Genetic algorithms + data structures = evolution programs (3rd ed.)
Genetic algorithms + data structures = evolution programs (3rd ed.)
DNA sequence design using templates
New Generation Computing
The Fidelity of the Tag-Antitag System
DNA 7 Revised Papers from the 7th International Workshop on DNA-Based Computers: DNA Computing
A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Algorithms for Testing That Sets of DNA Words Concatenate without Secondary Structure
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Development, evaluation and benchmarking of simulation software for biomolecule-based computing
Natural Computing: an international journal
Natural Computing: an international journal
Statistical thermodynamic analysis and designof DNA-based computers
Natural Computing: an international journal
Introduction to Computational Chemistry
Introduction to Computational Chemistry
Efficiency and reliability of DNA-based memories
GECCO'03 Proceedings of the 2003 international conference on Genetic and evolutionary computation: PartI
Statistical thermodynamic analysis and designof DNA-based computers
Natural Computing: an international journal
Designing nucleotide sequences for computation: a survey of constraints
DNA'05 Proceedings of the 11th international conference on DNA Computing
DNA'06 Proceedings of the 12th international conference on DNA Computing
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A principal challenge facing the development and scaling of biomolecular computers is the design of physically well-motivated, experimentally validated simulation tools. In particular, accurate simulations of computational behavior are needed to establish the feasibility of new architectures, and to guide process implementation, by aiding strand design. Key issues accompanying simulator development include model selection, determination of appropriate level of chemical detail, and experimental validation. In this work, each of these issues is discussed in detail, as presented at the workshop on simulation tools for biomolecular computers (SIMBMC), held at the 2003 Congress on Evolutionary Computation. The three major physical models commonly applied to model biomolecular processes, namely molecular mechanics, chemical kinetics, and statistical thermodynamics, are compared and contrasted, with a focus on the potential of each to simulate various aspects of biomolecular computers. The fundamental and practical limitations of each approach are considered, along with a discussion of appropriate chemical detail, at the biopolymer, process, and system levels. The relationship between system analysis and design is addressed, and formalized via the DNA Strand Design problem (DSD). Finally, the need for experimental validation of both underlying parameter sets and overall predictions is discussed, along with illustrative examples.