Force transmission and SUN-KASH higher-order assembly in the LINC complex models
Not provided.
Biophysics↗
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Results for “biophysical models”
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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Biophysical analysis of the plant-specific GIPC sphingolipids reveals multiple modes of membrane regulation
The plant plasma membrane (PM) is an essential barrier between the cell and the external environment, controlling signal perception and transmission. It consists of an asymmetrical lipid bilayer made up of three different lipid classes: sphingolipids, sterols, and phospholipids. The glycosyl inositol phosphoryl ceramides (GIPCs), representing up to 40% of total sphingolipids, are assumed to be almost exclusively in the outer leaflet of the PM. However, their biological role and properties are poorly defined. In this study, we investigated the role of GIPCs in membrane organization. Because GIPCs are not commercially available, we developed a protocol to extract and isolate GIPC-enriched fractions from eudicots (cauliflower and tobacco) and monocots (leek and rice). Lipidomic analysis confirmed the presence of trihydroxylated long chain bases and 2-hydroxylated very long-chain fatty acids up to 26 carbon atoms. The glycan head groups of the GIPCs from monocots and dicots were analyzed by gas chromatograph-mass spectrometry, revealing different sugar moieties. Multiple biophysics tools, namely Langmuir monolayer, ζ-Potential, light scattering, neutron reflectivity, solid state 2H-NMR, and molecular modeling, were used to investigate the physical properties of the GIPCs, as well as their interaction with free and conjugated phytosterols. We showed that GIPCs increase the thickness and electronegativity of model membranes, interact differentially with the different phytosterols species, and regulate the gel-to-fluid phase transition during temperature variations. These results unveil the multiple roles played by GIPCs in the plant PM.
59 BASIC BIOLOGICAL SCIENCES↗
Forest reorganisation effects on fuel moisture content can exceed changes due to climate warming in wet temperate forests
Abstract The distributions of vegetation and fire activity are changing rapidly in response to climate warming. In many regions, climate effects on dead fuel moisture content (FMC) are expected to increase future wildfire activity. However, forest FMC is largely driven by microclimate conditions, which are moderated from open weather by vegetation canopies. As shifts in vegetation increase under climate warming, the extent to which future fire activity will be driven by climate directly or associated vegetation shifts remains unresolved. Here, we present a study aimed at quantifying the relative magnitudes of (i) direct climate warming, and (ii) vegetation change, on FMC. Field sites to evaluate these effects were established in a natural laboratory of altered forest states to mature wet temperate forest in south‐eastern Australia. FMC was estimated using a process‐based model and 48 years of reconstructed climate data. Canopy effects on microclimate were captured by transferring inputs from climate to microclimate using models parameterised with field observations. To evaluate the relative magnitude of climate and vegetation effects, we calculated the maximum difference in mean annual FMC across annual climate replicates and compared this to FMC differences across reorganising forest sites. Our results show vegetation effects on FMC can exceed those related to expected climate change. Changes to forest structure and composition increased (+15.7%) and decreased (−12.3%) mean annual FMC, with a larger negative effect when forest cover was completely removed (−18.5%). In contrast, the largest climate effect on FMC was −6.6% across 48‐years of data. Our study demonstrates that the magnitude of vegetation effects on FMC can exceed expected climate change effects. Models of future fire activity that do not account for changing vegetation effects on microclimate are omitting a key biophysical control on FMC and therefore may not be accurately predicting future fire activity.
Brown, Tegan P.↗
The Use of Joint Models in Analysis of Aggregate Endpoints in RERF Cohort Studies
Not provided.
Biophysics↗
A tale of two extremes: Temperature sensitivity of carbon loss from cool and hot soils
Soils represent the largest terrestrial carbon (C) pool, and the flux of carbon dioxide (CO 2 ) from soils to the atmosphere is ~ 6-10 times more than anthropogenic emissions. Understanding responses of soil CO 2 emissions to warming is crucial for evaluating feedback to ongoing environmental changes. The relationship between microbial respiration and temperature is typically modeled using a Q 10 function. Generally, observations of the apparent Q 10 of soil respiration are higher for cold vs. warm ecosystems, reflecting expected biophysical controls of Arrhenius kinetics. However, results from two field warming experiments in the tropics contradict this expectation, both observing extraordinarily high soil respiration responses to in situ warming. Our overall objective for the proposed work is to reduce uncertainty in temperature sensitivity of soil C loss by systematically synthesizing underlying mechanisms related to soil C turnover and stabilization. We are evaluating the temperature sensitivity of soil respiration in ecosystems across temperature extremes (e.g., arctic/boreal and tropical systems) by integrating data collected from field warming experiments with machine learning and biogeochemical models.
