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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 109 records · Page 6

Defensive symbiosis against giant viruses in amoebae

Protists are important regulators of microbial communities and key components in food webs with impact on nutrient cycling and ecosystem functioning. In turn, their activity is shaped by diverse intracellular parasites, including bacterial symbionts and viruses. Yet, bacteria–virus interactions within protists are poorly understood. Here, we studied the role of bacterial symbionts of free-living amoebae in the establishment of infections with nucleocytoplasmic large DNA viruses (Nucleocytoviricota). To investigate these interactions in a system that would also be relevant in nature, we first isolated and characterized a giant virus (Viennavirus, family Marseilleviridae) and a sympatric potential Acanthamoeba host infected with bacterial symbionts. Subsequently, coinfection experiments were carried out, using the fresh environmental isolates as well as additional amoeba laboratory strains. Employing fluorescence in situ hybridization and qPCR, we show that the bacterial symbiont, identified as Parachlamydia acanthamoebae, represses the replication of the sympatric Viennavirus in both recent environmental isolates as well as Acanthamoeba laboratory strains. In the presence of the symbiont, virions are still taken up, but viral factory maturation is inhibited, leading to survival of the amoeba host. The symbiont also suppressed the replication of the more complex Acanthamoeba polyphaga mimivirus and Tupanvirus deep ocean (Mimiviridae). Our work provides an example of an intracellular bacterial symbiont protecting a protist host against virus infections. The impact of virus–symbiont interactions on microbial population dynamics and eventually ecosystem processes requires further attention.

59 BASIC BIOLOGICAL SCIENCES↗

Growth instabilities shape morphology and genetic diversity of microbial colonies

Abstract Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.

Golden, Alexander↗

Precision measurement of lifetime and branching ratios of the 4⁢𝑓 13⁡ 5⁢𝑑⁢6⁢𝑠 1 ⁢[5/2] 5/2 state in Yb + ions

We report spectroscopic and time-resolved experimental observations to characterize the [Xe]⁢4⁢𝑓 13 ⁡( 2 𝐹$^𝑜_{5/2}$)⁢5⁢𝑑⁢6⁢𝑠⁡( 1 𝐷)⁢ 1 ⁢[5/2]$^𝑜_{5/2}$ state in 172 Yb + ions. We access this state from the metastable 4⁢𝑓 14 ⁡5⁢𝑑⁡( 2 𝐷 3/2,5/2 ) manifold and observe an unexpectedly long lifetime of 𝜏 = 37.9⁢(9) ⁢µ⁢s that allows visible Rabi oscillations and resolved-sideband spectroscopy. Using a combination of coherent population dynamics, high-fidelity detection and heralded state preparation, and optical pumping methods, we measure the branching ratios to the 2 𝐷 3/2 , 2 𝐷 5/2 , and 2 𝑆 1/2 states to be 0.359⁢(2), 0.639(2), and 0.0023⁢(16), respectively. The branching ratio to the 4⁢𝑓 13⁡ 6⁢𝑠 2 ⁡( 2 𝐹 7/2 ) is compatible with zero within our experimental resolution. We also report measurements of Landé 𝑔-factor of the 1 ⁢[5/2]$^𝑜_{5/2}$ state. Further, the branching ratio of the 2 𝐷 5/2 to 2 𝑆 1/2 decay in 172 Yb + was measured to be 0.188(3), improving its relative uncertainty by an order of magnitude. Our measurements provide experimental benchmarks for better understanding the atomic structure of Yb + ions, which still lacks accurate numerical descriptions, and the use of high-lying excited states for partial detection and qubit manipulation in the omg architecture.

74 ATOMIC AND MOLECULAR PHYSICS↗

Optical coherence and energy-level properties of a Tm 3+ -doped LiNbO 3 waveguide at subKelvin temperatures

We characterize the optical coherence and energy-level properties of the 795-nm 3 H 6 to 3 H 4 transition of Tm 3+ in a Ti 4+ :LiNbO 3 waveguide at temperatures as low as 0.65 K. Coherence properties are measured with varied temperature, magnetic field, optical excitation power and wavelength, and measurement timescale. We also investigate nuclear spin-induced hyperfine structure and population dynamics with varying magnetic field and laser excitation power. Except for accountable differences due to different Ti 4+ - and Tm 3+ -doping concentrations, we find that the properties of Tm 3+ :Ti 4+ :LiNbO 3 produced by indiffusion doping are consistent with those of a bulk-doped Tm 3+ :LiNbO 3 crystal measured under similar conditions. Furthermore, our results, which complement previous work in a narrower parameter space, support using rare-earth ions for integrated optical and quantum signal processing.

