Results for “biophysical models” — Page 12

DOE OSTI2025

U-Surf: a global 1 km spatially continuous urban surface property dataset for kilometer-scale urban-resolving Earth system modeling

High-resolution urban climate modeling has faced substantial challenges due to the absence of a globally consistent, spatially continuous, and accurate dataset to represent the spatial heterogeneity of urban surfaces and their biophysical properties. This deficiency has long obstructed the development of urban-resolving Earth system models (ESMs) and ultra-high-resolution urban climate modeling, over large domains. Here, we present U-Surf, a first-of-its-kind 1 km resolution present-day (circa 2020) global continuous urban surface parameter dataset. Using the urban canopy model (UCM) in the Community Earth System Model as a base model for satisfying dataset requirements, U-Surf leverages the latest advances in remote sensing, machine learning, and cloud computing to provide the most relevant urban surface biophysical parameters, including radiative, morphological, and thermal properties, for UCMs at the facet and canopy level. Generated using a systematically unified workflow, U-Surf ensures internal consistency among key parameters, making it the first globally coherent urban canopy surface dataset. U-Surf significantly improves the representation of the urban land heterogeneity both within and across cities globally; provides essential, high-fidelity surface biophysical constraints to urban-resolving ESMs; enables detailed city-to-city comparisons across the globe; and supports next-generation kilometer-resolution Earth system modeling across scales. U-Surf parameters can be easily converted or adapted to various types of UCMs, such as those embedded in weather and regional climate models, as well as air quality models. The fundamental urban surface constraints provided by U-Surf can also be used as features for machine learning models and can have other broad-scale applications for socioeconomic, public health, and urban planning contexts. We expect U-Surf to advance the research frontier of urban system science, climate-sensitive urban design, and coupled human–Earth systems in the future. The dataset is publicly available at https://doi.org/10.5281/zenodo.11247598 (Cheng et al., 2024).

Cheng, Yifan [Univ. of Illinois at Urbana-Champaig↗

NASA NTRS2004

Spatially Complete Global Surface Albedos Derived from Terra/MODIS Data

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. Recent production of land surface anisotropy, diffuse bihemispherical (white-sky) albedo and direct beam directional hemispherical (black-sky) albedo from observations acquired by the MODIS instruments aboard NASA s Terra and Aqua satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal information on the land surface's radiative characteristics. Cloud cover, which cutails retrievals, and the presence of ephemeral and seasonal snow limit the snow-free data to approximately half the global land surfaces on an annual equal-angle basis. This precludes the MOD43B3 albedo products from being used in some remote sensing and ground-based applications, climate models, and global change research projects. An ecosystem-dependent temporal interpolation technique is described that has been developed to fill missing or seasonally snow-covered data in the official MOD43B3 albedo product. The method imposes pixel-level and local regional ecosystem-dependent phenological behavior onto retrieved pixel temporal data in such a way as to maintain pixel-level spatial and spectral detail and integrity. The phenological curves are derived from statistics based on the MODIS MOD12Q1 IGBP land cover classification product geolocated with the MOD43B3 data. The resulting snow-free value-added products provide the scientific community with spatially and temporally complete global white- and black-sky surface albedo maps and statistics. These products are stored on 1'(approximately 10 km) and coarser resolution equal-angle grids, and are computed for the first seven MODIS wavelengths, ranging from 0.47 through 2.1 microns, and for three broadband wavelengths, 0.3-0.7,0.3-5.0 and 0.7-5.0 microns.

King, Michael D.↗

NASA NTRS2005

Spatially Complete Global Surface Albedos Derived from Terra/MODIS Data

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. Recent production of land surface anisotropy, diffuse bihemispherical (white-sky) albedo and direct beam directional hemispherical (black-sky) albedo from observations acquired by the MODIS instruments aboard NASA's Terra and &la satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal information on the land surface's radiative characteristics. Cloud cover, which curtails retrievals, and the presence of ephemeral and seasonal snow limit the snow-free data to approximately half the global land surfaces on an annual equal-angle basis. This precludes the MOD43B3 albedo products from being used in some remote sensing and ground-based applications, &mate models, and global change research projects.

