Detection of Optical Activity as a Sign of Life
Gas liquid chromatographic techniques for detection of optical activity as sign of life
LIFE SCIENCE↗
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Results for “Biophysical techniques”
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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Bidirectional Reflectance of Flat, Optically Thick Particulate Layers: An Efficient Radiative Transfer Solution and Applications to Snow and Soil Surfaces
We describe a simple and highly efficient and accurate radiative transfer technique for computing bidirectional reflectance of a macroscopically flat scattering layer composed of nonabsorbing or weakly absorbing, arbitrarily shaped, randomly oriented and randomly distributed particles. The layer is assumed to be homogeneous and optically semi-infinite, and the bidirectional reflection function (BRF) is found by a simple iterative solution of the Ambartsumian's nonlinear integral equation. As an exact Solution of the radiative transfer equation, the reflection function thus obtained fully obeys the fundamental physical laws of energy conservation and reciprocity. Since this technique bypasses the computation of the internal radiation field, it is by far the fastest numerical approach available and can be used as an ideal input for Monte Carlo procedures calculating BRFs of scattering layers with macroscopically rough surfaces. Although the effects of packing density and coherent backscattering are currently neglected, they can also be incorporated. The FORTRAN implementation of the technique is available on the World Wide Web at http://ww,,v.giss.nasa.gov/-crmim/brf.html and can be applied to a wide range of remote sensing, engineering, and biophysical problems. We also examine the potential effect of ice crystal shape on the bidirectional reflectance of flat snow surfaces and the applicability of the Henyey-Greenstein phase function and the 6-Eddington approximation in calculations for soil surfaces.
Mishchenko, Michael I.↗
Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry
It is well known that the lipid distribution in the bilayer leaflets of mammalian plasma membranes (PMs) is not symmetric. Despite this, model membrane studies have largely relied on chemically symmetric model membranes for the study of lipid–lipid and lipid–protein interactions. This is primarily due to the difficulty in preparing stable, asymmetric model membranes that are amenable to biophysical studies. However, in the last 20 years, efforts have been made in producing more biologically faithful model membranes. Here, we review several recently developed experimental and computational techniques for the robust generation of asymmetric model membranes and highlight a new and particularly promising technique to study membrane asymmetry.
59 BASIC BIOLOGICAL SCIENCES↗
Atmospheric Correction of High-Spatial-Resolution Commercial Satellite Imagery Products Using MODIS Atmospheric Products
Remotely sensed ground reflectance is the basis for many inter-sensor interoperability or change detection techniques. Satellite inter-comparisons and accurate vegetation indices such as the Normalized Difference Vegetation Index, which is used to describe or to imply a wide variety of biophysical parameters and is defined in terms of near-infrared and redband reflectance, require the generation of accurate reflectance maps. This generation relies upon the removal of solar illumination, satellite geometry, and atmospheric effects and is generally referred to as atmospheric correction. Atmospheric correction of remotely sensed imagery to ground reflectance, however, has been widely applied to only a few systems. In this study, we atmospherically corrected commercially available, high spatial resolution IKONOS and QuickBird imagery using several methods to determine the accuracy of the resulting reflectance maps. We used extensive ground measurement datasets for nine IKONOS and QuickBird scenes acquired over a two-year period to establish reflectance map accuracies. A correction approach using atmospheric products derived from Moderate Resolution Imaging Spectrometer data created excellent reflectance maps and demonstrated a reliable, effective method for reflectance map generation.
