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NASA NTRS2017

Small Ion Channel Linking Molecular Simulations and Electrophysiology

Ion channels are pore-forming protein assemblies that mediate the transport of small ions across cell membranes. Otherwise, membrane bilayers would be almost impermeable to ions incapable to traverse the low dielectric constant, hydrophobic membrane core. Ion channels are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses, cardiac functions, muscle contraction and apoptosis. On the other extreme of biological complexity, viral ion channels (viroporins) influence many stages of the virus infection cycle either through regulating virus replication, such as entry, assembly and release or modulating the electrochemical balance in the subcellular compartments of host cells. Ion channels were crucial components of protocells. Their emergence facilitated adaptation of nascent life to different environmental conditions. The earliest ion channels must have been much simpler than most of their modern ancestors. Viral channels are among only a few naturally occurring models to study the structure, function and evolution of primordial channels. Experimental studies of these properties are difficult and often unreliable. In principle, computational methods, and molecular dynamics (MD) simulations in particular, can aid in providing information about both the structure and the function of ion channels. However, MD suffers from its own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. It is, therefore, essential to determine the reliability of MD simulations. We propose to do so on the basis of two criteria. One is channel stability on time scales that extend for several microseconds or longer. The other is the ability to reproduce the measured ionic conductance as a function of applied voltage. If both the stability and the calculated ionic conductance are satisfactory it will greatly increase our confidence that the structure and the function of a channel are described sufficiently accurately. To our knowledge, long time scale stability (approx.10 micro-sec) and the correct electrophysiology have been shown so far for only one channel - the synthetic LS3 hexamer). In this presentation, this approach will be discussed in application to two viral channels - Vpu, encoded by the HIV-1 genome and p7 of hepatitis C.

Pohorille, Andrzej↗

NASA NTRS1983

Examining functional acceptance testing with structural coverage metrics

Functionally generated acceptance tests are examined using structural coverage metrics. A method of comparing acceptance tests and operational usage was generated. Acceptance tests are prepresentative of operational usage except for the mix of statement types. Structural coverage metrics may provide insight into software faults.

Ramsey, J.↗

NASA NTRS2009

Phase Fluctuations at Goldstone Derived from 1-Year Site Testing Interferometer Data

A two-element site test interferometer has been deployed at the NASA Deep Space Network (DSN) tracking complex in Goldstone, California, since May 2007. The interferometer system consists of two offset-fed 1.2 m parabolic reflectors which monitor atmospheric-induced amplitude and phase fluctuations on an unmodulated beacon signal (20.199 GHz) broadcast from a geostationary satellite (Anik F2). The geometry of the satellite and the ground-based infrastructure imposes a 48.5 elevation angle with a separation distance of 256 m along an east-west baseline. The interferometer has been recording phase fluctuation data, to date, for 1 yr with an overall system availability of 95 percent. In this paper, we provide the cumulative distribution functions (CDFs) for 1 year of recorded data, including phase rms, spatial structure function exponent, and surface meteorological measurements: surface wind speed, relative humidity, temperature, barometric pressure, and rain rate. Correlation between surface measurements, phase rms, and amplitude rms at different time scales are discussed. For 1 year, phase fluctuations at the DSN site in Goldstone, are better than 23 for 90 percent of the time (at 48.5 elevation). This data will be used to determine the suitability of the Goldstone site as a location for the Next Generation Deep Space Network.

Nessel, James A.↗

NASA NTRS2012

Is Water a Universal Solvent for Life?

