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Faculty Publications

2007

San Jose State University

Articles 1 - 9 of 9

Full-Text Articles in Physical Sciences and Mathematics

Exceptionally Preserved Jellyfishes From The Middle Cambrian, Paulyn Cartwright, Susan L. Halgedahl, Jonathan R. Hendricks, Richard D. Jarrard, Antonio C. Marques, Allen G. Collins, Bruce S. Lieberman Oct 2007

Exceptionally Preserved Jellyfishes From The Middle Cambrian, Paulyn Cartwright, Susan L. Halgedahl, Jonathan R. Hendricks, Richard D. Jarrard, Antonio C. Marques, Allen G. Collins, Bruce S. Lieberman

Faculty Publications

Cnidarians represent an early diverging animal group and thus insight into their origin and diversification is key to understanding metazoan evolution. Further, cnidarian jellyfish comprise an important component of modern marine planktonic ecosystems. Here we report on exceptionally preserved cnidarian jellyfish fossils from the Middle Cambrian (~505 million years old) Marjum Formation of Utah. These are the first described Cambrian jellyfish fossils to display exquisite preservation of soft part anatomy including detailed features of structures interpreted as trailing tentacles and subumbrellar and exumbrellar surfaces. If the interpretation of these preserved characters is correct, their presence is diagnostic of modern jellyfish …

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Bedrock Channel Geometry Along An Orographic Rainfall Gradient In The Upper Marsyandi River Valley In Central Nepal, William Craddock, Douglas Burbank, Bodo Bookhagen, Emmanuel Gabet Jul 2007

Bedrock Channel Geometry Along An Orographic Rainfall Gradient In The Upper Marsyandi River Valley In Central Nepal, William Craddock, Douglas Burbank, Bodo Bookhagen, Emmanuel Gabet

Faculty Publications

Pronounced rainfall gradients combined with spatially uniform exhumation of rocks at Quaternary timescales and uniform rock strength make the upper Marsyandi River valley in central Nepal a useful natural laboratory in which to explore variations in bedrock channel width. We focus on small catchments (0.6–12.4 km2) along a more than tenfold gradient in monsoon rainfall. Rainfall data are gathered from a dense weather network and calibrated satellite observations, the pattern of Quaternary exhumation is inferred from apatite fission track cooling ages, and rock compressive strength is measured in the field. Bedrock channel widths, surveyed at high scour indicators, scale as …

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The Star Pile In Abell 545, R. Salinas, T. Richtler, M. J. West, Aaron J. Romanowsky, Y. Schuberth Jan 2007

The Star Pile In Abell 545, R. Salinas, T. Richtler, M. J. West, Aaron J. Romanowsky, Y. Schuberth

Faculty Publications

Context.Struble (1988, ApJ, 330, L25) found what appeared to be a cD halo without cD galaxy in the center of the galaxy cluster Abell 545. This remarkable feature has been passed almost unnoticed for nearly twenty years. Aims.Our goal is to review Struble's claim by providing a first (preliminary) photometric and spectroscopic analysis of this "star pile". Methods.Based on archival VLT-images and long-slit spectra obtained with Gemini-GMOS, we describe the photometric structure and measure the redshift of the star pile and of the central galaxy. Results.The star pile is indeed associated with Abell 545. Its velocity is higher by about …

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Algorithm Refinement For Fluctuating Hydrodynamics, Alejandro Garcia, S. Williams, J. B. Bell Jan 2007

Algorithm Refinement For Fluctuating Hydrodynamics, Alejandro Garcia, S. Williams, J. B. Bell

Faculty Publications

This paper introduces an adaptive mesh and algorithm refinement method for fluctuating hydrodynamics. This particle-continuum hybrid simulates the dynamics of a compressible fluid with thermal fluctuations. The particle algorithm is direct simulation Monte Carlo (DSMC), a molecular-level scheme based on the Boltzmann equation. The continuum algorithm is based on the Landau–Lifshitz Navier–Stokes (LLNS) equations, which incorporate thermal fluctuations into macroscopic hydrodynamics by using stochastic fluxes. It uses a recently developed solver for the LLNS equations based on third-order Runge–Kutta. We present numerical tests of systems in and out of equilibrium, including time-dependent systems, and demonstrate dynamic adaptive refinement by the …

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Numerical Methods For The Stochastic Landau-Lifshitz Navier-Stokes Equations, Alejandro Garcia, J. B. Bell, S. Williams Jan 2007

Numerical Methods For The Stochastic Landau-Lifshitz Navier-Stokes Equations, Alejandro Garcia, J. B. Bell, S. Williams

