SEARCH · Engineering Papers

Results for “native analysis”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12

All sources NASA NTRS DOE OSTI

NASA NTRS2014

Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

Thermodynamics↗

DOE OSTI2021

Covalent Functionalization of Nickel Phosphide Nanocrystals with Aryl-Diazonium Salts

Covalent functionalization of Ni 2 P nanocrystals was demonstrated using aryl-diazonium salts. Spontaneous adsorption of aryl functional groups was observed, with surface coverages ranging from 20 to 96% depending on the native reactivity of the salt as determined by the aryl substitution pattern. Increased coverage was possible for low reactivity species using a sacrificial reductant. Functionalization was confirmed using thermogravimetric analysis, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The structure and energetics of this nanocrystal electrocatalyst system, as a function of ligand coverage, were explored with density functional theory calculations. The Hammett parameter of the surface functional group was found to linearly correlate with the change in Ni and P core-electron binding energies and the nanocrystal's experimentally and computationally determined work function. The electrocatalytic activity and stability of the functionalized nanocrystals for hydrogen evolution were also improved when compared to the unfunctionalized material, but a simple trend based on electrostatics was not evident. Density functional theory was used to understand this discrepancy, revealing that H adsorption energies on the covalently functionalized Ni 2 P also do not follow the electrostatic trend and are predictive descriptors of the experimental results.

14 SOLAR ENERGY↗

DOE OSTI2022

Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology

Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

MicroResonators for Compacts Optical Sensors (μRCOS)

As the demand for continuous, in-situ surveillance of health of systems and environments rapidly increases, miniaturized sensors with fast responses are sought. Optical dielectric resonators supporting Whispering Gallery Modes (WGMs) have exceptional properties, like very high-power density, very narrow spectral linewidth, and extremely small mode volume. As the footprint of these sensors is drastically reduced, measurements of microvolumes samples with dramatic reduction in analysis time are possible, enabling large numbers of parallel analyses using microarrays. The high sensitivity and speed of WGM resonators combined with the ability to detect molecules in their native state have great future potential for basic and applied research such as reliable single molecule, trace-gas detection, environmental monitoring, chemical threat sensing, and biodefense Such appealing peculiarities motivated us developing WMG resonators (WGMRs) for Cavity Enhanced Absorption Spectroscopy (CEAS) for chem-bio detection. Specifically, we designed and batch-fabricated microspheres and fiber tapers for resonances excitation. We successfully detected gases (N 2 and CO 2 ) in customized environmental chambers, and bio-organisms (Inf. A and E. Coli) with integrated microfluidic systems. Background calibration and environmental isolation were always accounted for in proving the performances.

36 MATERIALS SCIENCE↗

DOE OSTI2021

MicroResonators for Compacts Optical Sensors (μRCOS)

36 MATERIALS SCIENCE↗

NASA NTRS2002

An Intercomparison of 2-D Models Within a Common Framework

A model intercomparison among the Atmospheric and Environmental Research (AER) 2-D model, the Goddard Space Flight Center (GSFC) 2-D model, and the Lawrence Livermore National Laboratory 2-D model allows us to separate differences due to model transport from those due to the model's chemical formulation. This is accomplished by constructing two hybrid models incorporating the transport parameters of the GSFC and LLNL models within the AER model framework. By comparing the results from the native models (AER and e.g. GSFC) with those from the hybrid model (e.g. AER chemistry with GSFC transport), differences due to chemistry and transport can be identified. For the analysis, we examined an inert tracer whose emission pattern is based on emission from a High Speed Civil Transport (HSCT) fleet; distributions of trace species in the 2015 atmosphere; and the response of stratospheric ozone to an HSCT fleet. Differences in NO(y) in the upper stratosphere are found between models with identical transport, implying different model representations of atmospheric chemical processes. The response of O3 concentration to HSCT aircraft emissions differs in the models from both transport-dominated differences in the HSCT-induced perturbations of H2O and NO(y) as well as from differences in the model represent at ions of O3 chemical processes. The model formulations of cold polar processes are found to be the most significant factor in creating large differences in the calculated ozone perturbations

