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The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
For many decades, quantum chemical method development has been dominated by algorithms which involve increasingly complex series of tensor contractions over one-electron orbital spaces. Procedures for their derivation and implementation…
Monte Carlo (MC) simulations allowing to describe photons propagation in statistical mixtures represent an interest that goes way beyond the domain of optics, and can cover, e.g., nuclear reactor physics, image analysis or life science just…
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these…
The PySCF package has emerged as a powerful and flexible open-source platform for quantum chemistry simulations. However, the efficiency of electronic structure calculations can vary significantly depending on the choice of computational…
An extensive comparison of the path uncertainty in single particle tracking systems for ion imaging was carried out based on Monte Carlo simulations. The spatial resolution as function of system parameters such as geometry, detector…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
We present PySCo, a fast and user-friendly Python library designed to run cosmological $N$-body simulations across various cosmological models, such as $\Lambda$CDM and $w_0w_a$CDM, and alternative theories of gravity, including $f(R)$,…
Single-molecule sensitive microscopies and spectroscopies are transforming biophysics and materials science laboratories. Techniques such as fluorescence correlation spectroscopy (FCS) and single-molecule sensitive fluorescence resonance…
Background: We describe an informatics framework for researchers and clinical investigators to efficiently perform parameter sensitivity analysis and auto-tuning for algorithms that segment and classify image features in a large dataset of…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
Simulation-guided design represents a fundamental contribution towards the development of modern semiconductor devices aiming to reach high-performance particle detection, identification and tracking, and constitutes a strategic element of…
Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the…
Super-resolution microscopy is rapidly gaining importance as an analytical tool in the life sciences. A compelling feature is the ability to label biological units of interest with fluorescent markers in living cells and to observe them…
Fast 3D super-resolution imaging is essential for decoding rapidly occurring biological processes. Encoding single molecules to their respective planes enable simultaneous multi-plane super-resolution volume imaging. This saves the…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
We present a detailed strong and weak scaling analysis of PICCANTE, an open source, massively parallel, fully-relativistic Particle-In-Cell (PIC) code. PIC codes are widely used in plasma physics and astrophysics to study the cases where…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
High-Content Digital Microscopy enhances user comfort, data storage and analysis throughput, paving the way to new researches and medical diagnostics. A digital microscopy platform aims at capturing an image of a cover slip, at storing…
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…