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Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…
Chemical reactions can be described as the stepwise redistribution of electrons in molecules. As such, reactions are often depicted using `arrow-pushing' diagrams which show this movement as a sequence of arrows. We propose an electron path…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
Background: Nuclear reactions are complex, with a large number of possible channels. Understanding how different channels contribute to a given reaction is investigated by perturbing the continuous spectrum. Purpose: To develop tools to…
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph transformation. In this framework, each elementary step is a…
We provide a category theoretical framework capturing two approaches to graph-based models of chemistry: formal reactions and disconnection rules. We model a translation from the latter to the former as a functor, which is faithful, and…
We develop random graph models where graphs are generated by connecting not only pairs of vertices by edges but also larger subsets of vertices by copies of small atomic subgraphs of arbitrary topology. This allows the for the generation of…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
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…
Chemical graphs are simple undirected connected graphs, where vertices represent atoms in a molecule and edges represent chemical bonds. A degree-based topological index is a molecular descriptor used to study specific physicochemical…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
Phase separation is the thermodynamic process that explains how droplets form in multicomponent fluids. These droplets can provide controlled compartments to localize chemical reactions, and reactions can also affect the droplets' dynamics.…
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…
We present a theory for rigorous quantum scattering calculations of probabilities for chemical reactions of atoms with diatomic molecules in the presence of an external electric field. The approach is based on the fully uncoupled basis set…
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…
The physical mechanism of nuclear reactions at low energies caused by spatial extension of electron is considered. Nuclear reactions of this type represent intra-electronic processes, more precisely, the processes occurring inside the area…
Nuclear reactions generate energy in nuclear reactors, in stars, and are responsible for the existence of all elements heavier than hydrogen in the universe. Nuclear reactions denote reactions between nuclei, and between nuclei and other…