Search NASASearch

SEARCH · Search NASA

Results for “Sequence Alignment”

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.

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

At least 127 records · Page 7

Generating local addresses and communication sets for data-parallel programs

Generating local addresses and communication sets is an important issue in distributed-memory implementations of data-parallel languages such as High Performance Fortran. We show that for an array A affinely aligned to a template that is distributed across p processors with a cyclic(k) distribution, and a computation involving the regular section A, the local memory access sequence for any processor is characterized by a finite state machine of at most k states. We present fast algorithms for computing the essential information about these state machines, and extend the framework to handle multidimensional arrays. We also show how to generate communication sets using the state machine approach. Performance results show that this solution requires very little runtime overhead and acceptable preprocessing time.

Chatterjee, Siddhartha

Telemetry-Based Ranging

A telemetry-based ranging scheme was developed in which the downlink ranging signal is eliminated, and the range is computed directly from the downlink telemetry signal. This is the first Deep Space Network (DSN) ranging technology that does not require the spacecraft to transmit a separate ranging signal. By contrast, the evolutionary ranging techniques used over the years by NASA missions, including sequential ranging (transmission of a sequence of sinusoids) and PN-ranging (transmission of a pseudo-noise sequence) whether regenerative (spacecraft acquires, then regenerates and retransmits a noise-free ranging signal) or transparent (spacecraft feeds the noisy demodulated uplink ranging signal into the downlink phase modulator) relied on spacecraft power and bandwidth to transmit an explicit ranging signal. The state of the art in ranging is described in an emerging CCSDS (Consultative Committee for Space Data Systems) standard, in which a pseudo-noise (PN) sequence is transmitted from the ground to the spacecraft, acquired onboard, and the PN sequence is coherently retransmitted back to the ground, where a delay measurement is made between the uplink and downlink signals. In this work, the telemetry signal is aligned with the uplink PN code epoch. The ground station computes the delay between the uplink signal transmission and the received downlink telemetry. Such a computation is feasible because symbol synchronizability is already an integral part of the telemetry design. Under existing technology, the telemetry signal cannot be used for ranging because its arrival-time information is not coherent with any Earth reference signal. By introducing this coherence, and performing joint telemetry detection and arrival-time estimation on the ground, a high-rate telemetry signal can provide all the precision necessary for spacecraft ranging.

Hamkins, Jon

Modeling Delamination in Postbuckled Composite Structures Under Static and Fatigue Loads

The ability of the Abaqus progressive Virtual Crack Closure Technique (VCCT) to model delamination in composite structures was investigated for static, postbuckling, and fatigue loads. Preliminary evaluations were performed using simple Double Cantilever Beam (DCB) and Mixed-Mode Bending (MMB) specimens. The nodal release sequences that describe the propagation of the delamination front were investigated. The effect of using a sudden or a gradual nodal release was evaluated by considering meshes aligned with the crack front as well as misaligned meshes. Fatigue simulations were then performed using the Direct Cyclic Fatigue (DCF) algorithm. It was found that in specimens such as the DCB, which are characterized by a nearly linear response and a pure fracture mode, the algorithm correctly predicts the Paris Law rate of propagation. However, the Abaqus DCF algorithm does not consider different fatigue propagation laws in different fracture modes. Finally, skin/stiffener debonding was studied in an aircraft fuselage subcomponent in which debonding occurs deep into post-buckling deformation. VCCT was shown to be a robust tool for estimating the onset propagation. However, difficulties were found with the ability of the current implementation of the Abaqus progressive VCCT to predict delamination propagation within structures subjected to postbuckling deformations or fatigue loads.

Bisagni, Chiara

Reverse draping of magnetic field lines in the boundary layer

An unexpected orientation of field lines has been found by ISEE satellite measurements of the earth magnetosphere boundary layer, perhaps indicating a reverse draping. Three-dimensional plasma flow measurements by ISEE 1 and 2 show the tailward flow in the boundary layer to have an equatorward component which suggests high-latitude plasma entry. Simultaneous magnetic field measurements with the two satellites during a boundary crossing sequence yielded data on the boundary layer electric currents and the boundary layer interface with plasma sheet and magnetosheath. The currents are found to be largely field-aligned, with intensities in the 0.03-0.06 microampere/sq m range.

Hones, E. W., Jr.

