common.bib

@comment{{Database of the Glasgow University  Centre for Systems and Control}}

@comment{{Abreviations for Journals }}

@comment{{Shortcuts for Institutions }}

@comment{{Shortcuts for Report Type }}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1967 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1968 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1970 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1971 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1972 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1973 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1974 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1975 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1976 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1977 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1978 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1979 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1980 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1981 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1982 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1983 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1984 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1985 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1986 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1987 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1988 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1989 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1990 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1991 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1992 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1993 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1994 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1995 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1996 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1997 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1998 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 1999 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2000 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2001 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2002 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2003 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2004 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2005 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2006 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2007 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2008 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2009 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2010 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2011 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2012 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2013 }}

@comment{{This is the file that should be edited to add CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2014 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{GawCra14,
  author = {Gawthrop, Peter J. and Crampin, Edmund J.},
  title = {Energy-based analysis of biochemical cycles using bond graphs},
  volume = 470,
  number = 2171,
  year = 2014,
  doi = {10.1098/rspa.2014.0459},
  archiveprefix = {arXiv},
  eprint = {1406.2447},
  abstract = {Thermodynamic aspects of chemical reactions have a long history in the physical chemistry literature. In particular, biochemical cycles require a source of energy to function. However, although fundamental, the role of chemical potential and Gibb's free energy in the analysis of biochemical systems is often overlooked leading to models which are physically impossible. The bond graph approach was developed for modelling engineering systems, where energy generation, storage and transmission are fundamental. The method focuses on how power flows between components and how energy is stored, transmitted or dissipated within components. Based on the early ideas of network thermodynamics, we have applied this approach to biochemical systems to generate models which automatically obey the laws of thermodynamics. We illustrate the method with examples of biochemical cycles. We have found that thermodynamically compliant models of simple biochemical cycles can easily be developed using this approach. In particular, both stoichiometric information and simulation models can be developed directly from the bond graph. Furthermore, model reduction and approximation while retaining structural and thermodynamic properties is facilitated. Because the bond graph approach is also modular and scaleable, we believe that it provides a secure foundation for building thermodynamically compliant models of large biochemical networks.},
  journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Science},
  pages = {1--25},
  note = {Available at {arXiv:1406.2447}}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2015 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{GawCurCra15,
  author = {Gawthrop, Peter J. and Cursons, Joseph and Crampin, Edmund J.},
  title = {Hierarchical bond graph modelling of biochemical networks},
  volume = 471,
  number = 2184,
  year = 2015,
  doi = {10.1098/rspa.2015.0642},
  publisher = {The Royal Society},
  abstract = {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 components as thermodynamically open systems exchanging mass and energy via ports. A key feature of this approach is that the resultant models are robustly thermodynamically compliant: the thermodynamic compliance is not dependent on precise numerical values of parameters. Moreover, the models are reusable owing to the well-defined interface provided by the energy ports. To extract bond graph model parameters from parameters found in the literature, general and compact formulae are developed to relate free-energy constants and equilibrium constants. The existence and uniqueness of solutions is considered in terms of fundamental properties of stoichiometric matrices. The approach is illustrated by building a hierarchical bond graph model of glycogenolysis in skeletal muscle.},
  issn = {1364-5021},
  journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
  archiveprefix = {arXiv},
  eprint = {1503.01814},
  pages = {1--23},
  note = {Available at {arXiv:1503.01814}}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2016 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{GawCra16,
  author = {P. J. Gawthrop and E. J. Crampin},
  journal = {IET Systems Biology},
  title = {Modular bond-graph modelling and analysis of biomolecular systems},
  year = 2016,
  volume = 10,
  number = 5,
  pages = {187-201},
  abstract = {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 diagram representations of the dynamics implied by these bond graphs are used to reveal implicit feedback structures and are linearised to allow the application of control-theoretical methods. Two concepts of modularity are examined: computational modularity where physical correctness is retained and behavioural modularity where module behaviour (such as ultrasensitivity) is retained. As well as providing computational modularity, bond graphs provide a natural formulation of behavioural modularity and reveal the sources of retroactivity. A bond graph approach to reducing retroactivity, and thus inter-module interaction, is shown to require a power supply such as that provided by the ATP ⇌ ADP + Pi reaction. The mitogen-activated protein kinase cascade (Raf-MEK-ERK pathway) is used as an illustrative example.},
  keywords = {biology computing;bond graphs;enzymes;hierarchical systems;molecular biophysics;physiological models;thermodynamics;ATP⇌ADP + Pi reaction;Michaelis-Menten kinetics;Raf-MEK-ERK pathway;behavioural modularity;biomolecular systems;block diagram representations;computational modularity;intermodule interaction;mitogen-activated protein kinase cascade;modular bond-graph modelling;retroactivity;signalling networks;thermodynamically-compliant hierarchical models},
  doi = {10.1049/iet-syb.2015.0083},
  issn = {1751-8849},
  month = {October},
  publisher = {Institution of Engineering and Technology},
  archiveprefix = {arXiv},
  eprint = {1511.06482},
  note = {Available at {arXiv:1511.06482}}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2017 }}

