Biochemistry 201 Biological Regulatory Mechanisms January 24, 2013
A Design of a Molecular Communication System Using Biological Communication Mechanisms
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A Design of a Molecular Communication System Using Biological Communication Mechanisms
T. Nakano*, A. Enomoto*, M. Moore*, R. Egashira*, T. Suda*,
K. Oiwa +, Y. Hiraoka +, T. Haraguchi+, R. Nakamori+, T. Koujin+
*University of California, Irvine+National Institute of Information and Communications Technology
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Outline
Nanomachine communicationNanomachinesOur approach
Molecular communicationExample systems
Conclusions
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Nanomachine Communication
GoalAchieve communication between nanomachines
Nanomachine: nano-scale or molecular scale objects that are capable of performing simple tasks
Figure: “Protonic Nanomachin Project”, Prof. Namba at Osaka University: http://www.npn.jst.go.jp/index.html
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Nanomachines Biological nanomachines
Dynein Molecular motors that walk along microtubule in a cell
F1ATPase Synthesizes ATP (energy) by using an influx of protons to rotate
Bacterium Swims toward the chemicals (e.g, food) using flagellum
Figures: Alberts, Molecular Biology of the CellDynein F1ATPase
Bacterium
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Nanomachines
Biological nanomachines logic gates made of biological components (e.g,
enzymes or bacteria) If both substrate and effector exist, product produced If no effector or no substrate, substrate remains unchanged
ANDC
SP
Enzyme
ProductSubstrate
Effector
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Nanomachines
Artificial nanomachinesNickel propeller
Size: 0.75 - 1.5 um
Micron motor Size: 100 um in diameter 10,000 rpm
MEMS/NEMS: http://www.fujita3.iis.u-tokyo.ac.jp/
“Engineering Issues in the fabrication of a hybrid nano-propeller system powered by F1-ATPase”
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Our Approach
Use communication mechanisms that biological systems use Intracellular communication Intercellular communication
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Intracellular Communication
Transport materials using molecular motors within a cell
Vesicles transported by molecular motors
Microtubules
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Cells coordinate through calcium signaling
J. Cell Biol. Jørgensen et al. 139 (2): 497, 1997
0 3 6 9
12 15 24 210
Intercellular communication
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Applications
Pinpoint drug deliveryTo deliver drug to (targeted) cancer cells
Molecular computing Coordination among distributed logical gates
AND
AND
OR
ANDC
SP
Enzyme
ProductSubstrate
Effector
<Bio nano-machine communication>
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Outline
Nanomachine communicationNanomachinesOur approach
Molecular communicationExample systems
Conclusions
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Molecular Communication
Sending and receiving of molecules as an information carrier
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Make nanomachines communicate using communication mechanisms in living organismsSenders/receivers = biological nanomachinesCommunication carrier = molecules (e.g., proteins,
ions, DNAs)Communication distance = nano/micro scaleA receiver (chemically/physically) reacts to
incoming molecules
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Receivers (nanomachines)
Senders (nanomachines)
Information molecules (Proteins, ions, DNA)
1. Encoding
2. Sending
3. Propagation
4. Receiving
5. Decoding
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Key System Components
A senderMolecule generationMolecule encodingMolecule emission
PropagationMolecule loading at a senderDirection controlMolecule unloading at a receiverMolecule recycling
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A receiverMolecule reception Molecule decodingMolecule decomposition or recycling
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System Characteristics
We want the system to beAutonomous (i.e., no human control)Closed (i.e., no energy supply from outside)Recycling (of carrier molecules and information
molecules) Other system characteristics
Probabilistic behaviorMany to many communicationSlow delivery of molecules
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Two Example Systems
Molecular CommunicationUsing a cellular networkUsing molecular motors
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Network of Biological Cells
Network of Biological Cells
Amplifier Switch
Engineering the network components using cells
0 sec 4 sec 6 sec 49 sec
Encoding information on calcium waves
Decoding information from calcium waves
Various cellular responses (e.g., contraction, secretion, growth, death)
Example 1: Molecular Communication Based on a Cellular Network
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1-n communication (broadcasting medium)
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1-1 communication
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Nanoscale protein channels connecting two adjacent cells
Allowing small molecules to be shared among cells, enabling coordinated action of the cells
Gap Junctions
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Example Networking
Filtering signals
Signal X is more permeable to channels formed between the cells
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Example Networking
Filtering signals
Signal Y is more permeable to channels formed between the cells
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Example Networking
Switching the direction of signalingExternal signal
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Example Networking
Switching the direction of signaling
Phosphorylation of channels increases/decreases permeability of the channels.
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Nanomachines communicate using molecular motors.
Molecules are transported by molecular motors that walk over a network of rail molecules.
Example 2: Molecular Communication
Using Molecular Motors
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Outline
Nanomachine communicationNanomachinesOur approach
Molecular communicationExample systems
Conclusions
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Research Issues
Developing applications that require communication among bio nanomachines
System designs using biological communication mechanisms Autonomous, closed, recycling system Various system components
Creating new “information” and “coding” concepts and models Various approaches
Feasibility test through experiments Theoretical modeling and analysis Simulations
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Conclusions
Molecular CommunicationNew paradigmNeed a lot of research
Integrating nano technology, bio technology and computer science