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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…
Chemistry plays a key role in many aspects of astrophysical fluids. Atoms and molecules are agents for heating and cooling, determine the ionization fraction, serve as observational tracers, and build the molecular foundation of life. We…
The impossibility of experiencing the molecular world with our senses hampers teaching and understanding chemistry because very abstract concepts (such as atoms, chemical bonds, molecular structure, reactivity) are required for this…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networks with separated timescales, uses solutions of the partial…
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…
The development of chemical engineering technology is a multi-stage process that encompasses laboratory research, scaling up, and industrial deployment. This process demands interdisciplinary col laboration and typically incurs significant…
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…
AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922-1930). This release features a number of new capabilities: rare-event molecular dynamics…
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, the dominant reaction chemistry, and the conditions for that…
We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from…
Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard…
This paper introduces ChemGen, a software package that uses code generation to integrate multispecies thermodynamics and chemical kinetics into C+-based computational physics codes. ChemGen aims to make chemical kinetics more accessible in…
CORSIKA 8 represents a significant update in the simulation of particle showers, building on the well-established foundation of CORSIKA 7. It has been entirely rewritten as a modular and modern C++ framework, addressing the limitations of…
In this work, we present RePlaChem, a software library for reducing detailed large-scale plasma chemical mechanisms to smaller skeletal ones. The library parses a plasma chemical mechanism in the well-established format compatible with the…
Chemists now routinely use software as part of their work. For example, virtual chemistry allows chemical reactions to be simulated. In particular, a selection of software is available for the visualisation of complex 3-dimensional…
Accurate simulation of dynamical processes in molecules and reactions is among the most challenging problems in quantum chemistry. Quantum computers promise efficient chemical simulation, but the existing quantum algorithms require many…
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…
The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage,…
We propose using semiconductor quantum dots for a simulation of chemical reactions as electrons are redistributed among such artificial atoms. We show that it is possible to achieve various reaction regimes and obtain different reaction…