相关论文: Context-Driven Exploration of Complex Chemical Rea…

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…

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These…

Sampled structure sequences obtained, for instance, from real-time reactivity explorations or first-principles molecular dynamics simulations contain valuable information about chemical reactivity. Eventually, such sequences allow for the…

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…

Graph transformation systems have the potential to be realistic models of chemistry, provided a comprehensive collection of reaction rules can be extracted from the body of chemical knowledge. A first key step for rule learning is the…

The analysis of complex reaction networks is of great importance in several chemical and biochemical fields (interstellar chemistry, prebiotic chemistry, reaction mechanism, etc). In this article, we propose to simultaneously refine and…

Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible…

A variety of natural phenomena comprises a huge number of competing reactions and short-lived intermediates. Any study of such processes requires the discovery and accurate modeling of their underlying reaction network. However, this task…

In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…

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…

Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…

We developed an automated approach to construct the complex reaction network and explore the reaction mechanism for several reactant molecules. The nanoreactor type molecular dynamics was employed to generate possible chemical reactions, in…

The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network…

We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and…

The development of chemical reaction models aids understanding and prediction in areas ranging from biology to electrochemistry and combustion. A systematic approach to building reaction network models uses observational data not only to…

Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical…

Rapid discovery of new reactions and molecules in recent years has been facilitated by the advancements in high throughput screening, accessibility to a much more complex chemical design space, and the development of accurate molecular…

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…

The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well represented as…

Investigating a reactive chemical system with automated reaction network exploration algorithms provides a more detailed picture of its chemical mechanism than what would be accessible by manual investigation. In general, exploration…