Related papers: Pythonic Black-box Electronic Structure Tool (PyBE…
Protein structure tokenizers (PSTs) are workhorses in protein language modeling, function prediction, and evolutionary analysis. However, existing PSTs only capture local geometry of static structures, and miss the correlated motions and…
PyPose is an open-source library for robot learning. It combines a learning-based approach with physics-based optimization, which enables seamless end-to-end robot learning. It has been used in many tasks due to its meticulously designed…
We present an introduction to the Quantum Toolbox in Python (QuTiP) in the context of an undergraduate quantum mechanics class and potential senior research projects. QuTiP provides ready-to-use definitions of standard quantum states and…
Probabilistic bits (p-bits) are stochastic hardware elements whose output probability can be tuned by an input bias, offering a route to energy-efficient architectures that exploit, rather than suppress, fluctuations. Here we report p-bit…
pSecDec is a computer tool to evaluate Feynman integrals and their weighted sums (amplitudes) using the method of sector decomposition and numerical integration. The new release of pySecDec version 1.6 comes with a significant performance…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…
In recent years, the concept of kirigami has been used in creating deployable structures for various scientific and technological applications. While high-fidelity Finite Element Analysis (FEA) is the standard for analyzing stress…
In a recent article [1], the FEAST algorithm has been presented as a general purpose eigenvalue solver which is ideally suited for addressing the numerical challenges in electronic structure calculations. Here, FEAST is presented beyond the…
We present PyTorch Connectomics (PyTC), an open-source deep-learning framework for the semantic and instance segmentation of volumetric microscopy images, built upon PyTorch. We demonstrate the effectiveness of PyTC in the field of…
PyPWA is a toolkit designed to optimize parametric models describing data and generate simulated distributions according to a model. Its software has been written within the python ecosystem with the goal of performing Amplitude or Partial…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
Summary: Medical researchers obtain knowledge about the prevention and treatment of disability and disease using physical measurements and image data. To assist in this endeavor, feature extraction packages are available that are designed…
Quantum computing (QC) promises to be a transformative technology with impact on various application domains, such as optimization, cryptography, and material science. However, the technology has a sharp learning curve, and practical…
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…
This study presents a novel optimisation technique for atomic structure calculations using the Flexible Atomic Code, focussing on complex multielectron systems relevant to $r$-process nucleosynthesis and kilonova modelling. We introduce a…
QwaveMPS is an open-source Python library for simulating one-dimensional quantum many-body waveguide systems using matrix product states (MPS). It provides a user-friendly interface for constructing, evolving, and analyzing quantum states…
In this paper, we present an open-source pure-Python library called PyPop7 for black-box optimization (BBO). As population-based methods (e.g., evolutionary algorithms, swarm intelligence, and pattern search) become increasingly popular for…
We present PyRigi, a novel Python package designed to study the rigidity properties of graphs and frameworks. Among many other capabilities, PyRigi can determine whether a graph admits only finitely many ways, up to isometries, of being…
Protein sequence analysis underpins research in biophysics, computational biology, and bioinformatics. We introduce BEER, a crossplatform graphical interface that accepts FASTA or Protein Data Bank (PDB) files, or manual sequence entry, and…
High-energy physics phenomenology often requires linking multiple computational tools to evaluate observables, likelihoods, and experimental constraints across nontrivial parameter spaces. In this work, we introduce Jarvis-HEP, a…