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Polarized Resonant Soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and…
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…
The Python package fluidfft provides a common Python API for performing Fast Fourier Transforms (FFT) in sequential, in parallel and on GPU with different FFT libraries (FFTW, P3DFFT, PFFT, cuFFT). fluidfft is a comprehensive FFT framework…
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these…
The Active Matter Evaluation Package (AMEP) is a Python library for analyzing simulation data of particle-based and continuum simulations. It provides a powerful and simple interface for handling large data sets and for calculating and…
Exascale computing delivers the raw power to simulate ever larger and more chemically realistic systems, but realizing this potential requires codes that can efficiently use thousands of processors. Our real-space multigrid (RMG) density…
This article presents a high-throughput computer program, called EasyDD, for batch processing, analyzing and visualizing of spectral data; particularly those related to the new generation of synchrotron detectors and X-ray powder…
We present a standalone implementation of a data-deconvolution method based on singular value decomposition. The tool is written in python and packaged in the open-source yonder package. yonder receives as input two matrices, one for the…
Diffusion models have recently achieved remarkable performance in image super-resolution (SR), but their high computational cost limits practical deployment in remote sensing applications. To address this issue, we propose SlimDiffSR, a…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
Current Flash X-ray single-particle diffraction Imaging (FXI) experiments, which operate on modern X-ray Free Electron Lasers (XFELs), can record millions of interpretable diffraction patterns from individual biomolecules per day. Due to…
The exotic internal structure of polar topologies in multi-ferroic materials offers a rich landscape for materials science research. As the spatial scale of these entities are often sub-atomic in nature, aberration corrected transmission…
We use the PyNeb 1.1.16 Python package to evaluate the atomic datasets available for the spectral modeling of [Fe II] and [Fe III], which list level energies, A-values, and effective collision strengths. Most datasets are reconstructed from…
Distribution of fluorescence resonance energy transfer (FRET) efficiency between the two ends of a Lennard-Jones polymer chain both at equilibrium and during folding and unfolding has been calculated, for the first time, by Brownian…
The Rutherford Backscattering Spectroscopy (RBS) and Particle Induced X-ray Emission (PIXE) techniques can be used to obtain complementary information about the characteristics of a sample but, traditionally, a gap has separated the…
Structural Equation Modeling (SEM) is an umbrella term that includes numerous multivariate statistical techniques that are employed throughout a plethora of research areas, ranging from social to natural sciences. Until recently, SEM…
An improved analysis for single particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the AMO instrument at the Linac Coherent Light Source (LCLS) as…
Fluorescence microscopy is essential in biological and medical research, providing critical insights into cellular structures. However, limited by optical diffraction and background noise, a substantial amount of hidden information is still…
In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…
We introduce the STAR-MELT Python package that we developed to facilitate the analysis of time-resolved emission line spectroscopy of young stellar objects. STAR-MELT automatically extracts, identifies and fits emission lines. We summarise…