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ABSTRACT
Along with the rapid development of synthetic biology, the technology of biological computers has become increasingly mature in recent years. In this paper, we propose a structure for a biological central processing unit (Bio-CPU) based on biological binary computing features. The Bio-CPU is constructed from a class of biological circuits with specific functions and a genetic clock source to trigger a series of sequential steps. The biological logic gates change their outputs at two protein concentration levels (active and inactive statuses), and the genetic clock provides a periodic signal to synchronize actions of related biological sequential logic circuits. Design of the Bio-CPU partly imitates a silicon CPU with modifications to fit the features of biological units. The proposed structure consists of three major parts: a biological arithmetic logic unit (Bio-ALU), a biological control unit (Bio-CU), and a biological memory unit (Bio-MU). Biological details of the system synthesis are explained. Demonstrations have been conducted and presented to illustrate the function of each functional module.
Nomenclature
| Ãi | = | Fourier coefficient |
| hi | = | Hill coefficients related to the cooperativity between TF protein inputs and the corresponding biding sites |
| K1 | = | independent binding strength of regulator X1 to the promoter |
| KR | = | independent binding strength of RNA polymerase to the promoter |
| M | = | sum of the total number of harmonics |
| mi | = | concentration of mRNA |
| n | = | Hill coefficient |
| pi, pj | = | protein concentrations of three genes |
| R | = | RNA polymerase concentration |
| si | = | shaping coefficients |
| t | = | time |
| wij | = | effect of environmental noises |
| X | = | single TF protein input |
| X1 | = | concentrations of regulator |
| α | = | maximal production |
| α0 | = | leakiness of promoter |
| αi | = | transcription rate of mRNA |
| β | = | degradation rate constant |
| γpi | = | decay rates of proteins |
| γmi | = | decay rates of mRNA |
| η | = | ratio of protein decay rate to the mRNA decay rate |
| ωi | = | cycle frequency |
Disclosure statement
No potential conflict of interest was reported by the authors.