Faculty Publications

The Landau-Lifshitz Navier-Stokes (LLNS) equations incorporate thermal fluctuations into macroscopic hydrodynamics by using stochastic fluxes. This paper examines explicit Eulerian discretizations of the full LLNS equations. Several computational fluid dynamics approaches are considered (including MacCormack’s two-step Lax-Wendroff scheme and the piecewise parabolic method) and are found to give good results for the variance of momentum fluctuations. However, neither of these schemes accurately reproduces the fluctuations in energy or density. We introduce a conservative centered scheme with a third-order Runge-Kutta temporal integrator that does accurately produce fluctuations in density, energy, and momentum. A variety of numerical tests, including the random walk …

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The Pn.S Elliptical Galaxy Survey: Data Reduction, Planetary Nebula Catalog, And Basic Dynamics For Ngc 3379, N. G. Douglas, N. R. Napolitano, Aaron J. Romanowsky, L. Coccato, K. Kuijken, M. R. Merrifield, M. Arnaboldi, O. Gerhard, K. C. Freeman, H. R. Merrett, E. Noordermeer, M. Capaccioli Jan 2007

The Pn.S Elliptical Galaxy Survey: Data Reduction, Planetary Nebula Catalog, And Basic Dynamics For Ngc 3379, N. G. Douglas, N. R. Napolitano, Aaron J. Romanowsky, L. Coccato, K. Kuijken, M. R. Merrifield, M. Arnaboldi, O. Gerhard, K. C. Freeman, H. R. Merrett, E. Noordermeer, M. Capaccioli

Faculty Publications

We present results from Planetary Nebula Spectrograph (PN.S) observations of the elliptical galaxy NGC 3379 and a description of the data reduction pipeline. We detected 214 planetary nebulae, of which 191 are ascribed to NGC 3379 and 23 to the companion galaxy NGC 3384. Comparison with data from the literature shows that the PN.S velocities have an internal error of lesssim20 km s-1 and a possible offset of similar magnitude. We present the results of kinematic modeling and show that the PN kinematics is consistent with absorption-line data in the region where they overlap. The resulting combined kinematic data set, …

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Biogeography And The Cambrian Radiation Of Arachnomorph Arthropods, Jonathan R. Hendricks, Bruce S. Lieberman Jan 2007

Biogeography And The Cambrian Radiation Of Arachnomorph Arthropods, Jonathan R. Hendricks, Bruce S. Lieberman

Faculty Publications

Biogeographic patterns in primarily Cambrian arachnomorph taxa are investigated using a recently constructed phylogenetic hypothesis in order to explore the biogeographic context of the Cambrian radiation. A modified version of Brooks Parsimony Analysis is employed to elucidate patterns of vicariance and geodispersal in taxa from six regions (Laurentia, Baltica, Siberia, Australia, Africa and China). Well resolved vicariance and geodispersal trees are very similar and reconstruct Laurentia and China as sister areas. This close area relationship between Laurentia and China provides extensive evidence for congruent vicariance and range expansion in Cambrian arachnomorphs, while data from trilobites do not show this pattern. …

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Comment: Boosting Algorithms: Regularization, Prediction And Model Fitting, A. Buja, David Mease, A. Wyner Jan 2007

Comment: Boosting Algorithms: Regularization, Prediction And Model Fitting, A. Buja, David Mease, A. Wyner

Faculty Publications

The authors are doing the readers of Statistical Science a true service with a well-written and up-to-date overview of boosting that originated with the seminal algorithms of Freund and Schapire. Equally, we are grateful for high-level software that will permit a larger readership to experiment with, or simply apply, boosting-inspired model fitting. The authors show us a world of methodology that illustrates how a fundamental innovation can penetrate every nook and cranny of statistical thinking and practice. They introduce the reader to one particular interpretation of boosting and then give a display of its potential with extensions from classification (where …

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Boosted Classification Trees And Class Probability/Quantile Estimation, David Mease, A. Wyner, A. Buja Jan 2007

Boosted Classification Trees And Class Probability/Quantile Estimation, David Mease, A. Wyner, A. Buja

Faculty Publications

The standard by which binary classifiers are usually judged, misclassification error, assumes equal costs of misclassifying the two classes or, equivalently, classifying at the 1/2 quantile of the conditional class probability function P[y = 1jx]. Boosted classification trees are known to perform quite well for such problems. In this article we consider the use of standard, off-the-shelf boosting for two more general problems: 1) classification with unequal costs or, equivalently, classification at quantiles other than 1/2, and 2) estimation of the conditional class probability function P[y = 1jx]. We first examine whether the latter problem, estimation of P[y = 1jx], …

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