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Plasmid-derived DNA Strand Displacement Gates for Implementing Chemical Reaction Networks

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Published on: November 25, 2015

Rule-based programming paradigm: a formal basis for biological, chemical and physical computation.

V Krishnamurthy¹, E V Krishnamurthy

¹Computer Sciences Laboratory, Research School of Information Sciences and Engineering, Australian National University, Canberra.

|April 8, 1999

Summary

This study introduces a rule-based programming paradigm for complex computations in biology, chemistry, and physics. It enables both deterministic and probabilistic modeling through element interactions and database support.

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Area of Science:

Computational Science
Theoretical Biology
Physical Chemistry

Background:

Traditional programming paradigms struggle with complex systems.
Biological, chemical, and physical systems involve intricate element interactions.

Purpose of the Study:

To present a formal rule-based programming paradigm for diverse scientific computations.
To model emergent behaviors and properties from element interactions.

Main Methods:

Interpreting computations as interactions within an object space governed by specific rules.
Utilizing a Gibbsian ensemble analogy for probabilistic rule applications.
Leveraging relational database concepts for query processing and transactions.

Main Results:

The paradigm supports parallel, cooperative, and competitive interactions among elements.
It can model deterministic computations with exact initial conditions.
Probabilistic computations for macroscopic properties are achievable.
The framework can be supported by database technologies.

Conclusions:

The rule-based paradigm offers a flexible and powerful approach for modeling complex scientific phenomena.
It unifies deterministic and probabilistic computational models.
Integration with database systems enhances its practical applicability.