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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 505 records · Page 28
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

FEED Study of Carbon Capture Inc. DAC and CarbonCure Utilization Using United States Steel's Gary Works Waste Plant

Direct Air Capture (DAC) has been proposed as a means of reducing atmospheric concentrations of CO2. While DAC has been evaluated through lab-scale, bench-scale, and small-scale pilot units, large-scale deployment has not been achieved. Feasibility studies are one tool to understand the potential design, operation, performance, and impact of commercial-scale DAC. This paper presents the results of a feasibility study for a passive DAC system deployed at >100,000 tpy scale in three different regions across the U.S. and awarded to Carbon Collect by the U.S. Department of Energy National Energy Technology Laboratory (DOE NETL). The MechanicalTree™technology has been designed and engineered by Carbon Collect based on the concept initially developed at Arizona State University Center for Negative Carbon Emissions. It uses a tower of stacked, sorbentcontaining disks supported by a lifting mechanism, exposed to the air to capture CO2 during the adsorption phase. The disks are then lowered into a regeneration chamber for vacuum and steam regeneration to produce CO2 product during the desorption step. The modular tree design allows large installations with repeatable, mass-manufactured units connected to common utilities such as steam supply, vacuum, and CO2 processing for compression and geologic storage. The passive DAC system eliminates the equipment and energy of forced air fans by using natural air circulation to contact the sorbent with the CO2 in the air. Because of this, the performance is dependent on the wind speed in addition to the temperature and relative humidity. Performance and flow rate fluctuations were incorporated into equipment and facility design with considerations for turndown to 10% of maximum rated flow to allow operation in all seasons. The feasibility study was undertaken to evaluate the technology in different regions and climates. Three locations were selected for this study representing different climates: Alabama (hot and humid), California (hot and arid), and Wyoming (continental). For each region, the adsorption/desorption cycle was optimized including tuning the heat integration and cycle timings. The performance of individual trees was then scaled to the full facility with the same design of more than 20,000 trees common between all regions. The installations had expected average CO2 capture rates of between 330,000 and 485,000 tonnes of CO2 per year depending on the climate. The initial engineering design for the facility at each location was performed with cost and performance estimates for the trees, carbon purification and compression, and the balance of plant. To supply thermal and electrical energy for the facility, carbon-free or low-carbon power must be considered. Options for low-carbon, continuous thermal and electrical energy were considered. The best-performing option from those considered was identified to be an electrically-heated molten salt energy storage system, powered by an on-site photovoltaic field. During molten salt thermal discharge, steam is produced from heat exchange with the molten salt and used to generate power in a steam turbine as well as steam for regenerating the DAC carbon trees. The thermal and electrical supply and analysis is presented in the context of low-carbon power for carbon removal. Modelling and economics of transportation and geologic storage of the CO2 is considered and presented for each location. The results of the feasibility study are incorporated into the presented techno-economic and life-cycle assessments. This work is intended to provide an understanding of the performance, cost, and impact of capturing CO2 at the commercial scale and the impact of climate and regional siting on the considered passive DAC system.

42 ENGINEERING↗
DOE OSTI2026

A Comprehensive Greenhouse Gas Assessment of Biomass-Based Carbon Dioxide Removal and Storage

Biomass-based Carbon Removal and Storage (BiCRS) is a suite of technological pathways that provide a relatively affordable and high-potential way to remove carbon dioxide from the atmosphere and simultaneously re-purpose residual biomass. BiCRS technologies are individually optimized to different biomass feedstocks, temperatures and oxygen, with the primary goal of capturing a high percentage of biomass-derived carbon dioxide and storing it in permanent below-ground storage (i.e. geologic storage), and a secondary goal of producing renewable energy. The current standard for BiCRS life cycle assessments does not account for greenhouse gas (carbon dioxide, methane and nitrous oxide) fluxes from surface soil amendment of BiCRS byproducts (e.g. char, ash) and their alternate fates. This is partly due to a paucity of empirical data due to the novelty of BiCRS conversion technologies, the range in feedstocks, and the heterogeneity of soils to which they might be amended. To fill this gap in in the life-cycle assessment and provide a realistic range of parameters for a soil amendment component of the BiCRS life cycle assessment, we conducted an incubation experiment to measure soil carbon changes, microbial respiration, methane fluxes, and nitrous oxide fluxes from two different soils amended with char- and ash- byproducts from biomass after gasification to hydrogen, fast pyrolysis to bio-oil, and torrefaction. Our results suggest that nitrous oxide and methane emission or consumption from BiCRS char amendments to soil are context dependent. Nitrous oxide emissions from amendments are higher in soils with higher pH, whereas some char amendments to low pH soil can reduce N 2 O emissions relative to control. In contrast, methane is emitted from BiCRS char amended to low pH soil, but consumed or neutral relative to control when amended to high pH soil. We present carbon and nitrogen mass balance throughout the experiment to help understand short-term durability of BiCRS chars and their counterfactuals, and preliminary suggestions for revisions to the broader BiCRS Measurement, Reporting, and Verification framework.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Systematic and objective evaluation of Earth system models: PCMDI Metrics Package (PMP) version 3