@comment{{This is the file that should be edited to add CSC publications}}

@incollection{Gaw17,
  author = {Gawthrop, Peter J.},
  editor = {Borutzky, Wolfgang},
  title = {Bond-Graph Modelling and Causal Analysis of Biomolecular Systems},
  booktitle = {Bond Graphs for Modelling, Control and Fault Diagnosis of Engineering Systems},
  year = {2017},
  publisher = {Springer International Publishing},
  address = {Berlin},
  pages = {587--623},
  isbn = {978-3-319-47434-2},
  doi = {10.1007/978-3-319-47434-2_16},
  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.}
}

@article{Gaw17a,
  author = {P. J. Gawthrop},
  journal = {IEEE Transactions on NanoBioscience},
  title = {Bond Graph Modeling of Chemiosmotic Biomolecular Energy Transduction},
  year = 2017,
  volume = 16,
  number = 3,
  pages = {177-188},
  abstract = { Engineering systems modeling and analysis based on the bond
                  graph approach has been applied to biomolecular
                  systems. In this context, 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. Redox reactions, and their
                  representation by half-reactions, are key components
                  of biological systems which involve both electrical
                  and chemical domains. A bond graph interpretation of
                  redox reactions is given which combines bond graphs
                  with the Faraday-equivalent chemical potential. This
                  approach is particularly relevant when the
                  biomolecular system implements chemoelectrical
                  transduction – for example chemiosmosis within the
                  key metabolic pathway of mitochondria: oxidative
                  phosphorylation. An alternative way of implementing
                  computational modularity using bond graphs is
                  introduced and used to give a physically based model
                  of the mitochondrial electron transport chain To
                  illustrate the overall approach, this model is
                  analyzed using the Faraday-equivalent chemical
                  potential approach and engineering intuition is used
                  to guide affinity equalisation: a energy based
                  analysis of the mitochondrial electron transport
                  chain.  },
  keywords = {Analytical models;Biological system modeling;Chemicals;Computational modeling;Context;Electric potential;Protons;Biological system modeling;computational systems biology;systems biology},
  doi = {10.1109/TNB.2017.2674683},
  issn = {1536-1241},
  month = {April},
  archiveprefix = {arXiv},
  eprint = {1611.04264},
  note = {Available at {arXiv:1611.04264}}
}

@article{GawCra17,
  author = {Gawthrop, Peter J. and Crampin, Edmund J.},
  title = {Energy-based analysis of biomolecular pathways},
  volume = 473,
  number = 2202,
  year = 2017,
  doi = {10.1098/rspa.2016.0825},
  publisher = {The Royal Society},
  archiveprefix = {arXiv},
  eprint = {1611.02332},
  note = {Available at {arXiv:1611.02332}},
  abstract = {Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about steady-state mass flows (reaction rates) through the network. In this work, we show how pathway analysis of biomolecular networks can be extended using an energy-based approach to provide information about energy flows through the network. This energy-based approach is developed using the engineering-inspired bond graph methodology to represent biomolecular reaction networks. The approach is introduced using glycolysis as an exemplar; and is then applied to analyse the efficiency of free energy transduction in a biomolecular cycle model of a transporter protein [sodium-glucose transport protein 1 (SGLT1)]. The overall aim of our work is to present a framework for modelling and analysis of biomolecular reactions and processes which considers energy flows and losses as well as mass transport.},
  issn = {1364-5021},
  journal = {Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences}
}

