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At least 19 records

Data for A Hybrid Biophysical-Machine Learning Framework for Diurnal Surface Energy Flux Estimation Using Proximal Sensing

Thermal infrared-based remote sensing of surface energy fluxes has traditionally relied on high spatial resolution satellite data with revisit frequencies on the order of weeks. In this study, we evaluate a biophysics-based analytical surface energy balance model for predicting latent energy (LE) and sensible heat (H) fluxes using proximal sensing observations. The Surface Temperature Initiated Closure (STIC1.2) model has been extensively validated across a wide range of spatial and temporal scales using various satellite-derived thermal infrared data sets. Here we extend this validation by applying STIC at sub-hourly temporal resolution over multiple growing seasons for four distinct agricultural systems. We further develop and evaluate novel STIC variants that incorporate machine learning (ML) techniques to eliminate the need for surface energy balance observations, specifically net radiation and soil heat flux, thereby enhancing model applicability in data-sparse settings. The integration of a ML component to estimate surface available energy is shown to have strong predictive performance for both LE (R2 = 0.81–0.94) and H (R2 = 0.46–0.72) across all agricultural systems examined here, demonstrating the potential of hybrid biophysical-machine learning approaches for surface energy balance modeling with minimal data requirements. This study concludes with a novel application of explainable machine learning (exML) to diagnose sources of model error. This exML framework attributes residual prediction errors to both model input variables and environmental drivers not explicitly included in the simulation experiments. This approach provides a new pathway for improving model design and integrating previously overlooked yet influential variables into future model iterations.

AI/ML↗

Space Biophysics: Accomplishments, Trends, Challenges

Physics and biology are inextricably linked. All the chemical and biological processes of life are dutifully bound to follow the rules and laws of physics. In space, these physical laws seem to turn on their head and biological systems, from microbes to humans, adapt and evolve in myriad ways to cope with the changed physical influences of the space environment. Gravity is the most prominent change in space that influences biology. In microgravity, the physical processes of sedimentation, density-driven convective flow, influence of surface tension and fluid pressure profoundly influence biology at the molecular and cellular level as well as at the whole-body level. Gravity sensing mechanisms are altered, structural and functional components of biology (such as bone and muscle) are reduced and changes in the way fluids and gasses behave also drive the way microbial systems and biofilms grow as well as the way plants and animals adapt. The radiation environment also effects life in space. Solar particle events and high energy cosmic radiation can cause serious damage to DNA and other biomolecules. The results can cause mutation, cellular damage or death, leading to health consequences of acute radiation damage or long-term health consequences such as increased cancer risk. Space Biophysics is the study and utilization of physical changes in space that cause changes in biological systems. The unique physical environment in space has been used successfully to grow high-quality protein crystals and 3D tissue cultures that could not be grown in the presence of unidirectional gravitational acceleration here on Earth. All biological processes that change in space have their root in a biophysical alteration due to microgravity and/or the radiation environment of space. In order to fully-understand the risks to human health in space and to fully-understand how humans, plants, animals and microbes can safely and effectively travel and eventually live for long periods beyond the protective environment of Earth, the biophysical properties underlying these changes must be studied, characterized and understood. This lecture reviews the current state of NASA biophysics research accomplishments and identifies future trends and challenges for biophysics research on the International Space Station and beyond.

Space Biophysics: Accomplishments↗

Past and Present Biophysical Redundancy of Countries as a Buffer to Changes in Food Supply

Spatially diverse trends in population growth, climate change, industrialization, urbanization and economic development are expected to change future food supply and demand. These changes may affect the suitability of land for food production, implying elevated risks especially for resource constrained, food-importing countries. We present the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Biophysical redundancy, defined as unused biotic and abiotic environmental resources, is represented by the potential food production of 'spare land', available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. In 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as 'Low Income Economies (LIEs)' since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

biophysics↗

Reconstructed Historical Land Cover and Biophysical Parameters for Studies of Land-Atmosphere Interactions within the Eastern United States

