To simulate the cell dynamics within mouse and human colonic crypts, many computational models have been developed. While real colonic crypts are shaped like test tubes, crypts were assumed as cylinders in several such models. However, possible drawbacks by modeling the crypt as a cylinder have not been investigated. Here we constructed a model considering a test-tube-like-shaped crypt in three-dimensional space, and simulated cell dynamics within it. The simulation results were compared with those obtained with a model using a cylinder crypt. We found that these two models showed different simulation results for the dynamics of expansion of a mutation occurred in a stem cell at the crypt bottom, and that the model using a test-tube-like-shaped crypt simulated the stem cell expansion more accurately. To simulate cell dynamics occurred in the lower part of the crypt, such as apoptosis and initial expansion of mutation, using a test-tube-like-shaped crypt is preferable. In a model assuming a cylinder crypt, it is considered that reported values for the required time of monoclonal conversion in a colonic crypt and its occurrence rate were overestimated and underestimated, respectively.

中文翻译：

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模拟肠道隐窝作为圆柱体以模拟小鼠和人类结肠隐窝内干细胞动力学的作用

为了模拟小鼠和人类结肠隐窝内的细胞动力学，已经开发了许多计算模型。虽然真实的结肠隐窝的形状像试管，但在几种这样的模型中，隐窝被假定为圆柱体。但是，尚未研究通过将隐窝建模为圆柱体而可能产生的缺陷。在这里，我们构建了一个模型，该模型考虑了三维空间中类似试管形的隐窝，并在其中模拟了细胞动力学。将仿真结果与使用圆柱隐窝的模型获得的仿真结果进行了比较。我们发现这两个模型对于隐窝底部干细胞中发生的突变的扩展动力学显示出不同的模拟结果，并且使用类似试管形隐窝的模型更准确地模拟了干细胞的扩展。为了模拟在隐窝下部发生的细胞动力学，例如凋亡和突变的初始扩展，优选使用试管状隐窝。在假设为圆柱隐窝的模型中，认为在结肠隐窝中进行单克隆转化所需时间的报告值及其发生率分别被高估和低估。