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Results for “sequence development”

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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
NASA NTRS1981

Evaluation and verification of epitaxial process sequence for silicon solar-cell production

Several process sequences are shown to be of potentially low cost and to perform effectively when applied to the high quality silicon crystals for which they were developed. The extent to which such process sequences can also perform effectively when applied to lower cost thin film solar cells formed by epitaxial deposition of Si on potentially inexpensive substrates of upgraded metallurgical grade Si was investigated.

Redfield, D.↗
DOE OSTI2024

A dynamic solvent chamber propagation estimation framework using RNN for warm solvent injection in heterogeneous reservoirs

Warm solvent injection (WSI), injecting low-temperature solvent into formations to reduce the viscosity of heavy oil, is a clean technology for heavy oil production through reducing greenhouse gas emissions and water usage. The success of WSI operation depends on the uniform development and propagation of solvent chambers in reservoirs. However, reservoir heterogeneity stemming from shale barriers plays a detrimental role in the conformance of solvent chamber development and oil production rate. In this work, we developed a novel recurrent neural network (RNN)-based framework with the capability of efficiently tracking and estimating the solvent chamber positions in heterogeneous reservoirs based on only production time-series data. The developed estimation model utilizes the “sequence-to-sequence" mapping methodology to correlate observed production time-series sequence and solvent chamber edge sequence via a long short-term memory (LSTM) algorithm. The trained RNN models exhibit high accuracy, evidenced by the predicted dynamic solvent chamber locations match the corresponding true locations from numerical simulation, with a high coefficient of determination (R 2 ) and a low mean squared error. Specifically, the achieved R 2 values exceed 0.98 on both the training and testing data. The developed RNN-based workflow was tested via several cases from both regularly- and irregularly-shaped shale barriers, and the results were promising. The predicted solvent chambers showed strong agreement with those obtained from numerical simulations. The major benefits of this workflow include reducing computational time and saving overall monitoring and tracking costs for conventional techniques. In conclusion, the present work would provide a good demonstration of the capability of practical integration of machine learning methods in solving engineering problems.

58 GEOSCIENCES↗
NASA NTRS1995

Aluminum U-groove weld enhancement based on experimental stress analyses

Though butt-welds are among the most preferred joining methods in aerostructures because of their sealing and assembly integrity and general elastic performance; their inelastic mechanics are generally the least understood. This study investigated experimental strain distributions across a thick aluminum U-grooved weld and identified two weld process considerations for improving the multipass weld strength. The extreme thermal expansion and contraction gradient of the fusion heat input across the tab thickness between the grooves produce severe peaking, which induces bending moment under uniaxial loading. The filler strain hardening decreased with increasing filler pass sequence. These combined effects reduce the weld strength, and a depeaking index model was developed to select filler pass thicknesses, pass numbers, and sequences to improve the welding process results over the current normal weld schedule.

Verderaime, V.↗
NASA NTRS1989

Interdependent figure-of-merit software development

This program was undertaken in order to understand the complex nature of interdependent performance in space missions. At the first step in a planned sequence of progress, a spread sheet program was developed to evaluate different fuel/oxidizer combinations for a specific Martian mission. This program is to be linked with output attained using sophisticated software produced by Gordon and McBride. The programming to date makes use of 11 independent parameters. Optimization is essential when faced with the incredible magnitude of costs, risks, and benefits involved with space exploration. A system of weights needs to be devised on which to measure the options. It was the goal to devise a Figure of Merit (FoM) on which different choices can be presented and made. The plan was to model typical missions to Mars, identify the parameters, and vary them until the best one is found. Initially, most of the focus was placed on propellant selection.

