Introduction to Chemical Reaction Networks
Background
This course contains multiple exercises that address different
aspects of chemical reaction networks. These are:
- Stochastic Cells:
a very simple chemical reaction network, introducing the Gillespie
algorithm, and comparison of stochastic and deterministic algorithms
- Simple Repressilator:
introduces the Repressilator synthetic gene regulatory network,
and examines the dynamics of a simple deterministic model
-
Stochastic and Deterministic Repressilators:
introduces a more complex model of the Repressilator, which is used
as the basis of both stochastic and deterministic simulation algorithms,
allowing for examining of the effects of noise on system dynamics
- Coupled Repressilators: introduces a model of Repressilator cells coupled by a quorum sensing
mechanism, allowing for the studying of oscillator synchronization
The Stochastic
Cells exercise is a useful prerequisite for the remainder of the
exercises. The Simple
Repressilator exercise is straightforward, builds upon techniques
introduced in other course modules (e.g., integration of coupled
ODEs), and introduces the phenomenology of the Repressilator. The Stochastic
and Deterministic Repressilators exercise is somewhat more
complicated, although it can be done without having worked on the
Simple Repressilator previously. Finally, the Coupled
Repressilators follows on the Simple Repressilator, and can be
completed without having done the Stochastic and Deterministic exercise.
James P. Sethna,
Christopher R. Myers,
Last modified: August 25, 2008