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At least 739 records · Page 41

Predicting Cognitive States Using Machine Learning Fusion Paradigms to Reduce Model Uncertainty

The development of a synergetic system between humans and technology is a challenge that the scientific community has been facing for many years. Our aeronautic research aims to enhance this synergy between humans and machines through predictive human performance modeling for systems to mitigate high-risk situations. By being able to predict and anticipate human states, the crew monitoring system should be able to adjust and support the pilot for aviation safety. Our work focusing on attention-related human performance-limiting states (AHPLS) that impact a pilot’s performance and introduce high-risk catastrophic situations [1]. For example, AHPLS has been cited as a causal factor in more than 50% of all loss control in flight and thus contributes significantly toward commercial aviation fatalities [1, 2]. Cognitive state and its physiological fingerprint can be valuable information for this detecting AHPLS, but human cognitive state detection is still a major limitation for these crew monitoring systems.

machine learning↗

Thermo-Mechanical Shock, X-Ray Transport and Radiation Response Analysis Experiments on NIF

The study of x-ray induced rapid heating and the resulting material responses - (thermomechanical shock (TMS) and thermo-structural response (TSR)) - is important to our understanding of material behavior in extreme environments. A series of high conversion efficiency (XRCE) x-ray sources have been developed for the NIF laser facility ranging in fluence and spectral content. In conjunction with source development, we have developed a new XTRRA (X-ray Transport and Radiation Response Analysis) test cassette to hold a set of samples, each at equal distance from target chamber center (TCC) where the x-ray source is placed. Design and performance details of the x-ray sources is discussed elsewhere. Here, we describe the development and use of this TMS XTRRA test cassette. The XTRRA test cassette is a snout mounted on a NIF Diagnostic Instrument Manipulator (DIM) designed to position six samples equidistant from the x-ray source to assure uniform irradiation of all samples. Photon Displacement interferometry (PDI) is used to measure the displacement of the rear surface of each sample resulting from x-ray exposure on the front of the sample. This will help determine the x-ray generated impulse on the sample. The samples are retrieved from the snout after the shot for inspection and post-shot analysis including the measurement of sample ablated mass and engineering tests examining changes in the material structure. The data from experiments are compared to predictions from LLNL’s ASC codes and used to inform models implemented in these codes. Thus, XRCE x-ray sources with the XTRRA snout at the National Ignition Facility (NIF) laser at the Lawrence Livermore National Laboratory provide the ability to expose a broad range of material samples directly to high x-ray fluence, measure shock transits, and recover the sample for further analysis post-shot.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

2022 Annual Site Environment Report, Princeton Plasma Physics Laboratory

This report provides the U.S. Department of Energy (DOE) and the public with information on the level of radioactive and non-radioactive pollutants (if any) that are added to the environment as a result of Princeton Plasma Physics Laboratory’s (PPPL) operations. This report fulfills the annual public reporting requirements of DOE Order 231.1B. The results of PPPL’s 2022 environmental surveillance and monitoring program are presented and discussed. The report also summarizes environmental initiatives, assessments, and community involvement programs that were undertaken in 2022. PPPL’s on-site operations started to be restored in 2022, following curtailments in 2020 and 2021 for the global coronavirus (COVID-19) pandemic. PPPL has engaged in fusion energy research since 1951 and at its current locations since 1958. The Laboratory’s mission is to develop the scientific knowledge and advanced engineering to enable fusion to power the U.S. and the world, and to develop the understanding of plasmas from the nano- to the astrophysical scale. PPPL’s primary experiment, the National Spherical Torus Experiment-Upgrade (NSTX-U) is a collaboration among national laboratories, universities, and national and international research institutions and is a major element in the US Fusion Energy Sciences Program. Its design tests the physics principles of spherical torus (ST) plasmas, playing an important role in the development of smaller, more economical fusion reactors. Due to previous operational issues, NSTX-U did not operate in 2022. PPPL is engaged in a project to replace key NSTX-U components and systems to enable the operation of this international magnetic fusion user facility. In 2022, PPPL’s radiological environmental monitoring program measured tritium in the air at onsite sampling stations. Using highly sensitive air monitors, PPPL is capable of detecting small changes in the ambient levels of tritium. The operation of monitors located on D-site is used to demonstrate compliance with the National Emission Standard for Hazardous Air Pollutants (NESHAPs) regulations. Also included in PPPL’s radiological environmental monitoring program, are water monitoring – ground, surface, and waste waters. PPPL’s radiological monitoring program characterized the background levels of tritium in the environment and those data are presented in this report. Ground water monitoring continued under New Jersey Department of Environmental Protection’s (NJDEP) Site Remediation Program regulations. PPPL monitored for non-radiological contaminants, mainly volatile organic compounds (components of common degreasing solvents). In 2022, PPPL complied with permit limits for surface water and sanitary wastewater discharges. PPPL was honored with an award for EPEAT-certified electronics purchasing from the Global Electronics Council.

