Related papers: Long-range interactions & parallel scalability in …
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
Current supercomputers often have a heterogeneous architecture using both CPUs and GPUs. At the same time, numerical simulation tasks frequently involve multiphysics scenarios whose components run on different hardware due to multiple…
We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU…
All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…
Quasi-2D Coulomb systems are of fundamental importance and have attracted much attention in many areas nowadays. Their reduced symmetry gives rise to interesting collective behaviors, but also brings great challenges for particle-based…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
We present implementations of a fourth-order symplectic integrator on graphic processing units for three $N$-body models with long-range interactions of general interest: the Hamiltonian Mean Field, Ring and two-dimensional self-gravitating…
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…
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…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
We present an algorithm for cluster dynamics to efficiently simulate large systems on MIMD parallel computers with large numbers of processors. The method divides physical space into rectangular cells which are assigned to processors and…
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…
The human neuromuscular system consisting of skeletal muscles and neural circuits is a complex system that is not yet fully understood. Surface electromyography (EMG) can be used to study muscle behavior from the outside. Computer…
The TREE method has been widely used for long-range interaction {\it N}-body problems. We have developed a parallel TREE code for two-component classical plasmas with open boundary conditions and highly non-uniform charge distributions. The…
We present Particle-Particle-Particle-Mesh (PPPM) and Tree Particle-Mesh (TreePM) implementations on GRAPE-5 and GRAPE-6A systems, special-purpose hardware accelerators for gravitational many-body simulations. In our PPPM and TreePM…
In this work, we develop a two-component coarse-grained molecular dynamics (CGMD) model for simulating the erythrocyte membrane. This proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton,…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
I describe here the performances of a parallel treecode with individual particle timesteps. The code is based on the Barnes-Hut algorithm and runs cosmological N-body simulations on parallel machines with a distributed memory architecture…