= WP2.3 Detailed kinetic modelling, identification and analysis of the citric acid cycle and respiratory chains of ''E. coli'' =
Project leader:  [wiki:public/OliverSawodny Oliver Sawodny] [[BR]]
Former Co-Project leader: [wiki:public/ThomasSauter Thomas Sauter] (now University of Luxembourg) [[BR]]
Sub-Project leader: [wiki:public/MichaelEderer Michael Ederer] [[BR]]
Postgraduate / Postdoc : [wiki:public/SebastianHenkel Sebastian Henkel]

This workpackage deals with the detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of ''E. coli''. In comparison to the [wiki:public/WP22 reduced order modelling] this work package aims to reproduce the fast dynamic behaviour of these processes by the insertion of detailed mechanistic components as well as the use of fewer reducing assumptions concerning dynamics. Especially for the identification and the analysis of the models fast dynamic measurement data is required.  

Primarily the modelling is divided into the establishment of a TCA cycle model and an ETC model as implicated by the WP's title. Probably at a future stage the two systems will be connected.

The following table shows the information about the available models, experiments and the link to the respective sources in the LIMS (ordered by descending date of first upload):

'''Models & Experiments'''
||'''date'''||'''name & link'''||'''short description'''||
|| 2010 || [wiki:LIMS/Models/WP23/ETCPrincipleModExtension3 Extended ETC principle model 3] || Due to recent ArcA~P phosgel measurement data and investigations concerning thermodynamics between quinones and ArcBA another model version was created. It considers only the oxidised quinones and not the quinone redox state being signal for ArcB. Apart from that it resembles the [wiki:LIMS/Models/WP23/ETCPrincipleModExtension2 former version]. The parameter identification is still in progress.||
|| 2009/2010 || [wiki:LIMS/Experiments/WP23/ETCMod2Results Model results] || This is in-silico data comparing measurement and simulation data used and created by [wiki:LIMS/Models/WP23/ETCPrincipleModExtension2 extended ETC principle model 2] ||
|| 2009/2010 || [wiki:LIMS/Models/WP23/ETCPrincipleModExtension2 Extended ETC principle model 2] || Due to the [wiki:LIMS/Experiments/WP23/PMSimSa1 sensitivity analysis] and the discussion about possible parameter changes, another ETC model extension was created. In comparison to the [wiki:LIMS/Models/WP23/ETCPrincipleModExtension1 last extension] again only one unifying oxidase is considered. In addition a simplified growth model was joined allowing the origin of electrons and possible changes due to different dilution rates. The parameter identification is still in progress. Preliminary results can be found [wiki:LIMS/Experiments/WP23/ETCMod2Results here].||
|| 2008 Nov. 5th || [wiki:LIMS/Experiments/WP23/PMSimSa1 Simulation/Sensitivity analysis] || Simulation and sensitivity analysis of this [wiki:LIMS/Models/WP23/ETCPrincipleModExtension1 extended ETC principle model 1].||
|| 2008 Nov. 5th || [wiki:LIMS/Models/WP23/ETCPrincipleModExtension1 Extended ETC principle model] || First extensions of the earlier ETC principle model: a) input of oxygen by ''aer'' variable; b) two oxidases (assumed partitioning). Parameter identified due to the use of measurement data. [wiki:LIMS/Experiments/WP23/PMSimSa1 Experiments].||
|| 2008 Jul. 10th || [wiki:LIMS/Models/WP23/SimpleArcAFNRMod ETC principle model] || Simplified model of the electron-transport chain of ''Escherichia coli'' and its regulation by ArcA and FNR to demonstrate a hypothetical design principle in the regulatory structure. ||
||2007 Sep. 2nd || [wiki:LIMS/Models/WP23/PreliminaryWork TCA preliminary work] || Preliminary work on the TCA cycle. ||