https://murray.cds.caltech.edu/index.php?action=history&feed=atom&title=Analysis_of_a_Digital_Clock_for_Molecular_Computing 2026-05-30T11:16:36Z Revision history for this page on the wiki MediaWiki 1.44.2 https://murray.cds.caltech.edu/index.php?title=Analysis_of_a_Digital_Clock_for_Molecular_Computing&diff=19843&oldid=prev 2016-05-15T06:17:30Z

<p>htdb2wiki: creating page for 2006t_udm07-acc.html</p> <p><b>New page</b></p><div>{{HTDB paper<br /> | authors = Johan Ugander, Mary J Dunlop, Richard M Murray<br /> | title = Analysis of a Digital Clock for Molecular Computing<br /> | source = American Control Conference, 2007 (submitted)<br /> | year = 2006<br /> | type = Preprint<br /> | funding = <br /> | url = http://www.cds.caltech.edu/~murray/preprints/udm07-acc_s.pdf<br /> | abstract = Gene expression is often controlled by natural genetic regulatory networks that govern the rates at which genes <br /> are transcribed. Recent work has shown that synthetic versions of genetic networks can be designed and built in living cells. Applications for these synthetic regulatory networks include intracellular decision-making and computation. In this study, <br /> we propose a new synthetic genetic network that behaves as a digital clock, producing square waveform oscillations. We analyze two models of the network, a deterministic model based on Michaelis-Menten kinetics, as well as a stochastic model based on the Gillespie algorithm. Both models predict regions of oscillatory behavior; the deterministic model provides insight into the conditions required to produce the oscillating clock-like behavior, while the stochastic model is truer to natural <br /> dynamics. Intracellular stochasticity is seen to contribute phase noise to the oscillator, and we propose improvements for the network and discuss the conceptual foundations of these improvements. <br /> | flags = <br /> | tag = udm07-acc<br /> | id = 2006t<br /> }}</div>

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