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At least 649 records · Page 36

A full-coordinate model of the polymerase domain of HIV-1 reverse transcriptase and its interaction with a nucleic acid substrate

We present a full-coordinate model of residues 1-319 of the polymerase domain of HIV-I reverse transcriptase. This model was constructed from the x-ray crystallographic structure of Jacobo-Molina et al. (Jacobo-Molina et al., P.N.A.S. USA 90, 6320-6324 (1993)) which is currently available to the degree of C-coordinates. The backbone and side-chain atoms were constructed using the MAXSPROUT suite of programs (L. Holm and C. Sander, J. Mol. Biol. 218, 183-194 (1991)) and refined through molecular modeling. A seven base pair A-form dsDNA was positioned in the nucleic acid binding cleft to represent the template-primer complex. The orientation of the template-primer complex in the nucleic acid binding cleft was guided by the positions of phosphorus atoms in the crystal structure.

Non-NASA Center↗

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↗

Meteorological Aspects of Two Modes of Lightning Triggered Upward Lightning (LTUL) Events in Sprite-Producing MCSs

During the 2013 convective storm season, a high resolution 3-D Lightning Mapping Array was deployed to north central Kansas (Cummins et al, this conference.) In conjunction with fixed and mobile camera systems and electric field mills, this allowed for detailed investigations of lightning induced upward lighting (LTUL) discharges from tall objects in the region, including wind turbines. Also, concurrent observations using a network of low-light cameras deployed over the central U.S. as part of the PhOCAL program detected transient luminous events (TLEs) above the Kansas LMA (KSLMA). During the night of 29-30 May 2013, waves of precipitation associated with several large MCSs traversing Kansas moved through the KSLMA domain. We focus on two LTUL events that exemplify two modes of upward lightning production from tall structures. At 0859Z, 30 May 2013, a nearby + 92 kA CG, with extensive in-cloud branching passing overhead a wind farm, was followed by complex LTUL discharges from four turbines. In addition, a sprite was confirmed by the Bennett, CO SpriteNet camera. The parent flash covered a very large area. It initiated near the MCS convective leading line ~150 km to the south, and traveled into a stratiform precipitation maximum over the KSLMA. Typically when a +CG precedes an LTUL, the triggering component is either 1) the return stroke that traverses the leader network which initially forms near the towers or 2) new negative leader activity that develops once the return stroke reaches the end of the initial leader network that may not have initially been near the tower. In the latter case, the new leader development passes near the towers and triggers upward positive leaders similar to those associated with only an intracloud flash. The +CG return stroke may hit >10 km from the towers and the new leader development may travel extensive distances before getting close enough to the towers to trigger upward lightning. In this case, there was the typical long delay between the +CG return stroke and LTUL initiation (10s to 100s of ms). The parent lightning discharges for both sprites and LTULs have many common aspects and tend to occur in similar meteorological regimes, with the two phenomena often occurring together. An earlier LUTL, at 2320Z, 29 May 2013 was captured at 9900 fps by a Phantom camera in the PhOCAL mobile Lightning Investigation Vehicle (LIV). This discharge, exhibiting numerous recoil leaders, also occurred in a stratiform region some ~50-100 km north of an MCS convective core. While there was no preceding +CG, there was an extensive network of IC channels, one of which passed overhead close to the turbine. These observations are consistent with the ongoing UPLIGHTS studies of LTULs from tall towers in Rapid City. While a +CG is usually involved (~85% of the time), the LTUL occurs because of the associated extensive in cloud components passing over towers. The earlier case without a +CG typifies this second mode where the triggering component is a negative leader associated with the IC activity passing near the towers initiates the upward positive leaders. We will discuss the parent discharges, shown in their meteorological (radar and satellite) context, and attempt to better understand the charge structures present in both the convective and stratiform regions of the MCS. The sprite and its relationship to the parent discharge will similarly be discussed

Lyons, W. A.↗

Polarized Resonant Soft X-ray Scattering (P-RSoXS) as a New Technique for Characterizing Amorphous Astromaterials

