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Results for “evolutionary computation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
NASA NTRS1971

Interaction of fast particles with intergalactic matter.

A discussion is given of the relaxation of power-law cosmic-ray spectra in the intergalactic medium. The theoretical time-dependent spectra obtained are used to calculate the nonthermal radiation produced by bremsstrahlung of subcosmic-ray electrons colliding with ambient protons of the intergalactic gas. A comparison is made between the theory and the observations of the diffuse X-ray and gamma-ray background. The calculated cosmic-ray proton spectra are applied to a computation of the heating of the intergalactic medium, and the resulting thermal bremsstrahlung radiation is compared with the suprathermal proton bremsstrahlung flux. We conclude that nonthermal bremsstrahlung is unlikely to be an important contributor to the isotropic X- and gamma-ray background. However, cosmic-ray heating can provide a plausible heat source for maintaining a hot intergalactic gas, especially when evolutionary effects are included in the distribution of cosmic-ray sources.

Arons, J.↗
NASA NTRS1989

Computer simulation of the mathematical modeling involved in constitutive equation development: Via symbolic computations

Development of new material models for describing the high temperature constitutive behavior of real materials represents an important area of research in engineering disciplines. Derivation of mathematical expressions (constitutive equations) which describe this high temperature material behavior can be quite time consuming, involved and error prone; thus intelligent application of symbolic systems to facilitate this tedious process can be of significant benefit. A computerized procedure (SDICE) capable of efficiently deriving potential based constitutive models, in analytical form is presented. This package, running under MACSYMA, has the following features: partial differentiation, tensor computations, automatic grouping and labeling of common factors, expression substitution and simplification, back substitution of invariant and tensorial relations and a relational data base. Also limited aspects of invariant theory were incorporated into SDICE due to the utilization of potentials as a starting point and the desire for these potentials to be frame invariant (objective). Finally not only calculation of flow and/or evolutionary laws were accomplished but also the determination of history independent nonphysical coefficients in terms of physically measurable parameters, e.g., Young's modulus, was achieved. The uniqueness of SDICE resides in its ability to manipulate expressions in a general yet predefined order and simplify expressions so as to limit expression growth. Results are displayed when applicable utilizing index notation.

Arnold, S. M.↗
DOE OSTI2026

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families

The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.

Nextflow↗
NASA NTRS1985

The solar-flare induced earth's environment

A composite numerical simulation model developed from a series of MHD models was used to compute the solar-flare-generated disturbances of physical parameters, such as density, temperature, velocity, and magnetic field from the solar surface (i.e., the photospheric level) to the earth's environment. It is shown that the disturbed earth's environment at high latitudes can be approximated by starting with the knowledge of the occurrence and the strength of a solar flare, then simulating the evolutionary consequences of the solar disturbance through interplanetary space up to and through the magnetosphere.

Wu, S. T.↗
DOE OSTI2023

Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype–phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ω C , which measures the error-corrected convergence rate of protein evolution. While ω C distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype–phenotype associations, even in lineages that diverged for hundreds of millions of years.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Aerodynamic Shape Optimization Using Hybridized Differential Evolution

An aerodynamic shape optimization method that uses an evolutionary algorithm known at Differential Evolution (DE) in conjunction with various hybridization strategies is described. DE is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Various hybridization strategies for DE are explored, including the use of neural networks as well as traditional local search methods. A Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the hybrid DE optimizer. The method is implemented on distributed parallel computers so that new designs can be obtained within reasonable turnaround times. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. (The final paper will include at least one other aerodynamic design application). The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated.

Madavan, Nateri K.↗
NASA NTRS2015

An Automatic Medium to High Fidelity Low-Thrust Global Trajectory Toolchain; EMTG-GMAT

Solving the global optimization, low-thrust, multiple-flyby interplanetary trajectory problem with high-fidelity dynamical models requires an unreasonable amount of computational resources. A better approach, and one that is demonstrated in this paper, is a multi-step process whereby the solution of the aforementioned problem is solved at a lower-fidelity and this solution is used as an initial guess for a higher-fidelity solver. The framework presented in this work uses two tools developed by NASA Goddard Space Flight Center: the Evolutionary Mission Trajectory Generator (EMTG) and the General Mission Analysis Tool (GMAT). EMTG is a medium to medium-high fidelity low-thrust interplanetary global optimization solver, which now has the capability to automatically generate GMAT script files for seeding a high-fidelity solution using GMAT's local optimization capabilities. A discussion of the dynamical models as well as thruster and power modeling for both EMTG and GMAT are given in this paper. Current capabilities are demonstrated with examples that highlight the toolchains ability to efficiently solve the difficult low-thrust global optimization problem with little human intervention.

