Contents

• Simulation setup and protocols
  • Building a crystal
  • Constructing synthetic nanopores
  • Generating the structure file
  • Calibrating the force field
  • Solvating the nanopore
  • Measuring ionic current
  
  
• Simulations of DNA permeation through nanopores
  • Manipulating DNA
  • Combining DNA and the synthetic nanopore
  • Measuring ionic current with DNA
  • Simulating DNA translocation
  
  
• Appendix