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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1974

Precision Attitude Determination System (PADS) system design and analysis: Single-axis gimbal star tracker

The feasibility is evaluated of an evolutionary development for use of a single-axis gimbal star tracker from prior two-axis gimbal star tracker based system applications. Detailed evaluation of the star tracker gimbal encoder is considered. A brief system description is given including the aspects of tracker evolution and encoder evaluation. System analysis includes evaluation of star availability and mounting constraints for the geosynchronous orbit application, and a covariance simulation analysis to evaluate performance potential. Star availability and covariance analysis digital computer programs are included.

Source record↗
DOE OSTI2020

Graph theory approach to determine configurations of multidentate and high coverage adsorbates for heterogeneous catalysis

Abstract Heterogeneous catalysts constitute a crucial component of many industrial processes, and to gain an understanding of the atomic-scale features of such catalysts, ab initio density functional theory is widely employed. Recently, growing computational power has permitted the extension of such studies to complex reaction networks involving either high adsorbate coverages or multidentate adsorbates, which bind to the surface through multiple atoms. Describing all possible adsorbate configurations for such systems, however, is often not possible based on chemical intuition alone. To systematically treat such complexities, we present a generalized Python-based graph theory approach to convert atomic scale models into undirected graph representations. These representations, when combined with workflows such as evolutionary algorithms, can systematically generate high coverage adsorbate models and classify unique minimum energy multidentate adsorbate configurations for surfaces of low symmetry, including multi-elemental alloy surfaces, steps, and kinks. Two case studies are presented which demonstrate these capabilities; first, an analysis of a coverage-dependent phase diagram of absorbate NO on the Pt 3 Sn(111) terrace surface, and second, an investigation of adsorption energies, together with identifying unique minimum energy configurations, for the reaction intermediate propyne (CHCCH 3 *) adsorbed on a PdIn(021) step surface. The evolutionary algorithm approach reproduces high coverage configurations of NO on Pt 3 Sn(111) using only 15% of the number of simulations required for a brute force approach. Furthermore, the screening of potentially hundreds of multidentate adsorbates is shown to be possible without human intervention. The strategy presented is quite general and can be applied to a spectrum of complex atomic systems.

36 MATERIALS SCIENCE↗
NASA NTRS1990

The evolution of horizontal-branch stars - Theoretical sequences

A new grid of standard (i.e., solar CNO/Fe, no core rotation, and including semiconvection) horizontal-branch evolutionary sequences are presented which extend the grid of Sweigart both by including the final phase of core helium exhaustion and by using a finer grid of compositions. These sequences were constructed specifically for the studies of the Sandage period-shift effect and the second parameter phenomenon among the Galactic globular clusters. The numerical results for the observable characteristics of the sequences are tabulated which can be directly used to synthesize the observed horizontal-branch distributions. The present computations suggest that the observed difference in period change of RR Lyrae stars in the globular clusters M3 and M15 could be attributed, at least in the mean, to stellar evolution.

Lee, Young-Wook↗
DOE OSTI2021

Evolution of eggshell structure in relation to nesting ecology in non-avian reptiles

Amniotic eggs are multifunctional structures that enabled early tetrapods to colonize the land millions of years ago, and are now the reproductive mode of over 70% of all terrestrial amniotes. Eggshell morphology is at the core of animal survival, mediating the interactions between embryos and their environment, and has evolved into a massive diversity of forms and functions in modern reptiles. These functions are critical to embryonic survival and may serve as models for new antimicrobial and/or breathable membranes. However, we still lack critical data on the basic structural and functional properties of eggs, particularly of reptiles. Here, we first characterized egg shape, shell thickness, porosity, and mineralization of eggs from 91 reptile species using optical images, scanning electron microscopy, and micro computed tomography, and collected data on nesting ecology from the literature. We then used comparative analyses to test hypotheses on the selective pressures driving their evolution. We hypothesized that eggshell morphology has evolved to protect shells from physical damage and desiccation, and, in support, found a positive relationship between thickness and precipitation, and a negative relationship between porosity and temperature. Although mineralization varied extensively, it was not correlated with nesting ecology variables. Ancestral state reconstructions show thinning and increased porosity over evolutionary time in squamates, but the opposite in turtles and crocodilians. Egg shape, size, porosity and calcification were correlated, suggesting potential structural or developmental tradeoffs. This study provides new data and insights into the morphology and evolution of reptile eggs, and raises numerous questions for additional research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The landscape of regulatory element evolution in a C4 perennial grass

