DNA simulation of boolean circuits

In this paper we describe a simulation of Boolean circuits using standard bio-molecular techniques. Previously proposed simulations have been shown to run in time proportional to the size of the circuit. The simulation we present here runs in time proportional to the depth of the circuit. We describe the abstract model and its laboratory implementation, before concluding with a brief analysis.

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

[2]  Gheorghe Paun,et al.  DNA computing based on splicing: universality results. , 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[3]  Neil Weste,et al.  Principles of CMOS VLSI Design , 1985 .

[4]  Lynn Conway,et al.  Introduction to VLSI systems , 1978 .

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

[6]  Warren D. Smith.  DNA computers in vitro and vivo , 1995, DNA Based Computers.

[7]  Guillermo A. Cecchi,et al.  DNA based molecular computation: Template-template interactions in PCR , 1996, DNA Based Computers.

[8]  Paul W. K. Rothemund,et al.  A DNA and restriction enzyme implementation of Turing machines , 1995, DNA Based Computers.

[9]  Michael A. Harrison,et al.  Introduction to switching and automata theory , 1965 .

[10]  Kenneth E. Batcher,et al.  Sorting networks and their applications , 1968, AFIPS Spring Joint Computing Conference.

[11]  Nicholas Pippenger,et al.  On simultaneous resource bounds , 1979, 20th Annual Symposium on Foundations of Computer Science (sfcs 1979).

[12]  Henry M. Sheffer.  A set of five independent postulates for Boolean algebras, with application to logical constants , 1913 .

[13]  Paul E. Dunne,et al.  The Complexity of Boolean Networks , 1988 .

[14]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[15]  Martyn Amos,et al.  The Complexity and Viability of DNA Computations , 1997, BCEC.

[16]  Ingo Wegener,et al.  The complexity of Boolean functions , 1987 .

[17]  Mitsunori Ogihara,et al.  Simulating Boolean circuits on a DNA computer , 1997, RECOMB '97.