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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Evolutionary Game and Simulation Research of Blockchain-Based Co-Governance of Emergency Supply Allocation

Recently, with the spread of COVID-19 pandemic, emergency supply allocation system is drawing more and more social attention. Emergency supply allocation system is an important part of emergency governance system. It reflects social organizations’ credibility, public safety, and the modernization level of social governance. However, emergency supply allocation system still has some problems, such as information asymmetry, different desires of participants, unreasonable allocation, and so on. At present, it is widely accepted that the advantage of blockchain in co-governance could be of great help in solving above problems. And in order to distinguish the effect of blockchain to the emergency supply allocation, the paper builds a tripartite evolutionary game model among the government, social organizations, and the public to analyse the impact of blockchain platform on emergency supply allocation. The simulation analysis shows the following: (1) The strategy choices of the government have a crucial impact on the evolution and stability of social organizations’ strategies. It needs a long-term process to guide social organizations practicing active allocation, and the government should accelerate to build the blockchain platform to promote this process. (2) With the help of blockchain platform, the increment of penalty intensity of the government is conductive to increasing the probabilities that social organizations practice active allocation and the government practices strict supervision. (3) Blockchain platform has a significant impact on social organizations’ choice for active allocation in many aspects, such as the positive and negative effects of social organizations, effect’s increasing multiple, and the cost of the public informing. In the end, some suggestions are presented to improve the co-governance of emergency supply allocation.

Zhao, Huawei↗
DOE OSTI2023

Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea

Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Generating Mixed Patterns of Residential Segregation: An Evolutionary Approach

The Schelling model of residential segregation has demonstrated that even the slightest preference for neighbors of the same race can be amplified into community-wide segregation. However, these models are unable to simulate mixed, coexisting patterns of segregation and integration, which have been seen to exist in cities. Using evolutionary model discovery we demonstrate how including social factors beyond racial bias when modeling relocation behavior enables the emergence of strongly mixed patterns. Our results indicate that the emergence of mixed patterns is better explained by multiple factors influencing the decision to relocate; the most important being the interaction of nonlinear, rapidly diminishing racial bias with a recent, historical tendency to move. Additionally, preference for less isolated neighborhoods or preference for neighborhoods with longer residing neighbors may produce weaker mixed patterns. Finally, this work highlights the importance of exploring the influence of multiple hypothesized factors of decision making, and their interactions, within agent rules, when studying emergent outcomes generated by agent-based models of complex social systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway

Terpenoids are a diverse class of compounds with wide-ranging uses including as industrial solvents, pharmaceuticals, and fragrances. Efforts to produce terpenoids sustainably by engineering microbes for fermentation are ongoing, but industrial production still largely relies on nonrenewable sources. The methylerythritol phosphate (MEP) pathway generates terpenoid precursor molecules and includes the enzyme Dxs and two iron–sulfur cluster enzymes: IspG and IspH. IspG and IspH are rate limiting-enzymes of the MEP pathway but are challenging for metabolic engineering because they require iron–sulfur cluster biogenesis and an ongoing supply of reducing equivalents to function. Therefore, identifying novel alternatives to IspG and IspH has been an on-going effort to aid in metabolic engineering of terpenoid biosynthesis. We report here an analysis of the evolutionary diversity of terpenoid biosynthesis strategies as a resource for exploration of alternative terpenoid biosynthesis pathways. Using comparative genomics, we surveyed a database of 4,400 diverse bacterial species and found that some may have evolved alternatives to the first enzyme in the pathway, Dxs making it evolutionarily flexible. In contrast, we found that IspG and IspH are evolutionarily rigid because we could not identify any species that appear to have enzymatic routes that circumvent these enzymes. The ever-growing repository of sequenced bacterial genomes has great potential to provide metabolic engineers with alternative metabolic pathway solutions. With the current state of knowledge, we found that enzymes IspG and IspH are evolutionarily indispensable which informs both metabolic engineering efforts and our understanding of the evolution of terpenoid biosynthesis pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

The little skate genome and the evolutionary emergence of wing-like fins

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate the origin of this phenotypic innovation by developing the little skate Leucoraja erinacea as a genomically enabled model. Analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes. Combining genome comparisons with extensive regulatory datasets in developing fins—including gene expression, chromatin occupancy and three-dimensional conformation—we find skate-specific genomic rearrangements that alter the three-dimensional regulatory landscape of genes that are involved in the planar cell polarity pathway. Functional inhibition of planar cell polarity signalling resulted in a reduction in anterior fin size, confirming that this pathway is a major contributor to batoid fin morphology. We also identified a fin-specific enhancer that interacts with several hoxa genes, consistent with the redeployment of hox gene expression in anterior pectoral fins, and confirmed its potential to activate transcription in the anterior fin using zebrafish reporter assays. Our findings underscore the central role of genome reorganization and regulatory variation in the evolution of phenotypes, shedding light on the molecular origin of an enigmatic trait.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory

The spatial organization of genes within plant genomes can drive evolution of specialized metabolic pathways. Terpenoids are important specialized metabolites in plants with diverse adaptive functions that enable environmental interactions. Here, we report the genome assemblies of Prunella vulgaris, Plectranthus barbatus, and Leonotis leonurus. We investigate the origin and subsequent evolution of a diterpenoid biosynthetic gene cluster (BGC) together with other seven species within the Lamiaceae (mint) family. Based on core genes found in the BGCs of all species examined across the Lamiaceae, we predict a simplified version of this cluster evolved in an early Lamiaceae ancestor. The current composition of the extant BGCs highlights the dynamic nature of its evolution. We elucidate the terpene backbones generated by the Callicarpa americana BGC enzymes, including miltiradiene and the terpene (+)-kaurene, and show oxidization activities of BGC cytochrome P450s. Our work reveals the fluid nature of BGC assembly and the importance of genome structure in contributing to the origin of metabolites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History

Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Abstract Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana . To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3 , a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis , and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4 . Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolutionary diversity of proton and water channels on the oxidizing side of photosystem II and their relevance to function

One of the reasons for the high efficiency and selectivity of biological catalysts arise from their ability to control the pathways of substrates and products using protein channels, and by modulating the transport in the channels using the interaction with the protein residues and the water/hydrogen-bonding network. Here, this process is clearly demonstrated in Photosystem II (PS II), where its light-driven water oxidation reaction catalyzed by the Mn 4 CaO 5 cluster occurs deep inside the protein complex and thus requires the transport of two water molecules to and four protons from the metal center to the bulk water. Based on the recent advances in structural studies of PS II from X-ray crystallography and cryo-electron microscopy, in this review we compare the channels that have been proposed to facilitate this mass transport in cyanobacteria, red and green algae, diatoms, and higher plants. The three major channels (O1, O4, and Cl1 channels) are present in all species investigated; however, some differences exist in the reported structures that arise from the different composition and arrangement of membrane extrinsic subunits between the species. Among the three channels, the Cl1 channel, including the proton gate, is the most conserved among all photosynthetic species. We also found at least one branch for the O1 channel in all organisms, extending all the way from Ca/O1 via the ‘water wheel’ to the lumen. However, the extending path after the water wheel varies between most species. The O4 channel is, like the Cl1 channel, highly conserved among all species while having different orientations at the end of the path near the bulk. The comparison suggests that the previously proposed functionality of the channels in T. vestitus (Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Hussein et al., Nat Commun 12:6531, 2021) is conserved through the species, i.e. the O1-like channel is used for substrate water intake, and the tighter Cl1 and O4 channels for proton release. The comparison does not eliminate the potential role of O4 channel as a water intake channel. However, the highly ordered hydrogen-bonded water wire connected to the Mn 4 CaO 5 cluster via the O4 may strongly suggest that it functions in proton release, especially during the S 0 → S 1 transition (Saito et al., Nat Commun 6:8488, 2015; Kern et al., Nature 563:421–425, 2018; Ibrahim et al., Proc Natl Acad Sci USA 117:12624–12635, 2020; Sakashita et al., Phys Chem Chem Phys 22:15831–15841, 2020; Hussein et al., Nat Commun 12:6531, 2021).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Online evolutionary neural architecture search for multivariate non-stationary time series forecasting

Time series forecasting (TSF) is one of the most important tasks in data science. TSF models are usually pre-trained with historical data and then applied on future unseen datapoints. However, real-world time series data is usually non-stationary and models trained offline usually face problems from data drift. Models trained and designed in an offline fashion can not quickly adapt to changes quickly or be deployed in real-time. To address these issues, this work presents the Online NeuroEvolution-based Neural Architecture Search (ONE-NAS) algorithm, which is a novel neural architecture search method capable of automatically designing and dynamically training recurrent neural networks (RNNs) for online forecasting tasks. Without any pre-training, ONE-NAS utilizes populations of RNNs that are continuously updated with new network structures and weights in response to new multivariate input data. ONE-NAS is tested on real-world, large-scale multivariate wind turbine data as well as the univariate Dow Jones Industrial Average (DJIA) dataset. These results demonstrate that ONE-NAS outperforms traditional statistical time series forecasting methods, including online linear regression, fixed long short-term memory (LSTM) and gated recurrent unit (GRU) models trained online, as well as state-of-the-art, online ARIMA strategies. Additionally, results show that utilizing multiple populations of RNNs which are periodically repopulated provide significant performance improvements, allowing this online neural network architecture design and training to be successful.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Evolutionary multi-objective optimization and Pareto-frontal uncertainty quantification of interatomic forcefields for thermal conductivity simulations

Predictive Molecular Dynamics simulations of thermal transport require forcefields that can simultaneously reproduce several structural, thermodynamic and vibrational properties of materials like lattice constants, phonon density of states, and specific heat. This requires a multi-objective optimization approach for forcefield parameterization. Existing methodologies for forcefield parameterization use ad-hoc and empirical weighting schemes to convert this into a single-objective optimization problem. Here, we provide and describe software to perform multi-objective optimization of Stillinger–Weber forcefields (SWFF) for two-dimensional layered materials using the recently developed 3rd generation non-dominated sorting genetic algorithm (NSGA-III). NSGA-III converges to the set of optimal forcefields lying on the Pareto front in the multi-dimensional objective space. This set of forcefields is used for uncertainty quantification of computed thermal conductivity due to variability in the forcefield parameters. We demonstrate this new optimization scheme by constructing a SWFF for a representative two-dimensional material, 2H-MoSe 2 and quantifying the uncertainty in their computed thermal conductivity.

97 MATHEMATICS AND COMPUTING↗