Related papers: Chemical concrete machine
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…
In many scientific fields, there is an interest in understanding the way in which complex chemical networks evolve. The chemical networks which researchers focus upon, have become increasingly complex and this has motivated the development…
A chemical reaction mechanism (CRM) is a sequence of molecular-level events involving bond-breaking/forming processes, generating transient intermediates along the reaction pathway as reactants transform into products. Understanding such…
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemical reaction networks sample? We begin tackling these…
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…
Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs…
Rewriting is a formalism widely used in computer science and mathematical logic. The classical formalism has been extended, in the context of functional languages, with an order over the rules and, in the context of rewrite based languages,…
The chemistry of an astrophysical environment is closely coupled to its dynamics, the latter often found to be complex. Hence, to properly model these environments a 3D context is necessary. However, solving chemical kinetics within a 3D…
Conversion of chemical energy into mechanical work is the fundamental mechanism of several natural phenomena at the nanoscale, like molecular machines and Brownian motors. Quantum mechanical effects are relevant for optimising these…
Reaction mechanisms are often presented as sequences of elementary steps, such as codified by arrow pushing. We propose an approach for representing such mechanisms using graph transformation. In this framework, each elementary step is a…
We introduce MetaChem, a language for representing and implementing Artificial Chemistries. We motivate the need for modularisation and standardisation in representation of artificial chemistries. We describe a mathematical formalism for…
We define a compilation scheme for a constructor-based, strongly-sequential, graph rewriting system which shortcuts some needed steps. The object code is another constructor-based graph rewriting system. This system is normalizing for the…
A scheme of universal quantum computation on a chain of qubits is described that does not require local control. All the required operations, an Ising-type interaction and spatially uniform simultaneous one-qubit gates, are…
Machine-learning generative methods for material design are constructed by representing a given chemical structure, either a solid or a molecule, over appropriate atomic features, generally called structural descriptors. These must be fully…
An inverse problem framework for constructing reaction systems with prescribed properties is presented. Kinetic transformations are defined and analysed as a part of the framework, allowing an arbitrary polynomial ordinary differential…
The computational power increases over the past decades havegreatly enhanced the ability to simulate chemical reactions andunderstand ever more complex transformations. Tensor contractions are the fundamental computational building block of…
Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
Validation of a presumably universal theory, such as quantum mechanics, requires a quantum mechanical description of systems that carry out theoretical calculations and experiments. The description of quantum computers is under active…
Precise reconstruction of top quark properties is a challenging task at the Large Hadron Collider due to combinatorial backgrounds and missing information. We introduce a physics-informed neural network architecture called the Covariant…