Simulation Studies of Biological Ion Channels

Biological ion channels are responsible for, and regulate the communication system in the body. In this thesis I develop, test and apply theoretical models of ion channels, that can relate their structure to their functional properties. Brownian dynamics simulations are introduced, in which the motions of individual ions are simulated as they move through the channel and in baths attached to each end. The techniques for setting boundary conditions which maintain ion concentrations in the baths and provide a driving potential are tested. Provided the bath size is large enough, all boundary conditions studied yield the same results. ..