Limits...
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

Barrier height and entropy production versus chemical rate parameters. A: Barrier changes with respect to changes of rate parameters (red: rate increase. green: rate decrease) k1, k2, ks, vm, vd, and vs. B. Barrier height and entropy production rate versus chemical rate parameters k1, k2, ks, vm, vd, and vs.
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Figure 11: Barrier height and entropy production versus chemical rate parameters. A: Barrier changes with respect to changes of rate parameters (red: rate increase. green: rate decrease) k1, k2, ks, vm, vd, and vs. B. Barrier height and entropy production rate versus chemical rate parameters k1, k2, ks, vm, vd, and vs.

Mentions: To explore the effects of the inherent chemical rate parameters on the robustness, we can try to find out which reactions are important, and further, which protein elements are crucial in maintaining the robustness. Fig. 11(A) shows the effects of rate parameters on the robustness. The six rate parameters increase by twenty percent (red), and decrease by twenty percent (green). The bars show the change in barrier height for different parameters. q is the percentage by which the rate constants are increase or decreased. Fig. 11(B) shows the barrier height (solid line) and the entropy production rate (dashed line) versus the six rate parameters. We can see that when the rate parameters k1 and vm increase, the barrier height increases and the entropy production rate decreases, as the system becomes more stable and robust. We can also see that when the other four rate parameters (k2, ks, vd, vs) increase, the barrier height decreases and the entropy production rate increases as the system becomes less stable and robust.


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

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

Barrier height and entropy production versus chemical rate parameters. A: Barrier changes with respect to changes of rate parameters (red: rate increase. green: rate decrease) k1, k2, ks, vm, vd, and vs. B. Barrier height and entropy production rate versus chemical rate parameters k1, k2, ks, vm, vd, and vs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 11: Barrier height and entropy production versus chemical rate parameters. A: Barrier changes with respect to changes of rate parameters (red: rate increase. green: rate decrease) k1, k2, ks, vm, vd, and vs. B. Barrier height and entropy production rate versus chemical rate parameters k1, k2, ks, vm, vd, and vs.
Mentions: To explore the effects of the inherent chemical rate parameters on the robustness, we can try to find out which reactions are important, and further, which protein elements are crucial in maintaining the robustness. Fig. 11(A) shows the effects of rate parameters on the robustness. The six rate parameters increase by twenty percent (red), and decrease by twenty percent (green). The bars show the change in barrier height for different parameters. q is the percentage by which the rate constants are increase or decreased. Fig. 11(B) shows the barrier height (solid line) and the entropy production rate (dashed line) versus the six rate parameters. We can see that when the rate parameters k1 and vm increase, the barrier height increases and the entropy production rate decreases, as the system becomes more stable and robust. We can also see that when the other four rate parameters (k2, ks, vd, vs) increase, the barrier height decreases and the entropy production rate increases as the system becomes less stable and robust.

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