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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

The matrix product approximation for the dynamic cavity method

Stochastic dynamics of classical degrees of freedom, defined on vertices of locally tree-like graphs, can be studied in the framework of the dynamic cavity method which is exact for tree graphs. Such models correspond for example to spin-glass systems, Boolean networks, neural networks, and other technical, biological, and social networks. The central objects in the cavity method are edge messages—conditional probabilities of two vertex variable trajectories. In this paper, we discuss a rather pedagogical derivation for the dynamic cavity method, give a detailed account of the novel matrix product edge message (MPEM) algorithm for the solution of the dynamic cavity equation as introduced, and present optimizations and extensions. Matrix product approximations of the edge messages are constructed recursively in an iteration over time. Computation costs and precision can be tuned by controlling the matrix dimensions of the MPEM in truncations. Without truncations, the dynamics is exact. Data for Glauber–Ising dynamics shows a linear growth of computation costs in time. In contrast to Monte Carlo simulations, the approach has a much better error scaling. Hence, it gives for example access to low probability events and decaying observables like temporal correlations. Here, we discuss optimized truncation schemes and an extension that allows to capture models which have a continuum time limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Data for Myers-Pigg et al. (2026), "Short-term coastal forest responses to a hurricane-scale freshwater and saltwater flooding experiment"

Coastal upland forests are exposed to intensifying precipitation regimes and sea level rise, increasing tree mortality and transforming these coastal forests into wetland ecosystems. Despite these well-known risks, the differing degrees to which hydrological, biogeochemical, and biological components of upland forests respond to novel salinity exposure is relatively unknown. The Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experiment decouples two distinct disturbances associated with hydrological extremes: (1) flooding from heavy precipitation and (2) exposure to saline conditions from storm surge. This dataset includes data reported in Myers-Pigg et al. (2025), which analyzed data from the first TEMPEST flooding treatment in 2022. This includes: - Colored dissolved organic matter in porewaters - Soil temperature and oxygen - Groundwater temperature and chemistry - Dissolved organic carbon concentrations in porewaters - Soil-to-atmosphere CH4 and CO2 fluxes - Soil temperature, water content, and electrical conductivity - Root-influenced CH4 and CO2 flux - Tree sap flow velocity - The R analytical code and documentation about the computational environmental in which it was run (the "sessionInfo.txt" file) All data files are plain-text comma separated value (CSV) and no special software is required to read them.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The tree of life describes a tripartite cellular world

The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ‘‘gaps.’’ In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Getting allometry right at the Oak Ridge free‐air CO 2 enrichment experiment: Old problems and new opportunities for global change experiments

Societal Impact Statement Free‐air CO 2 enrichment (FACE) experiments provide essential data on forest responses to increasing atmospheric CO 2 for evaluations of climate change impacts on humanity. Understanding and reducing the uncertainty in the experimental results is critical to ensure scientific and public confidence in the models and policy initiatives that derive therefrom. One source of uncertainty is the estimation of tree biomass using mathematical relationships between biomass and easily obtained and non‐destructive measurements (allometry). We evaluated the robustness of the allometric relationships established at the beginning of a FACE experiment and discuss the challenges and opportunities for the new generation of FACE experiments. Summary Long‐term field experiments to elucidate forest responses to rising atmospheric CO 2 concentration require allometric equations to estimate tree biomass from non‐destructive measurements of tree size. We analyzed whether the allometric equations established at the beginning of a free‐air CO 2 enrichment (FACE) experiment in a Liquidambar styraciflua plantation were still valid at the end of the 12 year experiment. Aboveground woody biomass was initially predicted by an equation that included bole diameter, taper, and height, assuming that including taper and height as predictors would accommodate changes in tree structure that might occur over time and in response to elevated CO 2 . At the conclusion of the FACE experiment, we harvested 23 trees, measured dimensions and dry mass of boles and branches, and extracted and measured the woody root mass of 10 trees. Although 10 of the harvested trees were larger than the trees used to establish the allometric relationship, measured aboveground woody biomass was well predicted by the original allometry. The initial linear equation between bole basal area and woody root biomass underestimated final root biomass by 28%, but root biomass was just 21% of total wood mass, and errors in aboveground and belowground estimates were offsetting. The allometry established at the beginning of the experiment provided valid predictions of tree biomass throughout the experiment. New allometric approaches using terrestrial laser scanning should reduce an important source of uncertainty in decade‐long forest experiments and in assessments of centuries‐long forest biomass accretion used in evaluating carbon offsets and climate mitigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

