Robust, Passive Clocking in BioDesign Automation

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Robust, Passive Clocking in Bio-Design Automation
Marc Riedel EE5393, Univ. of Minnesota
Brians Automated Modular Biochemical Instantiator
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Playing by the Rules
Biochemical Reactions how types of molecules
combine.
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Biochemical Reactions
Relative rates or (reaction propensities)
slow
medium
fast
Discrete chemical kinetics spatial homogeneity.
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Functional Dependencies
Exponentiation
Logarithm
Linear
Raising-to-a-Power
DAC 07, SB 3.0 The Synthesisof Stochastic
Biochemical Systems
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Contributions

• We describe a novel mechanism for locking the
  computation of biochemical modules.
• Our method synthesizes computation that is nearly
  rate independent, requiring at most two speeds
  (fast and slow).
• This allows us to map the design to libraries of
  biochemistry.

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Contribution Timing
Biochemical rules are inherently parallel.
Sequentialize?
Step 1
then
Step 2
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Composition
Rate separation increases with composition/modular
ity.
slow2
fast2
slow1
fast1
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Module Locking
Sequentialize computation with only two
rates fast and slow.
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Example Multiplication
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Module Locking
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Module Locking
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Key Generation
Two-phase protocol to ensure only one type of key
is present.
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Example Multiplication
Lock phases or modules with keys.
Keys are generated by keysmiths but indicators
consume keysmiths.
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A Comparison of the Accuracy of the Locked and
Unlocked Versions of Three Modules
Multiplication, Exponentiation, and Logarithm.
Unlocked
Locked
Accuracy
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Locking the log2(A) Module
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Biochemical Synthesis
Where are we?

• Methods and CAD tools for generating nearly rate
  independent biochemical netlists for nearly any
  memoryless function (e.g., curve-fitting).

• Methods for generating any register-to-register
  computation (e.g., DSP functions).

Where are we headed?

• The first technology-independent biochemical ALU
  and CPU.

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Communicating Ideas