King, Michael D.↗

NASA NTRS2006

Spatially Complete Global Surface Albedos Derived from Terra/MODIS Data

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. , Over five years of land surface anisotropy, diffuse bihemispherical (white-sky) albedo and direct beam directional hemispherical (black-sky) albedo from observations acquired by the MODIS instruments aboard NASA s Terra and Aqua satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal information on the land surface s radiative characteristics. However, roughly 30% of the global land surface, on an annual equal-angle basis, is obscured due to persistent and transient cloud cover, while another 207% is obscured due to ephemeral and seasonal snow effects. This precludes the MOD43B3 albedo products from being directly used in some remote sensing and ground-based applications, climate models, and global change research projects. To provide researchers with the requisite spatially complete global snow-free land surface albedo dataset, an ecosystem-dependent temporal interpolation technique was developed to fill missing or lower quality data and snow covered values from the official MOD43B3 dataset with geophysically realistic values. The method imposes pixel-level and local regional ecosystem-dependent phenological behavior onto retrieved pixel temporal data in such a way as to maintain pixel-level spatial and spectral detail and integrity. The phenological curves are derived from statistics based on the MODIS MOD12Q1 IGBP land cover classification product geolocated with the MOD43B3 data.

King, Michael D.↗

DOE OSTI2020

SIMPLE-G: A multiscale framework for integration of economic and biophysical determinants of sustainability

We introduce SIMPLE-G, a Simplified International Model of agricultural Prices, Land use, and the Environment- Gridded version, which is a novel tool for evaluating sustainability policies in a global context while factoring in local heterogeneity in land and water resources and natural ecosystem services. This multi-scale model can provide boundary conditions for local decision makers, as well as capturing feedback from local policies to national and global scales. Additionally, to illustrate its value in environmental analysis, we provide two applications of the model. First, we quantify the local stresses on land and water resources due to global changes in population, income, and productivity. Second, we quantify the global impacts of local policy responses and adaptations to water scarcity.

42 ENGINEERING↗

NASA NTRS1991

Remote sensing of earth terrain

In remote sensing, the encountered geophysical media such as agricultural canopy, forest, snow, or ice are inhomogeneous and contain scatters in a random manner. Furthermore, weather conditions such as fog, mist, or snow cover can intervene the electromagnetic observation of the remotely sensed media. In the modelling of such media accounting for the weather effects, a multi-layer random medium model has been developed. The scattering effects of the random media are described by three-dimensional correlation functions with variances and correlation lengths corresponding to the fluctuation strengths and the physical geometry of the inhomogeneities, respectively. With proper consideration of the dyadic Green's function and its singularities, the strong fluctuation theory is used to calculate the effective permittivities which account for the modification of the wave speed and attenuation in the presence of the scatters. The distorted Born approximation is then applied to obtain the correlations of the scattered fields. From the correlation of the scattered field, calculated is the complete set of scattering coefficients for polarimetric radar observation or brightness temperature in passive radiometer applications. In the remote sensing of terrestrial ecosystems, the development of microwave remote sensing technology and the potential of SAR to measure vegetation structure and biomass have increased effort to conduct experimental and theoretical researches on the interactions between microwave and vegetation canopies. The overall objective is to develop inversion algorithms to retrieve biophysical parameters from radar data. In this perspective, theoretical models and experimental data are methodically interconnected in the following manner: Due to the complexity of the interactions involved, all theoretical models have limited domains of validity; the proposed solution is to use theoretical models, which is validated by experiments, to establish the region in which the radar response is most sensitive to the parameters of interest; theoretically simulated data will be used to generate simple invertible models over the region. For applications to the remote sensing of sea ice, the developed theoretical models need to be tested with experimental measurements. With measured ground truth such as ice thickness, temperature, salinity, and structure, input parameters to the theoretical models can be obtained to calculate the polarimetric scattering coefficients for radars or brightness temperature for radiometers and then compare theoretical results with experimental data. Validated models will play an important role in the interpretation and classification of ice in monitoring global ice cover from space borne remote sensors in the future. We present an inversion algorithm based on a recently developed inversion method referred to as the Renormalized Source-Type Integral Equation approach. The objective of this method is to overcome some of the limitations and difficulties of the iterative Born technique. It recasts the inversion, which is nonlinear in nature, in terms of the solution of a set of linear equations; however, the final inversion equation is still nonlinear. The derived inversion equation is an exact equation which sums up the iterative Neuman (or Born) series in a closed form and, thus, is a valid representation even in the case when the Born series diverges; hence, the name Renormalized Source-Type Integral Equation Approach.

