Simulation of biological ion channels with technology computer-aided design.

Computer simulations of realistic ion channel structures have always been challenging and a subject of rigorous study. Simulations based on continuum electrostatics have proven to be computationally cheap and reasonably accurate in predicting a channel's behavior. In this paper we discuss the use of a device simulator, SILVACO, to build a solid-state model for KcsA channel and study its steady-state response. SILVACO is a well-established program, typically used by electrical engineers to simulate the process flow and electrical characteristics of solid-state devices. By employing this simulation program, we have presented an alternative computing platform for performing ion channel simulations, besides the known methods of writing codes in programming languages. With the ease of varying the different parameters in the channel's vestibule and the ability of incorporating surface charges, we have shown the wide-ranging possibilities of using a device simulator for ion channel simulations. Our simulated results closely agree with the experimental data, validating our model.