Berlin 2012 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 22: Statistical Physics of Biological Systems III (with DY)
BP 22.6: Vortrag
Donnerstag, 29. März 2012, 16:15–16:30, H 1058
Investigating intrinsic fluctuations in biochemical systems — •Joseph Challenger1, Jürgen Pahle2, Alan McKane1, and Pedro Mendes2 — 1School of Physics and Astronomy, The University of Manchester, Manchester, UK — 2Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK
In many biochemical reaction systems it is important to be able to quantify the stochastic fluctuations that are present. Deterministic rate equations, which are often used to describe these systems mathematically, do not allow for these fluctuations. An alternative, probabilistic, formalism is available, using the master equation. An approximate solution to this equation can be found using the van Kampen expansion, which provides leading order corrections to the rate equations. The terms in the expansion relate to objects in the rate equations in a very general way. We show how this approach can be generalised to biochemical systems which involve many neighbouring compartments.
We have incorporated this technique into COPASI, a software package designed to study biochemical reaction systems. This allows the procedure to be automated. Given a particular reaction system, COPASI calculates the fluctuations around the system's steady state. This analysis can be performed in tandem with the other tasks available in COPASI e.g. parameter scanning or optimisation. This is useful if there is uncertainty associated with numerical values of some of the reaction parameters. If the fluctuations are calculated via numerical simulation, these tasks can be computationally expensive. In contrast, these calculations can be done quickly using our approach.