Related papers: Computing Biomolecular System Steady-states
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…
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…
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…
In this paper, we use a variety of mathematical techniques to explore existence, local stability, and global stability of equilibria in abstract models of mitochondrial metabolism. The class of models constructed is defined by the…
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 methodology named LIFE (Linear-in-Flux-Expressions) was developed with the purpose of simulating and analyzing large metabolic systems. With LIFE, the number of model parameters is reduced by accounting for correlations among the…
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…
Network equilibrium models represent a versatile tool for the analysis of interconnected objects and their relationships. They have been widely employed in both science and engineering to study the behavior of complex systems under various…
A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole.…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
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…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
Arguing about the equilibrium distribution of continuous-time Markov chains can be vital for showing properties about the underlying systems. For example in biological systems, bistability of a chemical reaction network can hint at its…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…
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…
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…
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.…
We consider the general problem of determining the steady state of stochastic nonequilibrium systems such as those that have been used to model (among other things) biological transport and traffic flow. We begin with a broad overview of…
We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state…
We discuss metastable states in the mean-field version of the strong coupling BCS-model and study the evolution of a superconducting equilibrium state subjected to a dynamical semi-group with Lindblad generator in detailed balance w.r.t.…