Weisenstein, Debra K.↗

NASA NTRS2013

File Specification for GEOS-5 FP-IT (Forward Processing for Instrument Teams)

The GEOS-5 FP-IT Atmospheric Data Assimilation System (GEOS-5 ADAS) uses an analysis developed jointly with NOAA's National Centers for Environmental Prediction (NCEP), which allows the Global Modeling and Assimilation Office (GMAO) to take advantage of the developments at NCEP and the Joint Center for Satellite Data Assimilation (JCSDA). The GEOS-5 AGCM uses the finite-volume dynamics (Lin, 2004) integrated with various physics packages (e.g, Bacmeister et al., 2006), under the Earth System Modeling Framework (ESMF) including the Catchment Land Surface Model (CLSM) (e.g., Koster et al., 2000). The GSI analysis is a three-dimensional variational (3DVar) analysis applied in grid-point space to facilitate the implementation of anisotropic, inhomogeneous covariances (e.g., Wu et al., 2002; Derber et al., 2003). The GSI implementation for GEOS-5 FP-IT incorporates a set of recursive filters that produce approximately Gaussian smoothing kernels and isotropic correlation functions. The GEOS-5 ADAS is documented in Rienecker et al. (2008). More recent updates to the model are presented in Molod et al. (2011). The GEOS-5 system actively assimilates roughly 2 × 10(exp 6) observations for each analysis, including about 7.5 × 10(exp 5) AIRS radiance data. The input stream is roughly twice this volume, but because of the large volume, the data are thinned commensurate with the analysis grid to reduce the computational burden. Data are also rejected from the analysis through quality control procedures designed to detect, for example, the presence of cloud. To minimize the spurious periodic perturbations of the analysis, GEOS-5 FP-IT uses the Incremental Analysis Update (IAU) technique developed by Bloom et al. (1996). More details of this procedure are given in Appendix A. The analysis is performed at a horizontal resolution of 0.625-degree longitude by 0.5-degree latitude and at 72 levels, extending to 0.01 hPa. All products are generated at the native resolution of the horizontal grid. The majority of data products are time-averaged, but four instantaneous products are also available. Hourly data intervals are used for two-dimensional products, while 3-hourly intervals are used for three-dimensional products. These may be on the model's native 72-layer vertical grid or at 42 pressure surfaces extending to 0.1 hPa. This document describes the gridded output files produced by the GMAO near real-time operational GEOS-5 FP-IT processing in support of the EOS instrument teams. Additional details about variables listed in this file specification can be found in a separate document, the GEOS-5 File Specification Variable Definition Glossary.

3D Var↗

DOE OSTI2024

Technical Assistance Opportunities for Tribes

The National Renewable Energy Laboratory (NREL) offers many forms of technical assistance for Tribes to support local clean energy priorities and challenges. With broad support from the U.S. Department of Energy (DOE) and local partners, NREL provides technical expertise to enable data-driven, informed clean energy decision making. Technical assistance may address energy strategy, project financing, policy design and development, data analysis, economic development, infrastructure planning, energy justice, climate change, resilience, or other energy priorities. NREL has a long history of partnering with Tribes and Tribal organizations, including in Alaska Native Villages where the extreme Arctic climate poses unique energy challenges. NREL works directly with Tribes to find solutions that address their self-defined energy priorities, challenges, and goals.