There are strong reasons to believe that the laws, principles and constraints of physics and chemistry are universal. It is much less clear how this universality translates into our understanding of the origins of life. Conventionally, discussions of this topic focus on chemistry that must be sufficiently rich to seed life. Although this is clearly a prerequisite for the emergence of living systems, I propose to focus instead on self-organization of matter into functional structures capable of reproduction, evolution and responding to environmental changes. In biology, most essential functions are largely mediated by noncovalent interactions (interactions that do not involve making or breaking chemical bonds). Forming chemical bonds is only a small part of what living systems do. There are specific implications of this point of view for universality. I will concentrate on one of these implications. Strength of non-covalent interactions must be properly tuned. If they were too weak, the system would exhibit undesired, uncontrolled response to natural fluctuations of physical and chemical parameters. If they were too strong kinetics of biological processes would be slow and energetics costly. This balance, however, is not a natural property of complex chemical systems. Instead, it has to be achieved with the aid of an appropriate solvent for life. In particular, potential solvents for life must be characterized by a high dielectric constant to ensure solubility of polar species and sufficient flexibility of biological structures stabilized by electrostatic interactions. Among these solvents, water exhibits a remarkable trait that it also promotes solvophobic (hydrophobic) interactions between non-polar species, typically manifested by a tendency of these species to aggregate and minimize their contacts with the aqueous solvent. Hydrophobic interactions are responsible, at least in part, for many self-organization phenomena in biological systems, such as the formation of cellular boundary structures or protein folding. Strengths of electrostatic and hydrophobic interactions are similar and can be balanced over a wide range of temperatures, which considerably increases the repertoire of interactions that can be used to modulate biological functions. Some properties of water, e.g. its chemical activity against polymerization reactions, are considered as unfavorable to life. In actuality, this might be a favorable trait because life requires a balance between constructive and destructive processes. For example, molecules synthesized in response to specific conditions must be degraded once these conditions change. Otherwise regulation of biological processes would be virtually impossible. Water might not be the only liquid with favorable properties for supporting life. It has been proposed that formamide, which might be present elsewhere in the universe in sufficient quantities to warrant interest, could be a potential alternative to water for the origin of life. However, this will remain highly hypothetical until it is demonstrated in further studies on its physical, chemical and biological properties it is capable of mediating self-organization of matter and providing proper balance between different types of non-covalent interactions.

Pohorill, Andrew↗

NASA NTRS1993

Conceptual design of a device to measure hand swelling in a micro-gravity environment

In the design of pressurized suits for use by astronauts in space, proper fit is an important consideration. One particularly difficult aspect of the suit design is the design of the gloves. If the gloves of the suit do not fit properly, the grip strength of the astronaut can be decreased by as much as fifty percent. These gloves are designed using an iterative process and can cost over 1.5 million dollars. Glove design is further complicated by the way the body behaves in a micro-gravity environment. In a micro-gravity setting, fluid from the lower body tends to move into the upper body. Some of this fluid collects in the hands and causes the hands to swell. Therefore, a pair of gloves that fit well on earth may not fit well when they are used in space. The conceptual design process for a device which can measure the swelling that occurs in the hands in a micro-gravity environment is described. This process involves developing a specifications list and function structure for the device and generating solution variants for each of the sub functions. The solution variants are then filtered, with the variants that violate any of the specifications being discarded. After acceptable solution variants are obtained, they are combined to form design concepts. These design concepts are evaluated against a set of criteria and the design concepts are ranked in order of preference. Through this process, the two most plausible design concepts were an ultrasonic imaging technique and a laser mapping technique. Both of these methods create a three dimensional model of the hand, from which the amount of swelling can be determined. In order to determine which of the two solutions will actually work best, a further analysis will need to be performed.

Hysinger, Christopher L.↗

NASA NTRS1988

Enhanced image products by limb-correction and smoothing of VAS radiance measurements

Limb darkening and brightening affect the GOES satellite's VISSR Atmospheric Sounder instrument's imagery with varying satellite viewing angles and instrument noise; limb effects are also associated with a vertical shift of a wavelength's characteristic weighting function. The radiances in an image can be normalized to a reference zenith angle by limb-correcting the image. An additional undesirable effect is that of instrument noise, which varies as a function of channel characteristics and is greatest for channels sensitive to the upper atmosphere. The statistical structure function analysis method of Hillger et al. (1987) is used to obtain noise levels and optimal spatial averaging distances; the averaging domain size from the analysis is used to produce smoothed images, via a running average technique.

