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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 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 paper 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.
Signal transduction is an important and basic mechanism to cell life activities. The stochastic state transition of receptor induces the release of singling molecular, which triggers the state transition of other receptors. It constructs a nonlinear
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 conc
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 biophysical featur
A multiscale mathematical model is presented to describe the de novo granulation and the evolution of multispecies granular biofilms within a continuous reactor. The granule is modelled as a spherical free boundary domain with radial symmetry. The eq
The assembly of virus capsids from free coat proteins proceeds by a complicated cascade of association and dissociation steps, the great majority of which cannot be directly experimentally observed. This has made capsid assembly a rich field for comp