@article{GawSieKam17,
  author = {P. J. Gawthrop and I. Siekmann and T. Kameneva and S. Saha and M. R. Ibbotson and E. J. Crampin},
  journal = {IET Systems Biology},
  title = {Bond graph modelling of chemoelectrical energy transduction},
  year = 2017,
  volume = 11,
  number = 5,
  pages = {127-138},
  abstract = {Energy-based bond graph modelling of biomolecular systems is extended to include chemoelectrical transduction thus enabling integrated thermodynamically compliant modelling of chemoelectrical systems in general and excitable membranes in particular. Our general approach is illustrated by recreating a well-known model of an excitable membrane. This model is used to investigate the energy consumed during a membrane action potential thus contributing to the current debate on the trade-off between the speed of an action potential event and energy consumption. The influx of Na+ is often taken as a proxy for energy consumption; in contrast, this study presents an energy-based model of action potentials. As the energy-based approach avoids the assumptions underlying the proxy approach it can be directly used to compute energy consumption in both healthy and diseased neurons. These results are illustrated by comparing the energy consumption of healthy and degenerative retinal ganglion cells using both simulated and in vitro data.},
  keywords = {biochemistry;bioelectric potentials;biomembrane transport;eye;molecular biophysics;neurophysiology;sodium;Na;biomolecular systems;chemoelectrical energy transduction;chemoelectrical systems;degenerative retinal ganglion cells;diseased neurons;energy consumption;energy-based bond graph modelling;excitable membranes;healthy neurons;healthy retinal ganglion cells;integrated thermodynamically compliant modelling;membrane action potential},
  doi = {10.1049/iet-syb.2017.0006},
  issn = {1751-8849},
  archiveprefix = {arXiv},
  eprint = {1512.00956},
  note = {Available at {arXiv:1512.00956}}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2018 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{Gaw18,
  author = {P. Gawthrop},
  journal = {IEEE Transactions on NanoBioscience},
  title = {Computing Biomolecular System Steady-States},
  year = 2018,
  volume = 17,
  number = 1,
  pages = {36-43},
  abstract = {A new approach to compute the equilibria and the steady-states of biomolecular systems modeled by bond graphs is presented. The approach is illustrated using a model of a biomolecular cycle representing a membrane transporter and a model of the mitochondrial electron transport chain.},
  keywords = {Biological system modeling;Chemicals;Electric potential;Kinetic theory;Mathematical model;Nanobioscience;Steady-state;Biological system modeling;computational systems biology;systems biology},
  doi = {10.1109/TNB.2017.2787486},
  issn = {1536-1241},
  month = {March},
  note = {Published online 25th December 2017}
}

@inproceedings{GawCra18,
  author = {Peter J. Gawthrop and Edmund J. Crampin},
  title = {Biomolecular System Energetics},
  booktitle = {Proceedings of the 13th International Conference on Bond Graph Modeling ({ICBGM'18})},
  publisher = {Society for Computer Simulation},
  year = 2018,
  address = {Bordeaux},
  archiveprefix = {arXiv},
  eprint = {1803.09231},
  note = {Available at {arXiv:1803.09231}},
  abstract = {Efficient energy transduction is one driver of evolution;
                  and thus understanding biomolecular energy
                  transduction is crucial to understanding living
                  organisms. As an energy-orientated modelling
                  methodology, bond graphs provide a useful approach
                  to describing and modelling the efficiency of living
                  systems. This paper gives some new results on the
                  efficiency of metabolism based on bond graph models
                  of the key metabolic processes: glycolysis.}
}

