Contents -- Some New Directions in Science on Computers -- 1 Preface: -- Fluids -- CFD ANALYSIS AND DESIGN OPTIMIZATION USING PARALLEL COMPUTERS -- 1 INTRODUCTION -- 2 MATHEMATICAL MODEL -- 3 NUMERICAL METHOD -- 3.1 SPATIAL DISCRETIZATION -- 3.2 TIME STEPPING SCHEME FOR STEADY-STATE SOLUTIONS -- 3.3 ACCELERATION OF STEADY FLOW CALCULATIONS -- 3.4 A MULTIGRID IMPLICIT SCHEME FOR UNSTEADY FLOW -- 3.5 DYNAMIC REMESHING AND MESH MOVEMENT -- 4 DOMAIN DECOMPOSITION AND PARALLEL IMPLEMENTATION -- Parallel Efficiency -- 5 COMPUTATIONS OF STEADY AND TIME-DEPENDENT FLOWS -- 5.1 STEADY EULER AND RANS ANALYSIS -- 5.2 TIME-RESOLVED HELICOPTER ROTOR -- Rigid Rotor-Navier-Stokes Hover -- Rigid Rotor-Euler Forward Flight -- Aeroelastic Rotor-Euler Forward Flight -- 6 THE ADJOINT APPROACH TO OPTIMAL DESIGN -- 6.1 GENERAL FORMULATION -- 6.2 EXAMPLES OF DESIGN OPTIMIZATION -- Transonic Constrained Aircraft Design -- Supersonic Constrained Aircraft Design -- 7 CONCLUSIONS AND FUTURE DEVELOPMENTS -- ACKNOWLEDGMENTS -- NUMERICAL SIMULATIONS OF GROWTH KINETICS AND SPINODAL DECOMPOSITION IN FLUIDS -- 1 Introduction -- 2 Growth Kinetics -- 3 Quantities of Interest -- 4 Langevin method -- 5 Lattice Boltzmann -- 6 Finite Volume method -- Acknowledgments -- References -- MODERN SHOCK CAPTURING METHODS FOR CONSERVATION LAWS -- 1 Introduction -- 1.1 Hyperbolic Systems -- 1.2 The Development of Shocks -- 1.3 Viscous Solutions -- 1.4 Numerical Difficulties -- 2 Reconstructions -- 2.1 Conservative Schemes -- 2.2 Spatial Reconstruction -- 2.3 Nonlinear Systems -- 2.4 The Roe Average -- 2.5 Time Discretization -- 3 Time Evolution I: The Godunov Methods -- 3.1 Solutions of the Riemann Problem -- 3.2 The Godunov Method -- 3.3 Roe's Approximate Riemann Solver -- 3.4 An Entropy Fix -- 3.5 High Order Godunov Methods.

4 Time Evolution II: Methods Free of Riemann Solvers and Characteristic Decompositions -- 4.1 Non-Oscillatory Central Differencing -- 4.2 Kinetic Schemes -- 4.3 Relaxation Schemes -- 5 Higher Dimensional Problems -- 6 Concluding Remarks -- Acknowledgments -- References -- Materials -- SIMULATING MATERIALS FAILURE USING PARALLEL MOLECULAR DYNAMICS -- 1 Introduction -- 2 Methodology -- 3 Doing Parallel MD Computation -- 4 Computer Experiments For Two Dimensions -- 5 Computer Experiments For Three Dimensions -- Acknowledgments -- References -- SEMICONDUCTOR DEVICE PHYSICS AND THE MODELING OF SMALL SEMICONDUCTOR DEVICES -- 1 Introduction -- 2 Device Modeling Depends on Physics Modeling -- 2.1 Effect of the bandstructure model -- 2.2 Calibration of bulk energy bands and scattering rates -- 3 Physics Modeling Depends on Device Modeling -- 3.1 Energetic electrons at the Si-Si02 interface -- 3.2 Low energy electrons and quantization at the Si-Si02 interface -- 3.3 The importance of dynamic screening in electron-electron scattering -- 4 Conclusions -- Acknowledgments -- References -- Statistical Mechanics -- CELLULAR AUTOMATA AND SELF ORGANIZED CRITICALITY -- 1 Self-organized Criticality -- 2 Cellular Automata -- 3 Conway's Life -- 4 Fredkin's modulo two rule -- 5 Reversible rules -- 6 Forest fires and bunny wars -- 7 The sandpile revisited -- 8 An isomorphism -- 9 Concluding remarks -- Acknowledgments -- References -- Chemistry -- POLYMER SIMULATION USING CELLULAR AUTOMATA:2-D MELTS, GEL-ELECTROPHORESIS AND POLYMER COLLAPSE -- 1 Introduction -- 2 Cellular Automata -- 3 Cellular Automata for Polymer Dynamics4,9-12 -- 4 Two-Space Algorithm4,9-12 -- 5 Implementation of the Two-Space Algorithm4,9-12 -- 6 Application to 2-0 Melts -- 7 Application to Gel-electrophoresis -- 8 Application to Polymer Collapse -- Bibliography -- Biology.

