Computational Science ― ICCS 2003: International Conference, Melbourne, Australia and St. Petersburg, Russia, June 2–4, 2003. Proceedings, Part III (Lecture Notes in Computer Science, 2659)

Some of the most challenging problems in science and engineering are being addressed by the integration of computation and science, a research ?eld known as computational science. Computational science plays a vital role in fundamental advances in biology, physics, chemistry, astronomy, and a host of other disciplines. This is through the coordination of computation, data management, access to instrumentation, knowledge synthesis, and the use of new devices. It has an impact on researchers and practitioners in the sciences and beyond. The sheer size of many challenges in computational science dictates the use of supercomputing, parallel and distri- ted processing, grid-based processing, advanced visualization and sophisticated algorithms. At the dawn of the 21st century the series of International Conferences on Computational Science (ICCS) was initiated with a ?rst meeting in May 2001 in San Francisco. The success of that meeting motivated the organization of the - cond meeting held in Amsterdam April 21–24, 2002, where over 500 participants pushed the research ?eld further. The International Conference on Computational Science 2003 (ICCS 2003) is the follow-up to these earlier conferences. ICCS 2003 is unique, in that it was a single event held at two di?erent sites almost opposite each other on the globe – Melbourne, Australia and St. Petersburg, Russian Federation. The conference ran on the same dates at both locations and all the presented work was published in a single set of proceedings, which you hold in your hands right now. Computational Science - ICCS 2003 Preface Organization Table of Contents, Part III Table of Contents, Part I Table of Contents, Part II Table of Contents, Part IV A Bayes Algorithm for the Multitask Pattern Recognition Problem - Direct Approach Introduction Direct Approach to the Multitask Pattern Recognition Algorithm Multitask Recognition with Learning References The Development of a Virtual Reality Environment to Model the Experience of Schizophrenia Introduction The VISAC Laboratory and Remote Visualisation Aims of the Project Software Development Feedback Further Work Conclusion References An Optimization-Based Approach to Patient Grouping for Acute Healthcare in Australia Introduction The Nonsmooth Optimization Approach to Clustering An Optimization Algorithm for Solving Clustering Problem Complexity Reduction for Large-Scale Data Sets Feature Selection Number of Instances Reduction Case Study Results and Discussion Conclusions References Dynamic Parameterization to Simulate DIN Export Due to Gypsy Moth Defoliation Introduction Method Result Discussion Transformation of Organic Nitrogen to Inorganic Nitrogen Plant Uptake Evapotranspiration (ET) Soil Temperature Interception of Precipitation Conclusion References Multi-model Simulations of Chicken Limb Morphogenesis Introduction Computational Model The Cellular Potts Model (CPM) Reaction-Diffusion Equations State Transition Model Modeling of Zones Integration of Submodels Software Discussion of Simulation Results for Chicken Limb Development References PROTOMOL: A Molecular Dynamics Research Framework for Algorithmic Development Introduction Physical and Mathematical Background Numerical Integrators Force Evaluation Framework Design Force Design Performance Monitoring Performance Evaluation Discussion References An Efficient Navigation Method for Virtual Endoscopy Using Volume Ray Casting Introduction Related Work Navigation Method Using Volume Ray Casting Calculating Depth Information Determining the Direction of Rotation of Virtual Camera Calculating the Rotation Angle Experimental Results Conclusion References Constructing a Near-Minimal-Volume Computational Box for Molecular Dynamics Simulations with Periodic Boundary Conditions Introduction Boxes, Their Related Lattices and Calculating Lattice Packings Implementation Results Discussion and Conclusion References Recast of the Outputs of a Deterministic Model to Get a Better Estimate of Water Quality for Decision Makings Introduction Evaluation of CBEM Calibration Method for Recast of the CBEM Calibration Results of the Recast of CBEM Calibration Recast for the Cells without Observed Data Application to the Recast of Model Scenarios Discussion Assumption and Validity of the Method Problem with Ordered Data Regression on Paired or Non-paired Data Subdivision of Time Period for Regression Conclusion References A Fuzzy