bacteria conjugation based communication
TRANSCRIPT
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Multi-Hop Conjugation
Based BacteriaNanonetworks
SUMAS2.MTE
R
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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 afew hundreds nanometers
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Nanoscale communication
An emerging research paradigm that aims to p
communication capabilities between nanoscale ma(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
perform very simple computation, sensing and/or act
tasks.
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Top-Down
Main Challenge: Achieve
molecular
and atomic precision
Examples:
* Photolithography,
* Micro-contact
printing.
Design of Nano-Machines
Bottom-Up
Main Challenge:
* Controlling the assembly
process
* Obtaining complexstructures.
Examples:
* Molecular self-assembly
* Molecular recognition.
Bio-Hyb
Main Challeng
* Isolation of
biological
nano-machines
* Hybridization
Examples:
Bacteria transpor
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Design of Nano-machines
Nano-Material based
Nano-MachinesBiologically Inspired
Machines
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Biological nano-machines
CELL
The most sophisticated existing
nano-machine:
- Efficient energy consumption +
Harvesting Mechanisms
- Multi-task computing + DNAprocessing
- Multi-sensing + Actuation(Source:Ian F.Akyildiz,2008)
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Nanonetworks vs Traditional Communicat
Networks
Molecular
Communication
Traditional
Communication
(Source:Ian F.Akyildiz,2008)
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Molecular Communication
Defined as the transmission and reception of
information encoded in molecules
A new andinterdisciplinary field
that spans nano, ece, cs,
bio, physics, chemistry,
medicine, and
informationtechnologies
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Molecular Communication
Molecular Communication
Short Range(nm to m)
Wired
MolecularMotors
Wireless
Ion
Signaling
(e.g., calcium,
sodium,potassium,chlorine)
Medium Range(m to mm)
Wireless
Flagellated
Bacteria
Catalytic
Nanomotors
Long Range(mm to m)
Wired
Axons
Capillaries
Wireless
Pheromones
Lighttransduction
Pollen/Spores
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Nanonetwork architecture
Ion Sign
Molecu
Flag
bact
Cata
nano Pheromones
Pollen & Spores
(Source:Ian F.Akyildiz,2008)
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Bacteria based nanonetwork
Nodes-DPU(DNA processing unit)
-Emits attractants-
Reception 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 oneprokaryotic cell.
Flagellum allows them to convert chemical energy intomotion.
Escherichia coli (E. coli) has between 4 and 10 flagella, which
are moved by rotary motors, fuelledby 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.
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Basic communication steps
DNA packet is
introduced inside the
bacterias cytoplasm,
using:
Plasmids
Bacteriophages
Bacterial ArtificialChromosomes(BACs)
Encoding Transmission Propagation Reception Deco
Information is expressed as a set of DNA base pairs, the DNA packet,
inserted in a plasmid.
Bacteria sense gradients ofattractant particles.
They move towards the direction and
finds more attractants (chemotaxis).
The receiver releases attractants so thebacteria can reach it.
DNA packeextracted fr
plasmid usi
Restric
endon
enzym
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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 restrictionendonucleases.
Second the DNA packet containing the
desired information is added andlinked to the plasmid by means ofDNA ligase.
Finally, the plasmid is inserted insidebacterias cytoplasm usingtransformation or electroporation
techniques. (Source:sasitharan balusubrahmanian201
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Encoding
Nodes contain a DNA Processing Unit (DPU), which will be ato 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
33kbp (kilo base pairs) long . This region contains the genes and structures nec
for self-replication and transmission of the plasmid.
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The routing region:
contains a set of genes that implement the behavioral diff
between empty bacteria, with no data to deliver, and laden b
carrying a DNA message.
These genes encode new proteins or inhibit genes in the b
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 theplasmid.
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(Source:sasitharan balusubrahmanian2013)
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The DNA nucleotides -Adenine, Thymine, Cytosine and Guan
T, C and G) .
The information that the emitter nano-machine wants to send i
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
that are normally in close contact
Genetic transfer is operated by a protein complex called tsecretion systems, which forms the transferosome.
the plasmid needs to be prepared by another complex crelaxosome. The relaxosome makes a cut at a precise positionplasmid sequence called origin of Transfer
the bacterium attracts another bacterium by joining the pili, and thplasmid is passed through the pili connection
HOW BACTERIA TRANSFER INFORMATI
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HOW BACTERIA TRANSFER INFORMATI
(Source:sasitharan balusubrahmanian2013)
ROUTING OF DNA PACKET
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ROUTING OF DNA PACKET
A routing process that is usually applied to wireless networks.
The concept relies on intermediate nodes that have good immedqualities to forward packets to a destination node, in the event source to destination node link is poor or not within range.
One form of opportunistic routing is based on the concept oTolerant Networking (DTN) .
In DTN, mobile nodes opportunistically meet and passmesseach other,where eventually this message will reach the destinatio
Opportunistic Routing
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DELAY TOLERANCE NETWORK(DTN)
(Source:sasitharan balusubrahmanian2013)
Conjugation Based Opportunistic Routin
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Conjugation Based Opportunistic Routin
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 rela
2.
The chemoattractant from node 2 will attract bacteria travelingnode 1, while the chemoattractant from node 3 will attract bact
from node 2.
As the two groups of bacteria approach each other, a conjugati
process occurs, leading to messages of bacteria from node 1 toconjugate with bacteria from node 2.
The message will be transmitted to the destination node 3.
RECEPTION AND DECODING
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Once the plasmid is in the receivers gateway, the DNA pack
must be extracted from the plasmid.
This is done by restriction endonucleases enzymes that cleave
plasmid inrestriction sites.
DNA computers are able to separate different DNA strands b
lengths.
This allows the gateway node to recover the DNA packet am
the solution containing both the cleaved plasmid and the
DNA packet. Then, the gateway is able to process the DNA packet as requir
MAPPING OF NETWORK PROCESS TO BACTERIA
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PROCESS
ADVANTAGES
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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
CO C S O
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CONCLUSION
Here we have described a definition of molcommunication and its characteristics, and have
described initial designs for a molecular communi
system that uses bacteria as carrier for perfo
communication.
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(Source:sasitharan balusubrahmanian2013)
REFERENCE
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REFERENCE[1] Sasitharan balusubrahmanian, multihop cojugation based nanonetworks C
Netw., vol. 52, pp. 22602279, Jun. 2013.
[2] I. F. Akylidiz, F. Brunetti, and C. Blazquez, Nanonetworking: A communi
paradigm, Comput. Netw., vol. 52, pp. 22602279, Jun. 2008.
[3] T. Nakano and J. Q. Liu, Design and analysis of molecular relay channels
information theoretic approach, IEEE Trans.NanoBiosci., vol. 9, no. 3, pp
221, 2010.
[4] S. Balasubramaniam, N. T. Boyle, A. Della-Chiesa, F. Walsh, A. Mardinogl
D. B. A. Prina-Mello, Development of artificial neuronal networks for mo
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. 20
[6] P. Lio and S. Balasubramaniam, Opportunistic routing through conjugatiobacteria communication nanonetwork, Nano Commun.Netw., vol. 3, no. 1
3645, 2012.
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Thank you..
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