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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP

Abstract Bacterial DNA methylation is involved in diverse cellular functions, including modulation of gene expression, DNA repair, and restriction–modification systems for defense against viruses and other foreign DNA. Restriction systems hinder efforts to engineer organisms to produce fuels and chemicals from waste and renewable feedstocks by degrading DNA during transformation. Methylome analysis allows identification of motifs within a bacterial chromosome that may be targeted by native restriction enzymes. Further expression of the corresponding methyltransferases in Escherichia coli allows plasmid DNA to be protected from restriction in the target organism, thereby drastically enhancing transformation efficiency. Nanopore sequencing can detect methylated bases, but software is needed to transform modified base coordinates into methylated motifs. Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating incorrect motifs. MIJAMP also reports methylation data on specific, user-defined motifs. Using MIJAMP, we determined the methylated motifs both in a control strain (wild-type E. coli) and in Synecococcus sp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available at https://code.ornl.gov/alexander-public/mijamp/. One Sentence Summary: Here we describe software written to discover DNA methylation motifs from nanopore sequencing data.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2022

GRC MILab Software: Quick Start Guide

This document provides detailed installation and operating instructions for the GRC MILab Excel Add-In software developed at the NASA Glenn Research Center. The software described has been implemented to facilitate the process of importing into Microsoft Excel and analyzing materials test data from a wide range of materials tests. All resulting data is then ready for automated upload to the relevant table of the GRC Materials Intelligence (MI) database. This new software represents an update to the original MILab software developed by Granta Design Ltd.—a company specializing in materials software, data, and databases—for members of the Materials Data Management Consortium (MDMC), a collaboration between Granta, ASM International, NASA Glenn, and several other materials-oriented corporations and government agencies in the aerospace and defense industries. The updated software consists of the addition of two test type modules, the Generic and Generic Cyclic modules, with both representing a generalization of the original software. The Generic module supports the import and analysis of multiaxial data from any sequence of tensile, compression, relaxation, and/or creep test stages; and the Generic Cyclic module expands the functionality to include repeated sequences during cyclic testing. During processing, all imported data and analysis results are formatted by the software so as to be ready for immediate automated upload to the MI database, ensuring minimal overhead on the part of the user and access to persistent and reliable data for all relevant personnel.

Quick Start Guide↗
NASA NTRS1999

Orthologs, paralogs and genome comparisons

During the past decade, ancient gene duplications were recognized as one of the main forces in the generation of diverse gene families and the creation of new functional capabilities. New tools developed to search data banks for homologous sequences, and an increased availability of reliable three-dimensional structural information led to the recognition that proteins with diverse functions can belong to the same superfamily. Analyses of the evolution of these superfamilies promises to provide insights into early evolution but are complicated by several important evolutionary processes. Horizontal transfer of genes can lead to a vertical spread of innovations among organisms, therefore finding a certain property in some descendants of an ancestor does not guarantee that it was present in that ancestor. Complete or partial gene conversion between duplicated genes can yield phylogenetic trees with several, apparently independent gene duplications, suggesting an often surprising parallelism in the evolution of independent lineages. Additionally, the breakup of domains within a protein and the fusion of domains into multifunctional proteins makes the delineation of superfamilies a task that remains difficult to automate.

Non-NASA Center↗
DOE OSTI2024

Design and Characterization of a Transcriptional Repression Toolkit for Plants

Regulation of gene expression is essential for all life. Tools to manipulate the gene expression level have therefore proven to be very valuable in efforts to engineer biological systems. However, there are few well-characterized genetic parts that reduce gene expression in plants, commonly known as transcriptional repressors. We characterized the repression activity of a library consisting of repression motifs from approximately 25% of the members of the largest known family of repressors. Combining sequence information with our trans-regulatory function data, we next generated a library of synthetic transcriptional repression motifs with function predicted in advance. After characterizing our synthetic library, we demonstrated not only that many of our synthetic constructs were functional as repressors but also that our advance predictions of repression strength were better than random guesses. Finally, we assessed the functionality of known transcriptional repression motifs from a wide range of eukaryotes. Our study represents the largest plant repressor motif library experimentally characterized to date, providing unique opportunities for tuning transcription in plants.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Software For Graphical Representation Of A Network

