Date of Award

Spring 5-2014

Degree Type

Masters Thesis

Degree Name

Master of Science (MS)


Biological Sciences

Committee Chair

Kenneth J. Curry

Committee Chair Department

Biological Sciences

Committee Member 2

Richard H. Bennett

Committee Member 2 Department

Biological Sciences

Committee Member 3

Franklin T. Heitmuller

Committee Member 3 Department

Geography and Geology


Three-dimensional reconstructions of marine fine-grained sediment open a new dimension for studying nano- and microscale organo-clay fabric important to improving and advancing organic matter (OM) sequestration and fluid flow dynamics modeling. I created 3-D reconstructions of clay fabric and pore pathways from serial sections and photographic mosaics obtained using transmission electron microscopy. These reconstructions show aggregations of clay domains, surrounding OM, and pore networks. I examined a Model sample (laboratory consolidated) with 1% OM and a Natural sample (polychaete fecal pellet) with high levels of OM. Three-dimensional reconstructions were segmented into 300 nm cube subsamples to make highly localized qualitative observations and quantitative measurements of porosity, particle and pore orientation and volume, and pore network tortuosity.

Flow pathway spreadsheet maps were created based on pore size and orientation. This technique allows tortuosity to be calculated for 3-D reconstructions while restricting porosity to a minimum boundary condition prior to determining tortuous pathways. Measurements of 2-D photographs and 3-D reconstructions using the same serial photographs showed that pathlengths measured for tortuosity were for the most part statistically similar. The range of porosities and the number of pathways through which flow could pass through the sample are significantly higher in 3-D analyses. Thus, measurements made from 2-D sediment pathway studies provide limited information, omitting a significant number of diffusion and flow pathways that cannot be resolved in two dimensions.