Jones, Andrew S.↗

NASA NTRS2003

Modelling protein functional domains in signal transduction using Maude

Modelling of protein-protein interactions in signal transduction is receiving increased attention in computational biology. This paper describes recent research in the application of Maude, a symbolic language founded on rewriting logic, to the modelling of functional domains within signalling proteins. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. In general, Maude models can simulate biological signalling networks and produce specific testable hypotheses at various levels of abstraction. Developing symbolic models of signalling proteins containing functional domains is important because of the potential to generate analyses of complex signalling networks based on structure-function relationships.

Signal Transduction↗

NASA NTRS2019

Effects of Topography on Tropical Forest Structure Depend on Climate Context

Topography affects abiotic conditions which can influence the structure, function, and dynamics of ecological communities. An increasing number of studies have demonstrated biological consequences of fine-scale topographic heterogeneity but we have a limited understanding of how We merged high-resolution (1 sq. meter) data on topography and canopy height derived from airborne lidar with ground-based data from 15 forest plots in Puerto Rico distributed along a precipitation gradient spanning ca. 800 to 3,500 mm yr(exp -1). Ground-based data included species composition, estimated above-ground biomass (AGB), and two key functional traits (wood density and leaf mass per area, LMA) that reflect resource-use strategies and a trade-off between hydraulic safety and hydraulic efficiency. We used hierarchical Bayesian models to evaluate how the interaction between topography climate is related to metrics of forest structure (i.e., canopy height and AGB), as well as taxonomic and functional alpha- and beta-diversity. Fine-scale topography (characterized with the topographic wetness index, TWI) significantly affected forest structure and the strength (and in some cases direction) of these effects varied across the precipitation gradient. In all plots, canopy height increased with topographic wetness but the effect was much stronger in dry compared to wet forest plots. In dry forest plots, topographically wetter microsites also had higher levels of AGB but in wet forest plots, topographically drier microsites had higher AGB. Fine-scale topography influenced functional composition but had only weak or non-significant effects on taxonomic and functional alpha- and beta-diversity. For instance, community-weighted wood density followed a similar pattern to AGB across plots. We also found a marginally significant association between variation of wood density and topographic heterogeneity that depended on climate context. Synthesis: The effects of fine-scale topographic heterogeneity on tropical forest structure and composition depend on the climate context. Our study demonstrates how a stronger integration of topographic heterogeneity across precipitation gradients could improve estimates of forest structure and biomass, and may provide insight to the ways that topography might mediate species responses to drought and climate change.

Tropical dry forest↗

NASA NTRS1976

Effects of random path fluctuations on the accuracy of laser ranging systems

Effects of turbulence-induced pathlength fluctuations on the accuracy of single-color laser ranging systems are examined. Correlation and structure functions for the path deviations are derived using several proposed models for the variation of the turbulence structure parameter with altitude. For single-color systems, random pathlength fluctuations can limit the accuracy of a range measurement to a few centimeters when the turbulence is strong and the effective propagation path is long (greater than 10 km). Two-color systems can partially correct for the random path fluctuations so that in most cases their accuracy is limited to a few millimeters. However, at low elevation angles for satellite ranging (less than 20 deg) and over long horizontal paths, two-color systems can also have errors approaching a few centimeters.

Gardner, C. S.↗

NASA NTRS1985

Autocorrelation of wind observations

Autocorrelation and variance statistics are calculated for cloud motion measurements from four different sources, rawinsonde wind reports, synoptic land station reports, ship reports, aircraft reports, automatic aircraft reports gathered during the Global Weather Experiment, and Seasat scatterometer winds from September 1978. The last of these data sources exhibited the highest autocorrelations and lowest standard deviations over short distances. Structure function plots of autocovariances against separation distance between observations indicated that Seasat was most sensitive to wind field structure by having low autovariance at short distances.