Ramohalli, K.↗
DOE OSTI2024

Synthetic Biology PacBio/JAWS QC Analysis (PBJ) v3.0

This software was designed as a sequence validation tool for the assembly of synthetic constructs. It analyzes FASTQ files against a list of reference sequences, combining the results from eight sequencing libraries to generate a summary, and the files needed to view the results in the Integrative Genomics Viewer (IGV) application for manual verification. This was developed for FASTQ files generated by PacBio sequencing, but could be used on any FASTQ files that do not have paired end reads. It can be used to analyze one - eight libraries at a time, and assumes that each construct sequence in the reference will be in each pool, however, this is not a requirement. This is used to identify which libraries of pooled sequences contains a perfect match, or fixable match to the reference file. This pipeline uses many freely available open source libraries, the value added is that in our application the steps of the pipeline are defined in Workflow Description Language (WDL) and run through the Cromwell workflow engine in Docker containers, for easy distribution and set up, as well as the user friendly html summary that is generated.

Simirenko, Lisa↗
DOE OSTI2024

SynBio QC Dual Barcode QC (DBC) v1.0

This software was designed as a sequence validation tool for the assembly of synthetic constructs, where the constructs have a high degree of similarity and thus are barcoded prior to the sequencing library prep. It demultiplexes each FASTQ file for each barcode, then analyzes the resulting FASTQ files against a list of reference sequences for that barcode/library, combining the results from eight sequencing libraries to generate a summary, and the files needed to view the results in the Integrative Genomics Viewer (IGV) application for manual verification. This was developed for FASTQ files generated by PacBio sequencing, but could be used on any FASTQ files that do not have paired end reads. It can be used to analyze one - eight libraries at a time. Each construct is independently analyzed with only the sequences with the same barcode, in the same pooled library. Then the results are combined into a user friendly summary. This is used to identify which libraries of pooled sequences contains a perfect match, or fixable match to the reference file. This pipeline uses many freely available open source libraries, the value added is that in our application the steps of the pipeline are defined in Workflow Description Language (WDL) and run through the Cromwell workflow engine in Docker containers, for easy distribution and set up, as well as the user friendly html summary that is generated.

Simirenko, Lisa↗
NASA NTRS2021

Real-Time Culture-Independent Microbial Profiling Onboard the International Space Station using Nanopore Sequencing

For the past two decades, microbial monitoring of the International Space Station (ISS) has relied on culture-dependent methods that require return to Earth for analysis. This has a number of limitations, with the most significant being bias towards the detection of culturable organisms and the inherent delay between sample collection and ground-based analysis. In recent years, portable and easy-to-use molecular-based tools, such as Oxford Nanopore Technologies’ MinION™ sequencer and miniPCR bio’s miniPCR™ thermal cycler, have been validated onboard the ISS. Here, we report on the development, validation, and implementation of a swab-to-sequencer method that provides a culture-independent solution to real-time microbial profiling onboard the ISS. Method development focused on analysis of swabs collected in a low-biomass environment with limited facility resources and stringent controls on allowed processes and reagents. ISS-optimized procedures included enzymatic DNA extraction from a swab tip, bead-based purifications, altered buffers, and the use of miniPCR and the MinION. Validation was conducted through extensive ground-based assessments comparing current standard culture-dependent and newly developed culture-independent methods. Similar microbial distributions were observed between the two methods; however, as expected, the culture-independent data revealed microbial profiles with greater diversity. Protocol optimization and verification was established during NASA Extreme Environment Mission Operations (NEEMO) analog missions 21 and 22, respectively. Unique microbial profiles obtained from analog testing validated the swab-to-sequencer method in an extreme environment. Finally, four independent swab-to-sequencer experiments were conducted onboard the ISS by two crewmembers. Microorganisms identified from ISS swabs were consistent with historical culture-based data, and primarily consisted of commonly observed human-associated microbes. This simplified method has been streamlined for high ease-of-use for a non-trained crew to complete in an extreme environment, thereby enabling environmental and human health diagnostics in real-time as future missions take us beyond low-Earth orbit.

microbiology↗
NASA NTRS1981

A Module Experimental Process System Development Unit (MEPSDU)

The development of a cost effective process sequence that has the potential for the production of flat plate photovoltaic modules which meet the price goal in 1986 of 70 cents or less per Watt peak is described. The major accomplishments include (1) an improved AR coating technique; (2) the use of sand blast back clean-up to reduce clean up costs and to allow much of the Al paste to serve as a back conductor; and (3) the development of wave soldering for use with solar cells. Cells were processed to evaluate different process steps, a cell and minimodule test plan was prepared and data were collected for preliminary Samics cost analysis.

