相关论文: A network dynamics approach to chemical reaction n…
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…
In the first part of this paper, we propose new optimization-based methods for the computation of preferred (dense, sparse, reversible, detailed and complex balanced) linearly conjugate reaction network structures with mass action dynamics.…
We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of elementary reactions. Their dynamics is described by deterministic rate equations satisfying mass action law. Our most general framework…
Steady states are frequently used to investigate the long-term behaviors of (bio)-chemical systems. Recently, there has been a growing interest in network-based approaches due to their efficiency in deriving parametrizations of positive…
Stochastic reaction networks are dynamical models of biochemical reaction systems and form a particular class of continuous-time Markov chains on $\mathbb{N}^n$. Here we provide a fundamental characterisation that connects structural…
For chemical reaction networks described by a master equation, we define energy and entropy on a stochastic trajectory and develop a consistent nonequilibrium thermodynamic description along a single stochastic trajectory of reaction…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a…
We study a generic family of nonlinear dynamics on undirected networks generalising linear consensus. We find a compact expression for its equilibrium points in terms of the topology of the network and classify their stability using the…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
Chemical reaction network theory is a field of applied mathematics concerned with modeling chemical systems, and can be used in other contexts such as in systems biology to study cellular signaling pathways or epidemiology to study the…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
Chemical reaction network theory provides powerful tools for rigorously understanding chemical reactions and the dynamical systems and differential equations that represent them. A frequent issue with mathematical analyses of these networks…
Mass action systems capture chemical reaction networks in homogeneous and dilute solutions. We suggest a notion of generalized mass action systems that admits arbitrary nonnegative power-law rate functions and serves as a more realistic…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
Network translation has recently been used to establish steady state properties of mass action systems by corresponding the given system to a generalized one which is either dynamically or steady state equivalent. In this work we further…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
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…
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…
Complex chemical reaction networks, which underlie many industrial and biological processes, often exhibit non-monotonic changes in chemical species concentrations, typically described using nonlinear models. Such non-monotonic dynamics are…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…