Network thermodynamics of biological systems: A bond graph approach

Gawthrop, P.J.; Pan, Michael

doi:10.1016/j.mbs.2022.108899

Cited by 12 publications

(40 citation statements)

References 78 publications

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“…"Information and Energy/Matter" (Dodig-Crnkovic, 2012). As well, a recent interest in the consideration of the energy viewpoint has emerged, for instance in the free energy principle for biological systems (Friston, 2012) or the methodology of bond graphs models to consider energy transactions in biological processes (Gawthrop and Pan, 2022).…”

Section: Pathological States As Reduced Fluctuations In Energy Distri...mentioning

confidence: 99%

Is the Tendency to Maximise Energy Distribution an Optimal Collective Activity for Biological Purposes? A Proposal for a Global Principle of Biological Organization

Velázquez¹,

Mateos²,

Erra³

2023

Preprint

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Our purpose is to address the biological problem of finding foundations of the organization in the collective activity among cell networks in the nervous system, at the meso/macroscale, giving rise to cognition and consciousness. But in doing so, we encounter another problem related to the interpretation of methods to assess the neural interactions and organization of the neurodynamics, because thermodynamic notions, which have precise meaning only under specific conditions, have been widely employed in these studies. The consequence is that apparently contradictory results appear in the literature, but these contradictions diminish upon the considerations of the specific circumstances of each experiment. After clarifying some of these controversial points and surveying some experimental results, we propose that a necessary condition for cognition/consciousness to emerge is to have available enough energy, or cellular activity; and a sufficient condition is the multiplicity of configurations in which cell networks can communicate, resulting in non-uniform energy distribution, the generation and dissipation of energy gradients due to the constant activity. These ideas may reveal possible fundamental principles of brain organization and how healthy activity may derive to pathological states.

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Section: Pathological States As Reduced Fluctuations In Energy Distri...mentioning

confidence: 99%

Is the Tendency to Maximise Energy Distribution an Optimal Collective Activity for Biological Purposes? A Proposal for a Global Principle of Biological Organization

Velázquez¹,

Mateos²,

Erra³

2023

Preprint

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“…§ 2.1 summarises, in the form of a specific example, the basic ideas of modelling biochemical systems to be found in more detail in a recent paper [28]. § 2.2 introduces a normalisation approach to simplify the sensitivity analysis and § 2.3 considers the stoichiometry of bond graph models [28]. § 2.4 summarises the linearisation of biochemical systems [41].…”

Section: Bond Graph Modelling Of Biochemical Systemsmentioning

confidence: 99%

“…More complex biochemical system are needed to reveal the full power of the bond graph approach. For example detailed balance and Wegscheider conditions are automatically satisfied [28,56].…”

Section: Example: Modelling the Chemical Reactions A B Cmentioning

confidence: 99%

“…Because of the overlap between Engineering and Systems Biology, it is insightful to import methods from the former to the latter [25][26][27]. The bond graph technique provides one example of this methodological transfer, and has shown great potential in constraining models to be consistent with the laws of physics and thermodynamics [28,29]. Bond graphs were introduced by Paynter [30,31] to model the flow of energy though physical systems of interest to engineers and are described in several text books [32][33][34][35] and a tutorial for control engineers [36].…”

Section: Introductionmentioning

confidence: 99%

“…A detailed account is given by Oster et al [38] and an overview of the approach is given by Perelson [39]. This work has been extended to Systems Biology [28,[40][41][42][43][44][45][46].…”

Section: Introductionmentioning

confidence: 99%

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Sensitivity Analysis of Biochemical Systems Using Bond Graphs

Gawthrop

Pan

2023

Preprint

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The sensitivity of systems biology models to parameter variation can give insights into which parameters are most important for physiological function, and also direct efforts to estimate parameters. However, in general, kinetic models of biochemical systems do not remain thermodynamically consistent after perturbing parameters. To address this issue, we analyse the sensitivity of biological reaction networks in the context of a bond graph representation. We find that the parameter sensitivities can themselves be represented as bond graph components, mirroring potential mechanisms for controlling biochemistry. This approach naturally extends to finding sloppy parameters in biological models. We verify our approach using a model of the Pentose Phosphate Pathway, confirming the reactions and metabolites most essential to maintaining the function of the pathway.

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