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At least 613 records · Page 34

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

NASA Discipline Number 14-10↗

Reducing costs of managing and accessing navigation and ancillary data by relying on the extensive capabilities of NASA's spice system

The SPICE system of navigation and ancillary data possesses a number of traits that make its use in modern space missions of all types highly cost efficient. The core of the system is a software library providing API interfaces for storing and retrieving such data as trajectories, orientations, time conversions, and instrument geometry parameters. Applications used at any stage of a mission life cycle can call SPICE APIs to access this data and compute geometric quantities required for observation planning, engineering assessment and science data analysis. SPICE is implemented in three different languages, supported on 20+ computer environments, and distributed with complete source code and documentation. It includes capabilities that are extensively tested by everyday use in many active projects and are applicable to all types of space missions - flyby, orbiters, observatories, landers and rovers. While a customer's initial SPICE adaptation for the first mission or experiment requires a modest effort, this initial effort pays off because adaptation for subsequent missions/experiments is just a small fraction of the initial investment, with the majority of tools based on SPICE requiring no or very minor changes.

ancillary data↗

Reply to "Comment on 'A Self-Consistent Model of the Interacting Ring Current Ions and Electromagnetic Ion Cyclotron Waves, Initial Results: Waves and Precipitation Fluxes' and 'Self-Consistent Model of the Magnetospheric Ring Current and Propagating Electromagnetic Ion Cyclotron Waves: Waves in Multi-Ion Magnetosphere' by Khazanov et al. et al."

It is well-known that the effects of electromagnetic ion cyclotron (EMIC) waves on ring current (RC) ion and radiation belt (RB) electron dynamics strongly depend on such particle/wave characteristics as the phase-space distribution function, frequency, wavenormal angle, wave energy, and the form of wave spectral energy density. The consequence is that accurate modeling of EMIC waves and RC particles requires robust inclusion of the interdependent dynamics of wave growth/damping, wave propagation, and[ particles. Such a self-consistent model is being progressively developed by Khazanov et al. [2002, 2006, 2007]. This model is based on a system of coupled kinetic equations for the RC and EMIC wave power spectral density along with the ray tracing equations. Thome and Home [2007] (hereafter referred to as TH2007) call the Khazanov et al. [2002, 2006] results into question in their Comment. The points in contention can be summarized as follows. TH2007 claim that: (1) "the important damping of waves by thermal heavy ions is completely ignored", and Landau damping during resonant interaction with thermal electrons is not included in our model; (2) EMIC wave damping due to RC O + is not included in our simulation; (3) non-linear processes limiting EMIC wave amplitude are not included in our model; (4) growth of the background fluctuations to a physically significantamplitude"must occur during a single transit of the unstable region" with subsequent damping below bi-ion latitudes,and consequently"the bounce averaged wave kinetic equation employed in the code contains a physically erroneous 'assumption". Our reply will address each of these points as well as other criticisms mentioned in the Comment. TH2007 are focused on two of our papers that are separated by four years. Significant progress in the self-consistent treatment of the RC-EMIC wave system has been achieved during those years. The paper by Khazanov et al. [2006] presents the latest version of our model, and in this Reply we refer mostly to this paper.

Khazanov, G. V.↗

A Requirements-Driven Optimization Method for Acoustic Liners Using Analytic Derivatives

More than ever, there is flexibility and freedom in acoustic liner design. Subject to practical considerations, liner design variables may be manipulated to achieve a target attenuation spectrum. But characteristics of the ideal attenuation spectrum can be difficult to know. Many multidisciplinary system effects govern how engine noise sources contribute to community noise. Given a hardwall fan noise source to be suppressed, and using an analytical certification noise model to compute a community noise measure of merit, the optimal attenuation spectrum can be derived using multidisciplinary systems analysis methods. In a previous paper on this subject, a method deriving the ideal target attenuation spectrum that minimizes noise perceived by observers on the ground was described. A simple code-wrapping approach was used to evaluate a community noise objective function for an external optimizer. Gradients were evaluated using a finite difference formula. The subject of this paper is an application of analytic derivatives that supply precise gradients to an optimization process. Analytic derivatives improve the efficiency and accuracy of gradient-based optimization methods and allow consideration of more design variables. In addition, the benefit of variable impedance liners is explored using a multi-objective optimization.

Aircraft Noise↗

A 2D Kaleidoscope of Electron Heat Fluxes Driven by Auroral Electron Precipitation

Electron heat flux is an important value for ionospheric space weather modeling networks. Utilizing the 2D array of Time History of Events and Macroscale Interactions during Substorms all-sky-imager (ASI) observations, Gabrielse et al. (2021, https://doi.org/10.3389/fphy.2021.744298) described a new method that estimates the auroral scale sizes of intense precipitating electron energy fluxes and their mean energies during two substorms on 16 February 2010. These parameters in combination with SuperThermal Electron Transport code were used to develop a new methodology to calculate electron thermal fluxes from data inputs in 2D during one of the substorms at 09:40:00 UT across Canada and Alaska. To test the effect of various precipitation lifetimes on electron heat flux values, boxcar averages ranging from 0 to 900 s were applied to the ASI data. These data are then combined with the newly developed kinetic simulation to determine the thermal fluxes associated with the observed diffuse and discrete precipitation.

