Faulhammer, D.; Cukras, A.R.; Lipton, R.J.; Landweber, L.F. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. U. S. A. 2000, 97 (4), 1385 -- 1389.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....where for each i, 1 i t, S(i) is a set of strings, all having the same length l i . The l i are not required to be equal. Complete combinatorial sets are also used to represent solution spaces in biocomputation that find a satisfying assignment to an instance of the Satisfiability problem [6, 11]. Again, for this use, all strands in the complete combinatorial sets should form no secondary structure. These applications motivate the structure freeness problem for combinatorial sets: given the description of a complete combinatorial set S, determine whether all of the 2 t strands in S ....

D. Faulhammer, A.R. Cukras, R.J. Lipton, and L. F. Landweber, "Molecular computation: RNA solutions to chess problems," Proc. Natl. Acad. Sci. USA, 97, 2000, 1385--1389.

....sets that match or exceed the best previously known constructions. 1 Introduction DNA codes, i.e. sets of DNA strands that satisfy combinatorial constraints, play an important role in various approaches to biomolecular computation [7, 8] nanostructure design [16, 18] and molecular tagging [1, 2, 6]. Good code design is important in order to minimise errors due to non specific hybridization between distinct strands and their complements, to obtain a higher information density, and to obtain large sets of strands for large scale applications. For the types of combinatorial constraints ....

....DNA codes. Deaton et al. 3, 4] and Zhang and Shin [19] used genetic algorithms for designing DNA codes, and provide some small sets of code words that satisfy well motivated combinatorial constraints. However, some details of their algorithms are not specified in these papers. Faulhammer et al. [6] also use a stochastic search approach and provide an implementation of their algorithm. In all cases, while small sets of code words produced by the algorithms have been presented (and the papers make other contributions independent of the word design algorithms) little or no analysis of ....

[Article contains additional citation context not shown here]

D. Faulhammer, A.R. Cukras, R.J. Lipton, and L.F. Landweber, "Molecular computation: RNA solutions to chess problems," Proc. Natl. Acad. Sci. USA, 97: 1385-1389, 2000.

....actual coding sequences in the context of the space of possibilities. Our algorithms could also prove useful in the design of RNA sequences with speci c combinations of protein encoding and structure, for example in computing with nucleic acid molecules [1] A group at Princeton University [10, 12] recently solved the 3 3 knights tour problem using RNA, the largest such molecular computing experiment to date. This paper is organized as follows. Section 2 provides a quick overview of RNA secondary structure. Section 3 discusses the binding energy model for RNA folding in greater detail. ....

D. Faulhammer L. Landweber, R. Lipman and A. Cukras. Molecular computation: RNA solutions to chess problems. Proc. National Academy of Science, 97, 2000.

.... as a function of the free energy of the duplex and other parameters [57] Since multiple hybridization reactions involving distinct DNA words may happen in a single step of a DNA computation, it is desirable that the melting temperature of the duplexes created in each reaction be in a small range [10, 19, 61] or above some threshold [3] A third, much less accurate measure of the stability of a word is its GC content, or fraction of G s and C s. However because it is easy to measure and is amenable to combinatorial analysis, it is often used in constraining DNA words [21, 32, 49, 61] A related ....

....window spans at most two words. Many designs require that windows, pairs of windows, and windows and the complements of DNA words satisfy constraints based on the melting temperature, GC content, mismatch distance, repeated bases, and subwords distance measures listed in sections 2.2.1 and 2.2. 2 [4, 10, 19, 48, 54]. Since a window may span more than one word, such constraints in effect involve multiple words. For example, Braich et al. 4] design their word set so that words have length 15 and are over a three letter alphabet (no G s) The word set has no repeated runs of length more than 4. In addition, ....

[Article contains additional citation context not shown here]

Faulhammer, D., Cukras, A. R., Lipton, R.J., and L. F. Landweber, "Molecular computation: RNA solutions to chess problems," Proc. Natl. Acad. Sci. USA, 97: 1385-1389.

....take place at many molecules simultaneously, parallel computations involving millions of operations seem possible. Methods for solving several well known NP complete problems have been proposed, and have been performed on small examples in many cases [Adl94, Adl98, LWF 00] SGK 00, OKLL97, FCLL00] Moreover, based on certain biochemical reactions, formal models capturing the power of DNA computing have been developed [Lip95] Many arithmetical operations, like addition and multiplication of binary numbers can be performed in parallel on classical hardware. In this paper we consider the ....

