This material is based upon work supported by the National Science Foundation under Grant No. 1110947.

Disclaimer: Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

MoNaCo: Molecular
Nano-Communication Networks

Project Description

Nanomachines, Nanonetworks and Their Applications

In 1959, the Nobel laureate physicist Richard Feynman, in his famous speech entitled “There is Plenty of Room at the Bottom”, described for the first time how the manipulation of individual atoms and molecules would give rise to more functional and powerful man-made devices. More than half a century later, nanotechnology is providing a new set of tools to the engineering community to control entities at the atomic and molecular scales. Foremost amongst these new capabilities are nanomachines, integrated functional devices consisting of nanoscale components. Nanomachines used in applications today typically operate independently and accomplish tasks ranging from computing and data storing to sensing and actuation.

Enabling nanomachines to communicate with each other and hence form nanonetworks will considerably expand the types of applications they can be used in. Because of this, there is the need to define the way in which a single nanomachine communicates with other nanomachines based on their physical and practical limitations. In addition, the interconnection of nanomachines with the micro-world will require the development of nano-micro interfaces. Moreover, the communication among thousands or even millions of distributed nanomachines demands for novel cost-effective hardware and software solutions. Classical communication paradigms need to undergo a profound rethinking and redesign in order to meet the requirements (e.g., size, power consumption, etc.) of these new nanonetworks' applications. Existing networking architectures and communication protocols/software have to be completely rethought in light of these new communication paradigms.

While there is a large number of applications that nanonetworks could apply to, we briefly present three categories of applications below that are capture the significance of nanonetworks:

  • Biomedical applications The nanoscale is the natural domain of molecules, proteins, DNA, organelles and the major components of cells. As a result, a large number of applications of nanonetworks is in the biomedical field. Nanomachines can be deployed over (e.g., tattoo-like) or inside the human body (e.g., a pill or intramuscular injection) to monitor glucose, sodium, and cholesterol, to detect the presence of different infectious agents, or to identify specific types of cancer. Nanonetworks will also enable new smart drug delivery systems which combine the sensing capabilities of nanomachines with the abilities of nano-actuators to release specific drugs inside the body with great accuracy and in a timely manner.
  • Industrial applications The tools provided by nanotechnologies can be used to monitor and control the formation of biofilms in several industrial applications. A biofilm is an aggregate of nano and micro-organisms in which cells adhere to each other and usually onto a surface. Biofilms can have both beneficial and detrimental effects, depending on the application. For example, they can be used to clean residual waters coming from different manufacturing processes or organic waste. However, they can also be the tool for infectious diseases to spread through pipes and other liquid conducting mechanisms. In our vision, nanonetworks can be used to first detect the formation of biofilms and then to release specific chemical compounds to locally enhance or terminate their formation
  • Security/Safety applications Nanotechnology is enabling the development of biological and chemical nanosensors which have an unprecedented sensing accuracy. Nanonetworks composed by several of these nanosensors will serve as a countermeasure for surveillance against Nuclear, Biological and Chemical attacks at the nanoscale. For example, nanosensors can be used to detect chemical particles faster and in lower concentrations than conventional microsensors. Upon the detection of a toxic chemical compound, several nanomachines will transmit the information related to this event in a multi-hop way to a sink or command center. In addition, it will also be possible for the nanomachines to receive commands from the macroscale in order to, for example, change their behavior.

Several communication paradigms can be considered for use in nanonetworks, but our focus is on using molecular communication. [Back to top]

Molecular Communication and Molecular Nanonetworks

In molecular communication molecules are used to encode, transmit and receive information. There are several different reasons for why using molecular communication is seen as being especially attractive: (i) molecular communication between nanoscale entities occur in nature. Examples include inter-cellular and inter-bacterial communication, and such natural phenomena offer a readymade studying ground both to model nanonetworks and to develop solutions; (ii) nanonetworks can be built upon such naturally occurring phenomena with appropriate instrumentation and hence offer a faster engineering pathway to viable solutions; and (iii) perhaps most importantly, several of the aforementioned applications require bio-compatibility and hence necessitate properties that are readily offered by nanonetworks using molecular communication.