Pagnutti, Mary↗
A Technique for Assimilating GOES-Derived Land Surface Products into Regional Models to Improve the Representation of Land Surface Forcing
As the parameterizations of surface energy budgets in regional models have become more complete physically, models have the potential to be much more realistic in simulations of coupling between surface radiation, hydrology, and surface energy transfer. Realizing the importance of properly specifying the surface energy budget, many institutions are using land-surface models to represent the lower boundary forcing associated with biophysical processes and soil hydrology. However, the added degrees of freedom due to inclusion of such land-surface schemes require the specification of additional parameters within the model system such as vegetative resistances, green vegetation fraction, leaf area index, soil physical and hydraulic characteristics, stream flow, runoff, and the vertical distribution of soil moisture. A technique has been developed for assimilating GOES-IR skin temperature tendencies into the surface energy budget equation of a mesoscale model so that the simulated rate of temperature change closely agrees with the satellite observations. A critical assumption of the technique is that the availability of moisture (either from the soil or vegetation) is the least known term in the model's surface energy budget. Therefore, the simulated latent heat flux, which is a function of surface moisture availability, is adjusted based upon differences between the modeled and satellite-observed skin temperature tendencies. An advantage of this technique is that satellite temperature tendencies are assimilated in an energetically consistent manner that avoids energy imbalances and surface stability problems that arise from direct assimilation of surface shelter temperatures. The fact that the rate of change of the satellite skin temperature is used rather than the absolute temperature means that sensor calibration is not as critical. An advantage of this technique for short-range forecasts is that it does not require a complex land-surface formulation within the atmospheric model. As a result, the need to specify poorly known soil and vegetative characteristics is eliminated. The GOES assimilation technique has been incorporated into the PSU/NCAR MM5. Results will be presented to demonstrate the ability of the assimilation scheme to improve short-term simulations of near-surface air temperature and mixing ratio during the warm season for several selected cases during June of 1995 and June 1997 which exhibit a variety of atmospheric and land-surface conditions. In addition, the simulations produced by the assimilation technique will be compared with those produced by the MM5/BATS coupled model initialized with soil water content derived from a soil hydrology model.
Lapenta, William M.↗
Multiband radar characterization of forest biomes
The utility of airborne and orbital SAR in classification, assessment, and monitoring of forest biomes is investigated through analysis of orbital synthetic aperature radar (SAR) and multifrequency and multipolarized airborne SAR imagery relying on image tone and texture. Preliminary airborne SAR experiments and truck-mounted scatterometer observations demonstrated that the three dimensional structural complexity of a forest, and the various scales of temporal dynamics in the microwave dielectric properties of both trees and the underlying substrate would severely limit empirical or semi-empirical approaches. As a consequence, it became necessary to develop a more profound understanding of the electromagnetic properties of a forest scene and their temporal dynamics through controlled experimentation coupled with theoretical development and verification. The concatenation of various models into a physically-based composite model treating the entire forest scene became the major objective of the study as this is the key to development of a series of robust retrieval algorithms for forest biophysical properties. In order to verify the performance of the component elements of the composite model, a series of controlled laboratory and field experiments were undertaken to: (1) develop techniques to measure the microwave dielectric properties of vegetation; (2) relate the microwave dielectric properties of vegetation to more readily measured characteristics such as density and moisture content; (3) calculate the radar cross-section of leaves, and cylinders; (4) improve backscatter models for rough surfaces; and (5) relate attenuation and phase delays during propagation through canopies to canopy properties. These modeling efforts, as validated by the measurements, were incorporated within a larger model known as the Michigan Microwave Canopy Scattering (MIMICS) Model.
Dobson, M. Craig↗
Low cost and massively parallel force spectroscopy with fluid loading on a chip
Current approaches for single molecule force spectroscopy are typically constrained by low throughput and high instrumentation cost. Herein, a low-cost, high throughput technique is demonstrated using microfluidics for multiplexed mechanical manipulation of up to ~4000 individual molecules via molecular fluid loading on-a-chip (FLO-Chip). The FLO-Chip consists of serially connected microchannels with varying width, allowing for simultaneous testing at multiple loading rates. Molecular force measurements are demonstrated by dissociating Biotin-Streptavidin and Digoxigenin-AntiDigoxigenin interactions along with unzipping of double stranded DNA of varying sequence under different dynamic loading rates and solution conditions. Rupture force results under varying loading rates and solution conditions are in good agreement with prior studies, verifying a versatile approach for single molecule biophysics and molecular mechanobiology. FLO-Chip enables straightforward, rapid, low-cost, and portable mechanical testing of single molecules that can be implemented on a wide range of microscopes to broaden access and may enable new applications of molecular force spectroscopy.
