Related papers: Chemical concrete machine
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…
Chemputation reframes synthesis as the programmable execution of reaction code on a universally re-configurable hardware graph. Here we prove that a chemputer equipped with a finite, but extensible, set of reagents, catalysts and process…
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…
Given a graph rewrite system, a graph G is a quine graph if it has a non-void maximal collection of non-conflicting matches of left patterns of graphs rewrites, such that after the parallel application of the rewrites we obtain a graph…
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…
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…
The most fundamental abstraction underlying all modern computers is the Turing Machine, that is if any modern computer can simulate a Turing Machine, an equivalence which is called Turing completeness, it is theoretically possible to…
Modern computational chemistry has reached a stage at which massive exploration into chemical reaction space with unprecedented resolution with respect to the number of potentially relevant molecular structures has become possible. Various…
Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we…
Zipper logic is a graph rewrite system, consisting in only local rewrites on a class of zipper graphs. Connections with the chemlambda artificial chemistry and with knot diagrammatics based computation are explored in the article.
A simple model of the two-state ratchet type is proposed for molecular chemical engines that convert chemical free energy into mechanical work and vice versa. The engine works by catalyzing a chemical reaction and turning a rotor.…
We propose a simple theoretical model for a molecular chemical engine that catalyzes a chemical reaction and converts the free energy released by the reaction into mechanical work. Binding and unbinding processes of reactant and product…
A chemical turnstile is a device for transporting small, well-characterised doses of atoms from one location to another. A working turnstile has yet to be built, despite the numerous technological applications available for such a device.…
In recent years, the modeling interest has increased significantly from the molecular level to the atomic and quantum scale. The field of computational chemistry plays a significant role in designing computational models for the operation…
CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…
Chemical modelling serves two purposes in dynamical models: accounting for the effect of microphysics on the dynamics and providing observable signatures. Ideally, the former must be done as part of the hydrodynamic simulation but this…
Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all…
Recent technological advances allow us to view chemical mass-action systems as analog computers. In this context, the inputs to a computation are encoded as initial values of certain chemical species while the outputs are the limiting…
Structures of chemical compounds can be synthesized and categorized through mathematical means. Organic compounds are suitable targets because of their simple valences. Acyclic organic compounds made of hydrogen and second-row elements C,…