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The urgency of the energy transition requires improving the performance and longevity of hydrogen technologies. AlphaPEM is a dynamic one-dimensional (1D) physics-based PEM fuel cell system simulator, programmed in Python and experimentally…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
pyGDM is a python toolkit for electro-dynamical simulations of individual nano-structures, based on the Green Dyadic Method (GDM). pyGDM uses the concept of a generalized propagator, which allows to solve cost-efficiently monochromatic…
We present the Python Tree Tensor Network package (pyTTN) for the evaluation of dynamical properties of closed and open quantum systems that makes use of Tree Tensor Network (TTN), or equivalently the multi-layer multiconfiguration…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Structural analyses are an integral part of computational research on nucleation and supercooled water, whose accuracy and efficiency can impact the validity and feasibility of such studies. The underlying molecular mechanisms of these…
Denoising diffusion models (DDMs) have led to staggering performance leaps in image generation, editing and restoration. However, existing DDMs use very large datasets for training. Here, we introduce a framework for training a DDM on a…
Molecular dynamics simulations have been extensively used to predict thermal properties, but simulating different phases with similar precision using a unified force field is often difficult, due to the lack of accurate and transferrable…
A Python package for post-processing of plane two-dimensional data from computational fluid dynamics simulations is presented. The package, called turbulucid, provides means for scripted, reproducible analysis of large simulation campaigns…
This Letter introduces an approach for precisely designing surface friction properties using a conditional generative machine learning model, specifically a diffusion denoising probabilistic model (DDPM). We created a dataset of synthetic…
Due to the high computational cost of 3D particle-in-cell (PIC) simulations, lower-dimensional (2D or 1D) simulations are frequently used in their place. Our work shows that when modeling high-intensity laser ion acceleration, simulation…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
RapidSim is a lightweight application for the fast simulation of phase space decays of beauty and charm quark hadrons, allowing for quick studies of the properties of signal and background decays in particle physics analyses. Based upon the…
A laser-atom interaction simulator derived from quantum electrodynamics (LASED) is presented, which has been developed in the python programming language. LASED allows a user to calculate the time evolution of a laser-excited atomic system.…
Accurate and fast prediction of materials properties is central to the digital transformation of materials design. However, the vast design space and diverse operating conditions pose significant challenges for accurately modeling arbitrary…
Finite-temperature magnetism gives rise to many phenomena in alloy materials, such as magnetic phase transformations, short or medium range order in magnetic alloys, spin waves, critical phenomena, and the magnetocaloric effect. Lattice…
Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…
This paper presents catsim, the first package written in the Python language specialized in computerized adaptive tests and the logistical models of Item Response Theory. catsim provides functions for generating item and examinee…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
Correlation functions, such as static and dynamic structure factors, offer a versatile approach to analyzing atomic-scale structure and dynamics. By having access to the full dynamics from atomistic simulations, they serve as valuable tools…