@article{PanGawTra18,
  author = {Pan, Michael and Gawthrop, Peter J. and Tran, Kenneth and Cursons, Joseph and Crampin, Edmund J.},
  title = {Bond graph modelling of the~cardiac action potential: implications for drift and non-unique steady states},
  volume = 474,
  number = 2214,
  year = 2018,
  doi = {10.1098/rspa.2018.0106},
  publisher = {The Royal Society},
  abstract = {Mathematical models of cardiac action potentials have become increasingly important in the study of heart disease and pharmacology, but concerns linger over their robustness during long periods of simulation, in particular due to issues such as model drift and non-unique steady states. Previous studies have linked these to violation of conservation laws, but only explored those issues with respect to charge conservation in specific models. Here, we propose a general and systematic method of identifying conservation laws hidden in models of cardiac electrophysiology by using bond graphs, and develop a bond graph model of the cardiac action potential to study long-term behaviour. Bond graphs provide an explicit energy-based framework for modelling physical systems, which makes them well suited for examining conservation within electrophysiological models. We find that the charge conservation laws derived in previous studies are examples of the more general concept of a {\textquoteleft}conserved moiety{\textquoteright}. Conserved moieties explain model drift and non-unique steady states, generalizing the results from previous studies. The bond graph approach provides a rigorous method to check for drift and non-unique steady states in a wide range of cardiac action potential models, and can be extended to examine behaviours of other excitable systems.},
  issn = {1364-5021},
  journal = {Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences},
  archiveprefix = {arXiv},
  eprint = {1802.04548},
  note = {Available at {arXiv:1802.04548}}
}

@article{GawCra18a,
  author = {P. Gawthrop and E. J. Crampin},
  journal = {IEEE Transactions on NanoBioscience},
  title = {Bond Graph Representation of Chemical Reaction Networks},
  year = 2018,
  pages = {449-455},
  volume = 17,
  number = 4,
  month = {October},
  abstract = {The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction network concept of complexes. Both closed and open systems are discussed. The method is illustrated using a simple enzyme-catalysed reaction and a trans-membrane transporter.},
  keywords = {Chemicals;Junctions;Substrates;Standards;Nanobioscience;Biological system modeling;Open systems},
  doi = {10.1109/TNB.2018.2876391},
  issn = {1536-1241},
  archiveprefix = {arXiv},
  eprint = {1809.00449},
  note = {Available at {arXiv:1809.00449}}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2019 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{PanGawTra19,
  title = {A thermodynamic framework for modelling membrane transporters},
  journal = {Journal of Theoretical Biology},
  volume = 481,
  pages = {10 - 23},
  year = 2019,
  issn = {0022-5193},
  doi = {10.1016/j.jtbi.2018.09.034},
  author = {Michael Pan and Peter J. Gawthrop and Kenneth Tran and Joseph Cursons and Edmund J. Crampin},
  keywords = {Bond graph, Biochemistry, Chemical reaction network, Biomedical engineering, Systems biology},
  abstract = {Membrane transporters contribute to the regulation of the internal environment of cells by translocating substrates across cell membranes. Like all physical systems, the behaviour of membrane transporters is constrained by the laws of thermodynamics. However, many mathematical models of transporters, especially those incorporated into whole-cell models, are not thermodynamically consistent, leading to unrealistic behaviour. In this paper we use a physics-based modelling framework, in which the transfer of energy is explicitly accounted for, to develop thermodynamically consistent models of transporters. We then apply this methodology to model two specific transporters: the cardiac sarcoplasmic/endoplasmic Ca2+ ATPase (SERCA) and the cardiac Na+/K+ ATPase.},
  archiveprefix = {arXiv},
  eprint = {1806.04341},
  note = {Available at {arXiv:1806.04341}}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2020 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{GawCudCra20,
  title = {Physically-Plausible Modelling of Biomolecular Systems: A Simplified, Energy-Based Model of the Mitochondrial Electron Transport Chain},
  journal = {Journal of Theoretical Biology},
  pages = 110223,
  volume = 493,
  year = 2020,
  issn = {0022-5193},
  doi = {10.1016/j.jtbi.2020.110223},
  author = {Peter J. Gawthrop and Peter Cudmore and Edmund J. Crampin},
  keywords = {Systems biology, Thermodynamical modelling, Bond graph, Computational biology},
  abstract = {Advances in systems biology and whole-cell modelling demand increasingly comprehensive mathematical models of cellular biochemistry. Such models require the development of simplified representations of specific processes which capture essential biophysical features but without unnecessarily complexity. Recently there has been renewed interest in thermodynamically-based modelling of cellular processes. Here we present an approach to developing of simplified yet thermodynamically consistent (hence physically plausible) models which can readily be
                  incorporated into large scale biochemical
                  descriptions but which do not require full
                  mechanistic detail of the underlying processes. We
                  illustrate the approach through development of a simplified, physically plausible model of the mitochondrial electron transport chain and show that the simplified model behaves like the full system.}
}

