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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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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Key role of the REC lobe during CRISPR–Cas9 activation by ‘sensing’, ‘regulating’, and ‘locking’ the catalytic HNH domain

Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)–Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 – a specialized supercomputer capturing micro-to-millisecond biophysical events in real time and at atomic-level resolution – reveal the activation process of the endonuclease Cas9 toward DNA cleavage. Over the unbiased simulation, we observe that the spontaneous approach of the catalytic domain HNH to the DNA cleavage site is accompanied by a remarkable structural remodeling of the recognition (REC) lobe, which exerts a key role for DNA cleavage. Specifically, the significant conformational changes and the collective conformational dynamics of the REC lobe indicate a mechanism by which the REC1–3 regions ‘sense’ nucleic acids, ‘regulate’ the HNH conformational transition, and ultimately ‘lock’ the HNH domain at the cleavage site, contributing to its catalytic competence. By integrating additional independent simulations and existing experimental data, we provide a solid validation of the activated HNH conformation, which had been so far poorly characterized, and we deliver a comprehensive understanding of the role of REC1–3 in the activation process. Considering the importance of the REC lobe in the specificity of Cas9, this study poses the basis for fully understanding how the REC components control the cleavage of off-target sequences, laying the foundation for future engineering efforts toward improved genome editing.

59 BASIC BIOLOGICAL SCIENCES↗
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

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.↗
DOE OSTI2016

Peptide backbone modification in the bend region of amyloid-β inhibits fibrillogenesis but not oligomer formation

Current evidence suggests that oligomers of the amyloid-β (Aβ) peptide are involved in the cellular toxicity of Alzheimer’s disease, yet their biophysical characterization remains difficult because of lack of experimental control over the aggregation process under relevant physiologic conditions. Here in this paper, we show that modification of the Aβ peptide backbone at Gly29 allows for the formation of oligomers but inhibits fibril formation at physiologic temperature and pH. Our results suggest that the putative bend region in Aβ is important for higher-order aggregate formation.

2-nitrobenzyl↗
DOE OSTI2014

Understanding generalized inversions of nuclear magnetic resonance transverse relaxation time in porous media

The nuclear magnetic resonance transverse relaxation time T{sub 2}, measured using the Carr-Purcell-Meiboom-Gill (CPMG) experiment, is a powerful method for obtaining unique information on liquids confined in porous media. Furthermore, T{sub 2} provides structural information on the porous material itself and has many applications in petrophysics, biophysics, and chemical engineering. Robust interpretation of T{sub 2} distributions demands appropriate processing of the measured data since T{sub 2} is influenced by diffusion through magnetic field inhomogeneities occurring at the pore scale, caused by the liquid/solid susceptibility contrast. Previously, we introduced a generic model for the diffusion exponent of the form −ant{sub e}{sup k} (where n is the number and t{sub e} the temporal separation of spin echoes, and a is a composite diffusion parameter) in order to distinguish the influence of relaxation and diffusion in CPMG data. Here, we improve the analysis by introducing an automatic search for the optimum power k that best describes the diffusion behavior. This automated method is more efficient than the manual trial-and-error grid search adopted previously, and avoids variability through subjective judgments of experimentalists. Although our method does not avoid the inherent assumption that the diffusion exponent depends on a single k value, we show through simulation and experiment that it is robust in measurements of heterogeneous systems that violate this assumption. In this way, we obtain quantitative T{sub 2} distributions from complicated porous structures and demonstrate the analysis with examples of ceramics used for filtration and catalysis, and limestone of relevance to the construction and petroleum industries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1999

Remote Sensing of Urban Thermal Landscape Characteristics and Their Affects on Local and Regional Meteorology and Air Quality: An Overview of NASA EOS-IDS Project Atlanta

As an entity, the city is a manifestation of human "management" of the land. The act of city-building, however, drastically alters the biophysical environment, which ultimately, impacts local and regional land-atmosphere energy exchange processes. Because of the complexity of both the urban landscape and the attendant energy fluxes that result from urbanization, remote sensing offers the only real way to synoptically quantify these processes. One of the more important land-atmosphere fluxes that occurs over cities relates to the way that thermal energy is partitioned across the heterogeneous urban landscape. The individual land cover and surface material types that comprise the city, such as pavements and buildings, each have their own thermal energy regimes. As the collective urban landscape, the individual thermal energy responses from specific surfaces come together to form the urban heat island phenomena, which prevails as a dome of elevated air temperatures over cities. Although the urban heat island has been known to exist for well over 150 years, it is not understood how differences in thermal energy responses for land covers across the city interact to produce this phenomenon, or how the variability in thermal energy responses from different surface types drive its development. Additionally, it can be hypothesized that as cities grow in size through time, so do their urban heat islands. The interrelationships between urban sprawl and the respective growth of the urban heat island, however, have not been investigated. Moreover, little is known of the consequential effects of urban growth, land cover change, and the urban heat island as they impact local and regional meteorology and air quality.

Quattrochi, Dale A.↗
NASA NTRS2001

Retrieving LAI and FPAR from MERIS Data With Advanced Algorithms

The primary motivation of this research activity is to document the feasibility of deriving global fields of LAI (leaf area index) and FPAR (fraction of photosynthetically active radiation absorbed by vegetation) from atmosphere corrected ESA (European Space Agency) MERIS (Medium Resolution Imaging Spectrometer) data, validate and evaluate the MERIS LAI and FPAR products by intercomparison with MODIS (Moderate Resolution Imaging Spectrometer) LAI and FPAR products and with field data collected at the EOS Core sites distributed around the world. Our activities during Year 1 (January through December, 2001) have focused on the modification of the MODIS LAI/FPAR algorithm to facilitate its ability to process MERIS data. We considered a related but wider problem, i.e., fusion of biophysical parameters derived from data acquired by spectroradiometers of different spectral bands and different resolutions.

Myneni, Ranga B.↗
DOE OSTI2013

A line-source method for aligning on-board and other pinhole SPECT systems

Purpose: In order to achieve functional and molecular imaging as patients are in position for radiation therapy, a robotic multipinhole SPECT system is being developed. Alignment of the SPECT system—to the linear accelerator (LINAC) coordinate frame and to the coordinate frames of other on-board imaging systems such as cone-beam CT (CBCT)—is essential for target localization and image reconstruction. An alignment method that utilizes line sources and one pinhole projection is proposed and investigated to achieve this goal. Potentially, this method could also be applied to the calibration of the other pinhole SPECT systems.Methods: An alignment model consisting of multiple alignment parameters was developed which maps line sources in three-dimensional (3D) space to their two-dimensional (2D) projections on the SPECT detector. In a computer-simulation study, 3D coordinates of line-sources were defined in a reference room coordinate frame, such as the LINAC coordinate frame. Corresponding 2D line-source projections were generated by computer simulation that included SPECT blurring and noise effects. The Radon transform was utilized to detect angles (α) and offsets (ρ) of the line-source projections. Alignment parameters were then estimated by a nonlinear least squares method, based on the α and ρ values and the alignment model. Alignment performance was evaluated as a function of number of line sources, Radon transform accuracy, finite line-source width, intrinsic camera resolution, Poisson noise, and acquisition geometry. Experimental evaluations were performed using a physical line-source phantom and a pinhole-collimated gamma camera attached to a robot.Results: In computer-simulation studies, when there was no error in determining angles (α) and offsets (ρ) of the measured projections, six alignment parameters (three translational and three rotational) were estimated perfectly using three line sources. When angles (α) and offsets (ρ) were provided by the Radon transform, estimation accuracy was reduced. The estimation error was associated with rounding errors of Radon transform, finite line-source width, Poisson noise, number of line sources, intrinsic camera resolution, and detector acquisition geometry. Statistically, the estimation accuracy was significantly improved by using four line sources rather than three and by thinner line-source projections (obtained by better intrinsic detector resolution). With five line sources, median errors were 0.2 mm for the detector translations, 0.7 mm for the detector radius of rotation, and less than 0.5° for detector rotation, tilt, and twist. In experimental evaluations, average errors relative to a different, independent registration technique were about 1.8 mm for detector translations, 1.1 mm for the detector radius of rotation (ROR), 0.5° and 0.4° for detector rotation and tilt, respectively, and 1.2° for detector twist.Conclusions: Alignment parameters can be estimated using one pinhole projection of line sources. Alignment errors are largely associated with limited accuracy of the Radon transform in determining angles (α) and offsets (ρ) of the line-source projections. This alignment method may be important for multipinhole SPECT, where relative pinhole alignment may vary during rotation. For pinhole and multipinhole SPECT imaging on-board radiation therapy machines, the method could provide alignment of SPECT coordinates with those of CBCT and the LINAC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Simulating measurable ecosystem carbon and nitrogen dynamics with the mechanistically defined MEMS 2.0 model

