Contents

• Introduction
• stokes: Stokesian Dynamics Simulator
  • stokes3: Stokesian Dynamics Simulator
    • Output Parameters
    • System Parameters
    • Hydrodynamic Interaction Parameters
    • Non-Brownian Dynamics Parameters
    • Brownian Dynamics Parameters
    • Chain Interaction Parameters
    • Excluded-Volume Parameters
    • Confinement Force Parameters
    • Parameter Script
  • xi3: Tuning Program for the Ewald Summation
    • Sample Run
    • Help
  • Visualization and Other Utilities
  • Wrappers
    • C
    • Python
    • Perl
    • Ruby
    • Guile
    • Octave
  
  
• libstokes: Library for Stokesian Dynamics
  • API
    • System Parameters
    • NetCDF Interface
    • Solvers
  • Hydrodynamic Interaction in Stokes Flows
    • Many Body Problem
    • FTS formulation
    • Fixed Particles - Mixed Problem
    • Lubrication Correction
    • Ewald Summation
    • Navier Slip Boundary Condition
  • Brownian Dynamics
  • Chain Interaction among Particles
    • Bead-Spring Models -- Overview
    • Hookean Spring
    • Finitely Extensible Nonlinear Spring Models
    • Discrete Wormlike Chain Model
    • Bead-Rod Model
  • Confinements
  
  
• libiter: Library of Iterative Solvers
  • API
  • Iterative Method for Dense Matrix
  • Schemes
  
  
• libexp: Library for Multipole Expansion
  • Multipole Expansion
  • Ewald Summation
  • Fast Multipole Expansion
  • Linear Partial Differential Equations
  
  
• twobody: Exact Solutions of Two Rigid Spheres in Stokes Flows
• Postscript
• The GNU General Public License
• Bibliography