Modular bond-graph modelling and analysis of biomolecular systems.

@article{Gawthrop2016ModularBM,
  title={Modular bond-graph modelling and analysis of biomolecular systems.},
  author={Peter J. Gawthrop and Edmund J. Crampin},
  journal={IET systems biology},
  year={2016},
  volume={10 5},
  pages={
          187-201
        }
}
Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this study suggests that they can play the same rôle in the modelling, analysis and synthesis of biomolecular systems. The particular structure of bond graphs arising from biomolecular systems is established and used to elucidate the relation between thermodynamically closed and open systems. Block… 
Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction
  • P. Gawthrop
  • Chemistry
    IEEE Transactions on NanoBioscience
  • 2017
TLDR
The notion of a Faraday-equivalent chemical potential is introduced which allows chemical potential to be expressed in an analogous manner to electrical volts thus allowing engineering intuition to be applied to biomolecular systems.
Bond-Graph Modelling and Causal Analysis of Biomolecular Systems
TLDR
Bond graph modelling of the biomolecular systems of living organisms is introduced and Causality is used in this chapter to examine the properties of the junction structures of biomolecule systems and how they relate to biomolescular concepts.
Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data
TLDR
It is demonstrated how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems.
Modular assembly of dynamic models in systems biology
TLDR
It is argued that bond graphs are compatible with recent developments in modularity and abstraction in systems biology, and are thus a desirable framework for constructing large-scale models, and a new approach using bond graphs from engineering is proposed, where connections between models are defined using physical conservation laws.
Modular assembly of dynamic models in systems biology
TLDR
It is argued that bond graphs are compatible with recent developments in modularity and abstraction in systems biology, and are thus a desirable framework for constructing large-scale models.
A bond graph approach to integrative biophysical modelling
TLDR
Methods based on the bond graph framework to facilitate model reuse and integration are developed and used to facilitate the development of simple, thermodynamically consistent models of enzymes that are easily incorporated into larger models.
Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data
TLDR
It is demonstrated how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems.
Network Thermodynamics of Biological Systems: A Bond Graph Approach
Edmund Crampin (1973-2021) was at the forefront of Systems Biology research and his work will influence the field for years to come. This paper brings together and summarises the seminal work of his
Network Thermodynamical Modeling of Bioelectrical Systems: A Bond Graph Approach.
TLDR
Network Thermodynamics, as implemented with bond graphs, provide one approach to creating physically compatible mathematical models of bioelectrical systems, illustrated using simple models of ion channels, redox reactions, proton pumps and electrogenic membrane transporters, demonstrating that the approach can be used to build mathematical and computer models of a wide range of bioElectrical systems.
Bond graph modelling of chemoelectrical energy transduction
TLDR
An energy based model of action potentials is presented, which can be directly used to compute energy consumption in both healthy and diseased neurons and contributes to the current debate on the trade-off between the speed of an action potential event and energy consumption.
...
...

References

SHOWING 1-10 OF 98 REFERENCES
Hierarchical bond graph modelling of biochemical networks
The bond graph approach to modelling biochemical networks is extended to allow hierarchical construction of complex models from simpler components. This is made possible by representing the simpler
Energy-based analysis of biochemical cycles using bond graphs
  • P. Gawthrop, E. Crampin
  • Engineering
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
  • 2014
TLDR
The bond graph approach is found to be a secure foundation for building thermodynamically compliant models of large biochemical networks and both stoichiometric information and simulation models can be developed directly from the bond graph.
Bond Graph Modelling of Engineering Systems
This chapter introduces the reader to the concept-oriented approach to modeling that clearly separates ideal concepts from the physical components of a system when modeling its dynamic behavior for a
A control theoretic framework for modular analysis and design of biomolecular networks
Bond-graph modeling
The bond-graph method is a graphical approach to modeling in which component energy ports are connected by bonds that specify the transfer of energy between system components. Power, the rate of
METAMODELLING: Bond Graphs and Dynamic Systems [BOOKSHELF]
With the increasing complexity of processes to be analyzed, the control engineer often needs a model of the system to be controlled. However, in many practical cases, there is limited time for
Modular cell biology: retroactivity and insulation
TLDR
Here, the effect of interconnections on the input–output dynamic characteristics of transcriptional components are studied, focusing on a property, which is called ‘retroactivity’, that plays a role analogous to non‐zero output impedance in electrical systems.
Engineering principles in bio-molecular systems: From retroactivity to modularity
TLDR
This work proposes to design insulation devices based on a feedback mechanism inspired by the design of amplifiers in electronics, and introduces a bio-molecular realization of an insulation device based on phosphorylation.
Cell signaling pathways as control modules: complexity for simplicity?
  • D. Lauffenburger
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2000
TLDR
As biology begins to move into the “postgenomic” era, a key emerging question is how to approach the understanding of how complex biomolecular networks function as dynamical systems, with an intermediate concept suggesting a “modular” framework.
Control, responses and modularity of cellular regulatory networks: a control analysis perspective.
TLDR
A theoretical framework addressing integrated systems with gene expression, metabolic and signal transduction levels and a number of different approaches for the analysis of hierarchical systems are discussed, for example hierarchical control analysis and modular response analysis.
...
...