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On the time complexity of 2tag systems and small universal turing machines
 In 47th Annual IEEE Symposium on Foundations of Computer Science (FOCS
, 2006
"... We show that 2tag 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 improve ..."
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Cited by 16 (7 self)
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We show that 2tag 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
A small fast universal Turing machine
 Theoretical Computer Science
, 2005
"... We present a small timeefficient 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. ..."
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Cited by 15 (8 self)
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We present a small timeefficient 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.
Small semiweakly universal Turing machines
 Machines, Computations and Universality (MCU), volume 4664 of LNCS
, 2007
"... 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 semiweakly universal which means that on one side of the input they have an infinitely repeated word, and on the other s ..."
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Cited by 10 (4 self)
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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 semiweakly 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 semiweak machines. One of our machines has only 17 transition rules, making it the smallest known semiweakly universal Turing machine. Interestingly, two of our machines are symmetric with Watanabeâ€™s 7state and 3symbol, and 5state and 4symbol machines, even though we use a different simulation technique. 1.
Small weakly universal Turing machines
"... Abstract. We give small universal Turing machines with statesymbol 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 ..."
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Cited by 7 (4 self)
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Abstract. We give small universal Turing machines with statesymbol 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
How Crystals that Sense and Respond to Their Environments Could Evolve
"... Abstract. An enduring mystery in biology is how a physical entity simple enough to have arisen spontaneously could have evolved into the complex life seen on Earth today. CairnsSmith has proposed that life might have originated in clays which stored genomes consisting of an arrangement of crystal m ..."
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Cited by 6 (3 self)
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Abstract. An enduring mystery in biology is how a physical entity simple enough to have arisen spontaneously could have evolved into the complex life seen on Earth today. CairnsSmith has proposed that life might have originated in clays which stored genomes consisting of an arrangement of crystal monomers that was replicated during growth. While a clay genome is simple enough to have conceivably arisen spontaneously, it is not obvious how it might have produced more complex forms as a result of evolution. Here, we examine this possibility in the tile assembly model, a generalized model of crystal growth that has been used to study the selfassembly of DNA tiles. We describe hypothetical crystals for which evolution of complex crystal sequences is driven by the scarceness of resources required for growth. We show how, under certain circumstances, crystal growth that performs computation can predict which resources are abundant. In such cases, crystals executing programs that make these predictions most accurately will grow fastest. Since crystals can perform universal computation, the complexity of computation that can be used to optimize growth is unbounded. To the extent that lessons derived from the tile assembly model might be applicable to mineral crystals, our results suggest that resource scarcity could conceivably have provided the evolutionary pressures necessary to produce complex clay genomes that sense and respond to changes in their environment. 1
The complexity of small universal Turing machines: a survey
, 2007
"... 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 e ..."
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Cited by 4 (2 self)
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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 wellknown elementary cellular automaton, is also efficiently universal. We also mention some old and new universal programsize results, including new small universal Turing machines and new weakly, and semiweakly, universal Turing machines. We then discuss some ideas for future work arising out of these, and other, results.
On the boundaries of solvability and unsolvability in tag systems. Theoretical and Experimental Results.
, 2008
"... Several older and more recent results on the boundaries of solvability and unsolvability in tag systems are surveyed. Emphasis will be put on the significance of computer experiments in research on very small tag systems. 1 ..."
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Several older and more recent results on the boundaries of solvability and unsolvability in tag systems are surveyed. Emphasis will be put on the significance of computer experiments in research on very small tag systems. 1
Internal Examiner: Dr. James Power
"... My supervisor Damien Woods deserves a special thank you. His help and guidance went far beyond the role of supervisor. He was always enthusiastic, and generous with his time. This work would not have happened without him. I would also like to thank my supervisor Paul Gibson for his advice and suppor ..."
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My supervisor Damien Woods deserves a special thank you. His help and guidance went far beyond the role of supervisor. He was always enthusiastic, and generous with his time. This work would not have happened without him. I would also like to thank my supervisor Paul Gibson for his advice and support. Thanks to the staff and postgraduates in the computer science department at NUI Maynooth for their support and friendship over the last few years. In particular, I would like to mention Niall Murphy he has always been ready to help whenever he could and would often lighten the mood in dark times with some rousing Gilbert and Sullivan. I thank the following people for their interesting discussions and/or advice: