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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…
We present an open-source simulation framework for optically detected magnetic resonance, developed in Python. The framework allows users to construct, manipulate, and evolve multipartite quantum systems that consist of spins and electronic…
We propose algorithms and software for computing projections onto the intersection of multiple convex and non-convex constraint sets. The software package, called SetIntersectionProjection, is intended for the regularization of inverse…
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…
In rustworkx, we provide a high-performance, flexible graph library for Python. rustworkx is inspired by NetworkX but addresses many performance concerns of the latter. rustworkx is written in Rust and is particularly suited for…
ixpeobssim is a simulation and analysis framework, based on the Python programming language and the associated scientific ecosystem, specifically developed for the Imaging X-ray Polarimetry Explorer (IXPE). Given a source model and the…
We introduce Atomistic learned potentials in JAX (apax), a flexible and efficient open source software package for training and inference of machine-learned interatomic potentials. Built on the JAX framework, apax supports GPU acceleration…
QC Lab is an open-source Python package for QC dynamics simulations aimed to promote the development of QC algorithms, and their application to a wide variety of relevant model problems. It follows a modular design that facilitates…
BlackJAX is a library implementing sampling and variational inference algorithms commonly used in Bayesian computation. It is designed for ease of use, speed, and modularity by taking a functional approach to the algorithms' implementation.…
Basket trials are a new type of clinical trial in which a treatment is investigated in several subgroups. For the analysis of these trials, information is shared between the subgroups based on the observed data to increase the power. Many…
stopp is a novel R package specifically designed for the analysis of spatio-temporal point patterns which might have occurred in a subset of the Euclidean space or on some specific linear network, such as roads of a city. It represents the…
Medical image analysis plays a key role in precision medicine as it allows the clinicians to identify anatomical abnormalities and it is routinely used in clinical assessment. Data curation and pre-processing of medical images are critical…
SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…
An R package SpatialPack that implements routines to compute point estimators and perform hypothesis testing of the spatial association between two stochastic sequences is introduced. These methods address the spatial association between…
When modeling astronomical objects throughout the universe, it is important to correctly treat the limitations of the data, for instance finite resolution and sensitivity. In order to simulate these effects, and to make radiative transfer…
Recent advances in theoretical atomic physics have enabled large-scale calculation of atomic parameters for a variety of atomic processes with high degree of precision. The development and application of these methods is the aim of the Iron…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
ArchNEMESIS is an open-source Python package developed for the analysis of remote sensing spectroscopic observations of planetary atmospheres. It is based on the widely used NEMESIS radiative transfer and retrieval tool, which has been…
This article summarizes new features and enhancements of the first major update of Package-X. Package-X 2.0 can now generate analytic expressions for arbitrarily high rank dimensionally regulated tensor integrals with up to four distinct…
Particle-based fluid simulations have emerged as a powerful tool for solving the Navier-Stokes equations, especially in cases that include intricate physics and free surfaces. The recent addition of machine learning methods to the toolbox…