Provider of Services for Urban Air Mobility (PSU) Prototype Simulation (X5) Final Report

Urban Air Mobility (UAM) is a new air transportation service concept to carry passengers or cargo in metropolitan areas, leveraged by innovative aircraft and air traffic automation technologies. NASA has conducted a series of simulations, called the X-series simulation, to evaluate the UAM concept of operations and support the development of airspace procedures and services for UAM operations. The simulation called “X5” was conducted in 2023 to test a Provider of Services for UAM (PSU) prototype developed by NASA for UAM flight planning, strategic conflict management support, and data exchange between UAM operators. In this simulation, two strategic conflict management capabilities, Demand-Capacity Balancing and Sequencing and Scheduling, were further investigated. This document describes the UAM system architecture modeled, the X5 simulation environment to be executed (e.g., traffic scenario and UAM airspace construct), and the strategic conflict management processes developed and evaluated in this study. Then, the simulation results are provided using several system performance metrics, such as the number of operations planned and activated, demand-capacity imbalances detected and resolved, and pre-departure delays. Based on these metrics, the test findings and lessons learned from this simulation are discussed. NASA developed a PSU prototype as part of a reference implementation of UAM system architecture and evolved strategic conflict management capabilities for UAM operations from the previous collaborative simulations with industry partners. Below is the summary of the achievements: - Aligned NASA’s UAM reference architecture with the FAA’s UAM ConOps notional architecture - Extended UAM airspace management capabilities to include 1) Demand-Capacity Balancing (DCB) to ensure operators coordinate planned usage of shared vertiports, and 2) Sequencing and Scheduling (S&S) at UAM corridor entry and exit points to help facilitate an orderly flow of traffic - Defined the PSU information exchange APIs and requirements towards informing industry standards - Developed and tested a NASA PSU prototype as reference implementation to validate the requirements and APIs - Developed a prototype service connecting NASA’s PSU and the FAA system for testing future PSU-ATM interface requirements - Tested NASA-developed assumptions for UAM operations such as airspace design, procedures, vehicle performance, and strategic conflict management methods to inform future Cooperative Operating Practices (COPs) development with industry - Evaluated system performance metrics such as number of simultaneous operations and ground delays that can help define system-level requirements. The simulation results showed that the UAM traffic demand could be managed to minimize the needs of tactical separation provision with ground delays assigned by DCB and S&S. These accomplishments and the lessons learned from the PSU Prototype X5 simulation activities will be valuable inputs for the Air Mobility Pathfinders (AMP) project, which is NASA’s new project to create and evaluate a reference architecture for safe, secure, and scalable UAM operations.

Simulation

Generating local addresses and communication sets for data-parallel programs

Generating local addresses and communication sets is an important issue in distributed-memory implementations of data-parallel languages such as High Performance FORTRAN. We show that, for an array A affinely aligned to a template that is distributed across p processors with a cyclic(k) distribution and a computation involving the regular section A(l:h:s), the local memory access sequence for any processor is characterized by a finite state machine of at most k states. We present fast algorithms for computing the essential information about these state machines, and extend the framework to handle multidimensional arrays. We also show how to generate communication sets using the state machine approach. Performance results show that this solution requires very little run-time overhead and acceptable preprocessing time.

Chatterjee, Siddhartha

Protein Kinase Classification with 2866 Hidden Markov Models and One Support Vector Machine

The main application considered in this paper is predicting true kinases from randomly permuted kinases that share the same length and amino acid distributions as the true kinases. Numerous methods already exist for this classification task, such as HMMs, motif-matchers, and sequence comparison algorithms. We build on some of these efforts by creating a vector from the output of thousands of structurally based HMMs, created offline with Pfam-A seed alignments using SAM-T99, which then must be combined into an overall classification for the protein. Then we use a Support Vector Machine for classifying this large ensemble Pfam-Vector, with a polynomial and chisquared kernel. In particular, the chi-squared kernel SVM performs better than the HMMs and better than the BLAST pairwise comparisons, when predicting true from false kinases in some respects, but no one algorithm is best for all purposes or in all instances so we consider the particular strengths and weaknesses of each.

