Related papers: Enumeration and Online Library of Mass-Action Reac…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
Under suitable assumptions, the dynamic behaviour of a chemical reaction network is governed by an autonomous set of polynomial ordinary differential equations over continuous variables representing the concentrations of the reactant…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of…
It has been recently observed that the dynamical properties of mass action systems arising from many models of biochemical reaction networks can be derived by considering the corresponding properties of a related generalized mass action…
Humans constantly interact with their surrounding environments. Current human-centric generative models mainly focus on synthesizing humans plausibly interacting with static scenes and objects, while the dynamic human action-reaction…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
One of the main tasks of post-genomic informatics is to systematically investigate all molecules and their interactions within a living cell so as to understand how these molecules and the interactions between them relate to the function of…
The automated inference of physically interpretable (bio)chemical reaction network models from measured experimental data is a challenging problem whose solution has significant commercial and academic ramifications. It is demonstrated,…
The nuclear reaction network is usually studied via precise calculation of differential equation sets, and much research interest has been focused on the characteristics of nuclides, such as half-life and size limit. In this paper, however,…
An important invariant of a chemical reaction network is its maximum number of positive steady states. This number, however, is in general difficult to compute. Nonetheless, there is an upper bound on this number -- namely, a network's…
In this work we present a reactions module for "Chaos Many-Body Engine" (Grossu et al., 2010 [1]). Following our goal of creating a customizable, object oriented code library, the list of all possible reactions, including the corresponding…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…
A variety of natural phenomena comprises a huge number of competing reactions and short-lived intermediates. Any study of such processes requires the discovery and accurate modeling of their underlying reaction network. However, this task…
We study the decay process for the reaction-diffusion process of three species on the small-world network. The decay process is manipulated from the deterministic rate equation of three species in the reaction-diffusion system. The particle…
Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signalling processes. Positive feedback loops,…
We consider a natural class of reaction networks which consist of reactions where either two species can inactivate each other (i.e., sequestration), or some species can be transformed into another (i.e., transmutation), in a way that gives…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…
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…