Gene regulatory evolution is a well-known source of phenotypic diversity and adaptive evolution. Although cis-regulatory elements (CREs) play a vital role in gene expression evolution, the molecular evolution of CREs remains mostly unknown due to the difficulty in identifying and characterizing these functional elements. Comparative genomic analyses of noncoding DNA can be leveraged to identify conserved noncoding sequences (CNS), many of which may harbor functional CREs conserved by purifying selection. However, purely computational inference of CREs from putative CNS can be erroneous due to the complex genomic architecture in plants. One promising experimental approach to identify CREs is by profiling accessible chromatin regions (ACRs) that are often associated with the location of CREs. In this study, we use comparative genomics along with the profiling of ACRs to study the molecular evolution of putative functional noncoding regulatory regions in Panicoid grasses. We identified sets of CNS that varied in relationship to the degree of evolutionary divergence among the studied taxa, including identifying core-Panicoid-CNS. We augmented this analysis by profiling ACRs in Panicum hallii ecotypes using ATAC-seq. ACRs had low SNP density at the summit, harbored a high frequency of core-Panicoid-CNS, and were enriched with expression QTL. These data help to annotate the P. hallii genome for putative functional elements and suggest that a large proportion of these ACRs are evolving under purifying selection. Turnover in CNS and ACR between ecotypes of P. hallii identifies a small set of putatively divergent CREs that may underlie differences in gene regulation between genotypes from inland and coastal habitats. In summary, we profiled ACRs in Panicoid grasses and integrated this data with our putative CNS prediction framework, which provides unique insight into patterns of polymorphism and divergence in CREs in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Turbopump Performance Improved by Evolutionary Algorithms

The development of design optimization technology for turbomachinery has been initiated using the multiobjective evolutionary algorithm under NASA's Intelligent Synthesis Environment and Revolutionary Aeropropulsion Concepts programs. As an alternative to the traditional gradient-based methods, evolutionary algorithms (EA's) are emergent design-optimization algorithms modeled after the mechanisms found in natural evolution. EA's search from multiple points, instead of moving from a single point. In addition, they require no derivatives or gradients of the objective function, leading to robustness and simplicity in coupling any evaluation codes. Parallel efficiency also becomes very high by using a simple master-slave concept for function evaluations, since such evaluations often consume the most CPU time, such as computational fluid dynamics. Application of EA's to multiobjective design problems is also straightforward because EA's maintain a population of design candidates in parallel. Because of these advantages, EA's are a unique and attractive approach to real-world design optimization problems.

Oyama, Akira↗
NASA NTRS1993

Dynamical instability as the cause of the massive outbursts in Eta Carinae and other luminous blue variables

A new type of stellar envelope structure has been computationally discovered at very high stellar masses. The outer part of the envelope resembles a nearly detached, diffusely filled shell overlying an ultrahot surface of small radius. This structural anomaly is caused by a large iron bump occurring in the new opacities of Iglesias et al. (1992). The new stellar models with normal metallicity encounter a strong ionization-induced dynamical instability in the outer envelope as they rapidly transit the H-R diagram after the end of central hydrogen burning. Preliminary evolutionary and hydrodynamical calculations successfully mimic the most basic observed properties of Eta Carinae and other very luminous blue variables. The Humphreys-Davidson sloped line in the H-R diagram, however, seems to be unrelated to these variables, and is instead the observed terminus of the main-sequence phase of evolution if convective core overshooting is insignificant.