Systematic, routine, and comprehensive evaluation of Earth system models (ESMs) facilitates benchmarking improvement across model generations and identifying the strengths and weaknesses of different model configurations. By gauging the consistency between models and observations, this endeavor is becoming increasingly necessary to objectively synthesize the thousands of simulations contributed to the Coupled Model Intercomparison Project (CMIP) to date. The Program for Climate Model Diagnosis and Intercomparison (PCMDI) Metrics Package (PMP) is an open-source Python software package that provides quick-look objective comparisons of ESMs with one another and with observations. The comparisons include metrics of large- to global-scale climatologies, tropical inter-annual and intra-seasonal variability modes such as the El Niño–Southern Oscillation (ENSO) and Madden–Julian Oscillation (MJO), extratropical modes of variability, regional monsoons, cloud radiative feedbacks, and high-frequency characteristics of simulated precipitation, including its extremes. The PMP comparison results are produced using all model simulations contributed to CMIP6 and earlier CMIP phases. An important objective of the PMP is to document the performance of ESMs participating in the recent phases of CMIP, together with providing version-controlled information for all datasets, software packages, and analysis codes being used in the evaluation process. Among other purposes, this also enables modeling groups to assess performance changes during the ESM development cycle in the context of the error distribution of the multi-model ensemble. Quantitative model evaluation provided by the PMP can assist modelers in their development priorities. In this paper, we provide an overview of the PMP, including its latest capabilities, and discuss its future direction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Bacteria export alarmone synthetases that produce (p)ppApp and (p)ppGpp

Guanosine penta- and tetraphosphate [(p)ppGpp] and their adenosine analogs [(p)ppApp] are bacterial second messengers known as alarmones. Members of the RelA-SpoT homolog (RSH) family synthesize (p)ppGpp to mediate the stringent response during nutrient starvation, whereas (p)ppApp synthetases have been identified as bactericidal toxins in diverse contexts including type VI secretion systems, toxin-antitoxin modules, and phages. Although alarmone synthesis has traditionally been viewed as a cytoplasmic process, early studies in Streptomyces suggested the existence of secreted alarmone synthetases. Here, we identify SaEAS, an exported alarmone synthetase (EAS) from Streptomyces albidoflavus, as the long-mysterious source of extracellular alarmone synthetase activity in Streptomyces. SaEAS produces both (p)ppGpp and (p)ppApp at rates exceeding 100,000 molecules per minute and has kinetic properties adapted to low substrate environments. A broader bioinformatic survey reveals ~600 EASs linked to a range of specialized bacterial secretion systems. Characterization of two additional EASs, VpEAS from Vibrio parahaemolyticus and AaEAS from Amycolatopsis azurea, shows that both produce (p)ppGpp exclusively and inhibit bacterial growth when localized to the cytoplasm. These findings challenge the longstanding view of (p)ppGpp as strictly pro-survival and unveil a diverse family of secreted RSH enzymes with potential roles in interbacterial antagonism and environmental signaling.

Ahmad, Shehryar↗
DOE OSTI2024

Defining weather scenarios for simulation-based assessment of thermal resilience of buildings under current and future climates: A case study in Brazil

In response to increasingly severe weather conditions, optimization of building performance and investment provides an opportunity to consider co-benefits of thermal resilience during energy efficiency retrofits. This work aims to assess thermal resilience of buildings using building performance simulation to evaluate the indoor overheating risk under nine weather scenarios, considering historical (2010s), mid-term future (2050s), and long-term future (2090s) typical meteorological years, and heat wave years. Such an analysis is based on resilience profiles that combine six integrated indicators. A case study with a district of 92 buildings in Brazil was conducted, and a combination of strategies to improve thermal resilience was identified. Results reflect the necessity of planning for resilience in the context of climate change. This is because strategies recommended under current conditions might not be ideal in the future. Therefore, an adaptable design should be prioritized. Cooling energy consumption could increase by 48 % by the 2050s, while excessive overheating issues could reach 37 % of the buildings. Simple passive strategies can significantly reduce the heat stress. A comprehensive thermal resilience analysis should ultimately be accompanied by a thorough reflection on the stakeholders’ objectives, available resources, and planning horizon, as well as the risks assumed for not being resilient.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2026