@article{PanGawCur20,
  author = {Michael Pan and Peter J. Gawthrop and Joseph Cursons and Kenneth Tran and Edmund J. Crampin},
  title = {{The cardiac Na+/K+ ATPase: An updated, thermodynamically consistent model}},
  year = 2020,
  month = 8,
  journal = {Physiome},
  doi = {10.36903/physiome.12871070.v1},
  abstract = {
The Na+/K+ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na+ and K+ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na+/K+ ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately there was no archived code associated with the original manuscript. Here we detail an updated version of the model and provide CellML and MATLAB code to ensure reproducibility and reusability. We note some errors within the original formulation which have been corrected to ensure that the model is thermodynamically consistent, and although this required some reparameterisation, the resulting model still provides a good fit to experimental measurements that demonstrate the dependence of Na+/K+ ATPase pumping rate upon membrane voltage and metabolite concentrations. To demonstrate thermodynamic consistency we also developed a bond graph version of the model. We hope that these models will be useful for community efforts to assemble a whole-cell cardiomyocyte model which facilitates the investigation of cellular energetics.
}
}

@article{GawPan20,
  author = {Gawthrop, Peter J.
		and Pan, Michael},
  title = {Network Thermodynamical Modeling of Bioelectrical Systems: A Bond Graph Approach},
  journal = {Bioelectricity},
  year = 2021,
  month = {Mar},
  day = 01,
  publisher = {Mary Ann Liebert, Inc., publishers},
  volume = 3,
  number = 1,
  pages = {3--13},
  abstract = {Interactions among biomolecules, electrons, and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance understanding but also to enable computer models to complement in vitro and in vivo experiments. Such models can never be entirely accurate; it is nevertheless important that the models are compatible with physical principles. Network Thermodynamics, as implemented with bond graphs, provide one approach to creating physically compatible mathematical models of bioelectrical systems. This is illustrated using simple models of ion channels, redox reactions, proton pumps, and electrogenic membrane transporters thus demonstrating that the approach can be used to build mathematical and computer models of a wide range of bioelectrical systems.},
  issn = {2576-3105},
  doi = {10.1089/bioe.2020.0042},
  note = {Published Online: 18 Dec 2020}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2021 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{Gaw21,
  author = {P. J. {Gawthrop}},
  journal = {IEEE Transactions on NanoBioscience},
  title = {Energy-Based Modeling of the Feedback Control of Biomolecular Systems With Cyclic Flow Modulation},
  year = 2021,
  volume = 20,
  number = 2,
  pages = {183-192},
  abstract = {Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to control engineering insight. In particular, a novel method is introduced to allow the transfer function based approach of classical linear control to be utilised in the analysis of feedback systems modelled by network thermodynamics and thus amalgamate energy-based modelling with control systems analysis. The approach is illustrated using a class of metabolic cycles with activation and inhibition leading to the concept of Cyclic Flow Modulation.},
  keywords = {Biological system modeling;Junctions;Transfer functions;Thermodynamics;Mathematical model;Feedback loop;Analytical models;Biological system modeling;computational systems biology;systems biology;negative feedback},
  doi = {10.1109/TNB.2021.3058440},
  issn = {1558-2639},
  month = {April}
}

