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At least 307 records · Page 17

Evolutionary Design of a Robotic Material Defect Detection System

During the post-flight inspection of SSME engines, several inaccessible regions must be disassembled to inspect for defects such as cracks, scratches, gouges, etc. An improvement to the inspection process would be the design and development of very small robots capable of penetrating these inaccessible regions and detecting the defects. The goal of this research was to utilize an evolutionary design approach for the robotic detection of these types of defects. A simulation and visualization tool was developed prior to receiving the hardware as a development test bed. A small, commercial off-the-shelf (COTS) robot was selected from several candidates as the proof of concept robot. The basic approach to detect the defects was to utilize Cadmium Sulfide (CdS) sensors to detect changes in contrast of an illuminated surface. A neural network, optimally designed utilizing a genetic algorithm, was employed to detect the presence of the defects (cracks). By utilization of the COTS robot and US sensors, the research successfully demonstrated that an evolutionarily designed neural network can detect the presence of surface defects.

Ballard, Gary↗

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗

Characterization of Aerodynamic Performance of Boundary-Layer-Ingesting Inlet Under Crosswind

NASA has been studying future transport concepts, envisioned to be technically realizable in the timeframe of 2020-2030, to meet environmental and performance goals. One concept receiving considerable interest involves a propulsion system embedded into a hybrid wing-body aircraft. While offering significant advantages in fuel savings and noise reduction by this concept, there are several technical challenges that are not encountered in the current fleet and must be overcome so as to deliver target performance and operability. One of these challenges is associated with an inlet system that ingests a significantly thick boundary layer, developing along the wing-body surface, into a serpentine diffuser before the flow meeting fan blades. The flow is subject to considerable total pressure loss and distorted at the fan face, much more significantly than in the inlet system of conventional aircraft. In our previous studies [1, 2], we have shown that through innovative design changes on the airframe surface, it is possible to simultaneously increase total pressure recovery and decrease distortion in the flow, without resorting to conventional penalty-ridden flow control concepts, such as vortex generator or boundary layer bleeding/suction. In the current study, we are interested in understanding the following issues: how the embedded propulsion system performs under a crosswind condition by studying in detail the flow characteristics of two inlets, the baseline and another optimized previously under the cruise condition. With the insight, it is hoped that it can help in the follow-on study by devising effective strategies to minimize flow distortion arising from the integration of an embedded-engine system into an airframe to the level acceptable to the operation and fuel consumption before 2030. To achieve these demanding goals, non-conventional concepts are called for; but technology gap is too big that it requires evolutionary approach by focusing various concepts and technologies needed in the next three generations of aircraft, respectively named as N+1, N+2, and N+3. Noticeably, considerable reduction in each category of 1 is required in N+2 (relative to Boeing 777-200 and GE90 engines) and N+3 (relative to Boeing 737-800 and CFM56-7B engines). In this study, concepts for N+2 is our interest. A concept that has potential to achieve these metrics and has been under intensive study is the hybrid wing body (HWB) airframe with a tightly integrated propulsion system, see Fig. 1. The inlet is non-circular at the entrance and the entering flow, no longer uniform or free of disturbances, and is now carrying with it a boundary layer developing along the fuselage; the inlet is thus known as boundary-layer-ingesting (BLI) inlet.

Liou, Meng-Sing↗

Phylogenomic discovery and engineering of nitrogen fixation into the bioenergy woody crop poplar

