相关论文: Artificial chemistry experiments with chemlambda, …
We provide a framework for experimentation at https://mbuliga.github.io/quinegraphs/ic-vs-chem.html#icvschem with two artificial chemistries: directed interaction combinators (dirIC, defined in section 2) and chemlambda. We are interested…
Here I report about the modifications of and relations between graphic lambda calculus, various formalisms which appeared under the name chemlambda and a version of directed interaction combinators. This is part of the study and experiments…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
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…
Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting…
We present chemlambda (or the chemical concrete machine), an artificial chemistry with the following properties: (a) is Turing complete, (b) has a model of decentralized, distributed computing associated to it, (c) works at the level of…
Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial…
Artificial Chemistries (ACs) are symbolic chemical metaphors for the exploration of Artificial Life, with specific focus on the origin of life. In this work we define a P system based artificial graph chemistry to understand the principles…
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…
Graph rewrite systems are powerful tools to model and study complex problems in various fields of research. Their successful application to chemical reaction modelling on a molecular level was shown but no appropriate and simple system is…
Analysis of chemical graphs is a major research topic in computational molecular biology due to its potential applications to drug design. One approach is inverse quantitative structure activity/property relationship (inverse QSAR/QSPR)…
Direct numerical simulations of turbulent reacting flows involving millions of grid points and detailed chemical mechanisms with hundreds of species and thousands of reactions are computationally prohibitive. To address this challenge, we…
In the $(G,H)$-isomorphism game, a verifier interacts with two non-communicating players (called provers) by privately sending each of them a random vertex from either $G$ or $H$, whose aim is to convince the verifier that two graphs $G$…
Analysis of chemical graphs is becoming a major research topic in computational molecular biology due to its potential applications to drug design. One of the major approaches in such a study is inverse quantitative structure…
A novel framework has recently been proposed for designing the molecular structure of chemical compounds with a desired chemical property using both artificial neural networks and mixed integer linear programming. In the framework, a…
Artificial chemistry simulations produce many intriguing emergent behaviors, but they are often difficult to steer or control. This paper proposes a method for steering the dynamics of a classic artificial chemistry model, known as AlChemy…
It is fundamental for science and technology to be able to predict chemical reactions and their properties. To achieve such skills, it is important to develop good representations of chemical reactions, or good deep learning architectures…
Molecular graphs of unsaturated carbon frameworks or hydrocarbons pruned of hydrogen atoms, are chemical graphs. A chemical graph is a connected simple graph of maximum degree $3$ or less. A nut graph is a connected simple graph with a…
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…
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…