Frontiers of Computational Science (eBook)

Preface 5
Contents 7
List of Contributors 13
Plenary & Keynote Papers
Computational Methods Combining Large Eddy Simulation with Approximate Wall- Layer Models for Predicting Separated Turbulent Near- Wall Flows 27
Numerical Experimentation: A Third Way to Study Nature 39
Recent Computational Developments in Quantum Conductance and Field Emission of Carbon Nanotubes 55
Energy Landscapes of Protein Self-Assembly: Lessons from Native Topology- Based Models 60
A Brief Introduction to Krylov Space Methods for Solving Linear Systems 75
Recent Developments in DNS and Modeling of Rotating Wall- Turbulent Shear Flows with Heat Transfer 85
Contribution of Computational Biology and Structural Genomics to Understand Genome and Transcriptome 96
Invited Papers 102
Achromatic and Chromatic Visual Information Processing and Discrete Wavelets 103
On Decaying Two-Dimensional Turbulence in a Circular Container 110
A Study Toward Improving Accuracy of Large Scale Industrial Turbulent Flow Computations 117
Direct Numerical Simulations of Turbulent Premixed Flames with Realistic Kinetic Mechanisms 124
Variational Monte Carlo Studies of Superconductivity in .-BEDT-TTF Salts 131
Simulation for Measurements of Electric Properties of Surface Nanostructures 135
Ultra-Fast Dynamics in Nanocarbon Explored by TDDFT- MD Simulations 141
Heat Transport in Nanoscale Objects: Classical to Quantum 147
Aromaticity Driven Rupture of CN and CC Multiple Bonds 153
Protein Function Prediction in Proteomics Era 159
What We can Learn about Protein Folding from Recent Progress in Structure Prediction 165
Brownian Dynamics Approach to Protein Folding 172
A Fourth Type of Secondary Structure Breaker 179
Neighborhood Parallel Simulated Annealing 185
New Computing System Architecture for Simulation of Biological Signal Transduction Networks 191
Convergence Analysis of GMRES Methods for Least Squares Problems 195
A Numerical Method for Calculating the Green’s Function Arising from Electronic Structure Theory 202
General Contribution 209
Direct Numerical Simulation of Turbulent Channel Flow Imposed with Spanwise Couette Flow 210
Reynolds-Number Dependence of Transport Barriers in Chaotic Mixing 215
On the Treatment of Long-range Electrostatic Interactions in Biomolecular Simulations 219
DNS of Turbulent Channel Flow Obstructed by Rectangular Ribs 225
Source Models of Gravity Waves in an F-plane Shallow Water System 231
Direct Numerical Simulation of Neutrally Stratified Ekman Boundary Layer 236
Application of the Renormalization Group Analysis to a Noisy Kuramoto– Sivashinsky Equation and its Numerical Simulation 240
Wavelet-Based Statistics in High-Resolution Direct Numerical Simulations of Three- Dimensional Homogeneous Isotropic Turbulence 244
Hydrophobic Hydration on Nanometer Length Scale 248
Ultra-Fast Genome Wide Simulation of Biological Signal Transduction Networks: Starpack 252
Molecular Dynamics Study on Interaction of C-Component Dislocation Loop and Edge Dislocation in a-Zirconium 256
Theoretical Analysis of Intramolecular Interaction 261
Effect of Nanoscale Structure of Solid Surface on Moving Droplet 266
Proximity Effect in NS Junctions in the Presence of Anderson Impurities 271
Wiedemann–Franz Law in Diffusive Normal Metal/p-Wave Superconductor Junctions 275
Nodal Structures of Wave Functions in Chaotic Billiards 279
Elongation of Water Residence Time at the Protein Interior in Aqueous Solution with Ectoine 283
Analytical Model for Protein Folding 288
Theoretical Research on Dynamics of the Genetic Toggle Switch 293
Non-Condon Theory for the Energy Gap Dependence of Electron Transfer Rate 297
Density Functional Molecular Orbital Calculations on Longer DNA– DNA and PNA– DNA Double Strands 302
A Parallel Computing Framework for Nonexperts of Computers: Easy Installation, Programming and Execution of Master– Worker Applications Using Spare Computing Power of PCs 307
Derivation of TIS for Search Performance Quantification on HC Method 311
Improvement of Search Performance of Genetic Algorithm Through Visualization of Search Process 315
A Proposal for Analysis of SD Evaluation Data by Using Clustering Method Focused on Data Distribution 319
Multiobjective Evolutionary RBF Networks and Its Application to Ensemble Learning 323
A New Concept of Cerebral Autoregulation Using Mathematical Expressions 328
Evolution Strategies on Desktop Grid Environment Using Scheduling Algorithms RR for Same Length Tasks 333
Solution of Black-Scholes Equation By Using RBF Approximation 338
Visualization of Differences on Two Subjects’Impression Words Based on Correlationof SD Data 343
Evaluation of High Imaging Quality LCDs Which Features Moving Picture: Comparison using Stabilometers 347
Template Translation for Multilingual Disaster Information System 351
An Application of Double-Wayland Algorithm to Detect Anomalous Signals 355