Approach for Overcurrent Relays Simulation Introduction The New Method Case Study Fuzzy Model Application Fuzzy Model of RSA20 OC Relay Fuzzy Model of CRP9 OC Relay Conclusion Glossary Refrences A Knowledge-Based Technique for Constraints Satisfaction in Manpower Allocation Introduction Problem Formulation Knowledge Representations and Relations Applying the Knowledge-BasedMA Algorithm Implementation and Methodologies Rule-Based Methodologies for Backtracking Fuzzification and De-fuzzification Implementation and E xperimental Results References A Symbolic Approach to Vagueness Management Introduction M-Valued Predicate Logic Representation of Nuanced Statements Linguistic Modifiers Exploitation of Nuanced Statements First GMP Rule GMP Rules Using Precision Modifiers Generalized Production System Conclusion References Development of Multiple Job Execution and Visualization System on ITBL System Infrastructure Software and Its Utilization for Parametric Studies in Environmental Modeling Introduction ITBL System and Its Infrastructure Software Applied Example and the Contents of the Development Details of Functions Summary References A Genetic Algorithm for Predicting RNA Pseudoknot Structures Introduction Genetic Algorithm Stem Pool Generation Initial Population Method and Results Conclusion References Computational Approach to Structural Analysis of Protein-RNA Complexes Introduction Terminology and Notation The Amino Acids: Main Chain, Side Chain The Nucleic Acids: Base, Backbone, Base Pair, Base Step The Interactions: Single, Bidentate and Complex Interaction The Hydrogen Bonds: Donor, Acceptor Framework for Analyzing Protein-RNA Binding Structures Dataset Hydrogen Bonds Algorithms Results and Discussion Amino Acids Nucleotide Conclusion References Improved Web Searching through Neural Network Based Index Generation Introduction A Hybrid System for Improved Web Searching Data Collection and Pre-processing Clustering of Web Query Terms Data Shift and Movement Identification Technique Experimental Results on Query Log Analysis Web Users’ Query Interest Pattern Analysis Adaptive Web Query Searching Current Work and Future Research Direction References Neural Network for Modeling Nonlinear Time Series: A New Approach Introduction Neural Net Architecture Nonlinear State Space Representation Bayesian Inferential Algorithm Based on Extended Kalman Filter Simulation Studies Analysis of (BVMT) Conclusion References Export Behaviour Modeling Using EvoNF Approach Introduction The Role of FIS for Explaining the Export Behaviour of MCS Parameterization of Membership Functions Parameterization of T-Norm Operators Chromosome Modeling and Representation Model Evaluation and Experimentation Results EvoNF Training Conclusions References Simulation Studies of a Multi-priority Dual Queue (MPDQ) with Preemptive and Non-preemptive Scheduling Introduction MPDQ Design and Simulation Scheduling Algorithm Preemptive MPDQ Simulation and Analytical Results Comparison of Scheduling Disciplines Loss by Queue Size CDF of Delay Waiting Time by Queue Size Regimes for Preemptive MPDQ CDF of Class 1 Waiting Times Conclusion References Visualization of Protein-Protein Interaction Networks Using Force-Directed Layout Introduction A Partitioned Approach to Graph Drawing Finding Groups Force-Directed Layout for Three-Dimensional Graph Drawing Finding Shortest Paths in Groups Analytical and Empirical Evaluation Discussion and Conclusions References Counting Polyominoes: A Parallel Implementation for Cluster Computing Introduction Enumeration of Polyominoes Transfer Matrix Algorithm Parallelization Results and Conclusion References Hyper-BLAST: A Parallelized BLAST on Cluster System Introduction Related Work Parallelization of BLAST on Cluster System Intra-search Parallelism in NCBI BLAST Extension of Intra-search Parallelism in Hyper-BLAST Performance Evaluation Conclusion and Future Work References Parallel Superposition for Bulk Synchronous Parallel ML Introduction Bulk Synchronous Parallelism \Flat" Functional Bulk Synchronous Parallel Programming The BSMLlib library Library Cost Model Parallel Superposition Examples Related Work References visPerf: Monitoring Tool for Grid Computing Introduction Support for Grid Computing Problems Requirements Monitoring System's Design Approach Local Monitor: {itshape visSensor} Managing and Presenting Monitored Information: {itshape visPerf} Peer-To-Peer Monitor Network Multiple Access Points: Monitor Proxy Case Study: visPerf for NetSolve Related Work Conclusion and Future Work References Design and Implementation of Intelligent Scheduler