Related papers: Sensitivity of metabolic networks: perturbing meta…
Perturbations are ubiquitous in metabolism. A central tool to understand and control their influence on metabolic networks is sensitivity analysis, which investigates how the network responds to external perturbations. We follow here a…
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,…
A sensitivity analysis of general stoichiometric networks is considered. The results are presented as a generalization of Metabolic Control Analysis, which has been concerned primarily with system sensitivities at steady state. An…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
We consider steady states of dynamics that have an underlying network structure. We study how a steady state responds to small perturbations in the network parameters and how this sensitivity is connected to the network structure. We…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
We study two specific measures of quality of chemical reaction networks, Precision and Sensitivity. The two measures arise in the study of sensory adaptation, in which the reaction network is viewed as an input-output system. Given a step…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
This paper presents an algebraic framework to study sign-sensitivities for reaction networks modeled by means of systems of ordinary differential equations. Specifically, we study the sign of the derivative of the concentrations of the…
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…
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and…
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…
The sensitivity (i.e. dynamic response) of complex networked systems has not been well understood, making difficult to predict whether new macroscopic dynamic behavior will emerge even if we know exactly how individual nodes behave and how…
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…
With the advance of efficient analytical methods for sensitivity analysis ofprobabilistic networks, the interest in the sensitivities revealed by real-life networks is rekindled. As the amount of data resulting from a sensitivity analysis…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…
Centrality metrics have been used in various networks, such as communication, social, biological, geographic, or contact networks. In particular, they have been used in order to study and analyze targeted attack behaviors and investigated…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Autocatalytic chemical networks play a predominant role in a large number of natural systems such as in metabolic pathways and in ecological networks. Despite recent efforts, the precise impact of thermodynamic constraints on these networks…