Identifying the parametric occurrence of multiple steady states for some biological networks

We consider a problem from biological network analysis of determining regions in a parameter space over which there are multiple steady states for positive real values of variables and parameters. We describe multiple approaches to address the problem using tools from Symbolic Computation. We describe how progress was made to achieve semi-algebraic descriptions of the multistationarity regions of parameter space, and compare symbolic and numerical methods. The biological networks studied are models of the mitogen-activated protein kinases (MAPK) network which has already consumed considerable effort using special insights into its structure of corresponding models. Our main example is a model with 11 equations in 11 variables and 19 parameters, 3 of which are of interest for symbolic treatment. The model also imposes positivity conditions on all variables and parameters. We apply combinations of symbolic computation methods designed for mixed equality / inequality systems, specifically virtual substitution, lazy real triangularization and cylindrical algebraic decomposition, as well as a simplification technique adapted from Gaussian elimination and graph theory. We are able to determine semi-algebraic conditions for multistationarity of our main example over a 2-dimensional parameter space. We also study a second MAPK model and a symbolic grid sampling technique which can locate such regions in 3-dimensional parameter space. © 2019 Elsevier Ltd

Авторы
Bradford R.1 , Davenport J.H.1 , England M.2 , Errami H.3 , Gerdt V. 4, 5 , Grigoriev D.6 , Hoyt C.7 , Košta M.8 , Radulescu O.9 , Sturm T.10, 11 , Weber A.3
Издательство
Academic Press
Язык
Английский
Страницы
84-119
Статус
Опубликовано
Том
98
Год
2020
Организации
  • 1 Department of Computer Science, University of Bath, United Kingdom
  • 2 Faculty of Engineering, Environment and Computing, Coventry University, United Kingdom
  • 3 Institute for Informatics, University of Bonn, Germany
  • 4 Joint Institute for Nuclear Research (JINR), Dubna, Russian Federation
  • 5 Friendship University of Russia (RUDN University), Moscow, Russian Federation
  • 6 CNRS & University of Lille, France
  • 7 Department of Life Science Informatics, B-IT, University of Bonn, Germany
  • 8 Slovak Academy of Sciences, Slovakia
  • 9 CNRS, University of Montpellier, France
  • 10 CNRS, Inria, the University of Lorraine, Nancy, France
  • 11 MPI Informatics, Saarland University, Saarbrücken, Germany
Ключевые слова
Biological networks; MAPK; Mixed equation/inequality solving; Real quantifier elimination; Signalling pathways
Дата создания
10.02.2020
Дата изменения
10.02.2020
Постоянная ссылка
https://repository.rudn.ru/ru/records/article/record/56496/