Discrete Biochemical Systems Theory
Almost every biomedical systems analysis requires early decisions regarding the choice of the most suitable representations to be used. De facto the most prevalent choice is a system of ordinary differential equations (ODEs). This framework is very popular because it is flexible and fairly easy to u...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Molecular Biosciences |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.874669/full |
| _version_ | 1828787501773357056 |
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| author | Eberhard O. Voit Daniel V. Olivença |
| author_facet | Eberhard O. Voit Daniel V. Olivença |
| author_sort | Eberhard O. Voit |
| collection | DOAJ |
| description | Almost every biomedical systems analysis requires early decisions regarding the choice of the most suitable representations to be used. De facto the most prevalent choice is a system of ordinary differential equations (ODEs). This framework is very popular because it is flexible and fairly easy to use. It is also supported by an enormous array of stand-alone programs for analysis, including many distinct numerical solvers that are implemented in the main programming languages. Having selected ODEs, the modeler must then choose a mathematical format for the equations. This selection is not trivial as nearly unlimited options exist and there is seldom objective guidance. The typical choices include ad hoc representations, default models like mass-action or Lotka-Volterra equations, and generic approximations. Within the realm of approximations, linear models are typically successful for analyses of engineered systems, but they are not as appropriate for biomedical phenomena, which often display nonlinear features such as saturation, threshold effects or limit cycle oscillations, and possibly even chaos. Power-law approximations are simple but overcome these limitations. They are the key ingredient of Biochemical Systems Theory (BST), which uses ODEs exclusively containing power-law representations for all processes within a model. BST models cover a vast repertoire of nonlinear responses and, at the same time, have structural properties that are advantageous for a wide range of analyses. Nonetheless, as all ODE models, the BST approach has limitations. In particular, it is not always straightforward to account for genuine discreteness, time delays, and stochastic processes. As a new option, we therefore propose here an alternative to BST in the form of discrete Biochemical Systems Theory (dBST). dBST models have the same generality and practicality as their BST-ODE counterparts, but they are readily implemented even in situations where ODEs struggle. As a case study, we illustrate dBST applied to the dynamics of the aryl hydrocarbon receptor (AhR), a signal transduction system that simultaneously involves time delays and stochasticity. |
| first_indexed | 2024-12-12T00:32:41Z |
| format | Article |
| id | doaj.art-109ad19901e24cb58828be8427466e49 |
| institution | Directory Open Access Journal |
| issn | 2296-889X |
| language | English |
| last_indexed | 2024-12-12T00:32:41Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-109ad19901e24cb58828be8427466e492022-12-22T00:44:26ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-05-01910.3389/fmolb.2022.874669874669Discrete Biochemical Systems TheoryEberhard O. VoitDaniel V. OlivençaAlmost every biomedical systems analysis requires early decisions regarding the choice of the most suitable representations to be used. De facto the most prevalent choice is a system of ordinary differential equations (ODEs). This framework is very popular because it is flexible and fairly easy to use. It is also supported by an enormous array of stand-alone programs for analysis, including many distinct numerical solvers that are implemented in the main programming languages. Having selected ODEs, the modeler must then choose a mathematical format for the equations. This selection is not trivial as nearly unlimited options exist and there is seldom objective guidance. The typical choices include ad hoc representations, default models like mass-action or Lotka-Volterra equations, and generic approximations. Within the realm of approximations, linear models are typically successful for analyses of engineered systems, but they are not as appropriate for biomedical phenomena, which often display nonlinear features such as saturation, threshold effects or limit cycle oscillations, and possibly even chaos. Power-law approximations are simple but overcome these limitations. They are the key ingredient of Biochemical Systems Theory (BST), which uses ODEs exclusively containing power-law representations for all processes within a model. BST models cover a vast repertoire of nonlinear responses and, at the same time, have structural properties that are advantageous for a wide range of analyses. Nonetheless, as all ODE models, the BST approach has limitations. In particular, it is not always straightforward to account for genuine discreteness, time delays, and stochastic processes. As a new option, we therefore propose here an alternative to BST in the form of discrete Biochemical Systems Theory (dBST). dBST models have the same generality and practicality as their BST-ODE counterparts, but they are readily implemented even in situations where ODEs struggle. As a case study, we illustrate dBST applied to the dynamics of the aryl hydrocarbon receptor (AhR), a signal transduction system that simultaneously involves time delays and stochasticity.https://www.frontiersin.org/articles/10.3389/fmolb.2022.874669/fullcanonical modeldelaydiscrete eventgeneralized mass action systempower-law approximationsystem |
| spellingShingle | Eberhard O. Voit Daniel V. Olivença Discrete Biochemical Systems Theory Frontiers in Molecular Biosciences canonical model delay discrete event generalized mass action system power-law approximation system |
| title | Discrete Biochemical Systems Theory |
| title_full | Discrete Biochemical Systems Theory |
| title_fullStr | Discrete Biochemical Systems Theory |
| title_full_unstemmed | Discrete Biochemical Systems Theory |
| title_short | Discrete Biochemical Systems Theory |
| title_sort | discrete biochemical systems theory |
| topic | canonical model delay discrete event generalized mass action system power-law approximation system |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.874669/full |
| work_keys_str_mv | AT eberhardovoit discretebiochemicalsystemstheory AT danielvolivenca discretebiochemicalsystemstheory |