for Gaussian Portal on Quantum Chemistry Grid Introduction Design Concept of the QC Grid QC Grid Architecture Web-Based User Interfaces Meta-scheduler Knowledge Database Results Database and I/O Archives Computing Nodes Gaussian Portal System Configuration Implementations Experience Discussion Conclusion and Future Plans References Extensions to Web Service Techniques for Integrating Jini into a Service-Oriented Architecture for the Grid Introduction Service Workflow Language Implementation Aspects Conclusions References Multiple-Level Grid Algorithm for Getting 2D Road Map in 3D Virtual Scene Introduction Related Work Virtual Terrain Acquisition Problem Problem Formulation Random Walk Approach Multiple-Level Grid Algorithm Grid Covering (GC) Algorithm Adjacent-Edge Rule The Complexity of the Multiple-Level Grid Algorithm Experiments Experiment 1: Small Virtual Scene Experiment 2: Large Virtual Scene Conclusion and Future Work References Parallelisation of Nonequilibrium Molecular Dynamics Code for Polymer Melts Using OpenMP Introduction The NEMD Code Parallelisation of the NEMD Code Data Dependencies Loop Fusion and Interchange: Performance Improvement by Increasing Parallel Loop Granularity Parallel Regions: Performance Improvement by Reducing fork/joins Efficient Use of Memory Parallelised Code Performance Simulation Results Summary References A Fault Tolerance Service for QoS in Grid Computing Introduction Related Work A Design of a Fault Tolerance Service System Model Expansion of Failure Definition Fault Tolerance Service Fault Detection Service Fault Management Service Simulation Conclusion References Performing Grid Computation with Enhanced Web Service and Service Invocation Technologies Introduction Enhancements to the Grid Job Submission Service Exploiting DIME for Data Transmission in Web Service Interactions Using WS-Security with the Grid Security Infrastructure Integration with General Grid Computing Environment The Client Tool for Service Oriented Grid Computing Exemplar of Grid Computing with Enhanced Web Services Conclusion and Future Work References Software Architecture and Performance Comparison of MPI/Pro and MPICH Background Architectural Characteristics Performance Results Profiler Output Future Work Conclusions References Virtual and Dynamic Hierarchical Architecture for E-science Grid Introduction Overview of VDHA Description of VDHA Formal Definition of VDHA Grid Group Management Protocol (GGMP) Query and Discovery Protocols Authentication Protocol (AP) Message-Based Implementation of VDHA Grid Service Description Framework (GSDF) Synchronizing Schema A Case Study Conclusion References Algorithmic Entropy, Phase Transition, and Smart Systems Introduction Conrad’s Principles Phase Transition Model for Smart System Role of Metric and Algorithmic Entropy Algorithmic Information and K Entropy Hierarchy among Machines Combining Zero and Positive Entropy Machines to Create Smartness Simulating a Mixture of Entropy in Systems Phase Transitions in AI Systems Simulating Nonequilibrium System: Evolutionary Optimization Boolean Satisfiability Problem and Phase Transition Do Critical Exponents and Scaling Laws Exist for Smartness? Matter and Life Conclusion References Computations of Coupled Electronic States in Quantum Dot/Wetting Layer Cylindrical Structures Introduction Position-Dependent Effective Mass Model for Quantum Dot/Wetting Layer Nanostructures Numerical Procedure Computational Analysis of Electronic States in QD/WL Coupled Systems References Deadlock Free Specification Based on Local Process Properties Introduction Theoretical Background The Synchronous Programming Model The Asynchronous Programming Model Conclusions References On the Reconfiguration Algorithm for Fault-Tolerant VLSI Arrays Introduction Preliminaries Algorithms Updating {sl RCRoute} Partial Computing for Logical Row Exclusion Main Algorithm and Complexity Experimental Results Conclusions References Automated Generation of Kinetic Chemical Mechanisms Using Rewriting Introduction Automatic Generation of Combustion Reactions Mechanisms Rewrite Systems Chemical Objects in {sf ELAN} Molecule Representation Reactant Representation Elementary Reactions in {sf ELAN} Generating All Visions Primary Mechanism in {sf ELAN} Conclusions and Further Work References Contraction versus Relaxation: A Comparison of Two Approaches for the Negative Cost Cycle Detection Problem Introduction The Vertex-Contraction Algorithm Implementation Machine Characteristics Graph Data Structures Experimental Setup for Sparse Graphs Conclusions Experimental Setup for Dense Graphs