Soft molecular computing

Molecular computing (MC) utilizes the complex interaction of biomolecules and molecular biology protocols to e ect computation. Lab experiments in MC are unreliable, ine cient, unscalable, and expensive compared to conventional computing standards. A critical issue in MC is therefore to test protocols to minimize errors and mishaps that can thwart experiments when actually run in vitro. The purpose of this paper is to describe Edna , an integrated software platform developed to address this problem. The platform will allow MC practicioners to use digital computers to gain insight on the performance of a protocol before it actually unfolds in the tube. Currently, Ednaprovides tools to nd good encodings for a given set of hybridization conditions, by design or evolution, tools to visualize the quality of these encodings, tools to estimate the complexity of given protocols based on bounded complexity, and a virtual test tube simulator based on local interactions between electronic DNA molecules. The virtual tube has allowed us to reproduce Adleman's experiment in silico. Edna includes graphical interfaces, click-and-drag facilities, is object-oriented, extensible, and so that it can easily evolve as the eld progresses.