Related papers: Chemical Reaction Network Decomposition Technique …
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
Mathematical modeling is now used commonly in the analysis of signaling networks. With advances in high resolution microscopy, the spatial location of different signaling molecules and the spatio-temporal dynamics of signaling microdomains…
In this paper, we consider networked systems comprised of interconnected sets of linear subsystems and propose a decentralized and compositional approach to stabilize or dissipativate such linear networked systems via optimally modifying…
In this paper, we derive two sufficient conditions to diagnose the persistence of two classes of delayed complex balanced chemical reaction network systems equipped with mass-action kinetics. One class is identified by $\dim…
We consider the question whether a chemical reaction network preserves the number and stability of its positive steady states upon inclusion of inflow and outflow reactions. Often a model of a reaction network is presented without inflows…
In this paper we introduce a new representation for the multistationarity region of a reaction network, using polynomial superlevel sets. The advantages of using this polynomial superlevel set representation over the already existing…
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…
Under mass-action kinetics, biochemical reaction networks give rise to polynomial autonomous dynamical systems whose parameters are often difficult to estimate. We deal in this paper with the problem of identifying the kinetic parameters of…
[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…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
Autocatalysis underlies the ability of chemical and biochemical systems to replicate. Recently, Blokhuis et al. gave a stoechiometric definition of autocatalysis for reaction networks, stating the existence of a combination of reactions…
We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…
We explore the emergence of complex structures within reaction networks, focusing on nuclear reaction networks relevant to stellar nucleosynthesis. The work presents a theoretical framework rooted in Chemical Organization Theory (COT) to…
A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the…
The long time behavior of a model for a first order, weakly reversible chemical reaction network is considered, where the movement of the reacting species is described by kinetic transport. The reactions are triggered by collisions with a…
In this paper, the applicability of the entropy method for the trend towards equilibrium for reaction-diffusion systems arising from first order chemical reaction networks is studied. In particular, we present a suitable entropy structure…
Quasi-steady state (QSS) reduction is a commonly used method to lower the dimension of a differential equation model of a chemical reaction network. From a mathematical perspective, QSS reduction is generally interpreted as a special type…
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical…
Dynamical systems in biology are complex, and one often does not have comprehensive knowledge about the interactions involved. Chemical reaction network (CRN) inference aims to identify, from observing species concentrations over time, the…
Network systems consist of subsystems and their interconnections, and provide a powerful framework for analysis, modeling and control of complex systems. However, subsystems may have high-dimensional dynamics, and the amount and nature of…