54 ENVIRONMENTAL SCIENCES↗

Turbulence statistical analysis of the L-H transition and RMPs in KSTAR

Here, we investigate the turbulence statistics associated with low-to-high confinement (L-H) transitions and externally applied resonant magnetic perturbations (RMPs) in KSTAR. Time-series fluctuations of electron density n e , electron temperature T e , and the time derivative of the poloidal magnetic field dB θ /dt (Mirnov coils) are analysed using information-geometric measures (information rate Γ and information length $\mathcal{L}$ = ∫ Γ dt), together with kurtosis κ and variance σ 2 . In low-density upper single-null plasmas (n e ~ 1.2 x 10 19 m -3 ), a ~80 kHz magnetic mode coupling n e , T e , dB θ /dt and emerges prior to the L-H transition and persists into the edge-localised modes H-mode. Edge-localised RMPs (ERMPs) suppress this coherent mode but enhance intermittency, producing frequent bursts that abruptly reshape the time-dependent probability density functions (PDFs) and generate large spikes in Γ (with smaller changes in κ), signalling ERMP-driven departures from quasi-stationarity. The impact of ERMPs on background fluctuation levels depends on density, radial location, and the fluctuating variable itself ($\tilde{n}$, $\tilde{T}$, $\dot{B}$ θ ), whereas $\mathcal{L}$ provides a robust, regime-agnostic measure of cumulative statistical reorganisation and spatial decorrelation. In particular, at low density we observe weaker coupling between $\tilde{n}$ and $\tilde{T}$, along with a tendency toward decreased radial correlation-most clearly for $\tilde{T}$-under ERMPs. Overall, information geometry cleanly captures intermittent events, quantifies non-equilibrium PDF evolution, and offers a compact, cross-diagnostic metric for assessing resonant magnetic perturbation effects on edge transport and correlation across densities, radial locations, and confinement states.

Kim, Eun-jin [Coventry Univ. (United Kingdom); Seo↗

Determining Magnetic Field Directions and Omni-directional Fluxes of Particles from STPSat-6 ZPS Plasma Measurements

This report summarizes our recent data derivation efforts on STPSat-6 ZPS plasma measurements, presenting final outcomes. We begin by outlining the methodology developed to determine local magnetic field directions from measured directional intensities of ~20 keV ions, leveraging symmetry in particles’ pitch-angle distributions, and the determined field directions over a storm period are shown with errors analyzed through comparison with NOAA GOES measurements. Next, we further assess the validity of the method and quantify its overall high performance while acknowledging certain caveats. Finally, given local magnetic field directions and ZPS data, we explain how omni-directional fluxes of particles can be derived from ZPS measurements with limited directional coverage, and estimate the related errors under several theoretical scenarios. The methods developed in this study can be applied for processing and augmenting ZPS data for the next, and the insights gained here can also inform instrument design in the future.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sensor selection and tool wear prediction with data‐driven models for precision machining