Alaska native village↗

DOE OSTI2026

Metalloproteins in an Era of Modern Crystallography and Why the Beamline Matters

The Structural Molecular Biology (SMB) macromolecular crystallography (MC) group at the Stanford Synchrotron Radiation Lightsource (SSRL) have developed state-of-the-art capabilities tailored for metalloenzyme structural analysis. Metalloproteins sit at the center of biology’s most audacious chemistry. From multi-electron redox catalysis to radical rearrangements and light-driven transformations, metal sites give proteins access to reaction landscapes that would otherwise be inaccessible under ambient conditions. Yet their study presents a fundamental paradox for MC studies: the very X-rays we use to reveal atomic structure can alter the electronic states we seek to understand. As the field moves beyond static snapshots toward mechanistic insight, success increasingly depends on our ability to maintain metal centers in their native state throughout the experiment. The SSRL SMB-MC beamlines integrate a suite of capabilities specifically designed to address these challenges. By combining in situ spectroscopic verification, intelligent dose management, controlled reaction initiation, optimized anomalous diffraction, and real-time crystallographic diffraction analysis, these tools enable researchers to interrogate metalloproteins with unprecedented rigor. This article explores how these complementary approaches are reshaping our ability to capture metalloprotein chemistry, and what this means for mechanistic studies at synchrotron beamlines.

Maggiolo, Ailiena O. [SLAC National Accelerator La↗

DOE OSTI2021

Quantifying the influence of natural climate variability on in situ measurements of seasonal total and extreme daily precipitation

Abstract While various studies explore the relationship between individual sources of climate variability and extreme precipitation, there is a need for improved understanding of how these physical phenomena simultaneously influence precipitation in the observational record across the contiguous United States. In this work, we introduce a single framework for characterizing the historical signal (anthropogenic forcing) and noise (natural variability) in seasonal mean and extreme precipitation. An important aspect of our analysis is that we simultaneously isolate the individual effects of seven modes of variability while explicitly controlling for joint inter-mode relationships. Our method utilizes a spatial statistical component that uses in situ measurements to resolve relationships to their native scales; furthermore, we use a data-driven procedure to robustly determine statistical significance. In Part I of this work we focus on natural climate variability: detection is mostly limited to DJF and SON for the modes of variability considered, with the El Niño/Southern Oscillation, the Pacific–North American pattern, and the North Atlantic Oscillation exhibiting the largest influence. Across all climate indices considered, the signals are larger and can be detected more clearly for seasonal total versus extreme precipitation. We are able to detect at least some significant relationships in all seasons in spite of extremely large (> 95%) background variability in both mean and extreme precipitation. Furthermore, we specifically quantify how the spatial aspect of our analysis reduces uncertainty and increases detection of statistical significance while also discovering results that quantify the complex interconnected relationships between climate drivers and seasonal precipitation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Metabolic engineering of the oleaginous yeast Yarrowia lipolytica PO1f for production of erythritol from glycerol

Abstract Background Sugar alcohols are widely used as low-calorie sweeteners in the food and pharmaceutical industries. They can also be transformed into platform chemicals. Yarrowia lipolytica , an oleaginous yeast, is a promising host for producing many sugar alcohols. In this work, we tested whether heterologous expression of a recently identified sugar alcohol phosphatase (PYP) from Saccharomyces cerevisiae would increase sugar alcohol production in Y. lipolytica . Results Y. lipolytica was found natively to produce erythritol, mannitol, and arabitol during growth on glucose, fructose, mannose, and glycerol. Osmotic stress is known to increase sugar alcohol production, and was found to significantly increase erythritol production during growth on glycerol. To better understand erythritol production from glycerol, since it was the most promising sugar alcohol, we measured the expression of key genes and intracellular metabolites. Osmotic stress increased the expression of several key genes in the glycerol catabolic pathway and the pentose phosphate pathway. Analysis of intracellular metabolites revealed that amino acids, sugar alcohols, and polyamines are produced at higher levels in response to osmotic stress. Heterologous overexpression of the sugar alcohol phosphatase increased erythritol production and glycerol utilization in Y. lipolytica . We further increased erythritol production by increasing the expression of native glycerol kinase (GK), and transketolase (TKL). This strain was able to produce 27.5 ± 0.7 g/L erythritol from glycerol during batch growth and 58.8 ± 1.68 g/L erythritol during fed-batch growth in shake-flasks experiments. In addition, the glycerol utilization was increased by 2.5-fold. We were also able to demonstrate that this strain efficiently produces erythritol from crude glycerol, a major byproduct of the biodiesel production. Conclusions We demonstrated the application of a promising enzyme for increasing erythritol production in Y. lipolytica . We were further able to boost production by combining the expression of this enzyme with other approaches known to increase erythritol production in Y. lipolytica . This suggest that this new enzyme provides an orthogonal route for boosting production and can be stacked with existing designs known to increase sugar alcohol production in yeast such as Y. lipolytica . Collectively, this work establishes a new route for increasing sugar alcohol production and further develops Y. lipolytica as a promising host for erythritol production from cheap substrates such as glycerol.