42 ENGINEERING↗
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↗
Visualizing 2D Probability Distributions from Satellite Image-Derived Data
Creating maps of biophysical and geophysical variables using Earth Observing System (EOS) satellite image data is an important component of Earth science. These 2D maps have a single value at every location and standard techniques are used to visualize them. Current tools fall short, however, when it is necessary to describe a distribution of values at each location. Distributions may represent a frequency of occurrence over time, frequency of occurrence from multiple runs of an ensemble forecast or possible values from an uncertainty model. 'Distribution data sets' are described, then a case study is presented to visualize such 2D distributions. Distribution data sets are different from multivariate data sets in the sense that the values are for a single variable instead of multiple variables. Our case study data consists of multiple realizations of percent forest cover, generated using a geostatistical technique that combines ground measurements and satellite imagery to model uncertainty about forest cover. We present several approaches for analyzing and visualizing such data sets. The first is a pixel-wise analysis of the probability density functions for the 2D image while the second is an analysis of features identified within the image. Such pixel-wise and feature-wise views will give Earth scientists a more complete understanding of distribution data sets.
Kao, David↗
Monatomic ions influence substrate permeation across bacterial microcompartment shells
Abstract Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.
59 BASIC BIOLOGICAL SCIENCES↗
Deciphering the Spectra of Flowers to Map Landscape-scale Blooming Dynamics
Like leaves, floral coloration is driven by inherent optical properties, which are determined by pigments, scattering structure, and thickness. However, establishing the relative contribution of these factors to canopy spectral signals is usually limited to in-situ observations. Modeling flowering dynamics (e.g., blooming duration, spatial distribution) at the landscape scale may reveal insights into ecological processes and phenological adaptations to environmental changes. Multitemporal visible to shortwave infrared (VSWIR) imaging spectroscopy observations are especially suited for such efforts. Reflectance in this spectral range is sensitive to major flower pigments, flowering phenology traces, and biophysical differences between flowers and other plant parts. We explored how flowers contribute to spectral signals using a time series of imagery from the Airborne Visible InfraRed Imaging Spectrometer - Next Generation (AVIRIS-NG) collected as part of the SBG High-Frequency Time Series (SHIFT) campaign as a case study. Airborne data were collected weekly during the spring of 2022 across two natural reserves in California. Field spectra were gathered from blooming plots at leaf, flower, and canopy levels at two time points during the campaign. The processed data was used to investigate flowering species' spectro-temporal variation and spatial distribution using Spectral Mixture Residual, Gaussian clustering techniques, and a proposed narrow-band flowering index. Linear spectral unmixing allowed the computation of the weighted contribution of four major high-variance endmembers (leaves, flowers, soil, dark) and low-variance residual signal that comprises subtle spectral features used to track biophysical processes. The reflectance residual was projected on a low principal component basis to characterize flowering clusters' variation and spatial distribution based on the Gaussian mixture model, providing an uncertainty metric to assess the results. Mapping flowering events from modeling spectro-temporal dynamics throughout the season, from pre-blooming to post-flowering stages, allowed us to identify gradient variations in spectral features within the VSWIR spectral range linked to flowering pigments. Time series of the Mixture Residual Blooming Index and the Red-Edge Normalized Difference Vegetation Index revealed specific flowering and greenness phenophases across the two main species (Coreopsis gigantea, Artemisia californica) in the flowering areas. Overall, our approach opens opportunities for future satellite monitoring of floral cycles at broader scales.
Yoseline Angel↗
Laboratory techniques and rhythmometry
Some of the procedures used for the analysis of rhythms are illustrated, notably as these apply to current medical and biological practice. For a quantitative approach to medical and broader socio-ecologic goals, the chronobiologist gathers numerical objective reference standards for rhythmic biophysical, biochemical, and behavioral variables. These biological reference standards can be derived by specialized computer analyses of largely self-measured (until eventually automatically recorded) time series (autorhythmometry). Objective numerical values for individual and population parameters of reproductive cycles can be obtained concomitantly with characteristics of about-yearly (circannual), about-daily (circadian) and other rhythms.
