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Lecture Notes in Computer Science

作者： Patro, Rob Sefer, Emre Malin, Justin Marçais, Guillaume Navlakha, Saket Kingsford, Carl Center for Bioinformatics and Computational Biology University of Maryland College Park MD 20742 United States Department of Computer Science University of Maryland College Park MD 20742 United States Computational Biology Bioinformatics and Genomics Concentration Biological Sciences Graduate Program University of Maryland College Park MD 20742 United States Program in Applied Mathematics Statistics and Scientific Computation University of Maryland College Park MD 20742 United States School of Computer Science Carnegie Mellon University Pittsburgh PA 15213 United States

ISBN: (纸本)9783642230370

We consider the problem of reconstructing a maximally parsimonious history of network evolution under models that support gene duplication and loss and independent interaction gain and loss. We introduce a combinatorial framework for encoding network histories, and we give a fast procedure that, given a set of duplication histories, in practice finds network histories with close to the minimum number of interaction gain or loss events. In contrast to previous studies, our method does not require knowing the relative ordering of unrelated duplication events. Results on simulated histories suggest that common ancestral networks can be accurately reconstructed using this parsimony approach. © 2011 Springer-Verlag.

关键词： Genes

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Continuum model of irradiation-induced spinodal decomposition in the presence of dislocations

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Physical Review B 2011年第17期83卷 174106-174106页

作者： J. J. Hoyt M. Haataja Department of Materials Science and Engineering McMaster University Hamilton Ontario Canada L8S4L7 Department of Mechanical and Aerospace Engineering Princeton Institute for the Science and Technology of Materials (PRISM) Program in Applied and Computational Mathematics (PACM) Princeton University Princeton New Jersey 08544

A model of phase-separation kinetics in systems exposed to energetic particle irradiation has been extended to include the effects of mobile dislocations. It is shown that when dislocations are allowed to participate in the decomposition reaction, phase separation can occur at temperatures above the coherent spinodal, which is in agreement with several experiments on irradiated alloys. A linear stability analysis of the governing kinetic equations is performed and three regimes of microstructural evolution are identified within the parameter space of damage cascade size vs incident flux: complete phase separation, solid-solution behavior, and compositional patterning. In addition, numerical simulations of the evolving dislocation density and composition fields are performed. The numerical results provide the amplitude and wavelength of the stable patterns that can form under irradiation and elucidate the role of misfit dislocations in reducing the coherency strain due to atomic size mismatch.

关键词： PHASE transformations (Physics) THERMODYNAMICS PARTICLES (Nuclear physics) ALLOYS IRRADIATION STRAINS & stresses (Mechanics)

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Anatomically adapted wavelets for integrated statistical analysis of fMRI data

Anatomically adapted wavelets for integrated statistical ana...

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IEEE International Symposium on Biomedical Imaging

作者： S. Görkem Özkaya Dimitri Van De Ville Program in Applied and Computational Mathematics Princeton University Princeton NJ USA Medical Image Processing Laboratory Universita de Genève Geneve Switzerland Medical Image Processing Laboratory Ecole Polytechnique Fédérale de Lausanne Lausanne Switzerland

Wavelets have been successfully used in statistical analysis of fMRI data as a spatial transform providing a compact representation of brain activation maps. However, conventional (tensor-product) wavelet transforms assume a rectangular domain, while the essential brain activity takes place in the convoluted gray-matter layer. We use the lifting scheme to design wavelet bases for more arbitrary domains which do not have a group structure. In particular, we have considered the grey-matter cortical layer as the domain. We then applied the new transform to fMRI data using the wavelet-based SPM (WSPM) framework. Preliminary results show that the adapted wavelets have superior performance in terms of sensitivity than the standard tensor-product wavelets, while having the same control over type-I error rate (specificity).

关键词： Wavelet transforms Wavelet domain Wavelet analysis Statistical analysis Sensitivity Vectors

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Improved reconstructions of random media using dilation and erosion processes

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Physical Review E 2011年第5期84卷 056102-056102页

作者： Chase E. Zachary Salvatore Torquato Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA

By using the most sensitive two-point correlation functions introduced to date, we reconstruct the microstructures of two-phase random media with heretofore unattained accuracy. Such media arise in a host of contexts, including porous and composite media, ecological structures, biological media, and astrophysical structures. The aforementioned correlation functions are special cases of the so-called canonical n-point correlation function Hn and generalize the ones that have been recently employed to advance our ability to reconstruct complex microstructures [Y. Jiao, F. H. Stillinger, and S. Torquato, Proc. Natl. Acad. Sci. 106, 17634 (2009)]. The use of these generalized correlation functions is tantamount to dilating or eroding a reference phase of the target medium and incorporating the additional topological information of the modified media, thereby providing more accurate reconstructions of percolating, filamentary, and other topologically complex microstructures. We apply our methods to a multiply connected “donut” medium and a dilute distribution of “cracks” (a set of essentially zero measure), demonstrating improved accuracy in both cases with implications for higher-dimensional and biconnected two-phase systems. The high information content of the generalized two-point correlation functions suggests that it would be profitable to explore their use to characterize the structural and physical properties of not only random media, but also molecular systems, including structural glasses.

关键词： FUNCTIONS (mathematics) MICROSTRUCTURE TOPOLOGY COMPOSITE materials PROBABILITY theory STATISTICS

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Phase Diagram and Structural Diversity of the Densest Binary Sphere Packings

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Physical Review Letters 2011年第12期107卷 125501-125501页

作者： Adam B. Hopkins Yang Jiao Frank H. Stillinger Salvatore Torquato Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Center for Theoretical Science Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

The densest binary sphere packings have historically been very difficult to determine. The only rigorously known packings in the α−x plane of sphere radius ratio α and relative concentration x are at the Kepler limit α=1, where packings are monodisperse. Utilizing an implementation of the Torquato-Jiao sphere-packing algorithm [S. Torquato and Y. Jiao, Phys. Rev. E 82, 061302 (2010)], we present the most comprehensive determination to date of the phase diagram in (α,x) for the densest binary sphere packings. Unexpectedly, we find many distinct new densest packings.

