bluuebunny/crossref_metadata_2025 huggingface dataset:
Fast probabilistic analysis of sequence function using scoring
matrices
Authors: Wu Thomas D. , Nevill-Manning Craig G. , Brutlag Douglas L.
Published: July 2002

*To whom correspondence should be addressed.

3Present address: Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. E-mail: twu@gene.com.

Motivation: We present techniques for increasing the speed of sequence analysis using scoring matrices. Our techniques are based on calculating, for a given scoring matrix, the quantile function, which assigns a probability, or p, value to each segmental score. Our techniques also permit the user to specify a p threshold to indicate the desired trade-off between sensitivity and speed for a particular sequence analysis. The resulting increase in speed should allow scoring matrices to be used more widely in large-scale sequencing and annotation projects.

Results: We develop three techniques for increasing the speed of sequence analysis: probability filtering, lookahead scoring, and permuted lookahead scoring. In probability filtering, we compute the score threshold that corresponds to the user-specified p threshold. We use the score threshold to limit the number of segments that are retained in the search process. In lookahead scoring, we test intermediate scores to determine whether they will possibly exceed the score threshold. In permuted lookahead scoring, we score each segment in a particular order designed to maximize the likelihood of early termination. Our two lookahead scoring techniques reduce substantially the number of residues that must be examined. The fraction of residues examined ranges from 62 to 6%, depending on the p threshold chosen by the user. These techniques permit sequence analysis with scoring matrices at speeds that are several times faster than existing programs. On a database of 12 177 alignment blocks, our techniques permit sequence analysis at a speed of 225 residues/s for a p threshold of 10−6, and 541 residues/s for a p threshold of 10−20.

In order to compute the quantile function, we may use either an independence assumption or a Markov assumption. We measure the effect of first- and second-order Markov assumptions and find that they tend to raise the p value of segments, when compared with the independence assumption, by average ratios of 1.30 and 1.69, respectively. We also compare our technique with the empirical 99.5th percentile scores compiled in the BLOCKSPLUS database, and find that they correspond on average to a p value of 1.5 × 10−5.

Availability: The techniques described above are implemented in a software package called EMATRIX. This package is available from the authors for free academic use or for licensed commercial use. The EMATRIX set of programs is also available on the Internet at http://motif.stanford.edu/ematrix.
Binary analysis and optimization-based normalization of gene
expression data
Authors: Shmulevich Ilya , Zhang Wei
Published: July 2002

Motivation: Most approaches to gene expression analysis use real-valued expression data, produced by high-throughput screening technologies, such as microarrays. Often, some measure of similarity must be computed in order to extract meaningful information from the observed data. The choice of this similarity measure frequently has a profound effect on the results of the analysis, yet no standards exist to guide the researcher.

Results: To address this issue, we propose to analyse gene expression data entirely in the binary domain. The natural measure of similarity becomes the Hamming distance and reflects the notion of similarity used by biologists. We also develop a novel data-dependent optimization-based method, based on Genetic Algorithms (GAs), for normalizing gene expression data. This is a necessary step before quantizing gene expression data into the binary domain and generally, for comparing data between different arrays. We then present an algorithm for binarizing gene expression data and illustrate the use of the above methods on two different sets of data. Using Multidimensional Scaling, we show that a reasonable degree of separation between different tumor types in each data set can be achieved by working solely in the binary domain. The binary approach offers several advantages, such as noise resilience and computational efficiency, making it a viable approach to extracting meaningful biological information from gene expression data.

Contact: is@ieee.org
Freezer anthropology: new uses for old blood
Authors: Merriwether D. Andrew
Published: July 2002

Archived blood fractions (plasma, settled red cells, white cells) have proved to be a rich and valuable source of DNA for human genetic studies. Large numbers of such samples were collected between 1960 and the present for protein and blood group studies, many of which are languishing in freezers or have already been discarded. More are discarded each year because the usefulness of these samples is not widely understood. Data from DNA derived from 10–35–year–old blood samples have been used to address the peopling of the New World and of the Pacific. Mitochondrial DNA haplotypes from studies using this source DNA support a single wave of migration into the New World (or a single source population for the New World) and that Mongolia was the likely source of the founding population. Data from Melanesia have shown that Polynesians are recent immigrants into the Pacific and did not arise from Melanesia.
Theoretical biology in the third millennium
Authors: Brenner Sydney
Published: July 2002

During the 20th century our understanding of genetics and the processes of gene expression have undergone revolutionary change. Improved technology has identified the components of the living cell, and knowledge of the genetic code allows us to visualize the pathway from genotype to phenotype. We can now sequence entire genes, and improved cloning techniques enable us to transfer genes between organisms, giving a better understanding of their function. Due to the improved power of analytical tools databases of sequence information are growing at an exponential rate. Soon complete sequences of genomes and the three–dimensional structure of all proteins may be known. The question we face in the new millennium is how to apply this data in a meaningful way. Since the genes carry the specification of an organism, and because they also record evolutionary changes, we need to design a theoretical framework that can take account of the flow of information through biological systems.
Fibrillin: from microfibril assembly to biomechanical function
Authors: Kielty C. M. , Baldock C. , Lee D. , Rock M. J. , Ashworth J. L. , Shuttleworth C. A.
Published: July 2002