Electron precipitation in aurora↗

Numerical solution of Space Shuttle Orbiter flow field

The supersonic, viscous laminar flow around the Space Shuttle Orbiter forebody has been computed with a parabolized Navier-Stokes code using a generalized coordinate transformation. The initial solution for the nose part of the Orbiter geometry was obtained with a three-dimensional time-dependent Navier-Stokes solver. It was necessary to employ a wind axis oriented coordinate system to obtain the initial solution with the time-dependent code. The generalized PNS technique used in this study allows the solution to be marched from the given initial data surface to any desired surface downstream. A grid point clustering scheme was employed to accurately describe the body shape by clustering points at the wing tip and at the wing body juncture. The computed heat transfer coefficients, pressure coefficients, and shock shapes are compared with the available experimental data for 0 degrees and 30 degrees angle of attack.

Venkatapathy, E.↗

Effects of cosmic rays on single event upsets

Assistance was provided to the Brookhaven Single Event Upset (SEU) Test Facility. Computer codes were developed for fragmentation and secondary radiation affecting Very Large Scale Integration (VLSI) in space. A computer controlled CV (HP4192) test was developed for Terman analysis. Also developed were high speed parametric tests which are independent of operator judgment and a charge pumping technique for measurement of D(sub it) (E). The X-ray secondary effects, and parametric degradation as a function of dose rate were simulated. The SPICE simulation of static RAMs with various resistor filters was tested.

Venable, D. D.↗

Probabilistic analysis of bladed turbine disks and the effect of mistuning

Probabilistic assessment of the maximum blade response on a mistuned rotor disk is performed using the computer code NESSUS. The uncertainties in natural frequency, excitation frequency, amplitude of excitation and damping are included to obtain the cumulative distribution function (CDF) of blade responses. Advanced mean value first order analysis is used to compute CDF. The sensitivities of different random variables are identified. Effect of the number of blades on a rotor on mistuning is evaluated. It is shown that the uncertainties associated with the forcing function parameters have significant effect on the response distribution of the bladed rotor.

Shah, A. R.↗

Probabilistic analysis of bladed turbine disks and the effect of mistuning

Probabilistic assessment of the maximum blade response on a mistuned rotor disk is performed using the computer code NESSUS. The uncertainties in natural frequency, excitation frequency, amplitude of excitation and damping have been included to obtain the cumulative distribution function (CDF) of blade responses. Advanced mean value first order analysis is used to compute CDF. The sensitivities of different random variables are identified. Effect of the number of blades on a rotor on mistuning is evaluated. It is shown that the uncertainties associated with the forcing function parameters have significant effect on the response distribution of the bladed rotor.

Shah, Ashwin↗

Techniques for hot structures testing

Hot structures testing have been going on since the early 1960's beginning with the Mach 6, X-15 airplane. Early hot structures test programs at NASA-Ames-Dryden focused on operational testing required to support the X-15 flight test program, and early hot structures research projects focused on developing lab test techniques to simulate flight thermal profiles. More recent efforts involved numerous large and small hot structures test programs that served to develop test methods and measurement techniques to provide data that promoted the correlation of test data with results from analytical codes. In Nov. 1988 a workshop was sponsored that focused on the correlation of hot structures test data with analysis. Limited material is drawn from the workshop and a more formal documentation is provided of topics that focus on hot structures test techniques used at NASA-Ames-Dryden. Topics covered include the data acquisition and control of testing, the quartz lamp heater systems, current strain and temperature sensors, and hot structures test techniques used to simulate the flight thermal environment in the lab.

