Simulating with AcCoRD: Actor-Based Communication via Reaction-Diffusion

TL;DR

AcCoRD is a versatile, open-source reaction-diffusion simulation tool designed for molecular communication research, combining microscopic and mesoscopic models for scalable and accurate analysis.

Contribution

The paper introduces AcCoRD, a novel hybrid reaction-diffusion simulator with detailed algorithms, open-source implementation, and applications to molecular communication system analysis.

Findings

Effective hybrid microscopic-mesoscopic modeling

Insights into parameter selection for hybrid models

Impact of reactive surfaces and environment size

Abstract

This paper introduces AcCoRD (Actor-based Communication via Reaction-Diffusion) version 1.0. AcCoRD is a sandbox reaction-diffusion solver designed for the study of molecular communication systems. It uses a hybrid of microscopic and mesoscopic simulation models that enables scalability via user control of local accuracy. AcCoRD is developed in C as an open source command line tool and includes utilities to process simulation output in MATLAB. The latest code and links to user documentation can be found at https://github.com/adamjgnoel/AcCoRD/. This paper provides an overview of AcCoRD's design, including the motivation for developing a specialized reaction-diffusion solver. The corresponding algorithms are presented in detail, including the computational complexity of the microscopic and mesoscopic models. Other novel derivations include the transition rates between adjacent mesoscopic subvolumes of different sizes. Simulation results demonstrate the use of AcCoRD as both an accurate reaction-diffusion solver and one that is catered to the analysis of molecular communication systems. A link is included to videos that demonstrate many of the simulated scenarios. Additional insights from the simulation results include the selection of suitable hybrid model parameters, the impact of reactive surfaces that are in the proximity of a hybrid interface, and the size of a bounded environment that is necessary to assume that it is unbounded. The development of AcCoRD is ongoing, so its future direction is also discussed in order to highlight improvements that will expand its potential areas of application. New features that are being planned at the time of writing include a fluid flow model and more complex actor behavior.