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Cilfone NA, Kirschner DE, Linderman JJ. Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cell Mol Bioeng. 2015;8(1):119-136doi: 10.1007/s12195-014-0363-6.
Cilfone, N. A., Kirschner, D. E., & Linderman, J. J. (2015). Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cellular and molecular bioengineering, 8(1), 119-136. https://doi.org/10.1007/s12195-014-0363-6
Cilfone, Nicholas A, et al. "Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems." Cellular and molecular bioengineering vol. 8,1 (2015): 119-136. doi: https://doi.org/10.1007/s12195-014-0363-6
Cilfone NA, Kirschner DE, Linderman JJ. Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cell Mol Bioeng. 2015 Mar;8(1):119-136. doi: 10.1007/s12195-014-0363-6. PMID: 26366228; PMCID: PMC4564133.
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Cell Mol Bioeng. 2015 Mar;8(1):119-136. doi: 10.1007/s12195-014-0363-6.

Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems.

Cellular and molecular bioengineering

Nicholas A Cilfone, Denise E Kirschner, Jennifer J Linderman

Affiliations

  1. Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
  2. Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.

PMID: 26366228 PMCID: PMC4564133 DOI: 10.1007/s12195-014-0363-6

Abstract

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

Keywords: Agent-Based Modeling; Hybrid Modeling; Linking Models; Multi-Scale Modeling; Numerical Implementation; Tuneable Resolution

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