Bacteria - Phage Biological Computer

Bio-computer research is an important part of computer science, its main idea is using biochemical reactions to stimulate computing manipulations. Based on biomolecules' tremendous parallel processing capability, the potential of bio-computer in solving NP problems has attracted more and more attentions. From 1994 to now is a decade of bio-computer's booming development, bio-computer transfers from theoretical research to experimental proving.Now almost all bio-computers are designed in vitro, not in vivo, in vitro means using biochemical reactions outside of life's body to stimulate computing. The advantage of in vitro computers is easily designing and realizing, their disadvantage is requiring human's participation and devices' assistance, and without these conditions, in vitro computers can not work automatically. Such computers do not use life's automaticity to control computing, but merely take biomolecules as data storage and tools in computing, like DNA computer.If embedding computing inside life's body, life's automaticity can be effective in controlling computing. The design of in vivo computers is more complex than in vitro computers, not only because the insufficiency of knowledge in cellular environment and self-control mechanism, but also the unknowing impact on life if computing is embedded inside."bacteria-bacteriophage" combining bio-computer (short in bacteria-phage computer) is an attempt to design an in vivo computer, and also an exploration of the possibility of embedding computing manipulation inside life's body. Bacteria-phage computer's basic idea is to insert biochemical reactions to simulate computing in the process of phages' infecting bacteria. Bacteria, phage and plasmid consist the hardware of bacteria-phage computer, bacteria's genome codes computing tool enzyme genes, phage's genome codes character tape and computing starting genes and plasmid codes insertion rules set. In one process of infection, computing starting genes are transcribed to express anti-inhibiting proteins which can combine with inhibiting proteins into complexes and disable their function, inhibiting proteins are some specific proteins which can inhibit computing tool enzyme genes' transcription. After that, computing tool enzyme genes' transcription will be activated. Computing tool enzymes are related to computing manipulation, like restriction endonucleases and ligase. Bacteria-phage computer takes insertion/deletion systems as its theoretical model, this model has the same computing capability as Turing machines.Bacteria-phage employs restriction-ligation mechanism to simulate insertion-deletion systems. Computing tool enzymes manipulate phage genome and plasmid DNA based on this mechanism.Although bacteria-phage computer's design is based basic life's principle and without unpractical imagination, to realize it will cost time. One hand is that the difficulty of designing in vivo computers restricts the development; the other hand is that the research on in vivo computers should synchronize the research on basic biology. Bacteria-phage computer can only be a certain stage in in vivo computers research, which makes a theoretical analysis of the feasibility, it would have symbolistic meaning rather than applied value.