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The high parallel scalability of the implementation allows for simulations of up to 10<jats:sup>9<\/jats:sup> individual cells (i.e., simulations at tissue spatial scales of up to 1\u2009cm<jats:sup>3<\/jats:sup> in size). With the recent advancements of the<jats:italic> Timothy<\/jats:italic> model, it has become critical to ensure appropriate performance level on emerging HPC architectures. For instance, the introduction of blood vessels supplying nutrients to the tissue is a very important step towards realistic simulations of complex biological processes, but it greatly increased the computational complexity of the model. In this paper, we describe the process of modernization of the application in order to achieve high computational performance on HPC hybrid systems based on modern Intel\u00ae MIC architecture. 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