相关论文: Sign patterns for chemical reaction networks
Families of ODE models characterized by a common sign structure of their Jacobi matrix are investigated within the formalism of qualitative differential equations. In the context of regulatory networks the sign structure of the Jacobi…
Persistency is the property, for differential equations in $\R^n$, that solutions starting in the positive orthant do not approach the boundary. For chemical reactions and population models, this translates into the non-extinction property:…
Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
We propose a unified framework that allows for the full mechanistic reconstruction of chemical reaction networks (CRNs) from concentration data. The framework utilizes an integral formulation of the differential equations governing the…
Living systems operate out of equilibrium, continuously consuming energy to sustain organised, functional states. Their emergent behaviour usually relies on a set of interconnected chemical reaction networks (CRNs) driven by external fluxes…
Two competing types of interactions often play an important part in shaping system behavior, such as activatory or inhibitory functions in biological systems. Hence, signed networks, where each connection can be either positive or negative,…
We present two quantitative behavioral equivalences over species of a chemical reaction network (CRN) with semantics based on ordinary differential equations. Forward CRN bisimulation identifies a partition where each equivalence class…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
Qualitative attributes of the region between order and disorder are examined to explore models of genetic and protein networks. Results show how the connectivity of vertices and the strength of their connections are related and how their…
Mathematical Epidemiology (ME) shares with Chemical Reaction Network Theory (CRNT) the basic mathematical structure of its dynamical systems. Despite this central similarity, methods from CRNT have been seldom applied to solving problems in…
Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all…
This paper presents a stability test for a class of interconnected nonlinear systems motivated by biochemical reaction networks. One of the main results determines global asymptotic stability of the network from the diagonal stability of a…
According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit;…
The historical quest for unifying the concepts and methods of Chemical Reaction Networks theory (CRNT), Mahematical Epidemiology (ME) and ecology has received increased attention in the last years and has led in particular to the…
The online estimation of the derivative of an input signal is widespread in control theory and engineering. In the realm of chemical reaction networks (CRN), this raises however a number of specific issues on the different ways to achieve…
Experiments with networks of discrete reactive bistable electrochemical elements organized in regular and nonregular tree networks are presented to confirm an alternative to the Turing mechanism for the formation of self-organized…
In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
We describe combinatorial approaches to the question of whether families of real matrices admit pairs of nonreal eigenvalues passing through the imaginary axis. When the matrices arise as Jacobian matrices in the study of dynamical systems,…