Conclusions Experimental Setup for Cruel Adversary Graphs Conclusions Conclusion References Direct Method for Solving a Transmission Problem with a Discontinuous Coefficient and the Dirac Distribution Introduction Finite Difference Approximation of Problem I Construction of the Solution of (13) Geometry of Domain and Principle of the Successive Elimination of Lines Numerical Algorithm Convergence of Approximate Solutions Function Space $V_h$ Approximate Solution in $V_h$ of Problem I Convergence Theorem References CORBA Based Real-Time Object-Group Platform in Distributed Computing Environments Introduction and Related Works Real-Time Object Group RTOG Structure Timing Constraints Interacting with Components in RTOGs Supporting Object Management Services in RTOGs Supporting Real-Time Services in RTOGs The Execution of RTOG Platform Conclusions References Structural Similarity between XML Documents and DTDs Introduction Related Work Local Similarity Consideration Matching XML Documents with DTD with Errors Allowed Determination of Edit Distance Normalization of Edit Distance Global Similarity Consideration Structural Similarity Experiment Results Conclusion References Web Personalisation with the Cover Coefficient Algorithm Introduction Collecting Click Stream Data The Cover Coefficient Technique and Web Personalisation Conclusions References Infrastructure of an Agile Supply Chain System: A Virtual Agent Modeling Approach Introduction Paradigms of Supply Chain Workflow Tools and Technologies Distributed Object Technology Neural Networks Rule-Based Reasoning Neural Object Module Infrastructure of an Agile Supply Chain System Testing and Evaluation Conclusion References Performance Improvement of Deflection Routing in Optical Burst Switching Networks Introduction Deflection Routing Algorithm Performance Evaluation Conclusion References A Performance Evaluation on Qos-Supporting Multicast Protocol over Conventional Multicast Protocol Introduction Multicast Protocol Source Based Tree Protocol Shared Tree Protocol Protocol Description: The QosMIC Overview Structure and Message Forwarding Method of the QosMIC Multicast Tree Searching Simulation Conclusion References Improving the Performance of Multistage Interconnection Networks under Nonuniform Traffic Pattern on Shorter Cycles Introduction The Proposed Model Calculations for the Required Measures Calculating r(ij), Throughput, and Delay Performance Verification of the Proposed Model Conclusion References Symmetric Tree Replication Protocol for Efficient Distributed Storage System Introduction Review of Earlier Protocols Logarithmic Replication Protocol Grid Protocol The Proposed Protocol Motivation The Proposed Symmetric Tree Protocol Performance Analysis Cost Analysis Logarithmic Protocol Symmetric Tree Protocol Availability Analysis Logarithmic Protocol Symmetric Tree Protocol Conclusion Reference A Group Key Management Supporting Individual Batch Rekeying and Fault Tolerance for Secure Multicast Introduction System Architecture GSM Component Operational Overview of System Group Initiation Member Join GSM Action Key Update Leave & Fault Tolerance Retransmission Key Update Message Data Distribution Performance Analysis Conclusions and Future Work References Architecture for Internal Communication in Multi-gigabit IP Routers Introduction Architecture for High-Speed IP Router Proposed Mechanism for Processing of Non-forwarded Packets Experimental Results Conclusion References Low-Cost Fault-Tolerance Protocol for Large-Scale Network Monitoring Introduction Domain Manager Fault-Tolerance Protocol (DMFTP) Failure Detection and Takeover Recovery Correctness Conclusion References Telecommunication Network Modeling and Planning Tool on ASP Clusters Introduction ASP Model Proposed Introduction AROMA WEB Portal Clusters and Application Administration Telecom Modeling Application Principle ASP Utilization Validation on ASP Cluster Conclusion References Fault-Tolerant Routing in Mesh-Connected 2D Tori Introduction Preliminaries Balanced 4-ary Partitioning Tree The Local Mesh-Connectivity Routing in Locally Mesh-Connected Tori Routing in a Locally $d$-Mesh-Connected Torus Routing in a Locally Mesh-Connected Torus Conclusion References Network-Tree Model and Shortest Path Algorithm Introduction Network-Tree Model Definition of Network-Tree Model Construction of Network-Tree Model Theory Of Path Optimization Shortest Path Algorithm of Expanded Network-Tree Model Preprocessing Procedure Network-Tree Shortest Path ($NTSP$) Algorithm Experimental Results Network-Tree Based on Lattice Structures Experimental Results