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Computing in Verotoxin.

Andrew Adamatzky¹

¹Unconventional Computing Centre, University of the West of England, Bristol, BS16 1QY, UK.

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry

|June 14, 2017

Summary

This study models protein verotoxin as an excitable automata, revealing logic gates and circuits through excitation patterns. The research quantifies gate frequencies, showing AND gates are most common, and explores the molecule's potential memory capacity.

Keywords:

logic gates molecular computing molecular logic proteins verotoxin

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Area of Science:

Computational Biology
Biophysics
Molecular Modeling

Background:

Protein verotoxin's complex structure and function remain incompletely understood.
Investigating molecular mechanisms can reveal novel computational capabilities within biological systems.

Purpose of the Study:

To develop an excitable automata model of protein verotoxin.
To demonstrate the realization of logic gates and circuits within this model.
To analyze the computational potential and memory capacity of the verotoxin molecule.

Main Methods:

Development of an excitable automata model for protein verotoxin.
Simulation of interacting excitation patterns to identify logic gate operations.
Systematic sampling of input pairs to calculate logic gate frequencies.
Analysis of specific circuit implementations like one-bit half-adder and controlled-not gates.

Main Results:

Logic gates and circuits are realized in the verotoxin model via interacting excitation patterns.
Frequencies of logic gates follow a hierarchy: AND > OR > AND-NOT > XOR.
Demonstrated realization of one-bit half-adder and controlled-not gates.
Estimated the memory capacity of the verotoxin molecule.

Conclusions:

Protein verotoxin exhibits inherent computational capabilities through its excitable automata dynamics.
The identified hierarchy of logic gate frequencies provides insights into the molecule's processing preferences.
The verotoxin molecule demonstrates potential for information processing and memory storage.