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Paradigms for Biomolecular Computation
 UNCONVENTIONAL MODELS OF COMPUTATION
, 1998
"... Biomolecular Computation (BMC) is computation done at the molecular scale, using Biotechnological techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental mile ..."
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Biomolecular Computation (BMC) is computation done at the molecular scale, using Biotechnological techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental milestones for the field of BMC.
From MicroSoft to BioSoft: computing with DNA
 Proc. BCEC’97 (BioComputing and Emergent Computation) Skovde, Sweden, World Scienti c
"... “Jump at the sun and you might at least catch hold of the moon” (Jamaican proverb) 1 From Digits and Beads to Bits and Biomolecules The notion of computing seems nowadays to be so synonymous with computers, that we often seem to forget that electronic computers are relatively new players on the worl ..."
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“Jump at the sun and you might at least catch hold of the moon” (Jamaican proverb) 1 From Digits and Beads to Bits and Biomolecules The notion of computing seems nowadays to be so synonymous with computers, that we often seem to forget that electronic computers are relatively new players on the world stage, [31]. Indeed, a brief look at the history of humanity shows that since the earliest days people needed to count and compute, either for measuring the months and the seasons or for commerce and constructions. The means used for performing calculations were whatever was available, and thus gradually progressed from manual to mechanical, and from there on to electrical devices. Indeed, man started off by counting on his digits, a fact attested by the use of the word digit to mean both “any of the ten numbers from 0 to 9 ” and “a finger, thumb or toe ” (Oxford Advanced Learner’s Dictionary). The need for counting and tracking occurrences in the physical world is witnessed by primitive calendars like the one at Stonehenge, 2,800 B.C., or by primitive calculators like the abacus. The abacus, the most common of which comes from China, was man’s first attempt at automating the counting process, and it involved the idea of positional representation: the value assigned to each bead (pebble, shell) was determined not by its shape but by its position. The transition to a qualitatively superior way of doing computation had to wait until the 17th century when Pascal built the first mechanical adding machine (1642), based on a gear system. In his machine, based on the design of Hero of Alexandria (2 A.D.), a wheel engaged its single tooth with a tenteeth ∗ This paper was written during my visit in Japan supported by the “Research for the
DNA starts to learn poker
 Proc. DNA7, Lecture Notes in Computer Science
, 2003
"... Abstract. DNA is used to implement a simplified version of poker. Strategies are evolved that mix bluffing with telling the truth. The essential features are (1) to wait your turn, (2) to default to the most conservative course, (3) to probabilistically override the default in some cases, and (4) to ..."
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Abstract. DNA is used to implement a simplified version of poker. Strategies are evolved that mix bluffing with telling the truth. The essential features are (1) to wait your turn, (2) to default to the most conservative course, (3) to probabilistically override the default in some cases, and (4) to learn from payoffs. Two players each use an independent population of strategies that adapt and learn from their experiences in competition. 1
Using DNA to solve the Bounded Post Correspondence Problem
, 2000
"... Theoretical research in DNA computing includes designing practical experiments for solving various computational problems by means of DNA manipulation. This paper proposes a DNA algorithm for an NPcomplete problem, The Bounded Post Correspondence Problem. The proposed experiment can be used to test ..."
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Theoretical research in DNA computing includes designing practical experiments for solving various computational problems by means of DNA manipulation. This paper proposes a DNA algorithm for an NPcomplete problem, The Bounded Post Correspondence Problem. The proposed experiment can be used to test several standard molecular biology laboratory procedures
Computing with DNA
 In Computer Methods in Molecular Biology, (S.Misener, S.Krawetz, Eds.), in Methods in Molecular Biology series
, 1998
"... A brief look at the history of humanity shows that since the earliest days people needed to count and compute, either for measuring the months and the seasons or for commerce and construction. The means used for performing calculations were whatever was available, and thus progressed gradually from ..."
