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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 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Thermophilic site-specific recombination system for rapid insertion of heterologous DNA into the Clostridium thermocellum chromosome

Clostridium thermocellum is an anaerobic thermophile capable of producing ethanol and other commodity chemicals from lignocellulosic biomass. The insertion of heterologous DNA into the C. thermocellum chromosome is currently achieved via a time-consuming homologous recombination process, where a single stable insertion can take 2–4 weeks or more to construct. In this work, we developed a thermostable version of the Serine recombinase Assisted Genome Engineering (tSAGE) approach for gene insertion in C. thermocellum utilizing a site-specific recombinase from Geobacillus sp. Y412MC61, enabling quick and easy insertion of DNA into the chromosome for accelerated genetic tool screening and heterologous gene expression. Using tSAGE, chromosomal insertion of plasmid DNA occurred at a maximum transformation efficiency of 5 × 10 3 CFU/µg, which is comparable to the transformation efficiency of a replicating control plasmid in C. thermocellum. Using tSAGE, we chromosomally integrated and characterized 17 reporter genes, 15 homologous and 31 heterologous constitutive promoters of varying strengths, 4 inducible promoters, and 5 riboswitches in C. thermocellum. We also determined that a 6–7 nucleotide gap between the ribosome binding site (RBS) and the start codon is optimal for high expression by employing a library of superfolder green fluorescent protein expression constructs driven by our strongest tested promoter (P clo1313_1194 ) with different distances between the RBS and start codon. The tools developed here will aid in accelerating C. thermocellum strain engineering for producing sustainable fuels and chemicals directly from plant biomass.

Biofuels↗
DOE OSTI2019

Undervalued potential of crassulacean acid metabolism for current and future agricultural production

The potential for crassulacean acid metabolism (CAM) to support resilient crops that meet demands for food, fiber, fuel, and pharmaceutical products far exceeds current production levels. This review provides background on five families of plants that express CAM, including examples of many species within these families that have potential agricultural uses. We summarize traditional uses, current developments, management practices, environmental tolerance ranges, and economic values of CAM species with potential commercial applications. The primary benefit of CAM in agriculture is high water use efficiency that allows for reliable crop yields even in drought conditions. Agave species, for example, grow in arid conditions and have been exploited for agricultural products in North and South America for centuries. Yet, there has been very little investment in agricultural improvement for most useful Agave varieties. Other CAM species that are already traded globally include Ananas comosus (pineapple), Aloe spp., Vanilla spp., and Opuntia spp., but there are far more with agronomic uses that are less well known and not yet developed commercially. Recent advances in technology and genomic resources provide tools to understand and realize the tremendous potential for using CAM crops to produce climate-resilient agricultural commodities in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Bacterial Glutathione S‐Transferases (GSTs) Involved in Breaking the β‐Aryl Ether Bond of Lignin Reveal Novel Catalytic Abilities and Reaction Mechanisms within the GST Superfamily

