Coupling kinetic models and advection–diffusion equations. 1. Framework development and application to sucrose translocation and metabolism in sugarcane
| Autor: | Johann M. Rohwer, Lafras Uys, Jan-Hendrik S. Hofmeyr |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0303 health sciences Sucrose Advection food and beverages Thermodynamics Chromosomal translocation Plant Science Metabolism Kinetic energy 01 natural sciences Biochemistry Genetics and Molecular Biology (miscellaneous) Coupling (electronics) 03 medical and health sciences chemistry.chemical_compound chemistry Modeling and Simulation Diffusion (business) Agronomy and Crop Science 030304 developmental biology 010606 plant biology & botany |
| Zdroj: | in silico Plants. 3 |
| ISSN: | 2517-5025 |
| DOI: | 10.1093/insilicoplants/diab013 |
| Popis: | The sugarcane stalk, besides being the main structural component of the plant, is also the major storage organ for carbohydrates. Previous studies have modelled the sucrose accumulation pathway in the internodal storage parenchyma of sugarcane using kinetic models cast as systems of ordinary differential equations. To address the shortcomings of these models, which did not include subcellular compartmentation or spatial information, the present study extends the original models within an advection–diffusion–reaction framework, requiring the use of partial differential equations to model sucrose metabolism coupled to phloem translocation. We propose a kinetic model of a coupled reaction network where species can be involved in chemical reactions and/or be transported over long distances in a fluid medium by advection or diffusion. Darcy’s law is used to model fluid flow and allows a simplified, phenomenological approach to be applied to translocation in the phloem. Similarly, generic reversible Hill equations are used to model biochemical reaction rates. Numerical solutions to this formulation are demonstrated with time-course analysis of a simplified model of sucrose accumulation. The model shows sucrose accumulation in the vacuoles of stalk parenchyma cells, and is moreover able to demonstrate the upregulation of photosynthesis in response to a change in sink demand. The model presented is able to capture the spatio-temporal evolution of the system from a set of initial conditions by combining phloem flow, diffusion, transport of metabolites between compartments and biochemical enzyme-catalysed reactions in a rigorous, quantitative framework that can form the basis for future modelling and experimental design. |
| Databáze: | OpenAIRE |
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