Biological nitrogen fixation (BNF) is a key process enabling plants in specific lineages to convert atmospheric dinitrogen (N₂) into bioavailable ammonia through symbioses with diazotrophic microbes. Expanding this capability beyond native nitrogen-fixing clades into non-nodulating crops would reduce synthetic fertilizer use, lowering energy inputs and environmental impacts in agriculture. Supported by DOE Funding Award DE-SC0018247, the NitFix project advanced foundational knowledge required to engineer root-nodule symbioses in new host species. The team generated the most comprehensive phylogenomic analysis to date of all known nodulating lineages, resolving the evolutionary history of nitrogen-fixing symbiosis and identifying core gene suites retained across nodulating taxa. Through multimodal genomics, transcriptomics, and functional analyses in Medicago truncatula and related species, the project mapped regulatory networks underlying nodule organogenesis, bacterial infection, and nitrogen-fixation efficiency. Key discoveries include the identification of conserved signaling modules for rhizobial recognition, transcription factors controlling nodule differentiation, and metabolic pathways integrating fixed nitrogen into plant growth. The project also developed enabling tools—including optimized transformation pipelines, gene-editing workflows, and imaging-based phenotyping—to accelerate engineering efforts in emerging models. Together, these results refine the mechanistic framework of symbiotic nitrogen fixation and highlight transferable components essential for rewiring these traits into non-nodulating crops.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative Analysis of TRGBs (CATs) from Unsupervised, Multi-halo-field Measurements: Contrast is Key

The tip of the red giant branch (TRGB) is an apparent discontinuity of the luminosity function (LF) due to the end of the red giant evolutionary phase and is used to measure distances in the local universe. In practice, tip localization via edge detection response (EDR) relies on several methods applied on a case-by-case basis. It is hard to evaluate how individual choices affect a distance estimation using only a single host field while also avoiding confirmation bias. To devise a standardized approach, we compare unsupervised, algorithmic analyses of the TRGB in multiple halo fields per galaxy. We first optimize methods for the lowest field-to-field dispersion, including spatial filtering, smoothing, and weighting of LF, color band selection, and tip selection based on the number of likely RGB stars and the ratio of stars below versus above the tip (R). We find R, which we call the tip contrast, to be the most important indicator of the quality of EDR measurements; higher R selection can decrease field-to-field dispersion. Further, since R is found to correlate with the age or metallicity of the stellar population based on theoretical modeling, it might result in a displacement of the detected tip magnitude. We find a tip-contrast relation with a slope of -0.023 ± 0.0046 mag/ratio, an ~5σ result that can be used to correct these variations in the detections. When using TRGB to establish a distance ladder, consistent TRGB standardization using tip-contrast relation across rungs is vital to make robust cosmological measurements.

79 ASTRONOMY AND ASTROPHYSICS↗

Rapid Preliminary Design of Interplanetary Trajectories Using the Evolutionary Mission Trajectory Generator

Preliminary design of interplanetary missions is a highly complex process. The mission designer must choose discrete parameters such as the number of flybys, the bodies at which those flybys are performed, and in some cases the final destination. In addition, a time-history of control variables must be chosen that defines the trajectory. There are often many thousands, if not millions, of possible trajectories to be evaluated. This can be a very expensive process in terms of the number of human analyst hours required. An automated approach is therefore very desirable. This work presents such an approach by posing the mission design problem as a hybrid optimal control problem. The method is demonstrated on notional high-thrust chemical and low-thrust electric propulsion missions. In the low-thrust case, the hybrid optimal control problem is augmented to include systems design optimization.

Design↗

An explicit solution to the optimal LQG problem for flexible structures with collocated rate sensors

We present a class of compensators in explicit form (not requiring numerical computer calculations) for stabilizing flexible structures with collocated rate sensors. They are based on the explicit solution, valid for both Continuum and FEM Models, of the LQG problem for minimizing mean square rate. They are robust with respect to system stability (will not destabilize modes even with mismatch of parameters), can be instrumented in state space form suitable for digital controllers, and can be specified directly from the structure modes and mode 'signature' (displacement vectors at sensor locations). Some simulation results are presented for the NASA LaRC Phase-Zero Evolutionary Model - a modal Trust model with 86 modes - showing damping ratios attainable as a function of compensator design parameters and complexity.

Balakrishnan, A. V.↗

Homology and the optimization of DNA sequence data

Three methods of nucleotide character analysis are discussed. Their implications for molecular sequence homology and phylogenetic analysis are compared. The criterion of inter-data set congruence, both character based and topological, are applied to two data sets to elucidate and potentially discriminate among these parsimony-based ideas. c2001 The Willi Hennig Society.