The glutathione S‐transferase (GST) protein superfamily contains thousands of known or predicted members, all of which contain an N‐terminal thioredoxin domain that binds a glutathione (GSH) molecule and activates it for catalysis. GSTs are important in many organisms for conjugating GSH to toxic molecules, making them more soluble and easier to excrete from cells. However, GSTs are also capable of catalyzing a wide and continually expanding range of other reactions using GSH as cofactor. Sphingomonad bacteria are capable of metabolizing low molecular weight oligomers and monomers derived from lignin, a heterogeneous polymer of aromatic subunits that is a major component of plant biomass. These bacteria and their enzymes have potential applications in converting naturally abundant lignin into valuable commodities. Sphingomonads use GSTs (called β‐etherases and GSH lyases) to catalyze two consecutive steps in their pathway for breaking the β‐aryl ether bond commonly found between aromatic subunits in the lignin polymer: β‐etherases stereospecifically break the β‐aryl ether bond by replacing it with a thioether bond involving GSH, and GSH lyases remove the GSH moiety from the resulting β‐thioether GSH conjugate. We have identified a heterodimeric β‐etherase (called BaeAB) that provides insight into the diversity of GSTs capable of acting as β‐etherases and into the evolution of the GST ability to break the β‐aryl ether bond. In addition, BaeAB has properties that are unique amongst characterized GSTs in general, including the majority of its catalytic activity apparently residing in only one of its subunits, and using an active site asparagine for catalysis (whereas most characterized GSTs use an amino acid residue with a side chain hydroxyl for catalysis). We have also identified a GSH lyase (called NaGST Nu ), which has close homologues in many different organisms, though the physiological roles of these homologues are largely unknown in other organisms besides sphingomonads. We found that the two homologues from Escherichia coli were able to catalyze the GSH lyase reaction in the pathway for breaking the β‐aryl ether bond, despite the fact that E. coli is not known to be able to metabolize lignin‐derived oligomers. This suggests that GSH lyase activity may be a common feature of these homologues (and that they likely act on GSH‐conjugated compounds naturally found within their respective organisms). In addition, the reaction mechanism of NaGST Nu involves binding two GSH molecules (whereas most characterized GSTs can only bind one GSH), as well as amino acid residues located in a channel leading from the active site to the protein exterior. Altogether, besides helping to identify novel GSTs that could potentially be used to generate value from lignin, our work is helping to uncover unique features of the large and widely studied, but relatively uncharacterized, GST superfamily. Support or Funding Information This work was supported by U.S. Department of Energy (DOE) Great Lakes Bioenergy Research Center grants (DOE Office of Science BER DE‐FC02‐07ER64494 and DE‐SC0018409). This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Kontur, Wayne S.↗
DOE OSTI2018

Synergistic effect of acidity and extraframework position in faujasite on renewable $p$-xylene production

p-Xylene is a commodity chemical used for the manufacture of plastic bottles and textiles. For the biomass-based route from 2,5-dimethylfuran (DMF) and ethylene, the properties of the catalyst such as acidity effect, product selectivity and catalyst activity play an important role. To determine the effect of acidity and extraframework position in faujasite zeolite on p-xylene selectivity, type Y (Si/Al = 40 and Si/Al = 2.55) and X (Si/Al = 1.25) zeolites containing the extraframework Lewis acids Na+, K+, Li+, Ag+ and Cu+, and a Brønsted acid-containing zeolite, HY (Si/Al = 40), were prepared and tested for p-xylene production under solvent-free conditions and at low conversions (less than 35%). Here it is reported that NaX zeolite catalyses DMF and ethylene conversion to p-xylene with 91% selectivity at 30% conversion, which is better than the 25% p-xylene selectivity obtained when using HY at similar conversion. ANOVA was used to show that there is a synergistic effect between acidity and extraframework position on the rate of p-xylene production. At 7% DMF conversion, Lewis acids were more selective than the Brønsted acid tested (50 versus 30% p-xylene selectivity). p-Xylene selectivity is optimal when using Lewis acids with moderate acidity and extraframework positions located in the faujasite supercage (sites II and III).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Reformulation of the No-Free-Lunch Theorem for Entangled Datasets

The No-Free-Lunch (NFL) theorem is a celebrated result in learning theory that limits one’s ability to learn a function with a training data set. With the recent rise of quantum machine learning, it is natural to ask whether there is a quantum analog of the NFL theorem, which would restrict a quantum computer’s ability to learn a unitary process with quantum training data. However, in the quantum setting, the training data can possess entanglement, a strong correlation with no classical analog. In this work, we show that entangled data sets lead to an apparent violation of the (classical) NFL theorem. This motivates a reformulation that accounts for the degree of entanglement in the training set. As our main result, we prove a quantum NFL theorem whereby the fundamental limit on the learnability of a unitary is reduced by entanglement. We employ Rigetti's quantum computer to test both the classical and quantum NFL theorems. In conclusion, our work establishes that entanglement is a commodity in quantum machine learning.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

MUCILAGE-RELATED10 Produces Galactoglucomannan That Maintains Pectin and Cellulose Architecture in Arabidopsis Seed Mucilage

