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The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
The chemistry of an astrophysical environment is closely coupled to its dynamics, the latter often found to be complex. Hence, to properly model these environments a 3D context is necessary. However, solving chemical kinetics within a 3D…
We present the modules for stellar nucleosynthesis, stellar mass loss, and turbulent diffusion of the new COLIBRE subgrid model for cosmological hydrodynamical simulations of galaxy formation. COLIBRE models the thermal evolution of the…
Molecular adsorption is the first important step of many surface-mediated chemical processes, from catalysis to tribology. This phenomenon is controlled by physical/chemical interactions, which can be accurately described by first…
The Cesam code is a consistent set of programs and routines which perform calculations of 1D quasi-hydrostatic stellar evolution including microscopic diffusion of chemical species and diffusion of angular momentum. The solution of the…
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,…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
We present an open-source, performant, pure-python molecular dynamics (MD) suite for non-ideal plasmas. The code, Sarkas, aims to accelerate the research process by providing an MD code but also pre- and post-processing tools. Sarkas offers…
Resource Balance Analysis (RBA) is a computational method based on resource allocation, which performs accurate quantitative predictions of whole-cell states (i.e. growth rate, meta-bolic fluxes, abundances of molecular machines including…
Chemical modeling and synthetic observations are powerful methods to interpret observations, both requiring a knowledge of the physical conditions. In this paper, we present the Analytical Protostellar Environment (APE) code, which aims at…
The emergence of data-driven computational materials science offers unprecedented opportunities to explore complex material landscapes, complementing experimental research with the discovery of novel compounds. To enable these developments,…
Summary: The DynaSig-ML (Dynamical Signatures - Machine Learning) Python package allows the efficient, user-friendly exploration of 3D dynamics-function relationships in biomolecules, using datasets of experimental measures from large…
The last decade showed an impressive observational effort from the photometric and spectroscopic point of view for ancient stellar clusters in our Galaxy and beyond. The theoretical interpretation of these new observational results requires…
Modules for Experiments in Stellar Astrophysics (MESA; (Paxton2011, 2013, 2015, 2018, 2019, Jermyn 2023) is a widely used open-source software for modelling stellar evolution. In many studies, the computational grids covers thousands of…
Multiscale modeling, which integrates material properties from ab initio calculations into continuum-scale simulations, is a promising strategy for optimizing semiconductor devices. However, a key challenge remains: while ab initio methods…
Abridged: We detail and benchmark two sophisticated chemical models developed by the Heidelberg and Bordeaux astrochemistry groups. The main goal of this study is to elaborate on a few well-described tests for state-of-the-art astrochemical…
Two features desired in a three-dimensional (3D) optical tomographic image reconstruction algorithm are the ability to reduce imaging artifacts and to do fast processing of large data volumes. Traditional iterative inversion algorithms are…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
A large scientific community depends on the precise modelling of complex processes in particle cascades in various types of matter. These models are used most prevalently in cosmic-ray physics, astrophysical-neutrino physics, and gamma-ray…