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Output time series data for Microzone simulation

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Created: Sep 24, 2019 at 6:22 p.m.
Last updated: Oct 04, 2019 at 4:20 p.m.
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Recent experimental studies have detected the presence of anoxic microzones in hyporheic sediments. These microzones are small-scale anoxic pores, embedded within oxygen-rich porous media and can act as anaerobic reaction sites producing reduction compounds such as nitrous oxide, a potent greenhouse gas. Microbes are a key control on nutrient transformation in hyporheic sediment, but their associated biomass growth is also capable of altering hydraulic flux, leading to potential bioclogging. Here, we developed one of the first computational modeling approaches that combined hydraulics and microbial conditions to explore the continuous evolution of microzones in stream sediments. The model assessed stream and sediment conditions with different hydraulic flux (0.1-1.0 md-1 Darcy flux), nutrient concentrations (O2 = 8 mgl-1, OrgC = 20 mgl-1, NO-3 = 1.5-3 mgl-1, NH3 = 0.5-1 mgl-1), and biomass scenarios (with and without). The model domain is a pore network model with random sized pore-throat radii creating heterogeneous and anisotropic flow that is representative of a natural streambed comprised of medium sand with a hydraulic conductivity of 0.8 md-1. Results from 30 d simulations indicate that hyporheic microzone formation will occur and microzone distributions are not simply controlled by residence time alone, rather by the complex interactions of hydraulic flux, nutrient concentrations and biomass, with bioclogging having strong feedbacks on both hydraulics and nutrients. Under all conditions with biomass growth, anoxic microzones were unstable, perishing a few days after formation, because bioclogging primarily occurs near the influent (downwelling) area of the hyporheic zone. This bioclogging then shifting transport conditions from advection- to diffusion-dominated transport, removing all oxic regions in the hyporheic zone. Overall, results from the modeling show that anoxic microzones are likely to form under many hyporheic zone conditions and are dependant on the hydraulic flux and the nutrient transport occurring with the flux.

Subject Keywords


Reading the folder names

Each folder name in the Microzone folder corresponds to a specific simulation.

  1. First 2 numbers: refers to the Darcy flux of the simulation
  2. hi/lw : Refers to the nutrient boundary conditions
  3. nclog/clog : Presence or absnce of n refers to no bioclogging or bioclogging scenario respectively

Reading the data files

Each file consists of 721 columns of data corresponding to 720 hours with 0 representing the initial conditions. Each column has to be reshaped in a column major-order into a 150X150 matrix which will generate the value distribution at the corresponding hour for a left to right flow through the domain. If reshaping is done in a row-major order then the values will be rotated 90 degrees clockwise. Any file name containing X or Y letters means the values are for pore throats aligned in either X or Y direction with Y representing flow-normal direction and X flow-wise direction.



People or Organizations that contributed technically, materially, financially, or provided general support for the creation of the resource's content but are not considered authors.

Name Organization Address Phone Author Identifiers
Instituted for Cyber Enabled Research Michigan State University

How to Cite

Roy Chowdhury, S. (2019). Output time series data for Microzone simulation, HydroShare,

This resource is shared under the Creative Commons Attribution CC BY.


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