Halberg, F.↗
Atmospheric Correction of High-Spatial-Resolution Commercial Satellite Imagery Products Using MODIS Atmospheric Products
Remotely sensed ground reflectance is the foundation of any interoperability or change detection technique. Satellite intercomparisons and accurate vegetation indices, such as the Normalized Difference Vegetation Index (NDVI), require the generation of accurate reflectance maps (NDVI is used to describe or infer a wide variety of biophysical parameters and is defined in terms of near-infrared (NIR) and red band reflectances). Accurate reflectance-map generation from satellite imagery relies on the removal of solar and satellite geometry and of atmospheric effects and is generally referred to as atmospheric correction. Atmospheric correction of remotely sensed imagery to ground reflectance has been widely applied to a few systems only. The ability to obtain atmospherically corrected imagery and products from various satellites is essential to enable widescale use of remotely sensed, multitemporal imagery for a variety of applications. An atmospheric correction approach derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) that can be applied to high-spatial-resolution satellite imagery under many conditions was evaluated to demonstrate a reliable, effective reflectance map generation method. Additional information is included in the original extended abstract.
Pagnutti, Mary↗
Quantifying the Relevance of Long-Range Forces for Crystal Nucleation in Water
Understanding nucleation from aqueous solutions is of fundamental importance in a multitude of fields, ranging from materials science to biophysics. The complex solvent-mediated interactions in aqueous solutions hamper the development of a simple physical picture, elucidating the roles of different interactions in nucleation processes. In this study, we make use of three complementary techniques to disentangle the role played by short- and long-range interactions in solvent-mediated nucleation. Specifically, the first approach we utilize is the local molecular field (LMF) theory to renormalize long-range Coulomb electrostatics. Second, we use well-tempered metadynamics to speed up rare events governed by short-range interactions. Third, the deep learning-based State Predictive Information Bottleneck approach is employed in analyzing the reaction coordinate of the nucleation processes obtained from the LMF treatment coupled with well-tempered metadynamics. We find that the two-step nucleation mechanism can largely be captured by the short-range interactions, while the long-range interactions further contribute to the stability of the primary crystal state under ambient conditions. Furthermore, by analyzing the reaction coordinate obtained from the combined LMF-metadynamics treatment, we discern the fluctuations on different time scales, highlighting the need for long-range interactions when accounting for metastability.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SAYANI'91 - A joint United States/Commonwealth of Independent States field campaign to investigate forest decline damage in the Krasnoyarsk region of southcentral Siberia
The field experiment described took place in the Sayani Mountains of Siberia. The purpose of the joint field campaign was to observe and exchange methodologies with Russian scientists with regard to the development of remote sensing techniques for the early detection and assessment of forest decline damage believed to be associated with atmospheric deposition and/or insect and disease infestations. Several types of passive and active remote sensing measurements were made in conjunction with biophysical measurements on vegetative samples collected from four study sites representing a strong elevational gradient. Relatively cloud-free SPOT data were also acquired over the study area. Moderate canopy damage was recorded at the mid-elevation site (3400 ft/1037 m). The lowest levels of damage were recorded at the lowest elevation site (2300 ft/701 m.) At all sites, east versus west flagging of the canopy was noted (i.e., full canopy on the west-facing side of the canopy, significantly less foliage on the east-facing side).
Williams, D. L.↗
Data for: A hybrid biophysical-machine learning framework for diurnal surface energy flux estimation using proximal sensing
Thermal-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 datasets. 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 specific surface energy balance observations, specifically net radiation and soil heat flux, thereby enhancing model applicability in data-sparse settings. The integration of an 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.
Agricultural Sciences↗
Determination of soil phosphatase activity by a fluorimetric technique.
Fluorimetric technique for phosphatase activity in soil based on beta-naphthol release from sodium- beta-naphthylphosphate
BIOPHYSICS↗
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↗