Related papers: Analyzing melts and fluids from ab initio molecula…
The package performs molecular-dynamics-like agent-based simulations for models of aligning self-propelled particles in two dimensions such as e.g. the seminal Vicsek model or variants of it. In one class of the covered models, the…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
The interaction of supercritical turbulent flows with granular sediment beds is challenging to study both experimentally and numerically; this challenging task has hampered the advances in understanding antidunes, the most characteristic…
The Python package fluidsim is introduced in this article as an extensible framework for Computational Fluid Mechanics (CFD) solvers. It is developed as a part of FluidDyn project (Augier et al., 2018), an effort to promote open-source and…
We present a user-friendly open-source MATLAB\textsuperscript{\textregistered} package developed by the research group Turbulence, Wind energy and Stochastics (TWiSt) at the Carl von Ossietzky University of Oldenburg. Firstly, this package…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms we show that the interactions between the emerging…
Molecular dynamics simulations are an essential tool in understanding protein structure, dynamics, and function at the atomic level. However, preparing high quality input files for MD simulations can be a time consuming and error prone…
Developing an efficient method to accelerate the speed of molecular dynamics is a central theme in the field of molecular simulation. One category among the methods are collective-variable-based methods, which rely on predefined collective…
Our work is motivated by the analysis of ash plume dynamics, arising in the study of volcanic eruptions. Such phenomena are characterized by large Reynolds number (exceeding $10^7$) and a large number of polydispersed particles~[1]. Thus,…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
\texttt{ml\_edm} is a Python 3 library, designed for early decision making of any learning tasks involving temporal/sequential data. The package is also modular, providing researchers an easy way to implement their own triggering strategy…
In several industrial applications, such as crystallization, pollution control, and flow assurance, an accurate understanding of the aqueous electrolyte solutions is crucial. Electrolyte equilibrium calculation contributes with the design…
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
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…
Software that processes real-world data or that models a physical system must have some way of managing units. While simple approaches like the understood convention that all data are in a unit system (such as the MKS SI unit system) do…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
The emergence of new nanoporous materials, based e.g. on 2D materials, offers new avenues for water filtration and energy. There is accordingly a need to investigate the molecular mechanisms at the root of the advanced performances of these…