programming biological cells ron weiss, george homsy, radhika nagpal tom knight, gerald sussman,...
Post on 20-Dec-2015
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![Page 1: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/1.jpg)
Programming Biological Cells
Ron Weiss, George Homsy, Radhika Nagpal
Tom Knight, Gerald Sussman, Nick PapadakisMIT Artificial Intelligence Laboratory
![Page 2: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/2.jpg)
Goal: program biological cells
Characteristics small (E.coli: 1x2m , 109/ml)
self replicating
energy efficient
Potential applications “smart” drugs / medicine
agriculture
embedded systems
Motivation
![Page 3: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/3.jpg)
Approach
Building biological digital circuits compute, connect gates, store values
High-level programming issues
Outline:
logiccircuit
microbialcircuit
compiler
genomehigh-levelprogram
![Page 4: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/4.jpg)
Compute: Biological Inverter
signal = protein concentration level computation = protein production + decay
[A][Z]
= 0= 1
[A] [Z]
[A][Z]
= 1= 0
Z
A
![Page 5: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/5.jpg)
activegene
Inverter Behavior
Simulation model based on phage biochemistry
[A]
[Z]
[ ]
time (x100 sec)
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Connect: Ring Oscillator
Connected gates show oscillation, phase shift
time (x100 sec)
[A]
[C]
[B]
![Page 7: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/7.jpg)
B_S
_R
Memory: RS Latch
time (x100 sec)
_[R]
[B]
_[S]
[A]
=A
![Page 8: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/8.jpg)
Microbial Circuit Design
Assigning proteins is hard. BioSPICE: Simulate a colony of cells
logiccircuit
microbialcircuit
compiler
genome
protein DBBioSPICE
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BioSPICE
Prototype protein level simulator intracellular circuits, intercellular
communication
Simulationsnapshot
cell
proteinconcentration
![Page 10: Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory](https://reader033.vdocuments.site/reader033/viewer/2022051315/56649d425503460f94a1ccbf/html5/thumbnails/10.jpg)
High Level Programming
Requires a new paradigm colonies are amorphous
cells multiply & die often
expose mechanisms cells can perform reliably
Microbial programming language example: pattern generation using aggregated
behavior
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Conclusions + Future Work
Biological digital gates are plausible
Now: Implement digital gates in E. coli
Also: Analyze robustness/sensitivity of gates
Construct a protein kinetics database
Study proteinprotein interactions for faster logic circuits