09 BIOMASS FUELS↗

DOE OSTI2021

Metabolic Engineering of the Oleaginous Yeast Yarrowia lipolytica PO1f for Production of Erythritol from Glycerol

Yarrowia lipolytica was found natively to produce erythritol, mannitol, and arabitol during growth on glucose, fructose, mannose, and glycerol. Osmotic stress is known to increase sugar alcohol production, and was found to significantly increase erythritol production during growth on glycerol. To better understand erythritol production from glycerol, since it was the most promising sugar alcohol, we measured the expression of key genes and intracellular metabolites. Osmotic stress increased the expression of several key genes in the glycerol catabolic pathway and the pentose phosphate pathway. Analysis of intracellular metabolites revealed that amino acids, sugar alcohols, and polyamines are produced at higher levels in response to osmotic stress. Heterologous overexpression of the sugar alcohol phosphatase increased erythritol production and glycerol utilization in Y. lipolytica . We further increased erythritol production by increasing the expression of native glycerol kinase (GK), and transketolase (TKL). These data show the growth and titers produced.

Conversion↗

NASA NTRS1994

FIFE data analysis: Testing BIOME-BGC predictions for grasslands

The First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE) was conducted in a 15 km by 15 km research area located 8 km south of Manhattan, Kansas. The site consists primarily of native tallgrass prairie mixed with gallery oak forests and croplands. The objectives of FIFE are to better understand the role of biology in controlling the interactions between the land and the atmosphere, and to determine the value of remotely sensed data for estimating climatological parameters. The goals of FIFE are twofold: the upscale integration of models, and algorithm development for satellite remote sensing. The specific objectives of the field campaigns carried out in 1987 and 1989 were the simultaneous acquisition of satellite, atmospheric, and surface data; and the understanding of the processes controlling surface energy and mass exchange. Collected data were used to study the dynamics of various ecosystem processes (photosynthesis, evaporation and transpiration, autotrophic and heterotrophic respiration, etc.). Modelling terrestrial ecosystems at scales larger than that of a homogeneous plot led to the development of simple, generalized models of biogeochemical cycles that can be accurately applied to different biomes through the use of remotely sensed data. A model was developed called BIOME-BGC (for BioGeochemical Cycles) from a coniferous forest ecosystem model, FOREST-BGC, where a biome is considered a combination of a life forms in a specified climate. A predominately C4-photosynthetic grassland is probably the most different from a coniferous forest possible, hence the FIFE site was an excellent study area for testing BIOME-BGC. The transition from an essentially one-dimensional calculation to three-dimensional, landscape scale simulations requires the introduction of such factors as meteorology, climatology, and geomorphology. By using remotely sensed geographic information data for important model inputs, process-based ecosystem simulations at a variety of scales are possible. The second objective of this study is concerned with determining the accuracy of the estimated fluxes from BIOME-BGC, when extrapolated spatially over the entire 15-km by 15-km FIFE site. To accomplish this objective, a topographically distributed map of soil depth at the FIFE site was developed. These spatially-distributed fluxes were then tested with data from aircraft by eddy-flux correlation obtained during the FIFE experiment.

