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NASA NTRS2024

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↗

NASA NTRS1969

Neutron therapy of cancer

Reports relate applications of neutrons to the problem of cancer therapy. The biochemical and biophysical aspects of fast-neutron therapy, neutron-capture and neutron-conversion therapy with intermediate-range neutrons are presented. Also included is a computer program for neutron-gamma radiobiology.

Frigerio, N. A.↗

NASA NTRS1985

Coupled atmosphere/canopy model for remote sensing of plant reflectance features

Solar radiative transfer through a coupled system of atmosphere and plant canopy is modeled as a multiple-scattering problem through a layered medium of random scatterers. The radiative transfer equation is solved by the discrete-ordinates finite-element method. Analytic expressions are derived that allow the calculation of scattering and absorption cross sections for any plant canopy layer form measurable biophysical parameters such as the leaf area index, leaf angle distribution, and individual leaf reflectance and transmittance data. An expression for a canopy scattering phase function is also given. Computational results are in good agreement with spectral reflectance measurements directly above a soybean canopy, and the concept of greenness- and brightness-transforms of Landsat MSS data is reconfirmed with the computed results. A sensitivity analysis with the coupled atmosphere/canopy model quantifies how satellite-sensed spectral radiances are affected by increased atmospheric aerosols, by varying leaf area index, by anisotropic leaf scattering, and by non-Lambertian soil boundary conditions. Possible extensions to a 2-D model are also discussed.

Gerstl, S. A.↗

NASA NTRS1985

Plant Growth Biophysics: the Basis for Growth Asymmetry Induced by Gravity

The identification and quantification of the physical properties altered by gravity when plant stems grow upward was studied. Growth of the stem in vertical and horizontal positions was recorded by time lapse photography. A computer program that uses a cubic spline fitting algorithm was used to calculate the growth rate and curvature of the stem as a function of time. Plant stems were tested to ascertain whether cell osmotic pressure was altered by gravity. A technique for measuring the yielding properties of the cell wall was developed.

Cosgrove, D.↗

NASA NTRS2013

Galactic Cosmic Ray Event-Based Risk Model (GERM) Code

This software describes the transport and energy deposition of the passage of galactic cosmic rays in astronaut tissues during space travel, or heavy ion beams in patients in cancer therapy. Space radiation risk is a probability distribution, and time-dependent biological events must be accounted for physical description of space radiation transport in tissues and cells. A stochastic model can calculate the probability density directly without unverified assumptions about shape of probability density function. The prior art of transport codes calculates the average flux and dose of particles behind spacecraft and tissue shielding. Because of the signaling times for activation and relaxation in the cell and tissue, transport code must describe temporal and microspatial density of functions to correlate DNA and oxidative damage with non-targeted effects of signals, bystander, etc. These are absolutely ignored or impossible in the prior art. The GERM code provides scientists data interpretation of experiments; modeling of beam line, shielding of target samples, and sample holders; and estimation of basic physical and biological outputs of their experiments. For mono-energetic ion beams, basic physical and biological properties are calculated for a selected ion type, such as kinetic energy, mass, charge number, absorbed dose, or fluence. Evaluated quantities are linear energy transfer (LET), range (R), absorption and fragmentation cross-sections, and the probability of nuclear interactions after 1 or 5 cm of water equivalent material. In addition, a set of biophysical properties is evaluated, such as the Poisson distribution for a specified cellular area, cell survival curves, and DNA damage yields per cell. Also, the GERM code calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle in a selected material. The GERM code makes the numerical estimates of basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at the NASA Space Radiation Laboratory (NSRL) for the purpose of simulating space radiation biological effects. In the first option, properties of monoenergetic beams are treated. In the second option, the transport of beams in different materials is treated. Similar biophysical properties as in the first option are evaluated for the primary ion and its secondary particles. Additional properties related to the nuclear fragmentation of the beam are evaluated. The GERM code is a computationally efficient Monte-Carlo heavy-ion-beam model. It includes accurate models of LET, range, residual energy, and straggling, and the quantum multiple scattering fragmentation (QMSGRG) nuclear database.