@article{GawPanCra21,
  author = {Gawthrop, Peter J.  and Pan, Michael  and Crampin, Edmund J. },
  title = {Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data},
  journal = {Journal of The Royal Society Interface},
  volume = 18,
  number = 181,
  pages = 20210478,
  year = 2021,
  doi = {10.1098/rsif.2021.0478},
  abstract = { Renewed interest in dynamic simulation models of biomolecular systems has arisen from advances in genome-wide measurement and applications of such models in biotechnology and synthetic biology. In particular, genome-scale models of cellular metabolism beyond the steady state are required in order to represent transient and dynamic regulatory properties of the system. Development of such whole-cell models requires new modelling approaches. Here, we propose the energy-based bond graph methodology, which integrates stoichiometric models with thermodynamic principles and kinetic modelling. We demonstrate 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. The approach is illustrated using a well-established stoichiometric model of Escherichia coli and published experimental data. }
}

@article{CudPanGaw21,
  author = {Cudmore, Peter
		and Pan, Michael
		and Gawthrop, Peter J.
		and Crampin, Edmund J.},
  title = {Analysing and simulating energy-based models in biology using {BondGraphTools}},
  journal = {The European Physical Journal E},
  year = 2021,
  month = {Dec},
  day = 13,
  volume = 44,
  number = 12,
  pages = 148,
  abstract = {Like all physical systems, biological systems are constrained by the laws of physics. However, mathematical models of biochemistry frequently neglect the conservation of energy, leading to unrealistic behaviour. Energy-based models that are consistent with conservation of mass, charge and energy have the potential to aid the understanding of complex interactions between biological components, and are becoming easier to develop with recent advances in experimental measurements and databases. In this paper, we motivate the use of bond graphs (a modelling tool from engineering) for energy-based modelling and introduce, BondGraphTools, a Python library for constructing and analysing bond graph models. We use examples from biochemistry to illustrate how BondGraphTools can be used to automate model construction in systems biology while maintaining consistency with the laws of physics.},
  issn = {1292-895X},
  doi = {10.1140/epje/s10189-021-00152-4}
}

@article{PanGawCur21,
  doi = {10.1371/journal.pcbi.1009513},
  author = {Pan, Michael AND Gawthrop, Peter J. AND Cursons, Joseph AND Crampin, Edmund J.},
  journal = {PLOS Computational Biology},
  publisher = {Public Library of Science},
  title = {Modular assembly of dynamic models in systems biology},
  year = 2021,
  month = 10,
  volume = 17,
  pages = {1-27},
  abstract = {It is widely acknowledged that the construction of large-scale dynamic models in systems biology requires complex modelling problems to be broken up into more manageable pieces. To this end, both modelling and software frameworks are required to enable modular modelling. While there has been consistent progress in the development of software tools to enhance model reusability, there has been a relative lack of consideration for how underlying biophysical principles can be applied to this space. Bond graphs combine the aspects of both modularity and physics-based modelling. In this paper, we argue 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. We use two examples to illustrate the utility of bond graphs in this context: a model of a mitogen-activated protein kinase (MAPK) cascade to illustrate the reusability of modules and a model of glycolysis to illustrate the ability to modify the model granularity.},
  number = 10
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of publications by CSC in 2022 }}

@comment{{This is the file that should be edited to add CSC publications}}

@article{GawPan22,
  title = {Network thermodynamics of biological systems: A bond graph approach},
  journal = {Mathematical Biosciences},
  volume = 352,
  pages = 108899,
  year = 2022,
  issn = {0025-5564},
  doi = {https://doi.org/10.1016/j.mbs.2022.108899},
  author = {Peter J. Gawthrop and Michael Pan},
  keywords = {Systems biology, Bond graph, Energy-based, Photosynthesis, Electrochemical transduction},
  abstract = {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 group in applying energy-based bond graph methods to biological systems. In particular, this paper: (a) motivates the need to consider energy in modelling biology; (b) introduces bond graphs as a methodology for achieving this; (c) describes extensions to modelling electrochemical transduction; (d) outlines how bond graph models can be constructed in a modular manner and (e) describes stoichiometric approaches to deriving fundamental properties of reaction networks. These concepts are illustrated using a new bond graph model of photosynthesis in chloroplasts.}
}

