nanoNS3: A network simulator for bacterial nanonetworks based on molecular communication

Abstract

We present nanoNS3, a network simulator for modeling Bacterial Molecular Communication (BMC) networks. nanoNS3 is built atop the Network Simulator 3 (ns-3). nanoNS3 is designed to achieve the following goals: 1) accurately and realistically model the real world BMC, 2) maintain high computational efficiency, 3) allow newly designed protocols to be implemented easily. nanoNS3 incorporates the channel, physical (PHY) and medium access control (MAC) layers of the network stack. The simulator has models that accurately represent receiver response, microfluidic channel loss, transfer rate and error analysis, modulation, and amplitude addressing designed specifically for BMC networks. We outline the design and architecture of nanoNS3, and then validate the aforementioned features through simulation and experimental results.

Porous monolith microfluidics for bacterial cell-to-cell communication assays

“…Previously, we developed a mathematical model for the receivers that predicted the fluorescence output given the AHL input, 15 and in reverse, we were able to determine the AHL input given the fluorescence output. 6 Inputting the fluorescent response of the receivers into the reverse model, we found that the AHL concentration level was approximately 8.5 lM. With the initial Comsol modeling, we predicted that 30% of the AHL would diffuse from transmitters to receivers.…”

“…Beyond elucidating the fundamental mechanisms in these physiological systems, understanding these communication signals could enable us to modulate, regulate, and even accelerate communication for both human health and engineered bacterial biosensors (e.g., Refs. [6][7][8].…”

Effective Geometry Monte Carlo: A Fast and Reliable Simulation Framework for Molecular Communication

“…Many different simulation frameworks for molecular communication have been proposed in the literature, such as N3Sim [18], NanoNS [19], BiNS2 [20], AcCoRD [21] and nanoNS3 [22]. The most commonly used simulation algorithm is the so called Monte Carlo (MC) Algorithm.…”

Design of networks with limited resources

“…However, this situation changes rapidly. Even though results in most works are derived through mathematical analysis, modelling and computer simulation, lately more and more such results are confirmed via wet lab experiments [108,109]. The communication technique we propose in chapter 4 is a response mainly to this technological limitation.…”

“…In that sense, in 2007 the first miniature antenna was built using carbon nanotubes [36]. In 2014, a demonstration of biological communications was performed in a wet lab experiment [38] and more recently simulation, results of the simulation tool nanoNS3 were confirmed in wet lab experiments [108,109].…”