updated October 28, 2007
(recovered from archive.org after a failed disk, site moved)

Kinetics for Artificial Gene Networks

In order to properly simulate gene expression dynamics, it is important to use reallistic kinetics for each transcription step. Much is already known about the kinetics of transcription at a microscopic level, i.e. for the steps of initiation, elongation and termination. However, those kinetics are too detailed to be useful for large scale models (of more than 50 genes, possibly thousands). It is then important to select phenomenological kinetic types that reflect the fundamental molecular properties of transcription.

In addition to the requirement of reallistic kinetics, it is also important for this work to have kinetic types that are scalable. By this we mean that the software must be able to define all kinetic types in a model automatically, while still retaining a good level of realism.

The main characteristics of the kinetic types used here are:

The kinetis used by our models follow one of the two generic types below. Unless stated otherwise, the data presented in this site follows Eq. 1.

Eq. 1

Eq. 2

The parameters are:

The transcription rate for each gene have an arbitrary number of inhibitors and activators, which are other genes. This number is governed by the nature of the gene network topology used.

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