Multicellular Models Bridging Subcellular Biochemistry to Population Dynamics
Cell signaling and gene transcription occur at faster time scales compared to cellular death, division, and evolution. Bridging these multiscale events in a model is computationally challenging. We introduce a framework for the systematic development of multiscale cell population models. Using message passing interface (MPI) parallelism, the framework creates a population model from a single-cell biochemical network model. It launches parallel simulations on a single-cell model and treats each stand-alone parallel process as a cell object. MPI mediates cell-to-cell and cell-to-environment communications in a server-client fashion. In the framework, model-specific higher level rules link the intracellular molecular events to cellular functions, such as death, division, or phenotype change. Cell death is implemented by terminating a parallel process, while cell division is carried out by creating a new process (daughter cell) from an existing one (mother cell). We first demonstrate these capabilities by creating two simple example models. In one model, we consider a relatively simple scenario where cells can evolve independently. In the other model, we consider interdependency among the cells, where cellular communication determines their collective behavior and evolution under a temporally evolving growth condition. We then demonstrate the framework's capability by simulating a full-scale model of bacterial quorum sensing, where the dynamics of a population of bacterial cells is dictated by the intercellular communications in a time-evolving growth environment.
M. A. Islam et al., "Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics," Processes, vol. 6, no. 11, MDPI AG, Nov 2018.
The definitive version is available at https://doi.org/10.3390/pr6110217
Chemical and Biochemical Engineering
Intelligent Systems Center
Second Research Center/Lab
Center for High Performance Computing Research
Keywords and Phrases
Cell population dynamics; Gillespie method; Message passing interface; Multiscale modeling; Quorum sensing
International Standard Serial Number (ISSN)
Article - Journal
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01 Nov 2018