Related papers: MATILDA.FT, a Mesoscale Simulation Package for Inh…
Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale…
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for…
Matrix factorization (MF) is employed by many popular algorithms, e.g., collaborative filtering. The emerging GPU technology, with massively multicore and high intra-chip memory bandwidth but limited memory capacity, presents an opportunity…
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…
We compare different Poisson solvers within the context of an electrostatic Vlasov-Poisson system. These schemes are implemented as part of the IPPL (Independent Parallel Particle Layer) library (Frey et al., 2024), which provides…
Parameter estimation via unbinned maximum likelihood fits is a central technique in particle physics. This article introduces MoreFit, which aims to provide a more optimised, rapid and efficient fitting solution for unbinned maximum…
We modified a MPI-friendly density functional theory (DFT) source code within hybrid parallelization including CUDA. Our objective is to find out how simple conversions within the hybrid parallelization with mid-range GPUs affect DFT code…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
We present a novel parallel algorithm for cloth simulation that exploits multiple GPUs for fast computation and the handling of very high resolution meshes. To accelerate implicit integration, we describe new parallel algorithms for sparse…
To achieve high performance on modern computers, it is vital to map algorithmic parallelism to that inherent in the hardware. From an application developer's perspective, it is also important that code can be maintained in a portable manner…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
The Smoothed Particles Hydrodynamics (SPH) is a particle-based, meshfree, Lagrangian method used to simulate multidimensional fluids with arbitrary geometries, most commonly employed in astrophysics, cosmology, and computational…
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…
A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when…
Density functional theory (DFT) has been a cornerstone in computational chemistry, physics, and materials science for decades, benefiting from advancements in computational power and theoretical methods. This paper introduces a novel,…
Discrete cosine transform (DCT) and other Fourier-related transforms have broad applications in scientific computing. However, off-the-shelf high-performance multi-dimensional DCT (MD DCT) libraries are not readily available in parallel…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
A major challenge in light-matter simulations is bridging the disparate time and length scales of electrodynamics and molecular dynamics. Current computational approaches often rely on heuristic approximations of either the electromagnetic…