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↗
DOE OSTI2021

Declining carbohydrate content of Sitka-spruce treesdying from seawater exposure

Abstract Increasing sea levels associated with climate change threaten the survival of coastal forests, yet the mechanisms by which seawater exposure causes tree death remain poorly understood. Despite the potentially crucial role of nonstructural carbohydrate (NSC) reserves in tree survival, their dynamics in the process of death under seawater exposure are unknown. Here we monitored progressive tree mortality and associated NSC storage in Sitka-spruce (Picea sitchensis) trees dying under ecosystem-scale increases in seawater exposure in western Washington, USA. All trees exposed to seawater, because of monthly tidal intrusion, experienced declining crown foliage during the sampling period, and individuals with a lower percentage of live foliated crown (PLFC) died faster. Tree PLFC was strongly correlated with subsurface salinity and needle ion contents. Total NSC concentrations in trees declined remarkably with crown decline, and reached extremely low levels at tree death (2.4% and 1.6% in leaves and branches, respectively, and 0.4% in stems and roots). Starch in all tissues was almost completely consumed, while sugars remained at a homeostatic level in foliage. The decreasing NSC with closer proximity to death and near zero starch at death are evidences that carbon starvation occurred during Sitka-spruce mortality during seawater exposure. Our results highlight the importance of carbon storage as an indicator of tree mortality risks under seawater exposure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Local carbon reserves are insufficient for phloem terpene induction during drought in Pinus edulis in response to bark beetle–associated fungi

Stomatal closure during drought inhibits carbon uptake and may reduce a tree's defensive capacity. Limited carbon availability during drought may increase a tree's mortality risk, particularly if drought constrains trees' capacity to rapidly produce defenses during biotic attack. We parameterized a new model of conifer defense using physiological data on carbon reserves and chemical defenses before and after a simulated bark beetle attack in mature Pinus edulis under experimental drought. Attack was simulated using inoculations with a consistent bluestain fungus (Ophiostoma sp.) of Ips confusus, the main bark beetle colonizing this tree, to induce a defensive response. Trees with more carbon reserves produced more defenses but measured phloem carbon reserves only accounted for c. 23% of the induced defensive response. Our model predicted universal mortality if local reserves alone supported defense production, suggesting substantial remobilization and transport of stored resin or carbon reserves to the inoculation site. Our results show that de novo terpene synthesis represents only a fraction of the total measured phloem terpenes in P. edulis following fungal inoculation. Without direct attribution of phloem terpene concentrations to available carbon, many studies may be overestimating the scale and importance of de novo terpene synthesis in a tree's induced defense response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Active layer depth and soil properties impact specific leaf area variation and ecosystem productivity in a boreal forest

Specific leaf area (SLA, leaf area per unit dry mass) is a key canopy structural characteristic, a measure of photosynthetic capacity, and an important input into many terrestrial process models. Although many studies have examined SLA variation, relatively few data exist from high latitude, climate-sensitive permafrost regions. We measured SLA and soil and topographic properties across a boreal forest permafrost transition, in which dominant tree species changed as permafrost deepened from 54 to >150 cm over 75 m hillslope transects in Caribou-Poker Creeks Research Watershed, Alaska. We characterized both linear and threshold relationships between topographic and edaphic variables and SLA and developed a conceptual model of these relationships. We found that the depth of the soil active layer above permafrost was significantly and positively correlated with SLA for both coniferous and deciduous boreal tree species. Intraspecific SLA variation was associated with a fivefold increase in net primary production, suggesting that changes in active layer depth due to permafrost thaw could strongly influence ecosystem productivity. While this is an exploratory study to begin understanding SLA variation in a non-contiguous permafrost system, our results indicate the need for more extensive evaluation across larger spatial domains. These empirical relationships and associated uncertainty can be incorporated into ecosystem models that use dynamic traits, improving our ability to predict ecosystem-level carbon cycling responses to ongoing climate change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stochastic events using pedigree-based DNA methylation data as input. We demonstrate how AlphaBeta can be employed to study transgenerationally heritable epimutations in clonal or sexually derived mutation accumulation lines, as well as somatic epimutations in long-lived perennials. Application of our method to published and new data reveals that spontaneous epimutations accumulate neutrally at the genome-wide scale, originate mainly during somatic development and that they can be used as a molecular clock for age-dating trees.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Plant carbohydrate storage: intra- and inter-specific trade-offs reveal a major life history trait

Trade-offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade-offs typically fall along a productive growth to conservative, bet-hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade-off framework is not well understood. Here, we examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database. We demonstrate that storage is actively accumulated, as part of a conservative, bet-hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the species Populus trichocarpa, genetic trade-offs show that for each additional unit of wood area growth (in cm 2 yr –1 ) that genotypes invest in, they lose 1.2 to 1.7 units (mg g –1 NSC) of storage. Across species, for each additional unit of area growth (in cm 2 yr –1 ), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots. Our findings impact our understanding of basic plant biology, fit storage into a widely used growth-survival trade-off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

A catastrophic tropical drought kills hydraulically vulnerable tree species

Drought-related tree mortality is now a widespread phenomenon predicted to increase in magnitude with climate change. However, the patterns of which species and trees are most vulnerable to drought, and the underlying mechanisms have remained elusive, in part due to the lack of relevant data and difficulty of predicting the location of catastrophic drought years in advance. In this work, we used long-term demographic records and extensive databases of functional traits and distribution patterns to understand the responses of 20–53 species to an extreme drought in a seasonally dry tropical forest in Costa Rica, which occurred during the 2015 El Niño Southern Oscillation event. Overall, species-specific mortality rates during the drought ranged from 0% to 34%, and varied little as a function of tree size. By contrast, hydraulic safety margins correlated well with probability of mortality among species, while morphological or leaf economics spectrum traits did not. This firmly suggests hydraulic traits as targets for future research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Use of a Black-Tailed Prairie Dog Burrow by Honey Bees in the Texas Panhandle