关键词： SPHERE packings PHASE diagrams SOLID geometry KEPLER'S laws CRYSTALLOGRAPHY CELLS

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A NUMERICAL STUDY OF THE GAUSSIAN BEAM METHODS FOR SCHR(O|¨)DINGER-POISSON EQUATIONS

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Journal of computational mathematics 2010年第2期28卷 261-272页

作者： Shi Jin Hao Wu Xu Yang Department of Mathematics University of Wisconsin Madison W1 53706 USA Department of Mathematical Sciences Tsinghua University Beijing 100084 China Department of Mathematics University of Wisconsin Madison WI 53706 USA Program in Applied and Computational Mathematics Princeton University Princeton NJ 08544USA

As an important model in quantum semiconductor devices, the SchrSdinger-Poisson equations have generated widespread interests in both analysis and numerical simulations in recent years. In this paper, we present Gaussian beam methods for the numerical simulation of the one-dimensional Schrodinger-Poisson equations. The Gaussian beam methods for high frequency waves outperform the geometrical optics method in that the former are accurate even around caustics. The purposes of the paper are first to develop the Gaussian beam methods, based on our previous methods for the linear SchrSdinger equation, for the Schrodinger-Poisson equations, and then check their validity for this weakly-nonlinear system.

关键词： Schrodinger-Poisson equations Gaussian beam methods Vlasov-Poisson equations

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Fat Arcs for Implicitly Defined Curves

Fat Arcs for Implicitly Defined Curves

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7th International Conference on Mathematical Methods for Curves and Surfaces

作者： Bela, Szilvia Juettler, Bert Doctoral Program in Computational Mathematics Austria Institute of Applied Geometry Johannes Kepler University Linz 4040 Altenberger Str. 69 Austria

ISBN: (纸本)9783642116193

We present an algorithm generating a collection of fat arcs which bound the zero set of a given bivariate polynomial in Bernstein-Bezier representation. We demonstrate the performance of the algorithm (in particular the convergence rate) and we apply the results to the computation of intersection curves between implicitly defined algebraic surfaces and rational parametric surfaces.

关键词： Polynomial approximation

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4D seismic monitoring of CO2 sequestration based upon spectral-element and adjoint methods: Comparison of acoustic, elastic and poroelastic theories 80

4D seismic monitoring of CO2 sequestration based upon spectr...

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Society of Exploration Geophysicists International Exposition and 80th Annual Meeting 2010, SEG 2010

作者： Morency, Christina Luo, Yang Tromp, Jeroen Department of Geosciences Princeton University United States Department of Geosciences and Program in Applied and Computational Mathematics Princeton University United States

ISBN: (纸本)9781617389801

The key issues in CO2 sequestration monitoring involve accurate monitoring, from the injection stage to prediction & verification, of CO2 movement over time for environmental considerations. A natural non-intrusive monitoring technique is referred to as "4D seismics", which involves 3D time-lapse seismic surveys. The success of monitoring the CO2 movement is subject to a proper description of the physical properties of the structure. We realize time-lapse migrations comparing acoustic, elastic, and poroelastic simulations of 4D seismic imaging to characterize the storage zone, based solely upon the first arrival traveltime anomaly arising from the injection of CO2. This approach highlights the influence of using different physical theories on interpreting seismic data, and, more importantly, on extracting the CO2 signature from the seismic wave field. Simulations are performed using a spectral-element method, which allows for highly accurate results. Biot? Equations are implemented to account for poroelastic effects. The sensitivity of observables to the model parameters is quantified based upon finite-frequency sensitivity kernels calculated using an adjoint method. © 2010 SEG.

关键词： Carbon dioxide

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Recovery of frequency-sparse signals from compressive measurements

Recovery of frequency-sparse signals from compressive measur...

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48th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2010

作者： Duarte, Marco F. Baraniuk, Richard G. Program in Applied and Computational Mathematics Princeton University United States Department of Electrical and Computer Engineering Rice University United States

ISBN: (纸本)9781424482146

Compressive sensing (CS) is a new approach to simultaneous sensing and compression for sparse and compressible signals. While the discrete Fourier transform has been widely used for CS of frequency-sparse signals, it provides optimal sparse representations only for signals with components at integral frequencies. There exist redundant frames that provide compressible representations for frequency-sparse signals, but such frames are highly coherent and severely affect the performance of standard CS recovery. In this paper, we show that by modifying standard CS recovery algorithms to prevent coherent frame elements from being present in the signal estimate, it is possible to bypass the shortcomings introduced by the coherent frame. The resulting algorithm comes with theoretical guarantees and is shown to perform significantly better for frequency-sparse signal recovery than its standard counterparts. The algorithm can also be extended to similar settings that use coherent frames. ©2010 IEEE.

关键词： Compressed sensing

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Publisher’s Note: “Enhanced damping of ion acoustic waves in dense plasmas” [Phys. Plasmas 18, 014505 (2011)]

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Physics of Plasmas 2011年第3期18卷

作者： S. Son Sung Joon Moon 118 Caleb Lane Princeton New Jersey 08540 USA 2Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

This article was originally published online on 11 January 2011 with an error in S. Son’s affiliation. AIP apologizes for this error.

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