Related papers: Stability of Metabolic Networks via Linear-In-Flux…
This paper serves as a framework for designing advanced models for drug action on metabolism. Drug treatment may affect metabolism by either enhancing or inhibiting metabolic reactions comprising a metabolic network. We introduce the…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
The theory of complex networks and of disordered systems is used to study the stability and dynamical properties of a simple model of material flow networks defined on random graphs. In particular we address instabilities that are…
A basic model of a dynamical distribution network is considered, modeled as a directed graph with storage variables corresponding to every vertex and flow inputs corresponding to every edge, subject to unknown but constant inflows and…
Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…
We study dynamical transportation networks in a framework that includes extensions of the classical Cell Transmission Model to arbitrary network topologies. The dynamics are modeled as systems of ordinary differential equations describing…
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…
In a recent paper, Marr, Muller-Linow and Hutt [Phys. Rev. E 75, 041917 (2007)] investigate an artificial dynamic system on metabolic networks. They find a less complex time evolution of this dynamic system in real networks, compared to…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
The metabolic networks are very well characterized for a large set of organisms, a unique case in within the large-scale biological networks. For this reason they provide a a very interesting framework for the construction of analytically…
We present a linear stability analysis of stationary states (or fixed points) in large dynamical systems defined on random directed graphs with a prescribed distribution of indegrees and outdegrees. We obtain two remarkable results for such…
We study a statistical model describing the steady state distribution of the fluxes in a metabolic network. The resulting model on continuous variables can be solved by the cavity method. In particular analytical tractability is possible…
We consider a basic model of a dynamical distribution network, modeled as a directed graph with storage variables corresponding to every vertex and flow inputs corresponding to every edge, subject to unknown but constant inflows and…
Many natural and man-made network systems need to maintain certain patterns, such as working at equilibria or limit cycles, to function properly. Thus, the ability to stabilize such patterns is crucial. Most of the existing studies on…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
A metabolic model can be represented as bipartite graph comprising linked reaction and metabolite nodes. Here it is shown how a network of conserved fluxes can be assigned to the edges of such a graph by combining the reaction fluxes with a…
We analyze from a far field the evolution of an interface that separates ideal incompressible fluids of different densities and has an interfacial mass flux. We develop and apply the general matrix method to rigorously solve the boundary…
This paper investigates the mathematical modeling and the stability of multi-lane traffic in the microscopic scale, studying a model based on two interaction terms. To do this we propose simple lane changing conditions and we study the…
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…
This paper analyses the stability of cycles within a heteroclinic network lying in a three-dimensional manifold formed by six cycles, for a one-parameter model developed in the context of game theory. We show the asymptotic stability of the…