Related papers: COEL: A Web-based Chemistry Simulation Framework
Stochastic evolution of Chemical Reactions Networks (CRNs) over time is usually analysed through solving the Chemical Master Equation (CME) or performing extensive simulations. Analysing stochasticity is often needed, particularly when some…
Chemical systems are interpreted through the species they contain and the reactions they may undergo, i.e., their chemical reaction network (CRN). In spite of their central importance to chemistry, the structure of CRNs continues to be…
The historical quest for unifying the concepts and methods of Chemical Reaction Networks theory (CRNT), Mahematical Epidemiology (ME) and ecology has received increased attention in the last years and has led in particular to the…
Chemically reacting flows are common in engineering, such as hypersonic flow, combustion, explosions, manufacturing processes and environmental assessments. For combustion, the number of reactions can be significant (over 100) and due to…
The complexity of molecular and cellular processes forces experimental studies to focus on subsystems. To study the functioning of biological systems across levels of structural and functional organisation, we require tools to compose and…
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…
Organic reaction, the foundation of modern chemical industry, is crucial for new material development and drug discovery. However, deciphering reaction mechanisms and modeling multi-molecular relationships remain formidable challenges due…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Recent improvements in large language models have opened new opportunities for accelerating and automating scientific workflows. In parallel, modern collider analyses are becoming increasingly complex and demand substantial programming and…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
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…
Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize…
In the field of chemical engineering, traditional data-processing and prediction methods face significant challenges. Machine-learning and large-language models (LLMs) also have their respective limitations. This paper explores the…
Virtual screening plays a critical role in modern drug discovery by enabling the identification of promising candidate molecules for experimental validation. Traditional machine learning methods such, as Support Vector Machines (SVM) and…
Nuclear magnetic resonance (NMR) spectroscopy provides an experimental readout of local chemical environments, but its use in molecular representation learning has been constrained by heterogeneous data and incomplete atom-level…
Predicting the degradation processes of molecules over long timescales is a key aspect of industrial materials design. However, it is made computationally challenging by the need to construct large networks of chemical reactions that are…
Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the…
With the prospect of automating a number of chemical tasks with high fidelity, chemical language processing models are emerging at a rapid speed. Here, we present a cloud-based real-time platform that allows users to virtually screen…
Reconstruction of biochemical reaction networks is a central topic in systems biology which raises crucial theoretical challenges in system identification. Nonlinear Ordinary Differential Equations (ODEs) that involve polynomial and…
In order to fully exploit the potential of molecular communication (MC) for intra-body communication, practically implementable cellular receivers are an important long-term goal. A variety of receiver architectures based on chemical…