Yueh, Herng-Aung↗

DOE OSTI2020

Validation of the Community Land Model Version 5 over the Contiguous United States (CONUS) using in-situ and remote sensing datasets

The Community Land Model (CLM) is an effective tool to simulate the biophysical and biogeochemical processes and their interactions with the atmosphere. Although CLM Version 5 (CLM5) constitutes various updates in these processes, its performance in simulating energy, water and carbon cycles over the Contiguous United States (CONUS) at scales which land surface changes and hydrometeorological and hydroclimatological applications are more locally relevant is yet to be assessed. In this study, we conducted three simulations at 0.125? during 1979-2018 over the CONUS using different configurations of CLM, namely CLM5-biogeochemistry (CLM5BGC), CLM4.5BGC, and CLM5-satellite phenology (CLM5SP). We validated and compared their simulations against multiple remote-sensed and in-situ datasets. Overall, the parametric and structural updates (e.g., carbon cost for nitrogen uptake, variable soil thickness, dry surface layer) in CLM5 improve its ability in capturing terrestrial biogeochemical dynamics. The low evapotranspiration in CLM5BGC is associated with biases in simulating vegetation phenological characteristics rather than soil water limitations. The mismatch between CLM5BGC-simulated peak leaf area index and reference data can be attributed to CLM5BGC's inability in simulating phenology of trees and grasses. The differences between CLM-simulated irrigation and reference estimates can be attributed to differences between processes represented in models and in reality, and uncertainties in input and validation datasets. Evaluation against observations at small catchments suggest that hydrologic parameters needed to be calibrated to improve simulations of runoff, especially subsurface runoff. Additional efforts are needed to incorporate spatially-distributed plant phenology and physiology parameters and regional-specific agricultural management practices (e.g., planting, harvest).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Contrasting Parametric Sensitivities in Two Global Vegetation Models Using Parameter Perturbation Ensembles

Uncertainty in land model projections remains high and the roles of parametric and structural uncertainty are difficult to disentangle. To compare parametric sensitivity across model structures we present two parameter perturbation ensembles using the Community Land Model (CLM) operating in satellite phenology mode. The ensembles contrast two vegetation modules: (a) the default CLM vegetation module and (b) the Functionally Assembled Terrestrial Ecosystem Simulator (CLM-FATES). We perturbed over 300 parameters and quantified their effects on biophysical fluxes globally and across biomes. Most parameters have minimal impact on biophysical fluxes, with only a few substantially influencing results. While both models exhibit similar parameter sensitivity for some fluxes, CLM-FATES shows larger spread in gross primary productivity (GPP), driven by strong sensitivity to carboxylation rate. CLM-FATES also shows a weaker GPP response to soil hydrology parameters and exhibits higher water use efficiency (WUE). Cross-model comparisons reveal similar sensitivities for some parameters (e.g., leaf dimension) but divergent responses to others (e.g., stomatal intercept), highlighting underlying structural differences. Differences in WUE and sensitivity to hydrology and stomatal conductance parameters underscore how model structure fundamentally alters parametric sensitivity. The data sets generated from these ensembles can be used to identify influential parameters and guide future calibration efforts.

Foster, A. C. [NSF National Center for Atmospheric↗

DOE OSTI2025

Bringing Inorganic Carbon to Life: Developing Model Metalloenzymes for C1 Conversion Reactions

The global carbon cycle is carefully balanced through the use of specialized enzymes in plants, algae, bacteria, and archaea. A primordial metabolic pathway for the conversion of inorganic carbon into cellular biomass uses a large, nickel-containing enzyme called carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS). This system fixes carbon dioxide (CO 2 ) into carbon monoxide (CO) at the CODH site. The carbon monoxide is then used to generate acetyl coenzyme A, a biological building block, through a key carbon-carbon bond forming step at the nickel site in ACS. Despite the significance of these processes in the context of energy conversion, the fundamental chemistry underlying these transformations has remained elusive, in part due to the complexity of the natural enzyme. To better understand the principles governing these biological processes, which represent one-carbon (C 1 ) activation reactions, this project will develop functional models of CODH and ACS based on modifications to a small metalloprotein scaffold. Comprehensive characterization of these systems using advanced spectroscopic and biophysical techniques will reveal key elements responsible for conferring high levels of activity to the model systems, with implications for gaining insight into the mechanisms of the natural enzymes. Moreover, the principles learned from this research can be used to guide design of robust catalysts for efficient conversion of CO 2 and CO into liquid fuels.

10 SYNTHETIC FUELS↗

NASA NTRS2001

Once we know all the radiobiology we need to know, how can we use it to predict space radiation risks and achieve fame and fortune?

