Distributed Acceleration of Adhesive Dynamics Simulations.

Abstract

Cell adhesion plays a critical role in processes ranging from leukocyte migration to cancer cell transport during metastasis. Adhesive cell interactions can occur over large distances in microvessel networks with cells traveling over distances much greater than the length scale of their own diameter. Therefore, biologically relevant investigations necessitate efficient modeling of large field-of-view domains, but current models are limited by simulating such geometries at the sub-micron scale required to model adhesive interactions which greatly increases the computational requirements for even small domain sizes. In this study we introduce a hybrid scheme reliant on both on-node and distributed parallelism to accelerate a fully deformable adhesive dynamics cell model. This scheme leads to performant system usage of modern supercomputers which use a many-core per-node architecture. On-node acceleration is augmented by a combination of spatial data structures and algorithmic changes to lessen the need for atomic operations. This deformable adhesive cell model accelerated with hybrid parallelization allows us to bridge the gap between high-resolution cell models which can capture the sub-micron adhesive interactions between the cell and its microenvironment, and large-scale fluid-structure interaction (FSI) models which can track cells over considerable distances. By integrating the sub-micron simulation environment into a distributed FSI simulation we enable the study of previously unfeasible research questions involving numerous adhesive cells in microvessel networks such as cancer cell transport through the microcirculation.