Abstract. For decades, predominant soil biogeochemical models have used conceptual soil organic matter (SOM) pools and only simulated them to a shallow depth in soil. Efforts to overcome these limitations have prompted the development of the new generation SOM models, including MEMS 1.0, which represents measurable biophysical SOM fractions, over the entire root zone, and embodies recent understanding of the processes that govern SOM dynamics. Here we present the result of continued development of the MEMS model, version 2.0. MEMS 2.0 is a full ecosystem model with modules simulating plant growth with above- and belowground inputs, soil water and temperature by layer, decomposition of plant inputs and SOM, and mineralization and immobilization of nitrogen (N). The model simulates two commonly measured SOM pools – particulate and mineral-associated organic matter (POM and MAOM, respectively). We present results of calibration and validation of the model with several grassland sites in the US. MEMS 2.0 generally captured the soil carbon (C) stocks (R2 of 0.89 and 0.6 for calibration and validation, respectively) and their distributions between POM and MAOM throughout the entire soil profile. The simulated soil N matches measurements but with lower accuracy (R2 of 0.73 and 0.31 for calibration and validation of total N in SOM, respectively) than for soil C. Simulated soil water and temperature were compared with measurements, and the accuracy is comparable to the other commonly used models. The seasonal variation in gross primary production (GPP; R2 = 0.83), ecosystem respiration (ER; R2 = 0.89), net ecosystem exchange (NEE; R2 = 0.67), and evapotranspiration (ET; R2 = 0.71) was well captured by the model. We will further develop the model to represent forest and agricultural systems and improve it to incorporate new understanding of SOM decomposition.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1984

Fundamental Remote Sensing Science Research Program. Part 1: Scene Radiation and Atmospheric Effects Characterization Project

Brief articles summarizing the status of research in the scene radiation and atmospheric effect characterization (SRAEC) project are presented. Research conducted within the SRAEC program is focused on the development of empirical characterizations and mathematical process models which relate the electromagnetic energy reflected or emitted from a scene to the biophysical parameters of interest.

R E Murphy↗
NASA NTRS2007

Unofficial Road Building in the Amazon: Socioeconomic and Biophysical Explanations

Roads have manifold social and environmental impacts, including regional development, social conflicts and habitat fragmentation. 'Road ecology' has emerged as an approach to evaluate the various ecological and hydrological impacts of roads. This article aims to complement road ecology by examining the socio-spatial processes of road building itself. Focusing on the Brazilian Amazon, a heavily-studied context due to forest fragmentation by roads, the authors consider non-state social actors who build 'unofficial roads' for the purpose of gaining access to natural resources to support livelihoods and community development. They examine four case studies of roads with distinct histories in order to explain the socio-spatial processes behind road building in terms of profit maximization, land tenure claims, co-operative and conflictive political ecologies, and constraints as well as opportunities afforded by the biophysical environment. The study cases illustrate the need for a multi-pronged theoretical approach to understanding road building, and call for more attention to the role of non-state actors in unofficial road construction.

Perz, Stephen G.↗
DOE OSTI2014

Cytochrome c{sub 6B} of Synechococcus sp. WH 8102 – Crystal structure and basic properties of novel c{sub 6}-like family representative

Highlights: • Crystal structure of cytochrome c{sub 6B} from Synechococcus sp. WH 8102 was solved. • Basic biophysical properties of cytochrome c{sub 6B} were determined. • Cytochrome c{sub 6B} exhibits similar architecture to cytochrome c{sub 6}. • Organization of heme binding pocket of cytochrome c{sub 6B} differs from that of c{sub 6}. • Midpoint potential of cytochrome c{sub 6B} is significantly lower than of cytochrome c{sub 6}. - Abstract: Cytochromes c are soluble electron carriers of relatively low molecular weight, containing single heme moiety. In cyanobacteria cytochrome c{sub 6} participates in electron transfer from cytochrome b{sub 6}f complex to photosystem I. Recent phylogenetic analysis revealed the existence of a few families of proteins homologous to the previously mentioned. Cytochrome c{sub 6A} from Arabidopsis thaliana was identified as a protein responsible for disulfide bond formation in response to intracellular redox state changes and c{sub 550} is well known element of photosystem II. However, function of cytochromes marked as c{sub 6B}, c{sub 6C} and c{sub M} as well as the physiological process in which they take a part still remain unidentified. Here we present the first structural and biophysical analysis of cytochrome from the c{sub 6B} family from mesophilic cyanobacteria Synechococcus sp. WH 8102. Purified protein was crystallized and its structure was refined at 1.4 Å resolution. Overall architecture of this polypeptide resembles typical I-class cytochromes c. The main features, that distinguish described protein from cytochrome c{sub 6}, are slightly red-shifted α band of UV–Vis spectrum as well as relatively low midpoint potential (113.2 ± 2.2 mV). Although, physiological function of cytochrome c{sub 6B} has yet to be determined its properties probably exclude the participation of this protein in electron trafficking between b{sub 6}f complex and photosystem I.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Defect-driven anomalous transport in fast-ion conducting solid electrolytes