Interpretation of Results Conclusions References Parallel Genetic Algorithm for a Flow-Shop Problem with Multiprocessor Tasks Introduction Parallel Genetic Algorithm Hardware and Software Environment The Sequential Genetic Algorithm Design of Migration Property of SGA Experimental Results Number of Subgroups Design of Migrations PGAs with Different Crossover Operations Conclusions References Performance Variability of Highly Parallel Architectures Motivation Variation Exists in Application Performance Hypothesis The Basic Tests Architectures Evaluated Test Results EP Variation Changing the Number of Adapters High Variation on the Cray T3E Detecting and Reacting to Variation Conclusions References JDOS: A Jini Based Distributed Operating System Introduction Other Systems Description Communications Remote Execution Remote File System Performance Results Conclusions and Future Developments References Parallel Blocked Sparse Matrix-Vector Multiplication with Dynamic Parameter Selection Method Introduction Experimental Environments Local Computation Optimization The New Blocking Method Selection of the Optimal Blocking Parameter Set The Blocking Parameter Selection Method Data Communication Optimization Implementation of Communication Method Application of New Blocking to the Parallel Environment Numerical Experiment The Dynamic Parameter Selection Method The Performance of Our Parallel SpMxV Library Concluding Remarks References Parallelization of the Discrete Gradient Method of Non-smooth Optimization and Its Applications Introduction Discrete Gradient Method Parallelization Strategies Application: Polyatomic Clusters Problem Results Conclusion References A Parallel Prime Edge-Length Crystallographic FFT Introduction Background Parallel Prime Edge-Length Crystallographic FFT (PCFFT) Computer Experiments References A Service-Oriented Framework for Parallel Medical Image Reconstruction Introduction Parallel Fully 3D Image Reconstruction Parallelization for SMP Clusters Performance Experiments The eMERGE System Reconstruction Services and Server-Side Components Service Manager and Service Registry User Interface and Client-Side Components Service Technologies Jini Web Services Open Grid Service Architecture Experimental Results Conclusions References Parallel Implicit Solution of Full Navier-Stokes Equations Introduction Formulation Navier-Stokes Equations FEM Formulation Numerical Formulation Domain Decomposition For the Momentum Equation Parallel Implementation Results and Discussion References Application of the Confidence Measure in Knowledge Acquisition Process Introduction Decision Problem Statement Rule-Based Decision Algorithm Proposition of Knowledge Confidence Measure Definition Using Confidence Measure for Rule Base Modification Confidence Measure for the Statistical Estimation Contradictions Elimination Algorithm Conclusion References Computational Science and Data Mining Introduction Background PAC-Learnability Framework Agnostic Learning Local and Global Issues in Data Mining PAC-Learnability Analysis for Mining Discussion and Further Work References Data Sharing Model for Sequence Alignment to Reduce Database Retrieve Introduction Traditional Model Traditional Architecture Cost Analysis Grouping Model Grouping Architecture Cost Analysis Carpool Model Carpool Architecture Cost Analysis Performance Evaluation Cost Analysis Simulation Conclusion References Self-Adapting Software for Numerical Linear Algebra Library Routines on Clusters Introduction Related E6orts LAPACK for Clusters Overview Typical Usage Scenario Performance Results Conclusions and Future Work References V-Invariant Methods for Generalised Least Squares Problems Introduction $Vtmspace -thinmuskip {.1667em}$-Invariance $Vtmspace -thinmuskip {.1667em}$-Invariant Factorization Does the Use of the $LDL^{T}$ Factorization of $V$ Make Sense? References Parallelisation of Sparse Grids for Large Scale Data Analysis Introduction Sparse Grids for Predictive Modelling Multiresolution Analysis and Sparse Grids Penalised Least Squares on Sparse Grids Solution of the Penalised Least Squares System Strategies for Exploiting Parallelism Parallelisation across Grids Parallelisation across Data Parallelisation of Solvers Combination of Coarse and Fine Grain Parallelism Conclusion References An Augmented Lanczos Algorithm for the Efficient Computation of a Dot-Product of a Function of a Large Sparse Symmetric Matrix Introduction The Augmented Lanczos Algorithm Alternative Approaches Some Properties Numerical Experiments Example 1 Example 2 Conclusion References Memory Hierarchy