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At least 163 records · Page 9

Computational Aerothermodynamic Design Issues for Hypersonic Vehicles

A brief review of the evolutionary progress in computational aerothermodynamics is presented. The current status of computational aerothermodynamics is then discussed, with emphasis on its capabilities and limitations for contributions to the design process of hypersonic vehicles. Some topics to be highlighted include: (1) aerodynamic coefficient predictions with emphasis on high temperature gas effects; (2) surface heating and temperature predictions for thermal protection system (TPS) design in a high temperature, thermochemical nonequilibrium environment; (3) methods for extracting and extending computational fluid dynamic (CFD) solutions for efficient utilization by all members of a multidisciplinary design team; (4) physical models; (5) validation process and error estimation; and (6) gridding and solution generation strategies. Recent experiences in the design of X-33 will be featured. Computational aerothermodynamic contributions to Mars Pathfinder, METEOR, and Stardust (Comet Sample return) will also provide context for this discussion. Some of the barriers that currently limit computational aerothermodynamics to a predominantly reactive mode in the design process will also be discussed, with the goal of providing focus for future research.

Gnoffo, Peter A.↗

The REH theory of protein and nucleic acid divergence - A retrospective update

The random evolutionary hits (REH) theory of evolutionary divergence, originally proposed in 1972, is restated with attention to certain aspects of the theory that have caused confusion. The theory assumes that natural selection and stochastic processes interact and that natural selection restricts those codon sites which may fix mutations. The predicted total number of fixed nucleotide replacements agrees with data for cytochrome c, a-hemoglobin, beta-hemoglobin, and myoglobin. The restatement analyzes the magnitude of possible sources of errors and simplifies calculational methodology by supplying polynomial expressions to replace tables and graphs.

Holmquist, R.↗

Rapid evolution of cis-regulatory sequences via local point mutations

Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

Non-NASA Center↗

Genomic Language model for Annotation of Repetitive Elements (GLARE) v1.0

GLARE (Genomic Language model for Annotation of Repetitive Elements) is a tool that classifies transposable elements (TEs)—the mobile, repetitive DNA sequences that make up large fractions of eukaryotic genomes. GLARE fine-tunes the NTv3-650M genomic language model on a harmonized collection of curated TE sequences from the PanTEon and Repbase reference databases, assigning each input sequence to one of 11 orders and 32 superfamilies in a Wicker-compatible taxonomy. Features. From nucleotide FASTA input, GLARE outputs per-sequence predictions, class summaries, composition figures, and an annotated FASTA. It provides calibrated confidence scores with optional abstention and runs on CPU or GPU. Uses. GLARE serves as a classification component in genome-annotation pipelines, downstream of TE discovery, supporting genome annotation and comparative and evolutionary genomics. Advantages. GLARE is the first repeat-element classifier to leverage a pretrained genomic language model. Combined with multi-database training, this approach outperformed all nine classifiers in the PanTEon benchmark, generalized better to unseen taxonomic clades, and remained robust to sequence orientation—a common failure mode of existing tools.

Bruna, Tomas [Lawrence Berkeley National Laborator↗

Century-long timelines of herbarium genomes predict plant stomatal response to climate change

Abstract Dissecting plant responses to the environment is key to understanding whether and how plants adapt to anthropogenic climate change. Stomata, plants’ pores for gas exchange, are expected to decrease in density following increased CO 2 concentrations, a trend already observed in multiple plant species. However, it is unclear whether such responses are based on genetic changes and evolutionary adaptation. Here we make use of extensive knowledge of 43 genes in the stomatal development pathway and newly generated genome information of 191 Arabidopsis thaliana historical herbarium specimens collected over 193 years to directly link genetic variation with climate change. While we find that the essential transcription factors SPCH, MUTE and FAMA, central to stomatal development, are under strong evolutionary constraints, several regulators of stomatal development show signs of local adaptation in contemporary samples from different geographic regions. We then develop a functional score based on known effects of gene knock-out on stomatal development that recovers a classic pattern of stomatal density decrease over the past centuries, suggesting a genetic component contributing to this change. This approach combining historical genomics with functional experimental knowledge could allow further investigations of how different, even in historical samples unmeasurable, cellular plant phenotypes may have already responded to climate change through adaptive evolution.

Environmental Sciences & Ecology↗

A Fully Associative, Non-Linear Kinematic, Unified Viscoplastic Model for Titanium Based Matrices

Specific forms for both the Gibb's and complementary dissipation potentials are chosen such that a complete (i.e., fully associative) potential based multiaxial unified viscoplastic model is obtained. This model possesses one tensorial internal state variable that is associated with dislocation substructure, with an evolutionary law that has nonlinear kinematic hardening and both thermal and strain induced recovery mechanisms. A unique aspect of the present model is the inclusion of non-linear hardening through the use of a compliance operator, derived from the Gibb's potential, in the evolution law for the back stress. This non-linear tensorial operator is significant in that it allows both the flow and evolutionary laws to be fully associative (and therefore easily integrated) and greatly influences the multiaxial response under non-proportional loading paths. In addition to this nonlinear compliance operator, a new consistent, potential preserving, internal strain unloading criterion has been introduced to prevent abnormalities in the predicted stress-strain curves, which are present with nonlinear hardening formulations, during unloading and reversed loading of the external variables. Specification of an experimental program for the complete determination of the material functions and parameters for characterizing a metallic matrix, e.g., TIMETAL 21S, is given. The experiments utilized are tensile, creep, and step creep tests. Finally, a comparison of this model and a commonly used Bodner-Partom model is made on the basis of predictive accuracy and numerical efficiency.

Arnold, S. M.↗

NASA Tech Briefs, July 2009

Topics covered include: Dual Cryogenic Capacitive Density Sensor; Hail Monitor Sensor; Miniature Six-Axis Load Sensor for Robotic Fingertip; Improved Blackbody Temperature Sensors for a Vacuum Furnace; Wrap-Around Out-the-Window Sensor Fusion System; Wide-Range Temperature Sensors with High-Level Pulse Train Output; Terminal Descent Sensor Simulation; A Robust Mechanical Sensing System for Unmanned Sea Surface Vehicles; Additive for Low-Temperature Operation of Li-(CF)n Cells; Li/CFx Cells Optimized for Low-Temperature Operation; Number Codes Readable by Magnetic-Field-Response Recorders; Determining Locations by Use of Networks of Passive Beacons; Superconducting Hot-Electron Submillimeter-Wave Detector; Large-Aperture Membrane Active Phased-Array Antennas; Optical Injection Locking of a VCSEL in an OEO; Measuring Multiple Resistances Using Single-Point Excitation; Improved-Bandwidth Transimpedance Amplifier; Inter-Symbol Guard Time for Synchronizing Optical PPM; Novel Materials Containing Single-Wall Carbon Nanotubes Wrapped in Polymer Molecules; Light-Curing Adhesive Repair Tapes; Thin-Film Solid Oxide Fuel Cells; Zinc Alloys for the Fabrication of Semiconductor Devices; Small, Lightweight, Collapsible Glove Box; Radial Halbach Magnetic Bearings; Aerial Deployment and Inflation System for Mars Helium Balloons; Steel Primer Chamber Assemblies for Dual Initiated Pyrovalves; Voice Coil Percussive Mechanism Concept for Hammer Drill; Inherently Ducted Propfans and Bi-Props; Silicon Nanowire Growth at Chosen Positions and Orientations; Detecting Airborne Mercury by Use of Gold Nanowires; Detecting Airborne Mercury by Use of Palladium Chloride; Micro Electron MicroProbe and Sample Analyzer; Nanowire Electron Scattering Spectroscopy; Electron-Spin Filters Would Offer Spin Polarization Greater than 1; Subcritical-Water Extraction of Organics from Solid Matrices; A Model for Predicting Thermoelectric Properties of Bi2Te3; Integrated Miniature Arrays of Optical Biomolecule Detectors; A Software Rejuvenation Framework for Distributed Computing; Kurtosis Approach to Solution of a Nonlinear ICA Problem; Robust Software Architecture for Robots; R4SA for Controlling Robots; Bio-Inspired Neural Model for Learning Dynamic Models; Evolutionary Computing Methods for Spectral Retrieval; Monitoring Disasters by Use of Instrumented Robotic Aircraft; Complexity for Survival of Living Systems; Using Drained Spacecraft Propellant Tanks for Habitation; Connecting Node; and Electrolytes for Low-Temperature Operation of Li-CFx Cells.

Source record↗

Pathways and Challenges to Innovation in Aerospace

This paper explores impediments to innovation in aerospace and suggests how successful pathways from other industries can be adopted to facilitate greater innovation. Because of its nature, space exploration would seem to be a ripe field of technical innovation. However, engineering can also be a frustratingly conservative endeavor when the realities of cost and risk are included. Impediments like the "find the fault" engineering culture, the treatment of technical risk as almost always evaluated in terms of negative impact, the difficult to account for expansive Moore's Law growth when making predictions, and the stove-piped structural organization of most large aerospace companies and federally funded research laboratories tend to inhibit cross-cutting technical innovation. One successful example of a multi-use cross cutting application that can scale with Moore's Law is the Evolutionary Computational Methods (ECM) technique developed at the Jet Propulsion Lab for automated spectral retrieval. Future innovations like computational engineering and automated design optimization can potentially redefine space exploration, but will require learning lessons from successful innovators.

Terrile, Richard J.↗

Correlational selection and genetic architecture shape the evolution of the leaf economics spectrum in a perennial grass

The generality of the worldwide leaf economics spectrum (LES) has made it a pillar of trait-based ecological research. Yet, few studies have examined the processes shaping the evolution of the LES within species, in part, because most species occupy only a small portion of the LES. Here, to address this gap, we took advantage of the distinct leaf economics strategies present in different ecotypes of the phenotypically diverse perennial grass Panicum virgatum (switchgrass) to generate a genetic mapping population, which we planted in common gardens at three sites spanning 12 degrees of latitude in the central United States. With this genetic mapping population, we evaluated two potentially interacting causes of LES evolution: 1) genetic architecture, where multiple traits are influenced by either the same gene (pleiotropy) or by genes in close physical proximity (genetic linkage), and 2) correlational selection, where selection acts on traits in combination rather than in isolation. We found that shared genetic architecture influenced covariation between photosynthetic rate (A MASS ) and leaf nitrogen (N MASS ) and between A MASS and leaf mass per area (LMA). We also found that correlational selection favored the trait combinations predicted by the LES (e.g., high LMA with low N MASS or low LMA with high N MASS ) and disfavored other, mismatched trait combinations at two of the three sites. Together, these results demonstrate how the evolution of an integrated LES within species can arise from multiple evolutionary causes.

59 BASIC BIOLOGICAL SCIENCES↗

High-Order Methods in NASA’s Next Generation of Computational Fluid Dynamics Tools

The missions of the National Aeronautics and Space Administration (NASA) routinely produce unique requirements and challenges for development and application of Computational Fluid Dynamics (CFD) methods. NASA presently embodies four distinct Mission Directorates: Aeronautics Research, Exploration Systems, Science, and Space Operations. These missions generate requirements for systems that operate in a wide variety of environments. They range from the high-speed flight of aerodynamically optimized vehicles operating in the earth’s atmosphere to spacecraft designed for missions that don’t favor aerodynamic optimization, some operating in the atmosphere of planets and planetary moons such as Mars and Venus or Saturn’s moon Titan. Systems supporting these vehicles, such as rocket and jet propulsion, reaction control systems, fluid and thermal transfer systems, etc. can also generate their own unique set of flow phenomena that challenge today’s CFD methodology. Through the NASA Engineering and Safety Center (NESC), NASA annually conducts state-of-the-discipline assessments in fifteen distinct engineering disciplines. These assessments are performed by the NASA Technical Fellows that lead Technical Discipline Teams (TDT) of recognized experts in these fifteen areas. In the Aerosciences discipline, three topics have been identified as the top challenges for the discipline: aero-plume interaction prediction, unsteady separated flows, and aerothermodynamic prediction. These challenge areas are defined by the Agency’s high-risk projects and problems on which the NESC is requested to perform independent testing, analysis, and assessments. When viewed as a whole, these tests, analyses, and assessments provide a clear view of the recurring technical challenges facing Agency engineers and researchers and can be used to guide future research and technology development. The present state-of-the-art in the application of CFD at NASA is the use of Reynolds-Averaged Navier- Stokes (RANS) solvers, primarily executed in a steady-state mode of operation. In isolated cases, Unsteady RANS (URANS) solvers have been employed when steady RANS solutions produce poorly converging or oscillating results or in cases, such as aeroelastic analysis, which require unsteady aerodynamic simulation. For most traditional external and internal aerodynamic flows, structured overset grids or unstructured grids are employed to minimize geometric modeling and grid generation times. Grid adaptation, primarily as a series of coarse-grain intermediate processing steps is also seeing use on particularly complex flow problems and configurations. In the case of aerothermodynamic flows, engineers have been forced to continue to employ structured grid techniques as the present unstructured grid methodology has proven inadequate in the prediction of surface heating. In the area of aero-plume interaction modeling, two-gas, frozen chemistry simulation is generally the state-of-the- art, with some production solvers capable of predicting flows with only a single gas component. Prediction of flows falling into the afore-mentioned top Aerosciences technical challenges have severely stressed the present state-of-the-art in CFD prediction and for some problems, such as unsteady separated flows and aero-plume interaction cases, engineers have begun employing Large Eddy Simulation (LES) and Hybrid RANS/LES techniques. In some isolated aero-propulsion interaction cases, chemically reacting flow simulations have been applied. These methods are highly evolutionary and engineers have little experience in their application, so they cannot be heavily relied upon in today’s application environment. Therefore, this leads one to muse over which numerical technologies will be included in the CFD tools that will be employed 30 years in the future. This presentation will describe specific technical problems that have stressed NASA’s traditional CFD methods to their breaking point and will link these issues to the Agency’s top Aerosciences technical challenges. The discussion will then shift to the characteristics of future CFD solvers that will be required to attack these challenges and how these characteristics differ from the present state-of-the- art. High-order methods certainly appear to have a place in the development of future CFD tools and some of the physical characteristics of our most challenging problems suggest that high-order methods are the only way to effectively solve them. But there are some relatively severe implementation issues that face these methods, particularly in the area of general applicability and robust operation as an engineering tool. Desired characteristics of next-generation CFD solvers will be discussed and the author’s view of which emerging numerical technologies might be employed to address these attributes will also be presented

