Nonlinear kinetics evolution

The simplest manifestation of nonlinear kinetics is the clock reaction—a reaction exliibiting an identifiable mduction period , during which the overall reaction rate (the rate of removal of reactants or production of final products) may be practically indistinguishable from zero, followed by a comparatively sharp reaction event during which reactants are converted more or less directly to the final products. A schematic evolution of the reactant, product and intenuediate species concentrations and of the reaction rate is represented in figure A3.14.2. Two typical mechanisms may operate to produce clock behaviour. 

In their early theoretical studies of the mitotic oscillator, Kauffman et al (Kauffman, 1975 Kauffman Wille, 1975 Tyson Kauffman, 1975) resorted to the abstract, Brusselator model (Lefever Nicolis, 1971) for their simulations of mixing experiments in which Physarum plasmodia taken at different phases of the cell cycle were fused. Like most models proposed for limit cycle behaviour, the Brusselator relies on an autocatalytic step for producing the instability leading to oscillations an advantage of this simple model is that the temporal evolution is governed by two polynomial, nonlinear kinetic equations (Lefever Nicolis, 1971). 

The existence of oscillatory phenomena in complex biochemical pathways is a function of the existence of servomechanisms. Oscillatory phenomena are expressions of nonlinear kinetics in a system displaced far from equilibrim and are thus examples of the dissipative structures necessary for the maintenance and evolution of biological systems (Chapter 2). Such structures are termed "dissipative" because they require the dissipation of energy through the system both for creation and stabilization of the new structure. 

We now consider how one extracts quantitative infonnation about die surface or interface adsorbate coverage from such SHG data. In many circumstances, it is possible to adopt a purely phenomenological approach one calibrates the nonlinear response as a fiinction of surface coverage in a preliminary set of experiments and then makes use of this calibration in subsequent investigations. Such an approach may, for example, be appropriate for studies of adsorption kinetics where the interest lies in die temporal evolution of the surface adsorbate density N. ... 

In their subsequent works, the authors treated directly the nonlinear equations of evolution (e.g., the equations of chemical kinetics). Even though these equations cannot be solved explicitly, some powerful mathematical methods can be used to determine the nature of their solutions (rather than their analytical form). In these equations, one can generally identify a certain parameter k, which measures the strength of the external constraints that prevent the system from reaching thermodynamic equilibrium. The system then tends to a nonequilibrium stationary state. Near equilibrium, the latter state is unique and close to the former its characteristics, plotted against k, lie on a continuous curve (the thermodynamic branch). It may happen, however, that on increasing k, one reaches a critical bifurcation value k, beyond which the appearance of the... 

Tavare and Garside ( ) developed a method to employ the time evolution of the CSD in a seeded isothermal batch crystallizer to estimate both growth and nucleation kinetics. In this method, a distinction is made between the seed (S) crystals and those which have nucleated (N crystals). The moment transformation of the population balance model is used to represent the N crystals. A supersaturation balance is written in terms of both the N and S crystals. Experimental size distribution data is used along with a parameter estimation technique to obtain the kinetic constants. The parameter estimation involves a Laplace transform of the experimentally determined size distribution data followed a linear least square analysis. Depending on the form of the nucleation equation employed four, six or eight parameters will be estimated. A nonlinear method of parameter estimation employing desupersaturation curve data has been developed by Witkowki et al (S5). 

The first one is that this particular form of H can also be used to prove the approach to equilibrium in the case of Boltzmann s kinetic equation for dilute gases. The Boltzmann equation is nonlinear and a different technique is needed to prove that all solutions tend to equilibrium. This technique is based on (5.6) other convex functions cannot be used. Incidentally, the Boltzmann equation is not a master equation for a probability density, but an evolution equation for the particle density in the six-dimensional one-particle phase space ( /i-space ). The linearized Boltzmann equation, however, has the same structure as a master equation (compare XIV.5). 

The irreversibility inherent in the equations of evolution of the state variables of a macroscopic system, and the maintenance of a critical distance from equilibrium, are two essential ingredients for this behavior. The former confers the property of asymptotic stability, thanks to which certain modes of behavior can be reached and maintained against perturbations. And the latter allows the system to reveal the potentialities hidden in the nonlinearity of its kinetics, by undergoing a series of symmetry breaking transitions across bifurcation points. 

Indeed, one can analyze In the same manner the evolution of the system under consideration under conditions of reversibility of all of the elementary reactions in scheme (3.30). Unfortunately, in this situation the analytic solution of the eigenvalue equation in respect to parameter X appears unreasonably awkward. However, if the kinetic irreversibility of both nonlinear steps are a priori assumed, it is easy to find stationary valued (Y, Z ), and we come to the preceding oscillating solution. At the same time, near thermodynamic equilibrium (i.e., at R aa P), there exits only a sole and stable stationary state of the system with (Y Z R). 

The time evolution of the nonlinear O-H stretching absorption shows pronounced oscillatory signals for all types of dimers studied. In Fig. 15.5, data for OD/OD dimers are presented which were recorded at 3 different spectral positions in the O-D stretching band. For positive delay times, one finds rate-like kinetics which is due to population and thermal relaxation of the excited dimers and, more importantly, superimposed by very strong oscillatory absorption changes. In contrast to the intramolecular hydrogen bonds discussed above, the time-dependent amplitude of the oscillations displays a slow modulation with an increase and a decrease on a time scale of several hundreds of femtoseconds. 

Each of the two enzymes thus behaves as phosphofructokinase in the model considered for glycolytic oscillations (chapter 2). To limit the study to temporal organization phenomena, the system is considered here as spatially homogeneous, as in the case of experiments on glycolytic oscillations (Hess et ai, 1969). In the case where the kinetics of the two enzymes obeys the concerted allosteric model (Monod et al, 1965), the time evolution of the model is governed by the kinetic equations (4.1), which take the form of three nonlinear, ordinary differential equations ... 

In order to reproduce the observed intensity of the 001 reflection and the 4-point pattern in the SAXS region, we performed a nonlinear least square fit by using Eqs. (2), (6.8)-(6.10), and (14). The solid and dotted curves in Fig. 6.4 were obtained by the above fitting procedure. In Fig. 6.4, it is found that the time evolution of the intensities of both the 001 reflection and the 4-point pattern in the SAXS region can be weU reproduced simultaneously by the present kinetic model. In the next sections, we will discuss the several parameters obtained by the fitting. 

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