Optimizations and Performance Bounds for Sparse ATAx Introduction Memory Hierarchy Optimizations for Sparse $A^TAx$ Upper Bounds on Performance A Latency-Based Execution Time Model A Lower Bound on Cache Misses Experimental Results and Analysis Related Work Conclusions and Future Directions References Issues in the Design of Scalable Out-of-Core Dense Symmetric Indefinite Factorization Algorithms Introduction Diagonal Pivoting Algorithms Challenges for the Parallel Out-of-Core Case Elimination Block Search Strategies Diagonal Pivoting Methods for a Parallel Out-of-Core Algorithm Blocking and Data Layout Issues A Slab-Based Algorithm Exploiting Locality in Interchanges The Need for Improved Memory Scalability A Block-Based Algorithm Conclusions and Future Work References Application of the Multi-level Parallelism (MLP) Software to a Finite Element Groundwater Program Using Iterative Solvers with Comparison to MPI Introduction Purpose The MLP Parallel Programming Paradigm Description of the Application Flow Equations Parallel Paradigm Solvers Tested MLP and MPI Programming Details Initialization Reduction Updating Ghost Nodes Performance Results Conclusions References Visual Parameteric Modeler for Rapid Composition of Parameter-Sweep Applications for Processing on Global Grids Introduction Related Work Architecture Design and Implementation Use Case Study – Molecular Docking Application Conclusion References Method Call Acceleration in Embedded Java Virtual Machines Motivations Related Work Approach Lookup Caching Synchronization Results Conclusion and Future Work References Jade: A Parallel Message-Driven Java Introduction Related Work Jadefuturelet next Parallel Constructs Jadefuturelet next Comparison with Charmkern -0.0emraise 0.3exhbox {++}futurelet next Comparison with Java Translation Issues Implementation Summary and Future Work References Parallel Finite Element Analysis Platform for the Earth Simulator: GeoFEM Introduction Software System Configuration Hybrid Parallel Iterative Solver on the ES [5–7] Parallel Visualization Concluding Remark References Mantle Convection Modeling with Viscoelastic/Brittle Lithosphere: Numerical and Computational Methodology Introduction Mathematical Model Numerical Implementation Computational Method Efficient Parallel Implementation Typical Problem Solver Scaling with Problem Size Parallel Efficiency Discussion References Anisotropic Convection Model for the Earth's Mantle Introduction Mathematical Formulation Numerical Method Application Power Law Induced Anisotropy References Finite Element Simulation of Stress Evolution in a Frictional Contact System Introduction Finite Element Formulation Numerical Investigation of Stress Evolution Discussion and Conclusions References Transparent Boundary Conditions for Wave Propagation on Unbounded Domains Introduction Theoretical Approach The One-Dimensional Wave Equation Transparent Boundary Conditions in Higher Dimensions Numerical Results Using Finite Di .erences Concluding Remarks References A 2D Numerical Model for Simulating the Physics of Fault Systems Introduction Numerical Model Calculation of Forces Elastic Forces Viscous Forces Thermal Noise Vertical Component of Elastic Forces on Split Nodes Horizontal Component of Frictional and Elastic Forces on Split Nodes Time Integration Scheme Numerical Examples Waves Traveling through a Locked Fault Rupture of a Homogeneous Fault Rupture of a Heterogeneous Fault Multi-fault Simulation Conclusions References Strategies for the Detection and Analysis of Space-Time Patterns of Earthquakes on Complex Fault Systems Introduction Earthquakes Numerical Simulations Unobservable Dynamics Multiscale Dynamics The Virtual California Model Software Technology Community Grid Final Remarks References Texture Alignment in Simple Shear Introduction Mathematical Formulation Cosserat Deformation Measures Constitutive Relationships for Granular Materials Director Theory Specific Viscous Relationships Applications Silo Discharge Self-Alignment Conclusions References Mechanical Properties of the Earth's Crust with Self-Similar Distribution of Faults Introduction Elastic Moduli of Earth’s Crust with Self-Similar Distributions of Faults On the Possibility of Wave Propagation Conclusions References Performance Modeling Codes for the QuakeSim Problem Solving Environment Introduction Scientific Significance Technology Accomplishments Status and Plans References Interacting Data Services for Distributed Earthquake Modeling Introduction QuakeSim Portal Architecture Overview XML Schemas for Code I/O Implementing Services for the Data Model Data