Stothers, Richard B.↗
DOE OSTI2026

MAL33 drives natural variation in maltose metabolism in Saccharomyces eubayanus

Maltose is one of the most abundant sugars in brewer’s wort, and its efficient utilization is critical for successful fermentation. However, maltose consumption varies naturally among Saccharomyces eubayanus strains isolated from different host trees, such as Quercus and Nothofagus. To identify the genetic determinants underlying these phenotypic differences, we performed bulk segregant analysis (BSA) and quantitative trait loci (QTL) mapping using an F 2 offspring derived from QC18 (Quercus-associated) and CL467.1 (Nothofagus-associated) strains. QTL mapping identified two significant genomic regions on subtelomeric loci of chromosomes V-R and XVI-L, each containing complete MAL loci composed of MAL32 (encoding maltase), MAL31 (transporter), and MAL33 (transcriptional activator) genes. Comparative polymorphism analyses identified mutations in MAL32 and MAL33 of QC18, including frameshift mutations resulting in premature stop codons. Functional validation demonstrated that the heterologous expression of MAL33 ChrV from CL467.1 fully restored maltose utilization in QC18, indicating the functional presence of MAL33 cis-regulatory sequences and MAL32 and MAL31 genes in QC18. While structural protein predictions identified truncation and impaired functionality in the maltose-responsive activation domain of Mal33p from QC18, overexpression of QC18’s own MAL33 ChrV allele also improved maltose metabolism, suggesting dosage-dependent transcriptional limitations rather than complete functional loss. These results indicate that allelic variations in the maltose-responsive activation domain of Mal33p result in differences in maltose consumption between strains. Here, we hypothesized that reduced maltose metabolism in QC18 is an adaptive response to the distinct sugar composition in Quercus robur bark, contrasting with the starch-rich environment of Nothofagus pumilio. These findings highlight subtelomeric MAL gene diversity as a reservoir of genetic variation, representing a key evolutionary mechanism that influences maltose adaptation among natural Saccharomyces isolates.

evolutionary plasticity↗
NASA NTRS2004

Generative Representations for Computer-Automated Design Systems

With the increasing computational power of Computers, software design systems are progressing from being tools for architects and designers to express their ideas to tools capable of creating designs under human guidance. One of the main limitations for these computer-automated design programs is the representation with which they encode designs. If the representation cannot encode a certain design, then the design program cannot produce it. Similarly, a poor representation makes some types of designs extremely unlikely to be created. Here we define generative representations as those representations which can create and reuse organizational units within a design and argue that reuse is necessary for design systems to scale to more complex and interesting designs. To support our argument we describe GENRE, an evolutionary design program that uses both a generative and a non-generative representation, and compare the results of evolving designs with both types of representations.

Hornby, Gregory S.↗
NASA NTRS2001

Arthropod phylogeny based on eight molecular loci and morphology

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

Non-NASA Center↗
DOE OSTI2023

Top-down design of protein architectures with reinforcement learning

As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in a manner not achievable by current design approaches. We describe a “top-down” reinforcement learning–based design approach that solves this problem using Monte Carlo tree search to sample protein conformers in the context of an overall architecture and specified functional constraints. Cryo–electron microscopy structures of the designed disk-shaped nanopores and ultracompact icosahedra are very close to the computational models. The icosohedra enable very-high-density display of immunogens and signaling molecules, which potentiates vaccine response and angiogenesis induction. Our approach enables the top-down design of complex protein nanomaterials with desired system properties and demonstrates the power of reinforcement learning in protein design.

Science & Technology - Other Topics↗
NASA NTRS1993

A synopsis of test results and knowledge gained from the Phase-0 CSI evolutionary model

The Phase-0 CSI Evolutionary Model (CEM) is a testbed for the study of space platform global line-of-sight (LOS) pointing. Now that the tests have been completed, a summary of hardware and closed-loop test experiences is necessary to insure a timely dissemination of the knowledge gained. The testbed is described and modeling experiences are presented followed by a summary of the research performed by various investigators. Some early lessons on implementing the closed-loop controllers are described with particular emphasis on real-time computing requirements. A summary of closed-loop studies and a synopsis of test results are presented. Plans for evolving the CEM from phase 0 to phases 1 and 2 are also described. Subsequently, a summary of knowledge gained from the design and testing of the Phase-0 CEM is made.