Cucinotta, Francis A.↗

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↗

NASA NTRS2014

Towards Co-evolution of Membrane Transport and Metabolism

Protocellular boundaries were inextricably connected to the metabolism they encapsulated: to be inheritable, early metabolism must have led to an increased rate of growth and division of vesicles and, similarly, transport through vesicle boundaries must have supported the evolution of metabolism. Even though explaining how this coupling emerged and evolved in the absence of the complex machinery of modern cells is one of the key issues in studies on the origin of life, little is known about the biochemical and biophysical processes that might have been involved. This gap in our knowledge is a major impediment in efforts to construct scenarios for the origin of life and laboratory models of protocells. A combination of experimental and computational studies carried out by us and our collaborators is aimed at helping to close this gap. Properties of membranes might have contributed to the selection of RNA as an early biopolymer. A kinetic mechanism was proposed (Sacerdote & Szostak, 2005) in which ribose was supplied more quickly than other aldopentoses to primordial cells for preferential incorporation of ribonucleotides into nucleic acids. This proposal is based on a finding that ribose permeates membranes an order of magnitude faster than its diastereomers, arabinose and xylose. Our computer simulations, which yield permeation rates in excellent agreement with experiment, and kinetic modeling explain this phenomenon in terms of inter- and intramolecular interactions involving exocyclic hydroxyl groups attached to carbon atoms of the pyranose ring (Wei and Pohorille, 2009). They also constrain scenarios for the formation of the earliest nucleic acids (Wei and Pohorille, 2013). In one scenario, sugars permeate protocellular walls and subsequently are used to synthesize nucleic acids inside protocells. As long as this process proceeds at the rate faster than 6x10(exp -3)/s, ribose derivatives will be available for synthesis easier than their diastereomers. If nucleosides or their activated derivatives are synthesized outside protocells and subsequently transported across protocellular membranes the kinetic mechanism does not apply because all diastereomers, which have their sugars in the furanose rather than pyranose form, permeate the membrane at approximately the same rate. Properties of membranes might have been also coupled to metabolism involving peptides. Recently, Adamala and Szostak (2013) have shown that a dipeptide inside fatty-acid vesicles catalyzes the formation of another dipeptide that binds to vesicle walls and, by doing so, promotes their growth at the expense of other vesicles. This coupling of metabolism, permeability of vesicles and their growth is the first demonstration of evolutionary advantage imparted by small, membrane-bound peptides. Building on this work we have calculated the rate at which different blocked amino acids are delivered to a protocell for synthesis of dipeptides. We have further shown that the dipeptides are located at the water-membrane interface rather than in the center of the bilayer. On these basis it is anticipated that other dipeptides containing aromatic, but not necessarily hydrophobic amino acids (e.g. tyrosine) could have the same catalytic effects. Insight from these studies allows for estimating the rate of vesicle growth and the rates of dipeptide synthesis required to keep the system in balance. These results, in combination with our earlier studies, lead to a general scenario for evolution from membrane-bound dipeptides to ion channels in the origin of life.

Metabolism↗

NASA NTRS2010

GUI to Facilitate Research on Biological Damage from Radiation

A graphical-user-interface (GUI) computer program has been developed to facilitate research on the damage caused by highly energetic particles and photons impinging on living organisms. The program brings together, into one computational workspace, computer codes that have been developed over the years, plus codes that will be developed during the foreseeable future, to address diverse aspects of radiation damage. These include codes that implement radiation-track models, codes for biophysical models of breakage of deoxyribonucleic acid (DNA) by radiation, pattern-recognition programs for extracting quantitative information from biological assays, and image-processing programs that aid visualization of DNA breaks. The radiation-track models are based on transport models of interactions of radiation with matter and solution of the Boltzmann transport equation by use of both theoretical and numerical models. The biophysical models of breakage of DNA by radiation include biopolymer coarse-grained and atomistic models of DNA, stochastic- process models of deposition of energy, and Markov-based probabilistic models of placement of double-strand breaks in DNA. The program is designed for use in the NT, 95, 98, 2000, ME, and XP variants of the Windows operating system.