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Cited by 2 (0 self)
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A brief look at the history of humanity shows that since the earliest days people needed to count and compute, either for measuring the months and the seasons or for commerce and construction. The means used for performing calculations were whatever was available, and thus progressed gradually from manual (digits) to mechanical (abacus, mechanical adding engine), and from there on to electronic devices. Electronic computers are only the latest in a long chain of human efforts to use the best technology available for performing computations. Although it is true that their appearance, some 50 years ago, has revolutionized computing, electronic computers mark neither the beginning nor the end of the history of computation. Indeed, even electronic computers have their limitations: There is a limit to the amount of data they can store, and physical laws dictate the speed thresholds they will soon reach. The most recent attempt to break down these barriers is to replace, once more, the tools for performing computations with biological ones instead of electrical ones. DNA computing (also sometimes referred to as biomolecular computing or molecular computing) is a new computational paradigm that employs (bio)molecule manipulation to solve computational problems, at the same time exploring natural processes as computational models. Research in this area began with an experiment by Leonard Adleman, who surprised the scientific community in 1994 (1) by using the tools of molecular biology to solve a difficult computational problem. Adleman’s experiment solved an instance of the Directed Hamiltonian Path Problem solely by manipulating DNA strands. This marked the first solution of a mathematical problem by use of biology.
Recent Developments in DNAComputing
 IN PROCEEDINGS OF THE 1997 27TH INTERNATIONAL SYMPOSIUM ON MULTIPLEVALUED LOGIC
, 1997
"... In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models was introduced and ..."
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In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models was introduced and examined, concerning their computional power (universality as well as time and space complexity), their efficiency and their error resistance. The main results are presented in this survey.
Computing with Molecules
, 1997
"... In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models have been introduc ..."
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In 1994 Adleman published the description of a lab experiment, where he computed an instance of the Hamiltonian path problem with DNA in test tubes. He initiated a flood of further research on computing with molecular means in theoretical computer science. A great number of models have been introduced, and their computational power has been examined, with results on universality, complexity, efficient algorithms, and error resistance. The main results are presented in this survey.
Noncommutative computer algebra and molecular computing
, 2001
"... Noncommutative calculations are considered from the molecular computing point of view. The main idea is that one can get more advantage in using molecular computing for noncommutative computer algebra compared with a commutative one. The restrictions, connected with the coefficient handling in Gröb ..."
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Noncommutative calculations are considered from the molecular computing point of view. The main idea is that one can get more advantage in using molecular computing for noncommutative computer algebra compared with a commutative one. The restrictions, connected with the coefficient handling in Gröbner basis calculations are investigated. Semigroup and group cases are considered as more appropriate. SAGBI basis constructions and possible implementations are discussed.
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"... Massively Parallel Machines. BMC also has the potential to supply massive computational power. General use of BMC is to construct parallel machines where each processor's state is encoded by a DNA strand. BMC can perform massively parallel computations by executing recombinant DNA operations th ..."
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Massively Parallel Machines. BMC also has the potential to supply massive computational power. General use of BMC is to construct parallel machines where each processor's state is encoded by a DNA strand. BMC can perform massively parallel computations by executing recombinant DNA operations that act on all the DNA molecules at the same time. These recombinant DNA operations may be performed to execute massively parallel local memory read/write, logical operations and also further basic operations on words such as parallel arithmetic. As we discuss in Section 2, DNA in weak solution in one liter of water can encode the state of about 10 18 processors, and since certain recombinant DNA operations can take many minutes, the overall potential for a massively parallel BMC machines is about 1; 000 teraops. (This assumes the parallel machine uses local rather than global shared memory. To allow such a parallel machine to use global shared memory, we need to do massively parallel message (DNA strand) routing. Reif's [R95] BMC simulation of a PRAM with shared memory required volume growing at least quadratically with size of the storage of the PRAM, but Gehani and Reif [GR98a] describe a MEMS micro ow device technology that can do the massively parallel message routing with a substantial decrease in the volume.)