CC3D Model of Cells on Plate with Growth and Division

3D Model of Cells on Plate with Growth and DivisionSudin Bhattacharya

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Wan-Yun ChengChristopher EklundRory Conolly MotivationComputational modeling of in vitro data is sensitive to the surface area that cells present to the culture medium.Surface area varies with degree of confluency of the culture and among cells at a given degree of confluency.Agent-based computational modeling can provide spatially realistic simulations of cells growing in a culture dish, and of the surface area that each cell presents to the medium.Expect to help with characterization of how degree of confluency contributes to variability of in vitro data.Directly relevant to IVIVE.

2Agent-based modeling as a means for testing biological hypothesesAgent-based modeling (ABM) is a style of modeling in which individuals (cells) and their interaction with each other and their environment are explicitly represented.- Jeff Schank http://www.agent-based-models.com/blog/category/agent-based-modeling/

Virtual tissues

Cells in a culture dishWe use Monte Carlo (MC) simulations of a 3D multicellular ABM developed in CompuCell3D (free tool, Glazier et al. , Indiana U.)3Assumptions used for model developmentCells grow on a culture dish.Cells strongly adhere to dish.Cells adhere to each other less strongly.Periodic Boundary Conditions models growth and flux of cells in a square section of the dish.There is a distribution of initial cell sizes (cells are initially in different stages of cycle).Each cell grows gradually volume incremented by 1 unit every 5th MC step, and symmetrically divides into two when volume is roughly doubled (normal distribution about a mean doubling volume).Orientation of cell division is random.Cells unattached to dish die with an 80% probability monolayer of cells.4

Cell Growth5

Cell Growth top view6

Distribution of Initial Cell Volumes (125 245 units) and Normal Distribution of Doubling Volume(225 275 units)

78Surface Area Vs. Time

Surface Area Vs. Confluence9

Confluence Vs. Time

10Surface Area Distribution among Cellst(MCS) = 0t(MCS) = 500t(MCS) = 1000t(MCS) = 1500t(MCS) = 2000t(MCS) = 2500t(MCS) = 2750t(MCS) = 3000

1112Data NeedsTime-course of confluence? Imaging of cell growth?

Distribution of cellular surface areas at various levels of confluence?

Laboratory measurementsCells under different confluenceAiming for different levels of confluence: low, medium, high, and over confluenceLow (10%-25% confluence)Imaging for 5 consecutive daysImage acquisition2D imageDIC or fluorescence image10 images at each level of confluence3D image (Z-stack)5 Z-stack images at each level of confluenceImage post processing2D image: cell surface area (NIS Elements)3D image: cell thickness (NIS Elements) and cell volume (MatLab)1313