  Molecular dynamics simulations are used to study the equilibrium distribution
of monovalent ions in a nanopore connecting two water reservoirs separated by a
membrane, both for the empty pore and that with a single stranded DNA molecule
inside. In the presence of DNA, the counterions condense on the stretched
macromolecule effectively neutralizing it, and nearly complete depletion of
coions from the pore is observed. The implications of our results for
experiments on DNA translocation through alpha-hemolysin nanopores are
discussed.