Weber, Ryan

Spin-Orbit Interaction in Neutron Star/Main Sequence Binaries and Implications for Pulsar Timing

The spin-induced quadrupole moment of a rapidly rotating star changes the orbital dynamics in a binary system, giving rise to advance (or regression) of periastron and precession of the orbital plane. We show that these effects are important in the recently discovered radio pulsar/mail sequence star binary system PSR J0045-7319, and reliably account for the observed peculiar timing residuals. Precise measurements of the apsidal motion and orbital plane precession can yield valuable information on the internal structure and rotation of the star. The detection of orbital precession implies that the spin of the companion star is not aligned with the orbital angular momentum, and suggests that the supernova gave the pulsar a kick out of the original orbital plane. Excitations of g-mode oscillations near periastron (the dynamical tide) can induce measurable changes in the orbital period and eccentricity at each passage for this system. We also discuss the spin-orbit coupling effects for the accreting X-ray pulsars and the other know radio pulsar/main sequence binary, PSR B1259-63.

neutron stars

KELT-24b: A 5M(J) Planet on a 5.6 day Well-aligned Orbit around the Young V=8.3 F-star HD 93148

We present the discovery of KELT-24 b, a massive hot Jupiter orbiting a bright (V=8.3 mag, K=7.2 mag) young F-star with a period of 5.6 days. The host star, KELT-24 (HD 93148), has a Teff=-+65094950K, a mass of M*=+1.4600.0590.055Me, a radius of R*=1.506±0.022Re, and an age of +0.780.420.61Gyr. Its planetary companion (KELT-24 b) has a radius of RP=1.272±0.021RJ and a mass of MP=-+5.180.220.21MJ, and from Doppler tomographic observations, we find that the planet’s orbit is well aligned to its host star’s projected spin axis (l=-+2.63.65.1). The young age estimated for KELT-24 suggests that it only recently started to evolve from the zero-age main sequence. KELT-24 is the brightest star known to host a transiting giant planet with a period between 5 and 10 days. Although the circularization timescale is much longer than the age of the system, we do not detect a large eccentricity or significant misalignment that is expected from dynamical migration. The brightness of its host star and its moderate surface gravity make KELT-24b an intriguing target for detailed atmospheric characterization through spectroscopic emission measurements since it would bridge the current literature results that have primarily focused on lower mass hot Jupiters and a few brown dwarfs.

Transit photometry

A systolic architecture for the correlation and accumulation of digital sequences

A fully systolic architecture for the implementation of digital sequence correlator/accumulators is described. These devices consist of a two-dimensional array of processing elements that are conceived for efficient fabrication in Very Large Scale Integrated (VLSI) circuits. A custom VLSI chip that was implemented using these concepts is described. The chip, which contains a four-lag three-level sequence correlator and four bits of accumulation with overflow detection, was designed using the Integrated UNIX-Based Computer Aided Design (CAD) System. Applications of such devices include the synchronization of coded telemetry data, alignment of both real time and non-real time Very Large Baseline Interferometry (VLBI) signals, and the implementation of digital filters and processes of many types.

Deutsch, L. J.

Fiber optic phase stepping system for interferometry

A closed loop phase control system using an all-fiber optical configuration has been developed for use in phase-stepping interferometry. This system drives the relative phase of two interfering beams through a sequence of pi/2 rad increments so that the initial relative phase of these beams can be determined. This phase-stepping system uses optical fibers to provide spatially uniform phase steps from a flexible, easily aligned optical configuration. In addition, this system uses phase feedback to eliminate phase modulator errors and to compensate for phase drifts caused by environmental disturbances.

Mercer, Carolyn R.

Microelectronics Instrument Products Shock and Vibration Electro-Optics: Acceptance Data Package - Section B

The motor/encoder (henceforth referred to as the UUT) test sequence began with a baseline functional evaluation, which demonstrated that the motor satisfied the operating torque, cogging torque, winding resistance, and mechanical requirements of SOW. In addition, the encoder electrical requirements were verified, as well as the alignment of the encoder outputs relative to the motor shaft position. There were no discrepancies observed in this portion of the test. The UUT was then exposed to a number of environments, including thermal vacuum, thermal cycling, random and sine vibration, and mechanical shock. During the thermal environments, the performance of the UUT under load was verified at specified points in the cycles, as described in ATP 20049. In addition, the UUT was bench tested between the two thermal environments. No anomalies were observed during the thermal tests. The vibration and shock tests were performed by East-West Technology Corporation, West Babylon, New York. The UUT was delivered to the lab in a sealed vibration fixture in order to maintain the cleanliness levels required by the SOW. In addition, a three ounce load was attached to the motor shaft. The attachment method of this load caused damage to the shaft and bearing during random vibration of S/N 0003 on April 28, 1995, and is described further in NCR 00168.

