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Three-dimensional reconstructions of clay fabric open a new dimension to fluid flow dynamic modeling. The tortuosity of pore pathways (ratio of shortest tortuous path to a straight line point-to-point) is an important property of flow dynamics at the clay nano- and microscales. Transmission electron micrographs and image analysis software were used to create 3D images of model (laboratory consolidated) and natural (polychaete fecal pellet) marine clay sediment for analyzing pore network properties. Our 3D renderings were segmented into 300 nm subsample cubes, orientation and volume measurements were made, and short pathways were identified. Flow pathway spread sheet maps were created based on orientation and pore diameter size. Tortuosity measurements were compared between 2D images and 3D renderings of model and natural sediments.

The natural sediment was more densely packed with higher organic content than our model sample which contained 10% chitin. Three-dimensional renderings have significantly more accessible pathways than their comparable 2D counterparts, but if a path can be traversed though a comparable 2D and 3D sample, the path lengths will be similar. For example, we measured 3D tortuosity through a series of 300 nm subsample cubes having paths oriented in the X-direction within the 40–100% porosity range to be 1.04 for the model sample and 1.15 for the natural sample. The 2D tortuosity through sampling cubes with the sample parameters was measured as 1.05 for the model sample, but there were no flow paths with these parameters for the natural sample, thus flow paths are porosity dependent here.

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