Service Architecture Summary and Conclusions References Apparent Strain Localization and Shear Wave Dispersion in Elastic Fault Gouge with Microrotations Introduction Three-Dimensional Continuum Elastic Model of Granulate Materials Simple Shear of Elastic Gouge with Microrotations On the Possibility of Determining the Localization Regime from Wave Velocity Measurements Conclusion References Efficient Implementation of Complex Particle Shapes in the Lattice Solid Model Introduction The Algorithm Contact Detection Calculation of Forces and Particle Motions Verification Test Conclusions References A Method of Hidden Markov Model Optimization for Use with Geophysical Data Sets Introduction Hidden Markov Models Optimization Procedure for the HMM Multimodality of the HMM Objective Function Q-Function Penalty Terms Experimental Results Conclusions and Future Work References A Performance Model of Non-deterministic Particle Transport on Large-Scale Systems Introduction MCNP Performance Model Application Model System Model Performance Study of MCNP Conclusion References A Compiler Approach to Performance Prediction Using Empirical-Based Modeling Introduction State-of-the-Art Performance-Aware Compilation Performance Prediction Performance Modeling & Understanding Empirical Modeling Overview Program Skeletons How to Derive Models Applications Compiler Optimizations Generating Performance Assertions Interactive Performance Understanding Research Challenges Summary References A Performance Prediction Framework for Scientific Applications Introduction The Convolution Method Speeding Up Tracing Results and Discussion References Identification of Performance Characteristics from Multi-view Trace Analysis Introduction Identification of Performance Characteristics from Multiple Executions Call-Graph Collection Multi-view Visualisation Future Work and Conclusions References Compiler Directed Parallelization of Loops in Scale for Shared-Memory Multiprocessors Introduction Scale Reference Groups Machine Model Optimization Algorithm Implementation MemoryOrder and NearbyPermutation LoopStripMine markParallel Results Execution Time Cache Performance Related Work Locality Optimizations Parallelizing Compilers Conclusion References A New Data Compression Technique for Event Based Program Traces Introduction Construction of Meta-events Model Implementation Naming Extending Meta-events to Event-Patterns Comparison of Timestamp Vectors Event-Patterns Over-All Data Compression Ratio Further Details Correction Pairs Name Spaces Examples Future Plans Related Work References Exploiting Stability to Reduce Time-Space Cost for Memory Tracing Introduction Memory Trace Break-Down Detecting Memory Stride Patterns Application Signatures Generating Memory Traces: Analysis of Results Conclusion and Future Work References Oh Behave! Agents-Based Behavioral Representations in Problem Solving Environments Introduction EMCAS Automatic Ontology Construction and Extension Personalization Real-Time Visual Representations within PSE Conclusion References JBeanStudio: A Component-Oriented Visual Software Authoring System for a Problem Solving Environment - Supporting Exploratory Visualization - Introduction Diversity of Computational Tools Need for Better Integration JBeanStudio System Architecture Component Wiring and Dataflow Interactively Building a Visualization Application Example: Exploratory Visualization Limitations and Future Works Conclusion References Multi-agent Approach for Visualisation of Fuzzy Systems Introduction Fuzzy Systems and Their Visualisation Requirements A Multi-agent Visualisation Framework Control Agent Computation Agent Symbolic Agent Visualization Agent Visual Features Higher Spatial Representations Profile Agent Conclusion and Future Work References Towards Biomedical Problem Solving in a Game Environment Introduction System Architecture Biological “World Model” Biological Characters Biological Interactions Implementation A Case S The four-volume set LNCS 2657, LNCS 2658, LNCS 2659, and LNCS 2660 constitutes the refereed proceedings of the Third International Conference on Computational Science, ICCS 2003, held concurrently in Melbourne, Australia and in St. Petersburg, Russia in June 2003. The four volumes present more than 460 reviewed contributed and invited papers and span the whole range of computational science, from foundational issues in computer science and algorithmic mathematics to advanced applications in virtually all application fields making use of computational techniques. These proceedings give a unique account of recent results in the field