TY - JOUR
T1 - Accelerating Whole-Cell Simulations of mRNA Translation Using a Dedicated Hardware
AU - Shallom, David
AU - Naiger, Danny
AU - Weiss, Shlomo
AU - Tuller, Tamir
N1 - Publisher Copyright:
© 2021 The Authors. Published by American Chemical Society
PY - 2021/12/17
Y1 - 2021/12/17
N2 - In recent years, intracellular biophysical simulations have been used with increasing frequency not only for answering basic scientific questions but also in the field of synthetic biology. However, since these models include networks of interaction between millions of components, they are extremely time-consuming and cannot run easily on parallel computers. In this study, we demonstrate for the first time a novel approach addressing this challenge by using a dedicated hardware designed specifically to simulate such processes. As a proof of concept, we specifically focus on mRNA translation, which is the process consuming most of the energy in the cell. We design a hardware that simulates translation in Escherichia coli and Saccharomyces cerevisiae for thousands of mRNAs and ribosomes, which is in orders of magnitude faster than a similar software solution. With the sharp increase in the amount of genomic data available today and the complexity of the corresponding models inferred from them, we believe that the strategy suggested here will become common and can be used among others for simulating entire cells with all gene expression steps.
AB - In recent years, intracellular biophysical simulations have been used with increasing frequency not only for answering basic scientific questions but also in the field of synthetic biology. However, since these models include networks of interaction between millions of components, they are extremely time-consuming and cannot run easily on parallel computers. In this study, we demonstrate for the first time a novel approach addressing this challenge by using a dedicated hardware designed specifically to simulate such processes. As a proof of concept, we specifically focus on mRNA translation, which is the process consuming most of the energy in the cell. We design a hardware that simulates translation in Escherichia coli and Saccharomyces cerevisiae for thousands of mRNAs and ribosomes, which is in orders of magnitude faster than a similar software solution. With the sharp increase in the amount of genomic data available today and the complexity of the corresponding models inferred from them, we believe that the strategy suggested here will become common and can be used among others for simulating entire cells with all gene expression steps.
KW - FPGA
KW - TASEP
KW - gene expression optimization
KW - hardware acceleration
KW - mRNA translation
KW - whole-cell translation simulation
UR - http://www.scopus.com/inward/record.url?scp=85120430240&partnerID=8YFLogxK
U2 - 10.1021/acssynbio.1c00415
DO - 10.1021/acssynbio.1c00415
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C2 - 34813269
AN - SCOPUS:85120430240
SN - 2161-5063
VL - 10
SP - 3489
EP - 3506
JO - ACS Synthetic Biology
JF - ACS Synthetic Biology
IS - 12
ER -