The local environment where we live within the Earth's biosphere is often taken for granted. This environment can vary depending on whether the land cover is a forest, grassland, wetland, water body, bare soil, pastureland, agricultural field, village, residential suburb, or an urban complex with concrete, asphalt, and large buildings. In general, the type and characteristics of land cover influence surface temperatures, sunlight exposure and duration, relative humidity, wind speed and direction, soil moisture amount, plant life, birds, and other wildlife in our backyards. The physical and biological properties (biophysical characteristics) of land cover help to determine our surface environment because they directly affect surface radiation, heat, and soil moisture processes, and also feedback to regional weather and climate. Depending on the spatial scale and land use intensity, land cover changes can have profound impacts on our local and regional environment. Over the past 350 years, the eastern half of the United States, an area extending from the grassland prairies of the Great Plains to the Gulf and Atlantic coasts, has experienced extensive land cover and land use changes that began with land clearing in the 1600s, led to extensive deforestation and intensive land use practices by 1920, and then evolved to the present-day landscape. Determining the consequences of such land cover changes on regional and global climate is a major research issue. Such research requires detailed historical land cover data and modeling experiments simulating historical climates. Given the need to understand the effects of historical land cover changes in the eastern United States, some questions include: - What were the most important land cover transformations and how did they alter biophysical characteristics of the land cover at key points in time since the mid-1600s? - How have land cover and land use changes over the past 350 years affected the land surface environment including surface weather, hydrologic, and climatic variability? - How do the potential effects of regional human-induced land cover change on the environment compare to similar changes that are caused by the natural variations of the Earth's climate system? To help answer these questions, we reconstructed a fractional land cover and biophysical parameter dataset for the eastern United States at 1650, 1850, 1920, and 1992 time-slices. Each land cover fraction is associated with a biophysical parameter class, a suite of parameters defining the biophysical characteristics of that kind of land cover. This new dataset is designed for use in computer models of land-atmosphere interactions, to understand and quantify the effects of historical land cover changes on the water, energy, and carbon cycles

Steyaert, Louis T.↗

Selection of Hyperspectral Narrowbands (HNBs) and Composition of Hyperspectral Twoband Vegetation Indices (HVIs) for Biophysical Characterization and Discrimination of Crop Types Using Field Reflectance and Hyperion-EO-1 Data

The overarching goal of this study was to establish optimal hyperspectral vegetation indices (HVIs) and hyperspectral narrowbands (HNBs) that best characterize, classify, model, and map the world's main agricultural crops. The primary objectives were: (1) crop biophysical modeling through HNBs and HVIs, (2) accuracy assessment of crop type discrimination using Wilks' Lambda through a discriminant model, and (3) meta-analysis to select optimal HNBs and HVIs for applications related to agriculture. The study was conducted using two Earth Observing One (EO-1) Hyperion scenes and other surface hyperspectral data for the eight leading worldwide crops (wheat, corn, rice, barley, soybeans, pulses, cotton, and alfalfa) that occupy approx. 70% of all cropland areas globally. This study integrated data collected from multiple study areas in various agroecosystems of Africa, the Middle East, Central Asia, and India. Data were collected for the eight crop types in six distinct growth stages. These included (a) field spectroradiometer measurements (350-2500 nm) sampled at 1-nm discrete bandwidths, and (b) field biophysical variables (e.g., biomass, leaf area index) acquired to correspond with spectroradiometer measurements. The eight crops were described and classified using approx. 20 HNBs. The accuracy of classifying these 8 crops using HNBs was around 95%, which was approx. 25% better than the multi-spectral results possible from Landsat-7's Enhanced Thematic Mapper+ or EO-1's Advanced Land Imager. Further, based on this research and meta-analysis involving over 100 papers, the study established 33 optimal HNBs and an equal number of specific two-band normalized difference HVIs to best model and study specific biophysical and biochemical quantities of major agricultural crops of the world. Redundant bands identified in this study will help overcome the Hughes Phenomenon (or "the curse of high dimensionality") in hyperspectral data for a particular application (e.g., biophysical characterization of crops). The findings of this study will make a significant contribution to future hyperspectral missions such as NASA's HyspIRI. Index Terms-Hyperion, field reflectance, imaging spectroscopy, HyspIRI, biophysical parameters, hyperspectral vegetation indices, hyperspectral narrowbands, broadbands.

