Friedland2009_Ara_RTC3_counter

This is the model of the RTC3 counter described in the article:
Synthetic gene networks that count.

Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Science. 2009 May 29;324(5931):1199-202. PMID:19478183, DOI:10.1126/science.1172005

Abstract:
Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.

The 3 arabinose pulses are implemented using events, one for the start of pulses and one for the end. The variable pulse_flag changes arabinose consumption to fit behaviour during pulses and in between. To simulate two pulses only, set the pulse length of the third pulse to a negative value (though with an absolute value smaller than the pulse intervall length).

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