Related papers: pyMBE: the Python-based Molecule Builder for ESPRe…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the…
Code completion has become an essential tool for daily software development. Existing evaluation benchmarks often employ static methods that do not fully capture the dynamic nature of real-world coding environments and face significant…
Coarse-graining (CG) reduces molecular details to extend the time and length scales of molecular dynamics simulations to microseconds and micrometers. However, the CG approaches have long been limited by the difficulty of constructing both…
In recent years, promising deep learning based interatomic potential energy surface (PES) models have been proposed that can potentially allow us to perform molecular dynamics simulations for large scale systems with quantum accuracy.…
Polymer-Attenuated Coulombic Self-Assembly (PACS) is a flexible experimental approach for generating crystals from simple colloidal building blocks. The central components are charged spherical particles coated with a polymer brush that…
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…
High-quality data is essential for modern machine learning, yet many valuable corpora are sensitive and cannot be freely shared. Synthetic data offers a practical substitute for downstream development, and large language models (LLMs) have…
This article presents an open-source Python package for simulating micro-thermoelectric generators, based on the work by D. Beretta et al. (Sustainable Energy Fuels, 2017). Featuring a user-friendly graphical user interface and robust…
ixpeobssim is a simulation and analysis framework, based on the Python programming language and the associated scientific ecosystem, specifically developed for the Imaging X-ray Polarimetry Explorer (IXPE). Given a source model and the…
Peppytides is a coarse-grained, accurate, physical model of the polypeptide chain. I have shared instructions to make your own polypeptide chain and STL files of Peppytides in MAKE magazine in Jan 2014 issue. However, Peppytides involves a…
GMP-Featurizer is a lightweight, accurate, efficient, and scalable software package for calculating the Gaussian Multipole (GMP) features \cite{GMP} for a variety of atomic systems with elements across the periodic table. Starting from the…
Electroencephalography (EEG)-based Brain-Computer Interfaces (BCIs) have emerged as a transformative technology with applications spanning robotics, virtual reality, medicine, and rehabilitation. However, existing BCI frameworks face…
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using the family of CALVADOS models of biomolecules including…
Process Execution Engines are a vital part of Business Process Management (BPM) and Manufacturing Orchestration Management (MOM), as they allow the business or manufacturing logic (expressed in a graphical notation such as BPMN) to be…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Liquid chromatography-mass spectrometry (LC-MS/MS) data analysis requires adaptable software solutions to meet diverse analytical needs. We present eMZed 3, a modern Python framework for flexible and interactive analysis of LC-MS/MS data.…
ControlBurn is a Python package to construct feature-sparse tree ensembles that support nonlinear feature selection and interpretable machine learning. The algorithms in this package first build large tree ensembles that prioritize basis…
We present ForSE (Foreground Scale Extender), a novel Python package which aims at overcoming the current limitations in the simulation of diffuse Galactic radiation, in the context of Cosmic Microwave Background experiments (CMB). ForSE…
Research into the processes of photoionised nebulae plays a significant part in our understanding of stellar evolution. It is extremely difficult to visually represent or model ionised nebula, requiring astronomers to employ sophisticated…