John Reif. Parallel molecular computation: Models and simulations. Algorithmica, Special Issue on Computational Biology, 1998.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....field of biomedical engineering particularly in recombinant DNA and RNA manipulating. Basic principles about recombinant DNA can be found in [37, 38] In this section we describe some biological operations that are useful for molecular computation. Some of our descriptions are similar to those in [8, 15, 25]. For a string x we denote by x the single DNA strand whose sequence is x and whose orientation is 5 , as x is read from left to right. Similarly, #x denotes the strand complementary to x. Finally, lx denotes the double strand that results when x and #x anneal. 2.2.1. Merge This is to ....

J. Reif. Parallel molecular computation: Models and simulations. In Proceedings he Seventh Annual ACM Symposium on Parallel Algorithms and Archi tectures, pages 213--223, 1995.

....models are characterised by the nature of the operations within them, and fall into three natural categories: ffl Filtering ffl Splicing ffl Constructive The major models are listed in table 3.1 according to the category in which they lie. 23 Filtering Splicing Constructive Adleman [2] Reif [66] Ogihara Ray [61] Lipton [52] Freund Kari Paun [21] Baum Boneh [11] Amos Gibbons Hodgson [7] Guarnieri Fliss Bancroft [39] Karp Kenyon Waarts [48] Winfree Yang Seeman [80] Liu Guo et al. 53] Roweis Winfree et al. 69] Table 3.1: A taxonomy of models of DNA computation 3.3 Filtering models ....

....show that the generative power of finite extended splicing systems is equal to that of Turing Machines. See [22] for a review of splicing systems. 39 a b d g S T (b) a b S T g d (a) Figure 3.2: a) Two strings, S and T (b) The result of splice(S; T ) 3.4. 1 Reif s PAM model In [66], Reif within his so called Parallel Associative Memory Model describes a Parallel Associative Matching (PA Match) operation. The essential constituent of the PA Match operation is a restricted form of the splicing operation which we denote here by Rsplice, and describe as follows. If S = S 1 S 2 ....

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John H. Reif. Parallel molecular computation: Models and simulations. In Proceedings of the Seventh Annual ACM Symposium on Parallel Algorithms 126 and Architectures (SPAA95), Santa Barbara, June 1995, pages 213--223. Association for Computing Machinery, June 1995.

....to note, however, that estimates lead us to believe that our model will perform more rapid computations than conventional computers on a range of feasible problem sizes. One possible way around the weight problem is to look for implementation of existing computing paradigms in DNA. Reif [14] points to one possible way forward, describing a method for simulating a CREW P RAM in vitro. However, Reif uses the error prone hybridization separation method described earlier, which we believe may be avoided by our methodology. Another development is the proposed [15] DNA and restriction ....

John H. Reif. Parallel molecular computation: Models and simulations. In Proceedings of the Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA), Santa Barbara, June 1995.

....Computing is a novel computing paradigm recently emerged from and stimulated by a groundbreaking wet lab experimental work by Adleman in 1994. Since then, a great number of computation models have been proposed in the context of both biomolecular experiments and theoretical computer science (e.g. [2, 3, 7, 9, 10, 11, 13, 17, 19, 20]) trying to break through the so called NP completeness barrier or to establish new computation paradigms with universal capability. This paper proposes new computing paradigms based on self assembly and conformational change. These two principles have already appeared in an extensive variety of ....

J.H.Reif. Parallel Molecular Computation : Models and Simulations. Proc. of Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'95), pp.213-223, 1995.

....paper we describe one such translation, that of transitive closure. We argue that this method demonstrates the feasibility of constructing a general framework for the translation of P RAM algorithms into DNA. 1. Introduction Since the publication of Adleman s seminal work [1] several models [9, 11] have been proposed which, in principle, establish the Turing completeness of DNA computation. Although these simulations are of theoretical interest, their practical significance remains unclear. These models are often biologically infeasible, or have an unacceptable run time. In addition, models ....

....for further work. Research Report CTAG 98004 y Email: martyn csc.liv.ac.uk 2. Motivation Although several Turing complete models of DNA computation have been proposed, they often require unrealistic resources (in terms of time or DNA volume) For instance, the model described by Reif [11] requires exponentially sized volumes of DNA. It is clear that if such models of computation are to be realistic they should require, at most, a volume of DNA that is polynomial in the problem size. However, it is unlikely to be enough to simply have polynomial volumed computations. We ought, at ....

John H. Reif. Parallel molecular computation: Models and simulations. In Proceedings of the Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA95), Santa Barbara, June 1995, pages 213--223. Association for Computing Machinery, June 1995.

