Models
In our institute we develope and reimplement mathematical models of biological systems. By exploring systematically the mathematical description of a complex biological phenomenon we analyse its dynamics and response to perturbations. For implementing models we use the Python package modelbase, which was developed in our group.
On our official QTB gitlab page you can find and download the implemented models as Python files. Moreover, most of our projects provide Jupiter Notebooks with which you can reproduce several of the figures from the original papers
In the following list you can find some of the models that are used in our institut.
| Model | Reference | Link |
|---|---|---|
| Calvin-Benson-Bassham cycle | Poolman, M.G., Fell, D.A., and Thomas, S. (2000). Modelling photosynthesis and its control. Journal of Experimental Botany 51, 319–328.; Pettersson, G., and Ryde-Pettersson, U. (1988). A mathematical model of the Calvin photosynthesis cycle. European Journal of Biochemistry 175, 661–672. | cbb-cycle |
| Labels in the Calvin-Benson-Bassham cycle | Poolman, M.G., Fell, D.A., and Thomas, S. (2000). Modelling photosynthesis and its control. Journal of Experimental Botany 51, 319–328.; Pettersson, G., and Ryde-Pettersson, U. (1988). A mathematical model of the Calvin photosynthesis cycle. European Journal of Biochemistry 175, 661–672. | cbb-cycle-labelling |
| Labels in the pentose phosphat pathway | Mcintyre, L.M., Thorburn, D.R., Bubb, W.A., and Kuchel, P.W. (1989). Comparison of computer simulations of the F-type and L-type non-oxidative hexose monophosphate shunts with 31P-NMR experimental data from human erythrocytes. European Journal of Biochemistry 180, 399–420. Berthon, H.A., Bubb, W.A., and Kuchel, P.W. (1993). 13C n.m.r. isotopomer and computer-simulation studies of the non-oxidative pentose phosphate pathway of human erythrocytes. Biochemical Journal 296, 379–387. | ppp-labelling |
| Photosynthetic electron transport chain | Ebenhöh, O., Fucile, G., Finazzi, G., Rochaix, J.-D., and Goldschmidt-Clermont, M. (2014). Short-term acclimation of the photosynthetic electron transfer chain to changing light: a mathematical model. Philosophical Transactions of the Royal Society B: Biological Sciences 369, 20130223. | petc-2014 |
| Non-photochemical Quenching | Matuszyńska, A., Heidari, S., Jahns, P., and Ebenhöh, O. (2016). A mathematical model of non-photochemical quenching to study short-term light memory in plants. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857, 1860–1869. | npqmodel-2016 |
| Photosynthesis (ETC + CBC) | Matuszyńska, A., Saadat, N.P., and Ebenhöh, O. (2019). Balancing energy supply during photosynthesis – a theoretical perspective. Physiologia Plantarum 166, 392–402. | photosynthesismodel-2019 |
| HIV dynamics | Perelson, A.S., Kirschner, D.E., and De Boer, R. (1993). Dynamics of HIV infection of CD4+ T cells. Mathematical Biosciences 114, 81–125. | HIV-t4cellsinfection-1993photosynthesismodel-2019 |
| Label propagation in stationary metabolic networks | Sokol, S., and Portais, J.-C. (2015). Theoretical Basis for Dynamic Label Propagation in Stationary Metabolic Networks under Step and Periodic Inputs. PLOS ONE 10, e0144652. | label-propagation-2015 |
| Describtion of the movement of particles (ribosomes) along a lattice (the mRNA) | McFarland, M. R., Keller, C. D., Childers, B. M., Adeniyi, S. A., Corrigall, H., Raguin, A., ... & Stansfield, I. (2020). The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. Nucleic acids research, 48(6), 3071-3088. | Global Translation Model |
| A codon tuning tool for the expression of heterologous proteins in host microorganisms | ExpressInHost |