Multi‐Objective Urban Observational Strategies: A Risk‐Based Framework for Expanding Flood Sensor Networks

In coupled human and natural systems, developing an observation strategy which maximizes insight into both the natural system and the human system is a challenging multi-objective optimization problem. In this article, we describe the expansion of a flood risk observation system in Southeast Texas designed to improve our understanding of both physical and socioeconomic exposure to hydrological hazards at fine spatial scales, in the context of a structured hazard-exposure-vulnerability risk framework. We describe a new approach for assessing the spatial extent through which a flood sensor's observations can be assumed to be relevant, and estimate the population served within each sensor's area of information using downscaled socio-demographic data. As hydrological observations and modeling move to ever finer scale, assessing the information they contain in the context of both social and natural systems becomes increasingly important for developing actionable scientific insights.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Flash droughts present a new challenge for subseasonal-to-seasonal prediction

Flash droughts are a recently recognized type of extreme event distinguished by sudden onset and rapid intensification of drought conditions with severe impacts. They unfold on subseasonal-to-seasonal timescales (weeks to months), presenting a new challenge for the surge of interest in improving subseasonal-to-seasonal prediction. In this perspective we discuss existing prediction capability for flash droughts and what is needed to establish their predictability. We place them in the context of synoptic to centennial phenomena, consider how they could be incorporated into early warning systems and risk management, and propose two definitions. The growing awareness that flash droughts involve particular processes and severe impacts, and probably a climate change dimension, makes them a compelling frontier for research, monitoring and prediction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Analysis of the performance of different culvert boundary conditions in 2D shallow flow models

Culverts allow roads to safely traverse small streams or drainage ditches, and their proper design is critical to ensure a safe and reliable transportation network. A correct modelization of these hydraulic structures becomes crucial in the assessment of flood footprints or discharge peak estimation in a risk evaluation plan. The question of how to include culverts comes up frequently when assembling a hydraulic model that requires the presence of as many singular elements as possible. In this work, three different culvert integrations with the surface domain are studied and compared in the context of a 2D shallow water (SW) model. All of them are based on the Federal Highway Administration (FHWA) formulation for the culvert discharge estimation but differ in complexity and in the interaction with the numerical model for surface flow, some of them as internal boundary conditions. Several steady and unsteady validation test cases are presented and the numerical results are compared with the predictions from HEC-RAS 1D and HY-8 software. Furthermore, the culvert area, shape and their sensitivity to the 2D computational mesh is also analyzed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Migrating Populus with climate change: Phenology, coppice management, cold spell susceptibility, leaf dynamics, and biomass production

Understanding the phenology and productivity of Populus species is crucial for effective management and conservation strategies amid climate change. We investigated leaf budbreak timing, susceptibility to cold damage, leaf dynamics, and biomass production of 168 Populus genotypes with diverse provenances in the southeastern United States. Our study revealed significant variation in budbreak timing across different taxa and years, with genotypes inheriting traits adapted to their parents’ local climates. Temperature emerged as a key factor triggering budbreak, while leaf development depended on other environmental cues such as photoperiod. Notably, budbreak occurred approximately 20 days earlier in 2023 compared to 2022 due to higher accumulated degree days (ADDs). Short-rotation-coppice (SRC) management delayed budbreak by five to ten days. Cold damage was significant in 2023, particularly for genotypes from northern provenances and those with P. maximowiczii parentage. Severe damage was also observed in eastern cottonwood ( Populus deltoides ​× ​ Populus deltoides (D ​× ​D)) genotypes, despite most having southeastern US parentages. Leaf dynamics, including leaf duration and leaf area index (LAI), varied across taxa and sites, with earlier budbreak correlating with extended growing seasons and increased LAI. Biomass production was intricately linked to phenological events, with earlier budbreak leading to increased biomass production and greater susceptibility to cold damage. Our findings highlight the importance of genetics, environment, and coppicing management in understanding and managing Populus phenology and biomass production. These insights provide valuable guidance for developing effective breeding, conservation, and management strategies for Populus species in the context of climate change.

