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Self-assembling automata: a model of conformational self-assembly

K Saitou1

  • 1Department of Mechanical Engineering and Applied Mechanics, University of Michigan, Ann Arbor 48109-2125, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|August 11, 1998
PubMed
Summary

This study introduces a self-assembling automaton model using conformational switches for assembly instructions. Three component conformations are sufficient for encoding any assembly sequence, regardless of string length.

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Area of Science:

  • Computational modeling
  • Systems chemistry
  • Theoretical computer science

Background:

  • Self-assembly is a fundamental process in nature and materials science.
  • Designing self-assembling systems requires precise control over component interactions.
  • Existing models may not efficiently capture the complexity of rule-based assembly instructions.

Purpose of the Study:

  • To present an abstract model for self-assembling systems based on local rules.
  • To define a computational framework, the self-assembling automaton, for modeling assembly processes.
  • To determine the minimum number of conformations required for encoding assembly sequences.

Main Methods:

  • Development of the self-assembling automaton model.
  • Definition of automata classes based on subassembly sequences.

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  • Analysis of conformational requirements for encoding arbitrary-length sequences.

    • Main Results:

    • The self-assembling automaton operates as a sequential rule-based machine on one-dimensional strings.
    • Classes of automata are categorized by their subassembly sequence properties.
    • It is proven that three conformations per component are universally sufficient for encoding any subassembly sequence.

    Conclusions:

    • The proposed model provides a theoretical framework for understanding rule-based self-assembly.
    • The finding on three conformations offers a concise and efficient encoding strategy.
    • This work contributes to the design principles of complex self-assembling systems.