Source record↗
NASA NTRS1986

Space power system scheduling using an expert system

A most pressing problem in space exploration is timely spacecraft power system sequence generation, which requires the scheduling of a set of loads given a set of resource constraints. This is particularly important after an anomaly or failure. This paper discusses the power scheduling problem and how the software program, Plan-It, can be used as a consultant for scheduling power system activities. Modeling of power activities, human interface, and two of the many strategies used by Plan-It are discussed. Preliminary results showing the development of a conflict-free sequence from an initial sequence with conflicts is presented. It shows that a 4-day schedule can be generated in a matter of a few minutes, which provides sufficient time in many cases to aid the crew in the replanning of loads and generation use following a failure or anomaly.

Bahrami, K. A.↗
DOE OSTI2024

Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance

Abstract A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron . From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a d -glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

Evolutionary changes in transcriptional regulation undoubtedly play an important role in creating morphological diversity. However, there is little information about the evolutionary dynamics of cis-regulatory sequences. This study examines the functional consequence of evolutionary changes in the Endo16 promoter of sea urchins. The Endo16 gene encodes a large extracellular protein that is expressed in the endoderm and may play a role in cell adhesion. Its promoter has been characterized in exceptional detail in the purple sea urchin, Strongylocentrotus purpuratus. We have characterized the structure and function of the Endo16 promoter from a second sea urchin species, Lytechinus variegatus. The Endo16 promoter sequences have evolved in a strongly mosaic manner since these species diverged approximately 35 million years ago: the most proximal region (module A) is conserved, but the remaining modules (B-G) are unalignable. Despite extensive divergence in promoter sequences, the pattern of Endo16 transcription is largely conserved during embryonic and larval development. Transient expression assays demonstrate that 2.2 kb of upstream sequence in either species is sufficient to drive GFP reporter expression that correctly mimics this pattern of Endo16 transcription. Reciprocal cross-species transient expression assays imply that changes have also evolved in the set of transcription factors that interact with the Endo16 promoter. Taken together, these results suggest that stabilizing selection on the transcriptional output may have operated to maintain a similar pattern of Endo16 expression in S. purpuratus and L. variegatus, despite dramatic divergence in promoter sequence and mechanisms of transcriptional regulation.

NASA Discipline Evolutionary Biology↗
NASA NTRS2000

Multi-Agent Diagnosis and Control of an Air Revitalization System for Life Support in Space

An architecture of interoperating agents has been developed to provide control and fault management for advanced life support systems in space. In this adjustable autonomy architecture, software agents coordinate with human agents and provide support in novel fault management situations. This architecture combines the Livingstone model-based mode identification and reconfiguration (MIR) system with the 3T architecture for autonomous flexible command and control. The MIR software agent performs model-based state identification and diagnosis. MIR identifies novel recovery configurations and the set of commands required for the recovery. The AZT procedural executive and the human operator use the diagnoses and recovery recommendations, and provide command sequencing. User interface extensions have been developed to support human monitoring of both AZT and MIR data and activities. This architecture has been demonstrated performing control and fault management for an oxygen production system for air revitalization in space. The software operates in a dynamic simulation testbed.

