Programming in biomolecular computation

TY - GEN

T1 - Programming in biomolecular computation

AU - Hartmann, Lars Røeboe

AU - Jones, Neil

AU - Simonsen, Jakob Grue

N1 - Conference code: 1

PY - 2010/12/21

Y1 - 2010/12/21

N2 - Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new “hardware” is not needed to solve new problems; and (last but not least) it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level.

AB - Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new “hardware” is not needed to solve new problems; and (last but not least) it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level.

U2 - 10.1016/j.entcs.2010.12.008

DO - 10.1016/j.entcs.2010.12.008

M3 - Conference article

SN - 1571-0661

VL - 268

SP - 97

EP - 114

JO - Electronical Notes in Theoretical Computer Science

JF - Electronical Notes in Theoretical Computer Science

T2 - 1st International Workshop on Interactions between Computer Science and Biology

Y2 - 10 June 2010 through 10 June 2010

ER -