Aspects of Biomolecular Computing

This paper is intended as a survey of the state of the art of some branches of Biomolecular Computing. Biomolecular Computing aims to use biological hardware (biomare), rather than chips, to build a computer. We discuss the following three main research directions: DNA computing, membrane systems, and gene assembly in ciliates. DNA computing combines practical results together with theoretical algorithm design. Various search problems have been implemented using DNA strands. Membrane systems are a family of computational models inspired by the membrane structure of living cells. The process of gene assembly in ciliates has been formalized as an abstract computational model. Biomolecular Computing is a field in full development, with the promise of important results from the perspective of both Computer Science (models of computation) and Biology (understanding biological processes).

[1]  Rudolf Freund,et al.  Membrane Systems with Symport/Antiport Rules: Universality Results , 2002, WMC-CdeA.

[2]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[3]  Gheorghe Paun,et al.  DNA Computing: New Computing Paradigms , 1998 .

[4]  Gheorghe Paun,et al.  Regular Extended H Systems are Computationally Universal , 1996, J. Autom. Lang. Comb..

[5]  T. Head.  Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors. , 1987, Bulletin of mathematical biology.

[6]  Marian Gheorghe,et al.  Population P Systems , 2004, J. Univers. Comput. Sci..

[7]  Mario J. Pérez-Jiménez,et al.  A Linear Solution for QSAT with Membrane Creation , 2005, Workshop on Membrane Computing.

[8]  F Guarnieri,et al.  Maya Blue Paint: An Ancient Nanostructured Material , 1996, Science.

[9]  Ion Petre,et al.  Computation in Living Cells: Gene Assembly in Ciliates (Natural Computing Series) , 2003 .

[10]  Mark Daley,et al.  Template-guided DNA recombination , 2005, Theor. Comput. Sci..

[11]  Minyi Guo,et al.  Solving the Independent-set Problem in a Dna-based Supercomputer Model , 2005, Parallel Process. Lett..

[12]  Stuart A. Kurtz,et al.  Biological computing , 1998 .

[13]  Matteo Cavaliere.  Evolution-Communication P Systems , 2002, WMC-CdeA.

[14]  Gheorghe Paun,et al.  DNA computing, sticker systems, and universality , 1998, Acta Informatica.

[15]  K Sakamoto,et al.  Molecular computation by DNA hairpin formation. , 2000, Science.

[16]  Donald Beaver.  Computing with DNA , 1995, J. Comput. Biol..

[17]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[18]  M. Bétermier,et al.  Large-scale genome remodelling by the developmentally programmed elimination of germ line sequences in the ciliate Paramecium. , 2004, Research in microbiology.

[19]  Achim Schnaufer,et al.  Complex management: RNA editing in trypanosomes. , 2005, Trends in biochemical sciences.

[20]  Selim G. Akl,et al.  An analysis of the effect of parallelism in the control of dynamical systems , 2005, Parallel Algorithms Appl..

[21]  L F Landweber,et al.  Molecular computation: RNA solutions to chess problems , 2000, Proc. Natl. Acad. Sci. USA.

[22]  Andrzej Ehrenfeucht,et al.  Molecular operations for DNA processing in hypotrichous ciliates , 2001 .

[23]  Mario J. Pérez-Jiménez,et al.  A Linear-Time Solution to the Knapsack Problem Using P Systems with Active Membranes , 2003, Workshop on Membrane Computing.

[24]  Ion Petre,et al.  Formal systems for gene assembly in ciliates , 2003, Theor. Comput. Sci..

[25]  Ion Petre,et al.  Gene Assembly in Ciliates: Molecular operations , 2003 .

[26]  L. Adleman.  Computing with DNA , 1998 .

[27]  Richard J. Lipton,et al.  Breaking DES using a molecular computer , 1995, DNA Based Computers.

[28]  Masami Hagiya,et al.  From Molecular Computing to Molecular Programming , 2000, DNA Computing.

[29]  Giancarlo Mauri,et al.  Solving NP-Complete Problems Using P Systems with Active Membranes , 2000, UMC.

[30]  P D Kaplan,et al.  DNA solution of the maximal clique problem. , 1997, Science.

[31]  Gheorghe Paun,et al.  On the Splicing Operation , 1996, Discret. Appl. Math..

[32]  Michael D. Vose,et al.  The simple genetic algorithm - foundations and theory , 1999, Complex adaptive systems.

[33]  Raghavan Rama,et al.  P Systems with Replicated Rewriting , 2001, J. Autom. Lang. Comb..

[34]  Selim G. Akl.  Inherently Parallel Geometric Computations , 2006, Parallel Process. Lett..

[35]  A. E. Eiben,et al.  Introduction to Evolutionary Computing , 2003, Natural Computing Series.

[36]  Hiroshi Yoshida,et al.  Solution to 3-SAT by breadth first search , 1999, DNA Based Computers.

[37]  Lloyd M. Smith,et al.  DNA computing on surfaces , 2000, Nature.

[38]  Clifford R. Johnson,et al.  Solution of a 20-Variable 3-SAT Problem on a DNA Computer , 2002, Science.