The Fidelity of the Tag-Antitag System
DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
Physical modeling of biomolecular computers: Models, limitations, and experimental validation
Natural Computing: an international journal
Natural Computing: an international journal
Physical modeling of biomolecular computers: Models, limitations, and experimental validation
Natural Computing: an international journal
International Journal of Knowledge-based and Intelligent Engineering Systems - Selected papers from the KES2004 conference
Successful preparation and analysis of a 5-site 2-variable DNA library
Natural Computing: an international journal
Dynamic neighborhood searches for thermodynamically designing DNA sequence
DNA13'07 Proceedings of the 13th international conference on DNA computing
Displacement whiplash PCR: optimized architecture and experimental validation
DNA'06 Proceedings of the 12th international conference on DNA Computing
DNA'06 Proceedings of the 12th international conference on DNA Computing
Analysing the density of subgroups in valued relationships based on DNA computing
KES'06 Proceedings of the 10th international conference on Knowledge-Based Intelligent Information and Engineering Systems - Volume Part III
Hi-index | 0.00 |
A principal research area in biomolecular computing is the development of analytical methods for evaluating computational fidelity and efficiency. In this work, the equilibrium theory of the DNA helix-coil transition is reviewed and expanded, as applied to the analysis and design of oligonucleotide-based computers. After a review of the equilibrium apparatus for modeling the helix-coil transition for single dsDNA species, application to complex hybridizing systems is discussed, via decomposition into component equilibria, which are presumed to proceed independently. The alternative approach, which involves estimation of a mean error probability per hybridized structure, or computational incoherence, ε is then presented, along with a discussion of a special-case exact solution (directed dimer formation), and an approximate general solution, applicable to conditions of uniform fractional-saturation. In order to clarify the opposing nature of the predictions of these two models, simulations are presented for the uniform saturation solution for ε, as applied to a small Tag--Antitag (TAT) system, along with the behavior expected via isolated melting curves. By a comparison with the predictions of a recent, TAT-specific solution for ε, the views provided by these generalized approximate models are shown to define the opposing limits of a more general error-response.