In the coming years, samples will be returned from several asteroids, the lunar surface, and the first material returned directly from the Martian surface. Previous in-situ and remote studies indicate these samples will contain abundant amorphous or weakly crystalline materials. However, detailed characterization and quantification of these amorphous materials remains challenging. Conventional techniques, including electron microscopy and X-ray diffraction, provide important information on material structure, but are generally limited to crystalline materials. Polarized resonant soft X-ray scattering (P-RSoXS) is a synchrotron-based X-ray scattering technique that has been used to characterize and quantify weakly crystalline systems, including soft materials. This research aims to translate this technique to geologic and extraterrestrial materials, building off the knowledge of using P-RSoXS to interrogate soft materials. P-RSoXS is well-suited to interrogate geologic materials, which are often multiphase, heterogeneous systems with crystalline and amorphous components, and domain sizes on the order of tens of nanometers. It is anticipated that future work will help reveal new chemical and structural information in geologic materials. Maturation of this preliminary work to develop P-RSoXS to characterize astromaterial-relevant samples will provide new understanding of the secondary processes responsible for the development of amorphous astromaterials and further elucidate our knowledge of the geologic history and past alteration processes.

Joshua H Litofsky↗

Experimental implementation of adaptive control for flexible space structures

On-going research at The Aerospace Corporation studying the feasibility of applying adaptive control methodologies to the control of flexible space structures is described. A laboratory testbed was established to test system identification and control approaches. The laboratory set-up and controller design approach are discussed. The ARX least squares parameter estimation technique is analyzed in terms of frequency domain transfer function bias error. This analysis approach enables the determination of the effects of sampling rate, sensor type, and data prefiltering on the estimation performance. The ability to identify space structure dynamics over a range of frequencies is shown to be heavily dependent on these factors.

Mcgraw, Gary A.↗

Ray propagation path analysis of acousto-ultrasonic signals in composites

The most important result was the demonstration that acousto-ultrasonic (AU) energy introduced into a laminated graphite/resin propagates by two modes through the structure. The first mode, along the graphite fibers, is the faster. The second mode, through the resin matrix, besides being slower is also more strongly attenuated at the higher frequencies. This demonstration was accomplished by analyzing the time and frequency domain of the composite AU signal and comparing them to the same for a neat resin specimen of the same chemistry and geometry as the composite matrix. Analysis of the fine structure of AU spectra was accomplished by various geometrical strategies. It was shown that the multitude of narrow peaks associated with AU spectra are the effect of the many pulse arrivals in the signal. The shape and distribution of the peaks is mainly determined by the condition of nonnormal reflections of ray paths. A cepstrum analysis was employed which can be useful in detecting characteristic times. Analysis of propagation modes can be accomplished while ignoring the fine structure.

Kautz, Harold E.↗

Optical fiber sensors and signal processing for intelligent structure monitoring

Few mode optical fibers have been shown to produce predictable interference patterns when placed under strain. The use is described of a modal domain sensor in a vibration control experiment. An optical fiber is bonded along the length of a flexible beam. Output from the modal domain sensor is used to suppress vibrations induced in the beam. A distributed effect model for the modal domain sensor is developed. This model is combined with the beam and actuator dynamics to produce a system suitable for control design. Computer simulations predict open and closed loop dynamic responses. An experimental apparatus is described and experimental results are presented.

Thomas, Daniel↗

Development of an integrated BEM approach for hot fluid structure interaction

A comprehensive boundary element method is presented for transient thermoelastic analysis of hot section Earth-to-Orbit engine components. This time-domain formulation requires discretization of only the surface of the component, and thus provides an attractive alternative to finite element analysis for this class of problems. In addition, steep thermal gradients, which often occur near the surface, can be captured more readily since with a boundary element approach there are no shape functions to constrain the solution in the direction normal to the surface. For example, the circular disc analysis indicates the high level of accuracy that can be obtained. In fact, on the basis of reduced modeling effort and improved accuracy, it appears that the present boundary element method should be the preferred approach for general problems of transient thermoelasticity.

