Basic Phytochrome B Calculations

Robert W. Smith*, Christian Fleck

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

Abstract

Mathematical models are important tools in helping us to understand complex biological systems. Models of phytochrome-regulated systems in Arabidopsis thaliana have shown the importance of dimerization, nuclear transport, and thermal/dark reversion in mediating phytochrome activity and plant development. Here we go through the steps required to calculate the steady-state amounts of phytochrome subspecies relative to the total phytochrome molecule population. Starting from a simplified two-state system we expand and apply the technique to the extended phytochrome dimer model. Additionally, we provide a Python package that can automatically calculate the proportion of phytochrome B in a particular state given specific experimental conditions.

Original languageEnglish
Title of host publicationPhytochromes
Subtitle of host publicationMethods and Protocols
EditorsAndreas Hiltbrunner
PublisherHumana Press Inc.
Pages121-133
Number of pages13
ISBN (Electronic)9781493996124
ISBN (Print)9781493996117
DOIs
Publication statusPublished - 18 Jul 2019

Publication series

NameMethods in Molecular Biology
Volume2026
ISSN (Print)1064-3745

Keywords

  • Computer programming
  • Mathematical modeling
  • Ordinary differential equations
  • Phytochromes

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