Source record

Microelectronics Instrument Products Shock and Vibration Electro-optics: C-Qualification Test Report

In this test report all measurements made during testing are recorded in ATP 20049 DS data sheets and are included in the log. The motor/encoder (henceforth referred to as the UUT) test sequence began with a baseline functional evaluation, which demonstrated that the motor satisfied the operating torque, cogging torque, winding resistance, and mechanical requirements of SOW. In addition, the encoder electrical requirements were verified, as well as the alignment of the encoder outputs relative tc, the motor shaft position. There were no discrepancies observed in this portion of the test. The UUT was then exposed to a number of environments, including thermal vacuum, thermal cycling, random and sine vibration, and mechanical shock. During the thermal environments, the performance of the UUT under load was verified at specified points in the cycles, as described in ATP 20049. In addition, the UUT was bench tested between the two thermal environments. No anomalies were observed during the thermal tests. The load attachment method was subsequently corrected, and vibration of S/N 0002 began while 0003 was being repaired.

Source record

Spherulitic Growth of Hematite Under Hydrothermal Conditions: Insights into the Growth Mechanism of Hematite Spherules at Meridiani Planum Mars.

Hematite-rich spherules were discovered embedded in sulfate-rich outcrop rock and as lag deposits of whole and broken spherules by the Opportunity rover at Meridiani Planem [1-6]. The Mars Global Surveyor (MGS) Thermal Emission Spectrometer (TES), which has a wider spectral range compared to the Mars Exploration Rover Mini-TES, provided an important constraint that hematite-rich spherules are dominated by emission along the crystallographic c-axis [7-10]. We have previously synthesized hematite spherules whose mineralogic, chemical, and crystallographic properties are strikingly similar to those for the hematite-rich spherules at Meridiani Planum [11]. The spherules were synthesized in the laboratory along with hydronium jarosite and minor hydronium alunite from Fe-Al-Mg-S-Cl acid sulfate solutions under hydrothermal conditions. The reaction sequence was (1) precipitation of hydronium jarosite, (2) jarosite dissolution and precipitation of hematite spherules, and (3) precipitation of hydronium alunite upon depletion of hydronium jarosite. The spherules exhibit a radial growth texture with the crystallographic c-axis aligned along the radial direction, so that thermal emission spectra have no hematite emissivity minimum at approx.390/cm similar to the emission spectra returned by MGS TES. The objective of this paper is to expand on our initial studies [11] to examine the morphological evolution during growth of spherules starting from sub-micrometer crystals to spherules many orders of magnitude in size.

Ming, Douglas W.

Tissue Photolithography

Tissue lithography will enable physicians and researchers to obtain macromolecules with high purity (greater than 90 percent) from desired cells in conventionally processed, clinical tissues by simply annotating the desired cells on a computer screen. After identifying the desired cells, a suitable lithography mask will be generated to protect the contents of the desired cells while allowing destruction of all undesired cells by irradiation with ultraviolet light. The DNA from the protected cells can be used in a number of downstream applications including DNA sequencing. The purity (i.e., macromolecules isolated form specific cell types) of such specimens will greatly enhance the value and information of downstream applications. In this method, the specific cells are isolated on a microscope slide using photolithography, which will be faster, more specific, and less expensive than current methods. It relies on the fact that many biological molecules such as DNA are photosensitive and can be destroyed by ultraviolet irradiation. Therefore, it is possible to protect the contents of desired cells, yet destroy undesired cells. This approach leverages the technologies of the microelectronics industry, which can make features smaller than 1 micrometer with photolithography. A variety of ways has been created to achieve identification of the desired cell, and also to designate the other cells for destruction. This can be accomplished through chrome masks, direct laser writing, and also active masking using dynamic arrays. Image recognition is envisioned as one method for identifying cell nuclei and cell membranes. The pathologist can identify the cells of interest using a microscopic computerized image of the slide, and appropriate custom software. In one of the approaches described in this work, the software converts the selection into a digital mask that can be fed into a direct laser writer, e.g. the Heidelberg DWL66. Such a machine uses a metalized glass plate (with chrome metallization) on which there is a thin layer of photoresist. The laser transfers the digital mask onto the photoresist by direct writing, with typical best resolution of 2 micrometers. The plate is then developed to remove the exposed photoresist, which leaves the exposed areas susceptible to chemical chrome etch. The etch removes the unprotected chrome. The rest of the photoresist is then removed, by either ultraviolet organic solvent or over-development. The remaining chrome pattern is quickly oxidized by atmospheric exposure (typically within 30 seconds). The ready chrome mask is now applied to the tissue slide and aligned manually, or using automatic software and pre-designed alignment marks. The slide plate sandwich is then exposed to UV to destroy the DNA of the unwanted cells. The slide and plate are separated and the slide is processed in a standard way to prepare for polymerase chain reaction (PCR) and potential identification of cancer sequences.

