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At least 73 records · Page 4

Influence of the size and protonation state of acidic residue 85 on the absorption spectrum and photoreaction of the bacteriorhodopsin chromophore

The consequences of replacing Asp-85 with glutamate in bacteriorhodopsin, as expressed in Halobacterium sp. GRB, were investigated. Similarly to the in vitro mutated and in Escherichia coli expressed protein, the chromophore was found to exist as a mixture of blue (absorption maximum 615 nm) and red (532 nm) forms, depending on the pH. However, we found two widely separated pKa values (about 5.4 and 10.4 without added salt), arguing for two blue and two red forms in separate equilibria. Both blue and red forms of the protein are in the two-dimensional crystalline state. A single pKa, such as in the E. coli expressed protein, was observed only after solubilization with detergent. The photocycle of the blue forms was determined at pH 4.0 with 610 nm photoexcitation, and that of the red forms at pH 10.5 and with 520 nm photoexcitation, in the time-range of 100 ns to 1 s. The blue forms produced no M, but a K- and an L-like intermediate, whose spectra and kinetics resembled those of blue wild-type bacteriorhodopsin below pH 3. The red forms produced a K-like intermediate, as well as M and N. Only the red forms transported protons. Specific perturbation of the neighborhood of the Schiff base by the replacement of Asp-85 with glutamate was suggested by (1) the shift and splitting of the pKa for what is presumably the protonation of residue 85, (2) a 36 nm blue-shift in the absorption of the all-trans red chromophore and a 25 nm red-shift of the 13-cis N chromophore, as compared to wild-type bacteriorhodopsin and its N intermediate, and (3) significant acceleration of the deprotonation of the Schiff base at pH 7, but not of its reprotonation and the following steps in the photocycle.

Non-NASA Center↗

Nanoactuators Based on Electrostatic Forces on Dielectrics

Nanoactuators of a proposed type would exploit the forces exerted by electric fields on dielectric materials. As used here, "nanoactuators" includes motors, manipulators, and other active mechanisms that have dimensions of the order of nanometers and/or are designed to manipulate objects that have dimensions of the order of nanometers. The underlying physical principle can be described most simply in terms of the example of a square parallel-plate capacitor in which a square dielectric plate is inserted part way into the gap between the electrode plates (see Figure Typically, the force is small from our macroscopic human perspective. The above equation shows that the force depends on the ratio between the capacitor dimensions but does not depend on the size. In other words, the force remains the same if the capacitor and the dielectric slab are shrunk to nanometer dimensions. At the same time, the masses of all components are proportional to third power of their linear dimensions. Therefore the force-to-mass ratio (and, consequently, the acceleration that can be imparted to the dielectric slab) is much larger at the nanoscale than at the macroscopic scale. The proposed actuators would exploit this effect. The upper part of Figure 2 depicts a simple linear actuator based on a parallel- plate capacitor similar to Figure 1. In this case, the upper electrode plate would be split into two parts (A and B) and the dielectric slab would be slightly longer than plate A or B. The actuator would be operated in a cycle. During the first half cycle, plate B would be grounded to the lower plate and plate A would be charged to a potential, V, with respect to the lower plate, causing the dielectric slab to be pulled under plate A. During the second half cycle, plate A would be grounded and plate B would be charged to potential V, causing the dielectric slab to be pulled under plate B. The back-and-forth motion caused by alternation of the voltages on plates A and B could be used to drive a nanopump, for example. A rotary motor, shown in the middle part of Figure 2, could include a dielectric rotor sandwiched between a top and a bottom plate containing multiple electrodes arranged symmetrically in a circle. Voltages would be applied sequentially to electrode pairs 1 and 1a, then 2 and 2a, then 3 and 3a in order to attract the dielectric rotor to sequential positions between the electrode pairs.