David M Schuster↗

Unlocking expanded flagellin perception through rational receptor engineering

Abstract The surface-localized receptor kinase FLS2 detects the flg22 epitope from bacterial flagella. FLS2 is conserved across land plants, but bacterial pathogens exhibit polymorphic flg22 epitopes. Most FLS2 homologues possess narrow perception ranges, but four with expanded perception have been identified. Using diversity analyses, AlphaFold modelling and amino acid properties, key residues enabling expanded recognition were mapped to FLS2’s concave surface, interacting with the co-receptor and polymorphic flg22 residues. Synthetic biology enabled engineering of expanded recognition from QvFLS2 (Quercus variabilis) into a homologue with canonical perception. A similar approach enabled transfer ofAgrobacteriumperception from FLS2 XL (Vitis riparia) into VrFLS2. Evolutionary analyses across three plant orders showed residues under positive selection aligning with those binding the co-receptor and flg22’s C terminus, suggesting more alleles with expanded perception exist. Our experimental data enabled the identification of specific receptor amino acid properties and AlphaFold3 metrics that facilitate predicting FLS2–flg22 recognition. This study provides a framework for rational receptor engineering to enhance pathogen restriction.

Plant Sciences↗

Thermoviscoplastic model with application to copper

A viscoplastic model is developed which is applicable to anisothermal, cyclic, and multiaxial loading conditions. Three internal state variables are used in the model; one to account for kinematic effects, and the other two to account for isotropic effects. One of the isotropic variables is a measure of yield strength, while the other is a measure of limit strength. Each internal state variable evolves through a process of competition between strain hardening and recovery. There is no explicit coupling between dynamic and thermal recovery in any evolutionary equation, which is a useful simplification in the development of the model. The thermodynamic condition of intrinsic dissipation constrains the thermal recovery function of the model. Application of the model is made to copper, and cyclic experiments under isothermal, thermomechanical, and nonproportional loading conditions are considered. Correlations and predictions of the model are representative of observed material behavior.

Freed, Alan D.↗

Probing Mechanism of Evolution of Simple Genomes

Our overarching goal is to discover how the structure of the genotypic space of RNA polymers affects their ability to evolve. Specifically, we will address several fundamental questions that, so far, have remained largely unanswered. Was the genotypic space explored globally or only locally? Was the outcome of early evolution predictable or was it, instead, govern by chance? What was the role of neutral mutations in the evolution of increasing complex systems? As the first step, we study the problem in the example of RNA ligases. We obtain the complete, empirical fitness landscapes for short ligases and examine possible evolutionary paths for RNA molecules that are sufficiently long to preclude exhaustive search of the genotypic space.

