Related papers: Parallel implementation of three-dimensional molec…
State-of-the-art numerical simulations of laser plasma by means of the Particle-in-Cell method are often extremely computationally intensive. Therefore there is a growing need for development of approaches for efficient utilization of…
We discuss two topics that we have encountered in our lattice-Boltzmann simulations of complex fluids: the sizes of droplets in particle-stabilised emulsions and deformable particles in fluid flow. The common factor in these seemingly…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
This master thesis introduces the idea of dynamic cutoffs in molecular dynamics simulations, based on the distance between particles and the interface, and presents a solution for detecting interfaces in real-time. Our dynamic cutoff method…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
The development and the implementation of a Particle-in-Cell code written in the Unified Parallel C (UPC) language for plasma simulations with application to astrophysics and fusion nuclear energy machines are presented. A simple one…
Optimal multiple sequence alignment by dynamic programming, like many highly dimensional scientific computing problems, has failed to benefit from the improvements in computing performance brought about by multi-processor systems, due to…
Numerical simulations are a prominent tool in laser-plasma experiments. Their role, as a guide in new regime explorations and as a support for understanding laboratory results, is undisputed. But as the experiments themselves are growing in…
We present an efficient parallel algorithm for statistical Molecular Dynamics simulations of ion tracks in solids. The method is based on the Rare Event Enhanced Domain following Molecular Dynamics (REED-MD) algorithm, which has been…
We present an optimized version of a cluster labeling algorithm previously introduced by the authors. This algorithm is well suited for large-scale Monte Carlo simulations of spin models using cluster dynamics on parallel computers with…
We present the basic idea, implementation, measured performance and performance model of FDPS (Framework for developing particle simulators). FDPS is an application-development framework which helps the researchers to develop particle-based…
Theoretical and experimental investigations of water vapor interaction with porous materials are very needful for various fields of science and technology. Not only studies of the interaction of water vapor and porous material as a…
Direct studies of intense laser-solid interactions is still of great challenges, because of the many coupled physical mechanisms, such as direct laser heating, ionization dynamics, collision among charged particles, and electrostatic or…
Due to the high computational cost of 3D particle-in-cell (PIC) simulations, lower-dimensional (2D or 1D) simulations are frequently used in their place. Our work shows that when modeling high-intensity laser ion acceleration, simulation…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Agent-based modelling constitutes a versatile approach to representing and simulating complex systems. Studying large-scale systems is challenging because of the computational time required for the simulation runs: scaling is at least…
This paper is about partitioning in parallel and distributed simulation. That means decomposing the simulation model into a numberof components and to properly allocate them on the execution units. An adaptive solution based on…
The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…