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13th International Conference on AIS 2004

作者： Kim, Jae-Kyung Sohn, Won-Sung Cho, Beom-Joon Lim, Soon-Bum Choy, Yoon-Chul Dept. of Computer Science Yonsei University Shinchon-dong Seodaemun-gu 120-749 Seoul Korea Republic of Computational Design Program School of Architecture Carnegie Mellon University Pittsburgh PA 15213 United States Department of Computer Engineering Chosun University Kwangju Korea Republic of Department of Multimedia Science Sookmyung Women's University Chungpa-dong Yongsan-gu 140-742 Seoul Korea Republic of

The paper proposes a layered scripting language technique for representation and control of avatar behavior for simpler avatar control in various domain environments. We suggest three layered architecture which is consisted of task-level behavior, high-level motion, and primitive motion script language. These layers brides gap between application domain and implementation environments, so that end user can control the avatar through easy and simple task-level scripting language without concerning low-level animation and the script can be applied various implementations regardless of application domain types. Our goal is to support flexible and extensible representation and control of avatar behavior by layered approach separating application domains and implementation tools. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Computer programming languages

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Fluid permeabilities of triply periodic minimal surfaces

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Physical Review E 2005年第5期72卷 056319-056319页

作者： Y. Jung S. Torquato Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

It has recently been shown that triply periodic two-phase bicontinuous composites with interfaces that are the Schwartz primitive (P) and diamond (D) minimal surfaces are not only geometrically extremal but extremal for simultaneous transport of heat and electricity. The multifunctionality of such two-phase systems has been further established by demonstrating that they are also extremal when a competition is set up between the effective bulk modulus and electrical (or thermal) conductivity of the bicontinuous composite. Here we compute the fluid permeabilities of these and other triply periodic bicontinuous structures at a porosity ϕ=1∕2 using the immersed-boundary finite-volume method. The other triply periodic porous media that we study include the Schoen gyroid (G) minimal surface, two different pore-channel models, and an array of spherical obstacles arranged on the sites of a simple cubic lattice. We find that the Schwartz P porous medium has the largest fluid permeability among all of the six triply periodic porous media considered in this paper. The fluid permeabilities are shown to be inversely proportional to the corresponding specific surfaces for these structures. This leads to the conjecture that the maximal fluid permeability for a triply periodic porous medium with a simply connected pore space at a porosity ϕ=1∕2 is achieved by the structure that globally minimizes the specific surface.

关键词： EXACT COMPUTATION FLOW SIMULATIONS COMPOSITES TRANSPORT SYSTEMS PHASES STEP

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Recognition of binding patterns common to a set of protein structures

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9th Annual International Conference on Research in computational Molecular Biology, RECOMB 2005

作者： Shatsky, Maxim Shulman-Peleg, Alexandra Nussinov, Ruth Wolfson, Haim J. School of Computer Science Faculty of Exact Sciences Tel Aviv University Tel Aviv 69978 Israel Sackler Inst. of Molecular Medicine Sackler Faculty of Medicine Tel Aviv University Tel Aviv 69978 Israel Basic Research Program SAIC-Frederick Inc. Lab. of Experimental and Computational Biology Frederick MD 21702 United States

ISBN: (纸本)3540258663

We present a novel computational method, MultiBind, for recognition of binding patterns common to a set of protein structures. It is the first method which performs a multiple alignment between protein binding sites in the absence of overall sequence, fold or binding partner similarity. MultiBind recognizes common spatial arrangements of physico-chemical properties in the binding sites. These should be important for recognition of function, prediction of binding and drug design. We discuss the theoretical aspects of the computational problem of multiple structure alignment. This problem involves solving a 3D k-partite matching problem, which we show to be NP-Hard. The MultiBind method, applies an efficient Geometric Hashing technique to detect a potential set of multiple alignments of the given binding sites. To overcome the exponential number of possible multiple combinations it applies a very efficient filtering procedure which is heavily based on the selected scoring function. Our method guarantees detection of an approximate solution in terms of pattern proximity as well as cardinality of multiple alignment. We show applications of MultiBind to several biological targets. The method recognizes patterns which are responsible for binding small molecules such as estradiol, ATP/ANP and transition state analogues. The presented computational results agree with the available biological ones. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Proteins

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Supporting the comparison of choropleth maps using an evolutionary algorithm

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Cartography and Geographic Information science 2005年第4期32卷 347-358页

作者： Xiao, Ningchuan Armstrong, Marc P. Department of Geography The Ohio State University 1036 Derby Hall Columbus OH 4320 United States Department of Geography Program in Applied Mathematical and Computational Science The University of Iowa Iowa City IA 52242 United States

Choropleth maps can be used to compare the patterns exhibited by different spatial variables. In this paper, we develop an evolutionary algorithm that can be used to generate classifications that allow a user to explore the spatial patterns of multiple choropleth maps in terms of their visual correlation and the equality of area contained in each class. Synthetic and census data are used to demonstrate the effectiveness of our approach.

