mRNA Translation Hardware Accelerator

Background: The Totally Asymmetric Simple Exclusion Process (TASEP) model has proved to be useful for describing the dynamics for ribosomal movement over mRNA molecules inside a cell. Till now the simulations of this model have been implemented via Software (SW) which requires long simulation time. Thus, in this project we aimed at implementing for the first time this model in Hardware (HW).

Results: We demonstrated the ability of our approach to generate TASEP HW which is based on real E. coli mRNAs. The implementation was fitted to the resources available on FPGA chip (logic gates and memories) and describes the dynamics of several hundreds of mRNA’s and ribosomes on an FPGA. We have demonstrated that the rate of the simulation in HW is significantly higher than in SW.

Conclusion: HW implementation of the algorithm will allow faster estimation of the dynamics of mRNA translation using smaller space. It could also be used for various biomedical applications including synthetic biology.