2018/06/28 by Adrien Coulier, Andreas Hellander, Coulier, Adrien +1
Biochemistry, Genetics and Molecular Biology · Engineering · #Cell Behavior (q-bio.CB) #FOS: Biological sciences #Gene Regulatory Network Analysis #Molecular Communication and Nanonetworks #Quantitative Methods (q-bio.QM) #Single-cell and spatial transcriptomics
paper · pdf · doi:10.48550/arxiv.1806.10889
openalex publication_date 2018/06/28 · openalex created_date 2022/09/21 · openalex updated_date 2026/07/28
We develop a modeling and simulation framework capable of massively parallel\nsimulation of multicellular systems with spatially resolved stochastic kinetics\nin individual cells. By the use of operator-splitting we decouple the\nsimulation of reaction-diffusion kinetics inside the cells from the simulation\nof molecular cell-cell interactions occurring on the boundaries between cells.\nThis decoupling leverages the inherent scale separation in the underlying model\nto enable highly horizontally scalable parallel simulation, suitable for\nsimulation on heterogeneous, distributed computing infrastructures such as\npublic and private clouds. Thanks to its modular structure, our frameworks\nmakes it possible to couple just any existing single-cell simulation software\ntogether with any cell signaling simulator. We exemplify the flexibility and\nscalability of the framework by using the popular single-cell simulation\nsoftware eGFRD to construct and simulate a multicellular model of Notch-Delta\nsignaling over OpenStack cloud infrastructure provided by the SNIC Science\nCloud.\n