Development of an Integrated Circuit that Performs Simulations of mRNA Translation Dynamics

Computational whole cell biophysical models of gene expression have revolutionized various bio-medical fields in recent years. Among others, they enable predicting the effect of mutations on diseases, designing various biotechnological products, and understanding various biomedical phenomena. However, the computational time of such models is extremely high, and often requires `cumbersome` usage of various servers and parallel computing.

In this project we develop the first compact hardware (integrated circuit) that performs a whole cell simulative model of mRNA translation in an efficient manner. Typically mRNA translation in eukaryotic cells is performed by an order of magnitude of 200,000 ribosomes that simultaneously translate 50,000 mRNAs (each of typical length of over 200 codons); thus, whole cell simulation of such models consumes very large amounts of computational resources. The ability of parallel processing is one of the most important features that separate the integrated circuit from a processor.

We specifically perform the following steps: 1) Design a whole cell simulation of mRNA translation for debugging/verification of the hardware; the model includes all the fundamental aspects of the process and multiple mRNA molecules and ribosomes. 2) Design and simulate the logic of the integrated circuit in an efficient manner using Verilog. 3) Burn the logic in to a Artix-7 FPGA (A field-programmable gate array) technology integrated in ZedBoard-Zynq development board. 4) Perform various types of validations of the FPGA.