Plants invest a lot of their resources into the production of an extracellular matrix built of polysaccharides. While the composition of the cell wall is relatively well characterized, the functions of the individual polymers and the enzymes that catalyze their biosynthesis remain poorly understood. We exploited the Arabidopsis ( Arabidopsis thaliana ) seed coat epidermis (SCE) to study cell wall synthesis. SCE cells produce mucilage, a specialized secondary wall that is rich in pectin, at a precise stage of development. A coexpression search for MUCILAGE-RELATED (MUCI) genes identified MUCI10 as a key determinant of mucilage properties. MUCI10 is closely related to a fenugreek ( Trigonella foenumgraecum ) enzyme that has in vitro galactomannan α-1,6-galactosyltransferase activity. Our detailed analysis of the muci10 mutants demonstrates that mucilage contains highly branched galactoglucomannan (GGM) rather than unbranched glucomannan. Muci10 likely decorates glucomannan, synthesized by CELLULOSE SYNTHASE-LIKE A2, with galactose residues in vivo. The degree of galactosylation is essential for the synthesis of the GGM backbone, the structure of cellulose, mucilage density, as well as the adherence of pectin. We propose that GGM scaffolds control mucilage architecture along with cellulosic rays and show that Arabidopsis SCE cells represent an excellent model in which to study the synthesis and function of GGM. Arabidopsis natural varieties with defects similar to muci10 mutants may reveal additional genes involved in GGM synthesis. Since GGM is the most abundant hemicellulose in the secondary walls of gymnosperms, understanding its biosynthesis may facilitate improvements in the production of valuable commodities from softwoods.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2011

Distributed structure determination at the JCSG

The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures. The Joint Center for Structural Genomics (JCSG), one of four large-scale structure-determination centers funded by the US Protein Structure Initiative (PSI) through the National Institute for General Medical Sciences, has been operating an automated distributed structure-solution pipeline, Xsolve, for well over half a decade. During PSI-2, Xsolve solved, traced and partially refined 90% of the JCSG’s nearly 770 MAD/SAD structures at an average resolution of about 2 Å without human intervention. Xsolve executes many well established publicly available crystallography software programs in parallel on a commodity Linux cluster, resulting in multiple traces for any given target. Additional software programs have been developed and integrated into Xsolve to further minimize human effort in structure refinement. ConsensusModeler exploits complementarities in traces from Xsolve to compute a single optimal model for manual refinement. Xpleo is a powerful robotics-inspired algorithm to build missing fragments and qFit automatically identifies and fits alternate conformations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Real-time streaming tomographic reconstruction with on-demand data capturing and 3D zooming to regions of interest

Complex dynamic tomographic experiments at brilliant X-ray light sources require real-time feedback on the sample changes with respect to environmental conditions, selecting representative regions of interest for high-resolution scanning, and on-demand data saving mechanisms for storing only relevant projections acquired by fast area detectors and reducing data volumes. Here the implementation details of a 3D real-time imaging monitoring instrument, with zooming to a volume of interest with easy-to-use visualization via ImageJ , a tool familiar to most beamline users, is presented. The instrument relies on optimized data flow between the detector and processing machines and is implemented on commodity computers. The instrument has been developed at beamline 2-BM of the Advanced Photon Source, where the automatic lens changing mechanism for zooming is implemented with an Optique Peter microscope. Performance tests demonstrate the ability to process more than 3 GB of projection data per second and generate real-time 3D zooming with different magnification. These new capabilities are essential for new APS Upgrade instruments such as the projection microscope under development at beamline 32-ID. The efficacy of the proposed instrument was demonstrated during an in situ tomographic experiment on ice and gas hydrate formation in porous samples.

