Related papers: Molecular dynamics simulations with many-body pote…
Recently, a fully implicit, energy- and charge-conserving particle-in-cell method has been proposed for multi-scale, full-f kinetic simulations [G. Chen, et al., J. Comput. Phys. 230,18 (2011)]. The method employs a Jacobian-free…
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
Cutting-edge embedded system applications, such as self-driving cars and unmanned drone software, are reliant on integrated CPU/GPU platforms for their DNNs-driven workload, such as perception and other highly parallel components. In this…
Three-dimensional neutron transport calculations using the Method of Characteristics (MOC) are highly regarded for their exceptional computational efficiency, precision, and stability. Nevertheless, when dealing with extensive-scale…
Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
For many years, systems running Nvidia-based GPU architectures have dominated the heterogeneous supercomputer landscape. However, recently GPU chipsets manufactured by Intel and AMD have cut into this market and can now be found in some of…
Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2)…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…
One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
Autonomous marine vehicles play an essential role in many ocean science and engineering applications. Planning time and energy optimal paths for these vehicles to navigate in stochastic dynamic ocean environments is essential to reduce…
Mixed-precision algorithms have been proposed as a way for scientific computing to benefit from some of the gains seen for artificial intelligence (AI) on recent high performance computing (HPC) platforms. A few applications dominated by…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Monte Carlo (MC) method has been recognized the most accurate dose calculation method for radiotherapy. However, its extremely long computation time impedes clinical applications. Recently, a lot of efforts have been made to realize fast MC…
The recent trend of using Graphics Processing Units (GPU's) for high performance computations is driven by the high ratio of price performance for these units, complemented by their cost effectiveness. At first glance, computational fluid…
PPMLR-MHD is a new magnetohydrodynamics (MHD) model used to simulate the interactions of the solar wind with the magnetosphere, which has been proved to be the key element of the space weather cause-and-effect chain process from the Sun to…
The recent evolution of software and hardware technologies is leading to a renewed computational interest in Particle-In-Cell (PIC) methods such as the Material Point Method (MPM). Indeed, provided some critical aspects are properly…