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At least 91 records · Page 5

Scaling features of noncoding DNA

We review evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene, and utilize this fact to build a Coding Sequence Finder Algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. Finally, we describe briefly some recent work adapting to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function, and reporting that noncoding regions in eukaryotes display a larger redundancy than coding regions. Specifically, we consider the possibility that this result is solely a consequence of nucleotide concentration differences as first noted by Bonhoeffer and his collaborators. We find that cytosine-guanine (CG) concentration does have a strong "background" effect on redundancy. However, we find that for the purine-pyrimidine binary mapping rule, which is not affected by the difference in CG concentration, the Shannon redundancy for the set of analyzed sequences is larger for noncoding regions compared to coding regions.

Non-NASA Center

Information, entropy and fidelity in visual communication

This paper presents an assessment of visual communication that integrates the critical limiting factors of image gathering and display with the digital processing that is used to code and restore images. The approach focuses on two mathematical criteria, information and fidelity, and on their relationships to the entropy of the encoded data and to the visual quality of the restored image.

Huck, Friedrich O.

Efficiency of a model human image code

Hypothetical schemes for neural representation of visual information can be expressed as explicit image codes. Here, a code modeled on the simple cells of the primate striate cortex is explored. The Cortex transform maps a digital image into a set of subimages (layers) that are bandpass in spatial frequency and orientation. The layers are sampled so as to minimize the number of samples and still avoid aliasing. Samples are quantized in a manner that exploits the bandpass contrast-masking properties of human vision. The entropy of the samples is computed to provide a lower bound on the code size. Finally, the image is reconstructed from the code. Psychophysical methods are derived for comparing the original and reconstructed images to evaluate the sufficiency of the code. When each resolution is coded at the threshold for detection artifacts, the image-code size is about 1 bit/pixel.

Watson, Andrew B.

An Easy-to-implement Coding Scheme for Multifrequency PPM

In implementing multifrequency PPM, a naturally arising question is: Let P be a fixed number; among all integer valued processes X1, X2, X3, with E ( X(n+1)-X(n) squared) less than or = P, which has the largest entropy? Earlier work by McEliece and Rodemich answered this question, but there is no obvious way to use this process to implement a code for multifrequency PPM. The present article describes an easy-to-implement process X1, X2, with E ( X(n+1)-X(n) squared) less than or = P, whose entropy is nearly as great as that of the McEliece-Rodemich process.

Mceliece, R. J.

Block adaptive rate controlled image data compression

A block adaptive rate controlled (BARC) image data compression algorithm is described. It is noted that in the algorithm's principal rate controlled mode, image lines can be coded at selected rates by combining practical universal noiseless coding techniques with block adaptive adjustments in linear quantization. Compression of any source data at chosen rates of 3.0 bits/sample and above can be expected to yield visual image quality with imperceptible degradation. Exact reconstruction will be obtained if the one-dimensional difference entropy is below the selected compression rate. It is noted that the compressor can also be operated as a floating rate noiseless coder by simply not altering the input data quantization. Here, the universal noiseless coder ensures that the code rate is always close to the entropy. Application of BARC image data compression to the Galileo orbiter mission of Jupiter is considered.

Rice, R. F.

Necessary conditions for the optimality of variable rate residual vector quantizers

Residual vector quantization (RVQ), or multistage VQ, as it is also called, has recently been shown to be a competitive technique for data compression. The competitive performance of RVQ reported in results from the joint optimization of variable rate encoding and RVQ direct-sum code books. In this paper, necessary conditions for the optimality of variable rate RVQ's are derived, and an iterative descent algorithm based on a Lagrangian formulation is introduced for designing RVQ's having minimum average distortion subject to an entropy constraint. Simulation results for these entropy-constrained RVQ's (EC-RVQ's) are presented for memory less Gaussian, Laplacian, and uniform sources. A Gauss-Markov source is also considered. The performance is superior to that of entropy-constrained scalar quantizers (EC-SQ's) and practical entropy-constrained vector quantizers (EC-VQ's), and is competitive with that of some of the best source coding techniques that have appeared in the literature.

Kossentini, Faouzi

Visual communication - Information and fidelity

This assessment of visual communication deals with image gathering, coding, and restoration as a whole rather than as separate and independent tasks. The approach focuses on two mathematical criteria, information and fidelity, and on their relationships to the entropy of the encoded data and to the visual quality of the restored image. Past applications of these criteria to the assessment of image coding and restoration have been limited to the link that connects the output of the image-gathering device to the input of the image-display device. By contrast, the approach presented in this paper explicitly includes the critical limiting factors that constrain image gathering and display. This extension leads to an end-to-end assessment theory of visual communication that combines optical design with digital processing.

Huck, Freidrich O.

