Related papers: Chemical concrete machine
Chemical reaction networks (CRNs) are a standard formalism used in chemistry and biology to reason about the dynamics of molecular interaction networks. In their interpretation by ordinary differential equations, CRNs provide a…
A nut graph is a graph on at least 2 vertices whose adjacency matrix has nullity 1 and for which non-trivial kernel vectors do not contain a zero. Chemical graphs are connected, with maximum degree at most three. We present a new algorithm…
We construct an information-geometric structure for chemical thermodynamics, applicable to a wide range of chemical reaction systems including non-ideal and open systems. For this purpose, we explicitly construct dual affine coordinate…
Finding the main product of a chemical reaction is one of the important problems of organic chemistry. This paper describes a method of applying a neural machine translation model to the prediction of organic chemical reactions. In order to…
Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the…
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…
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…
Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…
Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or…
A construction sequence for a graph is a listing of the elements of the graph (the set of vertices and edges) such that each edge follows both its endpoints. The construction number of the graph is the number of such sequences. We determine…
For decades, computational chemistry has been posited as one of the areas in which quantum computing would revolutionize. However, the algorithmic advantages that fault-tolerant quantum computers have for chemistry can be overwhelmed by…
A quantum Matter-Photonics framework is adapted to help scrutinize chemical reaction mechanisms and used to explore a process mapped from chemical tree topological model. The chemical concept of bond knitting/breaking is reformulated via…
One of the most promising suggested applications of quantum computing is solving classically intractable chemistry problems. This may help to answer unresolved questions about phenomena like: high temperature superconductivity, solid-state…
The purpose of this review is to introduce the reader to graph kernels and the corresponding literature, with an emphasis on those with direct application to chemoinformatics. Graph kernels are functions that allow for the inference of…
Chemical reactions are a prominent feature of molecular communication (MC) systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes or the communication…
Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic…
The mathematical formulation of Quantum Mechanics is derived from purely operational axioms based on a general definition of "experiment" as a set of transformations. The main ingredient of the mathematical construction is the postulated…
Topotactic chemical reaction (TCR) is a chemical process that transforms one crystalline phase to another while maintaining one or more of the original structural frameworks, typically induced by the local insertion, removal, or replacement…
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…
With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based…