  This paper presents a software platform, named BiNS2, able to simulate
diffusion-based molecular communications with drift inside blood vessels. The
contribution of the paper is twofold. First a detailed description of the
simulator is given, under the software engineering point of view, by
highlighting the innovations and optimizations introduced. Their introduction
into the previous version of the BiNS simulator was needed to provide to
functions for simulating molecular signaling and communication potentials
inside bounded spaces. The second contribution consists of the analysis,
carried out by using BiNS2, of a specific communication process happening
inside blood vessels, the atherogenesis, which is the initial phase of the
formation of atherosclerotic plaques, due to the abnormal signaling between
platelets and endothelium. From a communication point of view, platelets act as
mobile transmitters, endothelial cells are fixed receivers, sticky to the
vessel walls, and the transmitted signal is made of bursts of molecules emitted
by platelets. The simulator allows evaluating the channel latency and the
footprint on the vessel wall of the transmitted signal as a function of the
transmitter distance from the vessels wall, the signal strength, and the
receiver sensitivity.
