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In this thesis, we develop the theoretical and numerical foundations for a self-consistent model for the simulation of the properties of ion channels - their conductivity and selectivity - from their structure. We begin by revising the one-dimensional theory of the ionic current by setting up the self-consistent coupled Langevin Poisson equations in one-dimension, as a prototype of the three dimensional simulations. The solution of a one-dimensional approximation of the Poisson's equation for a channel modelled as a long and narrow cylindrical tube is derived. Using this solution, we calculate the ion trajectory as it traverses the channel.

Regulation of transmembrane ion transport is a vital aspect in the maintenance of a healthy organism. To understand how this highly selective process occurs, how it can become impaired and how impairment may be treated, model compounds are useful tools. Several systems are presently being explored but one of the most widely applicable combines a rigid macrocycle, capable of size-based ion recognition, with membrane spanning substituents that allow the target ions to transverse a phospholipid bilayer. The calixarene class of macrocycles is ideally suited to this task. Previous work had shown that oxacalix[3]arenes could act as models for the filters in natural transmembrane ion channels. Nitrogen-containing analogues of these calixarenes, azacalix[3]arenes, were investigated with a view to constructing a chloride transporting system. Synthetic difficulties encountered when introducing lower rim substitutents precluded the use of azacalix[3]arenes and attention turned to 4-t-butylcalix[n]arenes. 4-t-Butylcalix[4]- and [6]arenes were derivatised with a commercial, membrane disrupting surfactant, Triton X-IOO®, forming compounds designed to form lipid bilayer-spanning, channel-like structures. The ion transporting ability of these, and other bilayer-spanning O-substituted calixarene derivatives, was determined by planar bilayer electrophysiological methods. Results showed that this modular approach to artificial ion channel construction was successful; calixarene derivatives formed transmembrane channels that allowed sodium ions to pass through but not the larger potassium ions.

Torpedo AChR structure was used to make models of other LGICs. Coarse-grain MD allowed the identification of residues in the TM domain interacting with the lipid-bilayer. Born energy profiles through LGIC pores reveal that the EC domain plays a key role in ion selectivity.