Fibrillins form the structural framework of a unique and essential class of extracellular microfibrils that endow dynamic connective tissues with long–range elasticity. Their biological importance is emphasized by the linkage of fibrillin mutations to Marfan syndrome and related connective tissue disorders, which are associated with severe cardiovascular, ocular and skeletal defects. These microfibrils have a complex ultrastructure and it has proved a major challenge both to define their structural organization and to relate it to their biological function. However, new approaches have at last begun to reveal important insights into their molecular assembly, structural organization and biomechanical properties. This paper describes the current understanding of the molecular assembly of fibrillin molecules, the alignment of fibrillin molecules within microfibrils and the unique elastomeric properties of microfibrils.
The N‐terminal portion of mature aldehyde dehydrogenase affects protein folding and assembly
Authors: Zhou Jianzhong , Weiner Henry
Published: July 2002

Human liver cytosolic (ALDH1) and mitochondrial (ALDH2) aldehyde dehydrogenases are both encoded in the nucleus and synthesized in the cytosol. ALDH1 must fold in the cytosol, but ALDH2 is first synthesized as a precursor and must remain unfolded during import into mitochondria. The two mature forms share high identity (68%) at the protein sequence level except for the first 21 residues (14%); their tertiary structures were found to be essentially identical. ALDH1 folded faster in vitro than ALDH2 and could assemble to tetramers while ALDH2 remained as monomers. Import assay was used as a tool to study the folding status of ALDH1 and ALDH2. pALDH1 was made by fusing the presequence of precursor ALDH2 to the N‐terminal end of ALDH1. Its import was reduced about 10‐fold compared to the precursor ALDH2. The exchange of the N‐terminal 21 residues from the mature portion altered import, folding, and assembly of precursor ALDH1 and precursor ALDH2. More of chimeric ALDH1 precursor was imported into mitochondria compared to its parent precursor ALDH1. The import of chimeric ALDH2 precursor, the counterpart of chimeric ALDH1 precursor, was reduced compared to its parent precursor ALDH2. Mature ALDH1 proved to be more stable against urea denaturation than ALDH2. Urea unfolding improved the import of precursor ALDH1 and the chimeric precursors but not precursor ALDH2, consistent with ALDH1 and the chimeric ALDHs being more stable than ALDH2. The N‐terminal segment of the mature protein, and not the presequence, makes a major contribution to the folding, assembly, and stability of the precursor and may play a role in folding and hence the translocation of the precursor into mitochondria.
Reversible formation of on‐pathway macroscopic aggregates during the folding of maltose binding protein
Authors: Ganesh C. , Zaidi Faisal. N. , Udgaonkar Jayant. B. , Varadarajan Raghavan
Published: July 2002

Maltose binding protein (MBP) is widely used as a model for protein folding and export studies. We show here that macroscopic aggregates form transiently during the refolding of MBP at micromolar protein concentrations. Disaggregation occurs spontaneously without any aid, and the refolded material has structure and activity identical to those of the native, nondenatured protein. A considerable fraction of protein undergoing folding partitions into the aggregate phase and can be manually separated from the soluble phase by centrifugation. The separated MBP precipitate can be resolubilized and yields active, refolded protein. This demonstrates that both the soluble and aggregate phases contribute to the final yield of refolded protein. SecB, the cognate Escherichia coli cytosolic chaperone in vivo for MBP, reduces but does not entirely prevent aggregation, whereas GroEL and a variety of other control proteins have no effect. Kinetic studies using a variety of spectroscopic probes show that aggregation occurs through a collapsed intermediate with some secondary structure. The aggregate formed during refolding can convert directly to a near native state without going through the unfolded state. Further, optical and electron microscopic studies indicate that the MBP precipitate is not an amyloid.
The physics of sliding cylinders and curling rocks
Authors: Penner A. Raymond
Published: July 2002

The lateral deflection of a rotating cylindrical shell sliding on one of its ends is considered and both theoretical and experimental results are presented. The coefficient of kinetic friction between a curling rock and an ice surface is then derived and compared with experiment. Current models of the motion of a curling rock are discussed and an alternate hypothesis is presented.
Short solution of the radioactive decay chain equations
Authors: Pressyanov Dobromir S.
Published: July 2002

In most textbooks on nuclear physics1–3 the set of radioactive decay chain equations is solved analytically for a maximum of three nuclides. The general Bateman solution4 is given as a final result or only with a brief mention of the elaborate recursive procedure needed to obtain it.3 Here, a short method for obtaining the general solution is demonstrated.
Two-particle interference
Authors: Gottfried Kurt
Published: July 2002

