Molecular Circuits for Dynamic Noise Filtering

Tran Quoc Hoan

@k09ht haduonght.wordpress.com/

Paper Alert 2016-07-22, Hasegawa lab., Tokyo

The University of Tokyo

PNAS(2016-04), vol. 113 no. 17, Christoph Zechner, 4729–4734, doi: 10.1073/pnas.1517109113

Findings

Molecular Circuits for Dynamic Noise Filtering 2

• Developed the Possion noise filter by biochemical reactions as a molecular analog of the Kalman filter applied for molecular systems.

• Potential to improve the reliability of synthetic biological circuits and plan an important role in the development of new medical therapies.

Background

Molecular Circuits for Dynamic Noise Filtering 3

Electrical circuits Biological circuits

• Robust with noise and changing environmental conditions

• Context-dependency (Ex. hot cells)

• Noise-filter: build a circuit that evaluates what the noise looks like (Ex. Kalman filter)

• Noise-filter: cancel out the effects of molecular environment

Poisson filter

Optimal Signal Estimation

Molecular Circuits for Dynamic Noise Filtering 4

Kinetic model driven by an external input dY(t)

Optimal Signal Estimation

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• When cYZ(t) is large, we have Gamma Filter

• When cY is small (V(t) = M(t)), we have Posson filter

Poison filter can be implemented by below reactions

General Filtering Circuits

6Molecular Circuits for Dynamic Noise Filtering

In Vitro Estimation of Dynamic Signals

7Molecular Circuits for Dynamic Noise Filtering

Others

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• Ensemble Averaging

Molecular Circuits for Dynamic Noise Filtering

• Adaptive System Identification

• Extinct Noise Cancellation