Wang, Yu↗

Preconditioning for the Navier-Stokes equations with finite-rate chemistry

The preconditioning procedure for generalized finite-rate chemistry and the proper preconditioning for the one-dimensional Navier-Stokes equations are presented. Eigenvalue stiffness is resolved and convergence-rate acceleration is demonstrated over the entire Mach-number range from the incompressible to the hypersonic. Specific benefits are realized at low and transonic flow speeds. The extended preconditioning matrix accounts for thermal and chemical non-equilibrium and its implementation is explained for both explicit and implicit time marching. The effect of higher-order spatial accuracy and various flux splittings is investigated. Numerical analysis reveals the possible theoretical improvements from using proconditioning at all Mach numbers. Numerical results confirm the expectations from the numerical analysis. Representative test cases include flows with previously troublesome embedded high-condition-number regions.

Godfrey, Andrew G.↗

A fast upwind solver for the Euler equations on three-dimensional unstructured meshes

An upwind scheme is presented for solving the three-dimensional Euler equations on unstructured tetrahedral meshes. Spatial discretization is accomplished by a cell-centered finite-volume formulation using flux-difference splitting. Higher-order differences are formed by a novel cell reconstruction process which results in computational times per cell comparable to those of structured codes. The approach yields highly resolved solutions in regions of smooth flow while avoiding oscillations across shocks without explicit limiting. Solutions are advanced in time by a 3-stage Runge-Kutta time-stepping scheme with convergence accelerated to steady state by local time stepping and implicit residual smoothing. Solutions are presented for a range of configurations in the transonic speed regime to demonstrate code accuracy, speed, and robustness. The results include an assessment of grid sensitivity and convergence acceleration by mesh sequencing.

Frink, Neal T.↗

A Fast Upwind Solver for the Euler Equations on Three-Dimensional Unstructured Meshes

An upwind scheme is presented for solving the three-dimensional Euler equations on unstructured tetrahedral meshes. Spatial discretization is accomplished by a cell-centered finite-volume formulation using flux-difference splitting. Higher-order differences are formed by a novel cell reconstruction process which results in computational times per cell comparable to those of structured codes. The approach yields highly resolved solutions in regions of smooth flow while avoiding oscillations across shocks without explicit limiting. Solutions are advanced in time by a 3-stage Runge-Kutta time-stepping scheme with convergence accelerated to steady state by local time stepping and implicit residual smoothing. Solutions are presented for a range of configurations in the transonic speed regime to demonstrate code accuracy, speed, and robustness. The results include an assessment of grid sensitivity and convergence acceleration by mesh sequencing.

Frink, Neal T.↗

The Problem of the Propeller in Yaw with Special Reference to Airplane Stability

The quantity of air which the disk area described by propeller blades travels through, is accelerated rearward conformably to the momentum of the forces acting on the propeller. The accelerated air mass forms behind the propeller the so-called slipstream, in which among others, the mean velocity of advance is increased. If the propeller axis slopes toward the relative flight direction, the slipstream direction likewise changes, i.e., it sets up a downwash behind the propeller. It was shown how this deviation can be mathematically defined. With appreciable slope the momentum of the slipstream is partially split up in the surrounding air because of the circulation, and the downwash of the slipstream is diminished.

Misztal, Franz↗

Upwind scheme for solving the Euler equations on unstructured tetrahedral meshes

An upwind scheme is presented for solving the three-dimensional Euler equations on unstructured tetrahedral meshes. Spatial discretization is accomplished by a cell-centered finite-volume formulation using flux-difference splitting. Higher-order differences are formed by a multidimensional linear reconstruction process. The solution gradients required for the higher-order differenes are computed by a novel approach that yields highly resolved solutions in regions of smooth flow while avoiding oscillations across shocks without explicitly applying a limiter. Solutions are advanced in time by a three-stage Runge-Kutta time-stepping scheme with convergence accelerated to steady state by local time stepping and implicit residual smoothing. Transonic solutions are presented for two meshes around the ONERA M6 wing and demonstrate substantial accuracy and insensitivity to mesh size.