The superposition principle leads to coherence phenomena that have no counterpart in classical optics. A gedanken experiment, due to Horne and Zeilinger, provides an especially clear illustration of such phenomena, and is presented in a manner suitable to an introductory quantum mechanics course. The experiment displays an interference pattern in the correlation between two particles produced in a momentum-conserving decay, but no interference pattern when either particle is observed separately; it also has interesting Einstein–Podolsky–Rosen-type correlations.
Nonlinear output control in hysteretic, saturating materials
Authors: Piquette Jean C. , McLaughlin Elizabeth A. , Yang G. , Mukherjee B. K.
Published: July 2002

The problem of determining the drive waveform that produces a desired output from a hysteretic, saturating material is considered both theoretically and experimentally. The specific problem of interest is the production of a high-amplitude, but monofrequency, sinusoidal polarization response. (The techniques presented could also be used to control other physical variables, such as the strain, if desired.) Two sample materials were considered, one of which is characterized by relatively low hysteresis (tan δ≈0.03) and tested using mechanical prestresses of 20.7 MPa (3 kpsi) and 41.4 MPa (6 kpsi), and the other of which is characterized by relatively high hysteresis (tan δ≈0.11), and tested without a prestress. Both samples were fabricated from the electrostrictive material lead magnesium niobate (PMN), although a magnetostrictive material (such as Terfenol-D) could have been tested instead. The samples were subjected to a bias voltage and prestress in order to simulate conditions that might arise in a full transducer. By analytically inverting a theory of hysteresis [J. C. Piquette and S. E. Forsythe, J. Acoust. Soc. Am. 106, 3317–3327 (1999) and J. Acoust Soc. Am. 106, 3328–3334 (1999)], the required (predistorted) drive waveform was determined. Both semi-major and minor hysteresis loops, in both polarization and strain, were measured and the parameters of the theory determined by least-squares fitting. The measurements were obtained under quasi-static conditions, with drive frequencies at or below 10 Hz. The observed fits of theory to data are of high quality. The theory was then inverted analytically to determine the drive required to produce the desired monofrequency polarization response, having a peak polarization value approximately equal to that achieved using a biased sinusoid of AC amplitude equal to the bias. The total harmonic distortion (THD) in the output polarization resulting from the inverting drive, computed using 10 harmonics, was experimentally observed to be about an order of magnitude less than that resulting from a biased sinusoid in all cases. It is shown that the hysteresis loop arising when using the distortion-reducing drive is of smaller area than that obtained when driving with a sinusoid to achieve the same polarization amplitude. Thus, the distortion-reducing drive results in a smaller loss per cycle than is obtained with a sinusoidal drive.
On the relative role of sea-surface roughness and bubble plumes in shallow-water propagation in the low-kilohertz region
Authors: Norton Guy V. , Novarini Jorge C.
Published: July 2002

In the low-kilohertz frequency range, acoustic transmission in shallow water deteriorates as wind speed increases. Although the losses can be attributed to two environmental factors, the rough sea surface and the bubbles produced when breaking- or spilling waves are present, the relative role of each is still uncertain. For simplicity, in terms of an average bubble population, the time- and space-varying assemblage of microbubbles is usually assumed to be uniform in range and referred to as “the subsurface bubble layer.” However the bubble population is range- and depth-dependent. In this article, results of an experiment [Weston et al., Philos. Trans. R. Soc. London, Ser. A 265, 507–606 (1969)] involving fixed source and receivers, and observations during an extended period of time under varying weather conditions are re-examined by exercising a numerical model that allows for the dissection of the problem. Calculations are made at 2- and 4-kHz. It is shown that at these frequencies and at wind speeds capable of generating breaking waves the main mechanism responsible for the excess loss in the shallow-water waveguide is the patchy nature of the subsurface bubble field. Refraction and attenuation within the pockets of high void fraction are minor contributors to the losses.
Wave reflection from a transitional layer between the seawater and the bottom
Authors: Carbó Rafael
Published: July 2002

This paper presents a theoretical study of sound wave propagation through media whose properties change along one of the coordinate rectangular axes, and remain constant in the plane orthogonal to this axis. The uppermost sea bottom layer could be modeled as such an inhomogeneous medium where the density, sound velocity, and absorption of acoustical energy varies along one axis. The results were applied to obtain the reflection coefficient of the water-bottom surface considering that there is a transitional inhomogeneous layer with density, velocity, and absorption gradient, and without discontinuity with the bottom. It was concluded that the reflection coefficient of the bottom surface shows a frequency variation, dependent on the physical property gradients in the uppermost sea bottom layer.
Mean and mean-square responses of a prototypical master/fuzzy structure
Authors: Weaver R. L.
Published: July 2002