Deangelis, V. Michael↗

An Icy Kuiper Belt Around the Young Solar-type Star HD 181327

Context. HD 181327 is a young main sequence F5/F6 V star belonging to the Beta Pictoris moving group (age approx.. 12 Myr). It harbors an optically thin belt of circumstellar material at radius approx.. 90 AU, presumed to result from collisions in a population of unseen planetesimals. Aims. We aim to study the dust properties in the belt in details, and to constrain the gas-to-dust ratio. Methods. We obtained far-infrared photometric observations of HD 181327 with the PACS instrument onboard the Herschel Space Observatory, complemented by new 3.2 mm observations carried with the ATCA array. The geometry of the belt is constrained with newly reduced HST/NICMOS scattered light images that allow the degeneracy between the disk geometry and the dust properties to be broken. We then use the radiative transfer code GRaTeR to compute a large grid of models, and we identify the grain models that best reproduce the spectral energy distribution (SED) through a Bayesian analysis. We attempt to detect the oxygen and ionized carbon fine-structure lines with Herschel/PACS spectroscopy, providing observables to our photochemical code ProDiMo. Results. The HST observations confirm that the dust is confined in a narrow belt. The continuum is detected with Herschel/PACS completing nicely the SED in the far-infrared. The disk is marginally resolved with both PACS and ATCA. A medium integration of the gas spectral lines only provides upper limits on the [OI] and [CII] line fluxes.We show that the HD 181327 dust disk consists of micron-sized grains of porous amorphous silicates and carbonaceous material surrounded by an important layer of ice, for a total dust mass of approx.. 0.05 Solar Mass (in grains up to 1 mm). We discuss evidences that the grains consists of fluffy aggregates. The upper limits on the gas atomic lines do not provide unambiguous constraints: only if the PAH abundance is high, the gas mass must be lower than approx. 17 Solar Mass. Conclusions. Despite the weak constraints on the gas disk, the age of HD 181327 and the properties of the dust disk suggest that it has passed the stage of gaseous planets formation. The dust reveals a population of icy planetesimals, similar to the primitive Edgeworth-Kuiper belt, that may be a source for the future delivery of water and volatiles onto forming terrestrial planets.

HD 181327↗

The effects of rotational flow, viscosity, thickness, and shape on transonic flutter dip phenomena

The transonic flutter dip phenomena on thin airfoils, which are employed for propfan blades, is investigated using an integrated Euler/Navier-Stokes code and a two degrees of freedom typical section structural model. As a part of the code validation, the flutter characteristics of the NACA 64A010 airfoil are also investigated. In addition, the effects of artificial dissipation models, rotational flow, initial conditions, mean angle of attack, viscosity, airfoil thickness, and shape on flutter are investigated. The results obtained with an Euler code for the NACA 64A010 airfoil are in reasonable agreement with published results obtained by using transonic small disturbance and Euler codes. The two artifical dissipation models, one based on the local pressure gradient scaled by a common factor and the other based on the local presure gradient scaled by a spectral radius, predicted the same flutter speeds except in the recovery region for the case studied. The effects of rotation flow, initial conditions, mean angle of attack, and viscosity for the Reynolds number studied seem to be negligible or small on the minima of the flutter dip.

Reddy, T. S. R.↗

Experimental flutter boundaries with unsteady pressure distributions for the NACA 0012 Benchmark Model

The Structural Dynamics Div. at NASA-Langley has started a wind tunnel activity referred to as the Benchmark Models Program. The objective is to acquire test data that will be useful for developing and evaluating aeroelastic type Computational Fluid Dynamics codes currently in use or under development. The progress is described which was achieved in testing the first model in the Benchmark Models Program. Experimental flutter boundaries are presented for a rigid semispan model (NACA 0012 airfoil section) mounted on a flexible mount system. Also, steady and unsteady pressure measurements taken at the flutter condition are presented. The pressure data were acquired over the entire model chord located at the 60 pct. span station.

Rivera, Jose A., Jr.↗

The benchmark aeroelastic models program: Description and highlights of initial results

An experimental effort was implemented in aeroelasticity called the Benchmark Models Program. The primary purpose of this program is to provide the necessary data to evaluate computational fluid dynamic codes for aeroelastic analysis. It also focuses on increasing the understanding of the physics of unsteady flows and providing data for empirical design. An overview is given of this program and some results obtained in the initial tests are highlighted. The tests that were completed include measurement of unsteady pressures during flutter of rigid wing with a NACA 0012 airfoil section and dynamic response measurements of a flexible rectangular wing with a thick circular arc airfoil undergoing shock boundary layer oscillations.

Bennett, Robert M.↗

WGM Temperature Tracker

This software implements digital control of a WGM (whispering-gallerymode) resonator temperature based on the dual-mode approach. It comprises one acquisition (dual-channel) and three control modules. The interaction of the proportional-integral loops is designed in the original way, preventing the loops from fighting. The data processing is organized in parallel with the acquisition, which allows the computational overhead time to be suppressed or often completely avoided. WGM resonators potentially provide excellent optical references for metrology, clocks, spectroscopy, and other applications. However, extremely accurate (below micro-Kelvin) temperature stabilization is required. This software allows one specifically advantageous method of such stabilization to be implemented, which is immune to a variety of effects that mask the temperature variation. WGM Temperature Tracker 2.3 (see figure) is a LabVIEW code developed for dual-mode temperature stabilization of WGM resonators. It has allowed for the temperature stabilization at the level of 200 nK with one-second integration time, and 6 nK with 10,000-second integration time, with the above room-temperature set point. This software, in conjunction with the appropriate hardware, can be used as a noncryogenic temperature sensor/ controller with sub-micro-Kelvin sensitivity, which at the time of this reporting considerably outperforms the state of the art.