Cynomys ludovicianus Baird (Black-Tailed Prairie Dog) is considered to be a keystone species in the prairie, providing food and habitat for a diversity of wildlife. In October of 2020, we observed an active Apis mellifera Linnaeus (European Honey Bee) hive visible within the entrance of a burrow made by Black-Tailed Prairie Dogs in the treeless plains of the Texas Panhandle. Furthermore, this observation suggests that prairie dogs could provide habitat for this economically important pollinator and in landscapes otherwise devoid of cavities such as are commonly found in trees, buildings, and other structures.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Genotypic and Phenotypic Characterization of Incompatibility Group FIB Positive Salmonella enterica Serovar Typhimurium Isolates from Food Animal Sources

Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modeling the mechanisms of conifer mortality under seawater exposure

Summary Relative sea level rise (SLR) increasingly impacts coastal ecosystems through the formation of ghost forests. To predict the future of coastal ecosystems under SLR and changing climate, it is important to understand the physiological mechanisms underlying coastal tree mortality and to integrate this knowledge into dynamic vegetation models. We incorporate the physiological effect of salinity and hypoxia in a dynamic vegetation model in the Earth system land model, and used the model to investigate the mechanisms of mortality of conifer forests on the west and east coast sites of USA, where trees experience different form of sea water exposure. Simulations suggest similar physiological mechanisms can result in different mortality patterns. At the east coast site that experienced severe increases in seawater exposure, trees loose photosynthetic capacity and roots rapidly, and both storage carbon and hydraulic conductance decrease significantly within a year. Over time, further consumption of storage carbon that leads to carbon starvation dominates mortality. At the west coast site that gradually exposed to seawater through SLR, hydraulic failure dominates mortality because root loss impacts on conductance are greater than the degree of storage carbon depletion. Measurements and modeling focused on understanding the physiological mechanisms of mortality is critical to reducing predictive uncertainty.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Recent land cover changes in the Southwestern US lead to an increase in surface temperature

The increase in large-scale land cover change (LCC) in recent decades, particularly in response to climate-driven disturbances, has potential to impact local and regional changes in climate due to modification of carbon sources and sinks, albedo, surface roughness and energy fluxes. Using observational data, we predict the impact of two of the most extensive LCCs occurring in the Southwestern US: drought-induced tree mortality and shrub encroachment into grasslands, on surface temperature. We developed a new energy balance method that extracts the biophysical responses to environmental conditions, to predict how structural changes in albedo, surface roughness and canopy conductance following LCC will alter surface temperature. This method allows us not only to explain the observed differences in surface temperature between two non-adjacent study sites with different environmental conditions, but also to separate the contribution of biophysical and non-biophysical properties to surface temperature. Our results suggest that changes in biophysical properties due to shrub encroachment and tree mortality in the Southwestern US (independent of changes in other environmental properties) can potentially lead to an increase in midday surface temperature (11AM to 2PM) of 1 to 2 degrees Celsius, comparable to changes in surface temperature following deforestation. Although the average surface temperature increase in response to both shrub encroachment and tree mortality is similar, the biophysical properties driving the temperature change are different in each scenario. Change in aerodynamic conductance following tree mortality is the largest contributor to heating, while reduced albedo and canopy conductance drive the increase in surface temperature following shrub encroachment. Finally, we also show how this increase in daytime surface temperature could be further intensified with future climate, especially with the expected reduction in soil water availability in the Southwest.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A new approach to zip–lignin: 3,4–dihydroxybenzoate is compatible with lignification

Renewed interests in the development of bioenergy, biochemicals, and biomaterials have elicited new strategies for engineering the lignin of biomass feedstock plants. Furthermore, this study shows, for the first time, that 3,4-dihydroxybenzoate (DHB) is compatible with the radical coupling reactions that assemble polymeric lignin in plants. We introduced a bacterial 3-dehydroshikimate dehydratase into hybrid poplar (Populus alba × grandidentata) to divert carbon flux away from the shikimate pathway, which lies upstream of lignin biosynthesis. Transgenic poplar wood had up to 33% less lignin with p-hydroxyphenyl units comprising as much as 10% of the lignin. Mild alkaline hydrolysis of transgenic wood released fewer ester-linked p-hydroxybenzoate groups than control trees, and revealed the novel incorporation of cell-wall-bound DHB, as well as glycosides of 3,4-dihydroxybenzoic acid (DHBA). Two-dimensional nuclear magnetic resonance (2D-NMR) analysis uncovered DHBA-derived benzodioxane structures suggesting that DHB moieties were integrated into the lignin polymer backbone. In addition, up to 40% more glucose was released from transgenic wood following ionic liquid pretreatment and enzymatic hydrolysis. This work highlights the potential of diverting carbon flux from the shikimate pathway for lignin engineering and describes a new type of ‘zip-lignin’ derived from the incorporation of DHB into poplar lignin.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tree architecture: A strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.

59 BASIC BIOLOGICAL SCIENCES↗