Analytical estimates are made for mean and mean-square transient responses of a single degree of freedom master oscillator attached to an undamped N degree of freedom random substructure. The ensemble averaged response is found to be, asymptotically for a large number of substructural degrees of freedom, in accord with the predictions of the Pierce–Sparrow–Russell theory. In particular the mean response of the master oscillator manifests an apparent damping. Corrections to this behavior are also predicted, but are found to lie well below the root-mean-square level of the fluctuations. The corrections are therefore, for practical purposes, unimportant. The ensemble average of the square of the response is also investigated and found to take a value at later times that is in accord with simple equipartition arguments advanced in an earlier paper. The power spectral density of the late time behavior is shown to be proportional to the square of the power spectrum of the early time response, and thus to be a narrower-band process than that of the early time behavior. Numerical simulations are presented which agree with the analytical predictions at moderate times, but also show an enhanced backscatter that develops over longer time scales.
Preliminary report on the summer ’96 joint China–U.S. internal wave/acoustic wave experiment in the Yellow Sea
Authors: Zhou Ji-Xun , Rogers Peter H. , Caille Gary W. , Zhang Renhe , Jin Guoliang , Lei Liangying , Dahl Peter H. , Spindel Robert C. , Gan Zijun
Published: July 2002

Simultaneous observations of internal wave activity and acoustic wave propagation in 70-m water in the Yellow Sea were made in the late summer of 1996. The primary objective of this experiment was to validate the predicated modal coupling and fluctuations induced by shallow-water internal waves. The Yellow Sea provides an ideal environment for such research because it has a very flat and homogeneous bottom and a very strong, sharp thermocline. The environment lends itself to relatively simple models for both the acoustic field and the internal wave field. Propagation was measured over distances up to 55 km in the frequency range of 50 Hz–5 kHz. The receivers were three moored and two suspended hydrophone arrays. Internal wave activity was monitored using thermistor chains, SAR satellite imagery, and high-frequency sonar. Propagation data were taken as a function of range, as a function of time at a fixed range, and as a function of azimuth in the presence of differing levels of internal wave activity. Supporting environmental data obtained during the experiment include ADCP, bottom profile and surface wave-height spectra, and bottom coring. Preliminary data on internal wave field, sound propagation, reverberation, and bottom acoustic parameters will be presented. [Work supported by ONR and the Chinese Academy of Sciences.]
Issues in modeling outdoor acoustical barriers
Authors: Putnam Robert A.
Published: July 2002

In the design of power generation facilities, whether classified as ‘‘indoor’’ or ‘‘outdoor,’’ it often happens that the economic evaluation of noise control measures indicates the use of free-standing outdoor noise barriers as part of the overall facility acoustical design. Additionally, the facility buildings and components themselves often function as acoustical barriers. Whenever such barriers are to be modeled, approximations to classical barrier theory are common. The reality of actual facility arrangements, the limitations regarding placement of acoustical barriers, and the physical or economic constraints on barrier height usually mean that the size and positions of the barriers are not optimal. Furthermore, the presence of nearby reflective surfaces, the finite width of any given barrier, and the compounding effect of successive barriers or surfaces also necessitates adjustments to ideal barrier theory. This paper will discuss a number of particular cases commonly encountered and will recommend specific measures to be used to approximate the reality of actual situations. In addition, a general discussion will be presented which compares the mapping of sound levels beyond acoustical barriers as a function of whether the source is modeled as an idealized point source or as a more realistic distributed source. [See NOISE-CON Proceedings for full paper.]
Noise control for a 210-MW cogeneration plant
Authors: Moritz Charles T. , Bruce Robert D. , Bicknell Reid , Jacobson Jeff
Published: July 2002

In this paper, the authors discuss a case study involving the design of noise control treatments for a 210-MW cogeneration plant. Residential property was located to the north, south, and east of the plant, with industrial zoned property to the west. The local noise regulations limited the A-weighted sound level that could be produced by the plant under all normal operating conditions to 55 dB at residential property lines and 75 dB at the industrial property lines. The nearest residential boundary was about 100-m east of the turbine buildings. Cost-effective noise control treatments were developed during the design phase of the plant. These treatments included not only sound-level specifications for all major equipment items, special building wall and roof construction, transformer barriers, and silencers for ventilation systems and vents, but also many noisy equipment items were located on the west side of the plant. [See NOISE-CON Proceedings for full paper.]
Thermoviscous effects in steady and oscillating superfluid flow with applications to Helmholtz oscillators
Authors: Backhaus Scott
Published: July 2002

The two fluid nature of superfluid 4He can lead to interesting behavior when it is used in a Helmholtz oscillator. If the oscillator’s constriction is narrow enough, the normal fluid can be locked by its own viscosity leaving only the superfluid component to flow in and out of the oscillator volume. This leads to an accompanying temperature oscillation that can cause dissipation and/or frequency shifts depending on the thermal properties of the walls of the oscillator. If the constriction is somewhat larger, the normal component is able to move and the thermal effects are partially canceled. These same effects lead to dissipation when steady flow is forced through the constriction. Equations have been derived which include superfluid flow, normal fluid flow, compressibility, thermal expansion, and the properties of the oscillator walls. These have been solved for the resistance to steady flow and the resonant frequency and Q of a Helmholtz oscillation. The calculations will be compared with a wide array of recent measurements. [Work partially supported by the Office of Naval Research and NASA.]
Control system analysis of an annular prime mover
Authors: Muehleisen Ralph T. , Lin Hsaio-Tseng , Atchley Anthony A.
Published: July 2002

The thermoacoustic prime mover in an annular resonator is analyzed as a linear feedback control system. Using the techniques of control system analysis, a closed-form solution for the acoustic gain of a constriction with linear temperature gradient in an annular resonator is developed. For a large enough gradient in the constriction, the acoustic gain of the system could become infinite, at which time the system goes into unstable positive feedback creating a thermoacoustic prime mover. An analysis of an existing annular resonator system is made and a comparison to more standard thermoacoustic numerical analysis is presented. [Work supported by the Office of Naval Research and the American Society for Engineering Education.]
Experimental results with a themoacoustically driven thermoacoustic refrigerator
Authors: Hofler Thomas J. , Adeff Jay A. , Atchley Anthony A.
Published: July 2002

The construction of a thermoacoustically (heat) driven, thermoacoustic refrigerator (TADTAR) has been completed. The design utilizes a novel resonator topology and should have a high cooling power density. While the design goal calls for a cooling power level of 500 W over a temperature span of 40 °C, the first refrigeration data recently obtained exhibited only small amounts of cooling. However, as the understanding of the engine improves, so does its performance. Variations in resonator tuning and stack location, gas type and pressure, and stack type and geometry are being explored. Low Prandtl number gas mixtures produce particularly strong improvements in onset conditions and amplitude. [Work supported by Office of Naval Research.]
Heat transfer measurements in a thermoacoustic refrigerator
Authors: Wetzel Martin , Herman Cila
Published: July 2002

In conventional heat transfer studies, mostly dealing with steady-state flow phenomena, a well-established database is available in the literature. In thermoacoustics, however, the flow oscillates with a zero mean velocity and heat transfer rates in this physical situation cannot be easily predicted. As it was shown previously [M. Wetzel and C. Herman, J. Acoust. Soc. Am. 100, 2846(A) (1996)], a tool to investigate such high-speed heat transfer phenomena is holographic interferometry combined with high-speed cinematography. Interferometric measurements were conducted for drive ratios from 1% to 3%. Applying digital image processing to the obtained interferometric fringe pattern, the oscillating temperature field was measured and acoustic temperature fluctuations of the order of 1 K could be resolved. From the temperature fields the important heat transfer parameters such as local heat fluxes, heat transfer coefficients, and Nusselt numbers were determined at the edge of two stack plates. [Work supported by the Office of Naval Research.]
Thermoacoustic streaming on a rigid sphere
Authors: Gopinath Ashok
Published: July 2002

The fundamental problem of thermoacoustic streaming in the presence of a rigid sphere in a strong standing acoustic field has been treated analytically. As a first step the compact sphere assumption is made, and the corresponding governing equations developed in dimensionless form to allow for a consistent treatment of all the energy-exchange mechanisms. It is found that the interaction of the strong acoustic field with the rigid boundaries of the sphere is capable of inducing a second-order time-averaged temperature distribution, in addition to the well known second-order time-averaged fluid motion. The associated temperature gradients cause localized heating and cooling effects on the surface of the sphere, even in the complete absence of any externally applied temperature potential. The role of a little known second-order thermal expansion coefficient is pointed out. A careful analysis of this conjugate problem coupling the solid–fluid time-averaged transport effects could help in the measurement of this second-order thermodynamics modulus. [Work supported by NASA.]
Asymmetrical effects and higher harmonics from nonlinear interactions in a driven vibrating wire
Authors: Hanson Roger J. , Macomber H. Kent , Kassakatis Michael P.
Published: July 2002

Inclusion of tensional changes and longitudinal motion result in coupled nonlinear equations for motion in, and perpendicular to, the plane of the driving force on a stretched wire. Earlier experimental measurements of nonlinear effects in a sinusoidally driven vibrating wire [Hanson et al., J. Acoust. Soc. Am. 96, 1549–1556 (1994)] will be briefly reviewed. Presented data will show that the onset of motion perpendicular to the plane of the driving force depends very sensitively on asymmetries which produce slight differences in free vibration frequencies in two orthogonal directions. Also reported will be results of amplitude and phase measurements of generated second, third, and fourth harmonics of the driving frequency, both in the plane of the driving force (vertical) and perpendicular to it. These higher harmonics, not significant at frequencies far off-resonance, become very significant near a resonance. With the wire driven at frequencies near its third natural resonance, a very pronounced subharmonic splitting of order three has been observed. Qualitative aspects will be illustrated on video tape.
The effects of a rib on the structural intensity in a cylindrical shell
Authors: Lang Derek C. , Burroughs Courtney B.
Published: July 2002