Accumulated degree days (ADDs)↗
DOE OSTI2023

Evaluation of Power Transmission Lines Hardening Scenarios Using a Machine Learning Approach

The power transmission infrastructure is vulnerable to extreme weather events, particularly hurricanes and tropical storms. A recent example is the damage caused by Hurricane Maria (H-Maria) in the archipelago of Puerto Rico in September 2017, where major failures in the transmission infrastructure led to a total blackout. Numerous studies have been conducted to examine strategies to strengthen the transmission system, including burying the power lines underground or increasing the frequency of tree trimming. However, few studies focus on the direct hardening of the transmission towers to accomplish an increase in resiliency. This machine learning-based study fills this need by analyzing three direct hardening scenarios and determining the effectiveness of these changes in the context of H-Maria. A methodology for estimating transmission tower damage is presented here in this study as well as an analysis of impact of replacing structures with a high failure rate with more resilient ones. We found the steel self-support-pole to be the best replacement option for the towers with high failure rate. Furthermore, the third hardening scenario, where all wooden poles were replaced, exhibited a maximum reduction in damaged towers in a single line of 66% while lowering the mean number of damaged towers per line by 10%.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

The Future of Sensitivity Analysis: An essential discipline for systems modeling and policy support

Sensitivity analysis (SA) is en route to becoming an integral part of mathematical modeling. The tremendous potential benefits of SA are, however, yet to be fully realized, both for advancing mechanistic and data-driven modeling of human and natural systems, and in support of decision making. In this perspective paper, a multidisciplinary group of researchers and practitioners revisit the current status of SA, and outline research challenges in regard to both theoretical frameworks and their applications to solve real-world problems. Six areas are discussed that warrant further attention, including (1) structuring and standardizing SA as a discipline, (2) realizing the untapped potential of SA for systems modeling, (3) addressing the computational burden of SA, (4) progressing SA in the context of machine learning, (5) clarifying the relationship and role of SA to uncertainty quantification, and (6) evolving the use of SA in support of decision making. An outlook for the future of SA is provided that underlines how SA must underpin a wide variety of activities to better serve science and society.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Reflections on the anomalous ANITA events: the Antarctic subsurface as a possible explanation

The Antarctic Impulsive Transient Antenna (ANITA) balloon experiment was designed to detect radio signals initiated by high-energy neutrinos and cosmic ray (CR) air showers. These signals are typically discriminated by the polarization and phase inversions of the radio signal. The reflected signal from CRs suffer phase inversion compared to a direct ‘tau neutrino’ event. In this paper, we study subsurface reflection, which can occur without phase inversion, in the context of the two anomalous up-going events reported by ANITA. It is found that subsurface layers and firn density inversions may plausibly account for the events, while ice fabric layers and wind ablation crusts could also play a role. This hypothesis can be tested with radar surveying of the Antarctic region in the vicinity of the anomalous ANITA events. Future experiments should not use phase inversion as a sole criterion to discriminate between down-going and up-going events, unless the subsurface reflection properties are well understood.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Facets of hydro power and future trends in a Nordic Context

Hydropower technologies bolster high penetration of variable renewable energies (VREs) in the net zero emissions scenarios. Nevertheless, there are various challenges to meeting the ambitious goal, such as stability, reliability, resiliency, security, lack of reactive power, voltage support and inertia, large-scale storage deployment and coordination, interconnectedness, demand-side response, higher thermal cycles with increased start/stops, and inadequate Levelized Cost of Energy (LCOE) for system-wise VRE integration and profitability. This survey conducts a bottom-up analysis to unveil the opportunities to utilize hydropower facilities and disentangle the nested problem for intertwining design features, control algorithms, operation, optimization approaches, incentives, services, and market mechanisms using a three-pillar framework perspective: grid owners, power producers, and machine designers. The survey identified emerging trends in real-time and capacity markets, flexible power systems, and enhanced grid capabilities, including advanced voltage support and updated grid codes. These developments present significant opportunities for hydropower, such as achieving super-flexibility through hybridization, expanded reactive power capabilities, and advanced operational modes like a synchronous condenser and power adequator functionalities. These opportunities require novel design philosophies — including new winding, stator, and rotor configurations, optimized ventilation, and active cooling systems — to enhance performance under stressed grid and climate conditions. Finally, integrating climate and energy models for multi-basin optimization with finer spatial and temporal granularity enhances the planning accuracy for water management of hydropower while addressing environmental challenges. The review delivers helpful prospective suggestions and tools that would serve researchers, power engineers, and stakeholders in making decisions about hydropower technologies and services in 2050 and beyond.

