Library Dependency

This is a placeholder model. It requires the BioChem library.

• The free BioChem library is an extendable, general purpose Modelica library for modeling, simulation and visualization of biological and biochemical systems. The library is designed to be used together with Wolfram SystemModeler, which enables several extra features such as Systems Biology Markup Language (SBML) import and export. BioChem can, for instance, be used for selecting drug targets with PK/PD modeling or searching for novel drug targets with mechanistic modeling of the reactions in a cell or organism.

The following documentation is taken from the main example of the downloadable model. Once you have downloaded all the model dependencies, the model can be downloaded here.

Enzyme Catalysis

Introduction

This model illustrates a standard enzyme reaction, together with a non-enzymatic, alternative reaction path. Most enzymes are proteins, and they increase the rate of reactions in organisms by lowering the activation energy required for the reaction. Without enzymes, some processes in the human body would take days, some even decades. Defective enzymes are linked to a number of different diseases and medical conditions such as lactose intolerance.

In order to get the full experience of this example, you need the following:

• A desktop Wolfram Language product; a free trial download is available at www.wolfram.com/mathematica/trial/
• The EnzymeCatalysis.nb notebook that came in the same bundle as this model

Model

The example model consists of a two-pathway reaction model, an enzymatic and a non-enzymatic reaction. The enzymatic reaction by default has a rate one million times higher than the non-enzymatic one.

Simulation

Simulating the model will make it possible to see how the enzyme concentration affects the reaction rate.

To simulate the model and plot the concentration changes, follow the steps below:

• Click the Simulate button .

If you want to see how a change in enzyme concentration, rate constant or anything else would affect the model, this is possible. To change the initial conditions, you can edit the values of Sc0, Pc0 and Ec0 n the Parameters tab to change the initial substrate, product or enzyme concentration. Modify the corresponding initial concentration or parameter that you would like to change and then click the Simulate button again.

Advanced

In the model, you can change how the enzyme complex is initialized. The default behavior is to initialize the enzyme complex with zero concentration. This corresponds to a situation were the enzyme and subtrate are quickly mixed together. By changing the enzymeInitialization parameter, you can force the concentrations to instead initialize in steady-state.

Terms and Conditions of Use