Bacteria employ restriction enzymes to cut or restrict DNA at or near specific words in a unique way. Many restriction enzymes cut the two strands of double-stranded DNA at different positions leaving overhangs of single-stranded DNA. Two pieces of DNA may be rejoined or ligated if their terminal overhangs are complementary. Using these operations fragments of DNA, or oligonucleotides, may be inserted and deleted from a circular piece of plasmid DNA. We propose an encoding for the transition table of a Turing machine in DNA oligonucleotides and a corresponding series of restrictions and ligations of those oligonucleotides that, when performed on circular DNA encoding an instantaneous description of a Turing machine, simulate the operation of the Turing machine encoded in those oligonucleotides. DNA based Turing machines have been proposed by Charles Bennett but they invoke imaginary enzymes to perform the state-symbol transitions. Our approach differs in that every operation can be pe...

We present a small time-efficient universal Turing machine with 5 states and 6 symbols. This Turing machine simulates our new variant of tag system. It is the smallest known universal Turing machine that simulates Turing machine computations in polynomial time.

We show that 2-tag systems efficiently simulate Turing machines. As a corollary we find that the small universal Turing machines of Rogozhin, Minsky and others simulate Turing machines in polynomial time. This is an exponential improvement on the previously known simulation time overhead and improves a forty year old result in the area of small universal Turing machines. 1

We show that the problem of predicting t steps of the 1D cellular automaton Rule 110 is P-complete. The result is found by showing that Rule 110 simulates deterministic Turing machines in polynomial time. As a corollary we find that the small universal Turing machines of Mathew Cook run in polynomial time, this is an exponential improvement on their previously known simulation time overhead.

We present universal Turing machines with state-symbol pairs of (5, 5), (6, 4), (9, 3) and (15, 2). These machines simulate our new variant of tag system, the bi-tag system and are the smallest known single-tape universal Turing machines with 5, 4, 3 and 2-symbols, respectively. Our 5-symbol machine uses the same number of instructions (22) as the smallest known universal Turing machine by Rogozhin. Also, all of the universal machines we present here simulate Turing machines in polynomial time.

Abstract. We present three small universal Turing machines that have 3 states and 7 symbols, 4 states and 5 symbols, and 2 states and 13 symbols, respectively. These machines are semi-weakly universal which means that on one side of the input they have an infinitely repeated word, and on the other side there is the usual infinitely repeated blank symbol. This work can be regarded as a continuation of early work by Watanabe on semi-weak machines. One of our machines has only 17 transition rules, making it the smallest known semi-weakly universal Turing machine. Interestingly, two of our machines are symmetric with Watanabe’s 7-state and 3-symbol, and 5-state and 4-symbol machines, even though we use a different simulation technique. 1.

Abstract. We present small polynomial time universal Turing machines with state-symbol pairs of (5, 5), (6, 4), (9, 3) and (18, 2). These machines simulate our new variant of tag system, the bi-tag system and are the smallest known universal Turing machines with 5, 4, 3 and 2-symbols respectively. Our 5-symbol machine uses the same number of instructions (22) as the smallest known universal Turing machine by Rogozhin. 1

Abstract. We give small universal Turing machines with state-symbol pairs of (6, 2), (3,3) and (2,4). These machines are weakly universal, which means that they have an infinitely repeated word to the left of their input and another to the right. They simulate Rule 110 and are currently the smallest known weakly universal Turing machines. Despite their small size these machines are efficient polynomial time simulators of Turing machines. 1

We survey some work concerned with small universal Turing machines, cellular automata, tag systems, and other simple models of computation. For example it has been an open question for some time as to whether the smallest known universal Turing machines of Minsky, Rogozhin, Baiocchi and Kudlek are efficient (polynomial time) simulators of Turing machines. These are some of the most intuitively simple computational devices and previously the best known simulations were exponentially slow. We discuss recent work that shows that these machines are indeed efficient simulators. As a related result we also find that Rule 110, a well-known elementary cellular automaton, is also efficiently universal. We also mention some old and new universal program-size results, including new small universal Turing machines and new weakly, and semi-weakly, universal Turing machines. We then discuss some ideas for future work arising out of these, and other, results.

Bacteria employ restriction enzymes to cut or restrict DNA at or near specific words in a unique way. Many restriction enzymes cut the two strands of double-stranded DNA at different positions leaving overhangs of single-stranded DNA. Two pieces of DNA may be rejoined or ligated if their terminal overhangs are complementary. Using these operations fragments of DNA, or oligonucleotides, may be inserted and deleted from a circular piece of plasmid DNA. We propose an encoding for the transition table of a Turing machine in DNA oligonucleotides and a corresponding series of restrictions and ligations of those oligonucleotides that, when performed on circular DNA encoding an instantaneous description of a Turing machine, simulate the operation of the Turing machine encoded in those oligonucleotides. DNA based Turing machines have been proposed by Charles Bennett but they invoke imaginary enzymes to perform the state--symbol transitions. Our approach differs in that every operation can be pe...