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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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

PoPLAR: Portal for Petascale Lifescience Applications and Research

Background: We are focusing specifically on fast data analysis and retrieval in bioinformatics that will have a direct impact on the quality of human health and the environment. The exponential growth of data generated in biology research, from small atoms to big ecosystems, necessitates an increasingly large computational component to perform analyses. Novel DNA sequencing technologies and complementary high-throughput approaches–such as proteomics, genomics, metabolomics, and meta-genomics–drive data-intensive bioinformatics. While individual research centers or universities could once provide for these applications, this is no longer the case. Today, only specialized national centers can deliver the level of computing resources required to meet the challenges posed by rapid data growth and the resulting computational demand. Consequently, we are developing massively parallel applications to analyze the growing flood of biological data and contribute to the rapid discovery of novel knowledge. Methods: The efforts of previous National Science Foundation (NSF) projects provided for the generation of parallel modules for widely used bioinformatics applications on the Kraken supercomputer. We have profiled and optimized the code of some of the scientific community’s most widely used desktop and small-cluster-based applications, including BLAST from the National Center for Biotechnology Information (NCBI), HMMER, and MUSCLE; scaled them to tens of thousands of cores on high-performance computing (HPC) architectures; made them robust and portable to next-generation architectures; and incorporated these parallel applications in science gateways with a web-based portal. Results: This paper will discuss the various developmental stages, challenges, and solutions involved in taking bioinformatics applications from the desktop to petascale with a front-end portal for very-large-scale data analysis in the life sciences. Conclusions: This research will help to bridge the gap between the rate of data generation and the speed at which scientists can study this data. The ability to rapidly analyze data at such a large scale is having a significant, direct impact on science achieved by collaborators who are currently using these tools on supercomputers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

How chip size impacts steam pretreatment effectiveness for biological conversion of poplar wood into fermentable sugars

We report that woody biomass is highly recalcitrant to enzymatic sugar release and often requires significant size reduction and severe pretreatments to achieve economically viable sugar yields in biological production of sustainable fuels and chemicals. However, because mechanical size reduction of woody biomass can consume significant amounts of energy, it is desirable to minimize size reduction and instead pretreat larger wood chips prior to biological conversion. To date, however, most laboratory research has been performed on materials that are significantly smaller than applicable in a commercial setting. As a result, there is a limited understanding of the effects that larger biomass particle size has on the effectiveness of steam explosion pretreatment and subsequent enzymatic hydrolysis of wood chips. To address these concerns, novel downscaled analysis and high throughput pretreatment and hydrolysis (HTPH) were applied to examine whether differences exist in the composition and digestibility within a single pretreated wood chip due to heterogeneous pretreatment across its thickness. Heat transfer modeling, Simons’ stain testing, magnetic resonance imaging (MRI), and scanning electron microscopy (SEM) were applied to probe the effects of pretreatment within and between pretreated wood samples to shed light on potential causes of variation, pointing to enzyme accessibility (i.e., pore size) distribution being a key factor dictating enzyme digestibility in these samples. Application of these techniques demonstrated that the effectiveness of pretreatment of Populus tremuloides can vary substantially over the chip thickness at short pretreatment times, resulting in spatial digestibility effects and overall lower sugar yields in subsequent enzymatic hydrolysis. Finally, these results indicate that rapid decompression pretreatments (e.g., steam explosion) that specifically alter accessibility at lower temperature conditions are well suited for larger wood chips due to the non-uniformity in temperature and digestibility profiles that can result from high temperature and short pretreatment times. Furthermore, this study also demonstrated that wood chips were hydrated primarily through the natural pore structure during pretreatment, suggesting that preserving the natural grain and transport systems in wood during storage and chipping processes could likely promote pretreatment efficacy and uniformity.

09 BIOMASS FUELS↗
DOE OSTI2011

Poplar Genome Microarrays

Microarray-based transcriptome profiling is arguably the most mature and widely practiced omics technology of the post-genomics era. It provides an intuitive measure of transcript abundance for comparative gene expression analysis and for construction of co-regulation networks. Whole-genome microarray analysis can also facilitate systems-level analysis and integration of data from other omics platforms that lack global coverage, such as proteome and metabolome analyses. Just as Populus expressed sequence tag collections have proven invaluable for gene discovery and functional characterization, the growing volume of whole-genome microarray data represents a rich resource that promises to support a wide range of scientific inquiries to advance Populus biology in years to come.