Cucinotta, Frances A.↗

NASA NTRS1993

Deriving the intermediate spectra and photocycle kinetics from time-resolved difference spectra of bacteriorhodopsin. The simpler case of the recombinant D96N protein

The bacteriorhodopsin photocycle contains more than five spectrally distinct intermediates, and the complexity of their interconversions has precluded a rigorous solution of the kinetics. A representation of the photocycle of mutated D96N bacteriorhodopsin near neutral pH was given earlier (Varo, G., and J. K. Lanyi. 1991. Biochemistry. 30:5008-5015) as BRhv-->K<==>L<==>M1-->M2--> BR. Here we have reduced a set of time-resolved difference spectra for this simpler system to three base spectra, each assumed to consist of an unknown mixture of the pure K, L, and M difference spectra represented by a 3 x 3 matrix of concentration values between 0 and 1. After generating all allowed sets of spectra for K, L, and M (i.e., M1 + M2) at a 1:50 resolution of the matrix elements, invalid solutions were eliminated progressively in a search based on what is expected, empirically and from the theory of polyene excited states, for rhodopsin spectra. Significantly, the average matrix values changed little after the first and simplest of the search criteria that disallowed negative absorptions and more than one maximum for the M intermediate. We conclude from the statistics that during the search the solutions strongly converged into a narrow region of the multidimensional space of the concentration matrix. The data at three temperatures between 5 and 25 degrees C yielded a single set of spectra for K, L, and M; their fits are consistent with the earlier derived photocycle model for the D96N protein.

NASA Program Exobiology↗

NASA NTRS1986

Physics through the 1990s: Scientific interfaces and technological applications

The volume examines the scientific interfaces and technological applications of physics. Twelve areas are dealt with: biological physics-biophysics, the brain, and theoretical biology; the physics-chemistry interface-instrumentation, surfaces, neutron and synchrotron radiation, polymers, organic electronic materials; materials science; geophysics-tectonics, the atmosphere and oceans, planets, drilling and seismic exploration, and remote sensing; computational physics-complex systems and applications in basic research; mathematics-field theory and chaos; microelectronics-integrated circuits, miniaturization, future trends; optical information technologies-fiber optics and photonics; instrumentation; physics applications to energy needs and the environment; national security-devices, weapons, and arms control; medical physics-radiology, ultrasonics, MNR, and photonics. An executive summary and many chapters contain recommendations regarding funding, education, industry participation, small-group university research and large facility programs, government agency programs, and computer database needs.

Source record↗

NASA NTRS2001

Monte Carlo track structure for radiation biology and space applications

Over the past two decades event by event Monte Carlo track structure codes have increasingly been used for biophysical modelling and radiotherapy. Advent of these codes has helped to shed light on many aspects of microdosimetry and mechanism of damage by ionising radiation in the cell. These codes have continuously been modified to include new improved cross sections and computational techniques. This paper provides a summary of input data for ionizations, excitations and elastic scattering cross sections for event by event Monte Carlo track structure simulations for electrons and ions in the form of parametric equations, which makes it easy to reproduce the data. Stopping power and radial distribution of dose are presented for ions and compared with experimental data. A model is described for simulation of full slowing down of proton tracks in water in the range 1 keV to 1 MeV. Modelling and calculations are presented for the response of a TEPC proportional counter irradiated with 5 MeV alpha-particles. Distributions are presented for the wall and wall-less counters. Data shows contribution of indirect effects to the lineal energy distribution for the wall counters responses even at such a low ion energy.

