Initial conditions were chosen for the system to evolve toward the desired pattern (the Lunatic fringe secretion model currently does not seek to address the initiation of oscillations). To account for cell-flow in the PSM, new variables were added at regular intervals at the "posterior" extremity, representing new cells entering the PSM, with fixed initial values (corresponding to the state of an isolated oscillator, 1/3rd of its oscillatory period after its L-fng peak). To account for the blocking of the clock once cells had segmented, derivatives in anterior-most cells were set to 0 once they had been reached by an expression wave, and segmented cells were considered not to influence other cells in the PSM anymore.
Integration was performed with the adaptive-stepsize Runge-Kutta algorithm (Press, 1992), which was implemented in a custom Ada program (source available on request). Simulations comprised 300 cells, and were executed on a Macintosh PowerPC running Mac OS 10.2. Graphs were plotted using gnuplot, converted to animated GIFs using gifsicle, and to QuickTime movies with QuickTimePro.