Cilfone Nicholas A, Kirschner Denise E, Linderman Jennifer J
Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
Cell Mol Bioeng. 2015 Mar;8(1):119-136. doi: 10.1007/s12195-014-0363-6.
Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level.
生物学相关过程在多个时空尺度上运行。为了使计算建模方法能够模拟这种生物学复杂性，各个尺度的模型必须以允许跨尺度动态信息交换的方式进行链接。一种强大的方法是将离散建模方法（基于主体的模型，ABM）与连续模型相结合，形成混合模型。混合多尺度ABM已被用于模拟生物系统的涌现反应。在这里，我们回顾混合多尺度ABM的两个方面：链接各个尺度的模型以及有效地求解所得模型。我们讨论与链接各个尺度模型相关的计算选择，同时保持模型的易处理性。我们展示了在混合多尺度ABM背景下现有数值方法的实现。通过一个描述感染的示例模型，我们展示了各种数值方法组合的相对计算速度。混合多尺度ABM的有效链接和求解是模型可移植性、模块化以及在系统层面理解生物现象中应用的关键。
