Ongoing Projects

Project accepted. Contract in preparation.

1 June 2017 - 1 June 2019

16 October 2017 - 15 October 2018

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Completed Projects

24 June 2013 - 24 December 2014

Optimization of Communication Parameters in Nanonetworking

(Funded by BAP under project number 7436)

01 October 2012 - 01 April 2015

MoleCom:
Moleculer Communications in Nano-Communication Networks 

(Funded by TUBITAK under 1001 programme)

24 March 2011 - 24 March 2013

MC Approaches

(Funded by BAP under project number 6024) 

Modeling and Experimental Verification of the Diffusion Channel for Nanonetworking


     In the literature, almost all research on nanonetworks has been done based on theoretical models and they all use conjecture of these theoretical models. Without a doubt, these models should be repeated in a practical environment (and corrected if necessary) is crucial for nanonetwork community. Forming a controllable test environment consist of many different parts. Firstly, carrier molecules should be sensed by the test bed. Then, measuring assembly which consist of a micro-manivela (cantilever) will be developed. After that, free diffusion model will be tested physically for different and realistic conditions. The micro-manivela are considered for different applications before however, for the first time in the literature they will be used as a nanonetwork receiver. It is expected that, such a receiver model will be a unique and valuable solution for possible future problems for a very fresh and challenging topic like nanonetworks.


Project scope also consists of developing a rectangular shaped microfluidic channel which uses nanobeads. Microfluidic channels are used in different applications however, using them on nanonetworks is something that has not been done in the literature. Moreover, Hall and GMR receivers are going to integrated with the channel. Since biomolecules and magnetic beans are combined with each other, the flow can be produced. With micropumps, the flow can be controlled and biomolecules can be located at a specific location on the channel. Thanks to the these features, many different case can be tested effectively. 


Finally, nanonetwork literature nearly always prefers the most basic theoretical approach when simulating some techniques or conditions. For example, most of the research based on 1-D or 2-D channel assumption. Unfortunately, these simulation tools would not be enough to simulate detailed and sophisticated channel models like in this project. Hence, a GPU based simulator is going to be designed. The simulator is going to use every effect ,which caused by the environment, to model the channel with a high precision. This simulator will be cross checked with the experiments and it will be open-source for the use of nanonetwork community.

MEDUSA
Modelling Diffusion in Vessel-like Environments for Molecular Communication and Healthcare Applications



Despite the existing channel models in the literature, verified by simulations, there is a need for more realistic models and simulators. For example, many previous works on diffusion-based propagation assume infinite boundary conditions, which may not hold for most health applications.

The problem considered in this project proposal is diffusion within vessel-like constrained environments, focusing mainly on communication aspects and medical applications. Diffusion in such environments varies vastly from the existing models for MC. This difference complicates the solution for various medical applications, such as locating the nanomachine/cell that emits the messenger molecules. In addition, from communications point of view, the Inter-symbol interference (ISI) modelling and signal reception change significantly compared to unbounded and symmetric environments. After developing realistic channel models, ISI modelling and the receptor deployment issues are very useful and critical problems to solve.


In this project, we propose to explore the feasibility of MC applications at small-scale from communication and healthcare perspectives. We will develop propagation models for MCvD in vessel-like bounded and realistic environments. Theoretical channel models will be developed and verified, first via simulations, and then via micro-scale testbed measurements. Inter-symbol interference (ISI) mitigation and emitter cell location estimation techniques will be developed - former one is related to communication while the latter item is related to healthcare applications. Moreover, receptor deployment planning techniques will be analyzed to enhance the signaling quality.

On the design of molecular communication networks with high performance

    In this project, we are working on proposing communication methods on different Molecular Nanonetworks . Our ultimate aim is developing these methods and demonstrate their validities both in theory and simulations. We are working on two different networks within the scope of this project. 

The first one is multi-hop networks aimed to convey message from source to sink. In Molecular Communication, as the distance increases from source to sink, the number of received molecules decreases drastically which increases the probability of error. In order to solve this issue, intermediate nodes between transmitter and receiver are required to forward intended symbols. In these networks, self interference needs to be considered in addition to inter symbol interference to achieve better performance. We are working on developing Network coding methods for such networks with arbitrary number of intermediate nodes to increase the performance of these systems.

   
            The second network is multiple access networks that involve one or more hubs and many transmitters that are aimed to convey their messages to these hubs. Such network can be used to collect data from sensors that makes measurement (e.g. for detection of a disease) and sends these measured data to hubs. Then hubs needs collect all these measured data and make a decision or forward it to an upper layer. Due to the diffusive nature of the molecules in the channel, molecules coming from transmitters are hard to distinguish from each other and therefore, decoding of the individual transmitted symbol from each transmitter is a very hard task. Our aim here is developing communication strategies to distinguish individual messages coming from transmitters to hub to make a more robust decision about the measurement.

