. Namely, this paradigm combines “off-the-shelf” biosensors with large library screening from producing cells in a cell-type agnostic manner.

Bowman, Emily K.↗
DOE OSTI2022

GASNet-EX RMA Communication Performance on Recent Supercomputing Systems

Partitioned Global Address Space (PGAS) programming models, typified by systems such as Unified Parallel C (UPC) and Fortran coarrays, expose one-sided Remote Memory Access (RMA) communication as a key building block for High Performance Computing (HPC) applications. Architectural trends in supercomputing make such programming models increasingly attractive, and newer, more sophisticated models such as UPC++, Legion and Chapel that rely upon similar communication paradigms are gaining popularity. GASNet-EX is a portable, open-source, high-performance communication library designed to efficiently support the networking requirements of PGAS runtime systems and other alternative models in emerging exascale machines. The library is an evolution of the popular GASNet communication system, building upon 20 years of lessons learned. We present microbenchmark results which demonstrate the RMA performance of GASNet-EX is competitive with MPI implementations on four recent, high-impact, production HPC systems. These results are an update relative to previously published results on older systems. The networks measured here are representative of hardware currently used in six of the top ten fastest supercomputers in the world, and all of the exascale systems on the U.S. DOE road map.

Hargrove, Paul H↗
NASA NTRS1994

MODIS Technical Report Series. Volume 4: MODIS data access user's guide: Scan cube format

The software described in this document provides I/O functions to be used with Moderate Resolution Spectroradiometer (MODIS) level 1 and 2 data, and could be easily extended to other data sources. This data is in a scan cube data format: a 3-dimensional ragged array containing multiple bands which have resolutions ranging from 250 to 1000 meters. The complexity of the data structure is handled internally by the library. The I/O calls allow the user to access any pixel in any band through 'C' structure syntax. The high MODIS data volume (approaching half a terabyte per day) has been a driving factor in the library design. To avoid recopying data for user access, all I/O is performed through dynamic 'C' pointer manipulation. This manual contains background material on MODIS, several coding examples of library usage, in-depth discussions of each function, reference 'man' type pages, and several appendices with details of the included files used to customize a user's data product for use with the library.

Kalb, Virginia L.↗
DOE OSTI2022

GridDS: Data Science Toolkit for Energy Grid Data

According to the U.S. Energy Information Administration (EIA), the demand for energy is expected to increase 50% by the year 20501. While energy standards, such as the Institute of Electrical and Electronics Engineers (IEEE) Standard 1547, (Basso 2015) and monitoring with wide area management systems (WAMS) (Liu 2017, Zhou 2016) have enabled large scale data collection and storage, the application of this data in mitigating costs associated with increased consumer demand is an ongoing focus for energy research. This ubiquitous data collection presents a promising opportunity for machine learning and data science to improve efficiency of distributed energy resources (DERs). The GridDS software toolkit is designed to leverage advanced metering infrastructure (AMI), outage management systems data (OMS), Supervisory control Data Acquisition (SCADA), and geographic information systems (GIS) to forecast future energy demands and detect incipient grid failures. GridDS is a python software library designed to be modular and generalizable to data recorded by DERs. In adapting to disparate datasets recorded by various WAMS, GridDS provides a range of unique functionality not presently implemented in current WAMS which have highly specific software infrastructure by design. GridDS functionality ranges from data specification and preparation, to training and validation for state of the art machine learning, to interactive data visualization. For data intake, GridDS combines: Pandera: a library for creating data specifications. TimeScaleDB: a postgresSQL database infrastructure for efficient storage of timeseries data. Dataset class: A custom dataset class / interface that ensures modularity between a range of synthetic and live recorded datasets. Is

Ladd, Alexander↗
DOE OSTI2021

NEAMS TH CRAB

The MOOSE framework is a library designed to make it straightforward for physicists and engineers to model partial differential equations using finite element and finite volume methods. Finite elements have been a part of the framework library since MOOSE's inception over a decade ago. Initial finite volume capability, however, was added only as recently as May of 2020. Since that time, significant work has been conducted to develop fluid modeling capability based on the finite volume method. Much of this work has taken place in MOOSE's navier_stokes module and in the NEAMS program's coarse mesh CFD code Pronghorn. We report here on development in MOOSE and Pronghorn of incompressible, porous incompressible, and weakly compressible finite volume simulation capabilities and their application to modeling of MSR and FHR advanced reactor concepts.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