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Bond Graphs for Modelling, Control and Fault Diagnosis of Engineering Systems pp 587–623Cite as

Bond-Graph Modelling and Causal Analysis of Biomolecular Systems

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Abstract

Bond graph modelling of the biomolecular systems of living organisms is introduced. Molecular species are represented by non-linear C components and reactions by non-linear two-port R components. As living systems are neither at thermodynamic equilibrium nor closed, open and non-equilibrium systems are considered and illustrated using examples of biomolecular systems. Open systems are modelled using chemostats: chemical species with fixed concentration. In addition to their role in ensuring that models are energetically correct, bond graphs provide a powerful and natural way of representing and analysing causality. Causality is used in this chapter to examine the properties of the junction structures of biomolecular systems and how they relate to biomolecular concepts.

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Notes

  1. 1.

    This was pointed out to me by the Editor of this volume, Wolfgang Borutzky.

  2. 2.

    In this context, a moiety is a part of a molecule; in some reactions, such moieties are conserved across different molecules.

  3. 3.

    The standard notation would be x A but this clashes with our bond graph notation.

  4. 4.

    Other extensive quantities such as internal energy, entropy, Gibbs energy also have molar versions.

  5. 5.

    Michael Pan, private communication.

  6. 6.

    SCAP is used for all the examples in this chapter. Unless otherwise stated, all C components have integral causality.

  7. 7.

    TF components representing reaction stoichiometry also occur—see example in Sect. 16.5.

  8. 8.

    ATP (Adenosine triphosphate) is the “fuel” which drives many biomolecular processes via its conversion to ADP (Adenosine diphosphate) and P inorganic phosphate [1].

  9. 9.

    The SS component is equivalent to the EN (environment) component introduced by Rosenberg and Andry [37].

  10. 10.

    The term chemostat was used by Polettini and Esposito [35] and is equivalent to the “concentration clamping” of Qian and Beard [36].

  11. 11.

    The term flowstat is equivalent to “boundary flux injection” [36].

  12. 12.

    A protein molecule with a given chemical composition may have many different geometric “shapes” or conformations with different Gibbs energy—this is the basis of much cell biology [1].

  13. 13.

    NADH (reduced nicotinamide adenine dinucleotide) is an electron transporter within biomolecular processes [1].

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Acknowledgements

Peter Gawthrop would like to thank the Melbourne School of Engineering for its support via a Professorial Fellowship. He would also like to thank Michael Pan and Joe Cursons for their close reading of the draft chapter.

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  1. Systems Biology Laboratory, Melbourne School of Engineering, University of Melbourne, Melbourne, VIC, 3010, Australia

    Peter J. Gawthrop

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Correspondence to Peter J. Gawthrop .

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  1. Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany

    Wolfgang Borutzky

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Gawthrop, P.J. (2017). Bond-Graph Modelling and Causal Analysis of Biomolecular Systems. In: Borutzky, W. (eds) Bond Graphs for Modelling, Control and Fault Diagnosis of Engineering Systems. Springer, Cham. https://doi.org/10.1007/978-3-319-47434-2_16

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