Non-NASA Center↗

Ship and satellite bio-optical research in the California Bight

Mesoscale biological patterns and processes in productive coastal waters were studied. The physical and biological processes leading to chlorophyll variability were investigated. The ecological and evolutionary significance of this variability, and its relation to the prediction of fish recruitment and marine mammal distributions was studied. Seasonal primary productivity (using chlorophyll as an indication of phytoplankton biomass) for the entire Southern California Bight region was assessed. Complementary and contemporaneous ship and satellite (Nimbus 7-CZCS) bio-optical data from the Southern California Bight and surrounding waters were obtained and analyzed. These data were also utilized for the development of multi-platform sampling strategies and the optimization of algorithms for the estimation of phytoplankton biomass and primary production from satellite imagery.

Smith, R. C.↗

An Evolutionary Algorithm Approach to Multi-Pass ERL Optics Design

An Energy Recovery Experiment at CEBAF (ER@CEBAF) is aimed at demonstrating high energy, low current, multi-pass energy recovery at the existing 12 GeV CEBAF accelerator. The beam break-up instability, limiting the maximum beam current, can be controlled through minimizing beta functions for the lowest energy pass, which gives a preference to strongly focusing optics, e.g. a semi-periodic FODO lattice. On the other hand, one needs to limit beta function excursions, caused by under focusing, at the higher energy passes, which in turn favors weakly focusing linac optics. Balancing both effects is the main objective of proposed multi-pass linac optics optimization. Here, we discuss an optics design process for ER@CEBAF transverse optics using a genetic algorithm.

Neththikumara, I.↗

Genomic clocks and evolutionary timescales

For decades, molecular clocks have helped to illuminate the evolutionary timescale of life, but now genomic data pose a challenge for time estimation methods. It is unclear how to integrate data from many genes, each potentially evolving under a different model of substitution and at a different rate. Current methods can be grouped by the way the data are handled (genes considered separately or combined into a 'supergene') and the way gene-specific rate models are applied (global versus local clock). There are advantages and disadvantages to each of these approaches, and the optimal method has not yet emerged. Fortunately, time estimates inferred using many genes or proteins have greater precision and appear to be robust to different approaches.

Evolution, Molecular↗

Rapid Preliminary Design of Interplanetary Trajectories Using the Evolutionary Mission Trajectory Generator

This set of tutorial slides is an introduction to the Evolutionary Mission Trajectory Generator (EMTG), NASA Goddard Space Flight Center's autonomous tool for preliminary design of interplanetary missions. This slide set covers the basics of creating and post-processing simple interplanetary missions in EMTG using both high-thrust chemical and low-thrust electric propulsion along with a variety of operational constraints.

optimization↗

Multi-Objective Scheduling for the Cluster II Constellation

This paper describes the application of the MUSE multiobjecctive scheduling framework to the Cluster II WBD scheduling domain. Cluster II is an ESA four-spacecraft constellation designed to study the plasma environment of the Earth and it's magnetosphere. One of the instruments on each of the four spacecraft is the Wide Band Data (WBD) plasma wave experiment. We have applied the MUSE evolutionary algorithm to the scheduling problem represented by this instrument, and the result has been adopted and utilized by the WBD schedulers for nearly a year. This paper describes the WBD scheduling problem, its representation in MUSE, and some of the visualization elements that provide insight into objective value tradeoffs.

observatory scheduilng↗

Heterologous expression of Arabidopsis laccase2, laccase4 and peroxidase52 driven under developing xylem specific promoter DX15 improves saccharification in populus