@article{GawPan22a,
  author = {Gawthrop, Peter J.  and Pan, Michael },
  title = {Energy-based advection modelling using bond graphs},
  journal = {Journal of The Royal Society Interface},
  volume = 19,
  number = 195,
  pages = 20220492,
  year = 2022,
  doi = {10.1098/rsif.2022.0492},
  abstract = { Advection, the transport of a substance by the flow of a fluid, is a key process in biological systems. The energy-based bond graph approach to modelling chemical transformation within reaction networks is extended to include transport and thus advection. The approach is illustrated using a simple model of advection via circulating flow and by a simple pharmacokinetic model of anaesthetic gas uptake. This extension provides a physically consistent framework for linking advective flows with the fluxes associated with chemical reactions within the context of physiological systems in general and the human physiome in particular. }
}

@comment{{-*-bibtex-*- used to set EMACS into bibtex-mode}}

@comment{{Database of Papers Produced by members of the Glasgow University
	Control Group}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of software }}

@comment{{This is the file that should be edited to add software}}

@comment{{-*-bibtex-*- used to set EMACS into bibtex-mode}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in  }}

@comment{{This contains pre 1960 publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1868 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1869 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1869 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1907 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in  }}

@comment{{This contains pre 1960 publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1932 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1932 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1934 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1936 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1940 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1947 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1948 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1952 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1953 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1954 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1955 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1956 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1956 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1958 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1960 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1961 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1962 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1963 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1964 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1965 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1966 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1967 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1968 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1969 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1970 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1971 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1972 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1973 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1974 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1975 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1976 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1977 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1978 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1979 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1980 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1981 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1982 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1983 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1984 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1985 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1986 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1987 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1988 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1989 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1990 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1991 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1992 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1993 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1994 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1995 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1996 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1997 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1998 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 1999 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2000 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2001 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2002 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2003 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2004 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2005 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2006 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2007 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2008 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2009 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2010 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2011 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2012 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2013 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2014 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2015 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2016 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2017 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2018 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2019 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2018 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2020 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2021 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@article{ShaPanSaf21,
  author = {Shahidi, Niloofar
		and Pan, Michael
		and Safaei, Soroush
		and Tran, Kenneth
		and Crampin, Edmund J.
		and Nickerson, David P.},
  title = {Hierarchical semantic composition of biosimulation models using bond graphs},
  journal = {PLOS Computational Biology},
  year = 2021,
  month = {May},
  day = 13,
  publisher = {Public Library of Science},
  volume = 17,
  number = 5,
  pages = {e1008859},
  abstract = {Author summary Biological and physiological systems usually involve multiple underlying processes, mechanisms, structures, and phenomena, referred to here as sub-systems. Modelling the whole system every time from scratch requires a huge amount of effort. An alternative is to model each sub-system in a modular fashion, i.e., containing meaningful interfaces for connecting to other modules. Such modules are readily combined to produce a whole-system model. For the combined model to be consistent, modules must be described using the same modelling scheme. One way to achieve this is to use energy-based models that are consistent with the conservation laws of physics. Here, we present an approach that achieves this using bond graphs, which allows modules to be combined faster and more efficiently. First, physically plausible modules are generated using a small number of template modules. Then a meaningful interface is added to each module to automate connection. This approach is illustrated by applying this method to an existing model of the circulatory system and verifying the results against the reference model.},
  doi = {10.1371/journal.pcbi.1008859}
}

