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CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…
Significant progress in the development of efficient and fast algorithms for quantum chemical calculations has been made in the past two decades. The main focus has always been the desire to be able to treat ever larger molecules or…
As quantum computing hardware systems continue to advance, the research and development of performant, scalable, and extensible software architectures, languages, models, and compilers is equally as important in order to bring this novel…
With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative…
Process simulation is a critical cornerstone of chemical engineering design. Current automated chemical design methodologies focus mainly on various representations of process flow diagrams. However, transforming these diagrams into…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
Chemical reaction networks can be automatically generated from graph grammar descriptions, where rewrite rules model reaction patterns. Because a molecule graph is connected and reactions in general involve multiple molecules, the rewriting…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
We propose the chemlambda artificial chemistry, whose behavior strongly suggests that real molecules which embed Interaction Nets patterns and real chemical reactions which resemble Interaction Nets graph rewrites could be a realistic path…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
Agentic AI systems integrating large language models (LLMs) with reasoning and tooluse capabilities are transforming various domains - in particular, software development. In contrast, their application in chemical process flowsheet…
Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogenous biological datasets, which can be challenging without sophisticated tools. We developed COMO, a user-friendly…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
The goal of this paper is to gather and develop some necessary and sufficient criteria for injectivity and multistationarity in vector fields associated with a chemical reaction network under a variety of more or less general assumptions on…
An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers a highly interactive visualization and…
Chemical laboratory automation has long been constrained by rigid workflows and poor adaptability to the long-tail distribution of experimental tasks. While most automated platforms perform well on a narrow set of standardized procedures,…
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…
We present the VECMA toolkit (VECMAtk), a flexible software environment for single and multiscale simulations that introduces directly applicable and reusable procedures for verification, validation (V&V), sensitivity analysis (SA) and…
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…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…