Abstract Estimation of tool wear in precision machining is vital in the traditional subtractive machining industry to reduce processing cost, improve manufacturing efficiency and product quality. In this vein, fusion of time and frequency‐domain features of commonly sensed signals can provide an early indication of tool wear and improve its prediction accuracy for prognostics and health management. This paper presents a data‐driven methodology and a complete tool chain for the inference of precision machining tool wear from fused machine measurements, such as cutting force, power, audio and vibration signals, and quantify the usefulness of each measurement. Indicators of tool wear are extracted from time‐domain signal statistics, frequency‐domain analysis, and time‐frequency domain analysis. Correlation coefficients between the extracted features (indicators) and the tool wear are used to select the most informative features. Principal Component Analysis and Partial Least‐Squares are used to reduce the dimensionality of the feature space. Regression models, including linear regression, support vector regression, Decision tree regression, neural network regression and Gaussian process regression, are used to predict the tool wear using data from a Haas milling machine performing spiral boss face milling. The performance of the regression models based on subsets of sensors validates the preliminary estimates about the saliency of the sensors. The experimental results show that the proposed methods can predict the machine tool wear precisely, with readily available sensor measurements. Neural network and Gaussian process regression were able to achieve good estimates of tool wear at different machine operating conditions. The most informative signal in predicting tool wear was shown to be the vibration signal. Time‐frequency domain features were the most informative features among the combination of features of three domains. In addition, using partial least squares components extracted from the original features of signals led to higher prediction accuracy.

Han, Seulki↗

A charged particle transport approximation for thick and thin plasmas

In this work, we will construct a simple method to be utilized in the interpretation of the properties of a thin plasma from a study of the transport of charged particles through it. We do so by first demonstrating how charged particle fluxes encode local plasma information in their spectra for sufficiently thick plasmas and then propose how to extend that analysis to the thin plasma limit where the extensive geometry cannot be neglected through arguments from scale separation. We provide a numerical treatment of the transport problem and demonstrate that it is in good agreement with the approximation we present. Finally, we utilize both the numerical solution and our novel approximation to study the impact of the extensive scale of the plasma on the yield and flux normalized high-energy neutron spectra resulting from the upscattering of charged fuel ions. Using this analysis, we show that (after controlling for fusion yield) for the same uniform densities and temperatures, larger plasmas have higher magnitude but softer reaction-in-flight (RIF) neutron spectra relative to smaller plasmas. This is because larger plasmas retain more knocked-on suprathermal ions within their bulk and can downscatter them to lower average energies, while smaller plasmas allow a larger fraction of high energy particles to “range out” of the system prior to substantial downscattering or inducing an RIF reaction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Laser-metal interaction dynamics during additive manufacturing resolved by detection of thermally-induced electron emission

In situ monitoring is required to improve the understanding and increase the reliability of additive manufacturing methods such as laser powder bed fusion (LPBF). Current diagnostic methods for LPBF capture optical images, X-ray radiographs, or measure the emission of thermal or acoustic signals from the component. Herein, a methodology based on the thermal emission of electrons - thermionic emission - from the metal surface during LPBF is proposed which can resolve laser-material interaction dynamics. The high sensitivity of thermionic emission to surface temperature and surface morphology is revealed to enable precise determination of the transition between conduction and keyhole mode melting regimes. Increases in thermionic emission are correlated to laser scanning conditions that give rise to pore formation and regions where surface defects are pronounced. The information presented here is a critical step in furthering our understanding and validation of laser-based metal additive manufacturing.

36 MATERIALS SCIENCE↗

Generative AI models for learning flow maps of stochastic dynamical systems in bounded domains

Simulating stochastic differential equations (SDEs) in bounded domains, presents significant computational challenges due to particle exit phenomena, which requires accurate modeling of interior stochastic dynamics and boundary interactions. Despite the success of machine learning-based methods in learning SDEs, existing learning methods are not applicable to SDEs in bounded domains because they cannot accurately capture the particle exit dynamics. We present a unified hybrid data-driven approach that combines a conditional diffusion model with an exit prediction neural network to capture both interior stochastic dynamics and boundary exit phenomena. Our ML model consists of two major components: a neural network that learns exit probabilities using binary cross-entropy loss with rigorous convergence guarantees, and a training-free diffusion model that generates state transitions for non-exiting particles using closed-form score functions. The two components are integrated through a probabilistic sampling algorithm that determines particle exit at each time step and generates appropriate state transitions. Here, the performance of the proposed approach is demonstrated via three test cases: a one-dimensional simplified problem for theoretical verification, a two-dimensional advection-diffusion problem in a bounded domain, and a three-dimensional problem of interest to magnetically confined fusion plasmas.

