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. 2012 Jan 26;8(1):e1002331. doi: 10.1371/journal.pcbi.1002331

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Hsia et al.

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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Included are color plots (left) and DCTs averaged over hours 50 to 80 (right). The stochasticity causes oscillations to arise naturally and can be seen as early as hour 20. See Figures S11, S12 for full simulation results. (A) Results for (top) and (bottom) are indicative of the behavior for mRNA and proteins for cI, TetR, LacI, and LuxI. While the DCT plots vary from species to species, certain wave numbers are found to be more pronounced across all species, particularly . (B) Results for AHL produce similar behavior in all downstream species in the quenching loop. Both the color plot and DCT are markedly different due to the effects of diffusion, which causes a “spreading” of the rapid peaks seen in mRNA and protein color plots and acts like a low-pass filter in the frequency domain. (C) Overlay plot of AHL and demonstrating the correspondence between the peaks in the species as well as the effect of diffusion. AHL was monochromed in red and in green, leading to the appearance of yellow in areas of large overlap.

Inline graphic — Included are color plots (left) and DCTs averaged over hours 50 to 80 (right). The stochasticity causes oscillations to arise naturally and can be seen as early as hour 20. See Figures S11, S12 for full simulation results. (A) Results for (top) and (bottom) are indicative of the behavior for mRNA and proteins for cI, TetR, LacI, and LuxI. While the DCT plots vary from species to species, certain wave numbers are found to be more pronounced across all species, particularly . (B) Results for AHL produce similar behavior in all downstream species in the quenching loop. Both the color plot and DCT are markedly different due to the effects of diffusion, which causes a “spreading” of the rapid peaks seen in mRNA and protein color plots and acts like a low-pass filter in the frequency domain. (C) Overlay plot of AHL and demonstrating the correspondence between the peaks in the species as well as the effect of diffusion. AHL was monochromed in red and in green, leading to the appearance of yellow in areas of large overlap.