Literature DB >> 19243161

Parameter identification for chemical reaction systems using sparsity enforcing regularization: a case study for the chlorite-iodide reaction.

Philipp Kügler1, Erwin Gaubitzer, Stefan Müller.   

Abstract

Complex chemical reactions are commonly described by systems of nonlinear ordinary differential equations. Rate and equilibrium constants of these models are usually not directly accessible and have to be indirectly inferred from experimental observations of the system. As a consequence, parameter identification problems have to be formulated and computationally solved. Because of a limited amount of information and uncertainties in the data, the solutions to such parameter identification problems typically lack uniqueness and stability properties and hence cannot be found in a reliable way by a pure minimization of the data mismatch (i.e., the discrepancy between experimental observations and simulated model output). To overcome these difficulties, so-called regularization methods have to be used. In this article, we suggest a sparsity promoting regularization approach that eliminates unidentifiable model parameters (i.e., parameters of low or no sensitivity to the given data). That way, the model is reduced to a core reaction mechanism with manageable interpretation while still remaining in accordance with the experimental observations. For the computational realization, we utilize the adjoint state technique for an efficient calculation of the gradient of the objective with respect to model parameters as well as uncertain initial and experimental conditions. Illustrations of our approach are given by means of the chlorite-iodide reaction for which reference parameter values are available.

Entities:  

Year:  2009        PMID: 19243161     DOI: 10.1021/jp808792u

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  5 in total

1.  Moment fitting for parameter inference in repeatedly and partially observed stochastic biological models.

Authors:  Philipp Kügler
Journal:  PLoS One       Date:  2012-08-10       Impact factor: 3.240

2.  miRNA regulatory circuits in ES cells differentiation: a chemical kinetics modeling approach.

Authors:  Zijun Luo; Xuping Xu; Peili Gu; David Lonard; Preethi H Gunaratne; Austin J Cooney; Robert Azencott
Journal:  PLoS One       Date:  2011-10-19       Impact factor: 3.240

Review 3.  Synthetic spatial patterning in bacteria: advances based on novel diffusible signals.

Authors:  Martina Oliver Huidobro; Jure Tica; Georg K A Wachter; Mark Isalan
Journal:  Microb Biotechnol       Date:  2021-11-29       Impact factor: 6.575

4.  Differentiation between genomic and non-genomic feedback controls yields an HPA axis model featuring hypercortisolism as an irreversible bistable switch.

Authors:  Clemens A Zarzer; Martin G Puchinger; Gottfried Köhler; Philipp Kügler
Journal:  Theor Biol Med Model       Date:  2013-11-09       Impact factor: 2.432

5.  Modeling miRNA-mRNA interactions: fitting chemical kinetics equations to microarray data.

Authors:  Zijun Luo; Robert Azencott; Yi Zhao
Journal:  BMC Syst Biol       Date:  2014-02-18
  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.