Dargush, G. F.↗

Efficient Multidisciplinary Analysis Procedure Using Multi-Level Parallelization Approach

Multidisciplinary applications are suitable for parallel computing environment by adopting the domain decomposition method. Immediately, a multidisciplinary application can be parallelized by solving each discipline separately. In order to perform coupled multidisciplinary analysis, coupling of each discipline can be accomplished by exchanging boundary data at the interfaces. This is regarded as discipline-level parallelization. Next level could be a "coarse-grain" parallelization of each discipline, which mainly depends on the physical geometry and nature of each discipline. For example, it is almost impossible for structured-grid based computational fluid dynamics codes to do flow analysis of an aircraft by using a single grid because of the complexity of its configuration. Thus, multi-block grid is commonly used to describe the details of complex geometry. Similarly, in structural analysis, the structure is frequently subdivided into substructures. Thus, the computation of each subdomain can be easily parallelized since each subdomain is solved separately independent of other domains. The parallelization is accomplished by solving each subdomain separately on a separate processor and exchanging the boundary conditions at domain interfaces periodically. However, the physical decomposition of the domain introduces explicit boundary conditions at the domain interfaces. This is not desirable for critical areas such as those containing shock waves or flow separations. Thus, a "fine-grain" parallelization is introduced to overcome this problem. The "fine-grain" parallelization is one that solves exactly the same system of equations of a subdomain by using more than one processors without introducing any explicit boundary conditions. An efficient multidisciplinary analysis procedure can be accomplished by successfully combining the above multi-level parallelism. A multidisciplinary analysis code, ENSAERO developed at NASA Ames Research Center is used in this study to implement the proposed approach. The communication data structure required for the proposed approach will be studied in detail. This work will demonstrate the feasibility of using multi-level parallelization approach in multidisciplinary analysis applications.

Byun, Chansup↗

A flight simulator for advanced aircraft - Servo design to realization.

Discussion of computer-aided design results obtained for a moving-base, three-man flight simulator. From a control viewpoint, the structure is discussed in terms of disturbance torques, damping ratios, natural frequencies, load acceleration, and smoothness. The use of inertia to achieve well-behaved structural transfer functions and smooth or high fidelity load accelerations is demonstrated. Transfer functions in the complex frequency domain, as well as time-dependent solutions to the system, are derived. The relative merits of using position and/or velocity as primary feedback, for a limited travel acceleration device, are discussed. Root locus plots, which were utilized in the control-system design, Bode plots, and time-dependent plots are drawn. In addition, the theoretical ratio of velocity to commanded input Bode plot is compared to the experimental results, and the dramatic effect on the load smoothness plot caused by selecting velocity over position as primary feedback is shown.

King, R. F.↗

Nonlinear soil-structure interaction calculations simulating the SIMQUAKE experiment using STEALTH 2D

Transient, nonlinear soil-structure interaction simulations of an Electric Power Research Institute, SIMQUAKE experiment were performed using the large strain, time domain STEALTH 2D code and a cyclic, kinematically hardening cap soil model. Results from the STEALTH simulations were compared to identical simulations performed with the TRANAL code and indicate relatively good agreement between all the STEALTH and TRANAL calculations. The differences that are seen can probably be attributed to: (1) large (STEALTH) vs. small (TRANAL) strain formulation and/or (2) grid discretization differences.

Tang, H. T.↗

Grid generation for general three-dimensional configurations

A suitable grid system for complex three dimensional configurations such as wing/body/nacelle shape for the solution of nonlinear transonic flow problems was constructed. Two approaches were explored based on Thompson's body fitted coordinate concept. The most general approach was to divide the computational domain into multiple rectangular blocks where the configuration itself was also represented by a set of blocks whose structure follows the natural lines of the configuration. The block structured grid system was adaptable to complex configurations and gives good grid quality near physical corners. However, it introduced algorithm issues for the flow solution concerning the treatment of nonanalytic grid block boundaries and nonstandard grid cells. These issues were explored in relation to the grid generation. A more limited approach treats a wing/body configuration with only a single rectangular block in computational space. The issues involving nonstandard cells were avoided, but other limitations on grid resolution appear. Both a linear and a nonlinear system of grid generation equations were developed including methods of grid control.

