相关论文: Absolute concentration robustness: Algebra and geo…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
A complex balanced kinetic system is absolutely complex balanced (ACB) if every positive equilibrium is complex balanced. Two results on absolute complex balancing were foundational for modern chemical reaction network theory (CRNT): in…
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…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…
Bifunctional enzymes, which catalyze both the forward and reverse steps of a substrate modification reaction, arise naturally in bacterial two-component signaling systems and metabolic regulation. Beyond their well-known role in conferring…
Robustness is an observable property for which a chemical reaction network (CRN) can maintain its functionalities despite the influence of different perturbations. In general, to verify whether a network is robust, it is necessary to…
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…
Homeostasis occurs in a biological system when a chosen output variable remains approximately constant despite changes in an input variable. In this work we specifically focus on biological systems which may be represented as chemical…
Analysis of large continuous-time stochastic systems is a computationally intensive task. In this work we focus on population models arising from chemical reaction networks (CRNs), which play a fundamental role in analysis and design of…
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…
Perfect adaptation is a well-studied biochemical homeostatic behavior lying at the core of biochemical regulation. While the concepts of homeostasis and perfect adaptation are not new, their underlying mechanisms and associated biochemical…
We consider a chemical reaction network governed by mass action kinetics and composed of N different species which can reversibly form heterodimers. A fast iterative algorithm is introduced to compute the equilibrium concentrations of such…
The catalytic reaction system (CRS) formalism by Hordijk and Steel is a versatile method to model autocatalytic biochemical reaction networks. It is particularly suited, and has been widely used, to study self-sustainment and…
Biological systems possess negative entropy. In them, one form of order produces another, more organized form of order. We propose a formal scheme to calculate robustness of an entire biological system by quantifying the negative entropy…
We address the challenge of identifying all real positive steady states in chemical reaction networks (CRNs) governed by mass-action kinetics. Traditional numerical methods often require specific initial guesses and may fail to find all the…
The stability properties of models of spontaneous mirror symmetry breaking in chemistry are characterized algebraically. The models considered here all derive either from the Frank model or from autocatalysis with limited…
The ability of a chemical reaction network to generate itself by catalyzed reactions from constantly present environmental food sources is considered a fundamental property in origin-of-life research. Based on Kaufmann's autocatalytic sets,…
We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT…
Chemical reaction networks (CRNs) are foundational models for describing complex biochemical processes. We study noncompetitive CRNs, a class of networks whose static states are rate-independent, and that can implement ReLU neural networks.…
In this essay, we investigate some relations between Chemical Reaction Networks (CRN) and Mathematical Epidemiology (ME) and report on several pleasant surprises which we had simply by putting these two topics together. Firstly, we propose…