Related papers: Disconnection Rules are Complete for Chemical Reac…
Chemistry's rules carry exceptions: the octet rule, Hess's Law, detailed balance, orbital symmetry selection rules, all with disclaimers memorised separately. Their cause: a question from a richer structural level posed in the vocabulary of…
We consider linear elimination of variables in steady state equations of a chemical reaction network. Particular subsets of variables corresponding to sets of so-called reactant-noninteracting species, are introduced. The steady state…
Traces and their extension called combined traces (comtraces) are two formal models used in the analysis and verification of concurrent systems. Both models are based on concepts originating in the theory of formal languages, and they are…
A central challenge in materials science is characterizing chemical processes that are elusive to direct measurement, particularly in functional materials operating under realistic conditions. Here, we demonstrate that mechanical strain…
It is useful to have complete lists of nonisomorphic chemical reaction networks (CRNs) of a given size, with or without various restrictions. One may, for example, be interested in exploring how often certain dynamical behaviours occur in…
This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…
Reaction networks are a general formalism for describing collections of classical entities interacting in a random way. While reaction networks are mainly studied by chemists, they are equivalent to Petri nets, which are used for similar…
In typical microscopic approaches, particularly when pairing correlations are present, nuclei and nuclear fragments do not have well defined quantum numbers and symmetries should be restored. I present here a formalism for the simultaneous…
Deterministic reaction networks (RNs) are tools to model diverse biological phenomena characterized by particle systems, when there are abundant number of particles. Examples include but are not limited to biochemistry, molecular biology,…
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…
Central to our understanding of chemical reactivity is the principle of mass conservation, which is fundamental for ensuring physical consistency, balancing equations, and guiding reaction design. However, data-driven computational models…
We study binomiality of the steady state ideals of chemical reaction networks. Considering rate constants as indeterminates, the concept of unconditional binomiality has been introduced and an algorithm based on linear algebra has been…
Understanding mechanisms of rare but important events in complex molecular systems, such as protein folding or ligand (un)binding, requires accurately mapping transition paths from an initial to a final state. The committor is the ideal…
Text-book concepts of diffusion- versus kinetic-control are well-defined for reaction-kinetics involving macroscopic concentrations of diffusive reactants that are adequately described by rate-constants -- the inverse of the…
The concept of the limiting step is extended to the asymptotology of multiscale reaction networks. Complete theory for linear networks with well separated reaction rate constants is developed. We present algorithms for explicit…
Developing accurate models for chemical reactors is often challenging due to the complexity of reaction kinetics and process dynamics. Traditional approaches require retraining models for each new system, limiting generalizability and…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…
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…
A chemical reaction mechanism (CRM) is a sequence of molecular-level events involving bond-breaking/forming processes, generating transient intermediates along the reaction pathway as reactants transform into products. Understanding such…
We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and…