Vegetation↗

Impacts of climate and biophysical variability on global agriculture markets

Agricultural production is highly sensitive to changes in climate and weather patterns. The focus of the great majority of studies assessing climate impacts on agriculture has been on mean changes in agricultural responses. However, the manner in which global agricultural markets respond to the interannual variability of the climate and biophysical shocks is poorly understood. Here we show a strong transmission of interannual variations in climate-induced biophysical yield shocks to agriculture markets, which is magnified further by endogenous market fluctuations. We demonstrate the importance of imperfect versus perfect expectations of market and weather in generating the market fluctuations that play a key role in transferring the interannual variations to markets. We find that the volatility of market prices and consumption could be potentially reduced on average by 55% and 41%, respectively, with improved expectations, where agricultural producers make better decisions to adapt to climate and biophysical variability. We also find much heterogeneity in interannual variability across crops and regions, which is considerably mediated by trade as part of the economic response. Our study provides new insights on climate impacts on agricultural market variability and lays a foundation for further investigating the full range of climate impacts on biophysical and human systems.

Zhao, Xin↗

SAR terrain classifier and mapper of biophysical attributes

In preparation for the launch of SIR-C/X-SAR and design studies for future orbital SAR, a program has made considerable progress in the development of an SAR terrain classifier and algorithms for quantification of biophysical attributes. The goal of this program is to produce a generalized software package for terrain classification and estimation of biophysical attributes and to make this package available to the larger scientific community. The basic elements of the SAR (Synthetic Aperture Radar) terrain classifier are outlined. An SAR image is calibrated with respect to known system and processor gains and external targets (if available). A Level 1 classifier operates on the data to differentiate: urban features, surfaces and tall and short vegetation. Level 2 classifiers further subdivide these classes on the basis of structure. Finally, biophysical and geophysical inversions are applied to each class to estimate attributes of interest. The process used to develop the classifiers and inversions is shown. Radar scattering models developed from theory and from empirical data obtained by truck-mounted polarimeters and the JPL AirSAR are validated. The validated models are used in sensitivity studies to understand the roles of various scattering sources (i.e., surface trunk, branches, etc.) in determining net backscatter. Model simulations of sigma (sup o) as functions of the wave parameters (lambda, polarization and angle of incidence) and the geophysical and biophysical attributes are used to develop robust classifiers. The classifiers are validated using available AirSAR data sets. Specific estimators are developed for each class on the basis of the scattering models and empirical data sets. The candidate algorithms are tested with the AirSAR data sets. The attributes of interest include: total above ground biomass, woody biomass, soil moisture and soil roughness.

Ulaby, Fawwaz T.↗

Improving Access to MODIS Biophysical Science Products for NACP Investigators

MODIS 4 NACP is a NASA-funded project supporting the North American Carbon Program (NACP). The purpose of this Advancing Collaborative Connections for Earth-Sun System Science (ACCESS) project is to provide researchers with Moderate Resolution Imaging Spectroradiometer (MODIS) biophysical data products that are custom tailored for use in NACP model studies. Standard MODIS biophysical products provide used to improve our understanding on the climate and ecosystem changes. However, direct uses of the MODIS biophysical parameters are constrained by retrieval quality and cloud contamination. Another challenge that NACP users face is acquiring MODIS data in formats and at spatial-temporal resolutions consistent with other data sets they use. We have been working closely with key NACP users to tailor the MODIS products to fit their needs. First, we provide new temporally smoothed and spatially continuous MODIS biophysical data sets. Second, we are distributing MODIS data at suitable spatial-temporal resolutions and in formats consistent with other data integration into model studies.