Secondary cell wall holds considerable potential as it has gained immense momentum to replace the lignocellulosic feedstock into fuels. Lignin one of the components of secondary cell wall tightly holds the polysaccharides thereby enhancing the recalcitrance and complexity in the biomass. Laccases (LAC) and peroxidases (PRX) are the major phenyl-oxidases playing key functions during the polymerization of monolignols into lignin. Yet, the functions of laccase and peroxidases gene families remained largely unknown. Hence, the objective of this conducted study is to understand the role of specific LAC and PRX in Populus wood formation and to further investigate how the altered Lac and Prx expression affects biomass recalcitrance and plant growth. This study of heterologous expression of Arabidopsis Lac and Prx genes was conducted in poplar to avoid any otherwise occurring co-suppression mechanism during the homologous overexpression of highly expressed native genes. In the pursuit of optimizing lignocellulosic biomass for biofuel production, the present study focuses on harnessing the enzymatic potential of Arabidopsis thaliana Laccase2, Laccase4, and Peroxidase52 through heterologous expression. We overexpressed selected Arabidopsis laccase2 (AtLac2), laccase4 (AtLac4), and peroxidase52 (AtPrx52) genes, based on their high transcript expression respective to the differentiating xylem tissues in the stem, in hybrid poplar (cv. 717) expressed under the developing xylem tissue-specific promoter, DX15 characterized the transgenic populus for the investigation of growth phenotypes and recalcitrance efficiency. Bioinformatics analyses conducted on AtLac2 and AtLac4 and AtPrx52, revealed the evolutionary relationship between the laccase gene and peroxidase gene homologs, respectively. Transgenic poplar plant lines overexpressing the AtLac2 gene (AtLac2-OE) showed an increase in plant height without a change in biomass yield as compared to the controls; whereas AtLac4-OE and AtPrx52-OE transgenic lines did not show any such observable growth phenotypes compared to their respective controls. The changes in the levels of lignin content and S/G ratios in the transgenic poplar resulted in a significant increase in the saccharification efficiency as compared to the control plants. Overall, saccharification efficiency was increased by 35–50%, 21–42%, and 8–39% in AtLac2-OE, AtLac4-OE, and AtPrx52-OE transgenic poplar lines, respectively, as compared to their controls. Moreover, the bioengineered plants maintained normal growth and development, underscoring the feasibility of this approach for biomass improvement without compromising overall plant fitness. This study also sheds light on the potential of exploiting regulatory elements of DX15 to drive targeted expression of lignin-modifying enzymes, thereby providing a promising avenue for tailoring biomass for improved biofuel production. These findings contribute to the growing body of knowledge in synthetic biology and plant biotechnology, offering a sustainable solution to address the challenges associated with lignocellulosic biomass recalcitrance.

09 BIOMASS FUELS↗

The Evolution of Technology in the Deep Space Network: A History of the Advanced Systems Program

The Deep Space Network (DSN) of 1995 might be described as the evolutionary result of 45 years of deep space communication and navigation, together with the synergistic activities of radio science and radar and radio astronomy. But the evolution of the DSN did not just happen - it was carefully planned and created. The evolution of the DSN has been an ongoing engineering activity, and engineering is a process of problem solving under constraints, one of which is technology. In turn, technology is the knowledge base providing the capability and experience for practical application of various areas of science, when needed. The best engineering solutions result from optimization under the fewest constraints, and if technology needs are well anticipated (ready when needed), then the most effective engineering solution is possible. Throughout the history of the DSN it has been the goal and function of DSN advanced technology development (designated the DSN Advanced Systems Program from 1963 through 1994) to supply the technology needs of the DSN when needed, and thus to minimize this constraint on DSN engineering. Technology often takes considerable time to develop, and when that happens, it is important to have anticipated engineering needs; at times, this anticipation has been by as much as 15 years. Also, on a number of occasions, mission malfunctions or emergencies have resulted in unplanned needs for technology that has, in fact, been available from the reservoir of advanced technology provided by the DSN Advanced Systems Program. Sometimes, even DSN engineering personnel fail to realize that the organization of JPL permits an overlap of DSN advanced technology activities with subsequent engineering activities. This can result in the flow of advanced technology into DSN engineering in a natural and sometimes almost unnoticed way. In the following pages, we will explore some of the many contributions of the DSN Advanced Systems Program that were provided to DSN Engineering and Implementation. These contributions are, for the most part, unique capabilities that have met the requirements of flight projects for 45 years. These unique capabilities include not only the world's best deep-space communications system, but also outstanding competency in the fields of radio metric measurement, radar and radio astronomy, and radio science.

