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Simple Kinetics 1

Run Simple Kinetics 1 in your browser uses NetLogo 4.0.4 requires Java 1.4.1+ (system requirements) Note: If you download the NetLogo application, every model in the Models Library (besides the Community Models) is included. If you have trouble running this model in your browser, you may wish to download the application instead.

WHAT IS IT?

This model demonstrates the kinetics of a simple reversible reaction. It demonstrates numerically that the application of the Principle of Stationary Concentrations is valid in this case.

In this model there are two kinds of molecules, green and red. Green turtles turn into red turtles bimolecularly whereas red turtles turn back into pairs of green turtles monomolecularly. You can control the rate at which this changes occur with sliders Kb and Ku.

The reaction here is a reversible reaction of the type:

                            Kb
           A + A <=======> B
                            Ku

An example of such a reaction would be dimerization of acetic acid:

                                     Kb
           2 H C-COOH <=======> H C-COOH~...~HOOC-C H
          3           Ku     3                 3

This reaction is an example of a complex reaction which consists of two elementary reactions. The forward bimolecular reaction

                           Kb
           A + A --------> B

is characterized by the constant Kb and the reverse unimolecular reaction

                Ku
           B ---------> A + A

is characterized by the constant Ku.

The system of ordinary differential equations (ODE) that describes the concentrations of A and B is given below:

           dA           2
           -- = -2Kb * A  + 2Ku * B        (1)
           dt

           dB         2
           -- = Kb * A  - Ku * B           (2)
           dt

The usual initial conditions are A(0) = Ao and B(0) = 0. While it is possible to solve this system of ODE analytically, chemists usually apply the Principle of Stationary Concentrations when they investigate the kinetics of reactions of this type. The Principle says that one can assume that the concentrations of the species stop changing from some point on after the system reaches equilibrium. If concentrations are stationary, the derivatives

           dA               dB
           --  and  --
           dt               dt

are zero. Hence one can replace the system of ODE above with the system of algebraic equations below:

                       2
           0 = -2Kb * A*   + 2Ku * B*              (1')

                     2
           0 = Kb * A*  - Ku * B*                  (2')

where concentrations marked with * are stationary concentrations. The second equation (2') is linearly dependent on the first equation (1'). Luckily we also have another equation coming from the law of the conservation of mass:

           A* + 2 * B* = Ao                        (3)

From equation (2') we can express B* in terms of A* :

                     Kb    2
           B*  = --  A*                    (4)
                     Ku

We can now plug in expression (4) into (3) and then we will have a quadratic equation in terms of A*:

                     Kb   2
           A*  + -- A*  = Ao               (5)
             Ku

whose solution is:

                _____________
                |
                |             Kb
                |  1 + 4 * --  - 1
               \|          Ku
              --------------------         (6)
                     Kb
                            2 * --
                                    Ku

One can now find the stationary concentration of B using equation (4).

HOW TO USE IT

Choose the values of Ku and Kb with appropriate sliders:
- Kb controls the rate of the forward reaction by which two green turtles turn bimolecularly into a single red turtle.
- Ku controls the rate of the reverse reaction, by which a red turtle turns unimolecularly into two green turtles.

Having chosen appropriate values of the constants, press SETUP to clear the world and create an initial number of green turtles. Note: we do not create red turtles initially, although this could be done in principle.

Press GO to start the simulation.

THINGS TO NOTICE

You will see turtles wandering around the world and changing color. Pay more attention to the plot of the concentrations. Do the plots soon reach stationary concentrations?

THINGS TO TRY

How do the stationary concentrations depend on the values of Kb and Ku? You can change Ku and Kb while the model is running. See if you can predict what the stationary concentrations will be with various combinations of Kb and Ku.

EXTENDING THE MODEL

Try to implement the following reaction:

                    Kb         K2
           A + A <======> B -------> C
                    Ku

This reaction underlines a vast number of microbiological processes (e.g. fermentation). You can read about its kinetics in any book on Biochemistry. Look up the so-called Michaeles-Menten equation. Does it check numerically?

Try to implement the following reaction:

                    Kb         K2
           A + B <======> C -------> D
                    Ku

NETLOGO FEATURES

It is a little tricky to ensure that a reactant never participates in two reactions simultaneously. The turtle variable REACTING? is used to control this. In the future, a primitive called GRAB may be added to NetLogo; then REACTING? won't be needed.

CREDITS AND REFERENCES

Thanks to Mike Stieff for his work on this model.

To refer to this model in academic publications, please use: Wilensky, U. (1998). NetLogo Simple Kinetics 1 model. http://ccl.northwestern.edu/netlogo/models/SimpleKinetics1. Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.

In other publications, please use: Copyright 1998 Uri Wilensky. All rights reserved. See http://ccl.northwestern.edu/netlogo/models/SimpleKinetics1 for terms of use.

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