Bounded domains↗

Update on Integrated Optical Design Analyzer

Updated information on the Integrated Optical Design Analyzer (IODA) computer program has become available. IODA was described in Software for Multidisciplinary Concurrent Optical Design (MFS-31452), NASA Tech Briefs, Vol. 25, No. 10 (October 2001), page 8a. To recapitulate: IODA facilitates multidisciplinary concurrent engineering of highly precise optical instruments. The architecture of IODA was developed by reviewing design processes and software in an effort to automate design procedures. IODA significantly reduces design iteration cycle time and eliminates many potential sources of error. IODA integrates the modeling efforts of a team of experts in different disciplines (e.g., optics, structural analysis, and heat transfer) working at different locations and provides seamless fusion of data among thermal, structural, and optical models used to design an instrument. IODA is compatible with data files generated by the NASTRAN structural-analysis program and the Code V (Registered Trademark) optical-analysis program, and can be used to couple analyses performed by these two programs. IODA supports multiple-load-case analysis for quickly accomplishing trade studies. IODA can also model the transient response of an instrument under the influence of dynamic loads and disturbances.

Moore, James D., Jr.↗

NSTX-U National Research Program: White Paper in Response to Call from FESAC Sub-Committee

Both scientific and technical innovation is needed for the realization of an attractive engineering solution for a timely and cost-effective Pilot Plant, the design and construction of which is the overarching recommendation of the FESAC Long Range Plan, and the 2021 NASEM Pilot Plant reports, which underpin the Bold Decadal Vision. The two most significant plasma physics gaps to close for a Compact Pilot Plant (CPP) are core confinement improvement and heat flux mitigation, neither of which have been closed in an integrated fashion for any planned fusion power production device. High core confinement and stability are essential for producing majority self-driven plasmas in CPPs with reduced size and auxiliary heating power requirements, with an improvement in confinement being the major driver for cost reduction of a CPP. The National Spherical Tokamak Experiment - Upgrade (NSTX-U) is a unique low aspect ratio research facility that will address the fundamental challenge of developing the science and technology basis for a CPP design that integrates high core and edge confinement with the ability to mitigate very high incident heat fluxes. NSTX-U capabilities will enable the high performance, already achieved on NSTX, to extend into physics regimes much closer to those anticipated in Spherical Tokamak (ST)-based CPPs. These confinement and stability properties will be assessed by a full complement of diagnostics and analysis tools, which will also aid in the development of the underlying theory and predictive models needed for further optimization. Both conventional and transformative heat flux mitigation methods, such as liquid lithium plasma-facing components, will be developed and tested in-situ in NSTX-U at incident heat fluxes of ~100 MW/m 2 , and will inform plans and reduce risk for a subsequent major upgrade to the device to fully heated, high-Z wall and full liquid lithium divertor capability, a technology that potentially could then be implemented on any magnetic confinement device at any aspect ratio. NSTX-U research is fully complementary to programs performed on other STs, nationally and internationally. Furthermore, NSTX-U research has a direct connection to the private sector by informing design choices for future power production facilities being developed by these companies. The NSTX-U program will operate as a national User Facility, with collaborating researchers, engineers, and graduate students from 19 outside institutions, and open to participation and experiments led by researchers from both public and private entities. The research program will advance workforce development through training of young scientists, engineers, and technicians, and it will also serve for further diagnostic innovation, especially for high heat flux and high-Z wall environments, and implementation of advanced artificial intelligence (AI) for plasma and heat flux control.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Spatial Distribution of Ultraviolet Emission from Cometary Activity at 67P/Churyumov-Gerasimenko

The Alice ultraviolet spectrograph on board the Rosetta orbiter provided the first near-nucleus ultraviolet observations of a cometary coma from arrival at comet 67P/Churyumov-Gerasimenko in 2014 August through 2016 September. The characterization of atomic and molecular emissions in the coma revealed the unexpected contribution of dissociative electron impact emission at large heliocentric distances and during some outbursts. This mechanism also proved useful for compositional analysis, and Alice observed many cases that suggested elevated levels of the supervolatile O{sub 2}, identifiable in part to their emissions resulting from dissociative electron impact. In this paper, we present the first two-dimensional UV maps constructed from Alice observations of atomic emission from 67P during an increase in cometary activity on 2015 November 7–8. Comparisons to observations of the background coma and an earlier collimated jet are used to describe possible changes to the near-nucleus coma and plasma. To verify the mapping method and place the Alice observations in context, comparisons to images derived from the MIRO and VIRTIS-H instruments are made. The spectra and maps we present show an increase in dissociative electron impact emission and an O{sub 2}/H{sub 2}O ratio of ~0.3 for the activity; these characteristics have been previously identified with cometary outbursts seen in Alice data. Further, UV maps following the increases in activity show the spatial extent and emission variation experienced by the near-nucleus coma, informing future UV observations of comets that lack the same spatial resolution.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Post-irradiation Examination of Eurofer-97 Steel Irradiated to 20 dpa at 200–400°C in HFIR under the EUROfusion (ORNL-KIT) Collaboration Program