low thrust↗
DOE OSTI2022

Large Scale MD to Predict Epitope Regions in HIV Env [Slides]

Highly dense carbohydrates located on the surface of the HIV Env protein play a key role in immune evasion. Such evolutionary adaptation hampers any attempt to obtain a full mechanistic understanding of the role played by the glycans in protecting the virus against an effective immune response. Moreover, and due to their chemical variability, an accurate molecular understanding of the so called “glycan shield” is still limited by the lack of effective resolution of state-of-the-art experimental technics. Here, we have used extensive computational modelling in order to fill this gap, addressing the presence of a large glycan variability as observed experimentally. Based on an automated pipeline, we were able to assemble, set-up and simulate via Molecular dynamics hundreds of different glycosylated Env variants at nearly atomic resolution, recapitulating the glycosylation distributions observed experimentally. Results from these simulations were subjected to machine learning and very accurate prediction of simulation derived glycan shielding areas of each glycan as a function of static sequence features. Such predictive models of per-glycan shielding, incorporating both glycan dynamics and heterogeneity, were used to develop a novel sequence-based glycan shield mapping strategy. Parallel to these studies, we also developed an accurate machine learning approach to predict glycan heterogeneity data using sequence features and found good prediction accuracy.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

Designing a training tool for imaging mental models

The training process can be conceptualized as the student acquiring an evolutionary sequence of classification-problem solving mental models. For example a physician learns (1) classification systems for patient symptoms, diagnostic procedures, diseases, and therapeutic interventions and (2) interrelationships among these classifications (e.g., how to use diagnostic procedures to collect data about a patient's symptoms in order to identify the disease so that therapeutic measures can be taken. This project developed functional specifications for a computer-based tool, Mental Link, that allows the evaluative imaging of such mental models. The fundamental design approach underlying this representational medium is traversal of virtual cognition space. Typically intangible cognitive entities and links among them are visible as a three-dimensional web that represents a knowledge structure. The tool has a high degree of flexibility and customizability to allow extension to other types of uses, such a front-end to an intelligent tutoring system, knowledge base, hypermedia system, or semantic network.

Dede, Christopher J.↗
DOE OSTI2023

Structurally Constrained Evolutionary Algorithm for the Discovery and Design of Metastable Phases

Metastable materials are abundant in nature and technology, showcasing remarkable properties that inspire innovative materials design. However, traditional crystal structure prediction methods, which rely solely on energetic factors to determine a structure’s fitness, are not suitable for predicting the vast number of potentially synthesizable phases that represent a local minimum corresponding to a state in thermodynamic equilibrium. Here, we present a new approach for the prediction of metastable phases with specific structural features, and interface this method with the XTALOPT evolutionary algorithm. Our method relies on structural features that include the local crystalline order (e.g., the coordination number or chemical environment), and symmetry (e.g., Bravais lattice and space group) to filter the breeding pool of an evolutionary crystal structure search. The effectiveness of this approach is benchmarked on three known metastable systems: XeN 8 , with a two-dimensional polymeric nitrogen sublattice, brookite TiO 2 , and a high pressure BaH 4 phase that was recently characterized. Additionally, a newly predicted metastable melaminate salt, P1¯WC 3 N 6 , was found to possess an energy that is lower than two phases proposed in a recent computational study. Here, the method presented here could help in identifying the structures of compounds that have already been synthesized, and developing new synthesis targets with desired properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The Influence of the Instantaneous Collapse of Tailings Pond on Downstream Facilities

