Related papers: Tinker-HP : Accelerating Molecular Dynamics Simula…

Real-time simulation of a large-scale biologically representative spiking neural network is presented, through the use of a heterogeneous parallelisation scheme and SpiNNaker neuromorphic hardware. A published cortical microcircuit model is…

To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…

We present Swarm-NG, a C++ library for the efficient direct integration of many n-body systems using highly-parallel Graphics Processing Unit (GPU), such as NVIDIA's Tesla T10 and M2070 GPUs. While previous studies have demonstrated the…

Particle-in-Cell (PIC) simulations spend most of their execution time on particle--grid interactions, where fine-grained atomic updates become a major bottleneck on traditional many-core CPUs. Recent CPU architectures integrate specialized…

We present novel algorithmic solutions together with implementation details utilizing non-Abelian symmetries in order to boost the current limits of tensor network state algorithms on high performance computing infrastructure. In our…

With the rapidly increasing rate of microlensing planet detections, microlensing modeling software faces significant challenges in computation efficiency. Here, we develop the Twinkle code, an efficient and robust binary-lens modeling…

Accurate simulations of various physical processes on digital computers requires huge computing performance, therefore accelerating these scientific and engineering applications has a great importance. Density of programmable logic devices…

Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering,…

We develop a GPU-accelerated dynamic programming (DP) method for valuing, operating, and bidding energy storage under multistage stochastic electricity prices. Motivated by computational limitations in existing models, we formulate DP…

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…

We present a novel, GPU-optimized algorithm for particle-mesh interactions in grid-based hydrodynamics simulations, designed for massively parallel architectures. This approach overcomes the inefficiency of particle neighbour searches or…

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…

The parallel simulation of Spiking Neural P systems is mainly based on a matrix representation, where the graph inherent to the neural model is encoded in an adjacency matrix. The simulation algorithm is based on a matrix-vector…

We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…

Dynamic programming (DP) based algorithms are essential yet compute-intensive parts of numerous bioinformatics pipelines, which typically involve populating a 2-D scoring matrix based on a recursive formula, optionally followed by a…

The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…

We propose a new hybrid topology optimization algorithm based on multigrid approach that combines the parallelization strategy of CPU using OpenMP and heavily multithreading capabilities of modern Graphics Processing Units (GPU). In…

The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…

Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a…

Microstructures forming during ternary eutectic directional solidification processes have significant influence on the macroscopic mechanical properties of metal alloys. For a realistic simulation, we use the well established…