PREDICTION OF DNA STRUCTURAL VARIABILITY: A NEW COMPUTATIONAL METHOD FOR FINDING DNA REGULATORY REGIONS -- 1 Introduction -- 2 DNA Superhelicity and Destabilization in vivo -- 3 The Calculation of DNA Destabilization Profiles -- 3.1 The Analysis of Superhelical Denaturation -- 4 Destabilization Occurs Preferentially at regulatory Regions -- 5 Discussion -- Acknowledgment -- References -- ANALYSIS OF POPULATION PHENOMENA IN NEURONAL NETWORKS WITH ELECTROPHYSIOLOGY AND COMPUTER SIMULATIONS -- 1 Introduction -- 2 Technical Aspects -- 3 Selected Examples -- 3.1 Bursting in Pyramidal Neurons -- 3.2 Ectopic Action Potentials -- 3.3 Rhythmic Dendritic Ca Spikes -- 3-4 Synchronization of Neuronal Bursts by Fast-acting Excitatory Synapses -- 3.5 Sustained Seizures In Vitro -- 3.6 Are Spikes Initiated in Dendrites of Interneurons? -- 3.7 Synchronization of Interneurons by Gap Junctions -- 3.8 The "40 Hz" Rhythm and Synchronization by Inhibition Between Interneurons -- 4 Concluding Lesson -- Acknowledgements -- References -- A SIMULATION OF THE IMMUNE SYSTEM: EXPERIMENTS IN MACHINA -- 1 Introduction -- 2 Model -- 2.1 The Automaton -- 2.2 The Cast of Characters -- 2.3 The Processing of Antigen -- 2.4 Receptor Diversity -- 2.5 Procedure -- 3 Immunization -- 4 Affinity Maturation -- 4.1 Mutations -- 4.2 Mutation-Dependent Maturation in a System with Artificial Holes in theRepertoire. -- 4.3 The Interaction Strength Scale and Affinity. -- 4.4 Mutation Rate. -- 5 The MHC -- 6 Conclusions -- References -- Astrophysics -- APPLICATIONS OF N-BODY METHODS TO STUDIES OF LARGE SCALE STRUCTURE FORMATION IN THE UNIVERSE -- 1 Introduction -- 2 Equations of Motion -- 2.1 Dynamical Equations -- 2.2 Initial Conditions -- 3 Numerical Methods -- 3.1 Background -- 3.2 Particle Mesh Methods -- Density Assignments -- 3.3 Potential Calculations -- 3.4 Time Integration Schemes.

4 Variants of the PM Method: The Quest for Higher Resolution -- 5 Analysis of the Simulations Using Percolation and the MST -- 6 Conclusions -- Acknowledgments -- Geophysics -- GLOBAL OCEAN SIMULATIONS WITH AN ISOPYCNIC COORDINATE MODEL -- 1 Introduction -- 2 Ocean Modeling in Isopycnic Coordinates -- 3 A Near-Global Coarse-Mesh Simulation Experiment -- 3.1 Zonally averaged overturning in individual basins -- 3.2 Annually averaged diapycnal flux fields -- 3.3 Interannual and Interdecadal Variability -- 3.4 Tracer transport by abyssal currents. -- 4 A Near-Global Fine-Mesh Simulation Experiment -- 5 Summary and Outlook -- Acknowledgment -- References.