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

机译：使用AcCoRD模拟：通过反应扩散的基于行为者的交流

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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/adamjgnoeI/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. Videos in the supplementary materials 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.
机译：本文介绍了AcCoRD（通过反应扩散的基于角色的通信）版本1.0。 AcCoRD是专为研究分子通讯系统而设计的沙箱反应扩散求解器。它使用了微观和介观仿真模型的混合体，可以通过用户控制局部精度来实现可扩展性。 AcCoRD是用C语言开发的一种开放源代码命令行工具，并包含用于处理MATLAB中模拟输出的实用程序。最新的代码和指向用户文档的链接可以在https://github.com/adamjgnoeI/AcCoRD/中找到。本文概述了AcCoRD的设计，包括开发专门的反应扩散求解器的动机。详细介绍了相应的算法，包括微观和介观模型的计算复杂性。其他新颖的推导包括不同大小的相邻介观子体积之间的过渡速率。仿真结果表明，AcCoRD既可以用作精确的反应扩散求解器，又可以用于分子通讯系统的分析。补充材料中的视频演示了许多模拟场景。从模拟结果中获得的其他见解包括：选择合适的混合模型参数，混合界面附近的反应性表面的影响以及假定无界所需的有界环境的大小。 AcCoRD的开发仍在进行中，因此也讨论了其未来的发展方向，以突出改进其潜在应用领域的改进。在撰写本文时，正在计划的新功能包括流体模型和更复杂的角色行为。

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