Related papers: Analyzing melts and fluids from ab initio molecula…
RevelsMD is a new open source Python library, which uses reduced variance force sampling based estimators to calculate 3D particle densities and radial distribution functions from molecular dynamics simulations. This short note describes…
An early-stage version of simulation package is developed for electronic structure calculation and dynamics of atom process in large-scale systems, particularly, nm-scale or 10nm-scale systems. We adopted the Extensible Markup Language…
All-atom molecular dynamics (MD) computer simulations are a valuable tool for characterizing the conformational ensembles of intrinsically disordered proteins (IDPs). IDP conformational ensembles are highly heterogeneous and contain…
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…
Metal coordination is ubiquitous in Nature and central in many applications ranging from nanotechnology to catalysis and environmental chemistry. Complex formation results from the subtle interplay between different thermodynamic, kinetic,…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the…
The Python package pylimer-tools is a comprehensive toolkit for computational studies of polymer networks, particularly bead-spring networks. The package provides functionality to generate polymer networks using Monte Carlo (MC) procedures…
We introduce PyMGal, a Python package for generating optical mock observations of galaxies from hydrodynamical simulations. PyMGal reads the properties of stellar particles from these simulations and generates spectral energy distributions…
Determining molecular abundances in astrophysical environments is crucial for interpreting observational data and constraining physical conditions in these regions. Chemical modelling tools are essential for simulating the complex processes…
Materials science is undergoing profound changes due to advances in characterization instrumentation that have resulted in an explosion of data in terms of volume, velocity, variety and complexity. Harnessing these data for scientific…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
Generation and analysis of time-series data is relevant to many quantitative fields ranging from economics to fluid mechanics. In the physical sciences, structures such as metastable and coherent sets, slow relaxation processes, collective…
Background and Objective: Hemodynamic analysis of blood flow through arteries and veins is critical for diagnosing cardiovascular diseases, such as aneurysms and stenoses, and for investigating cardiovascular parameters, such as turbulence…
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is…
For the self-consistent description of various plasma sources operated in the low-pressure (nonlocal, kinetic) regime, the Particle-In-Cell simulation approach, combined with the Monte Carlo treatment of collision processes (PIC/MCC), has…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…