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Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives.

Wang J, Xu L, Wang E - PMC Biophys (2008)

Bottom Line: We also found that the entropy production rate characterizing the dissipation or heat loss decreases as the fluctuations decrease.We also found that the properties from exploring the effects of the inherent chemical rate parameters on the robustness.Our approach is quite general and can be applied to other oscillatory cellular network.PACS Codes: 87.18.-h, 87.18.Vf, 87.18.Yt.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China. jin.wang.1@stonybrook.edu.

ABSTRACT
Finding the global probabilistic nature of a non-equilibrium circadian clock is essential for addressing important issues of robustness and function. We have uncovered the underlying potential energy landscape of a simple cyanobacteria biochemical network, and the corresponding flux which is the driving force for the oscillation. We found that the underlying potential landscape for the oscillation in the presence of small statistical fluctuations is like an explicit ring valley or doughnut shape in the three dimensional protein concentration space. We found that the barrier height separating the oscillation ring and other area is a quantitative measure of the oscillation robustness and decreases when the fluctuations increase. We also found that the entropy production rate characterizing the dissipation or heat loss decreases as the fluctuations decrease. In addition, we found that, as the fluctuations increase, the period and the amplitude of the oscillations is more dispersed, and the phase coherence decreases. We also found that the properties from exploring the effects of the inherent chemical rate parameters on the robustness. Our approach is quite general and can be applied to other oscillatory cellular network.PACS Codes: 87.18.-h, 87.18.Vf, 87.18.Yt.

No MeSH data available.


Related in: MedlinePlus

EPR. A:The diffusion coefficient D versus the entropy production rate. B:The barrier height Barrier1 = Ufix - Umin and Barrier2 = Ufix - Umax versus the entropy production rate.
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Figure 6: EPR. A:The diffusion coefficient D versus the entropy production rate. B:The barrier height Barrier1 = Ufix - Umin and Barrier2 = Ufix - Umax versus the entropy production rate.

Mentions: where ep = -∫(kBT∇ ln P - F)·J dx is the entropy production rate [38], and hd = ∫ F·J dx is the mean rate of the heat dissipation. For a steady state, = 0, and the entropy production ep is equal to the heat dissipation hd. In Fig. 6(A), we can see the dissipation (entropy production rate) decrease as the diffusion coefficient characterizing the fluctuations decreases; this shows that robust oscillation with less fluctuation dissipates less energy and is more stable. From Fig. 6(B), we also find that less dissipation leads to higher barrier heights for escaping from the oscillation cycle and therefore a more stable network. So, minimization of the dissipation cost might serve as a design principle for evolution of the network because the entropy production is a global characterization of the circadian network; it is intimately related to the robustness of the network.


Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives.

Wang J, Xu L, Wang E - PMC Biophys (2008)

EPR. A:The diffusion coefficient D versus the entropy production rate. B:The barrier height Barrier1 = Ufix - Umin and Barrier2 = Ufix - Umax versus the entropy production rate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667439&req=5

Figure 6: EPR. A:The diffusion coefficient D versus the entropy production rate. B:The barrier height Barrier1 = Ufix - Umin and Barrier2 = Ufix - Umax versus the entropy production rate.
Mentions: where ep = -∫(kBT∇ ln P - F)·J dx is the entropy production rate [38], and hd = ∫ F·J dx is the mean rate of the heat dissipation. For a steady state, = 0, and the entropy production ep is equal to the heat dissipation hd. In Fig. 6(A), we can see the dissipation (entropy production rate) decrease as the diffusion coefficient characterizing the fluctuations decreases; this shows that robust oscillation with less fluctuation dissipates less energy and is more stable. From Fig. 6(B), we also find that less dissipation leads to higher barrier heights for escaping from the oscillation cycle and therefore a more stable network. So, minimization of the dissipation cost might serve as a design principle for evolution of the network because the entropy production is a global characterization of the circadian network; it is intimately related to the robustness of the network.

Bottom Line: We also found that the entropy production rate characterizing the dissipation or heat loss decreases as the fluctuations decrease.We also found that the properties from exploring the effects of the inherent chemical rate parameters on the robustness.Our approach is quite general and can be applied to other oscillatory cellular network.PACS Codes: 87.18.-h, 87.18.Vf, 87.18.Yt.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, PR China. jin.wang.1@stonybrook.edu.

ABSTRACT
Finding the global probabilistic nature of a non-equilibrium circadian clock is essential for addressing important issues of robustness and function. We have uncovered the underlying potential energy landscape of a simple cyanobacteria biochemical network, and the corresponding flux which is the driving force for the oscillation. We found that the underlying potential landscape for the oscillation in the presence of small statistical fluctuations is like an explicit ring valley or doughnut shape in the three dimensional protein concentration space. We found that the barrier height separating the oscillation ring and other area is a quantitative measure of the oscillation robustness and decreases when the fluctuations increase. We also found that the entropy production rate characterizing the dissipation or heat loss decreases as the fluctuations decrease. In addition, we found that, as the fluctuations increase, the period and the amplitude of the oscillations is more dispersed, and the phase coherence decreases. We also found that the properties from exploring the effects of the inherent chemical rate parameters on the robustness. Our approach is quite general and can be applied to other oscillatory cellular network.PACS Codes: 87.18.-h, 87.18.Vf, 87.18.Yt.

No MeSH data available.


Related in: MedlinePlus