HLA based architecture for molecular communication simulation Ali Akkaya ⇑ , Gaye Genc, Tuna Tugcu Computer Networks Research Laboratory-NETLAB, Department of Computer Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey article info Article history: Available online 10 January 2014 Keywords: Molecular communication Distributed simulation HLA abstract In parallel to the developments in nano-scale machines and engineered cells, communica- tion among them is getting more attention. The use of molecules to transfer information from one nanomachine to another is one of the mechanisms to build networks at the nano-scale. The research activities on communication models and performance evaluation of molecular communication heavily depend on simulations to verify the proposed models. The existing simulation tools for computer networking can not be directly used for molec- ular communication due to different communication model and channel characteristics of the fluid environment and the carrier wave properties. Simulation of molecular communi- cation requires modeling the new communication paradigm that comprises different options for encoding, transmission, propagation, reception, and decoding. It should con- sider possible architectural design options and performance evaluation of molecular com- munication networks. Since molecular communication involves the modeling of large number of nano-scale objects, the scalability of the simulation tool is another important concern. In this paper, we introduce a simulator design that aims at fulfilling important design issues of the molecular communication model, focusing on scalability. High Level Architecture (HLA), which is standardized under IEEE 1516, is used to design and develop a distributed simulation tool for molecular communication. The results show that different scalability options can be used to benefit from additional processing power to shorten the execution time. This also enables modeling large systems, which may not be possible otherwise. Ó 2013 Elsevier B.V. All rights reserved. 1. Introduction The design of nano-scale machines and engineered cells established a new research area, focusing on the communication needs of these devices. The research on the communication of nano-scale machines has new types of motivations such as the use of molecules for message encoding as opposed to traditional communication where information is encoded using elec- tromagnetic, acoustic or optical signals, and the use of different forms of chemical energy instead of traditionally used elec- trical energy. It also has new constraints, such as slower propagation speed and additional noise due to chemical reactions [1]. For nanomachines, accomplishing complex tasks will only be possible via efficient communication among themselves and external systems. Molecular communication, which is used by many living organisms, is one of the methods that can be used for inter-nanomachine communication. In molecular communication, molecules are used to transfer information from one nanomachine to another. The information is encoded and transmitted by the transmitter nanomachine as mole- cules, which propagate in the medium and arrive at the receiver nanomachine. Research on channel characteristics, capacity, 1569-190X/$ - see front matter Ó 2013 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.simpat.2013.12.012 ⇑ Corresponding author. Tel.: +90 5439031207. E-mail addresses: ali.akkaya@boun.edu.tr (A. Akkaya), gaye.genc@boun.edu.tr (G. Genc), tugcu@boun.edu.tr (T. Tugcu). Simulation Modelling Practice and Theory 42 (2014) 163–177 Contents lists available at ScienceDirect Simulation Modelling Practice and Theory journal homepage: www.elsevier.com/locate/simpat