Related papers: Semigroup models for biochemical reaction networks
We investigate a broad family of chemical reaction networks (CRNs) assigned with mass action kinetics, called complex-balanced-produced-CRNs (CBP-CRNs), which are generated by any given complex balanced mass action system (MAS) and whose…
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,…
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…
While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem. Specifically…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
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…
Stochastic reaction networks with mass-action kinetics provide a useful framework for understanding processes -- biochemical and otherwise -- in homogeneous environments. However, cellular reactions are often compartmentalized, either at…
In this work, we design a type of controller that consists of adding a specific set of reactions to an existing mass-action chemical reaction network in order to control a target species. This set of reactions is effective for both…
Chemical transformations depend not only on the identities of the reacting species but also on the catalytic, environmental, and intermediate conditions under which they occur. Classical binary reaction formalisms usually treat such…
Continuous-time Markov chains are frequently used as stochastic models for chemical reaction networks, especially in the growing field of systems biology. A fundamental problem for these Stochastic Chemical Reaction Networks (SCRNs) is to…
Energy functions for pure and heterogenous systems are one of the backbones for molecular simulation of condensed phase systems. With the advent of machine learned potential energy surfaces (ML-PESs) a new era has started. Statistical…
We establish that mass conserving single terminal-linkage networks of chemical reactions admit positive steady states regardless of network deficiency and the choice of reaction rate constants. This result holds for closed systems without…
Multistationary chemical reaction networks are of interest to scientists and mathematicians alike. While some criteria for multistationarity exist, obtaining explicit reaction rates and steady states that exhibit multistationarity for a…
Stochastic chemical processes are described by the chemical master equation satisfying the law of mass-action. We first ask whether the dual master equation, which has the same steady state as the chemical master equation, but with inverted…
Absolute concentration robustness (ACR) and concordance are novel concepts in the theory of robustness and stability within Chemical Reaction Network Theory. In this paper, we have extended Shinar and Feinberg's reaction network analysis…
Chemotaxis is a fundamental guidance mechanism of cells and organisms, responsible for attracting microbes to food, embryonic cells into developing tissues, immune cells to infection sites, animals towards potential mates, and…
Signatures of self-organized criticality (SOC) have recently been observed in an ultracold atomic gas under continuous laser excitation to strongly-interacting Rydberg states [S. Helmrich et al., Nature, 577, 481--486 (2020)]. This creates…
The reconstruction theorem and the multilevel Schauder estimate have central roles in the analytic theory of regularity structures [17]. Inspired by [26], we provide elementary proofs for them by using the semigroup of operators.…
We extend the traditional framework of steady state energy transduction -- typically characterized by a single input and output -- to multi-resource transduction in open chemical reaction networks (CRNs). Transduction occurs when…