Tsai, Chung-Jui↗
DOE OSTI2017

Additive and Non-Additive Genetic Variances for Tree Growth in Several Hybrid Poplar Populations and Implications Regarding Breeding Strategy

Populus species (P. deltoides, P. maximowiczii, P. nigra) and their inter-specific hybrids were tested for growth rate over a five year period at four test locations in Minnesota, USA, to estimate genetic variance components. The breeding scheme incorporated recurrent selection of full-sib families of pure species parents, production of F 1 inter-specific hybrids from selected families, and selection of clones within the F 1 s. Improvement of yield through time using this scheme is predicated on the assumption that additive effects comprise a significant portion of the total genetic variance. The estimates of additive and non-additive variances reported are not traditional point estimates, because a fully balanced mating design was impossible due to parental incompatibilities which result in incomplete breeding matrices. Instead, bounded estimates, not previously used in tree genetics research, are derived from linear combinations of formulae of genetic expectations observed among-family, among-clone, and environmental variances. Our results suggest that combined family and mass selection would lead to increases in growth rate of 27 % and 47 % per generation in P. deltoides and P. nigra , respectively. Broad sense-based clonal selection within the F 1 could yield selection responses in excess of 90 % of the mean of such populations. Among-family variance comprised about 1/3 of total genetic variance while within-family variance was always about 2/3 of total genetic variance, regardless of pedigree. With this beind said, the results indicate that recurrent intraspecific selective breeding followed by interspecific hybridization and non-recurrent selection based on broad sense genetic variation would constitute an effective yield improvement strategy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2011

Conceptual Model of Primary Mercury Sources, Transport Pathways, and Flux at the Y-12 Complex and Upper East Fork Poplar Creek, Oak Ridge, Tennessee

The interactions between the key processes that control the fate and transport of mercury in the sediments, groundwater, and stream water within the Y-12 National Security Complex in Oak Ridge, Tennessee are extremely complicated, and many aspects are not well understood. In complex environments such as that at the Y-12 Complex, conceptual models are frequently developed to aid in visualization and understanding of the dynamic nature of the hydrologic, geochemical, and physical environment. These conceptual models represent the attempt of scientists to integrate known data in an internally consistent manner to understand processes that control the fate and transport of contaminants. Over the many years of environmental investigation at Y-12, a number of conceptual models have been developed to identify and define various technical processes at a variety of scales. Many of these models have value today as a historical summary of previous modeling efforts and are provided in Appendix A of this report. The main purpose of the activity described in this report was to develop a conceptual model that delineates the location of mercury sources, transport pathways, and flux based on the most recent data and knowledgeable scientific interpretation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Phylogenomic discovery and engineering of nitrogen fixation into the bioenergy woody crop poplar

Biological nitrogen fixation (BNF) is a key process enabling plants in specific lineages to convert atmospheric dinitrogen (N₂) into bioavailable ammonia through symbioses with diazotrophic microbes. Expanding this capability beyond native nitrogen-fixing clades into non-nodulating crops would reduce synthetic fertilizer use, lowering energy inputs and environmental impacts in agriculture. Supported by DOE Funding Award DE-SC0018247, the NitFix project advanced foundational knowledge required to engineer root-nodule symbioses in new host species. The team generated the most comprehensive phylogenomic analysis to date of all known nodulating lineages, resolving the evolutionary history of nitrogen-fixing symbiosis and identifying core gene suites retained across nodulating taxa. Through multimodal genomics, transcriptomics, and functional analyses in Medicago truncatula and related species, the project mapped regulatory networks underlying nodule organogenesis, bacterial infection, and nitrogen-fixation efficiency. Key discoveries include the identification of conserved signaling modules for rhizobial recognition, transcription factors controlling nodule differentiation, and metabolic pathways integrating fixed nitrogen into plant growth. The project also developed enabling tools—including optimized transformation pipelines, gene-editing workflows, and imaging-based phenotyping—to accelerate engineering efforts in emerging models. Together, these results refine the mechanistic framework of symbiotic nitrogen fixation and highlight transferable components essential for rewiring these traits into non-nodulating crops.

59 BASIC BIOLOGICAL SCIENCES↗