Cell receptors, Cellular signal transduction
Cellular receptor dynamics are often analyzed using differential equations, making system dynamics (SD) a candidate methodology. In some cases it may be useful to model the phenomena at the biomolecular level, especially when concentrations and reaction probabilities are low and might lead to unexpected behavior modes. In such cases, agent-based simulation (ABS) may be useful. We show the application of both SD and ABS to simulate non-equilibrium ligand-receptor dynamics over a broad range of concentrations, where the probability of interaction varies from low to very low. Both approaches offer much to the researcher and are complementary. We did not find a clear demarcation indicating when one paradigm or the other would be strongly preferred, although SD is an obvious choice when studying systems at a high level of aggregation and abstraction, and ABS is well suited to studying phenomena at the level of individual receptors and molecules.
Wakeland, Wayne W.; Gallaher, Edward J.; Macovsky, Louis; and Aktipis, C. Athena, "A Comparison of System Dynamics and Agent-Based SimulationApplied to the Study of Cellular Receptor Dynamics" (2004). Systems Science Faculty Publications and Presentations. 84.