Related papers: ESPResSo 4.0 -- An Extensible Software Package for…
This paper presents SPIROS (Streamlined, Precise, Intuitive, and Rapid Optical Simulator), a dedicated optical simulation tool developed for the design and analysis of particle physics detectors. Unlike general-purpose frameworks such as…
Context: Experiment replications play a central role in the scientific method. Although software engineering experimentation has matured a great deal, the number of experiment replications is still relatively small. Software engineering…
ePSproc provides codes for post-processing results from ePolyScat (ePS), a suite of codes for the calculation of quantum scattering problems, developed and released by Luchesse \& co-workers (Gianturco et al. 1994)(Natalense and Lucchese…
Runko is a new open-source plasma simulation framework implemented in C++ and Python. It is designed to function as an easy-to-extend general toolbox for simulating astrophysical plasmas with different theoretical and numerical models.…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…
Designing scientific instrumentation often requires exploring large, highly constrained design spaces using computationally expensive physics simulations. These simulators pose substantial challenges for integrating evolutionary computation…
We present an NPT extension of Ewald summation with prolates (ESP), a spectrally accurate and scalable particle-mesh method for molecular dynamics simulations of periodic, charged systems. Building on the recently introduced ESP framework,…
For many macromolecular systems the accurate sampling of the relevant regions on the potential energy surface cannot be obtained by a single, long Molecular Dynamics (MD) trajectory. New approaches are required to promote more efficient…
We provide an introduction to molecular dynamics simulations in the context of the Kob-Andersen model of a glass. We introduce a complete set of tools for doing and analyzing the results of simulations at fixed NVE and NVT. The modular…
Motivation: Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
This dissertation focuses on the development process of scientific software. It presents a methodology that has emerged over time during development of Monte Carlo tools for high energy physics experiments. A short description of the…
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.…
The need for computational resources grows as computational algorithms gain popularity in different sectors of the scientific community. This search has stimulated the development of several cloud platforms that abstract the complexity of…
Vibrational spectroscopy is an indispensable analytical tool that provides structural fingerprints for molecules, solids, and interfaces thereof. This study introduces THeSeuSS (THz Spectra Simulations Software) - an automated computational…
Traditional force-fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab-initio accuracy at low…
We present SPUX - a modular framework for Bayesian inference enabling uncertainty quantification and propagation in linear and nonlinear, deterministic and stochastic models, and supporting Bayesian model selection. SPUX can be coupled to…
Full dimensional potential energy surfaces (PESs) based on machine learning (ML) techniques provide means for accurate and efficient molecular simulations in the gas- and condensed-phase for various experimental observables ranging from…
ParticLS (\emph{Partic}le \emph{L}evel \emph{S}ets) is a software library that implements the discrete element method (DEM) and meshfree methods. ParticLS tracks the interaction between individual particles whose geometries are defined by…
SALMON (Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids…