Theory

• Introduction
  • The cell environment
  • Modeling approaches
• Theory and Methods
  • Rigid bead molecules
  • Compartments
  • Boundary Conditions
  • Reactions
  • Potentials
  • Observables
  • Berendsen barostat
  • Distribution of molecules
  • Fast algorithms for Brownian dynamics of reacting and interacting particles
  • Polydispersity
  • Simulation loop
  • Visualization
• Results and validation
  • Anisotropic diffusion
  • Diffusion tensor of igG3
  • Fixed concentration boundary
  • Choosing the right reaction rate and radius
  • Bi-molecular reactions between rigid bead molecules
  • Reactions between surface molecules
  • Hard sphere fluid
  • LLPs of Patchy Particles
  • Benchmarks
• Discussion
  • On hydrodynamic interactions
  • Limitations of the Brownian dynamics approach
• Appendix
  • Appendix A