Optimization of Communication Parameters in Nanonetworking

Improvements in nanotechnology and biotechnology provide promising developments regarding the production of nanoscale machines (nano-machines) that will perform various tasks in the nanoscale. However, since the mentioned devices are small and have limited capability, accomplishing complex tasks with them will only be possible via establishing efficient communication links between them. Due to its bio-inspired approach, molecular communication provides a truly applicable solution and promising prospects for inter-nanomachine communication.

Overall, a molecular communication via diffusion (MCvD) system can be analyzed under five main processes: encoding, sending, propagation, receiving, and decoding. In order to establish communication between the transmitter and receiver nano-machines, the transmitter first encodes the information in a physical property of a molecule. The information carrying molecules are called messenger molecules, and are released into the communication channel after the modulation. These messenger molecules propagate in the environment according to the laws of Brownian motion, which makes their receiver arrivals random. From the molecules that do arrive at the receiver, the receiver tries to estimate the transmitted data.     

   

In this project, the optimum achievable data rate is acknowledged as an important metric of molecular communications. With this in mind, the achievable data rate of an MCvD scenario between two nano-machines in the absence of co-channel interference and noise is analyzed. Since changing the symbol duration and the detection threshold directly affects the transmission success, the data rate maximization is considered with respect to these variables. Furthermore, models for co-channel interference and noise are developed, and their effects on the optimum data rate are investigated. After the first analysis, the effects of co-channel interference, channel noise, and counting noise on the achievable data rate is further analyzed, alongside the methods to combat them.

MoleCom
Molecular Communications in Nano-Communication Networks

In the context of molecular communications, the dynamics of diffusion have to be thoroughly understood, since the messenger molecules sent from one nano-machine to another spread in the medium with diffusion. Moreover, the dynamics of diffusion have to be modeled with nano-communication networks in mind, in order to develop structures consisting of more than one nano-machine and analyze their performance. Such modeling also enables new research mainly on the physical layer. In this project, we have analyzed the properties of the diffusion medium, how it is affected by various types of noise and possible enhancements to overcome noise and interference in the channel.


Specifically, this project covered six main tracks of research.


• Medium noise analysis: The inherent noise in the communication medium was investigated for calcium signaling and molecular degradation. Additionally, analytical derivations on the number of received molecules for the absorbing spherical receiver were completed. • Molecular signal interference analysis: Co-channel interference and inter-symbol interference were investigated for communication via diffusion. A two molecule-based pre-equalization method was proposed for handling inter-symbol interference.


• N-tap filter analysis: Decision Feedback Filter was designed for decoding on the receiver side, which is very energy efficient. Also, a new modulation technique was introduced to overcome inter-symbol interference.


• Pulse shaping: A tunnel based approach was designed with destroyer molecules in order to suppress the heavy tail of the received pulse. Also, the molecular channel characteristics were investigated for spherical receivers with surface receptors.


• Reception enhancement using cell protrusions: The biologically inspired protrusion mechanism was introduced for reception enhancement. The diffusion channel was shown to be a channel with memory and the mutual information was investigated the protrusion case.


• Simulation of molecular communication via diffusion: A high level architecture based distributed simulator was implemented, which enabled the production of fast and robust results. Additionally, a multi-zone simulation environment was designed and tested.

MC Approaches

Ion signaling is used as an intercell communication method in closely packed cells in living tissues using ion waves as the data carriers. At each cell, the ion waves are triggered with secondary messengers moving either through the cells (called Internal Pathway) or diffusing in the environment surrounding the cells (called External Pathway). Though the cell biologists know how ion signaling works, the energy model and channel capacity are not studied. Routing via ion signaling also remains unexplored.

In this project, we analyze the parts of the ion signaling system and develop a channel model for this system. Then, using this channel model and the components of the system, we build an analytical energy model that governs the performance capabilities of an ion signaling system.        

     In a communication via diffusion system, energy is spent for the production of the messenger molecules and their release to the environment. We model the steps of the messenger molecule production and release following the techniques used by eukaryotic cells. In molecular cell biology, this process is known as exocytosis and is mainly composed of four steps as shown in below figure.  

Lastly, we build higher level networking concepts namely, the routing mechanism upon this system for a complete communication system in molecular communication.

Address

Bogazici University
Computer Engineering       
TR-34342 Bebek,
Istanbul - TURKEY

Contact Info

Email: nrg@boun.edu.tr
Phone: +90-212-359 76 11
Fax: +90-212-287 24 61

Links

Dept. of Computer Engineering
Dept. of Electrical and Electronics Eng.
Bogazici University

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