Related papers: On persistence and cascade decompositions of chemi…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
We describe how noise propagates through a network by calculating the variance of the outputs. Using stochastic calculus and dynamical systems theory, we study the network topologies that accentuate or alleviate the effect of random…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
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…
In this chapter, we illustrate recently obtained thermodynamic bounds for a number of enzymatic networks by focusing on simple examples of unicyclic or multi-cyclic networks. We also derive complementary relations which constrain the…
Autocatalytic Sets are reaction networks theorised as networks at the basis of life. Their main feature is the ability of spontaneously emerging and self-reproducing. The Reflexively and Food-generated theory provides a formal definition of…
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…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
A crisp survey is given of chemical reaction networks from the perspective of general nonlinear network dynamics, in particular of consensus dynamics. It is shown how by starting from the complex-balanced assumption the reaction dynamics…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These…
Open chemical reaction systems involve matter-exchange with the surroundings. As a result, species can accumulate inside a system during the course of the reaction. We study the role of network topology in governing the concentration…
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Reaction networks have become a major modelling framework in the biological sciences from epidemiology and population biology to genetics and cellular biology. In recent years, much progress has been made on stochastic reaction networks…
Complex balanced mass-action systems (CBMASs) are of great importance in the filed of biochemical reaction networks. However analyzing the persistence of these networks with high dimensions and time delays poses significant challenges. To…
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist…
This paper analyses of a stochastic model of a chemical reaction network with three types of chemical species ${\cal R}$, ${\cal M}$ and ${\cal U}$ that interact to transform a flow of external resources, the chemical species ${\cal Q}$, to…
We define a subclass of Chemical Reaction Networks called Post-Translational Modification systems. Important biological examples of such systems include MAPK cascades and two-component systems which are well-studied experimentally as well…