Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware

Area of Science:

• Computational Biology
• Synthetic Biology
• Biophysics

Background:

• Intracellular biophysical simulations are increasingly vital for basic science and synthetic biology.
• Current software-based models are computationally intensive, limiting their scalability and speed due to millions of interacting components.
• Simulating complex biological processes like mRNA translation requires significant computational resources.

Purpose of the Study:

• To address the computational limitations of current intracellular biophysical simulations.
• To develop and demonstrate a novel hardware-based approach for accelerating these simulations.
• To specifically optimize the simulation of mRNA translation, a key cellular energy-consuming process.

Main Methods:

• Designed and implemented dedicated hardware specifically for intracellular biophysical simulations.
• Focused on simulating mRNA translation in *Escherichia coli* and *Saccharomyces cerevisiae* as a proof of concept.
• Enabled simulation of thousands of mRNAs and ribosomes concurrently.

Main Results:

• The developed hardware achieves simulation speeds orders of magnitude faster than comparable software solutions.
• Successfully simulated mRNA translation for thousands of mRNAs and ribosomes in model organisms.
• Demonstrated a significant acceleration in computational throughput for complex biological network modeling.

Conclusions:

• Dedicated hardware offers a viable and highly efficient solution for overcoming computational bottlenecks in biophysical simulations.
• This approach is crucial for handling the increasing volume of genomic data and the complexity of inferred biological models.
• The strategy holds promise for future applications, including the simulation of entire cells and all gene expression steps.