Malin, Jane T.↗
NASA NTRS1984

Delineating mid- and low-level water vapor patterns in pre-convective environments using VAS moisture channels

Infrared and visible imagery from VAS are used to delineate mid- and lower-tropospheric moisture fields for a variety of severe storm cases in the southern and central United States. The ability of sequences of images to isolate areas of large negative vertical moisture gradients and apparent convective instability prior to the onset of convective storms is assessed. A variety of image combination procedures are used to deduce the stability fields which are then compared with the available radiosonde data. The results for several severe storm cases indicate that VAS can detect mid- and low-level mesoscale water vapor fields as distinct radiometric signals. The VAS imagery shows a strong tendency for thunderstorms to develop along the edges of bands of midlevel dryness as they overtake either preexisting or developing low-level moisture maxima. Image sequences depict the speed with which deep moist and dry layers can develop and move.

Petersen, R. A.↗
NASA NTRS2009

Aerocapture Guidance and Performance at Mars for High-Mass Systems

The Mars Entry, Descent, and Landing System Analysis (EDL-SA) project has been tasked with performing systems analysis to identify the optimal technologies required to land a 20-50 MT Exploration-class mission on Mars. It has been shown that it is not possible to safely land these large systems using heritage Mars EDL systems, or analogous Earth or Moon EDL systems. In 2007, NASA conducted a Mars Exploration Architecture Study which included an in depth review of the science motivations and engineering technology requirements for a human Mars mission campaign. This study resulted in an update to the Mars Design Reference Architecture (DRA 5.0). Among the primary findings and recommendations was the conclusion that landing of large payloads (greater than 1 MT) on the surface of Mars remains a key architectural challenge. Additionally, research and system studies of fundamental EDL technologies were highly recommended. The EDL-SA project identified the candidate technologies and assembled them into full capture and EDL sequences so that simulations could be developed to evaluate them. The chosen architectures combine the various technologies of interest in eight different ways. For aerocapture, only two scenarios were considered. The first is a rigid mid-L/D aeroshell (AS), which is represented in architectures 1, 4, 5, and 7. This scenario calls for a vehicle that flies at a 55-degree angle of attack, resulting in ballistic coefficient and L/D values of 490 kg/m 2 and 0.43, respectively. The second is a lifting hypersonic inflatable aerodynamic decelerator (HIAD), which is represented in architectures 2, 6, and 8. This scenario requires the vehicle to fly at a 22.2- degree angle of attack, which correlates to an L/D of 0.3 and was sized to provide a ballistic coefficient of 165 kg/m 2 . Architecture 3 is an all-propulsive sequence, and is not considered in this study.

Zumwalt, Carlie H.↗
NASA NTRS1991

Annular denuder systems: Precision and applicability to stratospheric sampling

Annular denuder systems (ADS) are designed to sample both gases and particles from ambient air without cross interference. The ADS's were used to detect chemical gradients over rural forest canopies. Accurate and precise methods for the sampling and analysis of low concentrations of gaseous and particulate species over short sampling periods were developed. Typical analytical precision data for nitrate and sulfate are shown. Both sampling and analytical precision data for a 2 hour test using four collocated ADS's are presented. On this particular day, the overall precision for HNO3 was unusually poor. The overall precision for the major constituents of interest is generally about 3 to 5 percent for typical ambient concentrations. The ADS's could potentially be used to determine the concentrations of HNO3 and fine-particle nitrate in the stratosphere, and to simultaneously characterize the chemical composition of stratospheric aerosols. Assuming 50 mb pressure, a 2 hour sampling time, a 50 Lpm sampling rate, and a low blank value, an overal precision of about 15 percent should be possible for 1 ppbv of HNO3 or nitrate, which would include nitric-acid trihydrate (NAT); and pump-driven systems could accommodate more complex systems involving denuders and filter packs in sequence. Alternate coatings could possibly be developed to selectively sample species such as Cl2 and ClNO3. The ADS's might also be useful in laboratory studies of heterogeneous chemical reactions involving NAT aerosols.

Randtke, Stephen J.↗
NASA NTRS1997

The Carbon-Rich Dust Sequence: Infrared Spectral Classification of Carbon Stars

We have developed a classification system for the infrared spectral emission from carbon stars, using a sample of 96 bright carbon-rich variables associated with the asymptotic giant branch. In addition to the stellar contribution, most spectra include the 11.2 micron emission feature from SiC and either a smooth cool continuum from amorphous carbon or a secondary emission feature at 9.0 microns. We have identified a carbon-rich dust sequence along which the amorphous carbon component grows while the 9.0 micron feature declines in strength. Along this spectral sequence, the fraction of Miras increases, as does the period of variability, the mass-loss rate, and the thickness of the circumstellar shell. Thus the carbon-rich dust sequence appears to be an evolutionary sequence. One class of spectra shows a particularly strong 9.0 micron feature, Enhanced C/O ratio, and several other unusual properties that suggest a different sequence, perhaps related to J stars.

Solan, G. C.↗
NASA NTRS1993

Phase holograms in PMMA with proximity effect correction

Complex computer generated phase holograms (CGPH's) have been fabricated in PMMA by partial e-beam exposure and subsequent partial development. The CGPH was encoded as a sequence of phase delay pixels and written by the JEOL JBX-5D2 E-beam lithography system, a different dose being assigned to each value of phase delay. Following carefully controlled partial development, the pattern appeared rendered in relief in the PMMA, which then acts as the phase-delay medium. The exposure dose was in the range 20-200 micro-C/sq cm, and very aggressive development in pure acetone led to low contrast. This enabled etch depth control to better than plus or minus lambda(sub vis)/60. That result was obtained by exposing isolated 50 micron square patches and measuring resist removal over the central area where the proximity effect dose was uniform and related only to the local exposure. For complex CGPH's with pixel size of the order of the e-beam proximity effect radius, the patterns must be corrected for the extra exposure caused by electrons scattered back up out of the substrate. This has been accomplished by deconvolving the two-dimensional dose deposition function with the desired dose pattern. The deposition function, which plays much the same role as an instrument response function, was carefully measured under the exact conditions used to expose the samples. The devices fabricated were designed with 16 equal phase steps per retardation cycle, were up to 1 cm square, and consisted of up to 100 million 0.3-2.0 micron square pixels. Data files were up to 500 MB long and exposure times ranged to tens of hours. A Fresnel phase lens was fabricated that had diffraction limited optical performance with better than 85 percent efficiency.

Maker, Paul D.↗
DOE OSTI2025

Bottom-Up Simulation, Reconstruction, and Quantification of Macromolecule Sequences from Experimental Polymerizations

Motivated by the canonical sequence–structure–function paradigm, tools to characterize chemical patterning in natural biomacromolecules, from proteins to nucleic acids, have grown exponentially in recent years. However, analogous strategies for synthetic macromolecules remain in nascent stages, complicated by sequence polydispersity and analytical limitations. To address this, we have developed a comprehensive and open-source Python package, PRISM (polymer rate insights and sequence modeling), an end-to-end workflow that provides a path from experimental kinetics measurements to quantitative and qualitative metrics for describing chemical patterning in stochastic polymers. First, a numerical integration strategy was constructed to simulate and fit experimental data from reversible addition–fragmentation chain transfer (RAFT) polymerization kinetics, enabling the facile estimation of relevant reactivity ratios. These ratios were then used in a mechanism-specific stochastic kinetic simulation strategy to simulate sequence ensembles corresponding to model systems spanning experimental copolymers, classes of statistical polymers (e.g., alternating, block, and gradient), and multiblock copolymers. Lastly, inspired by sequence homology metrics from bioinformatics, we introduce visualization strategies and quantitative metrics to facilitate comparisons of different sequence ensembles. As the sequence–structure–function paradigm becomes increasingly central in de novo design of synthetic macromolecules, this toolkit provides a first step toward accurate and representative sequence description and featurization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