The capabilities of manipulating matter at the molecular scale has inspired a huge research effort for many years and has led to the design and implementation of sophisticated devices, commonly referred to as nanomachines. The potentials of these devices span numerous areas, including medical science, environmental control, and material science.
Although decades of research and implementation activities has lead to remarkable nanomachines capabilities, especially in the medical field, their networked coordination is still at an early stage of research. Recently, some possible solutions for allowing nanomachines to exchange information have been proposed.

A broad classification refers to the communication environment and the relevant transport medium:

• Dry communications, established through a communication medium without a prevalent presence of water, such as carbon nano-tubes. Information can be exchanged through extremely high frequency (terahertz) electromagnetic or ultrasonic waves. 
• Wet communications, which refer to the use of a communications medium consisting of watery solutions or biological environments. Information is transferred by diffusion of particles, typically referred to as carriers, which are emitted and received by cells. This class is also referred to as biological or inter-cell communications. 
• Direct communications, where information transmission happens through a physical contact of nanodevices. This contact may either be mechanically designed and be implemented through mechanical nano-transceivers or happen through a biological cell contact, as it commonly happens in most biological interactions. 

The need of exchanging information at nanoscale requires a deep exploration of the feasible mechanisms that allow designing the basic components of a communications system, such as an information encoder, a transmitter, a communication medium, and a receiver. Due to the heterogeneity of different environments at nanoscale, it is unfeasible to identify general models, valid for most of nano-communication systems. For example, communications within a lymph node, or within blood vessels, or between brain cells, make use of mechanisms specific of each environment, different from each other. Hence, their analysis require different models, strictly related to their environmental features. For this reason, through the combination of interdisciplinary expertise, for each specific environment that could host nanoscale communications, it is necessary to plan and execute suitable experiments for achieving a deep knowledge of it.

The main goal of our research is to identify suitable communication models exploiting interactions between cells in different environments (e.g. blood vessels, lymph nodes), and analyze it by means of the BiNS (Biological Nanoscale Simulator) simulator, a software package we developed to simulate biological nano-scale communications.
The BiNS simulator is highly customizable, giving the possibility to simulate several biological communication scenarios. A standard set of tools is available to create nodes and carriers for the specific communication needs. It is possible to specialize these tools in order to reproduce the behavior of the biological entities chosen as nodes or carriers and, for the same reasons, it is also possible to describe with an high degree of accuracy the properties of the communication channel (e.g. the blood stream, an internal tissue environment, an in vitro experiment).

The aim of this research is essentially medical, and consists of implementing a simulation-based method to gain additional insights in mechanisms governing the development of specific pathologies, such as the atherosclerosis. To this aim, we have also executed a number of biological experiments in collaboration with the Laboratory of Internal and Cardiovascular Medicine of the School of Medicine of the University of Perugia. These experiments were not simply aimed to observe the outcome of the investigated biological mechanisms, which was already known, but rather their dynamic nature. This way, through the knowledge of the transient behavior of the involved biological interactions, we have used these achievements for tuning the models implemented in the BiNS simulator. Clearly, these phases are not strictly sequential, since any achievement can contribute to improve understanding and thus to direct future experimental activities on specific aspects.

The short term objective of developing a reliable in-silico model for communications among cells consists of the possibility of focusing on targeted experiments and reduce the number of experimental animals needed and relevant costs. The effort to develop such models can open interactions among relevant research fields resulting in an improved understanding of the dynamics at the nanoscale in biological environments. In addition, in the mid term, a reliable simulation platform can allows to implement a software tools for personalized forecast about evolution of diseases, starting from a limited number of markers.
Finally, the long term objective of such studies consists of exploiting the acquired knowledge to design and implement nano-sensors/nano-actuators for the prevention and treatment of, e.g., cardiovascular diseases, also through a closed-loop interaction with the outer world.

Current release of BiNS2 simulator