相关论文: Chemical Reaction Systems with a Homoclinic Bifurc…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
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,…
Analyzing qualitative behaviors of biochemical reactions using its associated network structure has proven useful in diverse branches of biology. As an extension of our previous work, we introduce a graph-based framework to calculate steady…
Motivated by investigating multistationarity in biochemical systems, we address saddle-node bifurcations for chemical reaction networks endowed with general kinetics. At positive equilibria, we identify structural network conditions that…
Reaction rates of chemical reactions under nonequilibrium conditions can be determined through the construction of the normally hyperbolic invariant manifold (NHIM) [and moving dividing surface (DS)] associated with the transition state…
Retrosynthesis is essential for designing synthetic pathways for complex molecules and can be revolutionized by AI to automate and accelerate chemical synthesis planning for drug discovery and materials science. Here, we propose a…
Subcritical Turing bifurcations of reaction-diffusion systems in large domains lead to spontaneous onset of well-developed localised patterns via the homoclinic snaking mechanism. This phenomenon is shown to occur naturally when balancing…
In this work, we propose a general inversion framework to non-uniquely invert a very large class of ordinary differential equations (ODEs) into chemical reaction networks. A thorough treatment of the relevant chemical reaction network…
Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…
Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize…
Machine-learning generative methods for material design are constructed by representing a given chemical structure, either a solid or a molecule, over appropriate atomic features, generally called structural descriptors. These must be fully…
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…
In this work, we focus on an autocatalytic reaction-diffusion model and carry out multiple scale weakly nonlinear analysis. A cubic and a quadratic autocatalytic reaction system is analysed. We develop a framework to identify the critical…
Chemical reaction networks (CRNs) are prototypical complex systems because reactions are nonlinear and connected in intricate ways, and they are also essential to understand living systems. Here, I discuss how recent developments in…
Understanding how biological homochirality emerged remains a challenge for the researchers interested in the origin of life. During the last decades, stable non-racemic steady states of nonequilibrium chemical systems have been discussed as…
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 induced kinetic differential equation of a reaction network endowed with mass action type kinetics is a system of polynomial differential equations. The problem studied here is: Given a polynomial differential equation, is it possible…
The paper presents amended basic map of states of chemical systems in discrete thermodynamics of chemical equilibria. Uniting two previously found basic map types in one and covering a wider range of situations, it allows us to obtain more…
We apply spatial dynamical-systems techniques to prove that certain spatiotemporal patterns in reversible reaction-diffusion equations undergo snaking bifurcations. That is, in a narrow region of parameter space, countably many branches of…
We study the effect of changes in the parameters of a two-dimensional potential energy surface on the phase space structures relevant for chemical reaction dynamics. The changes in the potential energy are representative of chemical…