Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable
Sets

D 2017

Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets

MAZURENKO, Stanislav, Jiří DAMBORSKÝ and Zbyněk PROKOP

Basic information

Original name

Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets

Authors

MAZURENKO, Stanislav (643 Russian Federation, belonging to the institution), Jiří DAMBORSKÝ (203 Czech Republic, guarantor, belonging to the institution) and Zbyněk PROKOP (203 Czech Republic, belonging to the institution)

Edition

Německo, 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, p. 9-17, 9 pp. 2017

Publisher

Springer International Publishing

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10102 Applied mathematics

Country of publisher

Portugal

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

printed version "print"

References:

URL

RIV identification code

RIV/00216224:14310/17:00099434

Organization unit

Faculty of Science

ISBN

978-3-319-60816-7

ISSN

DOI

http://dx.doi.org/10.1007/978-3-319-60816-7_2

UT WoS

000465514300002

Keywords in English

Enzyme kinetics; Optimal control; Synthetic biology; Metabolic networks; Non-linear dynamics

Abstract

V originále

This article studies the time evolution of multi-enzyme pathways. The non-linearity of the problem coupled with the infinite dimensionality of the time-dependent input usually results in a rather laborious optimization. Here we discuss how the optimization of the input enzyme concentrations might be efficiently reduced to a calculation of reachable sets. Under some general conditions, the original system has star-shaped reachable sets that can be derived by solving a partial differential equation. This method allows a thorough study and optimization of quite sophisticated enzymatic pathways with non-linear dynamics and possible inhibition. Moreover, optimal control synthesis based on reachable sets can be implemented and was tested on several simulated examples.

Links

LM2011028, research and development project

Name: RECETOX ? Národní infrastruktura pro výzkum toxických látek v prostředí

Investor: Ministry of Education, Youth and Sports of the CR

LO1214, research and development project

Name: Centrum pro výzkum toxických látek v prostředí (Acronym: RECETOX)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

MAZURENKO, Stanislav, Jiří DAMBORSKÝ and Zbyněk PROKOP. Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. In Rocha M.,De Paz J.F.,Pinto T.,Fdez-Riverola. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics. Německo: Springer International Publishing, 2017, p. 9-17. ISBN 978-3-319-60816-7. Available from: https://dx.doi.org/10.1007/978-3-319-60816-7_2.

@inproceedings{1403832,
   author = {Mazurenko, Stanislav and Damborský, Jiří and Prokop, Zbyněk},
   address = {Německo},
   booktitle = {11th International Conference on Practical Applications of Computational Biology & Bioinformatics},
   doi = {http://dx.doi.org/10.1007/978-3-319-60816-7_2},
   editor = {Rocha M.,De Paz J.F.,Pinto T.,Fdez-Riverola},
   keywords = {Enzyme kinetics; Optimal control; Synthetic biology; Metabolic networks; Non-linear dynamics},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {Německo},
   isbn = {978-3-319-60816-7},
   pages = {9-17},
   publisher = {Springer International Publishing},
   title = {Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets},
   url = {https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2017/10/9783319608150-c2.pdf},
   year = {2017}
}

TY  - JOUR
ID  - 1403832
AU  - Mazurenko, Stanislav - Damborský, Jiří - Prokop, Zbyněk
PY  - 2017
TI  - Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets
PB  - Springer International Publishing
CY  - Německo
SN  - 9783319608167
KW  - Enzyme kinetics
KW  - Optimal control
KW  - Synthetic biology
KW  - Metabolic networks
KW  - Non-linear dynamics
UR  - https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2017/10/9783319608150-c2.pdf
L2  - https://loschmidt.chemi.muni.cz/peg/wp-content/uploads/2017/10/9783319608150-c2.pdf
N2  - This article studies the time evolution of multi-enzyme pathways. The non-linearity of the problem coupled with the infinite dimensionality of the time-dependent input usually results in a rather laborious optimization. Here we discuss how the optimization of the input enzyme concentrations might be efficiently reduced to a calculation of reachable sets. Under some general conditions, the original system has star-shaped reachable sets that can be derived by solving a partial differential equation. This method allows a thorough study and optimization of quite sophisticated enzymatic pathways with non-linear dynamics and possible inhibition. Moreover, optimal control synthesis based on reachable sets can be implemented and was tested on several simulated examples.
ER  -

MAZURENKO, Stanislav, Jiří DAMBORSKÝ and Zbyněk PROKOP. Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. In Rocha M.,De Paz J.F.,Pinto T.,Fdez-Riverola. \textit{11th International Conference on Practical Applications of Computational Biology \&{} Bioinformatics}. Německo: Springer International Publishing, 2017, p.~9-17. ISBN~978-3-319-60816-7. Available from: https://dx.doi.org/10.1007/978-3-319-60816-7\_{}2.

Detailed Information on Publication Record