关键词： Mapping

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MAPPIS: Multiple 3D alignment of protein-protein interfaces

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1st International Symposium on computational Life sciences, CompLife 2005

作者： Shulman-Peleg, Alexandra Shatsky, Maxim Nussinov, Ruth Wolfson, Haim J. School of Computer Science Raymond and Beverly Sackler Faculty of Exact Sciences Tel Aviv University Tel Aviv 69978 Israel Sackler Inst. of Molecular Medicine Sackler Faculty of Medicine Tel Aviv University Tel Aviv 69978 Israel Basic Research Program SAIC-Frederick Inc. Lab. of Experimental and Computational Biology Frederick MD 21702 United States

ISBN: (纸本)3540291040

A protein-protein interface (PPI) is defined by a pair of regions of two interacting protein molecules that are linked by non-covalent bonds. Recognition of conserved 3D patterns of physico-chemical interactions may suggest their importance for the function as well as for the stability and formation of the protein-protein complex. It may assist in discovery of new drug leads that target these interactions. We present a novel method, MAPPIS, for multiple structural alignment of PPIs which allows recognition of a set of common physico-chemical properties and their interactions without the need to assume similarity of sequential patterns or backbone patterns. We show its application to several biological examples, such as alignment of interfaces of G proteins with their effectors and regulators, as well as previously created clusters of interfaces. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Proteins

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Numerical Simulation of Nanopulse Penetration of Biological Matter Using the z -Transform

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Journal of Mathematical Modelling and Algorithms 2005年第1期4卷 99-110页

作者： S. Su W. Dai D. T. Haynie R. Nassar N. Simicevic Ph.D. Program in Computational Analysis and Modeling College of Engineering & Science Louisiana Tech University Ruston USA Mathematics & Statistics College of Engineering & Science Louisiana Tech University Ruston USA Biomedical Engineering College of Engineering & Science Louisiana Tech University Ruston USA Physics College of Engineering & Science Louisiana Tech University Ruston USA Institute for Micromanufacturing College of Engineering & Science Louisiana Tech University Ruston USA

Short duration, fast rise time ultra-wideband (UWB) electromagnetic pulses (“nanopulses”) are generated by numerous electronic devices in use today. Moreover, many new technologies involving nanopulses are under development and expected to become widely available soon. Study of nanopulse bioeffects is needed to probe their useful range in possible biomedical and biotechnological applications, and to ensure human safety. In this work we develop a computational approach to investigate electromagnetic fields in biological cells exposed to nanopulses. The simulation is based on a z-transformation of the electric displacement and a second-order Taylor approximation of a Cole–Cole expression for the frequency dependence of the dielectric properties of tissues, useful for converting from the frequency domain to the time domain. Maxwell’s equations are then calculated using the finite difference time domain method (FDTD), coupled with a perfectly matched layer to eliminate reflections from the boundary. Numerical results for a biological cell model are presented and discussed.

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Pretest probability assessment derived from attribute matching

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BMC Medical Informatics and Decision Making 2005年第1期5卷 1-11页

作者： Kline, Jeffrey A. Johnson, Charles L. Pollack Jr., Charles V. Diercks, Deborah B. Hollander, Judd E. Newgard, Craig D. Garvey, J. Lee Department of Emergency Medicine Carolinas Medical Center Charlotte NC United States Computational Biology Program BreathQuant Medical Systems Inc. Charlotte NC United States Department of Emergency Medicine Pennsylvania Hospital Philadelphia PA United States Department of Emergency Medicine University of California at Davis Sacramento CA United States Department of Emergency Medicine Hospital of the University of Pennsylvania Philadelphia PA United States Department of Emergency Medicine Oregon Health and Science University Medical Center Portland OR United States

Background: Pretest probability (PTP) assessment plays a central role in diagnosis. This report compares a novel attribute-matching method to generate a PTP for acute coronary syndrome (ACS). We compare the new method with a validated logistic regression equation (LRE). Methods: Eight clinical variables (attributes) were chosen by classification and regression tree analysis of a prospectively collected reference database of 14,796 emergency department (ED) patients evaluated for possible ACS. For attribute matching, a computer program identifies patients within the database who have the exact profile defined by clinician input of the eight attributes. The novel method was compared with the LRE for ability to produce PTP estimation <2% in a validation set of 8,120 patients evaluated for possible ACS and did not have ST segment elevation on ECG. 1,061 patients were excluded prior to validation analysis because of ST-segment elevation (713), missing data (77) or being lost to follow-up (271). Results: In the validation set, attribute matching produced 267 unique PTP estimates [median PTP value 6%, 1^st-3^rd quartile 1-10%] compared with the LRE, which produced 96 unique PTP estimates [median 24%, 1^st-3^rd quartile 10-30%]. The areas under the receiver operating characteristic curves were 0.74 (95% CI 0.65 to 0.82) for the attribute matching curve and 0.68 (95% CI 0.62 to 0.77) for LRE. The attribute matching system categorized 1,670 (24%, 95% CI = 23-25%) patients as having a PTP < 2.0%;28 developed ACS (1.7% 95% CI = 1.1-2.4%). The LRE categorized 244 (4%, 95% CI = 3-4%) with PTP < 2.0%;four developed ACS (1.6%, 95% CI = 0.4-4.1%). Conclusion: Attribute matching estimated a very low PTP for ACS in a significantly larger proportion of ED patients compared with a validated LRE. © 2005 Kline et al;licensee BioMed Central Ltd.

关键词： Acute Coronary Syndrome Pretest Probability Emergency Department Patient Validation Population Regression Tree Analysis

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Experiments on Random Packings of Ellipsoids

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Physical Review Letters 2005年第19期94卷 198001-198001页

作者： Weining Man Aleksandar Donev Frank H. Stillinger Matthew T. Sullivan William B. Russel David Heeger Souheil Inati Salvatore Torquato P. M. Chaikin Department of Physics and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Chemistry and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Chemical Engineering and Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Department of Psychology and Center for Neural Science New York University New York New York 10003 USA

Recent simulations indicate that ellipsoids can pack randomly more densely than spheres and, remarkably, for axes ratios near 1.25∶1∶0.8 can approach the densest crystal packing (fcc) of spheres, with a packing fraction of 74%. We demonstrate that such dense packings are realizable. We introduce a novel way of determining packing density for a finite sample that minimizes surface effects. We have fabricated ellipsoids and show that, in a sphere, the radial packing fraction ϕ(r) can be obtained from V(h), the volume of added fluid to fill the sphere to height h. We also obtain ϕ(r) from a magnetic resonance imaging scan. The measurements of the overall density ϕavr, ϕ(r) and the core density ϕ0=0.74±0.005 agree with simulations.

关键词： .ellipsoids Princeton New Jersey

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Mapping impervious surface type and sub-pixel abundance using hyperion hyperspectral imagery

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Geocarto International 2005年第4期20卷 3-10页

作者： Falcone, James A. Gomez, Richard National Water-Quality Assessment (NAWQA) Program U.S. Geological Survey Mail Stop 413 Reston VA 20192 12201 Sunrise Valley Dr. United States Center for Earth Observing and Space Research School of Computational Science George Mason University Fairfax VA 22030 4400 University Drive United States

Impervious surfaces have been identified as an important and quantifiable indicator of environmental degradation in urban settings. A number of research efforts have been directed at mapping impervious surface type using multispectral imagery. To date, however, no studies have compared equivalent techniques using multispectral and hyperspectral imagery to that end. In this study, data from NASA's 220-channel Hyperion instrument were used to: a) delineate three types of impervious surface, and b) map sub-pixel percent abundance for a study site near Washington, D.C., USA. The results were compared with the results of similar methods using same-spatial-resolution Landsat ETM+ data for mapping impervious surface type, and with the results of the U.S. Geological Survey's National Land Cover Data (NLCD) 2001 impervious surface data layer, which is derived from Landsat and high-resolution Ikonos data. The accuracy of discriminating impervious surface type using Hyperion data was assessed at 88% versus Landsat at 59%. The sub-pixel percent impervious map corresponded well with the NLCD 2001;impervious surface in the study area was calculated at 29.3% for NLCD 2001 and 28.4% for the Hyperion-derived layer. The results suggest that fairly simple techniques using hyperspectral data are effective for quantifying impervious surface type, and that high-spectral- resolution imagery may be a good alternative to high-spatial-resolution data.

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An Exponential Matrix Product Based Representation for Generalized Hypergeometric Functions of TypepFp

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Applied Numerical Analysis & computational Mathematics 2005年第1期2卷

作者： N. A. Baykara İrem Yaman Metin Demiralp Mathematics Department Faculty of Sciences and Letters Marmara University Göztepe 34722 İstanbul Turkey Group for Science and Methods of Computing Computational Science and Engineering Program Informatics Institute İstanbul Technical University Maslak 34469 İstanbul Turkey Phone: +90 212 285 70 77 Fax: +90 212 285 70 73 Phone: +90 212 285 70 82 Fax: +90 212 285 70 73

In this work, a new representation is developed for generalized hypergeometric functions of type p F p . To this end a first order vector differential equation is constructed in a way such that the derivative of the unknown vector has unit matrix coefficient. The solution vector differential equation is rewritten in the form of a series expansion. An infinite process of factor extractions and annihilations is employed to construct finally a vector differential equation that can be easily solved. Truncation of this scheme can be used to get approximations to hypergeometric functions of type p F p . A simple, yet meaningful, implementation seems to give quite promising results. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

关键词： Exponential matrix factorization generalized hypergemetric function

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