....field of biomedical engineering particularly in recombinant DNA and RNA manipulating. Basic principles about recombinant DNA can be found in [37, 38] In this section we describe some biological operations that are useful for molecular computation. Some of our descriptions are similar to those in [8, 15, 25]. For a string x we denote by x the single DNA strand whose sequence is x and whose orientation is 5 0 3 0 , as x is read from left to right. Similarly, #x denotes the strand complementary to x. Finally, lx denotes the double strand that results when x and #x anneal. 2.2.1. Merge This ....

J. Reif. Parallel molecular computation: Models and simulations. In Proceedings he Seventh Annual ACM Symposium on Parallel Algorithms and Archi tectures, pages 213--223, 1995.

....and Append, which appends the same bit to each strand in a test tube. For more information on the physical realization of these operations, the reader may wish to consult [1] Much recent work has explored the power of the model in terms of various classes of decision and optimization problems [1, 2, 3, 4, 5, 6, 7, 12, 16, 19]. The DNA computational model can evaluate any boolean formula in a number of operations proportional to the size of the formula. If enlarged to allow the Append operation, it can evaluate any boolean circuit in a number of operations proportional to its size. However, except for [7] which we ....

....the main issues that distinguish DNA computers from conventional computers. Not surprisingly, it also distinguishes the problem of making DNA computations error resilient from the issue of computing with unreliable operations on conventional computers, that has been the focus of much research (cf. [8, 9, 10, 11, 14, 15, 16, 17, 18]) 1.2 Our results In this paper we provide a method for making computations error resilient without a big sacrifice in their running time, and derive lower bounds on the cost of such methods. We start with the problem that is at the core of all error resilient DNA computations: simulate a ....

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J. H. Reif. Parallel molecular computation: Models and simulations. In Proceedings of the 7th ACM Symposium on Parallel Algorithms and Architectures, 1995.

.... condition: a splicing rule is applicable only when certain strings, called permitting contexts, are present in the terms of splicing (see [23] Constructions showing how to simulate the work of a Turing machine by a DNA model of computation have also been proposed in [2] 5] 9] 11] 13] [57], 58] 59] 63] 70] 71] In an optimistic way, one may think of an analogy between these results and the work on finding models of computation carried out in the 30 s, which has laid the foundation for the design of the electronic computers. In a similar fashion, the results obtained about ....

J.Reif. Parallel molecular computation: models and simulation. To appear in SPAA'95, also at http://www.cs.duke.edu/~reif/HomePage.html.

....successfully been dealt with in vivo, they should not have solutions in vitro. As a step in this direction, in [41] a mechanism is suggested, based on membranes that separate volumes (vesicles) and on active systems that transport selected chemicals across membranes. Moreover, 4] 61] 47] [52], suggest how familiar computer design principles for electronic computers can be exploited to build molecular computers. 4 Current Research: a Sample As mentioned before, the current research in DNA computing has two aspects: practical and theoretical. This section will give a sample of both, ....

J.Reif. Parallel molecular computation: models and simulations. Proceedings: 7th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'95) Santa Barbara, CA, July 1995, pp. 213-223.

....can be done and cannot be done with molecules, much more basic experiments are necessary. Our results would be a breakthrough for more realistic discussion about the computational power of molecules. Some papers have referred to the importance of rotation and join operation of DNA molecules [6] [7]. Our rotation procedure looks like what is mentioned in [6] but ours use less enzymes and is more reliable. Our concatenation (and join) procedure is much more efficient than previously proposed one[7] because we join tuples without examining contained data. II. Materials and Methods A. ....

....papers have referred to the importance of rotation and join operation of DNA molecules [6] 7] Our rotation procedure looks like what is mentioned in [6] but ours use less enzymes and is more reliable. Our concatenation (and join) procedure is much more efficient than previously proposed one[7], because we join tuples without examining contained data. II. Materials and Methods A. Sequence Design An optimal sequence for computation should not form secondary structure by itself, and should bind only to the specific site where it is expected to anneal. Short DNA such as PCR primers can ....

J.H. Reif, "Parallel molecular computation: Models and simulations, " in Proc. of the 7th Annual Symposium on Parallel Algorithms and Architectures, 1995, pp. 213--223.

....it requires O(n 3 ) biological steps in the worst case. In contrast to their technique, our approach does not need exponential size of solution soup. Further, the set of DNA sequences coding the simple Horn program can be repeatedly used for the recognition of the same grammar. Recently Reif ([Rei95]) has proposed a parallel molecular computation model PAM which can theoretically efficiently simulate a Non Deterministic Turing Machine and a PRAM, where a PA Match operation, equivalently the join operation in relational database, plays an important role. However, his biological proposal to ....

