Theoretical and Experimental DNA Computation (Natural ...

5
Physical Implementations
“No amount of experimentation can ever prove me right; a single
experiment can prove me wrong.” – Albert Einstein
5.1 Introduction
This chapter provides an introduction to the implementation of DNA computations.
We concentrate in particular on a full description of two filtering
models (Adleman’s and parallel filtering). We highlight the practical implementation
problems inherent in all models, and suggest possible ways to alleviate
these. We also describe other key successful experimental implementations
of DNA-based computations.
5.2 Implementation of Basic Logical Elements
In 1982, Bennett [29] proposed the concept of a “Brownian computer” based
around the principle of reactant molecules touching, reacting, and effecting
state transitions due to their random Brownian motion. Bennett developed
this idea by suggesting that a Brownian Turing Machine could be built from a
macromolecule such as RNA. “Hypothetical enzymes”, one for each transition
rule, catalyze reactions between the RNA and chemicals in its environment,
transforming the RNA into its logical successor.
Conrad and Liberman developed this idea further in [46], in which the
authors describe parallels between physical and computational processes (for
example, biochemical reactions being employed to implement basic switching
circuits). They introduce the concept of molecular level “word processing” by
describing it in terms of transcription and translation of DNA, RNA processing,
and genetic regulation. However, the paper lacks a detailed description
of the biological mechanisms highlighted and their relationship with “traditional”
computing. As the authors themselves acknowledge, “our aspiration is