3D zooming↗
DOE OSTI2025

Optimal Economic Dispatch and Load-Following Strategies for Nuclear Integrated Energy Systems

The need for distributed and adaptable energy resources that can handle the growing unpredictability in both supply and demand is rising as the power system continues to modernize. In order to satisfy those needs and maintain grid resilience, nuclear power plants can dynamically control their output, despite typically being used as baseload generators. By incorporating energy storage and renewable energy sources, nuclear integrated energy systems are designed to satisfy the electrical and thermal demands of different end-user applications while ensuring flexible power operation. These systems generate revenue by participating in both wholesale and ancillary services electricity markets, as well as commodity markets for various byproducts generated from coupled industrial processes. This study addresses the economic dispatch efficiency of a tightly coupled nuclear integrated energy system comprising a gigawatt-scale light water reactor, commercialized in the U.S., a high-temperature steam electrolysis unit, a district heating network, and specified electrical loads. To demonstrate the nuclear power plant’s flexibility within the day-ahead unit commitment and economic dispatch framework, while maintaining equilibrium even during periods of refueling outages, this paper develops a mixed-integer linear programming framework that models the subsystems and components of its nuclear steam supply system. A systematic comparative analysis of flexible versus baseload nuclear power plant operation under varying levels of renewable energy integration indicates that flexible operation enhances system profitability by more than 18% while also increasing energy storage utilization, improving reactor responsiveness to load fluctuations, and allowing for greater participation across numerous electricity markets.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

A Versatile Simulated Data Transport Layer for in Situ Workflows Performance Evaluation

In situ processing does not only allow scientific applications to face the explosion in data volume and velocity but also to address the time constraints of many simulation-analysis workflows by providing scientists with early insights about their applications at runtime. Multiple frameworks implement the concept of a data transport layer (DTL) to enable such in situ workflows. These tools are very versatile, directly or indirectly access the data generated on the same node, another node of the same compute cluster, or a completely distinct node, and allow data publishers and subscribers to run on the same computing resources or not. This versatility puts on researchers the onus of taking key decisions related to resource allocation and how to transport data to ensure the most efficient execution of their in situ workflows. However, domain scientists and workflow practitioners lack the appropriate tools to assess the respective performance of particular design and deployment options. In this paper we introduce a versatile simulated DTL designed to provide researchers with insights on the respective performance of different execution scenarios of in situ workflows. This open-source, standalone library builds on the SimGrid toolkit and can be linked to any SimGrid-based simulator. It facilitates the evaluation of the performance behavior, at scale, of different data transport configurations and the study of the effects of resource allocation strategies. We demonstrate the scalability, versatility, and accuracy of this simulated DTL by reproducing the execution of two synthetic benchmarks and of a real-world in situ workflow composed of an MPI application and a parallel data analysis. Results of simulations run on a single core show that the proposed library can simulate the interactions of tens of thousands of simulated processes deployed on two interconnected commodity clusters in a few seconds, and the execution by a thousand simulated processes of an in situ workflow in less than three minutes.

Suter, Fred [ORNL] (ORCID:0000000319021955)↗
DOE OSTI2022

Real-time Implementation of Grid Code Compliant Grid Edge Energy Management System

Integrated distributed energy resources (DER) in a distribution system need to follow grid codes to avoid violations that result in DER/circuit segment disconnection. To comply with grid code requirements at the grid edge level, network constrained grid edge energy management system (EMS) can be deployed. The objective of grid edge EMS is to provide economic solution for active and reactive power DER setpoints at each dispatch interval and ensure voltage regulation to support secure interconnection of the grid edge segment to the distribution system with multiple inverter based DER units. In this work, real-time simulation of grid code compliant grid edge EMS is deployed in a realistic feeder circuit segment. For real-time simulation, communication between the grid edge EMS and DERs is done exploiting IEC 61850-7-420. It enables interoperability among different DERs and grid edge EMS. No prior art has deployed IEC 61850-7-420 GOOSE communication protocol for grid edge EMS. Conversion of IEC 61850 GOOSE messages to Modbus communication protocol is also performed to communicate with grid edge EMS in commodity-off the shelf embedded boards in this work. The real-time simulation in OPAL-RT real-time digital simulator shows the out-performance of grid edge EMS by reducing the voltage violation in the distribution circuit.