54 ENVIRONMENTAL SCIENCES↗
An agent-based modeling tool supporting bioenergy and bio-product community communication regarding cellulosic bioeconomy development
The emergence of the cellulosic bioeconomy requires not only adequate technological, economic, and policy advances, but also effective communication and coordination among the multiple stakeholders in the bioeconomy community. Aiming to facilitate stakeholder communication and collaboration for cellulosic bioeconomy growth, an agent-based model is developed as a community communication tool in this study. The tool simulates the behaviors and interactions of key stakeholders, as well as the responses and interactions between the stakeholders and biophysical, socioeconomic, and environmental conditions. The agent behavior rules are developed and validated based on behavior and economic theories and information attained from a stakeholder focus group study and a land use survey. A pilot study in a Central Illinois watershed shows stakeholder synergies, i.e., positive feedback loops across multiple stakeholders. The modeling tool's role in facilitating community communication is demonstrated via the focus group study. A comparison of policy scenarios suggests that the cellulosic bioeconomy development is fastest under a portfolio of policies combining the views of the multiple stakeholders. Critically, subsidy for small-scale bio-facilities is essential as it rapidly initializes an early market for cellulosic feedstocks and the adoption of Miscanthus. As a result, the communication tool is applied to bringing stakeholders and researchers together to develop shared visions, assess barriers, and explore solution portfolios to initialize and speed up the regional cellulosic bioeconomy.
09 BIOMASS FUELS↗
Investigating the Diurnal Radiative, Turbulent, and Biophysical Processes in the Amazonian Canopy‐Atmosphere Interface by Combining LES Simulations and Observations
Abstract We investigate the atmospheric diurnal variability inside and above the Amazonian rainforest for a representative day during the dry season. To this end, we combine high‐resolution large‐eddy simulations that are constrained and evaluated against a comprehensive observation set, including CO 2 concentrations, gathered during GoAmazon2014/15. We design systematic numerical experiments to quantify whether a multilayer approach in solving the explicit canopy improves our canopy‐atmosphere representation. We particularly focus on the relationship between photosynthesis and plant transpiration, and their distribution at leaf and canopy scales. We found the variability of photosynthesis drivers like vapor pressure deficit and leaf temperature to be about 3 times larger for sunlit leaves compared to shaded leaves. This leads to a large spread on leaf stomatal conductance values with minimum and maximum values varying more than 100%. Regarding the turbulent structure, we find wind‐driven stripe‐like shapes at the canopy top and structures resembling convective cells at the canopy. Wind‐related variables provide the best spatiotemporal agreement between model and observations. The potential temperature and heat flux profiles agree with an observed decoupling near the canopy top interface, although with less variability and cold biases of up to 3 K. The increasing complexity on the biophysical processes leads to the largest disagreements for evaporation, CO 2 plant assimilation and soil efflux. The model is able to capture the correct dependences and trends with the magnitudes still differing. We finally discuss the need to revise leaf and soil models and to complete the observations at leaf and canopy levels.
54 ENVIRONMENTAL SCIENCES↗
ITreeForeCast: An integrated modeling software to simulate tree level growth and forest carbon storage
Healthy trees in forest act as a natural carbon sink, capturing carbon. As they grow, they store carbon in their trunks, leaves and roots. Not all trees store carbon at the same rate, or in the same quantities, as it depends on a variety of biophysical and climatic factors. Furthermore, although carbon estimation in trees can be complex, the precision of estimates is tightly linked to trees growth, both in diameter and height. However, the simulation of carbon uptake by forest and forest growth has each been modeled separately, and independently at differing levels of detail and spatial resolution. In this paper, we introduce ITreeForeCast, a simulation model combining the two types of modeling on a unified platform, enabling the investigation of impacts of management strategies on carbon sequestration and wood products. ITreeForeCast is a user-extendable framework that offers new opportunities to model, simulate, and visualize the dynamics of individual trees in a forest, simulate management strategies over time, and carbon uptake.