Wylie, D. P.↗

NASA NTRS1988

Spatial and temporal variability of VAS radiance measurements by structure and correlation analysis

The statistical structure function analysis presently applied to VISSR Atmospheric Sounder (VAS) measurements has been extended to include time, and yields structure plots in either two spatial dimensions or one spatial dimension and time that indicate three-dimensional measurement variability. The analyses that include time as a coordinate also yield an indication of the mean speed and direction of the analyzed data. Results for three-hourly VAS data indicate that sampling at a high, approximately 1-hour, frequency is required in order to correctly monitor VAS measurements' temporal variability in a way equivalent to high spatial resolution.

Hillger, Donald W.↗

NASA NTRS1983

Structural coverage of functional testing

A FORTRAN program was instrumened to produce structural coverage measures. The structural coverage profiles of functionally generated acceptance tests and operational usage are used to examine two areas in software engineering: the examination of faults and the applicability of reliability models.

Ramsey, J.↗

NASA NTRS1986

Biochemical changes in bone in a model of weightlessness

The amounts of nonmineralized and mineralized collagen in bone from control, immobilized, and immobilized reambulated monkeys were examined. In order to understand structure function relationships of bone collagen and the reponse of a variety of conditions on control of the three dimensional structure of the collagen fibril, the stereochemistry of the cross-linking reactions as well as the stereospecific packing of the collagen molecules were studied.

Mechanic, Gerald L.↗

NASA NTRS1990

Recognition and characterization of hierarchical interstellar structure. I - Correlation function

The problem of the quantitative description of multiscale structure in interstellar cloud complexes and gravitational collapse calculations is considered, emphasizing the recognition and characterization of hierarchical fragmentation structure. The response of the two-point correlation function to a variety of analytical models for density structure is discussed for simple clustering of pointlike clouds to more complex models involving clouds with a distribution of sizes and densities and hierarchical substructure. By expressing the density distribution as the superposition of individual clouds, it is shown that the correlation function generates two types of terms: those involving each cloud's density convolved with itself and those involving pairs of different clouds. Major distortion of the correlation function are introduced by the presence of any image features with size scales a significant fraction of the image size.

Houlahan, Padraig↗

NASA NTRS1980

Preliminary design of graphite composite wing panels for commercial transport aircraft

Subjectively assessed practical and producible graphite/epoxy designs were subjected to a multilevel screening procedure which considered structural functions, efficiency, manufacturing and producibility, costs, maintainability, and inspectability. As each progressive screening level was reviewed, more definitive information on the structural efficiency (weight), manufacturing, and inspection procedures was established to support the design selection. The configuration features that enhance producibility of the final selected design can be used as a generic base for application to other wing panel designs. The selected panel design showed a weight saving of 25 percent over a conventional aluminum design meeting the same design requirements. The estimated cost reduction in manufacturing was 20 percent, based on 200 aircraft and projected 1985 automated composites manufacturing capability. The panel design background information developed will be used in the follow-on tasks to ensure that future panel development represents practical and producible design approaches to graphite/epoxy wing surface panels.

Byers, B. A.↗

NASA NTRS2020

Robotic Specialization in Autonomous Robotic Structural Assembly

Robotic in-space assembly of large space structures is a long-term NASA goal to reduce launch costs and enable larger scale missions. Recently, researchers have proposed using discrete lattice building blocks and co-designed robots to build high-performance, scalable primary structure for various on-orbit and surface applications. These robots would locomote on the lattice and work in teams to build and reconfigure building-blocks into functional structure. However, the most reliable and efficient robotic system architecture, characterized by the number of different robotic 'species' and the allocation of functionality between species, is an open question. To address this problem, we decompose the robotic building-block assembly task into functional primitives and, in simulation, study the performance of the the variety of possible resulting architectures. For a set consisting of five process types (move self, move block, move friend, align bock, fasten block), we describe a method of feature space exploration and ranking based on energy and reliability cost functions. The solution space is enumerated, filtered for unique solutions, and evaluated against energy and reliability cost functions for various simulated build sizes. We find that a 2 species system, dividing the five mentioned process types between one unit cell transport robot and one fastening robot, results in the lowest energy cost system, at some cost to reliability. This system enables fastening functionality to occupy the build front while reducing the need for that functional mass to travel back and forth from a feed station. Because the details of a robot design affect the weighting and final allocation of functionality, a sensitivity analysis was conducted to evaluate the effect of changing mass allocations on architecture performance. Future systems with additional functionalities such as repair, inspection, and others may use this process to analyze and determine alternative robot architectures.

