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Chemical plants are complex and dynamical systems consisting of many components for manipulation and sensing, whose state transitions depend on various factors such as time, disturbance, and operation procedures. For the purpose of…
Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…
Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…
Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background,…
Machine learning interatomic potentials (MLIPs) are changing atomistic simulations in the field of chemistry and materials science. However, constructing a single universal MLIP that can accurately model molecular and crystalline systems…
Polynomial dynamical systems (DSs) can model a wide range of physical processes. A special subset of these DSs that can model chemical reactions under mass-action kinetics is called chemical dynamical systems (CDSs). A fundamental problem,…
In cyber-physical systems like automotive systems, there are components like sensors, actuators, and controllers that communicate asynchronously with each other. The computational model of actor supports modeling distributed asynchronously…
Large language models (LLMs) are beginning to reshape how chemists plan and run reactions in organic synthesis. Trained on millions of reported transformations, these text-based models can propose synthetic routes, forecast reaction…
Chemical reaction networks describe interactions between biochemical species. Once an underlying reaction network is given for a biochemical system, the system dynamics can be modelled with various mathematical frameworks such as continuous…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
We introduce \textsc{qcmath}, a user-friendly quantum chemistry software tailored for electronic structure calculations, implemented using the Wolfram Mathematica language and available at \url{https://github.com/LCPQ/qcmath}. This…
In this work, we propose a general inversion framework to non-uniquely invert a very large class of ordinary differential equations (ODEs) into chemical reaction networks. A thorough treatment of the relevant chemical reaction network…
A QM/MM implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on…
In this paper we present the Uppsala Quantum Chemistry package (UQUANTCHEM), a new and versatile computational platform with capabilities ranging from simple Hartree-Fock calculations to state of the art First principles Extended Lagrangian…
Automation is becoming ubiquitous in all laboratory activities, leading towards precisely defined and codified laboratory protocols. However, the integration between laboratory protocols and mathematical models is still lacking. Models…
Astrochemical modeling is needed for understanding the formation and evolution of interstellar molecules, and for extracting physical information from spectroscopic observations of interstellar clouds. The modeling usually involves handling…
We propose the use of quantum optical systems to perform universal simulation of quantum dynamics. Two specific implementations that require present technology are put forward for illustrative purposes. The first scheme consists of neutral…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
Since the first observations of interstellar molecules, astrochemical simulations have been employed to model and understand its formation and destruction path- ways. With the advent of high-resolution telescopes such as JWST and ALMA, the…