NASA Center JSC↗

NASA NTRS1998

Radiation-induced total-deletion mutations in the human hprt gene: a biophysical model based on random walk interphase chromatin geometry

PURPOSE: To develop a biophysical model that explains the sizes of radiation-induced hprt deletions. METHODS: Key assumptions: (1) Deletions are produced by two DSB that are closer than an interaction distance at the time of DSB induction; (2) Interphase chromatin is modelled by a biphasic random walk distribution; and (3) Misrejoining of DSB from two separate tracks dominates at low-LET and misrejoining of DSB from a single track dominates at high-LET. RESULTS: The size spectra for radiation-induced total deletions of the hprt gene are calculated. Comparing with the results of Yamada and coworkers for gamma-irradiated human fibroblasts the study finds that an interaction distance of 0.75 microm will fit both the absolute frequency and the size spectrum of the total deletions. It is also shown that high-LET radiations produce, relatively, more total deletions of sizes below 0.5 Mb. The model predicts an essential gene to be located between 2 and 3 Mb from the hprt locus towards the centromere. Using the same assumptions and parameters as for evaluating mutation frequencies, a frequency of intra-arm chromosome deletions is calculated that is in agreement with experimental data. CONCLUSIONS: Radiation-induced total-deletion mutations of the human hprt gene and intrachange chromosome aberrations share a common mechanism for their induction.

NASA Center JSC↗

NASA NTRS1996

Using naturally occurring polysaccharides to align molecules with nonlinear optical activity

The Biophysics and Advanced Materials Branch of the Microgravity Science and Applications Division at Marshall Space Flight Center has been investigating polymers with the potential for nonlinear optical (NLO) applications for a number of years. Some of the potential applications for NLO materials include optical communications, computing, and switching. To this point the branch's research has involved polydiacetylenes, phthalocyanins, and other synthetic polymers which have inherent NLO properties. The aim of the present research is to investigate the possibility of using naturally occurring polymers such as polysaccharides or proteins to trap and align small organic molecules with useful NLO properties. Ordering molecules with NLO properties enhances 3rd order nonlinear effects and is required for 2nd order nonlinear effects. Potential advantages of such a system are the flexibility to use different small molecules with varying chemical and optical properties, the stability and cost of the polymers, and the ability to form thin, optically transparent films. Since the quality of any polymer films depends on optimizing ordering and minimizing defects, this work is particularly well suited for microgravity experiments. Polysaccharide and protein polymers form microscopic crystallites which must align to form ordered arrays. The ordered association of crystallites is disrupted by gravity effects and NASA research on protein crystal growth has demonstrated that low gravity conditions can improve crystal quality.

Prasthofer, Thomas↗

NASA NTRS1983

Improving our understanding of the remote sensing process

Plans for two fundamental research programs aimed at improving an understanding of the physics and mathematics of remote sensing are discussed. The first program, Scene Radiation and Atmospheric Research Program, is concerned with developing the capability to determine biophysical attributes of terrestrial scenes through an improved understanding of the relationships between those properties and remotely sensed radiation. The research issues in the second program, Mathematical Pattern Recognition and Image Analysis, are discussed with reference to the following five categories: preprocessing, digital image representation, object scene inference, computational structures, and continuing studies.

Calabrese, M. A.↗

NASA NTRS2015

Spin-Up and Tuning of the Global Carbon Cycle Model Inside the GISS ModelE2 GCM

Planetary carbon cycle involves multiple phenomena, acting at variety of temporal and spacial scales. The typical times range from minutes for leaf stomata physiology to centuries for passive soil carbon pools and deep ocean layers. So, finding a satisfactory equilibrium state becomes a challenging and computationally expensive task. Here we present the spin-up processes for different configurations of the GISS Carbon Cycle model from the model forced with MODIS observed Leaf Area Index (LAI) and prescribed ocean to the prognostic LAI and to the model fully coupled to the dynamic ocean and ocean biology. We investigate the time it takes the model to reach the equilibrium and discuss the ways to speed up this process. NASA Goddard Institute for Space Studies General Circulation Model (GISS ModelE2) is currently equipped with all major algorithms necessary for the simulation of the Global Carbon Cycle. The terrestrial part is presented by Ent Terrestrial Biosphere Model (Ent TBM), which includes leaf biophysics, prognostic phenology and soil biogeochemistry module (based on Carnegie-Ames-Stanford model). The ocean part is based on the NASA Ocean Biogeochemistry Model (NOBM). The transport of atmospheric CO2 is performed by the atmospheric part of ModelE2, which employs quadratic upstream algorithm for this purpose.

