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. 2012 Jul 31;7(7):e41019. doi: 10.1371/journal.pone.0041019

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© 2012 Jayanthi, Del Vecchio

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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(a) When compared to the isolated system, the amplitude of oscillations in system (20) increases when we add exclusively DNA binding sites with affinity to the repressor (, ). However, if we simultaneously add DNA binding sites with affinity to the activator, the amplitude is not affected as much (). (b) The period of system (20) can be changed with no effect on the amplitude when DNA binding sites with affinity to both the repressor and the activator are added simultaneously. The upper plot shows that a similar increase of period observed via the addition of repressor load can be obtained via the simultaneous addition of activator and repressor load. This second method has the advantage of not generating an increase in the amplitude, as shown in the lower plot. In this simulation we assumed the ratio . Parameters of the activator repressor system used in the simulation were , , , , , and , . In the traces showing only repressor load , while the traces showing simultaneous repressor and activator load, .

Inline graphic — (a) When compared to the isolated system, the amplitude of oscillations in system (20) increases when we add exclusively DNA binding sites with affinity to the repressor (, ). However, if we simultaneously add DNA binding sites with affinity to the activator, the amplitude is not affected as much (). (b) The period of system (20) can be changed with no effect on the amplitude when DNA binding sites with affinity to both the repressor and the activator are added simultaneously. The upper plot shows that a similar increase of period observed via the addition of repressor load can be obtained via the simultaneous addition of activator and repressor load. This second method has the advantage of not generating an increase in the amplitude, as shown in the lower plot. In this simulation we assumed the ratio . Parameters of the activator repressor system used in the simulation were , , , , , and , . In the traces showing only repressor load , while the traces showing simultaneous repressor and activator load, .