Related papers: Energy-based Analysis of Biomolecular Pathways
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…
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…
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…
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…
Designing reaction pathways that maximize the production of a target compound in a given metabolic network is a fundamental problem in systems biology. In this study, we systematically explore the non-oxidative glycolysis metabolic network,…
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.…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
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…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…
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…
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…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
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…
An Elementary Flux Mode (EFM) is a pathway with minimum set of reactions that are functional in steady-state constrained space. Due to the high computational complexity of calculating EFMs, different approaches have been proposed to find…
We develop a model-independent reduction method of chemical reaction systems based on the stoichiometry, which determines their network topology. A subnetwork can be eliminated systematically to give a reduced system with fewer degrees of…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…