The amount of vibrational energy scattering by a rib in a cylindrical shell will depend on the shape of the rib. This redistribution of energy will affect the coupling between the shell vibration and acoustic radiation. Most models treat the rib attachment to the shell as a line attachment. Here, a rib with different widths and shapes is considered. Equations for the structural intensity in an infinite cylindrical shell without and with fluid loading are derived. The rib is treated as a change in the shell thickness specified by a rib function with parameters to control height, width and shape. The effects of the rib on the structural intensity in the in-vacuo shell in the farfield of the rib are modeled as a function of frequency and circumferential mode number.
Recent shallow water measurements of signal coherence and array performance in several shallow water areas
Authors: Carey William M. , Reese James
Published: July 2002

Experimental measurements of signal coherence and array signal gain are reviewed for both deep and shallow water sound channels. The signal gain is related to the horizontal coherence length through relationships from the statistical theory of antennas. Signal gain measurements in the transverse direction are proffered as a practical measure of coherence length for both broadband and narrow-band signals. Using this technique, measurements at frequencies near 400 Hz are presented that show for the deep water cases, lengths on the order of 100 wavelengths can be achieved, while in the downward, refraction conditions of shallow water waveguides with sand-silt bottoms, lengths on the order of 30 wavelengths are realized. Recent measurements of broadband and narrow-band coherence and signal gain are discussed with emphasis on the role of partly coherent noise backgrounds due to coastal shipping, multipath interference effects, and averaging constraints. In particular, the results of an experiment conducted in the Straits of Korea will be presented where array gain and sonar images were obtained in the presence of a strong coastal current.
Acoustic scintillation due to shallow-water internal solitary waves: Theory and experiment
Authors: Djachenko V. R. , Konyaev K. V. , Leikin D. E. , Sabinin K. D. , Tuzhilkin Yu. I.
Published: July 2002

In August–September 1990, an acoustics experiment was performed in the shallow-water region near Kamchatka. A 11/2-h time series representing amplitude fluctuations of 800-Hz, 160-Hz-bandwidth acoustic pulses was obtained by a hydrophone moored 34 km from the source. During the same period, a time series representing solitonlike vertical displacements of the thermocline near the receiver was recorded using a 37.5-m vertical temperature sensor. The two records were found to display abnormal similarity at time delays of 16.5 and 44.5 min. The effect is shown to be due to modal synchronism that may take place in shallow-water lossy-bottom regions with a small downward-positive gradient of the sound velocity. Theoretical explanation is verified by numerical simulation in which received signals are modeled by Fourier synthesis based on coupled-mode wave-field solutions in a stratified channel with a moving internal solitary wave. On the basis of the theory developed, new possible approaches for acoustic remote sensing are discussed.
Numerical load generation, vibration analysis, and acoustic signature prediction of a composite combat vehicle
Authors: Birkett Craig , Vlahopoulos Nickolas , Wu Zhen , Shalis Edward
Published: July 2002

Acoustic signatures of ground combat vehicles are very important to their survivability. In particular, low-frequency tones can be used to identify vehicles beyond the line of site. In the range of 10-200 Hz, the structure-borne acoustic radiation is mainly due to the track force/moment inputs. In this work, full-vehicle models were developed to simulate numerically the radiated acoustic signature as well as interior noise levels at its design stage. The loads applied on the hull of the vehicle were computed from a specialized code previously developed by the U. S. Tank Command. It simulates the interaction of the hull, sprocket, idler, roadwheels, roadarms, torsion bars, and track. The loads generated from this analysis comprise the excitation for the vibration calculations. The boundary element method was used to compute the radiated sound pressure in the semianechoic condition after mapping normal vibration velocities (calculated from a finite-element model) onto the vehicle’s surfaces. A description of the entire process of generating the loads, incorporating them in the finite-element analysis, and using the vibration results for the acoustic signature of the army vehicle is presented. [Program partially funded by a U. S. Army SBIR contract.] [See NOISE-CON Proceedings for full paper.]
Issues in heat recovery steam generator system noise
Authors: Hessler George F.
Published: July 2002

A heat recovery steam generator (HRSG) is a fundamental component of all combustion turbine-based combined cycle power plants. While it’s primary purpose is to convert exhaust gas heat to steam, an important secondary function is to reduce noise emissions from the combustion turbine exhaust. This source, at about 155 dB (overall) re: 1 pW for a 100-MW turbine, is the highest noise emission source in any combustion turbine plant. Therefore, the residual exhaust noise emissions leaving the HRSG walls and stack exit must be predicted with acceptable accuracy to determine the total plant noise level. The sources involved in this prediction methodology will be discussed. The issues include source power levels, wall and duct transmission loss, and the noise reduction characteristics through the HRSG flow path. Special measurement techniques required to quantify HRSG noise emissions are described. Whereas the HRSG is mainly a passive device that attenuates combustion turbine exhaust noise, two HRSG generated sources, steam venting and supplemental duct firing, will also be discussed. [See NOISE-CON Proceedings for full paper.]
Structure of the acoustical field generated by an underground tunnel
Authors: Rybak S. A.
Published: July 2002

