BioMOCA: A Transport Monte Carlo Model for Ion Channels

Ion channels are proteins that form natural water-filled nanotubes in the membranes of all biological cells. They regulate ion transport in and out of the cell thereby maintaining the correct internal ion composition that is crucial to cell survival and function. Every channel carries a strong permanent charge, which plays a critical role in the conduction mechanisms of the open channel. Many channels can selectively transmit or block a particular ion species and most have switching properties similar to electronic devices. These device-like features are appealing to the electronics community for their possible application in the design of novel bio-devices. Here we describe a three-dimensional (3-D) transport Monte Carlo ion channel simulation, BioMOCA, based on the approach taken in semiconductor device simulations. Since ion diameters are comparable with channel dimensions a physical model of the volume of the ions must also be included.