Bernus, Borbala↗

NASA NTRS2006

The Dryline on 22 May 2002 during IHOP_2002: Convective-Scale Measurements at the Profiling Site

A detailed analysis of the structure of a double dryline observed over the Oklahoma panhandle during the first International H2O Project (IHOP_2002) convective initiation (CI) mission on 22 May 2002 is presented. A unique and unprecedented set of high temporal and spatial resolution measurements of water vapor mixing ratio, wind, and boundary layer structure parameters were acquired using the National Aeronautics and Space Administration (NASA) scanning Raman lidar (SRL), the Goddard Lidar Observatory for Winds (GLOW), and the Holographic Airborne Rotating Lidar Instrument Experiment (HARLIE), respectively. These measurements are combined with the vertical velocity measurements derived from the National Center for Atmospheric Research (NCAR) Multiple Antenna Profiler Radar (MAPR) and radar structure function from the high-resolution University of Massachusetts frequency-modulated continuous-wave (FMCW) radar to reveal the evolution and structure of the late afternoon double-dryline boundary layer. The eastern dryline advanced and then retreated over the Homestead profiling site in the Oklahoma panhandle, providing conditions ripe for a detailed observation of the small-scale variability within the boundary layer and the dryline. In situ aircraft data, dropsonde and radiosonde data, along with NCAR S-band dual-polarization Doppler radar (S-Pol) measurements, are also used to provide the larger-scale picture of the double-dryline environment. Moisture and temperature jumps of about 3 g kg(sup -1) and 1 -2 K, respectively, were observed across the eastern radar fine line (dryline), more than the moisture jumps (1-2 g kg(sup -1)) observed across the western radar fine line (secondary dryline). Most updraft plumes observed were located on the moist side of the eastern dryline with vertical velocities exceeding 3 m s(sup -1) and variable horizontal widths of 2-5 km, although some were as wide as 7-8 km. These updrafts were up to 1.5 g kg(sup -1) moister than the surrounding environment. Although models suggested deep convection over the Oklahoma panhandle and several cloud lines were observed near the dryline, the dryline itself did not initiate any storms over the intensive observation region (IOR). Possible reasons for this lack of convection are discussed. Strong capping inversion and moisture detrainment between the lifting condensation level and the level of free convection related to an overriding drier air, together with the relatively small near-surface moisture values (less than 10 g kg(sup -1)), were detrimental to CI in this case.

Demoz, Belay↗

NASA NTRS1971

Analytical and experimental investigation of aircraft metal structures reinforced with filamentary composites. Phase 1: Concept development and feasibility

The analytical and experimental investigations are described in the first phase of a program to establish the feasibility of reinforcing metal aircraft structures with advanced filamentary composites. The interactions resulting from combining the two types of materials into single assemblies as well as their ability to function structurally were studied. The combinations studied were boron-epoxy reinforced aluminum, boron-epoxy reinforced titanium, and boron-polyimide reinforced titanium. The concepts used unidirectional composites as reinforcement in the primary loading direction and metal for carrying the transverse loads as well as its portion of the primary load. The program established that several realistic concepts could be fabricated, that these concepts could perform to a level that would result in significant weight savings, and that there are means for predicting their capability within a reasonable degree of accuracy. This program also encountered problems related to the application of polyimide systems that resulted in their relatively poor and variable performance.

Oken, S.↗