09 - BIOMASS FUELS↗
Explainable machine learning to quantify the value of proximal remote sensing in latent energy flux estimation
Proximal remote sensing has the potential to provide critical information on vegetation biophysical factors that can predict land-atmosphere exchange of water and energy. Latent energy (LE) flux is traditionally estimated using process-based models which rely on vegetation parameters that change during the growing season. Data-driven models have the potential to address these issues by offering flexible predictor selection and more efficient utilization of the information in predictor sets. These models require careful choice of predictors to avoid redundancy and allow robust cross-validation. In this study we present a systematic and comprehensive evaluation of machine learning (ML) models to assess the capability of meteorological and proximal sensing data for predicting LE at a half-hourly temporal resolution across multiple growing seasons for an agricultural system. The results presented here demonstrate that a model using four environmental predictors in combination with two proximal sensing variables can capture 88 % of the variability in LE. ML models using only three predictors (one meteorological and two proximal remote sensing) captured 81 % of LE variability, offering the best trade-off between performance and complexity. An ML model utilizing only two predictors, one proximal remote sensing variable and downwelling radiation, captured 77 % of LE variability. These results demonstrate the power of proximal remote sensing and meteorological observations to estimate land-atmosphere water vapor exchange, providing a solution where more direct methods such as eddy covariance are not available and for evaluations of agronomic management and genotypic variations.
60 APPLIED LIFE SCIENCES↗
Trends and Drivers of Terrestrial Sources and Sinks of Carbon Dioxide: An Overview of the TRENDY Project
The terrestrial biosphere plays a major role in the global carbon cycle, and there is a recognized need for regularly updated estimates of land-atmosphere exchange at regional and global scales. An international ensemble of Dynamic Global Vegetation Models (DGVMs), known as the “Trends and drivers of the regional scale terrestrial sources and sinks of carbon dioxide” (TRENDY) project, quantifies land biophysical exchange processes and biogeochemistry cycles in support of the annual Global Carbon Budget assessments and the REgional Carbon Cycle Assessment and Processes, phase 2 project. DGVMs use a common protocol and set of driving data sets. A set of factorial simulations allows attribution of spatio-temporal changes in land surface processes to three primary global change drivers: changes in atmospheric CO 2 , climate change and variability, and Land Use and Land Cover Changes (LULCC). Here, we describe the TRENDY project, benchmark DGVM performance using remote-sensing and other observational data, and present results for the contemporary period. Simulation results show a large global carbon sink in natural vegetation over 2012–2021, attributed to the CO 2 fertilization effect (3.8 ± 0.8 PgC/yr) and climate (–0.58 ± 0.54 PgC/yr). Forests and semi-arid ecosystems contribute approximately equally to the mean and trend in the natural land sink, and semi-arid ecosystems continue to dominate interannual variability. The natural sink is offset by net emissions from LULCC (–1.6 ± 0.5 PgC/yr), with a net land sink of 1.7 ± 0.6 PgC/yr. Despite the largest gross fluxes being in the tropics, the largest net land-atmosphere exchange is simulated in the extratropical regions.
58 GEOSCIENCES↗
APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics
The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.
97 MATHEMATICS AND COMPUTING↗
Semi-automated Design of Artificial Intelligence Earth Systems Models
Prediction and observation of water cycles at various scales involve not only patterns isolated in space and time, but also modeling of complex spatio-temporal relationships across multiple domains. For instance, evapotranspiration (ET) and leaf area indexes (LAI) are two parameters that are needed to accurately model and understand land-atmosphere processes. Accurate assessments of ET and LAI are critical for understanding hydrological processes, deforestation, crop yield, and irrigation impacts. However, ET estimates for global simulations are available at very coarse spatial resolution. They are usually derived from satellite data based on broad plant functional types (PFTs), which fail to capture fine-scale variations because of changes in vegetation type across the globe. Similarly LAI estimates have typically been derived from vegetation indices at global scales or estimated locally using physical models, both of which suffer from a range of uncertainties that impact model sensitivity. The new era of AI model development for Earth systems (ES) calls for data-driven methods that provide domain scientists with uncertainty-aware estimations of biophysical parameters such as ET and LAI in a generalizable, interpretable, and discoverable manner.
