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2008 International Conference on Bioinformatics and computational Biology, BIOCOMP 2008

作者： Zhang, Changjiang Shen, Wensheng Williams, Kimberly Forstern Fannon, Michael Zhang, Jun Dept. of Computer Science University of Kentucky Lexington KY 40506 United States Dept. of Computational Science SUNY Brockport Brockport NY 14420 United States Dept. of Chemical Engineering Virginia Tech. Blacksburg VA 24061 United States Dept. of Ophthalmology University of Kentucky Lexington KY 40506 United States

ISBN: (纸本)1601320558

This paper presents a convection-diffusion-reaction model to simulate fibroblast growth factor (FGF-2) binding on cell surface molecules of receptors and heparin sulfate proteoglycan (HSPG) and mitogen-activated protein (MAP) kinase signaling under flow condition. It includes three parts: the flow of media using incompressible Navier-Stokes equation, the transport of FGF-2 using a convection-diffusion transport equation, and the local binding and signaling by chemical kinetics. It consists of a set of coupled nonlinear partial differential equations (PDEs) and a set of coupled nonlinear ordinary differential equations (ODEs). To solve these PDEs, the second order implicit Euler method with finite volume discretization is used. The ODE system is stiff and is solved by an ODE solver VODE using backward differencing formulation (BDF). The spatial distribution of FGF-2, FGFR, HSPG and their complexes are obtained. Our simulation results may provide insight into the understanding of regulation of heparin-binding gowth factors in circulation.

关键词： Navier Stokes equations

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Epipolar geometry and log-polar transform in wide baseline stereo matching

Epipolar geometry and log-polar transform in wide baseline s...

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作者： Palander, Kimmo Brandt, Sami S. Dept. of Biomedical Engineering and Computational Science P.O. Box 9203 FI-02015 TKK Finland Machine Vision Group Information Processing Laboratory University of Oulu P.O. Box 4500 FI-90014 Finland

ISBN: (纸本)9781424421756

This paper presents an interesting observation that epipolar geometry and log-polar transform can be naturally combined by setting the center of the log-polar transform into the epipoles. This choice preserves the linearity of the epipolar lines. Moreover, the setting is especially advantageous, when camera moves towards the optical axis of the camera as the log-polar transform compensates the large scale changes in the scene. This practically implies that conventional matching techniques can be used with wide baseline images. We discuss the approach with both calibrated and uncalibrated cameras and show some dense wide baseline reconstruction examples where the epipoles are close to the image centers. © 2008 IEEE.

关键词： Cameras

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A prediction method of hydroelastic motion of aircushion type floating structures considering with draft effect into hydrodynamic forces

A prediction method of hydroelastic motion of aircushion typ...

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27th International Conference on Offshore Mechanics and Arctic engineering, OMAE 2008

作者： Ikoma, Tomoki Kobayashi, Masato Masuda, Koichi Rheem, Chang-Kyu Maeda, Hisaaki Dept. of Oceanic Architecture and Engineering Ninon University CST 7-24-1 Narashinodai Funabashi Chiba 274-8501 Japan NTT Data Science Corporation Ninon Univ. Japan University of Tokyo IIS Japan

ISBN: (纸本)9780791848234

An aircushion type floating structure can prevent to enlarge the wave drifting force restraining the hydroelastic response of it in water waves. The floating structure should be large scale to incident waves in order to make the best use of such advantages, i.e. it is a very large floating structure. The linear potential theory is useful to easily handle the wave force etc. on the aircushion type floating structure theoretically because it is predicted that its theory can give good results of behaviors of water elevation within aircushions and pressure and of wave loads on the structure qualitatively. The authors have confirmed from our past model experiments that non-linear effect does not always increase but for some exceptions. A prediction method of hydroelastic responses for the aircushion type very large floating structure by using the three-dimensional linear potential theory is shown in this paper. The validity of the method is proven and the application of the method is investigated by comparing the theoretical results with the results of the past model experiments. Copyright © 2008 by ASME.

关键词： Water waves

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Clustering of High-Dimensional Gene Expression data with Feature Filtering Methods and Diffusion Maps

Clustering of High-Dimensional Gene Expression Data with Fea...

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International Conference on BioMedical engineering and Informatics (BMEI)

作者： Rui Xu Steven Damelin Boaz Nadler Donald C. Wunsch Dept. of Electrical & Computer Engineering Missouri University of Science & Technology Rolla MO USA School of Applied and Computational Mathematics University of the Witwatersrand Wits South Africa Dept. of Computer Science and Applied Mathematics Weizmann Institute of Science Rechovot Israel

The importance of gene expression data in cancer diagnosis and treatment by now has been widely recognized by cancer researchers in recent years. However, one of the major challenges in the computational analysis of such data is the curse of dimensionality, due to the overwhelming number of measures of gene expression levels versus the small number of samples. Here, we use a two-step method to reduce the dimension of gene expression data. At first, we extract a subset of genes based on the statistical characteristics of their corresponding gene expression measurements. For further dimensionality reduction, we then apply diffusion maps, which interpret the eigenfunctions of Markov matrices as a system of coordinates on the original data set in order to obtain efficient representation of data geometric descriptions, to the reduced data. A neural network clustering theory, Fuzzy ART, is applied to the resulting data to generate clusters of cancer samples. Experimental results on the small round blue-cell tumor (SRBCT) data set, compared with other widely-used clustering algorithms, demonstrate the effectiveness of our proposed method in addressing multidimensional gene expression data.

关键词： Gene expression Filtering Cancer data analysis data mining Eigenvalues and eigenfunctions Neural networks Fuzzy neural networks Subspace constraints Neoplasms

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The hydrodynamic environment for the s process in the He-shell flash of AGB stars

The hydrodynamic environment for the s process in the He-she...

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10th Symposium on Nuclei in the Cosmos, NIC 2008

作者： Woodward, Paul R. Porter, David H. Herwig, Falk Pignatari, Marco Jayaraj, Jagan Lin, Pei-Hung University of Minnesota Laboratory for Computational Science and Engineering 117 Pleasant St. S.E. Minneapolis MN 55455 United States University of Victoria Dept. of Physics and Astronomy Victoria BC V8W 3P6 Canada Keele University Astrophysics Group North Staffordshire ST5 5BG United Kingdom

The He-shell flash convection in AGB stars is the site for the high-temperature component of the s-process in low- and intermediate mass giants, driven by the 22Ne neutron source. During this phase several s-process branchings are activated, including some with time scales similar to the convective turn-over time scale. In addition, uncertainties regarding convective mixing at both the bottom and the top of the convective shell are preventing accurate predictions of s-process yields. The upper convection boundary plays a critical role during the Hingestion episode that may lead to neutron-bursts in the most metal-poor AGB stars. We address these problems through global 3-dimensional hydrodynamic simulations including the entire spherical He-shell flash convection zone (as oposed to the 3D box-in-a-star simulations). An important aspect of our current effort is to establish the feasibility of our appoach. We explain why we favour the explicit treatment over the anelastic approximation for this problem. The simulations presented in this paper use a Cartesian grid of 5123 cells and have been run on four 8-core workstations for four days to simulate ∼ 5000s, which corresponds to almost ten convective turn-over times. The convection layer extends radially at the simulated point in the flash evolution over 7Hp pressure scale-heights and exceeds the size of the underlying core. Convection is dominated by large convective cells that fill more than an entire octant. In order to better understand the conditions of the s-process branchings in this environment we have extracted particle tracers, and we discuss the thermodynamic trajectories along those paths. © Copyright owned by the author(s) under the terms of the Creative Commons Attribution-NonCommercial-ShareAlikeLicence.

