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DOE OSTI2024

Reaction-diffusion modeling provides insights into biophysical carbon-concentrating mechanisms in land plants

Carbon-concentrating mechanisms (CCMs) have evolved numerous times in photosynthetic organisms. They elevate the concentration of CO 2 around the carbon-fixing enzyme rubisco, thereby increasing CO 2 assimilatory flux and reducing photorespiration. Biophysical CCMs, like the pyrenoid-based CCM (PCCM) of Chlamydomonas reinhardtii or carboxysome systems of cyanobacteria, are common in aquatic photosynthetic microbes, but in land plants appear only among the hornworts. To predict the likely efficiency of biophysical CCMs in C 3 plants, we used spatially resolved reaction-diffusion models to predict rubisco saturation and light use efficiency. We found that the energy efficiency of adding individual CCM components to a C 3 land plant is highly dependent on the permeability of lipid membranes to CO 2 , with values in the range reported in the literature that are higher than those used in previous modeling studies resulting in low light use efficiency. Adding a complete PCCM into the leaf cells of a C 3 land plant was predicted to boost net CO 2 fixation, but at higher energetic costs than those incurred by photorespiratory losses without a CCM. Two notable exceptions were when substomatal CO 2 levels are as low as those found in land plants that already use biochemical CCMs and when gas exchange is limited, such as with hornworts, making the use of a biophysical CCM necessary to achieve net positive CO 2 fixation under atmospheric CO 2 levels. This provides an explanation for the uniqueness of hornworts' CCM among land plants and the evolution of pyrenoids multiple times.

Kaste, Joshua A. M.↗

DOE OSTI2020

Biophysical impacts of Earth greening largely controlled by aerodynamic resistance

Satellite observations show widespread increasing trends of leaf area index (LAI), known as the Earth greening. However, the biophysical impacts of this greening on land surface temperature (LST) remain unclear. Here, we quantify the biophysical impacts of Earth greening on LST from 2000 to 2014 and disentangle the contributions of different factors using a physically based attribution model. We find that 93% of the global vegetated area shows negative sensitivity of LST to LAI increase at the annual scale, especially for semiarid woody vegetation. Further considering the LAI trends (P ≤ 0.1), 30% of the global vegetated area is cooled by these trends and 5% is warmed. Aerodynamic resistance is the dominant factor in controlling Earth greening’s biophysical impacts: The increase in LAI produces a decrease in aerodynamic resistance, thereby favoring increased turbulent heat transfer between the land and the atmosphere, especially latent heat flux.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Prospects for Engineering Biophysical CO 2 Concentrating Mechanisms into Land Plants to Enhance Yields

Although cyanobacteria and algae represent a small fraction of the biomass of all primary producers, their photosynthetic activity accounts for roughly half of the daily CO 2 fixation that occurs on Earth. These microorganisms are able to accomplish this feat by enhancing the activity of the CO 2 -fixing enzyme Rubisco using biophysical CO 2 concentrating mechanisms (CCMs). Biophysical CCMs operate by concentrating bicarbonate and converting it into CO 2 in a compartment that houses Rubisco (in contrast with other CCMs that concentrate CO 2 via an organic intermediate, such as malate in the case of C 4 CCMs). This activity provides Rubisco with a high concentration of its substrate, thereby increasing its reaction rate. The genetic engineering of a biophysical CCM into land plants is being pursued as a strategy to increase crop yields. This review focuses on the progress toward understanding the molecular components of cyanobacterial and algal CCMs, as well as recent advances toward engineering these components into land plants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Deka, Ranjit K.↗

NASA NTRS2002

Low-Cost Evaluation of EO-1 Hyperion and ALI for Detection and Biophysical Characterization of Forest Logging in Amazonia (NCC5-481)

