Related papers: PyStructureFactor: A Python code for the molecular…
We describe our contribution as industrial stakeholders to the existing open-source GPU4PySCF project (https: //github.com/pyscf/gpu4pyscf), a GPU-accelerated Python quantum chemistry package. We have integrated GPU acceleration into other…
Many tools and techniques measure local structure in materials in contexts ranging from biology to geology. We provide a survey of those tools and metrics that are especially useful for analyzing particulate soft matter. The metrics we…
Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the "twilight-zone" of sequence…
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are…
We present the python package DiPolMol-Py, which can be used to calculate the rotational and hyperfine structure of $^2\Sigma$ molecules. The calculations can be performed in the presence of dc magnetic fields, dc electric fields and far…
Focused optical fields are key to a multitude of applications involving light-matter interactions, such as optical microscopy, single-molecule spectroscopy, optical tweezers, lithography, or quantum coherent control. A detailed vectorial…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the…
We present PyMoosh, a Python-based simulation library designed to provide a comprehensive set of numerical tools allowing to compute essentially all optical characteristics of multilayered structures, ranging from reflectance and…
An efficient numerical algorithm for the laser driven multi-level ionization of high-atomic-number gases is proposed and implemented in an electromagnetic particle-in-cell code SPACE. The algorithm is based on analytical solutions to the…
A finite element solution of an ion channel dielectric continuum model such as Poisson-Boltzmann equation (PBE) and a system of Poisson-Nernst-Planck equations (PNP) requires tetrahedral meshes for an ion channel protein region, a membrane…
The prediction of material structure from chemical composition has been a long-standing challenge in natural science. Although there have been various methodological developments and successes with computer simulations, the prediction of…
This thesis details a Python-based software designed to calculate the Jones polynomial, a vital mathematical tool from Knot Theory used for characterizing the topological and geometrical complexity of curves in \( \mathbb{R}^3 \), which is…
Factor Engine is a high-performance, open-source Python library designed for the systematic computation and analysis of financial factors. Built around a modular and extensible API that leverages Python decorators, Factor Engine enables…
A large proportion of organic molecules relevant to medicine and biotechnology contain one or more ionizable groups, which means that fundamental physical and chemical properties (e.g. the charge of the molecule) depend on the pH of the…
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…
We introduce a Python framework designed to automate the most common tasks associated with the extraction and upscaling of the statistics of single-impact crater functions to inform coefficients of continuum equations describing surface…
Python has become the de-facto language for training deep neural networks, coupling a large suite of scientific computing libraries with efficient libraries for tensor computation such as PyTorch or TensorFlow. However, when models are used…
Scintillating molecular crystals have emerged as prime candidates for directional dark matter detector targets. This anisotropy makes them exquisitely sensitive due to the daily modulation induced by the directional dark matter wind.…
We present PyFCG, an open source software library that ports Fluid Construction Grammar (FCG) to the Python programming language. PyFCG enables its users to seamlessly integrate FCG functionality into Python programs, and to use FCG in…