74 ATOMIC AND MOLECULAR PHYSICS↗

Connectivity and edge effects increase bee colonization in an experimentally fragmented landscape

Though landscape corridors increase dispersal of many animals and plants, it remains unknown whether these positive effects extend to the process of colonization and establishment of new populations in fragments. Working in experimentally fragmented landscapes, we tested how two aspects of habitat fragments altered by corridors – connectivity and edge-to-area ratio – determine patterns of colonization by a solitary, cavity-nesting bee Megachile rotundata. We found that though connectivity initially affected rates of nest-site occupation, edge-to-area ratio ultimately determined the final patterns of patch occupation and nest building, likely due to habitat selection by our focal species. Bee colonization was also higher in patches with higher abundances of their preferred food resources, flowers from the Fabaceae family. Our results show the importance of considering the effects of both connectivity and edge on population dynamics in habitat-based conservation.

54 ENVIRONMENTAL SCIENCES↗

A general theory of avian migratory connectivity

Birds exhibit a remarkable array of seasonal migrations. Despite much research describing migratory behaviour, the underlying forces driving how a species’ breeding and wintering populations redistribute each year, that is, migratory connectivity, remain largely unknown. Here, we test the hypothesis that birds migrate in a way that minimises energy expenditure while considering intraspecific competition for energy acquisition, by developing a modelling framework that simulates an optimal redistribution of individuals between breeding and wintering areas. Using 25 species across the Americas, we find that the model accurately predicts empirical migration patterns, and thus offers a general explanation for migratory connectivity based on first ecological and energetic principles. Our model provides a strong basis for exploring additional processes underlying the ecology and evolution of migration, but also a framework for predicting how migration impacts local adaptation across seasons and how environmental change may affect population dynamics in migratory species.

60 APPLIED LIFE SCIENCES↗

Warming increased bark beetle-induced tree mortality by 30% during an extreme drought in California

Quantifying the responses of forest disturbances to climate warming is critical to our understanding of carbon cycles and energy balances of the Earth system. The impact of warming on bark beetle outbreaks is complex as multiple drivers of these events may respond differently to warming. Using a novel model of bark beetle biology and host tree interactions, we assessed how contemporary warming affected western pine beetle (Dendroctonus brevicomis) populations and mortality of its host, ponderosa pine (Pinus ponderosa), during an extreme drought in the Sierra Nevada, California, United States. When compared with the field data, our model captured the western pine beetle flight timing and rates of ponderosa pine mortality observed during the drought. In assessing the influence of temperature on western pine beetles, we found that contemporary warming increased the development rate of the western pine beetle and decreased the overwinter mortality rate of western pine beetle larvae leading to increased population growth during periods of lowered tree defense. We attribute a 29.9% (95% CI: 29.4%–30.2%) increase in ponderosa pine mortality during drought directly to increases in western pine beetle voltinism (i.e., associated with increased development rates of western pine beetle) and, to a much lesser extent, reductions in overwintering mortality. These findings, along with other studies, suggest each degree (°C) increase in temperature may have increased the number of ponderosa pine killed by upwards of 35%–40% °C-1 if the effects of compromised tree defenses (15%–20%) and increased western pine beetle populations (20%) are additive. Due to the warming ability to considerably increase mortality through the mechanism of bark beetle populations, models need to consider climate's influence on both host tree stress and the bark beetle population dynamics when determining future levels of tree mortality.

59 BASIC BIOLOGICAL SCIENCES↗

Linking remotely sensed ecosystem resilience with forest mortality across the continental United States

Episodes of forest mortality have been observed worldwide associated with climate change, impacting species composition and ecosystem services such as water resources and carbon sequestration. Yet our ability to predict forest mortality remains limited, especially across large scales. Time series of satellite imagery has been used to document ecosystem resilience globally, but it is not clear how well remotely sensed resilience can inform the prediction of forest mortality across continental, multi-biome scales. Here, we leverage forest inventories across the continental United States to systematically assess the potential of ecosystem resilience derived using different data sets and methods to predict forest mortality. Here we found high resilience was associated with low mortality in eastern forests but was associated with high mortality in western regions. The unexpected resilience–mortality relation in western United States may be due to several factors including plant trait acclimation, insect population dynamics, or resource competition. Overall, our results not only supported the opportunity to use remotely sensed ecosystem resilience to predict forest mortality but also highlighted that ecological factors may have crucial influences because they can reverse the sign of the resilience–mortality relationships.

59 BASIC BIOLOGICAL SCIENCES↗

Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses

ABSTRACT Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances. IMPORTANCE Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

Lui, Lauren M.↗

Plastome evolution in annual Brachypodium species reveals widespread heteroplasmy and chloroplast capture, lineage-specific codon usage bias, and low positive selection

Comparative genomics and plastome phylogenomics have advanced significantly in recent years, highlighting the diversity, possible admixture, and non-neutral evolution of the predominantly considered non-recombinant chloroplast genomes in angiosperms. The grass genus Brachypodium serves as a powerful model for studying evolutionary processes in monocots. We analyzed 287 plastomes across the native circum-Mediterranean range of the three annual Brachypodium species ( B. distachyon, B. stacei, B. hybridum ), focusing on their structural variation, selection patterns and phylogenomic relationships. Our analyses confirmed the differentiation of the S and D plastomes, inherited respectively from the diploid progenitor species B. stacei and B. distachyon . We identified novel structural rearrangements and indels, and unique repeat motifs, along with widespread heteroplasmy, particularly in ancestral B. hybridum -D plastotypes. SNP diversity varied among plastotypes, reflecting population dynamics and evolutionary histories, with B. hybridum -D plastotypes showing the highest normalized diversity and B. hybridum -S the lowest. Positive selection was detected in 29 plastid genes by Tajima’s neutrality test, and in nine genes by site and branch-site evolutionary models, including matK, ndhF, rbcL, and rpoC2. Phylogenomic analyses revealed well-supported clades corresponding to the S and D plastome lineages, with frequent chloroplast capture events and long-distance dispersals shaping their evolutionary trajectories.

allopolyploidy↗

The circular bioeconomy: a driver for system integration

Background: Human and earth system modeling, traditionally centered on the interplay between the energy system and the atmosphere, are facing a paradigm shift. The Intergovernmental Panel on Climate Change’s mandate for comprehensive, cross-sectoral climate action emphasizes avoiding the vulnerabilities of narrow sectoral approaches. Our study explores the circular bioeconomy, highlighting the intricate interconnections among agriculture, forestry, aquaculture, technological advancements, and ecological recycling. Collectively, these sectors play a pivotal role in supplying essential resources to meet the food, material, and energy needs of a growing global population. We pose the pertinent question of what it takes to integrate these multifaceted sectors into a new era of holistic systems thinking and planning. Results: The foundation for discussion is provided by a novel graphical representation encompassing statistical data on food, materials, energy flows, and circularity. This representation aids in constructing an inventory of technological advancements and climate actions that have the potential to significantly reshape the structure and scale of the economic metabolism in the coming decades. In this context, the three dominant mega-trends—population dynamics, economic developments, and the climate crisis—compel us to address the potential consequences of the identified actions, all of which fall under the four categories of substitution, efficiency, sufficiency, and reliability measures. Substitution and efficiency measures currently dominate systems modeling. Including novel bio-based processes and circularity aspects might require only expanded system boundaries. Conversely, paradigm shifts in systems engineering are expected to center on sufficiency and reliability actions. Effectively assessing the impact of sufficiency measures will necessitate substantial progress in inter- and transdisciplinary collaboration, primarily due to their non-technological nature. In addition, placing emphasis on modeling the reliability and resilience of transformation pathways represents a distinct and emerging frontier that highlights the significance of an integrated network of networks. Conclusions: Existing and emerging circular bioeconomy practices can serve as prime examples of system integration. These practices facilitate the interconnection of complex biomass supply chain networks with other networks encompassing feedstock-independent renewable power, hydrogen, CO 2 , water, and other biotic, abiotic, and intangible resources. Elevating the prominence of these connectors will empower policymakers to steer the amplification of synergies and mitigation of tradeoffs among systems, sectors, and goals.

09 BIOMASS FUELS↗

Analyzing the 2019 Chilean social outbreak: Modelling Latin American economies

In this work, we propose a quantitative model for the 2019 Chilean protests. We utilize public data for the consumer price index, the gross domestic product, and the employee and per capita income distributions as inputs for a nonlinear diffusion-reaction equation, the solutions to which provide an in-depth analysis of the population dynamics. Specifically, the per capita income distribution stands out as a solution to the extended Fisher-Kolmogorov equation. According to our results, the concavity of employee income distribution is a decisive input parameter and, in contrast to the distributions typically observed for Chile and other countries in Latin America, should ideally be non-negative. Based on the results of our model, we advocate for the implementation of social policies designed to stimulate social mobility by broadening the distribution of higher salaries.

Curilef, Sergio (ORCID:0000000283183206)↗

TRANSENSOR: Transformer Real-time Assessment INtelligent System with Embedded Network of Sensors and Optical Readout. Final Report

Utilities across the world are wrestling with evolving market dynamics, population growth and climate change. Distributed Energy Resources (DERs) such as solar photovoltaics, distributed generators and energy storage systems are becoming important parts of the U.S. energy mix. These factors are driving an increasing need for low-cost grid asset monitoring. Aside from being costly, traditional utility monitoring systems are not sufficiently robust and do not provide real-time visibility into the condition of grid assets such as transformers. Lack of accurate real-time measurements on performance has resulted in the use of lagging indicators, such as oil sample analysis. To address this need, an innovative embedded optical sensing technology, Transformer Real-time Assessment Intelligent System (TRANSENSOR) was developed, validated and demonstrated in this project. To date, TRANSENSOR has focused on transformers but is extendable to other grid assets. In addition to the technology being embedded into new transformers during manufacturing, a retrofit configuration that can be installed on existing transformers in the field was also developed. It is anticipated that the ability to retrofit existing transformers will help accelerate adoption of the underlying TRANSENSOR technology. Phase 1 of the project focused on laboratory development and qualification of the technology. Following iterations and exploration of relevant optical sensing modalities and multiplexed configurations of interest for the transformer environment, an effective candidate configuration was agreed upon, down-selected and custom-designed for embedding into General Electric (GE) network transformers. Two new GE 500 kilovolt ampere (kVA), 27 kilovolt (kV) distribution network transformers were built with embedded fiber-optic (FO) sensors and successfully qualified per industry standards at GE’s Shreveport, Louisiana facility during Phase 1 of the project. Following the successful completion of Phase 1, the team proceeded to Phase 2, which focused on a field demonstration of the technology. Over Phase 2, the first new GE transformer built with embedded fiber-optic sensors was installed in an above-ground cage and connected to the grid at Con Edison’s Astoria facility. A second transformer equipped with TRANSENSOR was installed in an underground vault. Additionally, an older (1982 year model) GE transformer in an above-ground cage was retrofitted with fiber- optic sensors and reconnected to the grid at ConEd’s facility. Analysis of data acquired from the sensors showed interesting correlations with transformer loading. Additionally, key events such as transformer low-voltage network connection, primary-side energizing, and a pressure loss event from an oil sampling were detected by the TRANSENSOR system. Online data processing/feature extraction algorithms for the second transformer in the underground vault detected key features and event alerts that were transmitted through a wireless 4G connection. The remote deployment concept showed promising results with data collection running for a total of 8 months across the three (3) GE transformers instrumented for the Phase 2 field demonstration. This sets the stage well for further development and commercialization.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Use of imaging and mass spectrometry-based capabilities to describe microbiome interactions (Q4 Performance Metric Report, 2021)

The LLNL “Microbes Persist” Soil Microbiome Scientific Focus Area (SFA) seeks to determine how microbial soil ecophysiology, population dynamics, and microbe-mineral-organic matter interactions regulate the persistence of microbial residues and formation of soil carbon (C). In much of our research, we use imaging, mass spectrometry, and related methods to study plantmicrobe-mineral interactions, viral and microbial particles from soil, and the signatures plant and microbial necromass contribute as part of soil organic matter (SOM). Our project’s signature techniques include NanoSIMS-enabled approaches (to understand cell-cell and OM-mineral interactions at the single cell and even viral particle scale), radiocarbon (14C) analyses (to determine both the age and turnover time of soil organic matter), and a suite of soil chemical characterization techniques we describe below, and collectively refer to as ‘Multi- dimensional SOM-mineral characterization’ (SEM, TEM, STXM, NEXAFS, NMR, FTICR-MS, LC-MS). In this report, we focus on how imaging, NMR, beamline and mass spectrometry approaches can deepen our understanding of soil microbiomes and their engagement with the soil matrix.