Wolfe, Robert E.↗

Hyperspectral Radiative Transfer Modeling to Explore the Combined Retrieval of Biophysical Parameters and Canopy Fluorescence from FLEX - Sentinel-3 Tandem Mission Multi-Sensor Data

The FLuorescence EXplorer (FLEX) satellite mission, selected as ESA's 8th Earth Explorer, has been designed forthe measurement of sun-induced fluorescence (F) spectra emitted by plants. This will be accomplished through amulti-sensor approach by placing it in a common orbit in tandem with the Sentinel-3 (S3) mission, which willhave two optical sensors on board, OLCI (Ocean and Land Colour Instrument) and SLSTR (Sea and Land SurfaceTemperature Radiometer) to complement FLEX. These S3 instruments will be used in combination with theimaging spectrometers on board FLEX to provide data useful for atmospheric correction of FLEX data. However,a fully synergetic approach, i.e. by exploiting the spectral and directional information from all tandem missioninstruments together, is an attractive alternative which is explored in this paper. By employing all combined topof-atmosphere (TOA) spectral radiance data, one can (i) characterize the relevant optical properties of the atmosphere,(ii) retrieve biophysical canopy properties including the associated reflectance anisotropy, and (iii)retrieve a more accurate and consistent canopy F.Regarding retrieval methods, Fraunhofer Line Depth (FLD) and Spectral Fitting (SF) are well-known techniquesapplied to hyperspectral data. Both methods depend on a high spectral resolution and assume aLambertian (isotropic) canopy reflectance. However, most vegetation canopies are non-Lambertian. This impliesthat, in particular when ignoring the anisotropic surface reflection, substantial retrieval errors can occur due tothe interaction between atmospheric absorption bands and surface reflectance anisotropy. In this paper, a novelmethod based on spectral radiative transfer (RT) modeling is proposed, in which coupled RT models are used tosimulate TOA radiance spectra. These are then matched with ‘measured' spectra in order to retrieve surfacefluorescence, along with a suite of biophysical parameters, by model inversion through optimization. By applyingcoupled RT models of the soil-leaf-canopy and the surface-atmosphere systems, TOA radiance spectra canbe simulated for all optical sensors of this tandem mission. In this way, complex effects due to surface reflectanceanisotropy and the spectral sampling by the various instruments, which are difficult to compensate for in the endproducts, are properly taken into account by their incorporation in the forward modeling. Next, by model inversionof TOA radiance data via optimization, the most accurate F retrievals can be achieved in a consistentmanner, along with important canopy level biophysical parameters that may help interpret the F spectrum, suchas chlorophyll content and leaf area index (LAI). The potential of this approach has been explored in a numericalexperiment, and the results are presented in this paper. We find that, with the assumed well-characterized andplausible FLEX/S3 instrument performances, the simultaneous retrieval of biophysical canopy parameters and Fspectra would be possible with a remarkable accuracy, provided the correct atmospheric characterization isavailable.

Verhoef, Wouter↗

Identifying and Forecasting Potential Biophysical Risk Areas within a Tropical Mangrove Ecosystem Using Multi-Sensor Data