Layland, J. W.↗

Asteroseismic Inversions of Mixed Acoustic-Gravity Modes to Probe the Stellar Core Structure

The discovery of mixed acoustic-gravity modes of oscillations of moderate mass stars opens a unique opportunity to infer the structure of the inner energy-generating cores and thus test the stellar evolution theory. The mixed modes have properties of internal gravity waves (g-modes) in the convectively stable helium core and properties of acoustic modes outside the core. We select several sets of the oscillation mode frequencies in the mass range from about 1.3 to 1.6 solar masses from the Kepler Legacy database, and apply the optimally localized averaging inversion technique previously developed for low-degree helioseismology. The inversion technique takes into account the uncertainties in the determination of the mass and radius of the stars, as well as the surface effects. The methodology provides sensitivity kernels for various structure properties, including the sound speed, density, and Ledoux parameter of convective stability, and, thus, the direct relationship between the stellar properties and the deviation of observed frequencies from the reference models. The inversion results reveal significant deviations in the core structure from the reference models calculated using the MESA evolutionary code for the stellar parameters obtained by the asteroseismic model grid fitting. Our analysis shows that the best resolution of the inner helium core and surrounding shell is achieved in inversions for the Ledoux parameter.

SMD↗

Robustness properties of LQG optimized compensators for collocated rate sensors

In this paper we study the robustness with respect to stability of the closed-loop system with collocated rate sensor using LQG (mean square rate) optimized compensators. Our main result is that the transmission zeros of the compensator are precisely the structure modes when the actuator/sensor locations are 'pinned' and/or 'clamped': i.e., motion in the direction sensed is not allowed. We have stability even under parameter mismatch, except in the unlikely situation where such a mode frequency of the assumed system coincides with an undamped mode frequency of the real system and the corresponding mode shape is an eigenvector of the compensator transfer function matrix at that frequency. For a truncated modal model - such as that of the NASA LaRC Phase Zero Evolutionary model - the transmission zeros of the corresponding compensator transfer function can be interpreted as the structure modes when motion in the directions sensed is prohibited.

Balakrishnan, A. V.↗

Warming is Associated With More Encoded Antimicrobial Resistance Genes and Transcriptions Within Five Drug Classes in Soil Bacteria: A Case Study and Synthesis

ABSTRACT The effect of warming on anti‐microbial resistance (AMR) genes in the environment has critical implications for public health but is little studied. We collected published soil bacterial genomes from the BV‐BRC database and tested the correlation between reported optimal growth temperature and the number of encoded AMR genes. Furthermore, we tested the relationship between temperature and AMR gene transcription in a natural ecosystem by analysing soil transcriptomes from a warming manipulation experiment in an Alaskan boreal forest. We hypothesised that there is a positive relationship between warming and AMR prevalence in gene content in bacterial genomes and transcriptomic sequences, and that this effect would vary by drug class. Regarding the bacterial genomes, we found a positive relationship between the fraction of encoded AMR genes and the reported optimal temperature of soil bacteria. The drug classes tetracycline and lincosamide/macrolide/streptogramin had the strongest positive relationship with reported optimal temperature. For the case study in a natural ecosystem, we found 61 significantly upregulated AMR gene‐associated transcripts spanning eight drug classes in warmed plots. In the Alaskan soil samples, we found that warming elicited the strongest positive effect on transcripts targeting lincosamide/streptogramin, beta‐lactam and phenicol/quinolone antibiotics. Overall, higher temperatures were linked to AMR gene prevalence.

Hacopian, Melanie T. [Department of Ecology and Ev↗