System Visualization Tool (SVT) computer program developed to provide systems engineers with means of graphically representing networks. Generates diagrams illustrating structures and states of networks defined by users. Provides systems engineers powerful tool simplifing analysis of requirements and testing and maintenance of complex software-controlled systems. Employs visual models supporting analysis of chronological sequences of requirements, simulation data, and related software functions. Applied to pneumatic, hydraulic, and propellant-distribution networks. Used to define and view arbitrary configurations of such major hardware components of system as propellant tanks, valves, propellant lines, and engines. Also graphically displays status of each component. Advantage of SVT: utilizes visual cues to represent configuration of each component within network. Written in Turbo Pascal(R), version 5.0.

Mcallister, R. William↗
NASA NTRS1992

Spatial orientation of the vestibular system

1. A simplified three-dimensional state space model of visual vestibular interaction was formulated. Matrix and dynamical system operators representing coupling from the semicircular canals and the visual system to the velocity storage integrator were incorporated into the model. 2. It was postulated that the system matrix for a tilted position was a composition of two linear transformations of the system matrix for the upright position. One transformation modifies the eigenvalues of the system matrix while another rotates the pitch and roll eigenvectors with the head, while maintaining the yaw axis eigenvector approximately spatially invariant. Using this representation, the response characteristics of the pitch, roll, and yaw eye velocity were obtained in terms of the eigenvalues and associated eigenvectors. 3. Using OKAN data obtained from monkeys and comparing to the model predictions, the eigenvalues and eigenvectors of the system matrix were identified as a function of tilt to the side or of tilt to the prone positions, using a modification of the Marquardt algorithm. The yaw eigenvector for right-side-down tilt and for downward pitch cross-coupling was approximately 30 degrees from the spatial vertical. For the prone position, the eigenvector was computed to be approximately 20 degrees relative to the spatial vertical. For both side-down and prone positions, oblique OKN induced along eigenvector directions generated OKAN which decayed to zero along a straight line with approximately a single time constant. This was verified by a spectral analysis of the residual sequence about the straight line fit to the decaying data. The residual sequence was associated with a narrow autocorrelation function and a wide power spectrum. 4. Parameters found using the Marquardt algorithm were incorporated into the model. Diagonal matrices in a head coordinate frame were introduced to represent the direct pathway and the coupling of the visual system to the integrator. Model simulations predicted the behavior of yaw and pitch OKN and OKAN when the animal was upright, as well as the cross-coupling in the tilted position. The trajectories in velocity space were also accurately simulated. 5. There were similarities between the monkey eigenvectors and human perception of the spatial vertical. For side-down tilts and downward eye velocity cross-coupling, there was only an Aubert (A) effect. For upward eye velocity cross-coupling there were both Muller (E) and Aubert (A) effects. The mean of the eigenvectors for upward and downward eye velocities overlay human 1 x g perceptual data.(ABSTRACT TRUNCATED AT 400 WORDS).

NASA Discipline Neuroscience↗
DOE OSTI2024

Impedance Scan of Inverter-Based Resources and Diesel Generator for Stability Analysis