Hunt, E. Raymond, Jr.↗

DOE OSTI2026

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing↗

DOE OSTI2021

Cost Analysis Framework for Comparing AC and DC Design Alternatives for Building Electrical Distribution Systems

In recent years, in response to the changing nature of building load, direct current (DC) distribution systems for buildings have been proposed as alternatives to traditional alternating current (AC) systems. DC distribution offers a closer match to the types of loads and generation sources found in modern buildings, the majority of which use DC electricity internally either natively or as a power conditioning stage. The proposed benefits of DC distribution compared to AC distribution within buildings include higher efficiency, lower installation cost, lower operating cost, higher reliability, improved communication and control, and simplicity. Most recent DC distribution research has focused on quantifying the efficiency advantage of DC distribution over AC distribution. However, energy savings alone do not guarantee cost savings; a more complete cost accounting is required to establish financial benefit. This report provides a framework for cost analysis and comparison of building electrical distribution systems, including common variants for both AC and DC distribution systems. The framework includes all major cost categories, including up-front costs (capital, installation labor, soft costs) and long-term costs (energy, operations and maintenance).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2025

Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture because they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. However, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. In this study we characterized a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. Here, we profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and we detected significant phylogenetic diversity (e.g. Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated that the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs in which an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in ~10% of SynComs that generally followed the diversity–invasion principle. Additionally, our approach enabled analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work has established a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessment of the persistence of a specific organism of interest and its interaction with native consortia.

biofertilizers↗

DOE OSTI2023

EvoProtGrad (Directed Evolution for Proteins with Gradients) [SWR-23-48]

A Python package for directed evolution on a protein sequence with gradient-based discrete Markov chain monte carlo (MCMC). Users are able to compose custom models that map sequence to function with pretrained models, including protein language models (PLMs), to guide and constrain search. Our package natively integrates with the HuggingFace platform and supports PLMs from transformers. Our MCMC sampler identifies promising amino acids to mutate via model gradients taken with respect to the input (i.e., sensitivity analysis). We allow users to compose their own custom target function for MCMC by leveraging the Product of Experts MCMC paradigm. Each model is an "expert" that contributes its own knowledge about the protein's fitness landscape to the overall target function. The sampler is designed to be more efficient and effective than brute force and random search while maintaining most of the generality and flexibility. Additional information can be found in the related publication: https://iopscience.iop.org/article/10.1088/2632-2153/accacd

Emami, Patrick↗

DOE OSTI2022

Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida

Abstract With the increasing need for microbial bioproduction to replace petrochemicals, it is critical to develop a new industrial microbial workhorse that improves the conversion of lignocellulosic carbon to biofuels and bioproducts in an economically feasible manner. Pseudomonas putida KT2440 is a promising microbial host due to its capability to grow on a broad range of carbon sources and its high tolerance to xenobiotics. In this study, we engineered P. putida KT2440 to produce isoprenoids, a vast category of compounds that provide routes to many petrochemical replacements. A heterologous mevalonate (MVA) pathway was engineered to produce potential biofuels isoprenol (C 5 ) and epi-isozizaene (C 15 ) for the first time in P. putida . We compared the difference between three different isoprenoid pathways in P. putida on isoprenol production and achieved 104 mg/L of isoprenol production in a batch flask experiment through optimization of the strain. As P. putida can natively consume isoprenol, we investigated how to prevent this self-consumption. We discovered that supplementing l -glutamate in the medium can effectively prevent isoprenol consumption in P. putida and metabolomics analysis showed an insufficient energy availability and an imbalanced redox status during isoprenol degradation. We also showed that the engineered P. putida strain can produce isoprenol using aromatic substrates such as p -coumarate as the sole carbon source, and this result demonstrates that P. putida is a valuable microbial chassis for isoprenoids to achieve sustainable biofuel production from lignocellulosic biomass. Graphical Abstract

09 BIOMASS FUELS↗