Mangroves are one of the most productive ecosystems known for provisioning of various ecosystem goods and services. They help in sequestering large amounts of carbon, protecting coastline against erosion, and reducing impacts of natural disasters such as hurricanes. Bhitarkanika Wildlife Sanctuary in Odisha harbors the second largest mangrove ecosystem in India. This study used Terra, Landsat and Sentinel-1 satellite data for spatio-temporal monitoring of mangrove forest within Bhitarkanika Wildlife Sanctuary between 2000 and 2016. Three biophysical parameters were used to assess mangrove ecosystem health: leaf chlorophyll (CHL), Leaf Area Index (LAI), and Gross Primary Productivity (GPP). A long-term analysis of meteorological data such as precipitation and temperature was performed to determine an association between these parameters and mangrove biophysical characteristics. The correlation between meteorological parameters and mangrove biophysical characteristics enabled forecasting of mangrove health and productivity for year 2050 by incorporating IPCC projected climate data. A historical analysis of land cover maps was also performed using Landsat 5 and 8 data to determine changes in mangrove area estimates in years 1995, 2004 and 2017. There was a decrease in dense mangrove extent with an increase in open mangroves and agricultural area. Despite conservation efforts, the current extent of dense mangrove is projected to decrease up to 10% by the year 2050. All three biophysical characteristics including GPP, LAI and CHL, are projected to experience a net decrease of 7.7%, 20.83% and 25.96% respectively by 2050 compared to the mean annual value in 2016. This study will help the Forest Department, Government of Odisha in managing and taking appropriate decisions for conserving and sustaining the remaining mangrove forest under the changing climate and developmental activities.

Shanti Shrestha↗

Climate-Driven Divergence in Biophysical and Economic Impacts of Agrivoltaics

Increasing global demands for food and energy necessitate innovative land-use solutions. Agrivoltaics, colocating solar photovoltaics with agriculture, shows promise, but its widespread adoption faces complex biophysical and economic trade-offs in a changing climate. Here, we develop an integrated biophysical-economic modeling framework to quantify how agrivoltaics affect biophysical and economic impacts across the Midwestern United States under both current and project climate conditions. We find strong regional divergences driven by climate gradients. In the humid eastern Midwest, solar panel shading limits photosynthesis, leading to reduced yields (maize -24%; soybean -16%) and lower farmers' profitability (maize -16%; soybean -2%) compared to conventional agriculture. Conversely, in the semiarid western region, shading alleviates heat and water stress, moderating yield reductions for maize (-12%) and even boosting soybean yields (+6%), resulting in improved economic returns (-6% for maize; +9% for soybean), for a scenario with 33% photovoltaic ground coverage ratio. Although agrivoltaics generate substantial electrical energy across all regions, high upfront installation costs challenge solar developers compared to standalone solar photovoltaics. However, our analysis identifies “win-win” opportunities where soybean-based agrivoltaics in the semiarid region produce economic benefits for both farmers and solar developers, highlighting the necessity for region-specific designs tailored to local climate conditions. Critically, future climate projections indicate eastward expansion of semiarid conditions, broadening areas where agrivoltaics can mitigate crop yield penalties (even boosting yield) and improve overall profitability, especially under high-emission scenarios. The results provide a mechanistic and economically integrated understanding essential for developing evidence-based and region-specific strategies to scale agrivoltaics in a changing climate.

14 SOLAR ENERGY↗

Integrated Biophysical Modeling and Image Analysis: Application to Neuro-Oncology

Central nervous system (CNS) tumors come with vastly heterogeneous histologic, molecular, and radiographic landscapes, rendering their precise characterization challenging. The rapidly growing fields of biophysical modeling and radiomics have shown promise in better characterizing the molecular, spatial, and temporal heterogeneity of tumors. Integrative analysis of CNS tumors, including clinically acquired multi-parametric magnetic resonance imaging (mpMRI) and the inverse problem of calibrating biophysical models to mpMRI data, assists in identifying macroscopic quantifiable tumor patterns of invasion and proliferation, potentially leading to improved (a) detection/segmentation of tumor subregions and (b) computer-aided diagnostic/prognostic/predictive modeling. This article presents a summary of (a) biophysical growth modeling and simulation,(b) inverse problems for model calibration, (c) these models' integration with imaging workflows, and (d) their application to clinically relevant studies. We anticipate that such quantitative integrative analysis may even be beneficial in a future revision of the World Health Organization (WHO) classification for CNS tumors, ultimately improving patient survival prospects.