Molecular nanonetworks are directly inspired by communication networks among living entities already present in nature, as explained in the following three examples:

  • Bacteria Communication: when a bacterium wants to transmit a message, it releases information molecules in the medium where the bacteria population lies. These molecules propagate in the medium constrained by the environment boundaries and finally reach another bacterium which senses the informa- tion molecules and receives the message.
  • Calcium Signaling: a sensory cell, a neuron, or a cardiomyocyte releases or adsorbs calcium molecules in response to various stimuli that open/close particular channels on the cell membrane. The molecular information in the variation of calcium ions concentration is propagated inside and outside the cell, causing a variation in the electrical charge of the cell membrane and, subsequently, the transduction of the information into an electrical signal.
  • Pheromone Communication: pheromones are a specific type of molecules released by plants, insects and other animals which trigger specific behaviors among the receptor members of the same species. Pheromones of a particular type are released into the environment and they propagate in the air until they are captured by the receptors of their same type.

The realization of molecular nanonetworks however demands novel engineering solutions, including the identification of existing molecular communication mechanisms, the establishment of the foundations of molecular information theory, or the development of architectures and networking protocols for nanomachines. The objective of this project is to establish the theoretical foundations of molecular nanonetworks and to pave the way for this new networking paradigm.

In this project, we take the position that not only will molecular nanonetworks have great relevance to biological physical systems, but also taking a bio-inspired approach to the design of nanonetworks is an optimal pathway to viable solutions. The outcome of this proposal will set the basis for future research and defines the firsts steps towards real implementable solutions. [Back to top]

Information Theoretical Foundations of Molecular Nanonetworks

From the Information Theoretical Foundation point of view, there are three main functional blocks comprising a molecular nanonetwork, namely, 1) the emission process (the transmitter), 2) the propagation process (the channel), and 3) the reception process (the receiver ). The transmitter generates a signal (transmitted signal) that encodes the information message to be exchanged. The propagation process receives the transmitted signal as input and propagates the information to the receiver. The receiver collects the incoming information from the received signal and recovers the transmitted message.

The scheme of a molecular nanonetwork with two nodes.

In our analysis, we assume that the molecular nanonetwork is deployed in a space filled with a fluid medium, such as the cellular cytoplasm or the air, where molecules can propagate. Information transmission is realized through the emission of molecules in the space. Each block is analytically modeled and investigated in terms of attenuation and delay. In addition, we analyze the noise that affects each block. Finally, we characterize the molecular nanonetwork with two nodes in terms of capacity.

Molecular Nanonetworks are not a simple extension of traditional communication networks at the nanoscale: they promote the definition of a complete new communication paradigm. Nanonetworks require innovative communication solutions according to the characteristics of the network components and the communication processes. Apart from the implicit limitations and challenges posted by physically working in the nanoscale (in terms of device manufacturing, deployment and range of operation, amongst others), the main differences between nano-communication and traditional electromagnetic communication paradigms can be summarized as follows.

Message
In molecular communication, a message is encoded by using internal parameters of the molecules such as the chemical structure, relative positioning of molecular elements, polarization, DNA encoding.
Propagation Speed
In molecular nanonetworks, the molecules have to be physically transported from the transmitter to the receiver either passively by means of diffusion or actively using alternative mechanisms such as molecular motors or bacteria.
Noise
In molecular nanonetworks, two different types of noise can affect the messages: the noise generated from the Brownian motion of the molecules in the environment and the noise generated by the randomness present in the chemical reactions which take place in molecular communication.
Power Consumption
In traditional communication networks, the communication processes consume electrical power that is obtained from batteries or from external sources. In molecular nanonetworks, most of the processes are chemically driven resulting in chemical energy consumtion.
Communication Electromagnetic Molecular
Communication carrier Electromagnetic waves Molecules
Signal type Electromagnetic Chemical
Propagation Speed Light Extremely low
Medium Conditions Affect electromagnetic waves propagation Affect diffusion of molecules
Noise Electromagnetic fields and signals Brownian motion and chemical
Power Consumption Electrical Chemical

We also consider a network composed by more than two nanomachines. The presence of several nanomachines sharing the same medium affects the attenuation, delay and noise present at the emission, propagation and reception of molecular information.

A nanonetwork composed of 5 nodes.