Major uncertainties exist regarding the rate and intensity of logging in tropical forests worldwide: these uncertainties severely limit economic, ecological, and biogeochemical analyses of these regions. Recent sawmill surveys in the Amazon region of Brazil show that the area logged is nearly equal to total area deforested annually, but conversion of survey data to forest area, forest structural damage, and biomass estimates requires multiple assumptions about logging practices. Remote sensing could provide an independent means to monitor logging activity and to estimate the biophysical consequences of this land use. Previous studies have demonstrated that the detection of logging in Amazon forests is difficult and no studies have developed either the quantitative physical basis or remote sensing approaches needed to estimate the effects of various logging regimes on forest structure. A major reason for these limitations has been a lack of sufficient, well-calibrated optical satellite data, which in turn, has impeded the development and use of physically-based, quantitative approaches for detection and structural characterization of forest logging regimes. We propose to use data from the EO-1 Hyperion imaging spectrometer to greatly increase our ability to estimate the presence and structural attributes of selective logging in the Amazon Basin. Our approach is based on four "biogeophysical indicators" not yet derived simultaneously from any satellite sensor: 1) green canopy leaf area index; 2) degree of shadowing; 3) presence of exposed soil and; 4) non-photosynthetic vegetation material. Airborne, field and modeling studies have shown that the optical reflectance continuum (400-2500 nm) contains sufficient information to derive estimates of each of these indicators. Our ongoing studies in the eastern Amazon basin also suggest that these four indicators are sensitive to logging intensity. Satellite-based estimates of these indicators should provide a means to quantify both the presence and degree of structural disturbance caused by various logging regimes. Our quantitative assessment of Hyperion hyperspectral and ALI multi-spectral data for the detection and structural characterization of selective logging in Amazonia will benefit from data collected through an ongoing project run by the Tropical Forest Foundation, within which we have developed a study of the canopy and landscape biophysics of conventional and reduced-impact logging. We will add to our base of forest structural information in concert with an EO-1 overpass. Using a photon transport model inversion technique that accounts for non-linear mixing of the four biogeophysical indicators, we will estimate these parameters across a gradient of selective logging intensity provided by conventional and reduced impact logging sites. We will also compare our physical ly-based approach to both conventional (e.g., NDVI) and novel (e.g., SWIR-channel) vegetation indices as well as to linear mixture modeling methods. We will cross-compare these approaches using Hyperion and ALI imagers to determine the strengths and limitations of these two sensors for applications of forest biophysics. This effort will yield the first physical ly-based, quantitative analysis of the detection and intensity of selective logging in Amazonia, comparing hyperspectral and improved multi-spectral approaches as well as inverse modeling, linear mixture modeling, and vegetation index techniques.

Asner, Gregory P.↗

NASA NTRS2003

Radiation dosimetry and biophysical models of space radiation effects

Estimating the biological risks from space radiation remains a difficult problem because of the many radiation types including protons, heavy ions, and secondary neutrons, and the absence of epidemiology data for these radiation types. Developing useful biophysical parameters or models that relate energy deposition by space particles to the probabilities of biological outcomes is a complex problem. Physical measurements of space radiation include the absorbed dose, dose equivalent, and linear energy transfer (LET) spectra. In contrast to conventional dosimetric methods, models of radiation track structure provide descriptions of energy deposition events in biomolecules, cells, or tissues, which can be used to develop biophysical models of radiation risks. In this paper, we address the biophysical description of heavy particle tracks in the context of the interpretation of both space radiation dosimetry and radiobiology data, which may provide insights into new approaches to these problems.

Review↗

NASA NTRS2020

Biophysical Impacts of Earth Greening Largely Controlled by Aerodynamic Resistance

Greening↗

DOE OSTI2025

Extreme hydroclimates amplify the biophysical effects of advanced green-up in temperate China

