相关论文: Cayley Graphs of Semigroups Applied to Atom Tracki…

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…

Thermodynamic aspects of chemical reactions have a long history in the Physical Chemistry literature. In particular, biochemical cycles - the building-blocks of biochemical systems - require a source of energy to function. However, although…

Chemical reactions can be understood as transformations of multigraphs (molecules) that preserve vertex labels (atoms) and degrees (sums of bonding and non-bonding electrons), thereby implying the atom-atom map of a reaction. The…

The paper fills gaps in knowledge about Kuratowski operations which are already in the literature. The Cayley table for these operations has been drawn up. Techniques, using only paper and pencil, to point out all semigroups and its…

Tiered graph autoencoders provide the architecture and mechanisms for learning tiered latent representations and latent spaces for molecular graphs that explicitly represent and utilize groups (e.g., functional groups). This enables the…

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…

For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…

Random graph models have been instrumental in characterizing complex networks, but chemical reaction networks (CRNs) are better represented as hypergraphs. Traditional models of random CRNs often reduce CRNs to bipartite graphs,…

Stereoisomers have the same molecular formula and the same atom connectivity and their existence can be related to the presence of different three-dimensional arrangements. Stereoisomerism is of great importance in many different fields…

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…

Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…

We introduce a new Collaborative Causal Discovery problem, through which we model a common scenario in which we have multiple independent entities each with their own causal graph, and the goal is to simultaneously learn all these causal…

Charged particle tracking has played a key role in the development of particle physics, particularly for understanding phenomena involving short-lived particles precisely. As a platform for high-resolution charged particle tracking, an…

We investigate Cayley graphs of finite semigroups and monoids. First, we look at semigroup digraphs, i.e., directed Cayley graphs of semigroups, and give a Sabidussi-type characterization in the case of monoids. We then correct a proof of…

High-throughput screening using cell images is an efficient method for screening new candidates for pharmaceutical drugs. To complete the screening process, it is essential to have an efficient process for analyzing cell images. This paper…

Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from…

We introduce a new distributed algorithm for aligning graphs or finding substructures within a given graph. It is based on the cavity method and is used to study the maximum-clique and the graph-alignment problems in random graphs. The…

Coupled-cluster theory is a powerful tool for first-principles calculations of atomic nuclei, enabling accurate predictions of nuclear observables across the Segr\`e chart. While coupled-cluster computations are especially efficient at…

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…

Bond graphs can be used to build thermodynamically-compliant hierarchical models of biomolecular systems. As bond graphs have been widely used to model, analyse and synthesise engineering systems, this paper suggests that they can play the…