To evaluate the evolutionary processes guiding the formation of the tailings‐water mixtures produced by the instantaneous collapse of tailings ponds and the influence of these on downstream facilities, a 2D simulation model with reasonable boundary and working conditions derived from actual engineering practice was built in this study, and the relationship between dam‐break elevation and impact on downstream facilities was also analyzed to determine the relevant mechanism of influence. Computational results indicated that lowering the dam‐break elevation caused the maximum velocity and flooding depth, along with the flooded area at monitoring points, to gradually increase. The occurrence times of maximum velocity and flooding depth were also gradually moved forward as the breaking elevation was reduced; this effect is directly related to the increase in the total potential energy at the lower break elevations. Further simulations of sand‐prevent dams with different heights located downstream from a tailings pond were carried out to identify methods for mitigating the impact of dam failure. The results revealed that increasing the height of the sand‐prevent dam reduced the production of tailings mixtures. Based on the results, the construction of a sand‐prevent dam with a crest elevation equal to that of the starter dam was recommended.

Wang, Sha (ORCID:0000000324875445)↗
DOE OSTI2021

Real-Time Evolution and Deployment of Neuromorphic Computing at The Edge

Extremely low power neuromorphic systems are well-suited for deployment to the edge for many applications. In many use cases of neuromorphic computing for control, a spiking neural network is trained off-line using a simulation and then deployed to a neuromorphic system at the edge, where it will operate without ongoing training or learning. However, it may be desirable to continue training or learning at the edge to refine or adapt to the real-world system. In this work, we propose an approach for performing real-time evolutionary optimization for spiking neural networks for neuromorphic deployment at the edge. In particular, we propose a combination of simulation and real-world evaluations, along with feedback from the real-world environment, to train spiking neural networks for continuous deployment to the edge. We show that the real-time evolution at the edge approach achieves comparable performance to an evolution approach that requires constant evaluation in the realworld environment.

Schuman, Catherine↗
NASA NTRS1990

Is there a classical Hyades lithium problem?

The distribution of surface lithium abundances in the Hyades cluster, as a function of effective temperature, has resisted a satisfactory theoretical explanation for more than two decades. Trends in the historically recomputed values of stellar opacity have stimulated a systematic investigation of the effects of larger opacities on lithium depletion during the premain-sequence evolution of low-mass stars. It is shown that the calculated depletion depends quite strongly on the opacities employed, and that both surface and interior opacities play an important role. By performing standard evolutionary calculations with parameterized increments in the opacities, the observed Hyades Li and T(eff) relation for G and K dwarfs have been determined in a manner consistent with the other observational constraints. The solution presented herein requires an increase in interior opacities at about 4 million K over older values by approximately less than 37 percent. Such a change is not incompatible with the historical trends in opacity computations and suggests that the resolution of this problem lies solely in the opacities, without recourse to other physical mechanisms such as turbulent diffusion or 'extra mixing'.

Swenson, Fritz J.↗
DOE OSTI2025

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

The Saccharomycotina fungi have evolved to inhabit a vast diversity of habitats over their 400-million-year evolution. There are, however, only a few known fungal pathogens of plants in this subphylum, primarily belonging to the genera Eremothecium and Geotrichum. We compared the genomes of 12 plant-pathogenic Saccharomycotina strains to 360 plant-associated strains to identify features unique to the phytopathogens. Characterization of the oxylipin synthesis genes, a compound believed to be involved in Eremothecium pathogenicity, did not reveal any differences in gene presence within or between the plant-pathogenic and plant-associated strains. A reverse-ecological approach, however, revealed that plant pathogens lack several metabolic enzymes known to assist other phytopathogens in overcoming plant defenses. This includes L-rhamnose metabolism, formamidase and nitrilase genes. This result suggests that the Saccharomycotina plant pathogens are limited to infecting ripening fruits as they are without the necessary enzymes to degrade common phytohormones and secondary metabolites produced by plants.