Energy management system↗
DOE OSTI2014

Thread Group Multithreading: Accelerating the Computation of an Agent-Based Power System Modeling and Simulation Tool -- C GridLAB-D

GridLAB-DTM is an open source next generation agent-based smart-grid simulator that provides unprecedented capability to model the performance of smart grid technologies. Over the past few years, GridLAB-D has been used to conduct important analyses of smart grid concepts, but it is still quite limited by its computational performance. In order to break through the performance bottleneck to meet the need for large scale power grid simulations, we develop a thread group mechanism to implement highly granular multithreaded computation in GridLAB-D. We achieve close to linear speedups on multithreading version compared against the single-thread version of the same code running on general purpose multi-core commodity for a benchmark simple house model. The performance of the multithreading code shows favorable scalability properties and resource utilization, and much shorter execution time for large-scale power grid simulations.

Jin, Shuangshuang↗
DOE OSTI2022

Model-Based Reconstruction for Collimated Beam Ultrasound Systems

Collimated beam ultrasound systems are a novel technology for imaging inside multi-layered structures such as geothermal wells. Such systems include a transmitter and multiple receivers to capture reflected signals. Common algorithms for ultrasound reconstruction use delay-and-sum (DAS) approaches; these have low computational complexity but produce inaccurate images in the presence of complex structures and specialized geometries such as collimated beams.In this paper, we propose a multi-layer, ultrasonic, model-based iterative reconstruction algorithm designed for collimated beam systems. We introduce a physics-based forward model to accurately ac-count for the propagation of a collimated ultrasonic beam in multi-layer media and describe an efficient implementation using binary search. We model direct arrival signals, detector noise, and a spatially varying image prior, then cast the reconstruction as a maximum a posteriori estimation problem. Using simulated and experimental data we obtain significantly fewer artifacts relative to DAS while running in near real time using commodity compute resources.

Alanazi, Abdulrahman M.↗
DOE OSTI2011

GMH: A Message Passing Toolkit for GPU Clusters

Driven by the market demand for high-definition 3D graphics, commodity graphics processing units (GPUs) have evolved into highly parallel, multi-threaded, many-core processors, which are ideal for data parallel computing. Many applications have been ported to run on a single GPU with tremendous speedups using general C-style programming languages such as CUDA. However, large applications require multiple GPUs and demand explicit message passing. This paper presents a message passing toolkit, called GMH (GPU Message Handler), on NVIDIA GPUs. This toolkit utilizes a data-parallel thread group as a way to map multiple GPUs on a single host to an MPI rank, and introduces a notion of virtual GPUs as a way to bind a thread to a GPU automatically. This toolkit provides high performance MPI style point-to-point and collective communication, but more importantly, facilitates event-driven APIs to allow an application to be managed and executed by the toolkit at runtime.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2013

Comparing the Performance of Blue Gene/Q with Leading Cray XE6 and InfiniBand Systems

Abstract—Three types of systems dominate the current High Performance Computing landscape: the Cray XE6, the IBM Blue Gene, and commodity clusters using InfiniBand. These systems have quite different characteristics making the choice for a particular deployment difficult. The XE6 uses Cray’s proprietary Gemini 3-D torus interconnect with two nodes at each network endpoint. The latest IBM Blue Gene/Q uses a single socket integrating processor and communication in a 5-D torus network. InfiniBand provides the flexibility of using nodes from many vendors connected in many possible topologies. The performance characteristics of each vary vastly along with their utilization model. In this work we compare the performance of these three systems using a combination of micro-benchmarks and a set of production applications. In particular we discuss the causes of variability in performance across the systems and also quantify where performance is lost using a combination of measurements and models. Our results show that significant performance can be lost in normal production operation of the Cray XT6 and InfiniBand Clusters in comparison to Blue Gene/Q.

