molecular communication: simulation of a molecular motor ... · 1. molecular communication:...
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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
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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
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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
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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
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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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