title: Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems.
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 describingMycobacterium tuberculosisinfection, 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.
authors.affiliation: Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Cilfone
authors.affiliation: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
authors.forename: Denise E
authors.initials: DE
authors.lastname: Kirschner
authors.affiliation: Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Linderman
keywords: Agent-Based Modeling; Hybrid Modeling; Linking Models; Multi-Scale Modeling; Numerical Implementation; Tuneable Resolution