关键词： Neutron sources

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Abstracts for 2009 Annual Meeting, in Program Order

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Bulletin, Southern California Academy of sciences 2009年第2期108卷 89-136页

作者： Mark Helvey C. Heberer C. A. Sepulveda S. A. Aalbers D. Bernal S. Kohin D. Lawson L. Enriquez C. Villafana M. McCorkle M. Castagnola M. F. Golden Sabrina L. Drill Camm Swift Christina C. Fahy Michael Bell D. M. Petschauer C. Cash J. A. Reyes K. M. Kelley M. J. Allen E. T. Jarvis C. Linardich C. F. Valle T. Mason C. G. Lowe Julianne E. Kalman Don Cadien J. Ananda Ranasinghe Giancarlo Cicchetti K. L. Martin J. E. Dugan U. L. Vidal D. S. Boskovic L. R. Brand A. S. Llaban P. J. Krug C. P. Kofron F. X. Villablanca Edward L. Ervin Clark R. Mahrdt La Rie Burgoyne Daryle Hinton-Hardin Gianna Ramos Mackenzie Shribbs Philippa M. Drennan Lisa Komoroske Rebecca Lewison Peter H. Dutton Jeffrey Seminoff Dimitri Deheyn A. Dalkey Jinwon Kim Jeremy S. Pal Sara A. Rauscher Noah S. Diffenbaugh J. W. O'Brien H. K. Hansen M. E. Stephens R. Uyehara C. Kumpu J. R. Thomlinson C. W. Solek L. A. Sam D. C. Zacherl T. M. Magrann S. G. Dunbar D. Boskovic Cordale Johnson John Thomlinson Connie Vadheim Roth D. Lim S. E. Walker Matthew P. Sutton Darren R. Sandquist S. L. Kelley A. W. Fredell D. A. Anaya John R. Thomlinson K. Bayley H. Chu M. Estrada Noelle Bidegainberry Alison Fujii Larisa Pender-Healy M.H REZAIE BOROON P RAMIREZ K GNANDI Doreen Emilee Carpio Lori Critchfield Kathryn Dickson Chris Chabot Donald Buth Camm Swift Jonathan Sim Thomas Dowling Larry Allen Angela Chapman Donald A. Rodriguez Christopher Kahler Christina Fahim Lisa Winfrey Amanda Goldstein A. M. Cooper G. A. Fox D. R. Nelsen W. K. Hayes A. G. Corbit A. A. Corcoran K. M. Reifel B. H. Jones R. F. Shipe N. Lim O. Saliu N. Wakama T. Duong J. Gov G. Liu Ali Forghani Ramtin Khanipour H. L. Gliniak O. Horning Nick Haring Tim Stebbins Ron Velarde A. K. James Bonnie R. Lei W. Liu C. Mac Miguel A. Macias V. G. Minnich H. Musharbash K. A. Dickson J. C. Notar J. Gessow Mark E. Parlow Marcia G. Narog Jan L. Beyers David R. Weise Philip J. Riggan Anna Wrona C. R. Pospisil Rene Carbajal Suong Tran J. Quintanilla L. Gabrielian V. Carmona-Galindo N. R. Rahman G. Ramírez G. Brelles-Mariñ National Marine Fisheries Service Southwest Region 6010 Hidden Valley Drive Carlsbad CA. 92011 Pfleger Institute of Environmental Research Oceanside CA University of Massachusetts Dartmouth Dartmouth MA National Marine Fisheries Service Southwest Fisheries Science Center La Jolla CA UC Cooperative Extension Los Angeles County 4800 E. Cesar Chavez Ave. Los Angeles CA 90022 Entrix Inc. 2140 Eastman Ave # 200 Ventura CA 93003 Southern California Coastal Water Research Project (SCCWRP) Costa Mesa CA 92626 US Environmental Protection Agency Narragansett RI 02882 Marine Science Institute University of California Santa Barbara California 93106 U.S.A. j_dugan@lifesci.lscf.ucsb.edu Department of Earth and Biological Sciences School of Science and Technology Loma Linda University Loma Linda CA 92350 Division of Biochemistry School of Medicine Loma Linda University Loma Linda CA 92350 Associate Biologist Merkel &amp Associates Inc. 5434 Ruffin Road San Diego CA 92123 Research Assistant San Diego Natural History Museum Dept. of Herpetology P.O. Box 121390 San Diego CA 92112-1390 San Diego State University NOAA- Southwest Fisheries Science Center Scripps Institution of Oceanography Palos Verdes Peninsula Land Conservancy Rolling Hills Estates CA 90274 UCLA Los Angeles CA Entrix Inc. Ventura CA Arizona State University Tempe AZ California State University Northridge CA Palos Verdes Peninsula High School Rolling Hills Estates CA 90274 U.S. Department of Agriculture Forest Service PSW Research Station Forest Fire Laboratory 4955 Canyon Crest Drive Riverside California 92507. Loyola Marymount University Department of Civil Engineering Los Angeles CA 90045 Marlborough School Los Angeles CA 90004 Loyola Marymount University Natural Science Department Los Angeles CA 90045 Department of Biological Science California State University Fullerton Department of Biology Fullerton CA 92831 Department of Evolution Ecology and Organismal Biology The Ohio State U

