Simulating an in vitro experiment on nanoscale communications by using BiNS2

Abstract Nanoscale communications is an emergent research topic with potential applications in many fields. In order to design nanomachines able to exploit the communication potentials of nanoscale environments, it is necessary to identify the basic communication mechanisms and the relevant parameters. In this paper, we show how system parameters can be derived by suitably matching the results of in vitro experiments with those obtained via simulations by using the BiNS2 simulator. In order to scale the simulation from micrometric settings, with timescale in the order of seconds, to real experiments lasting tens of minutes with millimetric size, we enhanced the BiNS2 simulator by introducing a space partition algorithm based on the octree. In this way, the simulator can exploit the high level of parallelism of modern multicore computer architectures. We have used this technique for simulating an experiment focused on the communication between platelets and endothelium through the diffusion of nanoparticles. Simulation results match experimental data, thus allowing us to infer useful information on the receiver operation.