Related papers: ls1 mardyn: The massively parallel molecular dynam…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Developing an efficient code for large, multiscale astrophysical simulations is crucial in preparing the upcoming era of exascale computing. RAMSES is an astrophysical simulation code that employs parallel processing based on the Message…
As the Large Hadron Collider (LHC) continues its upward progression in energy and luminosity towards the planned High-Luminosity LHC (HL-LHC) in 2025, the challenges of the experiments in processing increasingly complex events will also…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
We have developed an application and implemented parallel algorithms in order to provide a computational framework suitable for massively parallel supercomputers to study the unitary dynamics of quantum systems. We use renowned parallel…
The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de/ and contains presently intermolecular force fields for over 150 pure fluids. It was developed and is maintained by the Boltzmann-Zuse Society…
Molecular dynamics models materials by simulating each individual particle's trajectory. Many-body potentials lead to a more accurate trajectory simulation, and are used in materials science and computational chemistry. We present…
Since its inception in 1995, LAMMPS has grown to be a world-class molecular dynamics code, with thousands of users, over one million lines of code, and multi-scale simulation capabilities. We discuss how LAMMPS has adapted to the modern…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
Particle-in-cell methods couple mesh-based methods for the solution of continuum mechanics problems, with the ability to advect and evolve particles. They have a long history and many applications in scientific computing. However, they have…
We present a new approach for the two-temperature molecular dynamics (MD) model for coupled simulations of electronic and phonon heat conduction in nanoscale systems. The proposed method uses a master equation to perform heat conduction of…
We have developed a fully parallel C++/MPI based simulation code for variable-density particle-laden turbulent flows. The fluid is represented through a uniform Eulerian staggered grid, while particles are modeled using a Lagrangian…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
Creating a highly parallel and flexible discrete element software requires an interdisciplinary approach, where expertise from different disciplines is combined. On the one hand domain specialists provide interaction models between…
Simulations of electrochemical double layer capacitors based on porous carbon electrodes, energy storage systems which accumulate and release energy through reversible ion adsorption at electrode/electrolyte interfaces, are often performed…
Quantum Mechanics/Molecular Mechanics (QM/MM) simulations are a popular approach to study various features of large systems. A common application of QM/MM calculations is in the investigation of reaction mechanisms in condensed-phase and…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…