Application of unsteady aerodynamic methods for transonic aeroelastic analysis

Aerodynamic methods for aeroelastic analysis are applied to various flow problems. These methods include those that solve the three dimensional transonic small disturbance (TSD) potential equation, the two dimensional (2-D) full potential (FP) equation, and the 2-D thin layer Navier-Stokes equations. Flutter analysis performed using TSD aerodynamics show that such methods can be used to analyze some aeroelastic phenomena. For thicker bodies and larger amplitude motions, a nonisentropic FP method is presented. The unsteady FP equation is modified to model the entropy jumps across shock waves. The conservative form of the modified equation is solved in generalized coordinates using an implicit, approximate factorization method. Pressures calculated on the NLR 7301 and NACA 64A010A airfoils using the nonisentropic FP method are presented. It is shown that modeling shock generated entropy extends the range of validity of the FP method. A Navier-Stokes code is correlated with pressures measured on a supercritical airfoil at transonic speeds. When corrections are made for wind tunnel wall effects, the calculations correlate well with the measured data.

Whitlow, Woodrow, Jr.

Computational Aerothermodynamic Simulation Issues on Unstructured Grids

The synthesis of physical models for gas chemistry and turbulence from the structured grid codes LAURA and VULCAN into the unstructured grid code FUN3D is described. A directionally Symmetric, Total Variation Diminishing (STVD) algorithm and an entropy fix (eigenvalue limiter) keyed to local cell Reynolds number are introduced to improve solution quality for hypersonic aeroheating applications. A simple grid-adaptation procedure is incorporated within the flow solver. Simulations of flow over an ellipsoid (perfect gas, inviscid), Shuttle Orbiter (viscous, chemical nonequilibrium) and comparisons to the structured grid solvers LAURA (cylinder, Shuttle Orbiter) and VULCAN (flat plate) are presented to show current capabilities. The quality of heating in 3D stagnation regions is very sensitive to algorithm options in general, high aspect ratio tetrahedral elements complicate the simulation of high Reynolds number, viscous flow as compared to locally structured meshes aligned with the flow.

Gnoffo, Peter A.

Entropy Generation/Availability Energy Loss Analysis Inside MIT Gas Spring and "Two Space" Test Rigs

The results of the entropy generation and availability energy loss analysis under conditions of oscillating pressure and oscillating helium gas flow in two Massachusetts Institute of Technology (MIT) test rigs piston-cylinder and piston-cylinder-heat exchanger are presented. Two solution domains, the gas spring (single-space) in the piston-cylinder test rig and the gas spring + heat exchanger (two-space) in the piston-cylinder-heat exchanger test rig are of interest. Sage and CFD-ACE+ commercial numerical codes are used to obtain 1-D and 2-D computer models, respectively, of each of the two solution domains and to simulate the oscillating gas flow and heat transfer effects in these domains. Second law analysis is used to characterize the entropy generation and availability energy losses inside the two solution domains. Internal and external entropy generation and availability energy loss results predicted by Sage and CFD-ACE+ are compared. Thermodynamic loss analysis of simple systems such as the MIT test rigs are often useful to understand some important features of complex pattern forming processes in more complex systems like the Stirling engine. This study is aimed at improving numerical codes for the prediction of thermodynamic losses via the development of a loss post-processor. The incorporation of loss post-processors in Stirling engine numerical codes will facilitate Stirling engine performance optimization. Loss analysis using entropy-generation rates due to heat and fluid flow is a relatively new technique for assessing component performance. It offers a deep insight into the flow phenomena, allows a more exact calculation of losses than is possible with traditional means involving the application of loss correlations and provides an effective tool for improving component and overall system performance.

Ebiana, Asuquo B.

Thermodynamic and transport properties of gaseous tetrafluoromethane in chemical equilibrium

Equations and in computer code are presented for the thermodynamic and transport properties of gaseous, undissociated tetrafluoromethane (CF4) in chemical equilibrium. The computer code calculates the thermodynamic and transport properties of CF4 when given any two of five thermodynamic variables (entropy, temperature, volume, pressure, and enthalpy). Equilibrium thermodynamic and transport property data are tabulated and pressure-enthalpy diagrams are presented.

Hunt, J. L.

Accurate solutions, parameter studies and comparisons for the Euler and potential flow equations

Parameter studies are conducted using the Euler and potential flow equation models for unsteady and steady flows in both two and three dimensions. The Euler code is an implicit, upwind, finite volume code which uses the Van Leer method of flux-vector-splitting which has been recently extended for use on dynamic meshes and maintain all the properties of the original splitting. The potential flow code is an implicit, finite difference method for solving the transonic small disturbance equations and incorporates both entropy and vorticity corrections into the solution procedures thereby extending its applicability into regimes where shock strength normally precludes its use. Parameter studies resulting in benchmark type calculations include the effects of spatial and temporal refinement, spatial order of accuracy, far field boundary conditions for steady flow, frequency of oscillation, and the use of subiterations at each time step to reduce linearization and factorization errors. Comparisons between Euler and potential flows results are made as well as with experimental data where available.

Anderson, W. Kyle

Accurate solutions, parameter studies and comparisons for the Euler and potential flow equations

Parameter studies are conducted using the Euler and potential flow equation models for steady and unsteady flows in both two and three dimensions. The Euler code is an implicit, upwind, finite volume code which uses the Van Leer method of flux vector splitting which has been recently extended for use on dynamic meshes and maintain all the properties of the original splitting. The potential flow code is an implicit, finite difference method for solving the transonic small disturbance equations and incorporates both entropy and vorticity corrections into the solution procedures thereby extending its applicability into regimes where shock strength normally precludes its use. Parameter studies resulting in benchmark type calculations include the effects of spatial and temporal refinement, spatial order of accuracy, far field boundary conditions for steady flow, frequency of oscillation, and the use of subiterations at each time step to reduce linearization and factorization errors. Comparisons between Euler and potential flow results are made, as well as with experimental data where available.

Anderson, W. Kyle

Size and Structure of the Sequence Space of Repeat Proteins

The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family— the total number of sequences in that family—can be estimated using models of maximum entropy trained on multiple sequence alignments of naturally occurring amino acid sequences. We analyzed and calculated the size of three abundant repeat proteins families, whose members are large proteins made of many repetitions of conserved portions of *30 amino acids. While amino acid conservation at each position of the alignment explains most of the reduction of diversity relative to completely random sequences, we found that correlations between amino acid usage at different positions significantly impact that diversity. We quantified the impact of different types of correlations, functional and evolutionary, on sequence diversity. Analysis of the detailed structure of the coding space of the families revealed a rugged landscape, with many local energy minima of varying sizes with a hierarchical structure, reminiscent of frustrated energy landscapes of spin glass in physics. This clustered structure indicates a multiplicity of subtypes within each family and suggests new strategies for protein design.

Jacopo Marchi

A high-speed distortionless predictive image-compression scheme

A high-speed distortionless predictive image-compression scheme that is based on differential pulse code modulation output modeling combined with efficient source-code design is introduced. Experimental results show that this scheme achieves compression that is very close to the difference entropy of the source.

Cheung, K.-M.

Flight stagnation-point heating calculations on Aeroassist Flight Experiment vehicle

NASA's Aeroassist Flight Experiment (AFE) vehicle will be deployed from the Space Shuttle Orbiter in 1994 to make a data-gethering aeropass through the upper atmosphere before returning to orbit for Shuttle pickup. An axisymmetric, chemically-reacting viscous shock-layer code is presently used to calculate AFE heating rates which automatically accounts for the viscous-inviscid interaction and entropy layer-swallowing effects which are ignored by the conventional boundary-layer methods. Results are presented for the stagnation-point heating of the current AFE baseline trajectory.

Hamilton, H. H., II

Simplified curve fits for the thermodynamic properties of equilibrium air

New, improved curve fits for the thermodynamic properties of equilibrium air have been developed. The curve fits are for pressure, speed of sound, temperature, entropy, enthalpy, density, and internal energy. These curve fits can be readily incorporated into new or existing computational fluid dynamics codes if real gas effects are desired. The curve fits are constructed from Grabau-type transition functions to model the thermodynamic surfaces in a piecewise manner. The accuracies and continuity of these curve fits are substantially improved over those of previous curve fits. These improvements are due to the incorporation of a small number of additional terms in the approximating polynomials and careful choices of the transition functions. The ranges of validity of the new curve fits are temperatures up to 25 000 K and densities from 10 to the -7 to 10 to the 3d power amagats.

Srinivasan, S.

Approximate heating analysis for the windward-symmetry plane of Shuttle-like bodies at large angle of attack

An engineering method has been developed for computing the windward-symmetry plane convective heat-transfer rates on Shuttle-like vehicles at large angles of attack. The engineering code includes an approximate inviscid flowfield technique, laminar and turbulent heating-rate expressions, an approximation to account for the variable-entropy effects on the surface heating and the concept of an equivalent axisymmetric body to model the windward-ray flowfields of Shuttle-like vehicles at angles of attack from 25 to 45 degrees. The engineering method is validated by comparing computed heating results with corresponding experimental data measured on Shuttle and advanced transportation models over a wide range of flow conditions and angles of attack from 25 to 40 degrees and also with results of existing prediction techniques. The comparisons are in good agreement.

Zoby, E. V.