Stochastic Computing with BiomolecuStochastic Computing with Biomolecular Automatalar Automata

R. Adar, Y. Benenson, G. Linshiz, A. Rosner,N. Tishby, and E. Shapiro

PNAS, vol. 101, no. 27, pp. 9960-9965, July 2004.

Cho, Dong-Yeon

© 2004 SNU CSE Biointelligence Lab

2

IntroductionIntroduction

Stochastic Computing The choice between several alternative computation path

s (each with a prescribed probability) Random number generator

Biomolecular computer A stochastic biomolecular computer would be more suitable for

this biomedical tasks than a deterministic one.

A Design Principle for Stochastic Computers

© 2004 SNU CSE Biointelligence Lab

3

Deterministic and Stochastic Deterministic and Stochastic Finite AutomataFinite Automata

© 2004 SNU CSE Biointelligence Lab

4

Previous WorkPrevious Work

© 2004 SNU CSE Biointelligence Lab

5

Results (1/6)Results (1/6)

Calibration We performed calibration with the four-symbol inputs aaab and bbba.

Computation trees used for the calibration of transition probabilities

© 2004 SNU CSE Biointelligence Lab

6

Results (2/6)Results (2/6)

To determine the function mapping relative concentrations of transition molecules to transition probabilities

Transitions processing the symbol a provide a linear mapping.

Transitions processing b reveal a convex mapping.

This is apparently caused by the software molecules that result in state S1 (T4 and T8) having a higher reaction rate than the competing software molecules that result in state S0 (T3 and T7).

© 2004 SNU CSE Biointelligence Lab

7

Results (3/6)Results (3/6)

To verify that the system is insensitive to fluctuations in input concentration

Using the input bbba and T1-T2 transition pair The computation is insensitive to the different input concentrat

ions used and the transition probability is determined solely by the ration between the transition molecules.

© 2004 SNU CSE Biointelligence Lab

8

Results (4/6)Results (4/6)

Sensitivity of the probability distribution to the absolute concentration of the software molecules

The transition probability is indeed relatively insensitive to the absolute software concentrations and is defined mostly by the relative concentration ratio.

© 2004 SNU CSE Biointelligence Lab

9

Results (5/6)Results (5/6) Running 4 Programs with 9 Inputs

bbba, aaab, abbbbbba, babbaaab, baaaaaab, babbabbbbbba, baaaabbbbbba, abbbbabbaaab,

abbbbaaaaaab

© 2004 SNU CSE Biointelligence Lab

10

Results (6/6)Results (6/6)