Related papers: Every atom-atom map can be explained by electron p…
The atom graph of a graph is the graph whose vertices are the atoms obtained by clique minimal separator decomposition of this graph, and whose edges are the edges of all possible atom trees of this graph. We provide two efficient…
Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…
Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
Atomic-scale mapping of the chemical elements in materials is now possible using aberration-corrected electron microscopes but delocalization and multiple scattering can confound image interpretation. Here we report atomic-resolution…
Reaction networks (RNs) comprise a set $X$ of species and a set $\mathscr{R}$ of reactions $Y\to Y'$, each converting a multiset of educts $Y\subseteq X$ into a multiset $Y'\subseteq X$ of products. RNs are equivalent to directed…
Multiple electron processes occur widely in atoms, molecules, clusters, and condensed matters when they are interacting with energetic particles or intense laser fields. In this work, a unified and accurate theoretical formalism is proposed…
A computational procedure is developed for determining the conversion probability for reaction-diffusion systems in which a first-order catalytic reaction is performed over active particles. We apply this general method to systems on metric…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction…
Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and…
The study of a positive or negative charge when an atom loses or gains an electron is a custom in both physical and chemical sciences. However, the related principles and phenomena become confusing when studying the concepts of ionization.…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
We study alchemical atomic energy partitioning as a method to estimate atomisation energies from atomic contributions which are defined in physically rigorous and general ways through use of the uniform electron gas as a joint reference. We…
Conservation laws are time-invariant properties that constrain many physical systems. For systems of chemical reactions, the law of mass conservation constrains how atoms flow between chemical species. Chemical reaction networks can display…
A system of $N_a$ atoms of $n$-levels interacting dipolarly with $\ell$ modes of electromagnetic field is considered. The energy surface of the system is constructed from the direct product of the coherent states of U$(n)$ in the totally…
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…
Atom tracing is essential for understanding the fate of labeled atoms in biochemical reaction networks, yet existing computational methods either simplify label correlations or suffer from combinatorial explosion. We introduce a…
Chemical reaction mechanisms are the foundation of how chemists evaluate reactivity and feasibility, yet current Computer-Assisted Synthesis Planning (CASP) systems operate without this mechanistic reasoning. We introduce a computational…