Frink, Neal T.↗

Physics of the Cosmos: Program Annual Technology Report

From ancient times, humans have looked up at the night sky and wondered: Are we alone? How did the universe come to be? How does the universe work? PCOS focuses on that last question. Scientists investigating this broad theme use the universe itself as their laboratory, investigating its fundamental laws and properties. They test Einstein's General Theory of Relativity to see if our current understanding of space-time is borne out by observations. They examine the behavior of the most extreme environments - supermassive black holes, active galactic nuclei, and others - and the farthest reaches of the universe, to expand our understanding. With instruments sensitive across the spectrum, from radio, through infrared (IR), visible light, ultraviolet (UV), to X rays and gamma rays, as well as gravitational waves (GWs), they peer across billions of light-years, observing echoes of events that occurred instants after the Big Bang. The Laser Interferometer Gravitational-Wave Observatory (LIGO) recently recorded the first direct measurement of long-theorized GWs. Another surprising recent discovery is that the universe is expanding at an ever-accelerating rate, the first hint of so-called "dark energy," estimated to account for 75% of mass-energy in the universe. Dark matter, so called because we can only observe its effects on regular matter, accounts for another 20%, leaving only 5% for regular matter and energy. Scientists now also search for special polarization in the cosmic microwave background to support the notion that in the split-second after the Big Bang, the universe inflated faster than the speed of light! The most exciting aspect of this grand enterprise today is that we can finally develop the tools needed for such discoveries.

COR↗

Parabolized reduced Navier-Stokes computational techniques

A review is presented of methods in which composite or reduced Navier-Stokes (RNS) equations are treated with a pressure-gradient-based flux-vector splitting. The methods are similar to large Re asymptotic formulations, and streamwise diffusion terms are ignored in favor of an explicit deferred corrector based on higher-order diffusion terms. The methods can be used for 2D and 3D supersonic flows in which the effects of real gas are incorporated. Several examples of the procedure are given, and subsonic and supersonic flows are handled well with relaxation procedures that incorporate multigrid acceleration. Effective solutions are described for problems ranging from incompressible flows and supersonic flows to sharp shocks and reverse-flow capturing.

Rubin, Stanley G.↗

Program Annual Technology Report: Physics of the Cosmos Program Office

From ancient times, humans have looked up at the night sky and wondered: Are we alone? How did the universe come to be? How does the universe work? PCOS focuses on that last question. Scientists investigating this broad theme use the universe as their laboratory, investigating its fundamental laws and properties. They test Einstein’s General Theory of Relativity to see if our current understanding of space-time is borne out by observations. They examine the behavior of the most extreme environments – supermassive black holes, active galactic nuclei, and others – and the farthest reaches of the universe, to expand our understanding. With instruments sensitive across the spectrum, from radio, through infrared (IR), visible light, ultraviolet (UV), to X rays and gamma rays, as well as gravitational waves (GWs), they peer across billions of light-years, observing echoes of events that occurred instants after the Big Bang. Last year, the LISA Pathfinder (LPF) mission exceeded expectations in proving the maturity of technologies needed for the Laser Interferometer Space Antenna (LISA) mission, and the Laser Interferometer Gravitational-Wave Observatory (LIGO) recorded the first direct measurements of long-theorized GWs. Another surprising recent discovery is that the universe is expanding at an ever-accelerating rate, the first hint of so-called “dark energy,” estimated to account for 75% of mass-energy in the universe. Dark matter, so called because we can only observe its effects on regular matter, is thought to account for another20%, leaving only 5% for regular matter and energy. Scientists now also search for special polarization in the cosmic microwave background to support the notion that in the split-second after the Big Bang, the universe inflated faster than the speed of light! The most exciting aspect of this grand enterprise today is the extraordinary rate at which we can harness technologies to enable these key discoveries.