Impedance-based methods are widely used for power system stability analysis with inverter-based resources (IBRs), e.g., assessing dynamic interactions between the power grid and an IBR, control interactions between multiple IBRs, and the sub-synchronous oscillation and damping phenomenon. Since it is difficult to get a numerical model 100% matching with the hardware IBR, using the hardware inverter directly to obtain its output impedance has become a prominent approach nowadays. Therefore, this article presents the impedance scan using hardware IBRs, and also a hardware diesel generator as it still stays with the grid before the grid completely goes to renewable. The devices under test (DuTs) for the impedance scan includes two 3-..phi.., 480 V, 60 Hz commercial grid-forming IBRs (one of 250 kVA and another of 125 kVA rating) in series with ..delta..-Y transformers, one 3-..phi.., 480 V, 60 Hz commercial grid-following IBR (of 125 kVA rating), and a 3-..phi.., 480 V, 60 Hz commercial diesel generator (of 187.5 kVA rating). Using voltage signals perturbed with sub-, inter-, and higher harmonic components, and measuring the current response, the positive-sequence impedances are computed via an offline-based post-analysis. Moreover, best-fit transfer functions are estimated that closely resemble the measured data points of the positive-sequence impedances. Based on the observations from various outcomes of the hardware experiments, this article also provides some fundamental insights on the equivalent positive-sequence impedance of a combination of multiple hardware components by comparing the estimated and the empirically computed impedances. A comparative insight on the damping capability of the DuTs using the positive-sequence impedances of the hardware is also discussed.

current measurement↗
DOE OSTI2025

Meld: A project for exploring how to meet DUNE's framework needs

Existing data-processing frameworks for HEP experiments are largely based on collider-physics concepts, which may be based on rigid, event-based data hierarchies. These data organizations are not always helpful for neutrino experiments, which must sometimes work around such restrictions by manually splitting apart events into constructs that are better suited for neutrino physics. The purpose of Meld is to explore more flexible data organizations by treating a frameworks job as: (1) A graph of data-product sequences connected by (2) User-defined functions that serve as operations to (3) Framework-provided higher-order functions.

Knoepfel, KyleJ. [Fermi National Accelerator Labor↗
DOE OSTI2024

Impedance Scan of Inverter-Based Resources and Diesel Generator for Stability Analysis: Preprint

Impedance-based methods are widely used for power system stability analysis with inverter-based resources (IBRs), e.g., assessing dynamic interactions between the power grid and an IBR, control interactions between multiple IBRs, and the sub-synchronous oscillation and damping phenomenon. Since it is difficult to get a numerical model 100% matching with the hardware IBR, using the hardware inverter directly to obtain its output impedance has become a prominent approach nowadays. Therefore, this article presents the impedance scan using hardware IBRs, and also a hardware diesel generator as it still stays with the grid before the grid completely goes to renewable. The devices under test (DuTs) for the impedance scan includes two 3-..phi.., 480 V, 60 Hz commercial grid-forming IBRs (one of 250 kVA and another of 125 kVA rating) in series with ..delta..-Y transformers, one 3-..phi.., 480 V, 60 Hz commercial grid-following IBR (of 125 kVA rating), and a 3-..phi.., 480 V, 60 Hz commercial diesel generator (of 187.5 kVA rating). Using voltage signals perturbed with sub-, inter-, and higher harmonic components, and measuring the current response, the positive-sequence impedances are computed via an offline- based post-analysis. Moreover, best-fit transfer functions are estimated that closely resemble the measured data points of the positive-sequence impedances. Based on the observations from various outcomes of the hardware experiments, this article also provides some fundamental insights on the equivalent positive- sequence impedance of a combination of multiple hardware components by comparing the estimated and the empirically computed impedances. A comparative insight on the damping capability of the DuTs using the positive-sequence impedances of the hardware is also discussed.

grid following inverter↗
NASA NTRS2007

Improve Problem Solving Skills through Adapting Programming Tools

There are numerous ways for engineers and students to become better problem-solvers. The use of command line and visual programming tools can help to model a problem and formulate a solution through visualization. The analysis of problem attributes and constraints provide insight into the scope and complexity of the problem. The visualization aspect of the problem-solving approach tends to make students and engineers more systematic in their thought process and help them catch errors before proceeding too far in the wrong direction. The problem-solver identifies and defines important terms, variables, rules, and procedures required for solving a problem. Every step required to construct the problem solution can be defined in program commands that produce intermediate output. This paper advocates improved problem solving skills through using a programming tool. MatLab created by MathWorks, is an interactive numerical computing environment and programming language. It is a matrix-based system that easily lends itself to matrix manipulation, and plotting of functions and data. MatLab can be used as an interactive command line or a sequence of commands that can be saved in a file as a script or named functions. Prior programming experience is not required to use MatLab commands. The GNU Octave, part of the GNU project, a free computer program for performing numerical computations, is comparable to MatLab. MatLab visual and command programming are presented here.