....the hybridization kinetics. A possible approach to keep sequences to an expected constant length could be to involve splicing mechanisms. Splicing removes middle parts of the sequence, e.g. removes the q i p i 0 i A part from p i 1 A1 i q i p i A0 i 0) For example, if we use RNA instead of DNA [FCLL00] we could exploit self splicing reactions. Currently there are limitations in exploiting splicing mechanisms: 1) RNA is less stable than DNA. 2) Splicing mechanisms are complex but generally irreversible. They depend on consensus sequences. Self splicing introns, which could be used, are RNA ....

D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. USA 97, pages 1385-1389, 2000.

....procedure to solve instances of the satisfiability problem. Contact: hubert.hug medizin.uni ulm.de schuler informatik.uni ulm.de 2 Introduction DNA can be used to solve computational problems by DNA hybridization (Adleman, 1994; Guarnieri et al. 1996; Ouyang et al. 1997; Liu et al. 2000; Faulhammer et al. 2000). In a similar way antibodies which specifically recognize peptide sequences can be used for calculation. One peptide can contain more than one recognition site (epitope) for the same or different antibodies. In the proposed model, peptides represent the search space of a given problem and ....

Faulhammer, D., Cukras, A. R., Lipton, R. J., & Landweber, L. F. (2000). Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. USA, 97, 1385-1389.

....Matter, 812] Physics Letters, 172] Physics Letters A, 120, 169] Physics of the Earth and Planetary Interiors, 573] Plasma Phys. Controlled Fusion, 793] Proc. SPIE Int. Soc. Opt. Eng. USA) 788] Proceedings of the National Academy of Sciences of the United States of America, [629, 913, 923, 961, 1025, 1044] Proceedings of the National Science Council, Republic of China, Part A: Physical Science and Engineering, 144] Protein Engineering, 932, 949, 978, 1023, 1028, 1077] Protein Science, 916, 953, 997, 1015, 1034, 1100, 1106] Proteins: Structure, Function, and Genetics, 912, 936, 954, 967, ....

....A. 655, 665, 690] Cornet, F. H. 565] Couchman, Luise S. 28] Coulomb, J. L. 510] Coveney, Peter V. 1042] Cox, J. Colin, 616] Cremers, A. B. 889] Crutch eld, James P. 123] Csoka, R. 856, 872] Csoka, T. 325, 1182] Csukas, B. 309] Cui, Y. 1053] Cukras, Anthony R. [629] Cummings, M. D. 1149] Currey, Kathleen M. 636] Curtis, Andrew, 189] Cusick, T. A. 672] Cwaduru, Raghu K. 831] Cwik, Tom, 518, 750] Daeyaert, F. D. 1065] D Agostino, G. 304, 1172] Daida, Jason M. 838, 850, 558] Da Costa Filho, Paulo Augusto, 376] Dandekar, Thomas, 917, ....

[Article contains additional citation context not shown here]

Dirk Faulhammer, Anthony R. Cukras, Richard J. Lipton, and Laura F. Landweber. Molecular computation: RNA solutions to chess problems. Proceedings of the National Academy of Sciences of the United States of America, 97(4):1385-1389, 15. February 2000. ga00aFaulhammer.

No context found.

Faulhammer, D.; Cukras, A.R.; Lipton, R.J.; Landweber, L.F. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. U. S. A. 2000, 97 (4), 1385 -- 1389.

No context found.

D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber. Molecular computation: RNA solutions to chess problems. PNAS, vol. 97 (2000), 1385-1389.

No context found.

D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber. Molecular computation: RNA solutions to chess problems. PNAS, vol. 97 (2000), 1385--1389.

No context found.

D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber. Molecular computation: RNA solutions to chess problems. Proc. Natl Acad. Sci. USA, 97:1385 -- 1389, 2000.

No context found.

D. Faulhammer, A. R. Cukras, R. J. Lipton, and L. F. Landweber. Molecular computation: RNA solutions to chess problems. PNAS, vol. 97 (2000), 1385--1389.

No context found.

Faulhammer,D., Cukras,A.R., Lipton,R.J. and Landweber,L.F. (2000) Molecular computation: RNA solutions to chess problems. Proc. Natl Acad. Sci. USA, 97, 1385--1389.

No context found.

Faulhammer, D., Cukras, A. R., Lipton, R.J., and L. F. Landweber, \Molecular computation: RNA solutions to chess problems," Proc. Natl. Acad. Sci. USA, 97: 1385-1389.

No context found.

Faulhammer, D., Cukras, A. R., Lipton, R.J., and Landweber, L.F. Molecular computation: RNA solutions to chess problems. Proc. Natl. Acad. Sci. USA, 97: 1385-1389.

Online articles have much greater impact   More about CiteSeer.IST   Add search form to your site   Submit documents   Feedback  

CiteSeer.IST - Copyright Penn State and NEC