The Oak Ridge National Laboratory/Karlsruhe Institute of Technology (ORNL/KIT) collaboration focuses on research involving irradiation experiments and post-irradiation examinations (PIE) of isotopically modified Eurofer-97 steels for fusion reactor applications. This collaboration capitalizes on ORNL’s expertise in radiation effects on materials and its capabilities in irradiation and PIE. The research aims to qualify Fe-9Cr-based Eurofer-97 steel under simulated fusion conditions, which include high doses and high transmutation rates. A unique isotopic modification technique is utilized in the research, wherein high-transmutation isotopes such as Fe-54 and Ni-58 are alloyed into the Eurofer steel to align with the expected helium production rates in fusion reactor conditions. This report presents the results of post-irradiation mechanical testing activities for the EUROFER-97/2 specimens after irradiation to ~20 dpa at various irradiation temperatures. The irradiation doses and temperatures for the ES capsules ranged from 18.4–20.4 dpa and 202–256°C, respectively. The mechanical property datasets, obtained through baseline testing and PIE of the tensile and fracture specimens, include microhardness data from 93 irradiated and non-irradiated tensile specimens and 28 irradiated bend bar specimens, uniaxial tensile property data from 45 irradiated and non-irradiated tensile specimens, and fracture toughness data from the bend bar specimens. Further data analyses provide statistical information on the microhardness values and tensile properties, as well as the reference ductile-brittle transition temperature (T 0 ) data.

36 MATERIALS SCIENCE↗

GPS/Magnetometer Based Satellite Navigation and Attitude Determination

In recent years algorithms were developed for orbit, attitude and angular-rate determination of Low Earth Orbiting (LEO) satellites. Those algorithms rely on measurements of magnetometers, which are standard, relatively inexpensive, sensors that are normally installed on every LEO satellite. Although magnetometers alone are sufficient for obtaining the desired information, the convergence of the algorithms to the correct values of the satellite orbital parameters, position, attitude and angular velocity is very slow. The addition of sun sensors reduces the convergence time considerably. However, for many LEO satellites the sun data is not available during portions of the orbit when the spacecraft (SC) is in the earth shadow. It is here where the GPS space vehicles (SV) can provide valuable support. This is clearly demonstrated in the present paper. Although GPS measurements alone can be used to obtain SC position, velocity, attitude and angular-rate, the use of magnetometers improve the results due to the synergistic effect of sensor fusion. Moreover, it is possible to obtain these results with less than three SVs. In this paper we introduce an estimation algorithm, which is a combination of an Extended Kalman Filter (EKF) and a Pseudo Linear Kalman Filter (PSELIKA).

Deutschmann, Julie↗

Real-time Enhanced Vision System

Flying in poor visibility conditions, such as rain, snow, fog or haze, is inherently dangerous. However these conditions can occur at nearly any location, so inevitably pilots must successfully navigate through them. At NASA Langley Research Center (LaRC), under support of the Aviation Safety and Security Program Office and the Systems Engineering Directorate, we are developing an Enhanced Vision System (EVS) that combines image enhancement and synthetic vision elements to assist pilots flying through adverse weather conditions. This system uses a combination of forward-looking infrared and visible sensors for data acquisition. A core function of the system is to enhance and fuse the sensor data in order to increase the information content and quality of the captured imagery. These operations must be performed in real-time for the pilot to use while flying. For image enhancement, we are using the LaRC patented Retinex algorithm since it performs exceptionally well for improving low-contrast range imagery typically seen during poor visibility conditions. In general, real-time operation of the Retinex requires specialized hardware. To date, we have successfully implemented a single-sensor real-time version of the Retinex on several different Digital Signal Processor (DSP) platforms. In this paper we give an overview of the EVS and its performance requirements for real-time enhancement and fusion and we discuss our current real-time Retinex implementations on DSPs.