COR↗

A Fast Implementation of the ISOCLUS Algorithm

Unsupervised clustering is a fundamental tool in numerous image processing and remote sensing applications. For example, unsupervised clustering is often used to obtain vegetation maps of an area of interest. This approach is useful when reliable training data are either scarce or expensive, and when relatively little a priori information about the data is available. Unsupervised clustering methods play a significant role in the pursuit of unsupervised classification. One of the most popular and widely used clustering schemes for remote sensing applications is the ISOCLUS algorithm, which is based on the ISODATA method. The algorithm is given a set of n data points (or samples) in d-dimensional space, an integer k indicating the initial number of clusters, and a number of additional parameters. The general goal is to compute a set of cluster centers in d-space. Although there is no specific optimization criterion, the algorithm is similar in spirit to the well known k-means clustering method in which the objective is to minimize the average squared distance of each point to its nearest center, called the average distortion. One significant feature of ISOCLUS over k-means is that clusters may be merged or split, and so the final number of clusters may be different from the number k supplied as part of the input. This algorithm will be described in later in this paper. The ISOCLUS algorithm can run very slowly, particularly on large data sets. Given its wide use in remote sensing, its efficient computation is an important goal. We have developed a fast implementation of the ISOCLUS algorithm. Our improvement is based on a recent acceleration to the k-means algorithm, the filtering algorithm, by Kanungo et al.. They showed that, by storing the data in a kd-tree, it was possible to significantly reduce the running time of k-means. We have adapted this method for the ISOCLUS algorithm. For technical reasons, which are explained later, it is necessary to make a minor modification to the ISOCLUS specification. We provide empirical evidence, on both synthetic and Landsat image data sets, that our algorithm's performance is essentially the same as that of ISOCLUS, but with significantly lower running times. We show that our algorithm runs from 3 to 30 times faster than a straightforward implementation of ISOCLUS. Our adaptation of the filtering algorithm involves the efficient computation of a number of cluster statistics that are needed for ISOCLUS, but not for k-means.

Memarsadeghi, Nargess↗

URANS Application with CFL3D

This case was run using CFL3D, a multi-zone Reynolds-averaged Navier-Stokes code developed at NASA Langley [1]. It solves the thin-layer form of the Navier-Stokes equations in each of the (selected) coordinate directions. It can use 1-to-1, patched, or overset grids, and employs local time step scaling, grid sequencing, and multigrid to accelerate convergence to steady state. In time-accurate mode, CFL3D has the option to employ dual-time stepping with subiterations and multigrid, and it achieves second order temporal accuracy. CFL3D is a finite volume method. It uses third-order upwind-biased spatial differencing on the convective and pressure terms, and second-order differencing on the viscous terms; it is globally second-order spatially accurate. The flux difference-splitting (FDS) method of Roe is employed to obtain fluxes at the cell faces. It is advanced in time with an implicit three-factor approximate factorization method.

Rumsey, C. L.↗

RANS and URANS Application with CFL3D

This case was run using CFL3D, a multi-zone Reynolds-averaged Navier-Stokes code developed at NASA Langley [1]. It solves the thin-layer form of the Navier-Stokes equations in each of the (selected) coordinate directions. It can use 1-to-1, patched, or overset grids, and employs local time step scaling, grid sequencing, and multigrid to accelerate convergence to steady state. In time-accurate mode, CFL3D has the option to employ dual-time stepping with subiterations and multigrid, and it achieves second order temporal accuracy. CFL3D is a finite volume method. It uses third-order upwind-biased spatial differencing on the convective and pressure terms, and second-order differencing on the viscous terms; it is globally second-order spatially accurate. The flux difference-splitting (FDS) method of Roe is employed to obtain fluxes at the cell faces. It is advanced in time with an implicit three-factor approximate factorization method.

Rumsey, C. L.↗

A Pseubo-Temporal Multi-Grid Relaxation Scheme for Solving the Parabolized Navier-Stokes Equations

A multi-grid, flux-difference-split, finite-volume code, VULCAN, is presented for solving the elliptic and parabolized form of the equations governing three-dimensional, turbulent, calorically perfect and non-equilibrium chemically reacting flows. The space marching algorithms developed to improve convergence rate and or reduce computational cost are emphasized. The algorithms presented are extensions to the class of implicit pseudo-time iterative, upwind space-marching schemes. A full approximate storage, full multi-grid scheme is also described which is used to accelerate the convergence of a Gauss-Seidel relaxation method. The multi-grid algorithm is shown to significantly improve convergence on high aspect ratio grids.

Morrison, J. H.↗

A Pseudo-Temporal Multi-Grid Relaxation Scheme for Solving the Parabolized Navier-Stokes Equations

A multi-grid, flux-difference-split, finite-volume code, VULCAN, is presented for solving the elliptic and parabolized form of the equations governing three-dimensional, turbulent, calorically perfect and non-equilibrium chemically reacting flows. The space marching algorithms developed to improve convergence rate and or reduce computational cost are emphasized. The algorithms presented are extensions to the class of implicit pseudo-time iterative, upwind space-marching schemes. A full approximate storage, full multi-grid scheme is also described which is used to accelerate the convergence of a Gauss-Seidel relaxation method. The multi-grid algorithm is shown to significantly improve convergence on high aspect ratio grids.

