Related papers: Energy-based Analysis of Biochemical Cycles using …
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…
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…
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…
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…
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…
Engineering systems modelling 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…
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…
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…
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…
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…
Modern energy systems in vehicles and built infrastructure are governed by high-dimensional dynamics spanning multiple physical domains (e.g., electrical, thermal, mechanical) and timescales. This tutorial paper presents a graph-based…
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.…
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…
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…
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…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…