Emergent Computation: Emphasizing Bioinformatics

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Springer Science & Business Media, Jan 7, 2005 - Medical - 423 pages
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Emergent Computation emphasizes the interrelationship of the different classes of languages studied in mathematical linguistics (regular, context-free, context-sensitive, and type 0) with aspects to the biochemistry of DNA, RNA, and proteins. In addition, aspects of sequential machines such as parity checking and semi-groups are extended to the study of the Biochemistry of DNA, RNA, and proteins. Mention is also made of the relationship of algebraic topology, knot theory, complex fields, quaternions, and universal turing machines and the biochemistry of DNA, RNA, and proteins.

Emergent Computation tries to avoid an emphasis upon mathematical abstraction ("elegance") at the expense of ignoring scientific facts known to Biochemists. Emergent Computation is based entirely upon papers published by scientists in well-known and respected professional journals. These papers are based upon current research. A few examples of what is not ignored to gain "elegance":

- DNA exists as triple and quadruple strands

- Watson-Crick complementary bases have mismatches

- There can be more than four bases in DNA

- There are more than sixty-four codons

- There may be more that twenty amino acids in proteins

While Emergent Computation emphasizes bioinformatics applications, the last chapter studies mathematical linguistics applied to areas such as languages found in birds, insects, medical applications, anthropology, etc.

Emergent Computation tries to avoid unnecessary mathematical abstraction while still being rigorous. The demands made upon the knowledge of chemistry or mathematics is minimized as well. The collected technical references are valuable in itself for additional reading.

 

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Contents

Ligases
65
A Review of Aspects of Automata Theory
75
The Beginning Numbers
87
DNA and RNA
115
Restriction Languages
117
DNA and RNA
145
DNA RNA Proteins
197
Inversion
205
Splicing Systems H Systems
259
tRNA Structure
313
Semigroups and Bioinformatics
339
Automata Theory and Disciplines Other than Bioinformatics
345
Appendix Shape Grammars
375
References
391
Index
415
Copyright

Turing Machines and SubTuring Machines
235

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About the author (2005)

Matthew Simon is developing oceanfront condominiums on the island of Eleuthera, Bahamas. www.ButtonwoodReserve.com. He resides in Fort Myers, Florida.

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