Multi-Hop Conjugation Based Bacteria Nanonetworks

SUMAYYA P A S2.MTECH-CE Roll no:23 1 1

Nanotechnology
Study of the control of matter on an atomic and molecular scale.
Enabling the miniaturization and fabrication

of devices in a scale ranging from one to a few hundreds nanometers

Nanoscale communication
An emerging research paradigm that aims to provide communication capabilities between nanoscale machines (nanomachines).
The first publication at 2005 Nanomachine

The most basic functional unit in nanoscale systems.

Scale: one to a few hundred nanometers. Consists of biological materials (e.g., molecules) and perform very simple computation, sensing and/or actuation tasks. 3

Nanomaterials:
Graphene Carbon Nanotubes (CNT) Graphene Nanoribbons (GNR)

(Source:www.wikipedia.com)

Design of Nano-Machines
Bottom-Up Top-Down Bio-Hybrid
Main Challenge: Main Challenge: Achieve Main Challenge: * Controlling the assembly molecular process and atomic precision * Obtaining complex structures. Examples: Examples: * Photolithography, * Molecular self-assembly * Micro-contact * Molecular recognition.

* Isolation of biological nano-machines * Hybridization.

Examples:
Bacteria transport
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printing.

Design of Nano-machines

Nano-Material based Nano-Machines

Biologically Inspired NanoMachines

Biological nano-machines
CELL The most sophisticated existing nano-machine:
- Efficient energy consumption +

Harvesting Mechanisms
- Multi-task computing + DNA

processing
- Multi-sensing + Actuation
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(Source:Ian F.Akyildiz,2008)

Nanonetworks vs Traditional Communication Networks

Traditional Communication

Molecular Communication
(Source:Ian F.Akyildiz,2008)

NANO-COMMUNICATION PARADIGMS

EM Based Communication for

Nano-Material Based Nano-

Molecular Communication
for Biological Nano-Networks
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Networks

Molecular Communication
Defined as the transmission and reception of information encoded in molecules

A new and interdisciplinary field that spans nano, ece, cs, bio, physics, chemistry, medicine, and information technologies
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Molecular Communication
Molecular Communication

Short Range (nm to m)

Medium Range (m to mm)

Long Range (mm to m)

Wired

Wireless

Wireless

Wired

Wireless

Molecular Motors

Ion Signaling
(e.g., calcium, sodium, potassium, chlorine)

Pheromones
Flagellated Bacteria Catalytic Nanomotors

Axons Capillaries

Light transduction

Pollen/Spores
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Nanonetwork architecture
Flagellated bacteria Pheromones Catalytic nanomotors

Pollen & Spores

Ion Signaling Molecular Motors

(Source:Ian F.Akyildiz,2008)

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Bacteria based nanonetwork

Nodes -DPU(DNA processing unit) -Emits attractantsReception attractant RA & Transmission attractant TA Carrier -flagellated bacteria

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(Source:Ian F.Akyildiz,2008)

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Flagellated Bacteria
Bacteria are microorganisms composed only by one

prokaryotic cell. Flagellum allows them to convert chemical energy into motion. Escherichia coli (E. coli) has between 4 and 10 flagella, which are moved by rotary motors, fuelled by chemical compounds. E. coli bacteria is approximately 2 m long and 1 m in diameter.

(Source:sasitharan balusubrahmanian2013)

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Why Bacterial Communication?

Spans medium range to long range (m to tens of cm) No need of infrastructure
Better than molecular motors

Transfer of huge amount of information

Up to 100Kbyte per bacteria (400K base pairs) using a plasmid.

Basic communication steps

Information is expressed as a set of DNA base pairs, the DNA packet, which is inserted in a plasmid.

Encoding
DNA packet is introduced inside the bacterias cytoplasm, using: Plasmids Bacteriophages Bacterial Artificial Chromosomes (BACs)

Transmission Propagation
Bacteria sense gradients of attractant particles.

Reception

Decoding
DNA packet is extracted from the plasmid using: Restriction endonucleases enzymes
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They move towards the direction and finds more attractants (chemotaxis).
The receiver releases attractants so the bacteria can reach it.

Message Plasmid
Plasmids : circular sequences of DNA Length between 5.000 and 400.000

base pairs First, the plasmid is cleaved in the restriction sites by restriction endonucleases. Second the DNA packet containing the desired information is added and linked to the plasmid by means of DNA ligase. Finally, the plasmid is inserted inside bacterias cytoplasm using transformation or electroporation techniques.
(Source:sasitharan balusubrahmanian2013)
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Encoding
Nodes contain a DNA Processing Unit (DPU), which will be able

to encode an arbitrary strand of DNA

This DNA forms a plasmid it is divided into 3 parts

the transfer region the routing region the message region

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The transfer region: is present in typical plasmids as factor of E. coli and is 33kbp (kilo base pairs) long . This region contains the genes and structures necessary for self-replication and transmission of the plasmid.