@article{ShaPanTra21,
  title = {SBML to bond graphs: From conversion to composition},
  journal = {Mathematical Biosciences},
  volume = 352,
  pages = 108901,
  year = 2022,
  issn = {0025-5564},
  doi = {https://doi.org/10.1016/j.mbs.2022.108901},
  author = {Niloofar Shahidi and Michael Pan and Kenneth Tran and Edmund J. Crampin and David P. Nickerson},
  keywords = {SBML, BioModels, Bond graphs, Automatic conversion, Glycolysis, Pentose phosphate pathway},
  abstract = {The Systems Biology Markup Language (SBML) is a popular software-independent XML-based format for describing models of biological phenomena. The BioModels Database is the largest online repository of SBML models. Several tools and platforms are available to support the reuse and composition of SBML models. However, these tools do not explicitly assess whether models are physically plausible or thermodynamically consistent. This often leads to ill-posed models that are physically impossible, impeding the development of realistic complex models in biology. Here, we present a framework that can automatically convert SBML models into bond graphs, which imposes energy conservation laws on these models. The new bond graph models are easily mergeable, resulting in physically plausible coupled models. We illustrate this by automatically converting and coupling a model of pyruvate distribution to a model of the pentose phosphate pathway.}
}

@comment{{-*-bibtex-*- used to set Emacs into bibtex-mode}}

@comment{{Database of non-CSC publications  in 2022 }}

@comment{{This is the file that should be edited to add non-CSC publications}}

@article{ShaPanTra22,
  doi = {10.1371/journal.pone.0269497},
  author = {Shahidi, Niloofar AND Pan, Michael AND Tran, Kenneth AND Crampin, Edmund J. AND Nickerson, David P.},
  journal = {PLOS ONE},
  publisher = {Public Library of Science},
  title = {A semantics, energy-based approach to automate biomodel composition},
  year = 2022,
  month = 06,
  volume = 17,
  pages = {1-36},
  abstract = {Hierarchical modelling is essential to achieving complex, large-scale models. However, not all modelling schemes support hierarchical composition, and correctly mapping points of connection between models requires comprehensive knowledge of each model’s components and assumptions. To address these challenges in integrating biosimulation models, we propose an approach to automatically and confidently compose biosimulation models. The approach uses bond graphs to combine aspects of physical and thermodynamics-based modelling with biological semantics. We improved on existing approaches by using semantic annotations to automate the recognition of common components. The approach is illustrated by coupling a model of the Ras-MAPK cascade to a model of the upstream activation of EGFR. Through this methodology, we aim to assist researchers and modellers in readily having access to more comprehensive biological systems models.},
  number = 6
}

@article{RajAruHun22,
  author = {Rajagopal, Vijay and Arumugam, Senthil and Hunter, Peter J. and Khadangi, Afshin and Chung, Joshua and Pan, Michael},
  title = {The Cell Physiome: What Do We Need in a Computational Physiology Framework for Predicting Single-Cell Biology?},
  journal = {Annual Review of Biomedical Data Science},
  volume = 5,
  number = 1,
  pages = {341-366},
  year = 2022,
  doi = {10.1146/annurev-biodatasci-072018-021246},
  note = {PMID: 35576556},
  abstract = { Modern biology and biomedicine are undergoing a big data explosion, needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome Project: a framework and approach for creating, sharing, and using biophysics-based computational models of single-cell physiology. Using examples in calcium signaling, bioenergetics, and endosomal trafficking, we highlight the need for spatially detailed, biophysics-based computational models to uncover new mechanisms underlying cell biology. We review progress and challenges to date toward creating cell physiome models. We then introduce bond graphs as an efficient way to create cell physiome models that integrate chemical, mechanical, electromagnetic, and thermal processes while maintaining mass and energy balance. Bond graphs enhance modularization and reusability of computational models of cells at scale. We conclude with a look forward at steps that will help fully realize this exciting new field of mechanistic biomedical data science. }
}

@comment{{-*-bibtex-*- used to set EMACS into bibtex-mode}}

@comment{{Cross References for Conferences MUST go in footers}}

This file was generated by bibtex2html 1.99.