It has been over 40 years since occupational radiation exposures to NASA's astronauts began and more than 300 individuals have been exposed to low and intermediate doses of trapped protons and galactic cosmic rays (GCR). The International Space Station (ISS) will add substantially to this number and significantly increase average lifetime doses. We review these exposures in this report. After many years of investigation, the method used to assess risk have not changed significantly. However, molecular biology and genetics have made enormous progress in establishing the mechanisms of cancer formation, damage to the central nervous system, and individual variation in sensitivity to radiation. We discuss critical questions and possible new approaches to the prediction of risk from space radiation exposures. Experimental models can lead to testable theories that along with extensive biophysical and informatics approaches, will lead to fame and fortune by allowing for accurate projections of astronaut risks and for the development of biological countermeasures.

NASA Center JSC↗

DOE OSTI2025

A split luciferase system for studying coronavirus Mpro dimerization in vitro and in living cells

The main protease enzyme (Mpro) of coronaviruses cleaves the viral polyprotein into functional units essential for virus replication. Prior work has demonstrated that Mpro functions as a homodimer. However, studies on the mechanism of dimerization have been challenging because the purified protease is mostly dimeric, dimerization-defective mutants lack proteolytic activity, and robust cell-based assays have yet to be reported. To enable work on Mpro dimerization, we have developed a quantitative luciferase-based SARS-CoV-2 (SARS2) Mpro biosensor that accurately reports protein dimerization in living cells and, upon purification, also in vitro. Co-transfection of cells with a construct expressing Mpro fused to the 18 kDa LargeBiT of luciferase (LgBiT) and a second construct with Mpro fused to the 1 kDa SmallBiT of luciferase (SmBiT) results in a reconstitution of luciferase activity in a dose-dependent manner that requires conserved residues within the dimerization interface. Proteolytic activity is dispensable for dimerization and, uniquely, a C145A catalytically inactive mutant exhibits enhanced dimerization signal likely due to lower cytotoxicity. Mpro enzymes from multiple different coronaviruses also dimerize in this system, indicating mechanistic conservation. Interestingly, this dimerization biosensor also provides a quantitative read-out of inhibitor-facilitated dimerization. Covalent SARS2 Mpro inhibitors such as nirmatrelvir cause a 3- to 5-fold increase in luciferase activity. Together with corroborating structural, biophysical, and molecular dynamics experiments, our studies support a model in which covalent Mpro inhibitors such as nirmatrelvir simultaneously block catalytic activity and induce allosteric stabilization of the dimeric complex.

SARS-CoV-2 main protease (Mpro/3CLpro)↗

DOE OSTI2022

Interplay of River and Tidal Forcings Promotes Loops in Coastal Channel Networks

We report the dense populations that inhabit global coastlines have an uncertain future due to increased flooding, storms, and human modification. The channel networks of deltas and marshes that plumb these coastlines present diverse architectures, including well-studied dendritic topologies. However, the quasi-stable loops that exist in nearly all coastal networks have not yet been explained. We present a model for self-organizing networks inspired by vascular biophysics to show that loops emerge when the relative forcings between rivers and tides are comparable, resulting in interplay between hydrodynamic forcings at short time scales relative to network evolution. Using field data and satellite imaging, we confirm this control on 21 field networks. Our comparison provides compelling evidence that hydrodynamic fluctuations are capable of stabilizing loops in geophysical systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Beyond sequence similarity: toward function-based screening of nucleic acid synthesis

Synthetic nucleic acids are a key input to modern biotechnology, yet they represent dual-use materials that require robust screening to mitigate biosecurity risks. The prevailing screening paradigm, which identifies sequences of concern (SoCs) through sequence similarity to controlled pathogens and toxins, may not fully capture risks posed by AI tools that can decouple biomolecular function from reliance on known sequences. Rapidly advancing biodesign capabilities enable the generation of genes and proteins that might evade sequence-based detection. We highlight the critical need for function-based screening approaches that can detect sequences capable of hazardous biological functions, regardless of similarity to known SoCs. We examine the feasibility of function-based screening with an initial focus on proteins, arguing that, while protein sequence space is vast, biologically functional proteins are significantly constrained by biophysical and biochemical requirements that can be learned and modeled. We propose a concrete implementation framework organized along a continuum of complexity, starting with toxins as the most tractable targets before expanding to more complex pathogenic functions. We then discuss open challenges and describe a research and development strategy to address them.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2004

Spatially Complete Surface Albedo Data Sets: Value-Added Products Derived from Terra MODIS Land Products

