Related papers: Testing Binomiality of Chemical Reaction Networks …
An inverse problem framework for constructing reaction systems with prescribed properties is presented. Kinetic transformations are defined and analysed as a part of the framework, allowing an arbitrary polynomial ordinary differential…
In this paper, we propose a novel technique, referred to as the Lyapunov Function PDEs technique, to diagnose persistence of chemical reaction networks with mass-action kinetics. The technique allows that every network is attached to a…
Multistationarity is the property of a system to exhibit two distinct equilibria (steady-states) under otherwise identical conditions, and it is a phenomenon of recognized importance for biochemical systems. Multistationarity may appear in…
Complex systems of intracellular biochemical reactions have a central role in regulating cell identities and functions. Biochemical reaction systems are typically studied using the language and tools of graph theory. However, graph…
A reaction system exhibits "absolute concentration robustness" (ACR) in some species if the positive steady-state value of that species does not depend on initial conditions. Mathematically, this means that the positive part of the variety…
Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that…
Zero-one biochemical reaction networks play key roles in cell signalling such as signalling pathways regulated by protein phosphorylation. Multistability of reaction networks is a crucial dynamics feature enabling decision-making in cells.…
In this paper, we prove several new results that give new insights into bilinear systems. We discuss conditions for asymptotic stability using probabilistic arguments. Moreover, we provide a global characterization of reachability in…
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…
We analyze the Conradi-Kahle Algorithm for detecting binomiality. We present experiments using two implementations of the algorithm in Macaulay2 and Maple on biological models and assess the performance of the algorithm on these models. We…
Linear conjugacy offers a new perspective to broaden the scope of stable biochemical reaction networks to the systems linearly conjugated to the well-established complex balanced mass action systems ($\ell$cCBMASs). This paper addresses the…
Generalized mass-action systems are power-law dynamical systems arising from chemical reaction networks. Essentially, every nonnegative ODE model used in chemistry and biology (for example, in ecology and epidemiology) and even in economics…
We study the boundary value problem of two stationary BGK-type models - the BGK model for fast chemical reaction and the BGK model for slow chemical reaction - and provide a unified argument to establish the existence and uniqueness of…
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 introduce a mixed-integer linear programming (MILP) framework capable of determining whether a chemical reaction network possesses the property of being endotactic or strongly endotactic. The network property of being strongly endotactic…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
Maintaining stability in an uncertain environment is essential for proper functioning of living systems. Robust perfect adaptation (RPA) is a property of a system that generates an output at a fixed level even after fluctuations in input…
We study the set of output stable configurations of chemical reaction deciders (CRDs). It turns out that CRDs with only bimolecular reactions (which are almost equivalent to population protocols) have a special structure that allows for an…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Chemically active mixtures exhibit complex patterns that emerge from the interplay of physical interactions and reactions among components. Individually, these two processes are well-understood: Physical interactions can give rise to phase…