The diffusion-based molecular channel is conceptually a broadcast channel. The molecules released in the medium linger in the channel for a long time. We refer to this property as memory of the molecular channel. Furthermore, the concept of interference in the molecular network is radically different to that in electromagnetic or acoustic networks. As opposed to conventional networks, the interference between the molecular messages exchanged by different nodes occurs in the channel where molecules physically affect one another, not only at the receiver side. Based on this, we envision two types of nanonetworks: 1) a network that delivers information from a set of nodes to the corresponding set of destinations, 2) a collaborative nanonetwork that wishes to achieve a macro-scale goal. We envision that in collaborative nanonetworks, several nodes are organized to iteratively interact with each other in a group and perform a task collectively, that otherwise would not be possible due to the limited capabilities of a single node. The main purpose of cooperation is to orchestrate actuation of all the nodes to perform a macro-scale task as a whole, e.g. getting census, attacking a target or locating resources. [Back to top]

Protocols for Molecular Nanonetworks

Traditional notions for the design of communication protocols cannot be reused in nanonetworks due to their unique characteristics stemming from the diffusion-based propagation of molecules. Hence, a radical departure from conventional protocol design is necessary. In traditional protocol design, the end-systems and the inter- mediate entities are assumed to be able to perform complex tasks, whereas the channel itself is assumed to be simplistic. Nanomachines are simple entities that cannot perform complex tasks that render any traditional proto- col abstractions untenable, but at the same time a new degree of freedom that is available in nanonetworks is that the channel is programmable, and hence active, at the nanoscale. It is this degree of freedom that we exercise in constructing protocol abstractions for nanonetworks. We consider a broad nano-active channel paradigm within which we design and develop the proposed protocol solutions.

We approach the task of developing the paradigm of nano-active channel protocols by breaking down the solution into three distinct components: i) we first explore communication protocol primitives that can be derived from the capabilities and characteristics of the nanomachines; ii) we then identify and develop principles for nanoscale communication that we posit should be used as guiding concepts along with the primitives in designing higher order functionalities; and iii) we design communication protocol abstractions that are composites of the primitives, but whose construction is guided by the aforementioned principles. [Back to top]

Molecular Nanonetwork Simulation Tool

We propose to design, develop and maintain NanoSim, a new open-source simulator for molecular nanonetworks. NanoSim will be used to validate both the models for attenuation, delay, noise and capacity, as well as, the principles, primitives and protocols. Several open-source network simulators exist today, like the NS2, NS3, and Glomosim, but these cannot be used for molecular nanonetworks because:

  • These simulators are build on top of well-defined propagation models for electromagnetic or acoustic com- munication. In diffusion-based molecular nanonetworks, only very simple models are given in closed-form expression and they are only valid under very limiting assumptions.
  • These simulators are developed with the classic network stack in mind and will not work for molecular nanonetworks essentially due to the same reasons why traditional communication protocols do not work for these networks.
The key principle of NanoSim is that every molecule in the system is considered individually. By modeling the movements of a single molecule as well as its interactions with other molecules and the medium, we have a full control of the system, and we are not tight to any specific model. We plan to make the source code of our simulator public, so that other researchers can easily use it and also build upon the features we develop. [Back to top]

Validation Platform: Bacteria Quorum Sensing

Design and implementation of molecular nanonetworks requires a concerted effort ranging from modeling the system to experimentation of simple, tractable molecular cell networks. We are developing an experimental platform for validating our theoretical models using a well described molecular cellular communication system in bacteria called Quorum Sensing (QS). What is learned regarding the limits of molecular signaling in this simple system serve as a proof of concept and can be applied to more complex cellular systems.

Quorum Sensing is an example of communication by which bacteria synchronize gene expression on a population- wide scale. This process involves emission of the molecules into the medium where they accumulate in proportion to the number of cells in the population. As the concentration of the signal increases, binding of this extracellular signal molecule to its cellular receptor triggers regulatory changes within the bacterium that activates the expres- sion of genes encoding factors. These factors are unproductive and thus costly for individuals but beneficial on a macroscale level to the bacterial group. QS systems provide an apt environment that captures all of the elements of molecular communication systems and hence can be used to validate/refine our theoretical developments. In particular, we focus on the Vibrio fischeri (V. fischeri) paradigm, as a model nanonetwork.

We will use an experimental platform composed of a fabrication device in which we will incubate bacteria that are genetically engineered to encode a well described molecular signaling circuit. Specifically, the model organism E. coli will be engineered to encode components of a QS molecular communication network, from the bacterium Vibrio fischeri. This synthetic biology approach will recreate, in E. coli, a complex cellular behavior that can be perturbed and manipulated to understand the networking fundamental variables.

We propose to design, build, and demonstrate an experimental platform for studying molecular communication parameters between genetically engineered bacteria to provide experimental data for the validation of theory and models for molecular nano-communication networks. More specifically, we will engineer a microfluidic platform for stimulating and measuring the response of genetically engineered bacteria to both constant and time varying molecular signaling conditions, tailored for cellular populations at differing length scales. We will measure communication parameters such as delay vs. frequency, amplitude vs. frequency, noise and interference.

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