Shaykhian, Linda H.↗
DOE OSTI2024

Algorithm 1049: The Delaunay Density Diagnostic

Accurate approximation of a real-valued function depends on two aspects of the available data: the density of inputs within the domain of interest and the variation of the outputs over that domain. There are few methods for assessing whether the density of inputs is sufficient to identify the relevant variations in outputs—i.e., the “geometric scale” of the function—despite the fact that sampling density is closely tied to the success or failure of an approximation method. In this article, we introduce a general purpose, computational approach to detecting the geometric scale of real-valued functions over a fixed domain using a deterministic interpolation technique from computational geometry. The algorithm is intended to work on scalar data in moderate dimensions (2–10). Our algorithm is based on the observation that a sequence of piecewise linear interpolants will converge to a continuous function at a quadratic rate (in L 2 norm) if and only if the data are sampled densely enough to distinguish the feature from noise (assuming sufficiently regular sampling). We present numerical experiments demonstrating how our method can identify feature scale, estimate uncertainty in feature scale, and assess the sampling density for fixed (i.e., static) datasets of input–output pairs. Finally, we include analytical results in support of our numerical findings and have released lightweight code that can be adapted for use in a variety of data science settings.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1996

Refining Linear Fuzzy Rules by Reinforcement Learning

Linear fuzzy rules are increasingly being used in the development of fuzzy logic systems. Radial basis functions have also been used in the antecedents of the rules for clustering in product space which can automatically generate a set of linear fuzzy rules from an input/output data set. Manual methods are usually used in refining these rules. This paper presents a method for refining the parameters of these rules using reinforcement learning which can be applied in domains where supervised input-output data is not available and reinforcements are received only after a long sequence of actions. This is shown for a generalization of radial basis functions. The formation of fuzzy rules from data and their automatic refinement is an important step in closing the gap between the application of reinforcement learning methods in the domains where only some limited input-output data is available.

Berenji, Hamid R.↗
NASA NTRS1994

The luminosity function at the end of the main sequence: Results of a deep, large-area, CCD survey for cool dwarfs

The luminosity function at the end of the main sequence is determined from V, R, and I data taken by the charge coupled devices (CCD)/Transit Instrument, a dedicated telescope surveying an 8.25 min wide strip of sky centered at delta = +28 deg, thus sampling Galactic latitudes of +90 deg down to -35 deg. A selection of 133 objects chosen via R - I and V - I colors has been observed spectroscopically at the 4.5 m Multiple Mirror Telescope to assess contributions by giants and subdwarfs and to verify that the reddest targets are objects of extremely late spectral class. Eighteen dwarfs of type M6 or later have been discovered, with the latest being of type M8.5. Data used for the determination of the luminosity function cover 27.3 sq. deg down to a completeness limit of R = 19.0. This luminosity function, computed at V, I, and bolometric magnitudes, shows an increase at the lowest luminosities, corresponding to spectral types later than M6- an effect suggested in earlier work by Reid & Gilmore and Legget & Hawkins. When the luminosity function is segregated into north Galactic and south Galactic portions, it is found that the upturn at faint magnitudes exists only in the southern sample. In fact, no dwarfs with M(sub I) is greater than or equal to 12.0 are found within the limiting volume of the 19.4 sq deg northern sample, in stark contrast to the smaller 7.9 sq deg area at southerly latitudes where seven such dwarfs are found. This fact, combined with the fact that the Sun is located approximately 10-40 pc north of the midplane, suggests that the latest dwarfs are part of a young population with a scale height much smaller than the 350 pc value generally adopted for other M dwarfs. These objects comprise a young population either because the lower metallicities prevelant at earlier epochs inhibited the formation of late M dwarfs or because the older counterparts of this population have cooled beyond current detection limits. The latter scenario would hold if these late-type M dwarfs are substellar. The luminosity function data together with an empirical derivation of the mass-luminosity relation (from Henry & McCarthy) are used to compute a mass function independent of theory. This mass function increases toward the end of the main sequence, but the observed density of M dwarfs is still insufficient to account for the missing mass. If the increases seen in the luminosity and mass functions are indicative of a large, unseen, substellar population, brown dwarfs may yet add significantly to the mass of the Galaxy.

