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A comparative study of stochastic and deterministic simulation methods for transport-diffusion systems

Åström, Hampus LU (2016) FYTM01 20151
Computational Biology and Biological Physics
Department of Astronomy and Theoretical Physics
Abstract
The growth of tissues and organs in plants is governed by the morphogen auxin coupled with the membrane protein PIN, which together generate patterns that guide development. Systems of this kind have been studied extensively in experiments and computational system biology models. This thesis builds on that work by introducing a stochastic version of these models to examine differences between stochastic and deterministic behaviours of the patterning process. Stochastic simulations are found to exhibit a more dynamic behaviour while deterministic simulations produce patterns that are more sensitive to the underlying cell grid arrangement. The minimum distance between auxin concentration peaks also depends on the cell grid, but is found to... (More)
The growth of tissues and organs in plants is governed by the morphogen auxin coupled with the membrane protein PIN, which together generate patterns that guide development. Systems of this kind have been studied extensively in experiments and computational system biology models. This thesis builds on that work by introducing a stochastic version of these models to examine differences between stochastic and deterministic behaviours of the patterning process. Stochastic simulations are found to exhibit a more dynamic behaviour while deterministic simulations produce patterns that are more sensitive to the underlying cell grid arrangement. The minimum distance between auxin concentration peaks also depends on the cell grid, but is found to be conserved between simulation types. The difference between stochastic and deterministic simulations is significant under certain conditions, and future research should evaluate the system conditions before utilising deterministic algorithms when stochastic simulations might model the system more accurately. (Less)
Popular Abstract
Plants determine where to grow new limbs and leafs using the chemical auxin. Auxin is a hormone, and cells that have much of it grow more than others thereby initiating new structures. The concentrations of auxin in each cell are determined by how it is transported between cells. This thesis is a study in how different computer simulation methods of auxin patterns in plants can lead to different outcomes. The studied method types are deterministic (differential equations) and stochastic (probabilities and random selection). The stochastic simulations are found to be more dynamic and less influences by the arrangement of the cells in comparison to deterministic simulations. Under certain conditions there can be clear differences in results... (More)
Plants determine where to grow new limbs and leafs using the chemical auxin. Auxin is a hormone, and cells that have much of it grow more than others thereby initiating new structures. The concentrations of auxin in each cell are determined by how it is transported between cells. This thesis is a study in how different computer simulation methods of auxin patterns in plants can lead to different outcomes. The studied method types are deterministic (differential equations) and stochastic (probabilities and random selection). The stochastic simulations are found to be more dynamic and less influences by the arrangement of the cells in comparison to deterministic simulations. Under certain conditions there can be clear differences in results from the two simulation types, and this should be considered when using computer simulations. (Less)
Please use this url to cite or link to this publication:
author
Åström, Hampus LU
supervisor
organization
course
FYTM01 20151
year
type
H2 - Master's Degree (Two Years)
subject
keywords
Transport-Diffusion, Auxin, PIN, Stochastic, Deterministic, Simulation, Pattern, Plant, Morphogen
language
English
additional info
Henrik Jönsson was my main supervisor. Pawel Krupinski was assistant supervisor.
id
8892312
date added to LUP
2016-10-05 10:21:50
date last changed
2017-10-06 16:48:20
@misc{8892312,
  abstract     = {The growth of tissues and organs in plants is governed by the morphogen auxin coupled with the membrane protein PIN, which together generate patterns that guide development. Systems of this kind have been studied extensively in experiments and computational system biology models. This thesis builds on that work by introducing a stochastic version of these models to examine differences between stochastic and deterministic behaviours of the patterning process. Stochastic simulations are found to exhibit a more dynamic behaviour while deterministic simulations produce patterns that are more sensitive to the underlying cell grid arrangement. The minimum distance between auxin concentration peaks also depends on the cell grid, but is found to be conserved between simulation types. The difference between stochastic and deterministic simulations is significant under certain conditions, and future research should evaluate the system conditions before utilising deterministic algorithms when stochastic simulations might model the system more accurately.},
  author       = {Åström, Hampus},
  keyword      = {Transport-Diffusion,Auxin,PIN,Stochastic,Deterministic,Simulation,Pattern,Plant,Morphogen},
  language     = {eng},
  note         = {Student Paper},
  title        = {A comparative study of stochastic and deterministic simulation methods for transport-diffusion systems},
  year         = {2016},
}