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Actors and factors - Bridging social science findings and urban land use change modeling

Actors and factors - Bridging social science findings and ur...

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4th Biennial Meeting of International Congress on Environmental Modelling and Software: Integrating sciences and Information Technology for Environmental Assessment and Decision Making, iEMSs 2008

作者： Haase, D. Kabisch, S. Haase, A. Filatova, T. Van Der Veen, A. Tötzer, T. Loibl, W. Scatasta, S. Schetke, S. Zuin, A. Von Walter, F. UFZ Centre for Environmental Research Dept. of Computational Landscape Ecology Permoserstr. 15 D-04318 Leipzig Germany UFZ Centre for Environmental Research Dept. of Urban and Environmental Sociology Permoserstr. 15 D-04318 Leipzig Germany Department of Water Engineering and Management University of Twente Netherlands International Institute for Geo-Information Science and Earth Observation Netherlands Austrian Research Centers - ARC GmbH Systems Research A-1220 Vienna Austria Centre for European Economic Res. ZEW L7 1 Mannheim Germany Institute of Geodesy and Geoinformation Dept. of Urban Planning and Real Estate Management University of Bonn Germany Edinburgh College of Art OPENspace Research Centre United Kingdom Georg-August-Universität Göttingen Platz der Göttinger Sieben 5 37073 Göttingen Germany

ISBN: (纸本)9788476530740

Recent uneven land use dynamics in urban areas resulting from demographic change, economic pressure and the cities' mutual competition in a globalising world challenge both scientists and practitioners, among them social scientists, modellers and spatial planners. Processes of growth and decline specifically affect the urban environment, the requirements of the residents on social and natural resources. Social and environmental research is interested in a better understanding and ways of explaining the interactions between society and landscape in urban areas. And it is also needed for making life in cities attractive, secure and affordable within or despite of uneven dynamics. The position paper upon "Actors and factors - bridging social science findings and urban land use change modeling" presents approaches and ideas on how social science findings on the interaction of the social system (actors) and the land use (factors) are taken up and formalised using modelling and gaming techniques. It should be understood as a first sketch compiling major challenges and proposing exemplary solutions in the field of interest.

关键词： Demography

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Block ignition Inertial Confinement Fusion (ICF) for space propulsion

Block ignition Inertial Confinement Fusion (ICF) for space p...

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作者： Miley, George H. Hora, H. Cang, Yu Osman, F. Badziak, J. Wolowski, J. Sheng, Zheng-Ming Zhang, Jie Zhang, Weiyan He, Xia Department of Nuclear Plasma and Radiological Engineering University of Illinois Urbana 61801 United States Department of Theoretical Physics University of New South Wales Sydney Australia School of Computer Sciences University of Western Sydney Penrith Australia Institute of Plasma Physics and Laser Microfusion Warsaw Poland Beijing National Laboratory for Condensed Matter Physics Institute of Physics Chinese Academy of Science Beijing 100080 China Institute of Applied Physics and Computational Mathematics Beijing China Nuclear Plasma and Radiological Engineering 216 Talbot Lab. 104 S. Wright Urbana IL 61801 United States Emeritus Theoretical Physics Sydney Australia Prollerweg 4 Garching/Munich Germany Dept. Mathematics Trinity College Summerville/Sydney Australia Institute of Plasma Physics and Laser Fusion Warsaw Poland Inst. Physics Chinese Academy of Sciences Beijing China Shanghai Jiao Tong University Shanghai China China Academy of Engineering Physics Beijing China Chinese Academy of Science Beijing China