13 HYDRO ENERGY↗
DOE OSTI2024

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

Abstract Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Environmental drivers of increased ecosystem respiration in a warming tundra

Abstract Arctic and alpine tundra ecosystems are large reservoirs of organic carbon 1,2 . Climate warming may stimulate ecosystem respiration and release carbon into the atmosphere 3,4 . The magnitude and persistency of this stimulation and the environmental mechanisms that drive its variation remain uncertain 5–7 . This hampers the accuracy of global land carbon–climate feedback projections 7,8 . Here we synthesize 136 datasets from 56 open-top chamber in situ warming experiments located at 28 arctic and alpine tundra sites which have been running for less than 1 year up to 25 years. We show that a mean rise of 1.4 °C [confidence interval (CI) 0.9–2.0 °C] in air and 0.4 °C [CI 0.2–0.7 °C] in soil temperature results in an increase in growing season ecosystem respiration by 30% [CI 22–38%] (n = 136). Our findings indicate that the stimulation of ecosystem respiration was due to increases in both plant-related and microbial respiration (n = 9) and continued for at least 25 years (n = 136). The magnitude of the warming effects on respiration was driven by variation in warming-induced changes in local soil conditions, that is, changes in total nitrogen concentration and pH and by context-dependent spatial variation in these conditions, in particular total nitrogen concentration and the carbon:nitrogen ratio. Tundra sites with stronger nitrogen limitations and sites in which warming had stimulated plant and microbial nutrient turnover seemed particularly sensitive in their respiration response to warming. The results highlight the importance of local soil conditions and warming-induced changes therein for future climatic impacts on respiration.

Science & Technology - Other Topics↗
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗
DOE OSTI2022

A mutagenic analysis of NahE, a hydratase-aldolase in the naphthalene degradative pathway

NahE is a hydratase-aldolase that converts o-substituted trans-benzylidenepyruvates (H, OH, or CO 2 - ) to benzaldehyde, salicylaldehyde, or 2-carboxybenzaldehyde, respectively, and pyruvate. The enzyme is in a bacterial degradative pathway for naphthalene, which is a toxic and persistent environmental contaminant. Sequence, crystallographic, and mutagenic analysis identified the enzyme as a member of the N-acetylneuraminate lyase (NAL) subgroup in the aldolase superfamily. As such, it has a conserved lysine (Lys183) and tyrosine (Tyr155), for Schiff base formation, as well as a GXXGE motif for binding of the pyruvoyl carboxylate group. A crystal structure of the selenomethionine derivative of NahE shows these active site elements along with nearby residues that might be involved in the mechanism and/or specificity. Mutations of five active site amino acids (Thr65, Trp128, Tyr155, Asn157, and Asn281) were constructed and kinetic parameters measured in order to assess the effect(s) on catalysis. Here, the results show that the two Trp128 mutants (Phe and Tyr) have the least effect on catalysis, whereas amino acids with bulky side chains at Thr65 (Val) and Asn281 (Leu) have the greatest effect. Changing Tyr155 to Phe and Asn157 to Ala also hinders catalysis, and the effects fall in between these extremes. These observations are put into a structural context using a crystal structure of the Schiff base of the reaction intermediate. Trapping experiments with substrate, Na(CN)BH 3 , and wild type enzyme and selected mutants mostly paralleled the kinetic analysis, and identified two salicylaldehyde-modified lysines: the active site lysine (Lys183) and one outside the active site (Lys279). The latter could be responsible for the observed inhibition of NahE by salicylaldehyde. Together, the results provide new insights into the NahE-catalyzed reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nutrient Dynamics in a Coupled Terrestrial Biosphere and Land Model (ELM-FATES-CNP)

We present a representation of nitrogen and phosphorus cycling in the Functionally Assembled Terrestrial Ecosystem Simulator, a demographic vegetation model within the Energy Exascale Earth System land model. This representation is modular, and designed to allow testing of multiple hypothetical approaches for carbon-nutrient coupling in plants. Novel model hypotheses introduced in this work include, (a) the controls on plant acquisition of aqueous mineralized nutrients in the soil and (b) fairly straight forward methods of allocating nutrients to specific plant organs and their losses through live plant turnover as well as litter fluxes generated through plant mortality. This combines the new with pre-existing hypotheses (such as nitrogen fixation and soil decomposition) into a system that can accommodate plant-soil dynamics for a large number of size- and functional-type-resolved plant cohorts within a time-since-disturbance-resolved ecosystem. Root uptake of nutrients is governed by fine root biomass, and plants vary in their fine root biomass allocation in order to balance carbon and nutrient limitations to growth. We test the sensitivity of the model to a wide range of parameter variations and structural representations, and in the context of observations at Barro Colorado Island, Panama. A key model prediction is that plants in the high-light-availability canopy positions allocate more carbon to fine roots than plants in low-light understory environments, given the widely different carbon versus nutrient constraints of these two niches within a given ecosystem. This model provides a basis for exploring carbon-nutrient coupling with vegetation demography within Earth system models.

54 ENVIRONMENTAL SCIENCES↗