March 28, 2014

Speaker: Peter Colberg, Chemical Physics Theory Group, University of Toronto

Title: Ångström-Scale Chemically-Powered Motors Propelled With OpenCL on GPUs

Abstract: Molecular machines are ubiquitous in nature and play an important role in the biological cell, where they pump ions across membranes or transport cargo through the cell among many other functions. Synthetic chemically-powered motors mimic their biological role models using asymmetric catalytic activity to generate concentration gradients that lead to self-propulsion. Their motion in solution is influenced by thermal fluctuations and long-range hydrodynamic interactions.

We study Ångström-scale chemically-powered motors using full molecular dynamics simulations. Unlike nano-scale micron-size motors, Ångström-scale motors are comparable in size to the surrounding solvent molecules. Using a self-written molecular dynamics code we simulate solvent structure, solvent flow fields and long-time dynamics for a self-propelled sphere-dimer motor.

In this talk I will give an overview of the parallel algorithms used for the simulation, which are simple yet in combination form a powerful program. The computational kernels are written in OpenCL C and, using the same code across all devices, achieve satisfactory run times on multi-core CPUs and excellent run times on AMD and NVIDIA GPUs.