ISBN: (纸本)9781563479434

Use of laser-driven Inertial Confinement Fusion (ICF) for space propulsion has been examined in several earlier conceptual design studies. However, these designs used older ICF target technology. Important new directions opened following the development of "chirped" lasers capable of ultra-short ps pulses with powers of PWs. This allows fast ignition (FI) for high energy gain ICF power plants1. The FI approach uses a conventional laser to pre-compress the target to high density. The PW laser is then fired on the compressed target, creating an internal electron beam that ignites fusion in a central core of the target. It is estimated that using a 10 TW-ps laser for FI can achieve fusion energy gains >103. Here a new type of FI, termed block ignition, is considered2-4. This approach can further increase the fusion gain offered through FI. Application of block ignition to the earlier VISTA design for ICF space propulsion unit is considered here. With the improved performance obtained, it becomes feasible to bypass DT fusion and use tritium-lean D targets as a first step for development of fusion propulsion technology.

关键词： Inertial confinement fusion

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Molecular dynamics simulations of crystal rearrangement at grain boundaries and the vicinity

Molecular dynamics simulations of crystal rearrangement at g...

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作者： Uehara, Takuya Wakabayashi, Naoki Ohno, Nobutada Dept. Computational Science and Engineering Nagoya University Furo-cho Chikusa-ku Nagoya Aichi 464-8603 Japan Graduate School of Engineering Nagoya University Japan Dept. Computational Science and Engineering Nagoya University Japan

Molecular dynamics simulations of rearrangement of atoms around the grain boundaries are carried out. The purpose of this study is to estimate the stability of grain boundaries and to observe their motion based on the atomistic considerations, so that the results are able to be applied for multi-scale scheme such as the phase field model. First, the grain-boundary energy is calculated as a function of misorientation angle, which revealed that several specific angles exhibit cusp-like low values, for both symmetric and non-symmetric grain boundaries. Secondly, changes in morphology of a square grain embedded in a bulk single crystal are simulated. Grains surrounded by specific grain boundaries having low energy are stable and do not incorporate rotation or migration, while unstable grains change their shape or orientation. A circular-grain model is also applied for the simulations, and similar tendency is obtained. Finally, a simulation at a high temperature for the model which consist of a grain stable at low temperature is carried out, which reveals that grain contraction occurs resulting in disappearance of the grain.

关键词： Crystal atomic structure

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Implicit formulation of homogenization method for periodic elastoplastic solids

Implicit formulation of homogenization method for periodic e...

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作者： Asada, Takashi Ohno, Nobutada Nagoya University Dept. of Computational Science and Engineering Furo-cho Chikusa-ku Nagoya 464-8603 Japan

In this study, to determine incremental, perturbed displacement fields in periodic elastoplastic solids, an incremental homogenization problem is fully implicitly formulated, and an algorithm is developed to solve the homogenization problem. It is shown that the homogenization problem can be iteratively solved with quadratic convergences by successively updating strain increments in unit cells, and that the present formulation allows versatility in the initial setting of strain increments in contrast to previous studies. The homogenization algorithm developed is then examined by analyzing a holed plate, with an elastoplastic micro-structure, subjected to tensile loading. It is thus demonstrated that the convergence in iteratively solving the homogenization problem strongly depends on the initial setting of strain increments in unit cells, and that quick convergences can be attained if the initial setting of strain increments is appropriate.

关键词： Elastoplasticity

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