DNAQL: a query language for DNA sticker complexes

• Published in: Natural computing 2021-03, Vol.20 (1), p.161-189
• Main Authors: Brijder, Robert, Gillis, Joris J. M., Van den Bussche, Jan
• Format: Article
• Language: English
• Subjects: Artificial Intelligence; Complex Systems; Computation; Computer Science; Deoxyribonucleic acid; DNA; Evolutionary Biology; Functional programming; Processor Architectures; Programming languages; Query languages; Relational algebra; Theory of Computation; Tightness
• ISSN: 1567-7818; 1572-9796
• DOI: 10.1007/s11047-020-09839-7

DNA computing has a rich history of computing paradigms with great expressive power. However, far less expressive power is needed for data manipulation. Indeed, the relational algebra, the yardstick of database systems, is expressible in first-order logic, and thus less powerful than Turing-complete models. Turing-complete DNA computing models have to account for many and varied scenarios. A DNA implementation of data manipulations might be nimbler and perform its operation faster than a Turing-complete DNA computing model. Hence, we propose a restrictive model for implementing data manipulation operations, focused on implementability in DNA. We call this model the sticker complex model. A forte of the sticker complex model, is its ability to detect when hybridization becomes an uncontrolled chain reaction. Such chain reactions make hybridization less predictable and thus less attractive for deterministic computations. Next, we define a query language on sticker complexes, called DNAQL . DNAQL is a typed, applicative functional programming language, powerful enough to simulate the relational algebra on sticker complexes. The type system enjoys a number of desirable properties such as soundness, maximality, and tightness.