Vegetation phenology modulates climate by altering energy and water exchange between the land and atmosphere. However, how extreme hydroclimatic conditions modify these phenology-climate feedbacks is still poorly understood. Here, in this study, we used a land–atmosphere-coupled Weather Research and Forecasting model to explore the impacts of advanced green-up on air temperature under different hydroclimate conditions across temperate China and to Mechanistic analysis elucidate the underlying biophysical mechanisms. By imposing a 14-day earlier green-up in line with recent satellite observations, we found that under mean climate conditions, an earlier leaf-out induces immediate surface cooling of 0.14 °C during green-up and a lagging 0.02 °C warming during senescence averaged for temperate China. Extremely humid conditions amplify the cooling effects to 0.18 °C during green-up, extending this cooling into the senescence period. Conversely, under extremely arid conditions, earlier green-up cools air temperature by 0.09 °C, and amplified senescence warming to 0.16 °C. Mechanism analysis revealed that evapotranspiration-dominated non-radiative processes drive immediate cooling during green-up while radiation and circulation process dominates the delayed but opposite warming/cooling effects during senescence in extremely arid/humid hydroclimates. Given the projected continuation of warming trends and increased frequency of extreme climatic events, it is imperative to incorporate the biophysical effects of vegetation phenology into local climate adaptation strategies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

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 (R 2 = 0.81–0.94) and H (R 2 = 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.

evapotranspiration↗

DOE OSTI2021

Empirical estimation of weather-driven yield shocks using biophysical characteristics for U.S. rainfed and irrigated maize, soybeans, and winter wheat

Agricultural yields are highly susceptible to changes in weather system patterns, including both annual and sub-annual changes in temperature and precipitation. Understanding the impacts of future changes in meteorological variables on crop yields have been widely studied in both empirical and process-based models. This work presents a structural econometric approach that combines historical weather data with information about the biophysical growth cycles of maize, winter wheat, and soy to predict the year-to-year yield responses for rainfed crops. Modeled soil moisture and temperature are taken as key predictors, which allows testing the fitted rainfed model’s ability to predict irrigated yields by assuming irrigation produces the numerically optimal level of soil moisture. This approach is grounded in known biophysical processes, which improves confidence in the model predictions. It produces estimates of interannual variability in yields, which enable study of the effects of extreme events on agricultural productivity. Finally, it enables prediction of the potential impacts of changing weather patterns on irrigated crops in areas that are currently primarily rainfed. We present the results of the empirical model, fitted with rainfed data; out-of-sample validation on irrigated crops; and projections of yield shocks under multiple future climate scenarios. Under a bias-corrected GFDL RCP8.5 scenario, this approach predicts average yield change, relative to 2006-2020 average yields, across U.S. counties in the 2040-2060 period of -16.9% and -13.4% for rainfed and irrigated maize, of -19.1% and -18.4% for rainfed and irrigated soy, and of -4.0% and -2.0% for rainfed and irrigated winter wheat. And in the 2070-2090 period of -30.3% and -28.8 % for rainfed and irrigated maize, of -33.1% and -32.8% for rainfed and irrigated soy, and of -6.5% and -5.2%for rainfed and irrigated winter wheat.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1964

Report of travel grants to the international biophysics meeting, paris, june 22-27, 1964

Travel grants for international biophysics meeting, and membership list of international organization for pure and applied biophysics

BIOPHYSICS↗

NASA NTRS2015

Mapping Biophysical Parameters for Land Surface Modeling over the Continental US Using MODIS and Landsat

In terms of the space cities occupy, urbanization appears as a minor land transformation. However, it permanently modifies land's ecological functions, altering its carbon, energy, and water fluxes. It is therefore necessary to develop a land cover characterization at fine spatial and temporal scales to capture urbanization's effects on surface fluxes. We develop a series of biophysical vegetation parameters such as the fraction of photosynthetically active radiation, leaf area index, vegetation greenness fraction, and roughness length over the continental US using MODIS and Landsat products for 2001. A 13-class land cover map was developed at a climate modeling grid (CMG) merging the 500mMODIS land cover and the 30m impervious surface area from the National Land Cover Database. The landscape subgrid heterogeneity was preserved using fractions of each class from the 500 m and 30 m into the CMG. Biophysical parameters were computed using the 8-day composite Normalized Difference Vegetation Index produced by the North American Carbon Program. In addition to urban impact assessments, this dataset is useful for the computation of surface fluxes in land, vegetation, and urban models and is expected to be widely used in different land cover and land use change applications.

