• Home
  • Search
  • Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA
  • Cite Icon39
  • https://doi.org/10.1098/rsif.2016.0990Copy DOI Icon

Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA

Show More
  • Abstract
  • Highlights & Summary
  • PDF
  • Literature Map
  • References
  • Citations
  • Similar Papers
Abstract

The theory of computer science is based around universal Turing machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of classical UTMs. For the most important class of problem in computer science, non-deterministic polynomial complete problems, non-deterministic UTMs (NUTMs) are theoretically exponentially faster than both classical UTMs and quantum mechanical UTMs (QUTMs). However, no attempt has previously been made to build an NUTM, and their construction has been regarded as impossible. Here, we demonstrate the first physical design of an NUTM. This design is based on Thue string rewriting systems, and thereby avoids the limitations of most previous DNA computing schemes: all the computation is local (simple edits to strings) so there is no need for communication, and there is no need to order operations. The design exploits DNA's ability to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that the design works using both computational modelling and in vitro molecular biology experimentation: the design is thermodynamically favourable, microprogramming can be used to encode arbitrary Thue rules, all classes of Thue rule can be implemented, and non-deterministic rule implementation. In an NUTM, the resource limitation is space, which contrasts with classical UTMs and QUTMs where it is time. This fundamental difference enables an NUTM to trade space for time, which is significant for both theoretical computer science and physics. It is also of practical importance, for to quote Richard Feynman ‘there's plenty of room at the bottom’. This means that a desktop DNA NUTM could potentially utilize more processors than all the electronic computers in the world combined, and thereby outperform the world's current fastest supercomputer, while consuming a tiny fraction of its energy.

Loading PDF

Similar Papers
  • Research Article
  • Citations1

Impact of Mathematics on the Theoretical Computer Science Course Units in the General Degree Program in Computer Science at Sri Lankan State Universities

  • Jan 01, 2018
  • Issues in Informing Science and Information Technology
  • Sritharan Thambithurai
  • Conference Article

2008 Abstracts Collection -- IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science

  • Jan 01, 2008
  • DROPS (Schloss Dagstuhl – Leibniz Center for Informatics)
  • Ramesh Hariharan +2
  • Single Book
  • Citations1200

Locally Presentable and Accessible Categories

  • Mar 10, 1994
  • J Adamek +1
  • Research Article
  • Citations13

Topological Cones: Foundations for a Domain Theoretical Semantics Combining Probability and Nondeterminism

  • May 01, 2006
  • Electronic Notes in Theoretical Computer Science
  • Klaus Keimel
  • Book Chapter
  • Citations3

Non-Extensive Thermodynamics of Algorithmic Processing - the Case of Insertion Sort Algorithm

  • Jan 14, 2011
  • Dominik Strzaka +1
  • Supplementary Content
  • Citations3

Logics in Computer Science

  • Jan 01, 2013
  • Università degli Studi di Napoli Federico II
  • Fabio Mogavero
  • Research Article

Computability Theory (Dagstuhl Seminar 17081).

  • Jan 01, 2017
  • DROPS (Schloss Dagstuhl – Leibniz Center for Informatics)
  • Klaus Ambos-Spies +3
  • Research Article
  • Citations116

The correspondence between partial metrics and semivaluations

  • Dec 04, 2003
  • Theoretical Computer Science
  • M.P Schellekens
  • Conference Article
  • Citations28

Visualization in education of theoretical computer science

  • Jan 01, 2007
  • Daniela Chudá
  • Research Article
  • Citations5

Learning by game-building

  • Jun 25, 2007
  • ACM SIGCSE Bulletin
  • Laura Korte +3
  • Research Article
  • Citations8

The Dual Complexity Space as the Dual of a Normed Cone

  • Aug 01, 2006
  • Electronic Notes in Theoretical Computer Science
  • S Romaguera +2
  • Conference Article
  • Citations20

Invariance principle on the slice

  • May 29, 2016
  • Yuval Filmus +3
  • Conference Article
  • Citations11

Comparing the behavior of OpenMP Implementations with various Applications on two different Fujitsu A64FX platforms

  • Jul 17, 2021
  • Practice and Experience in Advanced Research Computing
  • Benjamin Michalowicz +5
  • Single Report

TOP500 Supercomputers for June 2005

  • Jun 22, 2005
  • Erich Strohmaier +3
  • Single Report

TOP500 Supercomputers for June 2004

  • Jun 23, 2004
  • Erich Strohmaier +3
Cactus Communications logo

Copyright 2026 Cactus Communications. All rights reserved.