J. H. Reif. Parallel Molecular Computation : Models and Simulations. Proc. of Seventh Annual ACM Symposium on Parallel Algorithms and Architectures, 1995.

....characterizations, while a clear difference of our models from others is that we use a collection of set (test tube) operations suitable for molecular biological implementation and our models benefit from a great efficiency of molecular parallelism in more natural manner. Recently Reif ([Rei95]) has proposed a parallel molecular computation model PAM which can theoretically efficiently simulate a nondeterministic Turing machine and a PRAM, where a PA Match operation, equivalently the join operation in relational database, is employed in an effective manner. Due to the complexity of the ....

J.H.Reif. Parallel Molecular Computation : Models and Simulations. Proc. of Seventh Annual ACM Symposium on Parallel Algorithms and Architectures(SPAA'95), pp.213-223, 1995.

....a mathematical foundation. To this aim, models of DNA computing have been proposed and studied from the point of view of their computational power and their in vitro feasibility (see, for example, 2] 3] 8] 21] 30] 35] 54] 50] 22] 40] 39] 16] 13] 51] 31] 9] 11] [41], 43] 44] 53] Overall, the existence of different models with complementing features shows the versatility of DNA computing and increases the likelihood of practically constructing a DNA computing based device. On the other side, the theoretical research on DNA computing includes designing ....

J.Reif. Parallel molecular computation: models and simulations. Proceedings: 7th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'95) Santa Barbara, CA, July 1995, pp. 213-223.

....believe that our model will perform more rapid computations than conventional computers on a range of feasible problem sizes. One possible way around the weight problem (for problems in the complexity class P , for example) is to look for implementation of existing computing paradigms in DNA. Reif [18] points to one possible way forward, describing a method for simulating a CREW PRAM using DNA. However, Reif uses the error prone hybridization separation method described earlier, which we believe may be avoided by our methodology. Another development is the proposed [19] DNA and restriction ....

John H. Reif. Parallel molecular computation: Models and simulations. In Proceedings of the Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA), Santa Barbara, June 1995.

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John Reif. Parallel molecular computation: Models and simulations. Algorithmica, Special Issue on Computational Biology, 1998.

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John Reif. Parallel molecular computation: Models and simulations. Algorithmica, Special Issue on Computational Biology, 1998.

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John Reif. Parallel molecular computation: Models and simulations. Algorithmica, Special Issue on Computational Biology, 1998.

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J. H. Reif. Parallel molecular computation: Models and simulations. In Proceedings: 7th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA'95) Santa Barbar,CA, pages 213--223, 1999.

....constant number of layers (as is done with VLSI models) Besides our contribution of this formal MF BMC model, the paper contains two other classes of results. The main result is the volume and time efficient algorithm for message routing in the MF BMC model, specifically useful for PA Match [23]. We will show that routing of strands between chambers will occur in time O( N DeltaD m Deltan ) where N is the number of strands in the MF BMC, n is the number of chambers where RDNA operations are occurring, D is the diameter of the topology of the layout of the chambers, and m is ....

....is perfect, has obvious benefits, such as classifying all the data into categories rapidly. However, most techniques developed and used in the field of BMC thus far have an implementation that closely matches but is not the perfect analogue of the abstraction that BMC algorithm designers use [1, 23]. The gap between reality and theory has many aspects to it and has been attacked in many different ways, such as the development of systematic techniques to reduce errors [1, 4, 18] An aspect which this paper seeks to address is the desired and undesired interaction of reactants. In certain ....

John Reif. Parallel molecular computation: Models and simulations. Algorithmica, Special Issue on Computational Biology, 1998.

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John H. Reif. Parallel molecular computation: Models and simulations. In Proceedings of the Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA95), Santa Barbara, June 1995.

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John H. Reif. Parallel molecular computation: Models and simulations. Algorithmica, 1998. Special issue on Computational Biology. See also [9].

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J. H. Reif. Parallel molecular computation: Models and simulations. In Proceedings of the 7th ACM Symposium on Parallel Algorithms and Architectures, 1995.

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J.H.Reif. Parallel Molecular Computation : Models and Simulations. Proc. of Seventh Annual ACM Symposium on Parallel Algorithms and Architectures(SPAA'95), pp.213-223, 1995.

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J.H. Reif. Parallel molecular computation: Models and simulations. Proceedings of the Seventh Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA95), Santa Barbara, pages 213--223, June 1995.

No context found.

J.H.Reif. Parallel Molecular Computation : Models and Simulations. Proc. of Seventh Annual ACM Symposium on Parallel Algorithms and Architectures(SPAA'95), pp.213-223, 1995.

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