Wade, Lawrence A.

Optical Navigation Attitude Estimation and Calibration Performance Improvement using Outlier Rejection

Spacecraft optical navigation (OpNav) systems process a sequence of images of celestial bodies against a starfield background to estimate the position and velocity of the vehicle. While attitude is sometimes available from an onboard star tracker, it is often desirable to recognize the background stars in the OpNav images to better align the image. While many image processing algorithms exist for finding stars, efficiency and reliability remain key issues in the presence of extended bodies(e.g. the Moon, Earth), especially when attempting to solve the full lost-in-space problem. Some star outliers(stars identified with high residuals)could appear in the camera field of view, however using them in the attitude estimation or camera calibration would lead to less accurate results. Therefore, we require new and robust approaches to remove these outliers before any further processing. The emphasis of the work is on developing a simple and robust iterative technique to detect and reject the outliers which could be found in any frame during the lost in space attitude determination or during the camera calibration. These outliers are determined based on the residuals of the centroids of the detected stars and the corresponding location using the star catalog. If the residuals exceed a predetermined threshold value, the object will be detected as an outlier and will be removed before another attitude determination and calibration iteration is performed. The performance for both attitude determination and on-orbit camera calibration are improved by an almost two-fold increase in accuracy when applying this outlier rejection technique.

OpNav

Pattern-Recognition System for Approaching a Known Target

A closed-loop pattern-recognition system is designed to provide guidance for maneuvering a small exploratory robotic vehicle (rover) on Mars to return to a landed spacecraft to deliver soil and rock samples that the spacecraft would subsequently bring back to Earth. The system could be adapted to terrestrial use in guiding mobile robots to approach known structures that humans could not approach safely, for such purposes as reconnaissance in military or law-enforcement applications, terrestrial scientific exploration, and removal of explosive or other hazardous items. The system has been demonstrated in experiments in which the Field Integrated Design and Operations (FIDO) rover (a prototype Mars rover equipped with a video camera for guidance) is made to return to a mockup of Mars-lander spacecraft. The FIDO rover camera autonomously acquires an image of the lander from a distance of 125 m in an outdoor environment. Then under guidance by an algorithm that performs fusion of multiple line and texture features in digitized images acquired by the camera, the rover traverses the intervening terrain, using features derived from images of the lander truss structure. Then by use of precise pattern matching for determining the position and orientation of the rover relative to the lander, the rover aligns itself with the bottom of ramps extending from the lander, in preparation for climbing the ramps to deliver samples to the lander. The most innovative aspect of the system is a set of pattern-recognition algorithms that govern a three-phase visual-guidance sequence for approaching the lander. During the first phase, a multifeature fusion algorithm integrates the outputs of a horizontal-line-detection algorithm and a wavelet-transform-based visual-area-of-interest algorithm for detecting the lander from a significant distance. The horizontal-line-detection algorithm is used to determine candidate lander locations based on detection of a horizontal deck that is part of the lander.

Huntsberger, Terrance

Microstructure of Al2O3 scales formed on NiCrAl alloys

The structure of transient scales formed on pure and Y or Zr-doped Ni-15Cr-13Al alloys oxidized for 0.1 hr at 1100 C was studied by the use of transmission electron microscopy. Crystallographically oriented scales were found on all three alloys, but especially for the Zr-doped NiCrAl. The oriented scales consisted of alpha-(Al,Cr)2O3, Ni(Al,Cr)2O4 and gamma-Al2O3. They were often found in intimate contact with each other such that the close-packed planes and directions of one oxide phase were aligned with those of another. The prominent structural features of the oriented scales were approximately equal to micrometer subgrains; voids, antiphase domain boundaries and aligned precipitates were also prevalent. Randomly oriented alpha-Al2O3 was also found and was the only oxide ever observed at the immediate oxide metal interface. These approximately 0.15 micrometer grains were populated by intragranular voids which decreased in size and number towards the oxide metal interface. A sequence of oxidation was proposed in which the composition of the growing scale changed from oriented oxides rich in Ni and Cr to oriented oxides rich in Al. At the same time the structure changed from cubic spinels to hexagonal corundums with apparent precipitates of one phase in the matrix of the other. Eventually randomly oriented pure alpha-Al2O3 formed as the stable oxide with an abrupt transition: there was no gradual loss of orientation, no gradual compositional change or no gradual decrease in precipitate density.

Smialek, J. L.