Related papers: RevelsMD: Reduced Variance Estimators of the Local…
Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions or local transport properties from molecular simulations, we show that the variance can be…
Even though the computation of local properties, such as densities or radial distribution functions, remains one of the most standard goals of molecular simulation, it still largely relies on straighforward histogram-based strategies. Here…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
We introduce rd-spiral, an open-source Python library for simulating 2D reaction-diffusion systems using pseudo-spectral methods. The framework combines FFT-based spatial discretization with adaptive Dormand-Prince time integration,…
relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…
Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such data benefits from estimating the minimal…
RadVel is an open source Python package for modeling Keplerian orbits in radial velocity (RV) time series. RadVel provides a convenient framework to fit RVs using maximum a posteriori optimization and to compute robust confidence intervals…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language…
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…
The interstellar medium (ISM) exhibits complex, multi-scale structures that are challenging to study due to their projection into two-dimensional (2D) column density maps. We present the Volume Density Mapper, a novel algorithm based on…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
The extraction of inhomogeneous 3-dimensional densities around tagged solutes from molecular simulations is known to have a very high computational cost because this is traditionally performed by collecting histograms, with each discrete…
Subatomic particle track reconstruction (tracking) is a vital task in High-Energy Physics experiments. Tracking is exceptionally computationally challenging and fielded solutions, relying on traditional algorithms, do not scale linearly.…
Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web…
Microfluidic devices are increasingly used in biological and chemical experiments due to their cost-effectiveness for rheological estimation in fluids. However, these devices often face challenges in terms of accuracy, size, and cost. This…
We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…
Dynamic mode decomposition (DMD) is a recently developed tool for the analysis of the behavior of complex dynamical systems. In this paper, we will propose an extension of DMD that exploits low-rank tensor decompositions of potentially…