MATLAB-based Simulation of Whole-Cell and Single-Channel Currents

Mathematical models of electrophysiological data are used to investigate biophysical mechanisms that underlie electrical excitability. Although the resources and time required for obtaining experimental data to create these models may not be available to undergraduates enrolled in a biophysics course, computational tools that simulate cellular or single-channel responses to electrophysiological stimuli can be utilized to provide these data. We have developed two MATLAB-based simulation packages that are being used in a cellular electrophysiology course for upper-level undergraduate engineering students to demonstrate the design of electrophysiological stimuli, and the analysis and modeling of ionic currents in excitable tissues. The first package simulates a Hodgkin-Huxley style voltage-gated current elicited during voltage-clamp experiments. Users specify the duration and magnitude of a voltage waveform; the model returns a simulated whole-cell current traces with superimposed noise, and various measurements including peak current, steady state current, and time constants from exponential fits of the current time course. The second package simulates a voltage- or ligand-gated single-channel current as a stochastic process using a state transition matrix. Users specify the membrane voltage, ligand concentration, and number of trials; the model returns simulated single-channel current traces with superimposed noise, and various measurements including amplitude and dwell time histograms. This software has been used during lectures to demonstrate various principles in class, and for class projects in which students derive kinetic models that underlie currents obtained during whole-cell and single-channel recordings. These software packages are freely available and can be downloaded at www.eng.utoledo.edu/∼smolitor/download.htm.