The problem considered is about relative magnitudes of the field exited by the modes of cylindrical shell oscillations in soil due to a periodical force on the shell’s inner side. The closed form of this problem includes the dynamical equations of the shell, the wave equations of the surrounding elastic medium, and the appropriate boundary conditions. The principal role of the Rayleigh waves in the vibration energy transmission is determined and its value calculated for some examples of layered ground with a free boundary. The effect of the waveguide in the system of elastic layers is estimated.
Analysis of elastic cavitating wing vibration
Authors: Kovinskaya Svetlana I. , Amromin Eduard L.
Published: July 2002

A two-dimensional unsteady potential flow outside an elastic partially cavitating wing is analyzed numerically by using the Birnbaum equation on the hydrofoil chord and the Lagrange–Cauchy integral on the cavity. The angle of attack has a small periodic perturbation, and cavity thickness and length also take perturbations. Wing vibration is considered to be vibration of a variable thickness beam with two clamp bolts near the beam center. A monofrequency flow perturbation induces monofrequency flexural vibration of a noncavitating wing, but the vibration of a cavitating wing has multifrequency. Computation of NACA-16009 hydrofoil vibration was made for various free-stream speeds, module of elasticity, fluid, and wing densities, and as a result, three frequency bands of a vibration increase are determined. The low-frequency band is connected with a cavity volume oscillation. There is a considerable influence of cavity length on vibration. The high-frequency band is connected with elastic resonances of the wing. A solitary resonance was found in the middle band. This resonance has a nonlinear dependence on the loss coefficient and does not have a dependence on cavity dimensions and wing elasticity. This resonance appearance is connected with an interaction of lift and media inertia forces.
Flow-induced self-noise on a spherical acoustic velocity sensor
Authors: Lauchle Gerald C. , Jones Andrew R.
Published: July 2002

An experimental effort to characterize the broadband flow-induced self-noise on a spherically shaped acoustic velocity sensor operating underwater is described. The transducer is a small geophone encased in a near-neutrally buoyant sphere, 76.2 mm in diameter. The research described in this paper quantifies the flow-induced self-noise signal as a function of the sphere diameter Reynolds number (2.15<Re<34 290) and it is found that the broadband (10- to 100-Hz) flow-induced signal may be separated into two regimes characterized by: (1) Stokes flow which scales on a viscous time scale, and (2) turbulent flow which scales on an inertial time scale. During Stokes flow and at higher sub-critical Reynolds numbers where the shed vortices are laminar, virtually no broadband noise is produced. The detected, but weak, flow noise appears to scale on the magnitude of the viscous forces in this range. Above the transition Reynolds numbers, turbulent flow structures shed by the bluff body generate the dominant flow noise. This noise scales on the inertial forces of the flow. [Work supported by NAWC/AD/WAR and ONR.]
CD-ROM development for a certificate program in acoustics
Authors: Sparrow Victor W. , Williams Vickie S.
Published: July 2002

The Pennsylvania State University is currently developing a computer-based certificate program in acoustics aimed at practicing noise control engineers. This presentation will describe the development of a CD-ROM to deliver instruction in the program. Supplemented by a study guide, reading assignments, and homework, the purpose of the CD-ROM is to take the place of, and improve upon, traditional lectures in a course in acoustics. On each CD-ROM are placed Hypertext Markup Language (HTML) files which are viewable in a provided World Wide Web browser. These HTML files contain text, graphics, sounds, animations, and equations, the latter in the form of Graphics Interchange Format (GIF) files. The students move at their own pace from page to page through the HTML files as they would view overheads in a lecture presentation, but the hypertext, sound, and animation links allow for a more thorough treatment of the material. Having the HTML files already on the CD-ROM eliminates the communications delays inherent if all the files were only on the Internet. [Work supported by the Sloan Foundation. The authors appreciate the advice and contributions of all of the members of the Cohort-based Asynchronous Learning in Acoustics development team.] [See NOISE-CON Proceedings for full paper.]
Acoustical resonator frequency shift due to the migration of particles and bubbles
Authors: Kwiatkowski Christopher S. , Marston Philip L.
Published: July 2002

A change of the resonant frequency of an acoustic chamber can arise due to the presence and migration of objects inside the chamber. In the investigations of collinear four-wave mixing mediated by a suspension, it was noticed that for sufficiently high particle concentrations, the resonant frequency of the chamber shifted as the particles formed periodically spaced bands, due to the induced radiation pressure from two counter-propagating pump waves. This frequency shift, which also affects the Q factor of the cavity, is another manifestation of the interaction of sound with sound. A transfer-matrix approach was developed which uses a continuum approximation for the particle suspension, and is in good agreement with previous theory and experiment. By using sufficiently gassy water, pump pressures of large enough amplitude led to the measurement of the response of the system to cavitation bubbles. By proper tuning, the frequency shift of higher azimuthal modes of the cylindrical cavity were probed, with experimental results showing both stable and unstable modes. [Work was supported by the Office of Naval Research.]
Comparisons of the calculated and measured acoustic pressure amplitude from single-bubble sonoluminescence
Authors: Matula Thomas J. , Crum Larry A. , Moss William C.
Published: July 2002