Strekalov, Dmitry V.↗

An Open-Science Approach to Address Individual Response to Simulated GCR In Genetically Diverse Populations of Mice and Humans

This project addresses the challenge of understanding and predicting individual radiation sensitivity by integrating genetics, demographics and biomarker characteristics across species (mice and humans). We hypothesize that ex vivo DNA repair response to GCR components is a central determinant of cancer risk from space radiation and can serve as a biomarker of radiation risk in combination with genetics. Automated image quantification of 53BP1+ radiation-induced foci (RIF) during the first 4-48 h post-irradiation was performed as a function of dose and LET in non-immortalized primary skin fibroblasts derived from 76 mice across 15 strains (5 inbred reference strains and 10 collaborative-cross strains) exposed to X rays (0.1, 1 and 4 Gy), 350 MeV/n 40Ar and 600 MeV/n 56Fe (1.1 and 3 particles/100sq. μm), as well as in peripheral blood mononuclear cells (PBMCs) from 768 healthy donors (matched ethnicity, 50/50 male/female, 18-70 years old) exposed to gamma rays (0.1 and 1 Gy), 350 MeV/n 28Si, 350 MeV/n 40Ar and 600 MeV/n 56Fe (1.1 and 3 particles/100sq. μm). A genome-wide association study (GWAS) was performed on the mouse strains between DNA damage responses to space radiation and single nucleotide polymorphisms (SNPs). We found SNPs, which were significantly associated to the RIF phenotype, mapped to genes and pathways that are functionally linked to health hazards for deep space exploration (e.g. carcinogenesis, nervous system damage and immune dysfunction). Some of these SNPs were located within protein coding regions, potentially interfering with protein functions and providing promising genetic targets for countermeasures. We also found correlations between both spontaneous and radiation-induced DNA damage and SNPs mapped to pathways associated with cellular metabolism. GWAS is undergoing for the human data. All data have been made available via the NASA Space Biology Open-Science database (genelab.nasa.gov) and we will discuss how various genomic and transcriptomic datasets can be accessed for modeling and integrated using machine learning methods for discovering new radiation biology.

Sylvain V Costes↗

Classical Flutter Analysis of X-57 Aircraft Mod II, III, and IV Configurations

To support airworthiness assessment of the X-57 electric propulsion demonstrator aircraft, the National Aeronautics and Space Administration (NASA) completed classical flutter analysis of the Mod II, Mod III, and Mod IV aircraft configurations. Aeroelastic analysis was primarily performed using the ZAERO analysis code developed by Zona Technology. Supplemental computational fluid dynamics (CFD) flutter analysis for the Mod III and Mod IV configurations was performed using NASA’s FUN3D software to verify the aeroelastic behavior at deployed flaps conditions. The NASTRAN finite element models (FEMs) used for aeroelastic analysis were developed by NASA. The final Mod II FEM utilized shell elements for the wing and fuselage, and beam elements for the tail and wing control surfaces. For Mod III and Mod IV aircraft models, shell element wing FEMs developed throughout the Mod III/IV wing design cycle were utilized. The fuselage and empennage FEM components were shared between the Mod II, III, and IV aircraft models. ZAERO analyses predicted flutter boundaries were >60% beyond the X-57 flight-test envelope never exceed airspeed (V NE ) for all configurations. Aeroelastic Reynolds-averaged Navier–Stokes (RANS) CFD simulations using FUN3D of the Mod III/IV configurations predicted flap mode instability did not occur until at least speeds of 60% higher than the Mod III/IV maximum flap deployment airspeed (V FE ).

Keerti K. Bhamidipati↗

The effects of rotational flow, viscosity, thickness, and shape on transonic flutter dip phenomena

The transonic flutter dip phenomena on thin airfoils, which are employed for propfan blades, is investigated using an integrated Euler/Navier-Stokes code and a two degrees of freedom typical section structural model. As a part of the code validation, the flutter characteristics of the NACA 64A010 airfoil are also investigated. In addition, the effects of artificial dissipation models, rotational flow, initial conditions, mean angle of attack, viscosity, airfoil thickness and shape on flutter are investigated. The results obtained with a Euler code for the NACA 64A010 airfoil are in reasonable agreement with published results obtained by using transonic small disturbance and Euler codes. The two artificial dissipation models, one based on the local pressure gradient scaled by a common factor and the other based on the local pressure gradient scaled by a spectral radius, predicted the same flutter speeds except in the recovery region for the case studied. The effects of rotational flow, initial conditions, mean angle of attack, and viscosity for the Reynold's number studied seem to be negligible or small on the minima of the flutter dip.

Reddy, T. S. R.↗