Saccharomycotina, fungi, phytopathogen, reverse ec↗
DOE OSTI2020

Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods

Researchers often measure changes in gene expression across conditions to better understand the shared functional roles and regulatory mechanisms of different genes. Analogous to this is comparing gene expression across species, which can improve our understanding of the evolutionary processes shaping the evolution of both individual genes and functional pathways. One area of interest is determining genes showing signals of coevolution, which can also indicate potential functional similarity, analogous to co-expression analysis often performed across conditions for a single species. However, as with any trait, comparing gene expression across species can be confounded by the non-independence of species due to shared ancestry, making standard hypothesis testing inappropriate. We compared RNA-Seq data across 18 fungal species using a multivariate Brownian Motion phylogenetic comparative method (PCM), which allowed us to quantify coevolution between protein pairs while directly accounting for the shared ancestry of the species. Our work indicates proteins which physically-interact show stronger signals of coevolution than randomly-generated pairs. Interactions with stronger empirical and computational evidence also showing stronger signals of coevolution. We examined the effects of number of protein interactions and gene expression levels on coevolution, finding both factors are overall poor predictors of the strength of coevolution between a protein pair. Simulations further demonstrate the potential issues of analyzing gene expression coevolution without accounting for shared ancestry in a standard hypothesis testing framework. Furthermore, our simulations indicate the use of a randomly-generated null distribution as a means of determining statistical significance for detecting coevolving genes with phylogenetically-uncorrected correlations, as has previously been done, is less accurate than PCMs, although is a significant improvement over standard hypothesis testing. These methods are further improved by using a phylogenetically-corrected correlation metric. Our work highlights potential benefits of using PCMs to detect gene expression coevolution from high-throughput omics scale data. This framework can be built upon to investigate other evolutionary hypotheses, such as changes in transcription regulatory mechanisms across species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens

The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including base pairs and base mis-pairs, that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase (aaRS) interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. We also identified Leishmania major threonyl-tRNA synthetase (ThrRS) inhibitors from the same library. We discuss why chemotherapies targeting multiple aaRSs should be less prone to the evolution of resistance than monotherapeutic or synergistic combination chemotherapies targeting only one aaRS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Casein kinase 1 dynamics underlie substrate selectivity and the PER2 circadian phosphoswitch

Post-translational control of PERIOD stability by Casein Kinase 1δ and ε (CK1) plays a key regulatory role in metazoan circadian rhythms. Despite the deep evolutionary conservation of CK1 in eukaryotes, little is known about its regulation and the factors that influence substrate selectivity on functionally antagonistic sites in PERIOD that directly control circadian period. Here we describe a molecular switch involving a highly conserved anion binding site in CK1. This switch controls conformation of the kinase activation loop and determines which sites on mammalian PER2 are preferentially phosphorylated, thereby directly regulating PER2 stability. Integrated experimental and computational studies shed light on the allosteric linkage between two anion binding sites that dynamically regulate kinase activity. We show that period-altering kinase mutations from humans to Drosophila differentially modulate this activation loop switch to elicit predictable changes in PER2 stability, providing a foundation to understand and further manipulate CK1 regulation of circadian rhythms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

DESI DR2 Galaxy luminosity functions

We present galaxy luminosity functions (LFs) for the Dark Energy Spectroscopic Instrument (DESI) DR2 Bright Galaxy Survey (BGS) in the g, r, z, and $w1$ bands over $0.002\lt z\lt 0.6$. Our analysis uses updated k-corrections and evolutionary corrections, including new polynomial kcorrection fits derived from BGS Year 1 data that supersede earlier GAMA-based prescriptions. Exploiting the statistical power of DESI, we measure LFs to very faint magnitudes, reaching $^{0.1}M_r-5\log h\sim -10$. Independent measurements from the North and South survey regions show excellent agreement around the LF knee, but the very small statistical uncertainties reveal that simple analytic forms fail to capture the full LF shape. The bright end departs from a pure exponential decline, while the faint end exhibits complex, non-powerlaw behaviour, including a pronounced upturn at $^{0.1}M_r-5\log h\gtrsim -15$, which is stronger for red galaxies than for blue. We show that our LFs are largely complete for galaxies with surface brightness $\mu _{50}\lt 25$, and that an apparent steepening fainter than $-13$ is driven primarily by local overdensity and fragmentation of large galaxies. A systematic North–South offset at the brightest magnitudes is traced to red galaxies and may reflect shallower North photometry underestimating extended earlytype profiles, although this remains inconclusive. We therefore also provide LFs based on model Petrosian magnitudes. Redshift splitting reveals small but significant residuals, indicating limitations of a simple global evolutionary model. Using the redshift limits of J. Loveday et al. (2012), we find excellent agreement with GAMA, with substantially reduced statistical errors. These measurements provide a precise reference for studies of environmental and population-dependent LFs and for testing galaxy formation models.

79 ASTRONOMY AND ASTROPHYSICS↗