In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this chapter we review four distinct theoretical and simulation frameworks: (i) non-spatial and deterministic, (ii) spatial and deterministic, (iii) non-spatial and stochastic and (iv) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models.
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Olaf Wolkenhauer; Peter Wellstead; Kwang-Hyun Cho
Review Article| September 30 2008
Modelling reaction kinetics inside cells
†Indiana University School of Informatics and Biocomplexity Institute, 1900 E 10th St, Eigenmann Hall 906, Bloomington, IN 47406, U.S.A.
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Essays Biochem (2008) 45: 41–56.
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Olaf Wolkenhauer, Peter Wellstead, Kwang-Hyun Cho, Ramon Grima, Santiago Schnell; Modelling reaction kinetics inside cells. Essays Biochem 30 September 2008; 45 41–56. doi: https://doi.org/10.1042/bse0450041
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