Related papers: What makes a reaction network "chemical"?
We identify the thermodynamic conditions necessary to observe indefinite growth in homogeneous open chemical reaction networks (CRNs) satisfying mass action kinetics. We also characterize the thermodynamic efficiency of growth by…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
The study of the dynamics of chemical reactions, and in particular phenomena such as oscillating reactions, has led to the recognition that many dynamical properties of a chemical reaction can be predicted from graph theoretical properties…
Many reaction networks arising in applications are multistationary, that is, they have the capacity for more than one steady state; while some networks exhibit absolute concentration robustness (ACR), which means that some species…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
The steady-state degree of a chemical reaction network is the number of complex steady-states, which is a measure of the algebraic complexity of solving the steady-state system. In general, the steady-state degree may be difficult to…
Power law dynamics is used to describe the stability behavior in metabolic networks such as chemical reaction networks (CRN's). These systems allow multiple steady states within a single stoichiometric class. On the other side thermodynamic…
We present a data-driven verification approach that determines whether or not a given chemical reaction network (CRN) satisfies a given property, expressed as a formula in a modal logic. Our approach consists of three phases, integrating…
Across many disciplines, chemical reaction networks (CRNs) are an established population model defined as a system of coupled nonlinear ordinary differential equations. In many applications, for example, in systems biology and epidemiology,…
We provide a sufficient and necessary condition in terms of the stoichiometric coefficients for a bi-reaction network to admit multistability. Also, this result completely characterizes the bi-reaction networks according to if they admit…
For dynamical systems arising from chemical reaction networks, persistence is the property that each species concentration remains positively bounded away from zero, as long as species concentrations were all positive in the beginning. We…
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…
Rapid discovery of new reactions and molecules in recent years has been facilitated by the advancements in high throughput screening, accessibility to a much more complex chemical design space, and the development of accurate molecular…
A family of results, referred to as inheritance results, tell us which enlargements of a chemical reaction network (CRN) preserve its capacity for nontrivial behaviours such as multistationarity and oscillation. In this paper, the following…
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…
Reaction networks taken with mass-action kinetics arise in many settings, from epidemiology to population biology to systems of chemical reactions. Bistable reaction networks are posited to underlie biochemical switches, which motivates the…
We consider discrete-space continuous-time Markov models of reaction networks and provide sufficient conditions for the following stability condition to hold: each state in a closed, irreducible component of the state space is positive…
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…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…