Kirkpatrick, J. Davy↗
NASA NTRS2016

Space Suit Portable Life Support System (PLSS) 2.0 Pre-Installation Acceptance (PIA) Testing

Following successful completion of the space suit Portable Life Support System (PLSS) 1.0 development and testing in 2011, the second system-level prototype, PLSS 2.0, was developed in 2012 to continue the maturation of the advanced PLSS design which is intended to reduce consumables, improve reliability and robustness, and incorporate additional sensing and functional capabilities over the current Space Shuttle/International Space Station Extravehicular Mobility Unit (EMU) PLSS. PLSS 2.0 represents the first attempt at a packaged design comprising first generation or later component prototypes and medium fidelity interfaces within a flight-like representative volume. Pre-Installation Acceptance (PIA) is carryover terminology from the Space Shuttle Program referring to the series of test sequences used to verify functionality of the EMU PLSS prior to installation into the Space Shuttle airlock for launch. As applied to the PLSS 2.0 development and testing effort, PIA testing designated the series of 27 independent test sequences devised to verify component and subsystem functionality, perform in situ instrument calibrations, generate mapping data to define set-points for control algorithms, evaluate hardware performance against advanced PLSS design requirements, and provide quantitative and qualitative feedback on evolving design requirements and performance specifications. PLSS 2.0 PIA testing was carried out from 3/20/13 - 3/15/14 using a variety of test configurations to perform test sequences that ranged from stand-alone component testing to system-level testing, with evaluations becoming increasingly integrated as the test series progressed. Each of the 27 test sequences was vetted independently, with verification of basic functionality required before completion. Because PLSS 2.0 design requirements were evolving concurrently with PLSS 2.0 PIA testing, the requirements were used as guidelines to assess performance during the tests; after the completion of PIA testing, test data served to improve the fidelity and maturity of design requirements as well as plans for future advanced PLSS functional testing.

Watts, Carly↗
NASA NTRS2016

Space Suit Portable Life Support System (PLSS) 2.0 Pre-Installation Acceptance (PIA) Testing

Following successful completion of the space suit Portable Life Support System (PLSS) 1.0 development and testing in 2011, the second system-level prototype, PLSS 2.0, was developed in 2012 to continue the maturation of the advanced PLSS design. This advanced PLSS is intended to reduce consumables, improve reliability and robustness, and incorporate additional sensing and functional capabilities over the current Space Shuttle/International Space Station Extravehicular Mobility Unit (EMU) PLSS. PLSS 2.0 represents the first attempt at a packaged design comprising first generation or later component prototypes and medium fidelity interfaces within a flight-like representative volume. Pre-Installation Acceptance (PIA) is carryover terminology from the Space Shuttle Program referring to the series of test sequences used to verify functionality of the EMU PLSS prior to installation into the Space Shuttle airlock for launch. As applied to the PLSS 2.0 development and testing effort, PIA testing designated the series of 27 independent test sequences devised to verify component and subsystem functionality, perform in situ instrument calibrations, generate mapping data, define set-points, evaluate control algorithms, evaluate hardware performance against advanced PLSS design requirements, and provide quantitative and qualitative feedback on evolving design requirements and performance specifications. PLSS 2.0 PIA testing was carried out in 2013 and 2014 using a variety of test configurations to perform test sequences that ranged from stand-alone component testing to system-level testing, with evaluations becoming increasingly integrated as the test series progressed. Each of the 27 test sequences was vetted independently, with verification of basic functionality required before completion. Because PLSS 2.0 design requirements were evolving concurrently with PLSS 2.0 PIA testing, the requirements were used as guidelines to assess performance during the tests; after the completion of PIA testing, test data served to improve the fidelity and maturity of design requirements as well as plans for future advanced PLSS functional testing.

