Partial evaluation and automatic program generation
Partial evaluation and automatic program generation
Computability and complexity: from a programming perspective
Computability and complexity: from a programming perspective
Evolution as a Computational Engine
CSL '97 Selected Papers from the11th International Workshop on Computer Science Logic
Theoretical Computer Science - Special issue: Computational systems biology
Computation: finite and infinite machines
Computation: finite and infinite machines
Theory of Self-Reproducing Automata
Theory of Self-Reproducing Automata
Toward molecular programming with DNA
Proceedings of the 13th international conference on Architectural support for programming languages and operating systems
The many facets of natural computing
Communications of the ACM
On the Computational Power of Biochemistry
AB '08 Proceedings of the 3rd international conference on Algebraic Biology
The κ-Lattice: Decidability Boundaries for Qualitative Analysis in Biological Languages
CMSB '09 Proceedings of the 7th International Conference on Computational Methods in Systems Biology
Turing universality of the biochemical ground form
Mathematical Structures in Computer Science
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Abstract interpretation of cellular signalling networks
VMCAI'08 Proceedings of the 9th international conference on Verification, model checking, and abstract interpretation
DNA'04 Proceedings of the 10th international conference on DNA computing
Computational biology: a programming perspective
Formal modeling
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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.