# OpenRBC: A Fast Simulator of Red Blood Cells at Protein Resolution

## TL;DR

OpenRBC is a highly efficient, parallelized molecular dynamics simulator capable of modeling entire mammalian red blood cells at protein resolution on standard workstations, enabling advanced biomechanical studies.

## Contribution

The paper introduces an adaptive Voronoi-based spatial-searching algorithm and a scalable, high-performance code for simulating large-scale red blood cell models at unprecedented detail.

## Key findings

- Outperforms legacy simulators by nearly tenfold in speed.
- Enables simulation of 4 million particles representing an entire red blood cell.
- Scales efficiently to hundreds of CPU threads.

## Abstract

We present OpenRBC, a coarse-grained molecular dynamics code, which is capable of performing an unprecedented in silico experiment --- simulating an entire mammal red blood cell lipid bilayer and cytoskeleton as modeled by 4 million mesoscopic particles --- using a single shared memory commodity workstation. To achieve this, we invented an adaptive spatial-searching algorithm to accelerate the computation of short-range pairwise interactions in an extremely sparse 3D space. The algorithm is based on a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated over the course of the simulation. The algorithm enables the construction of the key spatial searching data structure in our code, i.e. a lattice-free cell list, with a time and space cost linearly proportional to the number of particles in the system. The position and shape of the cells also adapt automatically to the local density and curvature. The code implements OpenMP parallelization and scales to hundreds of hardware threads. It outperforms a legacy simulator by almost an order of magnitude in time-to-solution and more than 40 times in problem size, thus providing a new platform for probing the biomechanics of red blood cells.