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Plant systems modelling

Plants have developed sophisticated mechanisms to capture and use resources efficiently. Complex internal molecular/biochemical mechanisms mediate the transport, accumulation, transformation of nutrients in the different compartments of the plant. Specialised structures are formed to exploit resources availability in space. While the components required for these basic processes are becoming increasingly well characterised, little is still known of their precise coordination and control in space and time. In the Plant Systems Modelling Group, we are developing new quantitative approaches to understand and predict the precise nature of the coupling between these genetic and biophysical processes. 

New: Collaboration starting to study competition for nitrogen funded by VolkswagenStifung


Modelling the genetic, physical and environmental processes of plant growth and development

Plants develop complex root architectures and form numerous associations with micro-organisms in order to acquire water and nutrients from soils. In natural environments, the growth of these networks is not well understood because of the complexity of interactions and biological responses to the varying soil conditions. We develop experimental and modelling approaches to better understand and characterise these responses.


Models of the growth of root networks in soil

Our approach is to use “more brain, less computer”. We simply theories in order to capture only the essence of the emerging behaviours in plant soil systems. For example, we showed the growth of root networks are explained by the dynamics of their meristems which propagating in space like waves. This concept simplified method allowed understand relationships between growth parameters and topological structures, improved the efficiency of computations and allows automated extraction growth parameter from phenotyping datasets.

Image of modelling root system using Continuous Deformable Domains

Mechanisms of early microbial colonisation of the rhizoplane


Bacteria use various strategies to feed on root exudates, including surface attachment using flagella or fimbriae motility or biofilm formation. Plants also control to a great extent the colonization of the rhizosphere. They secrete compounds that stimulate or repress specific members of the soil microbiota. To date, it has been very difficult to understand how such processes interact. We develop models that shows how elongation rate, attachment rate bacterial dispersion, exudation, and root development influence the early stages of microbial colonisation of the rhizoplane. Models have allowed identification of patterns associated with the mechanisms of colonisation (chemotaxis, attachement, colonisation of the root cap). Experiments are now being carried out to confort predictions from the theory, and to obtain precise quantification of growth parameters in a transparent soil system.


Multicellular models of plant morphogenesis

The networks of cell-cell interactions determine how new organs are initiated and regulated and modified by environmental signals. We are developing multicellular models to provide a fundamental understanding of how cell-cell interactions contribute to whole plant function.



Quantitative analysis of the plant architectural development

Computational tools for studying plant architecture and developmentImage of software tools for plant biometry

We are developing methods to quantify, understand and predict plant development. These methods include image capture, mathematical modelling and computer simulation. We are using these methods as tools to collect and analyse data, build models and simulate the processes involved during plant morphogenesis.

Imaging systems

We are developing imaging systems to characterise plant growth and development. We use techniques such as Optical Projection Tomography (OPT), Biospeckle Laser Imaging, and Single Plane Illumination Microscopy.

Transparent soil

We have developed a substrate called transparent soil, with a matrix of solid particles and a pore network containing liquid and air. The physical structure was manipulated with the aim of generating 3D optical images of soil biota in a physically complex yet controllable environment. More information is on the Transparent soils page.

Image showing segmentation of plant cell architectures


Areas of Interest

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The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.