相关论文: Pathfinder -- Navigating and Analyzing Chemical Re…
Embedding computation in biochemical environments incompatible with traditional electronics is expected to have wide-ranging impact in synthetic biology, medicine, nanofabrication and other fields. Natural biochemical systems are typically…
Chemical reaction networks (CRNs) are a standard formalism used in chemistry and biology to reason about the dynamics of molecular interaction networks. In their interpretation by ordinary differential equations, CRNs provide a…
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…
Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from…
We present a differentiable formulation of abstract chemical reaction networks (CRNs) that can be trained to solve a variety of computational tasks. Chemical reaction networks are one of the most fundamental computational substrates used by…
Chemical reaction networks (CRNs) are fundamental computational models used to study the behavior of chemical reactions in well-mixed solutions. They have been used extensively to model a broad range of biological systems, and are primarily…
The purpose of this review is to introduce the reader to graph kernels and the corresponding literature, with an emphasis on those with direct application to chemoinformatics. Graph kernels are functions that allow for the inference of…
Prediction of complete step-by-step chemical reaction mechanisms (CRMs) remains a major challenge. Whereas the traditional approaches in CRM tasks rely on expert-driven experiments or costly quantum chemical computations, contemporary deep…
Chemical reaction networks (CRNs) model systems where molecules interact according to a finite set of reactions such as $A + B \to C$, representing that if a molecule of $A$ and $B$ collide, they disappear and a molecule of $C$ is produced.…
Automated and high-throughput quantum chemical investigations into chemical processes have become feasible in great detail and broad scope. This results in an increase in complexity of the tasks and in the amount of generated data. An…
Understanding and predicting interface diffusion phenomena in materials is crucial for various industrial applications, including semiconductor manufacturing, battery technology, and catalysis. In this study, we propose a novel approach…
This paper studies the (discrete) \emph{chemical reaction network (CRN)} computational model that emerged in the last two decades as an abstraction for molecular programming. The correctness of CRN protocols is typically established under…
Chemical kinetics plays an important role in governing the thermal evolution in reactive flows problems. The possible interactions between chemical species increase drastically with the number of species considered in the system. Various…
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 Chemical Reaction Network (CRN) is a well-studied model that describes the interaction of molecules in well-mixed solutions. In 2014, Qian and Winfree [22] proposed the abstract surface chemical reaction network model (sCRN), which…
Stochastic chemical reaction networks (CRNs) are complex systems which combine the features of concurrent transformation of multiple variables in each elementary reaction event, and nonlinear relations between states and their rates of…
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…
The evolution of chemical reaction networks is often analyzed through kinetic models and energy landscapes, but these approaches fail to capture the deeper structural constraints governing complexity growth. In chemical reaction networks,…
The dynamics of a chemical reaction network (CRN) is often modelled under the assumption of mass action kinetics by a system of ordinary differential equations (ODEs) with polynomial right-hand sides that describe the time evolution of…
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…