Related papers: GPU-accelerated simulation of colloidal suspension…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
The cryosphere plays a significant role in Earth's climate system. Therefore, an accurate simulation of sea ice is of great importance to improve climate projections. To enable higher resolution simulations, graphics processing units (GPUs)…
The interaction between passive and active/driven particles has introduced a new way to control colloidal suspension properties from particle aggregation to crystallization. Here, we focus on the hydrodynamic interaction between a single…
Graphics research on Smoothed Particle Hydrodynamics (SPH) has produced fantastic visual results that are unique across the board of research communities concerned with SPH simulations. Generally, the SPH formalism serves as a spatial…
In the quest for highest performance in scientific computing, we present a novel framework that relies on high-bandwidth communication between GPUs in a compute cluster. The framework offers linear scaling of performance for explicit…
We present experimental confirmation of dynamic facilitation in monodisperse and bidisperse colloidal suspensions near the glass transition volume fraction. Correlations in particle dynamics are seen to exist not only in space (clusters and…
A new flow solver scalable on multiple Graphics Processing Units (GPUs) for direct numerical simulation of wall-bounded incompressible flow is presented. This solver utilizes a previously reported work (J. Comp. Physics, vol. 352 (2018),…
The motion of suspended colloidal particles generates fluid disturbances in the surrounding medium that create interparticle interactions. While such colloidal hydrodynamic interactions (HIs) have been extensively studied in viscous…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
Using both computational and experimental methods, the capacity of four different surfactant molecules to inhibit the agglomeration of sII hydrate particles was assessed. The computational simulations were carried out using both steered and…
This paper presents a generalised and efficient wall boundary treatment in the smoothed particle hydrodynamics (SPH) method for 3-D complex and arbitrary geometries with single- and multi-phase flows to be executed on graphics processing…
Simulation speed matters for neuroscientific research: this includes not only how quickly the simulated model time of a large-scale spiking neuronal network progresses, but also how long it takes to instantiate the network model in computer…
A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the…
We provide a quantitative description of the evolution of memory from the apparently random Markovian dynamics of a pair of optically trapped colloidal microparticles in water. The particles are trapped in very close proximity of each other…
Adaptive finite elements combined with geometric multigrid solvers are one of the most efficient numerical methods for problems such as the instationary Navier-Stokes equations. Yet despite their efficiency, computations remain expensive…
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…
A fifth-order implicit Runge-Kutta method and two fourth-order exponential integration methods equipped with Krylov subspace approximations were implemented for the GPU and paired with the analytical chemical kinetic Jacobian software…
Smoothed Particle Hydrodynamics (SPH) is essential for modeling complex large-deformation problems across various applications, requiring significant computational power. A major portion of SPH computation time is dedicated to the Nearest…
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…