Climate model↗

NASA NTRS2010

Shorebird Migration Patterns in Response to Climate Change: A Modeling Approach

The availability of satellite remote sensing observations at multiple spatial and temporal scales, coupled with advances in climate modeling and information technologies offer new opportunities for the application of mechanistic models to predict how continental scale bird migration patterns may change in response to environmental change. In earlier studies, we explored the phenotypic plasticity of a migratory population of Pectoral sandpipers by simulating the movement patterns of an ensemble of 10,000 individual birds in response to changes in stopover locations as an indicator of the impacts of wetland loss and inter-annual variability on the fitness of migratory shorebirds. We used an individual based, biophysical migration model, driven by remotely sensed land surface data, climate data, and biological field data. Mean stop-over durations and stop-over frequency with latitude predicted from our model for nominal cases were consistent with results reported in the literature and available field data. In this study, we take advantage of new computing capabilities enabled by recent GP-GPU computing paradigms and commodity hardware (general purchase computing on graphics processing units). Several aspects of our individual based (agent modeling) approach lend themselves well to GP-GPU computing. We have been able to allocate compute-intensive tasks to the graphics processing units, and now simulate ensembles of 400,000 birds at varying spatial resolutions along the central North American flyway. We are incorporating additional, species specific, mechanistic processes to better reflect the processes underlying bird phenotypic plasticity responses to different climate change scenarios in the central U.S.

Smith, James A.↗

NASA NTRS1994

Learning random networks for compression of still and moving images

Image compression for both still and moving images is an extremely important area of investigation, with numerous applications to videoconferencing, interactive education, home entertainment, and potential applications to earth observations, medical imaging, digital libraries, and many other areas. We describe work on a neural network methodology to compress/decompress still and moving images. We use the 'point-process' type neural network model which is closer to biophysical reality than standard models, and yet is mathematically much more tractable. We currently achieve compression ratios of the order of 120:1 for moving grey-level images, based on a combination of motion detection and compression. The observed signal-to-noise ratio varies from values above 25 to more than 35. The method is computationally fast so that compression and decompression can be carried out in real-time. It uses the adaptive capabilities of a set of neural networks so as to select varying compression ratios in real-time as a function of quality achieved. It also uses a motion detector which will avoid retransmitting portions of the image which have varied little from the previous frame. Further improvements can be achieved by using on-line learning during compression, and by appropriate compensation of nonlinearities in the compression/decompression scheme. We expect to go well beyond the 250:1 compression level for color images with good quality levels.

Gelenbe, Erol↗

NASA NTRS1993

Extended ecosystem signatures with application to Eos synergism requirements

The primary objective is to define the advantages of synergistically combining optical and microwave remote sensing measurements for the determination of biophysical properties important in ecosystem modeling. This objective was approached in a stepwise fashion starting with ground-based observations of controlled agricultural and orchard canopies and progressing to airborne observations of more natural forest ecosystems. This observational program is complemented by a parallel effort to model the visible reflectance and microwave scattering properties of composite vegetation canopies. The goals of the modeling studies are to verify our basic understanding of the sensor-scene interaction physics and to provide the basis for development of inverse models optimized for retrieval of key biophysical properties. These retrieval algorithms can then be used to simulate the expected performance of various aspects of Eos including the need for simultaneous SAR and HIRIS observations or justification for other (non-synchronous) relative timing constraints and the frequency, polarization, and angle of incidence requirements for accurate biophysical parameter extractions. This program completed a very successful series of truck-mounted experiments, made remarkable progress in development and validation of optical reflectance and microwave scattering models for vegetation, extended the scattering models to accommodate discontinuous and periodic canopies, developed inversion approaches for surface and canopy properties, and disseminated these results widely through symposia and journal publications. In addition, the third generation of the computer code for the microwave scattering models was provided to a number of other US, Canadian, Australian, and European investigators who are currently presenting and publishing results using the MIMICS research code.

Ulaby, Fawwaz T.↗