期刊
CELLULAR AND MOLECULAR BIOENGINEERING
卷 8, 期 1, 页码 119-136出版社
SPRINGER
DOI: 10.1007/s12195-014-0363-6
关键词
Multi-scale modeling; Hybrid modeling; Agent-based modeling; Numerical implementation; Linking models; Tuneable resolution
资金
- NIH [R01 EB012579, R01 HL 110811]
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 Mycobacterium tuberculosis 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.
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