54 ENVIRONMENTAL SCIENCES↗

The GREEN ‘omics of Nutrient Feedbacks to Soil Warming

The GREEN ‘omics of Nutrient Feedbacks in Soil project advanced the DOE Biological and Environmental Research (BER) mission by developing and applying isotope-enabled ’omics tools to understand how soil microbes regulate carbon and nutrient cycling. Guided by the Growth Rate, growth Efficiency, and stoichiometry of Essential Nutrients (GREEN ’omics) framework, the project aimed to build a predictive, systems-level understanding of microbial traits that control ecosystem biogeochemistry. In a collaboration among Northern Arizona University (lead), West Virginia University, Lawrence Livermore National Laboratory, and Pacific Northwest National Laboratory, we combined quantitative stable isotope probing (qSIP), Chip-SIP, NanoSIMS, and genome-resolved metagenomics across long-term experiments in Arctic, boreal, temperate, and tropical ecosystems. The project produced three key outcomes: 1) We showed that community-weighted temperature sensitivities of bacterial growth (Q10) can predict ecosystem-scale soil respiration responses across diverse soils. 2) We provided the first in situ evidence for density-dependent population dynamics in soil bacteria and demonstrated that nutrient additions intensify competition, concentrating carbon use into fewer taxa. 3) We improved and extended isotope-enabled ’omics methods by quantifying qSIP measurement error to guide experimental design and coupling SIP with genome-resolved metagenomics to reveal cross-kingdom interactions among bacteria, fungi, and viruses. Together, these results show that a small number of microbial traits and taxa exert disproportionate control over soil carbon and nutrient cycling, providing critical data and methods to improve representation of microbial processes in Earth system models.

54 ENVIRONMENTAL SCIENCES↗

LandCast Mosaic: Reconstructing Global Population Distributions, 1975-2025

LandCast Mosaic (LCM) provides a global, high-resolution gridded population dataset spanning 1975–2025, representing annual, scenario-consistent estimates of daytime, nighttime, and ambient population distributions. LCM builds on the 2025 LandScan Mosaic (LSM) population data by backcasting to earlier years using historical changes in built-surface area derived from the Global Human Settlement Layer (GHSL) and authoritative population counts from international datasets. The workflow scales 2025 building-informed gridded population estimates according to observed changes in built surface, applies linear interpolation for intermediate years, and normalizes estimates to match administrative- and country-level totals. The resulting dataset offers consistent, globally gridded population estimates over fifty years, suitable for temporal analyses of population dynamics, disaster risk modeling, and urban planning applications.

97 MATHEMATICS AND COMPUTING↗

A Comprehensive Comparison of Building Height Products at a Global Level

The built environment continues to expand due to increasing human populations with some projections indicating additional growth of 2.5 billion persons by 2050. Buildings are a key component of the built environment and information on building height and urban morphology in general can help to better understand and address a host of development and urban planning issues including energy consumption, urbanization, population dynamics, urban heat islands, environmental degradation, and others. To date, several approaches have been developed to address the need for mapping building height at scale. These approaches can be grouped into two main categories: 1) directly measure height from remote sensing products or 2) indirectly estimate height from footprint morphology features at the building-by-building level. Due to a number of these global height datasets now being available for consumption and use across domains, there is a critical need to understand the differences displayed between these products and how the use of these may influence the outcome when applied. In this analysis, we compare and evaluate 5 global building height datasets: Global Human Settlement, World Settlement Footprint 3D, Global Building Morphology dataset, three-dimensional Global Building Footprints, and an approach developed at Oak Ridge National Laboratory (ORNL). Our analysis shows that, across 5 cities at a global scale with high-quality building height reference data, the approach developed by ORNL of inferring height at the building-by-building level is more accurate and consistent. This was evidenced by the ORNL product improving upon the baseline in all 5 cities, the only product to do so. These findings will aid researchers in choosing a global building height product that best meets their needs and provides global availability, consistency, and accuracy.

42 ENGINEERING↗

Spatial Microsimulation and Activity Allocation in Python: An Update on the Likeness Toolkit

Understanding human security and social equity issues within human systems requires large-scale models of population dynamics that simulate high-fidelity representations of individuals and access to essential activities (work/school, social, errands, health). Likeness is a Python toolkit that provides these capabilities for Oak Ridge National Laboratory's (ORNL) UrbanPop spatial microsimulation project. In step with the initial development phase for Likeness (2021 - 2022), we built out several foundational examples of work/school and health service access. In this paper, we describe expansion and scaling of Likeness capabilities to metropolitan areas in the United States. We then provide an integrated demonstration of our methods based on a case study of Leon County, FL and perform validation exercises on 1) neighborhood demographic composition and 2) visits by demographic cohorts (gender/age) obtained from point of interest (POI) footfall data for essential services (grocery stores). Taking into account lessons learned from our case study, we scope improvements to our model as well as provide a roadmap of the anticipated Likeness development cycle into 2023 - 2024.

Tuccillo, Joe↗