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Whole-cell model simulations for medicine and bioengineering

Karr, Jonathan R; Goldberg, Arthur P

Whole-cell models predict cell behaviors by modeling all molecular components and their interactions. Recently, we and other developed the first whole-cell model. The model represents the functionality of all 409 characterized genes and 725 metabolites throughout one life cycle of the reduced bacterium Mycoplasma genitalium. This model was validated against a broad range of data and provided insights into many previously unobserved cellular behaviors.

Simulating the behavior of a single cell required modest computing resources – 1 core-day of an Intel E5520 CPU, capable of 3.3×1015 double-precision floating-point operations during the computation. Sampling the organism’s behavior required 128 simulations. Nevertheless, we anticipate that exascale computing resources will be required to use more comprehensive and more accurate whole-cell models to personalize medicine and engineer bacteria.

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