Lee, K. D.↗

The use of frequency methods in rotorcraft system identification

A new approach to model structure determination is examined. Flight data from the Rotor Systems Research Aircraft (RSRA) are transformed into the frequency domain and truncated to provide band limiting. The stepwise regression technique is then used to identify a quasistatic state-space model from the transformed data. The data processing requirements for both time domain and frequency domain identification are discussed and the results of the two techniques are compared.

Duval, R. W.↗

A flexible grid embedding technique with application to the Euler equations

An automated grid embedding procedure for solution of flows about complex geometries is described. The physical domain is subdivided into regions that can accommodate easily generated grids. The grids are organized in a hierarchical structure, and communication among grids is accomplished by interpolation of the flow variables at mesh boundaries. Algorithms for locating embedded boundaries, special treatment of the embedded grids, and the data structures required for manipulating the solution data are described. The method is demonstrated by solution of the Euler equations for transonic flow about a supercritical airfoil and a flapped airfoil.

Benek, J. A.↗

Epoxy/Fluoroether Composites

Composite materials made from unfilled and glass-fiber-reinforced epoxy toughened by copolymerization with elastomeric prepolymers of perfluoroalkyl ether diacyl fluoride (EDAF). Improved properties due to hydrogen bonding between rubber phase and epoxy matrix, plus formation of rubberlike phase domains that molecularly interpenetrate with epoxy matrix. With optimum rubber content, particle size, and particle shape, entire molecular structure reinforced and toughened. Improved composites also show increased failure strength, stiffness, glass-transition temperature, and resistance to water.

Rosser, R. W.↗

Interactive grid generation for turbomachinery flow field simulations

The control point form of algebraic grid generation presented provides the means that are needed to generate well structured grids for turbomachinery flow simulations. It uses a sparse collection of control points distributed over the flow domain. The shape and position of coordinate curves can be adjusted from these control points while the grid conforms precisely to all boundaries. An interactive program called TURBO, which uses the control point form, is being developed. Basic features of the code are discussed and sample grids are presented. A finite volume LU implicit scheme is used to simulate flow in a turbine cascade on the grid generated by the program.

Choo, Yung K.↗

Object oriented studies into artificial space debris

A prototype simulation is being developed under contract to the Royal Aerospace Establishment (RAE), Farnborough, England, to assist in the discrimination of artificial space objects/debris. The methodology undertaken has been to link Object Oriented programming, intelligent knowledge based system (IKBS) techniques and advanced computer technology with numeric analysis to provide a graphical, symbolic simulation. The objective is to provide an additional layer of understanding on top of conventional classification methods. Use is being made of object and rule based knowledge representation, multiple reasoning, truth maintenance and uncertainty. Software tools being used include Knowledge Engineering Environment (KEE) and SymTactics for knowledge representation. Hooks are being developed within the SymTactics framework to incorporate mathematical models describing orbital motion and fragmentation. Penetration and structural analysis can also be incorporated. SymTactics is an Object Oriented discrete event simulation tool built as a domain specific extension to the KEE environment. The tool provides facilities for building, debugging and monitoring dynamic (military) simulations.

Adamson, J. M.↗

Interactive grid generation for turbomachinery flow field simulations

The control point form of algebraic grid generation presented provides the means that are needed to generate well structured grids of turbomachinery flow simulations. It uses a sparse collection of control points distributed over the flow domain. The shape and position of coordinate curves can be adjusted from these control points while the grid conforms precisely to all boundaries. An interactive program called TURBO, which uses the control point form, is being developed. Basic features of the code are discussed and sample grids are presented. A finite volume LU implicit scheme is used to simulate flow in a turbine cascade on the grid generated by the program.

Choo, Yung K.↗