Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn

Seminar

Speaker: Sabrina Kleessen, AG Nikoloski, UP + MPI-MP

Title: Dynamic Flux Balance Analysis of Carbon Metabolism

Time: Wed, Nov 17, 2010, 10am

Place: MPI für Molekulare Pflanzenphysiologie, Room 0.21 in The Box

Abstract:
The rapidly developing field of systems biology depends on the analysis of metabolic networks, yielding quantification and understanding of different metabolic states at the systemic level. Flux balance analysis (FBA) is one of the most important tools for large-scale analysis of metabolic networks. Additionally, methods have been developed to combine static modeling, based on classical FBA, with kinetic modeling approaches, termed dynamic FBA (DFBA). Static approaches, such as: minimization of metabolic adjustment (MOMA) and regulatory on/off minimization (ROOM), as well as the dynamic approach, M-DFBA, were developed for perturbed networks. These approaches do not assume optimality principles, e.g., maximization of biomass.

This study presents a novel approach, called R-DFBA, for predicting metabolite concentrations and reaction rates over time. The method incorporates the static approach ROOM with DFBA to allow the analysis of perturbed networks without knowledge about the exact values of kinetic parameters. The objective function is modified to minimize the fluctuations of the profile of metabolite concentrations instead of the classical optimality assumption. Furthermore, we examine the influence of the objective function to the predictability of flux dynamics in networks with the help of the analyzed approaches.

Together with the proposed approach, a total of ten methods are used to investigate the behavior of metabolite concentrations and flux rates of reactions of two different carbon pathways. The first system focuses on the photosynthetic metabolism of C3-plants, whereas the second includes the most abundant sugars and sugar phosphates of the central carbon metabolism. Based on the underlying networks, we analyze the advantages and disadvantages of our approach, and compare the obtained results with those from the other FBA-based methods.

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Past NLD Seminars (1994-2007) & (2008 ...)

Students' seminar: Theoretical Physics, PIK, Modeling & TSA Berlin-Potsdam-Colloquia: PhysGesellschaft Berlin, TU Berlin, Pro Physik, AIP, AEI, MPI-KGF, GFZ, HMI, PIK, AWI, Max Planck Institute for the History of Science, Mathematik, DPG Disputationen, & Vorschau UP

Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
Phone: (+49-331) 977-1658, Fax : (+49-331) 977-1045

Email: Udo.Schwarz AT uni-potsdam.de

DFG SFB 1294

DFG Sonderforschungsbereich 1294 Data assimilation

DFG SPP 1488

DFG Schwerpunktprogramm 1488 Planetmag


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