We report solid-state ionic conduction is a key enabler of electrochemical energy storage and conversion. The mechanistic connections between material processing, defect chemistry, transport dynamics, and practical performance are of considerable importance, but remain incomplete. Here, inspired by studies of fluids and biophysical systems, we re-examine anomalous diffusion in the iconic two-dimensional fast-ion conductors, the β- and β"-aluminas. Using large-scale simulations, we reproduce the frequency dependence of alternating-current ionic conductivity data. We show how the distribution of charge-compensating defects, modulated by processing, drives static and dynamic disorder, which lead to persistent sub-diffusive ion transport at macroscopic timescales. We deconvolute the effects of repulsions between mobile ions, the attraction between the mobile ions and charge-compensating defects, and geometric crowding on ionic conductivity. Our quantitative framework based on these model solid electrolytes connects their atomistic defect chemistry to macroscopic performance with minimal assumptions and enables mechanism-driven 'atoms-to-device' optimization of fast-ion conductors.

25 ENERGY STORAGE↗
DOE OSTI2024

Isopycnal Submesoscale Stirring Crucially Sustaining Subsurface Chlorophyll Maximum in Ocean Cyclonic Eddies

Abstract Mesoscale and submesoscale processes have crucial impacts on ocean biogeochemistry, importantly enhancing the primary production in nutrient‐deficient ocean regions. Yet, the intricate biophysical interplay still holds mysteries. Using targeted high‐resolution in situ observations in the South China Sea, we reveal that isopycnal submesoscale stirring serves as the primary driver of vertical nutrient transport to sustain the dome‐shaped subsurface chlorophyll maximum (SCM) within a long‐lived cyclonic mesoscale eddy. Density surface doming at the eddy core increased light exposure for phytoplankton production, while along‐isopycnal submesoscale stirring disrupted the mesoscale coherence and drove significant vertical exchange of tracers. These physical processes play a crucial role in maintaining the elevated phytoplankton biomass in the eddy core. Our findings shed light on the universal mechanism of how mesoscale and submesoscale coupling enhances primary production in ocean cyclonic eddies, highlighting the pivotal role of submesoscale stirring in structuring marine ecosystems.

Cao, Haijin↗
DOE OSTI2018

DIALS : implementation and evaluation of a new integration package

The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Quantifying Climate Change Effects of Bioenergy and BECCS: Critical Considerations and Guidance on Methodology

Bioenergy is a critical element in many national and international climate change mitigation efforts, including as a carbon dioxide removal strategy combined with the capture and durable geological storage of flue gas emissions (BECCS). However, divergent results on the effectiveness of bioenergy as a climate change mitigation measure are reported in the scientific literature. Climate impacts of bioenergy depend on case-specific factors, primarily biophysical features of the biomass production system, and the design and efficiency of conversion and capture processes. Estimates of climate impacts are also strongly affected by methodological choices and assumptions, and much of the divergence between studies derives from differences in the assumed alternate use of the land or feedstock, the alternate energy source and the system boundaries applied. We present a methodology to support robust estimates of the climate change effects of bioenergy systems, updating the standard methodology developed by the International Energy Agency's Technology Collaboration Program on Bioenergy. We provide guidance on the key choices including the reference land use and energy system that bioenergy is assumed to displace, spatial and temporal system boundaries, co-product handling, climate forcers considered, metrics applied and time horizon of impact assessment. Researchers should consider the whole bioenergy system including all life cycle stages, and choose system boundaries, reference systems and treatment of co-products that are consistent with the intended application of the results. The assessment should be normalised to a functional unit that can be compared with other systems delivering an equivalent quantity of the same function. All significant climate forcers should be included, and climate effects should be quantified using appropriate impact assessment methods that distinguish the impact of time. Consistency in methodology and interpretation will facilitate comparison between studies of different bioenergy systems.

09 BIOMASS FUELS↗
NASA NTRS2001

Root elongation against a constant force: experiment with a computerized feedback-controlled device

Axial force was applied to the root tip of corn (Zea mays L. cv. Merit) seedlings using a computerized, feedback-controlled mechanical device. The system's feedback capability allowed continuous control of a constant tip load, and the attached displacement transducer provided the time course of root elongation. Loads up to 7.5 g decreased the root elongation rate by 0.13 mm h-1 g-1, but loads 7.5 to 17.5 g decreased the growth rate by only 0.04 mm h-1 g-1. Loads higher than 18 g stopped root elongation completely. Measurement of the cross-sectional areas of the root tips indicated that the 18 g load had applied about 0.98 MPa of axial pressure to the root, thereby exceeding the root's ability to respond with increased turgor pressure. Recorded time-lapse images of loaded roots showed that radial thickening (swelling) occurred behind the root cap, whose cross-sectional area increased with tip load.

Non-NASA Center↗