Evolution↗

Viscoplastic constitutive relationships with dependence on thermomechanical history

Experimental evidence of thermomechanical history dependence in the cyclic hardening behavior of some common high-temperature structural alloys is presented with special emphasis on dynamic metallurgical changes. The inadequacy of formulating nonisothermal constitutive equations solely on the basis of isothermal testing is discussed. A representation of thermoviscoplasticity is proposed that qualitatively accounts for the observed hereditary behavior. This is achieved by formulating the scalar evolutionary equation in an established viscoplasticity theory to reflect thermomechanical path dependence. To assess the importance of accounting for thermomechanical history dependence in practical structural analyses, two qualitative models are specified: (1) formulated as if based entirely on isothermal information; (2) to reflect thermomechanical path dependence using the proposed thermoviscoplastic representation. Predictions of the two models are compared and the impact the calculated differences in deformation behavior may have on subsequent lifetime predictions is discussed.

Robinson, D. N.↗

Annual Research Briefs - 2000: Center for Turbulence Research

This report contains the 2000 annual progress reports of the postdoctoral Fellows and visiting scholars of the Center for Turbulence Research (CTR). It summarizes the research efforts undertaken under the core CTR program. Last year, CTR sponsored sixteen resident Postdoctoral Fellows, nine Research Associates, and two Senior Research Fellows, hosted seven short term visitors, and supported four doctoral students. The Research Associates are supported by the Departments of Defense and Energy. The reports in this volume are divided into five groups. The first group largely consists of the new areas of interest at CTR. It includes efficient algorithms for molecular dynamics, stability in protoplanetary disks, and experimental and numerical applications of evolutionary optimization algorithms for jet flow control. The next group of reports is in experimental, theoretical, and numerical modeling efforts in turbulent combustion. As more challenging computations are attempted, the need for additional theoretical and experimental studies in combustion has emerged. A pacing item for computation of nonpremixed combustion is the prediction of extinction and re-ignition phenomena, which is currently being addressed at CTR. The third group of reports is in the development of accurate and efficient numerical methods, which has always been an important part of CTR's work. This is the tool development part of the program which supports our high fidelity numerical simulations in such areas as turbulence in complex geometries, hypersonics, and acoustics. The final two groups of reports are concerned with LES and RANS prediction methods. There has been significant progress in wall modeling for LES of high Reynolds number turbulence and in validation of the v(exp 2) - f model for industrial applications.

Source record↗

Artificial Intelligence Transforming Post-Translational Modification Research

Post-Translational Modifications (PTMs) are covalent changes to amino acids that occur after protein synthesis, including covalent modifications on side chains and peptide backbones. Many PTMs profoundly impact cellular and molecular functions and structures, and their significance extends to evolutionary studies as well. In light of these implications, we have explored how artificial intelligence (AI) can be utilized in researching PTMs. Initially, rationales for adopting AI and its advantages in understanding the functions of PTMs are discussed. Then, various deep learning architectures and programs, including recent applications of language models, for predicting PTM sites on proteins and the regulatory functions of these PTMs are compared. Finally, our high-throughput PTM-data-generation pipeline, which formats data suitably for AI training and predictions is described. We hope this review illuminates areas where future AI models on PTMs can be improved, thereby contributing to the field of PTM bioengineering.

59 BASIC BIOLOGICAL SCIENCES↗

Planet Hunters TESS IV: A Massive, Compact Hierarchical Triple Star System TIC 470710327

We report the discovery and analysis of a massive, compact, hierarchical triple system (TIC 470710327) initially identified by citizen scientists in data obtained by NASA’s Transiting Exoplanet Survey Satellite (TESS). Spectroscopic follow-up observations obtained with the HERMES spectrograph, combined with eclipse-timing variations (ETVs), confirm that the system is comprised of three OB stars, with a compact 1.10 d eclipsing binary and a non-eclipsing tertiary on a 52.04 d orbit. Dynamical modelling of the system (from radial velocity and ETVs) reveal a rare configuration wherein the tertiary star (O9.5-B0.5V; 14–17 M ꙩ ) is more massive than the combined mass of the inner binary (10.9–13.2 M ꙩ ). Given the high mass of the tertiary, we predict that this system will undergo multiple phases of mass transfer in the future, and likely end up as a double neutron star gravitational wave progenitor or an exotic Thorne–Żytkow object. Further observational characterization of this system promises constraints on both formation scenarios of massive stars as well as their exotic evolutionary end-products.

NASA's Transiting Exoplanet Survey Satellite (TESS↗

Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish

Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine–freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene ‘cassettes’. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.

59 BASIC BIOLOGICAL SCIENCES↗