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Molecular Communication:Simulation of a Molecular Motor Communication SystemMichael Moore, Akihiro Enomoto, Tadashi Nakano, Tatsuya SudaDepartment of Computer ScienceDonald Bren School of Information and Computer SciencesUniversity of California, Irvine, Irvine, CA 92697-3425 Web: http://bolero.ics.uci.edu/mc/index.htmlEmail: [email protected]
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Outline
Nanomachine communicationNanomachinesNano-Scale biological communication
Molecular communicationExample systemsApplications
My Simulation Work
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Molecular CommunicationCommunication paradigm for biological nanomachines
Molecules as information carriers
Figure: “Protonic Nanomachin Project”, Prof. Namba at Osaka University: http://www.npn.jst.go.jp/index.html
Nanomachines: nano-scale or molecular scale objects that are capable of performing simple tasks
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What are Nanomachines?Cellular components/cells
Dynein Molecular motors that walk along microtubule in a cell
Bacterium Swims toward the chemicals (e.g, food) using flagellum
Figures: Alberts, Molecular Biology of the CellDynein
Bacterium
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What are Nanomachines?
Molecules such as enzymesFunction as logic gates
If both substrate and effector exist, product producedIf no effector or no substrate, substrate remains unchanged
ANDCS P
Enzyme
ProductSubstrate
Effector
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Within a cell (vesicles transported by molecular motors)
A vesicle transported by a kinesin motor toward the periphery of the cell
A vesicle transported by a dynein motor toward the center of the cell
Nucleus
Centrosome
Microtubule Plasma-membrane
Nano-Scale Communication in Bio World
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Molecular MotorsKinesin
Consumes ATP energy to move along microtubuleBinds cargo according to tail domain
http://www.embl-heidelberg.de/CellBiophys/LocalProbes/motorproteins/kinesin.html
Microtubule
Kinesin
Bound Information Molecule
Motor Procession Along a Microtubule
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Outline
Nanomachine communicationNanomachinesNano-Scale biological communication
Molecular communicationExample systemsApplications
My Simulation Work
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Simplest Molecular Communication System: An Example
1. Encoding
Senders(nanomachines)
Information Source
Information molecules(Proteins, ions, DNAs, etc)
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Simplest Molecular Communication System: An Example
2. Sending
1. Encoding
Senders(nanomachines)
Information Source
Information molecules(Proteins, ions, DNAs, etc)
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Simplest Molecular Communication System: An Example
2. Sending
3. Propagation(directional）
1. Encoding
Senders(nanomachines)
Information Source
Information molecules(Proteins, ions, DNAs, etc)
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Simplest Molecular Communication System: An Example
2. Sending
4. Receiving(selective）
1. Encoding
Receivers(nanomachines)
Senders(nanomachines)
Information Source
Information molecules(Proteins, ions, DNAs, etc)
3. Propagation(directional）
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Simplest Molecular Communication System: An Example
2. Sending
5. Decoding1. Encoding
Receivers(nanomachines)
Senders(nanomachines)
Information Source
Information SinkInformation molecules(Proteins, ions, DNAs, etc)
3. Propagation(directional）
4. Receiving(selective）
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Simplest Molecular Communication System: An Example
2. Sending
5. Decoding1. Encoding
Receivers(nanomachines)
Senders(nanomachines)
Information Source
Information SinkInformation molecules(Proteins, ions, DNAs, etc)
3. Propagation(directional）
4. Receiving(selective）
5. Next hop commun
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ComponentsSenders/receivers = biological nanomachinesCommunication carrier = molecules (e.g., proteins, ions, DNA sequences)Communication distance = nano/micro scaleA receiver (chemically/physically) reacts to incoming molecules
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Application:Body Sensor Networks
Soft nanomachines that are bio-friendly are embedded into a body
Interact with each other Interact directly with cellsSelf-replicating, self healing
ApplicationsMedical treatment and health monitoringEnhancing various capabilities
Sense of smell, hearing capacities
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Application:New Ways of Problem Solving
Program simple behavior rules into biological nanomachinesSolving large scale problems (e.g., a maze) through collaboration and communication
T. Nakagaki, H. Yamada, Á. Tóth, "Intelligence: Maze-solving by an amoeboid organism," 2000 Nature
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Nanomachines communicate using molecular motors.Molecules are transported by molecular motors that walk over a network of rail molecules.
Prototype System 1: Molecular Communication Using Molecular Motors
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Self organizing creation of a rail molecule network
Nanomachine Seed of rail molecules (e.g., γ-tubulin)
CAP molecule Rail molecule
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Outline
Nanomachine communicationNanomachinesNano-Scale biological communication
Molecular communicationExample systemsApplications
My Simulation Work
My research: Simulation of Uni-cast Molecular Communication
Uni-castSimplest communicationOne sender transmits to one receiverE.g. sender encodes “1” and receiver decodes a “1”
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Sender: Receiver:
S R
Information molecules
Uni-cast Communication
Compare propagation approaches
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SR
Sender:
Receiver:
Microtubule:S R
Diffusion (D)No
Microtubule
S R
Motor (M)Connected
Microtubule
Hybrid (H)Microtubule Aster
S R
Multi-bit Communication ModelSignal
Probability to receive a “1”
Noise Causes error when receiving a 0
Significant ParametersDistance, time between sending events, number of information molecules
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SendingNextSending
Time for receiving
Signal Noise for Next Sending
Other Simulations Performed
Broadcast communicationMicrotubule topologies
Length, number of microtubulesReceiver location on microtubules
Optimize information rate in terms ofDecay of information moleculesNumber of information molecules sent/received
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Future Work
Communication using MoleculesReliability, Dynamics
General molecular communicationsApplicationsTheoretical information limitsHigher-layer networking
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