The acoustic emissions from single cavitation bubbles have been measured with a state-of-the-art needle hydrophone. The measurements correspond to a stable cavitation bubble driven below and above the sonoluminescence threshold. Previous measurements above this threshold indicated that the lower-bound peak pressure at a distance of 1 mm from the bubble was nearly 2 bar [I. M. Hallaj et al., J. Acoust. Soc. Am. 100, 2717(A) (1996)]. The measured pressure amplitude below the sonoluminescence threshold is much weaker. Comparisons of the measured amplitudes with calculations are considered. In one case the acoustic emission mechanism is considered as being due to internal shock waves diverging into the fluid. In a second case the acceleration of the bubble wall is considered as the mechanism for the acoustic pulse, assuming a spatially uniform gas pressure in the bubble. Both methods are consistent with the measured values. However, neither method agrees well with the measured pulse amplitudes of the afterbounces. The addition of damping mechanisms not currently considered in the theories should provide better agreement. [Work supported by NSF. WCM’s work was performed under the auspices of the U. S. Department of Energy at Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.]
Vibro-acoustic response reduction of a fluid-loaded beam using unequally spaced absorbers and concentrated masses
Authors: Cheng Chih-Chun
Published: July 2002

A systematic method based on optimization techniques has been developed to determine locations of absorbers or concentrated masses required to reduce the vibration level, surface sound-pressure level, and total acoustic radiation power from a fluid-loaded structure. The method is demonstrated using a simply supported, fluid-loaded beam driven by a harmonic point force. In the optimization procedure, the unequally spaced absorbers or concentrated mass locations are the design variables and the designated location of vibration level, surface pressure, and the radiated acoustic power serve as the objective functions, respectively. Results show that the displacement response, surface sound pressure, and total radiated acoustic power can be reduced or controlled due to the presence of the absorbers or concentrated masses in an optimal arrangement. Although the reduction in vibroacoustic response achieved through concentrated masses is not as efficient as that of absorbers (as expected) satisfactory results in local vibration and surface sound pressure confinement are achieved using the concentrated masses. Note that the structure demonstrated here is simple, but it is believed that this methodology can be simply applied to other complex fluid-loaded structures. [Work supported by NSC, Taiwan.]
Experimental validation of a finite element model predicting the vibro-acoustic behavior of double-plate structures with Biot poroelastic materials
Authors: Panneton Raymond , Atalla Noureddine , Dauchez Nicolas
Published: July 2002

Recently, a tri-dimensional finite-element model predicting the vibro-acoustic behavior of multilayer systems containing Biot poroelastic materials have been developed [R. Panneton and N. Atalla, J. Acoust. Soc. Am. 100, 346–354 (1996)]. The objective of the current paper is to validate the finite-element model with experimental measurements. Three experimental validations are proposed: (1) measurements versus FEM predictions of the surface impedance of a poroelastic material using an impedance tube; (2) measurements versus FEM predictions of the vibrations of a plate bonded to a poroelastic layer; and (3) measurements versus FEM predictions of the vibration transmission loss through a double plate system containing a poroelastic material. Results of the FEM predictions agree very well with the measurement results. [Work supported by NSERC, FCAR, and Bombardier Inc. Canadair.]
Vibration analysis of ship beams
Authors: Kara Fuat , Altay G. Aşkar , Dökmeci M. Cengiz
Published: July 2002

This paper is essentially addressed to the vibrations of ships which were extensively studied both experimentally and analytically by modeling a ship as a beam of uniform cross section and predicting its vibration characteristics by Euler’s theory of elastic beams. To begin with, the free vibration characteristics of a ship beam are predicted from Timoshenko’s theory of elastic beam of variable cross section by use of Galerkin’s method. The results are evaluated by use of those obtained recently from Euler’s theory [e.g., S. Abrate, J. Sound. Vib. 185 (4), 703–716 (1995)]. Next, a numerical algorithm that is based on the method of moments [e.g., G. A. Altary and M. C. Dökmeci, Z. angew. Math. Mech. 77, 1–17 (1997) and references therein] is developed so as to predict the vibration characteristics of a ship beam at both low and high frequencies. The equations derived include the effects of warping and shear deformations of cross section and, in fact, they incorporate as many higher order effects as deemed necessary in any case of interest. They govern all the extensional, flexural, and torsional as well as coupled motions of ship beam. Also, the results are compared with those of earlier ones. [Work supported in part by TÜBA.]