Related papers: Extension of the simulation code ACAT to treat rea…
Molecular dynamics (MD) simulation with modified Brenner's reactive empirical bond order (REBO) potential is a powerful tool to investigate plasma wall interaction on divertor plates in a nuclear fusion device. However, MD simulation box's…
This work describes extensions to existing level-set algorithms developed for application within the field of Atom Probe Tomography (APT). We present a new simulation tool for the simulation of 3D tomographic volumes, using advanced level…
AMDAT (Amorphous Molecular Dynamics Analysis Toolkit) is an open-source C++ toolkit for post-processing molecular dynamics trajectories, focused on high-performance static and dynamic analyses of amorphous, glassy, and polymer materials,…
The applications of machine learning techniques to chemistry and materials science become more numerous by the day. The main challenge is to devise representations of atomic systems that are at the same time complete and concise, so as to…
We present a coupled atomistic-continuum method for the modeling of defects and interface dynamics of crystalline materials. The method uses atomistic models such as molecular dynamics near defects and interfaces, and continuum models away…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
A new algorithm for calculating intermolecular pair forces in Molecular Dynamics (MD) simulations on a distributed parallel computer is presented. The Arbitrary Interacting Cells Algorithm (AICA) is designed to operate on geometrical…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
It is shown that the atom-molecule collision problem in the presence of an external electric field can be solved using the total angular momentum representation in the body-fixed coordinated frame, leading to a computationally efficient…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…
Particle-in-cell methods with stochastic collision models are commonly used to simulate collisional plasma dynamics, with applications ranging from hypersonic flight to semiconductor manufacturing. Code verification of such methods is…
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…
MOLSCAT is a general-purpose program for quantum-mechanical calculations on nonreactive atom-atom, atom-molecule and molecule-molecule collisions. It constructs the coupled-channel equations of atomic and molecular scattering theory, and…
Adaptive precision molecular dynamics simulations have developed along energy- and force-coupling approaches, which allow for a continuous transition between different particle descriptions or interaction potentials. Most approaches…
In studying solidification process by simulations on the atomic scale, the modeling of crystal nucleation or amorphisation requires the construction of interatomic interactions that are able to reproduce the properties of both the solid and…
The Accurate Particle Tracer (APT) code is designed for large-scale particle simulations on dynamical systems. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are…
Molecular dynamics simulations demand an unprecedented combination of accuracy and scalability to tackle grand challenges in catalysis and materials design. To bridge this gap, we present AlphaNet, a local-frame-based equivariant model that…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…