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Oscillations and multiscale dynamics in a closed chemical reaction system: Second law of thermodynamics and temporal complexity
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10.1063/1.2995855
/content/aip/journal/jcp/129/15/10.1063/1.2995855
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/15/10.1063/1.2995855
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Schematic comparison of qualitative dynamics between (a) standard damped oscillation and (b) reversible LV. The filled dots in (a) and (b) represent the equilibrium point of the system. The reversible LV system is 3D [Eq. (2)], with the vertical direction along the axis of the cone being intimately related to the total free energy of the system. The dynamics has two regimes: When far from equilibrium, chemical oscillations occur around the axis. (c) The motion is oscillatory, with a pair of complex eigenvalues and a third real eigenvalue. (e) When near the equilibrium, the motion is a monotonic, exponential relaxation with three real eigenvalues. The switch occurs when the pair of complex eigenvalues is equal and real (d). System in (b) has been termed either quasiplanar oscillation or “corkscrew oscillations” (Ref. 15), depending on the rate of free energy dissipation.

Image of FIG. 2.
FIG. 2.

Dynamics of reversible LV system (2) with a large total concentration of all molecules . Parameter used in the calculations: , , and . Initial value ; total run time . The “cone-shaped” dynamics is obligatory for quasiplanar oscillation in which the radial relaxation is faster than the vertical relaxation.

Image of FIG. 3.
FIG. 3.

Dynamics of reversible LV system (2) with a small total concentration of all molecules . Parameters used in the calculations: , , and initial values . All other parameters used are the same as in Fig. 2.

Image of FIG. 4.
FIG. 4.

Oscillation around the invariant curve (dashed). (a) is for initial point far from the invariant curve, . (b) is for initial point near the invariant curve, , which is much closer to the invariant curve. (c) and (d) are the projections of the 3D trajectory in (b) onto the and planes. Parameters used in the simulations are the same as in Fig. 2 except and .

Image of FIG. 5.
FIG. 5.

(a) Perturbed system (solid line) vs unperturbed system (dotted lines). For the perturbed system, all the parameters used are the same as in Fig. 3, with initial point (0.5,0.1,0.045). The five closed orbits for the unperturbed system, from top to bottom, are with , 0.0361, 0.027, 0.0186, and 0.0105, respectively. (b) Chemical dynamics in a closed system does not follow the negative gradient of the free energy of the system. On the solution curve, all the arrows represent the direction of the negative gradient of the free energy. Note that the directions of the free energy gradient in (b), which should be perpendicular to the constant energy level curves, are approximately perpendicular to the closed orbits in (a).

Image of FIG. 6.
FIG. 6.

The rate of free energy decreasing, , along a trajectory as a function of time . denotes the vector field of the 3D system and is the free energy function.

Image of FIG. 7.
FIG. 7.

Mechanical analog model according to Eq. (8) with and the initial values (5,5,45). This figure should be compared with Figs. 2(a) and 3(a).

Image of FIG. 8.
FIG. 8.

Contour plot of with and is drawn against . The red dashed line indicates the critical driving force , and the white one is for .

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/content/aip/journal/jcp/129/15/10.1063/1.2995855
2008-10-16
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Oscillations and multiscale dynamics in a closed chemical reaction system: Second law of thermodynamics and temporal complexity
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/15/10.1063/1.2995855
10.1063/1.2995855
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