Biology Portal

Agent-based Modeling of an Enzymatic Reaction using AgentSheets

Enzymes are the cell's molecular machines. They are macromolecules that are able to interact with specific molecular components of the cell and accelerate chemical or physical processes catalytically. Along with the cell's membranes, enzymes enable the cell to control it's composition and functional state, and to respond to it's environment. The materials here provide background on some of the molecular details of enzyme function and approaches to their study, derive basic mathematical descriptions of enzyme kinetic behavior, and describe the construction and use of agent-based models of enzyme kinetics using the AgentSheets software. The modeling exercises emphasize the use of dynamic modeling as a part of the computational scientific method.

Background Science: Describes, for the simplest case, the basic molecular events that underlie enzymatic reactions, how the rates of these events depend on various factors, and how enzyme kinetics are assayed.

Mathematics and Computation: Describes, the derivation of the Michaelis-Menton equation, methods for estimating the kinetic parameters of this equation, along with numerical and stochastic approaches for integrating rate equations for the reaction.

AgentSheets Introduction: Provides step-by-step instructions to the general approach for planning and building an agent-based model using AgentSheets.

Building the Model: Details, the construction of a basic model of an enzymatic reaction using AgentSheets, presuming familiarity with the AgentSheets software as presented in introduction above.

Model Limitations: Considers some of the assumptions of the basic model, suggesting some possible alternative approaches that might have been used.

Extending the Model: Provides additional scientific background on enzyme inhibitors, and multi-substrate enzyme mechanisms, with suggestions for projects that add these features to the basic model.