Belvin, W. Keith↗
NASA NTRS1975

Hydrodynamic models of a Cepheid atmosphere. I - Deep envelope models

The implicit hydrodynamic code of Kutter and Sparks has been modified to include radiative transfer effects. This modified code has been used to compute deep envelope models of a classical Cepheid with a period of 12 days. It is shown that in this particular model the hydrogen ionization region plays only a small role in producing the observed phase lag between the light and velocity curves. The cause of the bumps on the model's light curve is examined, and a mechanism is presented to explain those Cepheids with two secondary features on their light curves. This mechanism is shown to be consistent with the Hertzsprung sequence only if the evolutionary mass-luminosity law is used.

Karp, A. H.↗
NASA NTRS2001

Searching for Organics, Fossils, and Biology on Mars

One of the goals of Astrobiology is to understand life on a fundamental level. All life on Earth is constructed from the same basic biochemical building blocks consisting of 20 amino acids with left handed symmetry, five nucleotides, a few sugars of right handed symmetry and some lipids. Using the metaphor of computers this is equivalent to saying that all life shares the same hardware. Beyond hardware similarity, it is now known that all life has fundamentally the same software. The genetic code of life is common to all organisms. Some have argued that the "hammer of evolution is heavy" and life anywhere is likely to be composed of identical biochemical and genetic patterns. However, in a system as complex as biochemistry it is likely that there are numerous local optima and the details of the optimum found by evolutionary selection on another world would likely depend on the initial conditions and random developments in the early biological history on that world. To address these fundamental questions in Astrobiology we need a second example of life: a second genesis.

McKay, Christopher P.↗
NASA NTRS2017

Coupling Between Metabolism and Compartmentalization: Vesicle Growth in the Presence of Dipeptides

A fundamental unresolved question in studies on the origin of life is: how different, ubiquitous protocellular functions begun to work in concert setting the stage for Darwinian evolution of nascent life? From this perspective, of particular significance is coupling between growth of protocellular compartments and the encapsulated, primordial metabolism, which is one of the focal topics of the current ISSOL meeting. Specifically, growth and division of cells facilitated by the products of a metabolic reaction would confer an evolutionary advantage on protocells encapsulating this reaction, as their population would increase at the expense of other protocells. Along these lines, Adamala and Szostak have recently demonstrated that a dipeptide captured inside fatty acid vesicles catalyzes the formation of other dipeptides from activated monomers. Some of the newly synthesized dipeptides, in turn, are capable to promote competitive growth of vesicles in the presence of fatty acid micelles. As vesicles become larger, they adapt filamentous shape, which has been shown to promote their division. On the basis of computer simulations, we provide a molecularly detailed explanation of this process and draw conclusions about its generality.

Wei, C.↗
DOE OSTI2021

Chemical Complexity of Phosphorous-bearing Species in Various Regions of the Interstellar Medium

Phosphorus-related species are not known to be as omnipresent in space as hydrogen, carbon, nitrogen, oxygen, and sulfur-bearing species. Astronomers spotted very few P-bearing molecules in the interstellar medium and circumstellar envelopes. Limited discovery of the P-bearing species imposes severe constraints in modeling the P-chemistry. In this paper, we carry out extensive chemical models to follow the fate of P-bearing species in diffuse clouds, photon-dominated or photodissociation regions (PDRs), and hot cores/corinos. We notice a curious correlation between the abundances of PO and PN and atomic nitrogen. Since N atoms are more abundant in diffuse clouds and PDRs than in the hot core/corino region, PO/PN reflects <1 in diffuse clouds, ≪1 in PDRs, and >1 in the late warm-up evolutionary stage of the hot core/corino regions. During the end of the post-warm-up stage, we obtain PO/PN > 1 for hot core and <1 for its low-mass analog. We employ a radiative transfer model to investigate the transitions of some of the P-bearing species in diffuse cloud and hot core regions and estimate the line profiles. Our study estimates the required integration time to observe these transitions with ground-based and space-based telescopes. We also carry out quantum chemical computation of the infrared features of PH{sub 3}, along with various impurities. We notice that SO{sub 2} overlaps with the PH{sub 3} bending-scissoring modes around ∼1000–1100 cm{sup −1}. We also find that the presence of CO{sub 2} can strongly influence the intensity of the stretching modes around ∼2400 cm{sup −1} of PH{sub 3}.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