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. The availability of global albedo data over a large range of spectral channels and at high spatial resolution has dramatically improved with the launch of the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument aboard NASA s Earth Observing System (EOS) Terra spacecraft in December 1999. However, lack of spatial and temporal coverage due to cloud and snow effects can preclude utilization of official products in production and research studies. We report on a technique used to fill incomplete MOD43 albedo data sets with the intention of providing complete value-added maps. The technique is influenced by the phenological concept that within a certain area, a pixel s ecosystem class should exhibit similar growth cycle events over the same time period. The shape of an area s phenological temporal curve can be imposed upon existing pixel-level data to fill missing temporal points. The methodology will be reviewed by showcasing 2001 global and regional results of complete albedo and NDVl data sets.

Moody, E. G.↗

NASA NTRS2004

Spatially Complete Surface Albedo Data Sets: Value-Added Products Derived from Terra MODIS Land Products

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. Recent observations of diffuse bihemispherical (white-sky) and direct beam directional hemispherical (black-sky ) land surface albedo included in the MOD43B3 product from MODIS instruments aboard NASA's Terra and Aqua satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal characteristics. Cloud and seasonal snow cover, however, curtail retrievals to approximately half the global land surfaces on an annual equal-angle basis, precluding MOD43B3 albedo products from direct inclusion in some research projects and production environments.

Moody, Eric G.↗

NASA NTRS2017

NASA Wrangler: Automated Cloud-Based Data Assembly in the RECOVER Wildfire Decision Support System

NASA Wrangler is a loosely-coupled, event driven, highly parallel data aggregation service designed to take advantageof the elastic resource capabilities of cloud computing. Wrangler automatically collects Earth observational data, climate model outputs, derived remote sensing data products, and historic biophysical data for pre-, active-, and post-wildfire decision making. It is a core service of the RECOVER decision support system, which is providing rapid-response GIS analytic capabilities to state and local government agencies. Wrangler reduces to minutes the time needed to assemble and deliver crucial wildfire-related data.

decision support↗

DOE OSTI2023

Contrasting the Biophysical and Radiative Effects of Rising CO 2 Concentrations on Ozone Dry Deposition Fluxes

Abstract The dry deposition of ozone from the atmosphere to ecosystems is an important coupling mechanism between atmospheric chemistry and terrestrial biogeochemical processes. In most Earth system models, dry deposition is simulated using a resistor‐in‐series approach that aims to parameterize the governing biological, chemical, and physical processes through a series of functional approximations. Here, we evaluate the influence of carbon cycle‐climate responses on this parameterization using the results of the Energy Exascale Earth System Model v1.1 Biogeochemistry simulation campaign. This simulation campaign was designed in part to explore the biophysical and radiative effects of rising historical CO 2 concentrations on the Earth system. We find that while the global annual ozone dry deposition is relatively insensitive to these effects, regionally the influence can be up to 10%. The strongest regional sensitivities in ozone dry deposition are predominantly in higher latitudes over land in the northern hemisphere and are dominated by the radiative effect of CO 2 , with little net influence of biophysical responses. Of all the impacts of the radiative effect of CO 2 , we point to the potential importance of accurately representing ozone deposition to snow in Earth System Models and provide recommendations for future simulation campaigns.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2009

3D Visualization of Monte-Carlo Simulation's of HZE Track Structure and Initial Chemical Species

Heavy ions biophysics is important for space radiation risk assessment [1] and hadron-therapy [2]. The characteristic of heavy ions tracks include a very high energy deposition region close to the track (<20 nm) denoted as the track core, and an outer penumbra region consisting of individual secondary electrons (6-rays). A still open question is the radiobiological effects of 6- rays relative to the track core. Of importance is the induction of double-strand breaks (DSB) [3] and oxidative damage to the biomolecules and the tissue matrix, considered the most important lesions for acute and long term effects of radiation. In this work, we have simulated a 56Fe26+ ion track of 1 GeV/amu with our Monte-Carlo code RITRACKS [4]. The simulation results have been used to calculate the energy depiction and initial chemical species in a "voxelized" space, which is then visualized in 3D. Several voxels with dose >1000 Gy are found in the penumbra, some located ~0.1 mm from the track core. In computational models, the DSB induction probability is calculated with radial dose [6], which may not take into account the higher RBE of electron track ends for DSB induction. Therefore, these simulations should help improve models of DSB induction and our understanding of heavy ions biophysics.

Plante, Ianik↗