Hines, Glenn D.↗

TMS XTRRA experiments on NIF

The study of x-ray induced rapid heating and the resulting material responses - (thermomechanical shock (TMS) and thermo-structural response (TSR)) - is important to our understanding of material behavior in extreme environments. A series of high conversion efficiency (XRCE) x-ray sources have been developed for the NIF laser facility ranging in fluence and spectral content. In conjunction with source development, we have developed a new XTRRA (X-ray Transport and Radiation Response Analysis) test cassette to hold a set of samples, each at equal distance from target chamber center (TCC) where the x-ray source is placed. Design and performance details of the x-ray sources is discussed elsewhere. Here, we describe the development and use of this TMS XTRRA test cassette. The XTRRA test cassette is a snout mounted on a NIF Diagnostic Instrument Manipulator (DIM) designed to position six samples equidistant from the x-ray source to assure uniform irradiation of all samples. Photon Displacement interferometry (PDI) is used to measure the displacement of the rear surface of each sample resulting from x-ray exposure on the front of the sample. This will help determine the x-ray generated impulse on the sample. The samples are retrieved from the snout after the shot for inspection and post-shot analysis including the measurement of sample ablated mass and engineering tests examining changes in the material structure. The data from experiments are compared to predictions from LLNL’s ASC codes and used to inform models implemented in these codes. Thus, XRCE x-ray sources with the XTRRA snout at the National Ignition Facility (NIF) laser at the Lawrence Livermore National Laboratory [1,2] provide the ability to expose a broad range of material samples directly to high x-ray fluence, measure shock transits, and recover the sample for further analysis post-shot.

36 MATERIALS SCIENCE↗

Discoveries in Blast-Driven Turbulence of Astrophysical Relevance

The fluid mixing caused by variable-density instabilities is important in a wide variety of scenarios from ocean mixing and astrophysical phenomena to nuclear fusion techniques and atomic weapons. This thesis explores the mixing resulting from a specific instability known as the Blast Driven Instability (BDI). This work investigates the variable density mixing in an explosively driven environment due to the fluid instabilities at the material interfaces. Specifically, diverging Richtmyer-Meshkov (impulsive-acceleration environment) and Rayleigh-Taylor (variable-acceleration environment) instabilities (present in supernova and inertial confinement fusion) are studied using advanced high-speed diagnostics in carefully designed laboratory experiments. The BDI morphology is presented through a time development of Mie scattering images, and steps through the parameter space (varying density ratio and driver speed), highlighting the development of the structures that form during mixing. A scaling criterion is used to relate the two systems of vastly different spatiotemporal scales. Velocity fields in the BDI have been captured for the first time using the high temporal resolution PIV technique. Subsequent analysis of the dynamics of the instability from the velocity fields illustrates the distribution of kinetic energy, the transition to turbulence, and the characteristic growth of the instability are discussed. This study furthers understanding of how blast-driven instability pertains to supernova and inertial confinement fusion science. The morphology of the BDI has been characterized for the first time. This work steps through the parameter space covered in Mie scattering experiments, and how the different parameters contribute to development of structures and mixing. It also examines a scaling of the Atwood number for expanding predictive capabilities to other experimental conditions and simulations. The first collection of velocity fields acquired for the BDI are recorded, and subsequent analysis evaluating the distribution of kinetic energy throughout space and time for two density ratios from the overall parameter space, as well as the transition to turbulence, estimated from a Reynolds number calculated based on momentum mixing are all presented. This information is useful in advancing the development of models to predict physics of high energy density applications where experiments are not always readily available. This research has successfully demonstrated understanding for the time criteria defining regimes where the shock driven (Richtmyer-Meshkov instability) and the buoyancy driven (Rayleigh-Taylor instability) dominates through a parametric study of density variation (Atwood number) and driver speed (Mach number). All this furthers understanding of how the BDI pertains to SN and ICF.

79 ASTRONOMY AND ASTROPHYSICS↗

Orthologs, paralogs and genome comparisons

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

Non-NASA Center↗