White, J. A.↗

RNS Applications for Interacting Sub- and Supersonic Flows

A solution based grid adaptation method that combines elements of the multigrid method for solution acceleration and the domain decomposition philosophy for grid optimization is described. Unlike other solution based adaptive gridding schemes, wherein the overhead of recomputing the grid and re-evaluating the solution on the adapted grid leads to higher computational costs compared to a non-adapted calculation, the present methodology reduces the computational time required to obtain the solution. The computational effort involved in the present calculation is significantly lower than a non-adapted calculation that utilizes the multigrid method purely as a convergence acceleration tool. In addition to convergence acceleration, the multigrid framework provides a mechanism of information transfer from regions wherein grid refinement is specified to unrefined coarse grid regions. The basis for domain decomposition in the current procedure is the variation in grid refinement requirements for each coordinate direction in different portions of the flow field. The method is demonstrated herein on an efficient set of governing equations termed the reduced Navier Stokes equations, applied in conjunction with a set of physical boundary conditions. The governing equations are discretized through a pressure based flux splitting procedure that is uniformly applicable from incompressible to supersonic Mach numbers.

Rubin, Stanley G.↗

The physics of comets

This volume of the 'Fundamentals of Cosmic Physics' is concerned with the physics of comets. Aspects regarding the nucleus are discussed, taking into account observations, radius and albedo, mass, rotation, splitting and disruption, the temperature and sublimation of the cometary nucleus, the chemical composition, the electrostatic charging of the cometary nucleus, and the structure and evolution of the cometary nucleus. Other topics explored are related to the atmosphere and its interaction with the solar wind, the plasma tail, and the dust tail. Attention is given to excitation mechanisms, atmospheric abundances and production rates, chemical models of the inner coma, collisional processes and the multifluid approach, radiative transfer, the ionization processes, models of the inner layer, the outer coma, acceleration mechanisms in the plasma tail, the structure of the plasma tail, the cometary magnetosphere, dust grain orbits, gas-dust interaction in the inner coma, and the nature of the cometary dust.

Mendis, D. A.↗

Three-Dimensional Navier-Stokes Method with Two-Equation Turbulence Models for Efficient Numerical Simulation of Hypersonic Flows

A new computational efficient 3-D compressible Reynolds-averaged implicit Navier-Stokes method with advanced two equation turbulence models for high speed flows is presented. All convective terms are modeled using an entropy satisfying higher-order Total Variation Diminishing (TVD) scheme based on implicit upwind flux-difference split approximations and arithmetic averaging procedure of primitive variables. This method combines the best features of data management and computational efficiency of space marching procedures with the generality and stability of time dependent Navier-Stokes procedures to solve flows with mixed supersonic and subsonic zones, including streamwise separated flows. Its robust stability derives from a combination of conservative implicit upwind flux-difference splitting with Roe's property U to provide accurate shock capturing capability that non-conservative schemes do not guarantee, alternating symmetric Gauss-Seidel 'method of planes' relaxation procedure coupled with a three-dimensional two-factor diagonal-dominant approximate factorization scheme, TVD flux limiters of higher-order flux differences satisfying realizability, and well-posed characteristic-based implicit boundary-point a'pproximations consistent with the local characteristics domain of dependence. The efficiency of the method is highly increased with Newton Raphson acceleration which allows convergence in essentially one forward sweep for supersonic flows. The method is verified by comparing with experiment and other Navier-Stokes methods. Here, results of adiabatic and cooled flat plate flows, compression corner flow, and 3-D hypersonic shock-wave/turbulent boundary layer interaction flows are presented. The robust 3-D method achieves a better computational efficiency of at least one order of magnitude over the CNS Navier-Stokes code. It provides cost-effective aerodynamic predictions in agreement with experiment, and the capability of predicting complex flow structures in complex geometries with good accuracy.

Bardina, J. E.↗