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The Probe-Particle Model combine theories designed for the simulation of scanning probe microscopy experiments, employing non-reactive, flexible tip apices to achieve sub-molecular resolution. In the article we present the latest version of…

Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…

This paper describes a deep-SDM framework, MALPOLON. Written in Python and built upon the PyTorch library, this framework aims to facilitate training and inferences of deep species distribution models (deep-SDM) and sharing for users with…

Differential privacy (DP) is the state-of-the-art framework for guaranteeing privacy for individuals when releasing aggregated statistics or building statistical/machine learning models from data. We develop the open-source R package DPpack…

Phase diagrams (PDs) illustrate the relative stability of competing phases under varying conditions, serving as critical tools for synthesizing complex materials. Reliable phase diagrams rely on precise free energy calculations, which are…

Differentiable programming is the combination of classical neural networks modules with algorithmic ones in an end-to-end differentiable model. These new models, that use automatic differentiation to calculate gradients, have new learning…

We present a Python package called Modular Petri Net Assembly Toolkit (MPAT) that empowers users to easily create large-scale, modular Petri Nets for various spatial configurations, including extensive spatial grids or those derived from…

Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be…

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,…

The contribution of nuclear quantum effects (NQEs) to the properties of various hydrogen-bound systems, including biomolecules, is increasingly recognized. Despite the development of many acceleration techniques, the computational overhead…

Machine learning (ML) and artificial intelligence (AI) have the remarkable ability to classify, recognize, and characterize complex patterns and trends in large data sets. Here, we adopt a subclass of machine learning methods viz., deep…

In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…

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…

Multiscale dynamical systems, modeled by high-dimensional stiff ordinary differential equations (ODEs) with wide-ranging characteristic timescales, arise across diverse fields of science and engineering, but their numerical solvers often…

WavePacket is an open-source program package for numeric simulations in quantum dynamics. It can solve time-independent or time-dependent linear Schr\"odinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled…

Deep learning (DL) is one of the fastest growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and…

The MIRS software for the modeling of ro-vibrational spectra of polyatomic molecules was considerably extended and improved. The original version (Nikitin, et al. JQSRT, 2003, pp. 239--249) was especially designed for separate or…

Universal machine-learning interatomic potentials (uMLIPs) enable reactive molecular simulations with near-DFT accuracy, yet applying them efficiently to large, realistic condensed-phase systems remains computationally demanding. Here we…

Machine learning potential-driven molecular dynamics (MD) simulations have significantly enhanced the predictive accuracy of thermal transport properties across diverse materials. However, extracting phonon-mode-resolved insights from these…

Denoising Diffusion Probabilistic Models (DDPMs) are a very popular class of deep generative model that have been successfully applied to a diverse range of problems including image and video generation, protein and material synthesis,…