Towards Autonomous Molecular Computers

In this paper, we rst summarize the research that has been completed in the eld of DNA computing and the research problems that must be overcome if the technique of computing with molecules is to become practical. We then propose a new direction in research towards autonomous molecular computers , describe the author's work on the implementation of state machines using DNA molecules, and discuss the future of DNA computing from this perspective. DNA computing is an interdisciplinary eld of research straddling computer science and biochemistry (or bio-physics). It has been an area of active investigation since Adleman's paper in Science, which described a method for solving a DHPP (directed Hamiltonian path problem) using DNA molecules 1]. In this section, we brieey review the research into DNA computing that has been performed to date, summarize the research problems that must be solved for the eld to progress, and discuss the probable directions of future research in this eld. In the next section, we build upon the arguments developed in the rst section and propose a new direction in research, stemming from the idea of autonomous molecular computers, in connection with the author's work on the implementation of state machines using DNA molecules. We call a molecular computation autonomous if it proceeds without explicit operations performed from outside a test tube. At the end of the paper, we brieey touch upon DNA-based nano-scale construction, because autonomous computation is the key for the technology, and it is one of the promising areas to which DNA-computing will be applied. The paradigm of DNA computing, the Adleman-Lipton Paradigm, which was rst proposed by Adleman 1] and later expanded by Lipton 12], is one of data-parallel computation using DNA molecules. It aims to solve combi-natorial search problems such as DHPPs by generating and testing paths represented by DNA molecules. In the generation step, candidates for a solution to a search problem are randomly generated using hybridiza-tion between complementary sequences of DNA. Each DNA molecule that is generated represents one candidate for a solution. Within a test tube used in ordinary molecular biology experiments, about 10 12 candidates are generated, although there are many copies of each single candidate. In the testing step, techniques of molecular biology are then employed to check whether each candidate satisses the conditions necessary for it to represent a solution to the search problem. In this step, each condition is tested …