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Computational Biology

Model, simulate, and visualize biological and biochemical systems. Model and simulate reaction kinetics.

Enzyme Catalysis

Enzymes play a part in almost every biochemical reaction known, from human metabolism to beer brewing. This model showcases a generic substrate to product reaction and catalyzes it to illustrate the power of enzymes. The free BioChem Modelica library is needed to run this example; it can be downloaded here.

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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.

The Model

Complete model.

The model consists of a substrate that is converted either through an enzymatic reaction or a non-enzymatic reaction. Going through the enzymatic route is a much quicker alternative, even though it may be more complex. The enzyme complex stabilizes the transition state, reducing the activation energy for the reaction.

Substrate Becomes Product

The model contains both a non-enzymatic and an enzymatic pathway.


The download includes a Mathematica notebook with a graphical user interface built using the Manipulate function. Use it to explore the behavior of the reaction, with adjustable settings for the substrate and enzyme concentrations.

With no enzyme present, the substrate concentration is almost constant.
Adjusting the enzyme concentration greatly affects the reaction rate.

Analysis Made Simple

The enzyme’s effect can be easily analyzed using the simple dynamic GUI included in the download.