Biophysical↗

DOE OSTI2022

Examining polymer‐protein biophysical interactions with small‐angle x‐ray scattering and quartz crystal microbalance with dissipation

Abstract Polymer‐protein hybrids can be deployed to improve protein solubility and stability in denaturing environments. While previous work used robotics and active machine learning to inform new designs, further biophysical information is required to ascertain structure–function behavior. Here, we show the value of tandem small‐angle x‐ray scattering (SAXS) and quartz crystal microbalance with dissipation (QCMD) experiments to reveal detailed polymer‐protein interactions with horseradish peroxidase (HRP) as a test case. Of particular interest was the process of polymer‐protein complex formation under thermal stress whereby SAXS monitors formation in solution while QCMD follows these dynamics at an interface. The radius of gyration ( R g ) of the protein as measured by SAXS does not change significantly in the presence of polymer under denaturing conditions, but thickness and dissipation changes were observed in QCMD data. SAXS data with and without thermal stress were utilized to create bead models of the potential complexes and denatured enzyme, and each model fit provided insight into the degree of interactions. Additionally, QCMD data demonstrated that HRP deforms by spreading upon surface adsorption at low concentration as shown by longer adsorption times and smaller frequency shifts. In contrast, thermally stressed and highly inactive HRP had faster adsorption kinetics. The combination of SAXS and QCMD serves as a framework for biophysical characterization of interactions between proteins and polymers which could be useful in designing polymer‐protein hybrids.

60 APPLIED LIFE SCIENCES↗

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↗

DOE OSTI2022

Economic and biophysical limits to seaweed farming for climate change mitigation

Net-zero greenhouse gas (GHG) emissions targets are driving interest in opportunities for biomass-based negative emissions and bioenergy, including from marine sources such as seaweed. Yet the biophysical and economic limits to farming seaweed at scales relevant to the global carbon budget have not been assessed in detail. We use coupled seaweed growth and technoeconomic models to estimate the costs of global seaweed production and related climate benefits, systematically testing the relative importance of model parameters. Under our most optimistic assumptions, sinking farmed seaweed to the deep sea to sequester a gigaton of CO 2 per year costs as little as US$\$$480 per tCO 2 on average, while using farmed seaweed for products that avoid a gigaton of CO 2 -equivalent GHG emissions annually could return a profit of $\$$50 per tCO 2 -eq. However, these costs depend on low farming costs, high seaweed yields, and assumptions that almost all carbon in seaweed is removed from the atmosphere (that is, competition between phytoplankton and seaweed is negligible) and that seaweed products can displace products with substantial embodied non-CO 2 GHG emissions. Moreover, the gigaton-scale climate benefits we model would require farming very large areas (>90,000 km 2 )—a >30-fold increase in the area currently farmed. Our results therefore suggest that seaweed-based climate benefits may be feasible, but targeted research and demonstrations are needed to further reduce economic and biophysical uncertainties.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Biophysical and Biochemical Characterization of TP0037, a D-Lactate Dehydrogenase, Supports an Acetogenic Energy Conservation Pathway in Treponema pallidum

A longstanding conundrum in Treponema pallidum biology concerns how the spirochete generates sufficient energy to fulfill its complex pathogenesis processes during human syphilitic infection. For decades, it has been assumed that the bacterium relies solely on glucose catabolism (via glycolysis) for generation of its ATP. However, the organism’s robust motility, believed to be essential for human tissue invasion and dissemination, would require abundant ATP likely not provided by the parsimony of glycolysis. As such, additional ATP generation, either via a chemiosmotic gradient, substrate-level phosphorylation, or both, likely exists in T. pallidum. Along these lines, we have hypothesized that T. pallidum exploits an acetogenic energy conservation pathway that relies on the redox chemistry of flavins. Central to this hypothesis is the apparent existence in T. pallidum of an acetogenic pathway for the conversion of d-lactate to acetate. Herein we have characterized the structural, biophysical, and biochemical properties of the first enzyme (d-lactate dehydrogenase [d-LDH]; TP0037) predicted in this pathway. Binding and enzymatic studies showed that recombinant TP0037 consumed d-lactate and NAD+ to produce pyruvate and NADH. The crystal structure of TP0037 revealed a fold similar to that of other d-acid dehydrogenases; residues in the cofactor-binding and active sites were homologous to those of other known d-LDHs. The crystal structure and solution biophysical experiments revealed the protein’s propensity to dimerize, akin to other d-LDHs. This study is the first to elucidate the enzymatic properties of T. pallidum’s d-LDH, thereby providing new compelling evidence for a flavin-dependent acetogenic energy conservation (ATP-generating) pathway in T. pallidum.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Biophysical model of eelgrass and water quality in Coos Bay, OR shows greater mitigation potential for ocean acidification than hypoxia

Seagrass beds provide important ecosystem services and are valued, in part, for their potential to mediate stressors such as ocean acidification and hypoxia (OAH) for sensitive species. However, the susceptibility of seagrasses to anthropogenic impacts and recent declines motivate the need to better understand the drivers of seagrass and the water quality consequences that occur with variation in seagrass abundance. To meet this need, we leveraged existing monitoring data (water quality and seagrass), hydrodynamic circulation model, and biogeochemical model framework with seagrass submodel, to produce a biophysical model of Coos Bay estuary, Oregon, U.S. The model includes biogeochemical processes involving water quality, plankton, seagrass, and sediment-water interactions. Ecosystem models like this are useful for evaluating complex estuarine systems because they allow us to extend our understanding of system dynamics beyond existing observations and perform experiments to identify the processes driving observed patterns. We used the biophysical model of Coos Bay to evaluate the dynamics of water quality and native eelgrass (Zostera marina) under three eelgrass abundance scenarios (zero eelgrass, current extent, and maximum observed extent) to elucidate the relationship between eelgrass and OAH. Including eelgrass in the Coos Bay model produced results that more closely resembled water quality observations - dissolved oxygen (DO) and pH were more dynamic in simulations with eelgrass, often having both higher highs and lower lows. While there were some areas of the estuary where DO improved with the addition of eelgrass to the model there was overall a small net increase in harmful DO conditions (based on a salmon physiological threshold). In contrast, ocean acidification conditions, pH and calcium carbonate saturation state for aragonite (Ω), were improved (based on oyster requirements) with the addition of eelgrass - although the magnitude of improvement differed seasonally and spatially. Our new model represents a useful tool - one which accounts for and controls the relevant physical and biogeochemical processes - to evaluate conditions that confer resilience or enhance vulnerability to OAH in an important Pacific Northwest coastal estuary and results can inform the OAH-related dynamics occurring in other eastern boundary current estuaries.

FVCOM-ICM↗

DOE OSTI2022

Biophysical Characterization of Membrane Proteins Embedded in Nanodiscs Using Fluorescence Correlation Spectroscopy

Proteins embedded in biological membranes perform essential functions in all organisms, serving as receptors, transporters, channels, cell adhesion molecules, and other supporting cellular roles. These membrane proteins comprise ~30% of all human proteins and are the targets of ~60% of FDA-approved drugs, yet their extensive characterization using established biochemical and biophysical methods has continued to be elusive due to challenges associated with the purification of these insoluble proteins. In response, the development of nanodisc techniques, such as nanolipoprotein particles (NLPs) and styrene maleic acid polymers (SMALPs), allowed membrane proteins to be expressed and isolated in solution as part of lipid bilayer rafts with defined, consistent nanometer sizes and compositions, thus enabling solution-based measurements. Fluorescence correlation spectroscopy (FCS) is a relatively simple yet powerful optical microscopy-based technique that yields quantitative biophysical information, such as diffusion kinetics and concentrations, about individual or interacting species in solution. Here, we first summarize current nanodisc techniques and FCS fundamentals. We then provide a focused review of studies that employed FCS in combination with nanodisc technology to investigate a handful of membrane proteins, including bacteriorhodopsin, bacterial division protein ZipA, bacterial membrane insertases SecYEG and YidC, Yersinia pestis type III secretion protein YopB, yeast cell wall stress sensor Wsc1, epidermal growth factor receptor (EGFR), ABC transporters, and several G protein-coupled receptors (GPCRs).

59 BASIC BIOLOGICAL SCIENCES↗