Related papers: MDcraft -- a modern molecular dynamics simulation …
While discrete-event simulators are essential tools for architecture research, design, and development, their practicality is limited by an extremely long time-to-solution for realistic applications under investigation. This work describes…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Molecular dynamics (MD) simulations allow the exploration of the phase space of biopolymers through the integration of equations of motion of their constituent atoms. The analysis of MD trajectories often relies on the choice of collective…
WavePacket is an open-source program package for numeric simulations in quantum dynamics. It can solve time-independent or time-dependent linear Schr\"odinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
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…
Particle tracking in large-scale numerical simulations of turbulent flows presents one of the major bottlenecks in parallel performance and scaling efficiency. Here, we describe a particle tracking algorithm for large-scale parallel…
Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…
Computational quantum chemistry plays a critical role in drug discovery, chemical synthesis, and materials science. While first-principles methods, such as density functional theory (DFT), provide high accuracy in modeling electronic…
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…
Optimizing high-performance power electronic equipment, such as power converters, requires multiscale simulations that incorporate the physics of power semiconductor devices and the dynamics of other circuit components, especially in…
The MeMC is an open-source software package for monte-carlo simulation of elastic shells. It is designed as a tool to interpret the force-distance data generated by indentation of biological nano-vesicles by atomic force microscopes. The…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
Molecular dynamics (MD) simulations provide detailed insight into atomic-scale mechanisms but are inherently restricted to small spatio-temporal scales. Coarse-grained molecular dynamics (CGMD) techniques allow simulations of much larger…
We present MXtalTools, a flexible Python package for the data-driven modelling of molecular crystals, facilitating machine learning studies of the molecular solid state. MXtalTools comprises several classes of utilities: (1) synthesis,…
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…
Continuous dynamical systems, characterized by differential equations, are ubiquitously used to model several important problems: plasma dynamics, flow through porous media, weather forecasting, and epidemic dynamics. Recently, a wide range…
Conventional molecular dynamics (MD) simulations struggle when simulating particles with steeply varying interaction potentials, due to the need to use a very short time step. Here, we demonstrate that an event-driven Monte Carlo (EDMC)…
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…