Anchondo, Ian↗
NASA NTRS1987

Maximum likelihood estimation of parameterized 3-D surfaces using a moving camera

A new approach is introduced to estimating object surfaces in three-dimensional space from a sequence of images. A surface of interest here is modeled as a 3-D function known up to the values of a few parameters. The approach will work with any parameterization. However, in work to date researchers have modeled objects as patches of spheres, cylinders, and planes - primitive objects. These primitive surfaces are special cases of 3-D quadric surfaces. Primitive surface estimation is treated as the general problem of maximum likelihood parameter estimation based on two or more functionally related data sets. In the present case, these data sets constitute a sequence of images taken at different locations and orientations. A simple geometric explanation is given for the estimation algorithm. Though various techniques can be used to implement this nonlinear estimation, researches discuss the use of gradient descent. Experiments are run and discussed for the case of a sphere of unknown location. These experiments graphically illustrate the various advantages of using as many images as possible in the estimation and of distributing camera positions from first to last over as large a baseline as possible. Researchers introduce the use of asymptotic Bayesian approximations in order to summarize the useful information in a sequence of images, thereby drastically reducing both the storage and amount of processing required.

Hung, Y.↗
NASA NTRS1993

The Mars mapper science and mission planning tool

The Mars Mapper Program (MOm) is an interactive tool for science and mission design developed for the Mars Observer Mission (MO). MOm is a function of the Planning and Sequencing Element of the MO Ground Data System. The primary users of MOm are members of the science and mission planning teams. Using MOm, the user can display digital maps of Mars in various projections and resolutions ranging from 1 to 256 pixels per degree squared. The user can overlay the maps with ground tracks of the MO spacecraft (S/C) and footprints and swaths of the various instruments on-board the S/C. Orbital and instrument geometric parameters can be computed on demand and displayed on the digital map or plotted in XY-plots. The parameter data can also be saved into files for other uses. MOm is divided into 3 major processes: Generator, Mapper, Plotter. The Generator Process is the main control which spawns all other processes. The processes communicate via sockets. At any one time, only 1 copy of MOm may operate on the system. However, up to 5 copies of each of the major processes may be invoked from the Generator. MOm is developed on the Sun SPARCStation 2GX with menu driven graphical user interface (GUI). The map window and its overlays are mouse-sensitized to permit on-demand calculations of various parameters along an orbit. The program is currently under testing and will be delivered to the MO Mission System Configuration Management for distribution to the MO community in 3/93.

Lo, Martin W.↗
NASA NTRS1995

Selecting a general-purpose data compression algorithm

The National Space Science Data Center's Common Data Formate (CDF) is capable of storing many types of data such as scalar data items, vectors, and multidimensional arrays of bytes, integers, or floating point values. However, regardless of the dimensionality and data type, the data break down into a sequence of bytes that can be fed into a data compression function to reduce the amount of data without losing data integrity and thus remaining fully reconstructible. Because of the diversity of data types and high performance speed requirements, a general-purpose, fast, simple data compression algorithm is required to incorporate data compression into CDF. The questions to ask are how to evaluate and compare compression algorithms, and what compression algorithm meets all requirements. The object of this paper is to address these questions and determine the most appropriate compression algorithm to use within the CDF data management package that would be applicable to other software packages with similar data compression needs.

Mathews, Gary Jason↗