Related papers: Enumeration and Online Library of Mass-Action Reac…
The design and synthesis of complex and large mimicked biochemical networks de novo is an unsolved problem in synthetic biology. To address this limitation without resorting to ad hoc computations and experiments, a predictive mathematical…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
Nuclear reaction rates are quantities of fundamental importance in astrophysics. Substantial efforts have been devoted in the last decades to measure or calculate them. The present paper presents for the first time a detailed description of…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
The process of genetic recombination can be seen as a chemical reaction network with mass-action kinetics. We review the known results on existence, uniqueness, and global stability of an equilibrium in every compatibility class and for all…
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…
Massively multitask neural architectures provide a learning framework for drug discovery that synthesizes information from many distinct biological sources. To train these architectures at scale, we gather large amounts of data from public…
We developed an automated approach to construct the complex reaction network and explore the reaction mechanism for several reactant molecules. The nanoreactor type molecular dynamics was employed to generate possible chemical reactions, in…
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…
A highly efficient formulation of moment equations for stochastic reaction networks is introduced. It is based on a set of binomial moments that capture the combinatorics of the reaction processes. The resulting set of equations can be…
Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has…
We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
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…
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist…
A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations…
Reaction mechanism search tools have demonstrated the ability to provide insights into likely products and rate-limiting steps of reacting systems. However, reactions involving several concerted bond changes - as can be found in many key…