Layering in networks: The case of biochemical systems
Networked systems are characterised by their scale and structure. In particular, biochemical reaction networks involve complicated interconnections of chemical reaction pathways and cycles, occurring on a number of different time and space scales even within a cell. This paper seeks to formalise a m...
| Main Authors: | , , |
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| Format: | Journal article |
| Language: | English |
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2013
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| _version_ | 1826283379872497664 |
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| author | Prescott, T Papachristodoulou, A IEEE |
| author_facet | Prescott, T Papachristodoulou, A IEEE |
| author_sort | Prescott, T |
| collection | OXFORD |
| description | Networked systems are characterised by their scale and structure. In particular, biochemical reaction networks involve complicated interconnections of chemical reaction pathways and cycles, occurring on a number of different time and space scales even within a cell. This paper seeks to formalise a method of layering the dynamics of a biochemical network by decomposing its stoichiometric matrix into a sum of stoichiometric matrices, each of which we identify with a layer. We derive a condition to test when a given layer directly communicates with another. We also examine singular perturbation by considering decomposition into fast and slow layers, characterising the approximate dynamics through the quasi-steady state approximation in terms of a perturbation of the dynamics of the slow layer. © 2013 AACC American Automatic Control Council. |
| first_indexed | 2024-03-07T00:58:02Z |
| format | Journal article |
| id | oxford-uuid:88c2b001-17ab-406b-96b1-cb994ea5e3f0 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T00:58:02Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | oxford-uuid:88c2b001-17ab-406b-96b1-cb994ea5e3f02022-03-26T22:19:37ZLayering in networks: The case of biochemical systemsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:88c2b001-17ab-406b-96b1-cb994ea5e3f0EnglishSymplectic Elements at Oxford2013Prescott, TPapachristodoulou, AIEEENetworked systems are characterised by their scale and structure. In particular, biochemical reaction networks involve complicated interconnections of chemical reaction pathways and cycles, occurring on a number of different time and space scales even within a cell. This paper seeks to formalise a method of layering the dynamics of a biochemical network by decomposing its stoichiometric matrix into a sum of stoichiometric matrices, each of which we identify with a layer. We derive a condition to test when a given layer directly communicates with another. We also examine singular perturbation by considering decomposition into fast and slow layers, characterising the approximate dynamics through the quasi-steady state approximation in terms of a perturbation of the dynamics of the slow layer. © 2013 AACC American Automatic Control Council. |
| spellingShingle | Prescott, T Papachristodoulou, A IEEE Layering in networks: The case of biochemical systems |
| title | Layering in networks: The case of biochemical systems |
| title_full | Layering in networks: The case of biochemical systems |
| title_fullStr | Layering in networks: The case of biochemical systems |
| title_full_unstemmed | Layering in networks: The case of biochemical systems |
| title_short | Layering in networks: The case of biochemical systems |
| title_sort | layering in networks the case of biochemical systems |
| work_keys_str_mv | AT prescottt layeringinnetworksthecaseofbiochemicalsystems AT papachristodouloua layeringinnetworksthecaseofbiochemicalsystems AT ieee layeringinnetworksthecaseofbiochemicalsystems |