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The routing region: contains a set of genes that implement the behavioral differences between empty bacteria, with no data to deliver, and laden bacteria carrying a DNA message. These genes encode new proteins or inhibit genes in the bacterial DNA for Deactivate chemotaxis towards transmitters. Activate chemotaxis towards the receiver. Inhibit bacterial replication . Enable programmed death on timeout
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The message region: contains the destination network address and the message body, which occupies most of the length of the plasmid.

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(Source:sasitharan balusubrahmanian2013)

 The DNA nucleotides -Adenine, Thymine, Cytosine and Guanine (A,

T, C and G) . The information that the emitter nano-machine wants to send is expressed as a set of DNA base pairs - the DNA packet. The short-range packet is composed of different blocks . The wrapper The gateway . The cleaving sequence Receiver nano-machine address block Information. A single-stranded sequence

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PROPAGATION
Conjugation
involves the transfer of a plasmid between donor and recipient bacteria

that are normally in close contact Genetic transfer is operated by a protein complex called type IV secretion systems, which forms the transferosome. the plasmid needs to be prepared by another complex called a relaxosome. The relaxosome makes a cut at a precise position of the plasmid sequence called origin of Transfer the bacterium attracts another bacterium by joining the pili, and the plasmid is passed through the pili connection

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HOW BACTERIA TRANSFER INFORMATION

(Source:sasitharan balusubrahmanian2013)

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ROUTING OF DNA PACKET

Opportunistic Routing
A routing process that is usually applied to wireless networks.
The concept relies on intermediate nodes that have good immediate link

qualities to forward packets to a destination node, in the event that the source to destination node link is poor or not within range.
One form of opportunistic routing is based on the concept of Delay

Tolerant Networking (DTN) .

In DTN, mobile nodes opportunistically meet and passmessages to each other,where eventually this message will reach the destination point
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DELAY TOLERANCE NETWORK(DTN)

(Source:sasitharan balusubrahmanian2013)
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Conjugation Based Opportunistic Routing

the combined process of conjugation and

chemotaxis

(Source:sasitharan balusubrahmanian2013)
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 node 1 wants to transmit a message to node 3, by using the relay node

2. The chemoattractant from node 2 will attract bacteria traveling from node 1, while the chemoattractant from node 3 will attract bacteria from node 2. As the two groups of bacteria approach each other, a conjugation process occurs, leading to messages of bacteria from node 1 to conjugate with bacteria from node 2. The message will be transmitted to the destination node 3.

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RECEPTION AND DECODING

Once the plasmid is in the receivers gateway, the DNA packet must be extracted from the plasmid. This is done by restriction endonucleases enzymes that cleave the plasmid inrestriction sites. DNA computers are able to separate different DNA strands by lengths.
This allows the gateway node to recover the DNA packet among the solution containing both the cleaved plasmid and the DNA packet. Then, the gateway is able to process the DNA packet as required.
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MAPPING OF NETWORK PROCESS TO BACTERIA PROCESS

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ADVANTAGES

Less noise
Does not need external source of raw molecules Low message delivery delay

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APPLICATION
Biomedical applications
Industrial applications Security/Safety applications

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CONCLUSION
Here we have described a definition of molecular communication and its characteristics, and have also described initial designs for a molecular communication system that uses bacteria as carrier for performing communication.

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(Source:sasitharan balusubrahmanian2013)

[1] Sasitharan balusubrahmanian, multihop cojugation based nanonetworks Comput. Netw., vol. 52, pp. 22602279, Jun. 2013. [2] I. F. Akylidiz, F. Brunetti, and C. Blazquez, Nanonetworking: A communication paradigm, Comput. Netw., vol. 52, pp. 22602279, Jun. 2008. [3] T. Nakano and J. Q. Liu, Design and analysis of molecular relay channels: An information theoretic approach, IEEE Trans. NanoBiosci., vol. 9, no. 3, pp. 213 221, 2010.

REFERENCE

[4] S. Balasubramaniam, N. T. Boyle, A. Della-Chiesa, F. Walsh, A. Mardinoglu, and D. B. A. Prina-Mello, Development of artificial neuronal networks for molecular communication, Nano Commun. Netw., vol. 2, no. 23, Jun./Sep. 2011.
[5] L. C. Cobo-Rus and I. F. Akyildiz, Bacteria-based communication in nanonetworks, Nano Commun. Netw., vol. 1, no. 4, pp. 244256, Dec. 2010. [6] P. Lio and S. Balasubramaniam, Opportunistic routing through conjugation in bacteria communication nanonetwork, Nano Commun. Netw., vol. 3, no. 1, pp. 37 3645, 2012.

Thank you..
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