60 APPLIED LIFE SCIENCES↗

Editorial: Advances in computational molecular biophysics

This special issue of BBA is dedicated to Dr. Jeremy C. Smith on the occasion of his 60th birthday and his more than three decades as a practitioner of computational molecular biophysics. The special issue showcases cutting-edge work in computational molecular biophysics. The senior authors of the manuscripts in this issue are Dr. Smith’s previous or present collaborators. Their articles reflect Dr. Smith’s distinguished career integrating experimental and molecular simulation approaches into a unified description of the function, structure, and dynamics of biomolecules. Each of the articles presented here illustrates one aspect of the broad nature of computational molecular biophysics.

59 BASIC BIOLOGICAL SCIENCES↗

Elucidating lipid nanoparticle properties and structure through biophysical analyses

Designing lipid nanoparticle (LNP) delivery systems with specific targeting, potency and minimal side effects is crucial for their clinical use. However, traditional characterization methods, such as dynamic light scattering, cannot accurately quantify physicochemical properties of LNPs and how these are influenced by the lipid composition and mixing method. Here, we structurally characterize polydisperse LNP formulations by applying emerging solution-based biophysical methods that have higher resolution and provide biophysical data beyond size and polydispersity. These techniques include sedimentation velocity analytical ultracentrifugation, field-flow fractionation followed by multiangle light scattering and size-exclusion chromatography in line with synchrotron small-angle X-ray scattering. Here, we show that LNPs have intrinsic polydispersity in size, RNA loading and shape, which depend on both the formulation technique and the lipid composition. Lastly, we predict LNP transfection in vitro and in vivo by examining the relationship between mRNA translation and physicochemical characteristics. Solution-based biophysical methods will be essential for determining LNP structure–function relationships, facilitating the creation of new design rules for LNPs.

36 MATERIALS SCIENCE↗

Comprehensive single-shot biophysical cytometry using simultaneous quantitative phase imaging and Brillouin spectroscopy

Abstract Single-cell analysis, or cytometry, is a ubiquitous tool in the biomedical sciences. Whereas most cytometers use fluorescent probes to ascertain the presence or absence of targeted molecules, biophysical parameters such as the cell density, refractive index, and viscosity are difficult to obtain. In this work, we combine two complementary techniques—quantitative phase imaging and Brillouin spectroscopy—into a label-free image cytometry platform capable of measuring more than a dozen biophysical properties of individual cells simultaneously. Using a geometric simplification linked to freshly plated cells, we can acquire the cellular diameter, volume, refractive index, mass density, non-aqueous mass, fluid volume, dry volume, the fractional water content of cells, both by mass and by volume, the Brillouin shift, Brillouin linewidth, longitudinal modulus, longitudinal viscosity, the loss modulus, and the loss tangent, all from a single acquisition, and with no assumptions of underlying parameters. Our methods are validated across three cell populations, including a control population of CHO-K1 cells, cells exposed to tubulin-disrupting nocodazole, and cells under hypoosmotic shock. Our system will unlock new avenues of research in biophysics, cell biology, and medicine.

Steelman, Zachary A.↗

Biophysical principles of choanoflagellate self-organization

Inspired by the patterns of multicellularity in choanoflagellates, the closest living relatives of animals, we quantify the biophysical processes underlying the morphogenesis of rosette colonies in the choanoflagellate Salpingoeca rosetta . We find that rosettes reproducibly transition from an early stage of 2-dimensional (2D) growth to a later stage of 3D growth, despite the underlying variability of the cell lineages. Our perturbative experiments demonstrate the fundamental importance of a basally secreted extracellular matrix (ECM) for rosette morphogenesis and show that the interaction of the ECM with cells in the colony physically constrains the packing of proliferating cells and, thus, controls colony shape. Simulations of a biophysically inspired model that accounts for the size and shape of the individual cells, the fraction of ECM, and its stiffness relative to that of the cells suffices to explain our observations and yields a morphospace consistent with observations across a range of multicellular choanoflagellate colonies. Overall, our biophysical perspective on rosette development complements previous genetic perspectives and, thus, helps illuminate the interplay between cell biology and physics in regulating morphogenesis.

59 BASIC BIOLOGICAL SCIENCES↗