-High Performance Computing, Performance Evaluatio↗
DOE OSTI2012

Multithreaded Algorithms for Maximum Matching in Bipartite Graphs

Abstract—We design, implement, and evaluate algorithms for computing a matching of maximum cardinality in a bipartite graph on multi-core and massively multithreaded computers. As computers with larger number of slower cores dominate the commodity processor market, the design of multithreaded algorithms to solve large matching problems becomes a necessity. Recent work on serial algorithms based on searching for augmenting paths for this problem have shown that their performance is sensitive to the order in which the vertices are processed for matching. In a multithreaded environment, imposing a serial order in which vertices are considered for matching would lead to loss of concurrency and performance. But this raises the question: Would parallel matching algorithms on multithreaded machines improve performance over a serial algorithm? We answer this question in the affirmative. We report efficient multithreaded implementations of two key algorithms (Hopcroft- Karp based on breadth-first-search, and Pothen-Fan based on depth-first-search) and their variants, combined with the Karp- Sipser initialization algorithm. We report extensive results and insights using three shared-memory platforms (a 48-core AMD Opteron, a 32-core Intel Nehalem, and a 128-processor Cray XMT) on a representative set of real-world and synthetic graphs. To the best of our knowledge, this is the first extensive study of augmentation-based parallel algorithms for bipartite cardinality matching.

Azad, Md Ariful↗
DOE OSTI2014

Scaling Irregular Applications through Data Aggregation and Software Multithreading

Bioinformatics, data analytics, semantic databases, knowledge discovery are emerging high performance application areas that exploit dynamic, linked data structures such as graphs, unbalanced trees or unstructured grids. These data structures usually are very large, requiring significantly more memory than available on single shared memory systems. Additionally, these data structures are difficult to partition on distributed memory systems. They also present poor spatial and temporal locality, thus generating unpredictable memory and network accesses. The Partitioned Global Address Space (PGAS) programming model seems suitable for these applications, because it allows using a shared memory abstraction across distributed-memory clusters. However, current PGAS languages and libraries are built to target regular remote data accesses and block transfers. Furthermore, they usually rely on the Single Program Multiple Data (SPMD) parallel control model, which is not well suited to the fine grained, dynamic and unbalanced parallelism of irregular applications. In this paper we present {\bf GMT} (Global Memory and Threading library), a custom runtime library that enables efficient execution of irregular applications on commodity clusters. GMT integrates a PGAS data substrate with simple fork/join parallelism and provides automatic load balancing on a per node basis. It implements multi-level aggregation and lightweight multithreading to maximize memory and network bandwidth with fine-grained data accesses and tolerate long data access latencies. A key innovation in the GMT runtime is its thread specialization (workers, helpers and communication threads) that realize the overall functionality. We compare our approach with other PGAS models, such as UPC running using GASNet, and hand-optimized MPI code on a set of typical large-scale irregular applications, demonstrating speedups of an order of magnitude.

Aggregation↗
DOE OSTI2020

Population Count on Intel® CPU, GPU, and FPGA

Population count is a primitive used in many applications. Commodity processors have dedicated instructions for achieving high-performance population count. Motivated by the productivity of high-level synthesis and the importance of population count, in this paper we investigated the OpenCL implementations of population count algorithms, and evaluated their performance and resource utilizations on an FPGA. Based on the results, we select the most efficient implementation. Then we derived a reduction pattern from a representative application of population count. We parallelized the reduction with atomic functions, and optimized it with vectorized memory accesses, tree reduction, and compute-unit duplication. We evaluated the performance of the reduction kernel on an Intel (R) Xeon (R) CPU and an Intel (R) IrisT Pro integrated GPU, and an FPGA card that features an Intel (R) Arria (R) 10 FPGA. When DRAM memory bandwidth is comparable on the three computing platforms, the FPGA can achieve the highest kernel performance for large workload. On the other hand, we described performance bottlenecks on the FPGA. To make FPGAs more competitive in raw performance compared to high-performant CPU and GPU platforms, it is important to increase external memory bandwidth, minimize data movement between a host and a device, and reduce OpenCL runtime overhead on an FPGA.

heterogeneous computing↗