Related papers: Biochemical network decomposition reveals absolute…
The Turing completeness of continuous chemical reaction networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…
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…
The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…
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…
In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and…
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…
Here we propose a generic mechanism - networked buffering - for generating robust traits in complex systems that requires two basic conditions to be satisfied: 1) agents are versatile enough to perform more than one single functional role…
The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…
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…
Deciding whether and where a system of parametrized ordinary differential equations displays bistability, that is, has at least two asymptotically stable steady states for some choice of parameters, is a hard problem. For systems modeling…
A crisp survey is given of chemical reaction networks from the perspective of general nonlinear network dynamics, in particular of consensus dynamics. It is shown how by starting from the complex-balanced assumption the reaction dynamics…
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…
Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical…
Resilient ecological systems will be better able to maintain their structure and function in the emerging Anthropocene. Estimating the resilience of different systems will therefore provide valuable insight for conservation decision-makers,…
Most of the current complex networks that are of interest to practitioners possess a certain community structure that plays an important role in understanding the properties of these networks. Moreover, many machine learning algorithms and…
A recent article by Weidner et al. [2021] presents a method to extract graph properties that are predictive of the dynamical behavior of multivariate, discrete models of biochemical regulation. In other words, a method that uses only…
Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…
Controlling stochastic reactions networks is a challenging problem with important implications in various fields such as systems and synthetic biology. Various regulation motifs have been discovered or posited over the recent years, the…
Existing part-aware person re-identification methods typically employ two separate steps: namely, body part detection and part-level feature extraction. However, part detection introduces an additional computational cost and is inherently…
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…