title: A minimal and self-consistent in silico cell model based on macromolecular interactions.
abstract: A self-consistent minimal cell model with a physically motivated schema for molecular interaction is introduced and described. The genetic and metabolic reaction network of the cell is modelled by multidimensional nonlinear ordinary differential equations, which are derived from biochemical kinetics. The strategy behind this modelling approach is to keep the model sufficiently simple in order to be able to perform studies on evolutionary optimization in populations of cells. At the same time, the model should be complex enough to handle the basic features of genetic control of metabolism and coupling to environmental factors. Thereby, the model system will provide insight into the mechanisms leading to important biological phenomena, such as homeostasis, (circadian) rhythms, robustness and adaptation to a changing environment. One example of modelling a molecular regulatory mechanism, cooperative binding of transcription factors, is discussed in detail.
authors.affiliation: Theoretical Biochemistry Group, Institut für Theoretische Chemie, Universität Wien, Währingerstrasse 17, 1090 Wien, Austria. xtof@tbi.univie.ac.at
authors.forename: Christoph
authors.initials: C
authors.lastname: Flamm
authors.forename: Lukas
authors.initials: L
authors.lastname: Endler
authors.forename: Stefan
authors.initials: S
authors.lastname: Müller
authors.forename: Stefanie
authors.initials: S
authors.lastname: Widder
authors.forename: Peter
authors.initials: P
authors.lastname: Schuster
mesh_terms: D005075:Biological Evolution; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D005786:Gene Expression Regulation; D005838:Genotype; D046911:Macromolecular Substances / Q000737:chemistry*; D008954:Models, Biological
chemical_list: D046911:Macromolecular Substances