Combining computational chemistry and computational electronics to understand protein ion channels

Abstract

Nanoscale computational engineering can be achieved by combining atomic and molecular scale methods of computational chemistry with coarser-grained continuum theories used in computational electronics. Each computational discipline is quite different; yet both must give the same results if they are done correctly. Here we apply both classes of simulation technique to the specific problem of computing ion current in protein channels. In the biological tradition, ion channels are transport enzymes, catalyzing the movement of ions from one side of a membrane to the other. In the tradition of nanodevices, ion channels can be viewed as transistors with unusual properties_exquisite sensitivity to specific environment factors and ability to self-assemble.