54 ENVIRONMENTAL SCIENCES↗
A Radiative Transfer Model for Patchy Landscapes Based on Stochastic Radiative Transfer Theory
The availability of global high-resolution land cover maps provides promising a priori knowledge for characterizing subpixel heterogeneity and improving predictions of directional reflectance of coarse-resolution pixels. Due to mutual shadowing and sheltering effects between the adjacent forest and cropland patches, the spectral nonlinear mixing of patchy ecotones is significant, especially when the sun illuminates the ecotone from the forest side with high solar zenith angle. The spectral linear mixture (SLM) approach leads to overestimation of the bidirectional reflectance factor (BRF) in the red band in the principal plane (PP), with a maximum absolute error (MAE) of 0.0063 and a maximum relative error (MRE) of 52.5%, and to underestimation in the near-infrared band in PP with an MAE of 0.0940 and an MRE of 14.5%. In a scenario with randomly distributed boundary orientations, the overestimation of SLM increases with the degree of fragmentation and the view zenith angle. We propose a Radiative Transfer model for patchy ECotones (RTEC). which improves R² from 0.61 to 0.94 in the red band of Landsat-8 directional reflectance at the validation site. The RTEC model provides an efficient and analytical approach for directional reflectance predictions over heterogeneous patchy landscapes at coarse resolution and will be used for biophysical parameter retrievals [e.g., the leaf area index (LAI)] in future applications.
Zeng, Yelu↗
Deforestation strengthens atmospheric transport of mineral dust and phosphorus from North Africa to the Amazon
Phosphorus contained in atmospheric mineral dust aerosol originating from Africa fertilizes tropical forests in Amazonia. However, the mechanisms influencing this nutrient transport pathway remain poorly understood. Here we use the Community Earth System Model to investigate how large-scale deforestation affects mineral dust aerosol transport and deposition in the tropics. We find that the surface biophysical changes that accompany deforestation produce a warmer, drier and windier surface environment that perturbs atmospheric circulation and enhances long-range dust transport from North Africa to the Amazon. Tropics-wide deforestation weakens the Hadley circulation, which in turn, leads to a northward expansion of the Hadley cell and increases surface air pressure over the Sahara Desert. Additionally, the high pressure anomaly over the Sahara, in turn, increases northeasterly winds across North Africa and the tropical North Atlantic Ocean, which subsequently increases dust transport to the South America continent. We estimate that the annual atmospheric phosphorus deposition from dust significantly increases by 27% (P < 0.01) in the Amazon under a scenario of complete deforestation. These interactions exemplify how land surface changes can modify tropical nutrient cycling, which in turn, may have consequences for long-term changes in tropical ecosystem productivity and biodiversity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Go with the flow: modeling unique biological flows in engineered in vitro platforms
Interest in recapitulating in vivo phenomena in vitro using organ-on-a-chip technology has grown rapidly and with it, attention to the types of fluid flow experienced in the body has followed suit. These platforms offer distinct advantages over in vivo models with regards to human relevance, cost, and control of inputs (e.g., controlled manipulation of biomechanical cues from fluid perfusion). Given the critical role biophysical forces play in several tissues and organs, it is therefore imperative that engineered in vitro platforms capture the complex, unique flow profiles experienced in the body that are intimately tied with organ function. In this review, we outline the complex and unique flow regimes experienced by three different organ systems: blood vasculature, lymphatic vasculature, and the intestinal system. Here, we highlight current state-of-the-art platforms that strive to replicate physiological flows within engineered tissues while introducing potential limitations in current approaches.
42 ENGINEERING↗
Distinct roles of land cover in regulating spatial variabilities of temperature responses to radiative effects of aerosols and clouds
Surface temperature responses to radiative perturbations due to aerosols and clouds are complicated by the land surface properties. To disentangle these complexities, this study, from a terrestrial surface energy budget perspective, isolates the underlying biophysical processes from the instantaneous radiative effects of aerosols and clouds on surface temperature using the National Center for Atmospheric Research Community Earth System Model version 1.2.1. It is found that in comparison with the global heterogeneous distributions of instantaneous radiative perturbations at the surface induced by aerosols and clouds, the spatial variations of the corresponding surface temperature responses to aerosol direct radiative effects (DRE) during the daytime and cloud radiative effects (CRE) during the nighttime are amplified. It is because of the consistent global distribution of the local surface climate sensitivity (a function of land cover properties such as surface roughness and Bowen ratio) with those of daytime DRE and nighttime CRE. By applying identical anthropogenic aerosol and precursor emissions over eight major past, present and projected future anthropogenic aerosol emitting regions (i.e. Brazil, China, East Africa, India, Indonesia, South Africa, United States and Western Europe), surface temperature responses to aerosol radiative cooling in the daytime and cloud radiative warming in the nighttime over these regions positively regulated by local surface climate sensitivities are prominent.
54 ENVIRONMENTAL SCIENCES↗