Related papers: Bond Graph Modelling of Chemiosmotic Biomolecular …
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 paper suggests that they can play the…
Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…
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…
Interactions between 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…
Energy-based bond graph modelling of biomolecular systems is extended to include chemoelectrical trans- duction thus enabling integrated thermodynamically-compliant modelling of chemoelectrical systems in general and excitable membranes in…
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…
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…
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…
Whole-cell modelling is constrained by the laws of nature in general and the laws of thermodynamics in particular. This paper shows how one prolific source of information, stoichiometric models of biomolecular systems, can be integrated…
A new approach to computing the equilibria and steady-states of biomolecular systems modelled by bond graphs is presented. The approach is illustrated using a model of a biomolecular cycle representing a membrane transporter and a model of…
Understanding how the electronic structure of electrodes influences electrocatalytic reactions has been a longstanding topic in the electrochemistry community, with predominant attention paid to metallic electrodes. In this work, we present…
Electrosorption is a promising technique for brackish water deionization and waste water remediation. Faradaic materials with redox activity have recently been shown to enhance both the adsorption capacity and the selectivity of…
Hybrid Bond Graph (HBG) is a Bond Graph-based modelling approach which provides an effective tool not only for dynamic modeling but also for fault detection and isolation (FDI) of switching systems. Bond graph (BG) has been proven useful…
Bio-oil molecule assessment is essential for the sustainable development of chemicals and transportation fuels. These oxygenated molecules have adequate carbon, hydrogen, and oxygen atoms that can be used for developing new value-added…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
In the 20th century, individual technology products like the generator, telephone, and automobile were connected to form many of the large-scale, complex, infrastructure networks we know today: the power grid, the communication…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…