Flow Partitioning in Fully Saturated Soil Aggregates

Transport in Porous Media

Volumn 103, Issue 2, 2014, Pages 295-314

  Yang, Xiaofan ^a   Richmond, Marshall C ^a   Scheibe, Timothy D ^a   Perkins, William A ^a   Resat, Haluk ^a,b  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b Washington State University   (United States)

Author keywords

Computational fluid dynamics; Flow partitioning; Hydraulic conductivity; Nutrient transport; Pore scale modelling; Porous media; Preferential flow pathways; Soil aggregate; Water saturation

Indexed keywords

ACCESS CONTROL; BIOGEOCHEMISTRY; CARBON; COMPUTATIONAL FLUID DYNAMICS; GROUNDWATER FLOW; HYDRAULIC CONDUCTIVITY; MICROORGANISMS; NUMERICAL METHODS; NUTRIENTS; ORGANIC COMPOUNDS; PORE SIZE; POROUS MATERIALS; SOILS; SOLUTE TRANSPORT;

FLOW PARTITIONING; NUTRIENT TRANSPORT; PORE-SCALE MODELLING; PREFERENTIAL FLOWS; SOIL AGGREGATE; WATER SATURATIONS;

AGGREGATES;

COMPUTATIONAL FLUID DYNAMICS; FLOW PATTERN; HYDRAULIC CONDUCTIVITY; NUTRIENT; PARTITIONING; POROUS MEDIUM; PREFERENTIAL FLOW; SATURATED MEDIUM; SATURATION; SOIL AGGREGATE; TRANSPORT PROCESS;

EID: 84899987199     PISSN: 01693913     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11242-014-0302-y     Document Type: Article

References (52)

1. Bailey, V. L., Bilskis, C. L., Fansler, S. J., McCue, L. A., Smith, J. L., Konopka, A.: Measurements of microbial community activities in individual soil macroaggregates. Soil Biol. Biochem. 48, 192-195 (2012). doi: 10. 1016/j. soilbio. 2012. 01. 004.
2. Balay, S., Brown, J., Buschelman, K., Gropp, W. D., Kaushik, D., Knepley, M. G., McInnes, L. C., Smith, B. F., Zhang, H.: PETSc Web page. http://www. mcs. anl. gov/petsc (2012).
3. Blunt, M. J.: Flow in porous media-pore-network models and multiphase flow. Curr. Opin. Colloid Interface Sci. 6(3), 197-207 (2001).
4. Cardenas, M. B.: Three-dimensional vortices in single pores and their effects on transport. Geophys. Res. Lett. 38(18), L18402 (2008). doi: 10. 1029/2008gl035343.
5. Carminati, A., Kaestner, A., Lehmann, P., Fluhler, H.: Unsaturated water flow across soil aggregate contacts. Adv. Water Resour. 31(9), 1221-1232 (2008). doi: 10. 1016/j. advwatres. 2008. 01. 008.
6. Celia, M. A., Dahle, H. K., Hassanizadeh, S. M.: Dynamic pore-scale network models for two-phase flow in porous media. Comput. Methods Water Resour. 1, 2, 217-223 (2000).
7. de Rochefort, L., Vial, L., Fodil, R., Maitre, X., Louis, B., Isabey, D., Caillibotte, G., Thiriet, M., Bittoun, J., Durand, E., Sbirlea-Apiou, G.: In vitro validation of computational fluid dynamic simulation in human proximal airways with hyperpolarized (3)He magnetic resonance phase-contrast velocimetry. J. Appl. Physiol. 102(5), 2012-2023 (2007). doi: 10. 1152/japplphysiol. 01610. 2005.
8. Dixon, A. G., Nijemeisland, M.: CFD as a design tool for fixed-bed reactors. Ind. Eng. Chem. Res. 40(23), 5246-5254 (2001). doi: 10. 1021/ie001035a.
9. Elkins, C. J., Alley, M. T.: Magnetic resonance velocimetry: applications of magnetic resonance imaging in the measurement of fluid motion. Exp. Fluids 43(6), 823-858 (2007). doi: 10. 1007/s00348-007-0383-2.
10. Eppinger, T., Seidler, K., Kraume, M.: DEM-CFD simulations of fixed bed reactors with small tube to particle diameter ratios. Chem. Eng. J. 166(1), 324-331 (2011). doi: 10. 1016/j. cej. 2010. 10. 053.
11. Feeney, D. S., Crawford, J. W., Daniell, T., Hallett, P. D., Nunan, N., Ritz, K., Rivers, M., Young, I. M.: Three-dimensional microorganization of the soil-root-microbe system. Microb. Ecol. 52(1), 151-158 (2006).
12. Ferziger, J. H., Peric, M.: Computational Methods for Fluid Dynamics, 3rd edn. Springer, Berlin (2001).
13. Gradwell, M. W.: Internal air contents of subsoil aggregates in some clay soils. N. Z. J. Agric. Res. 22(4), 615-620 (1979).
14. Kang, Q. J., Lichtner, P. C., Viswanathan, H. S., Abdel-Fattah, A. I.: Pore scale modeling of reactive transport involved in Geologic CO2 sequestration. Transp. Porous Media 82(1), 197-213 (2010). doi: 10. 1007/s11242-009-9443-9.
15. Kausch, M. F., Pallud, C. E.: Modeling the impact of soil aggregate size on selenium immobilization. Biogeosciences 10, 1323-1336 (2013). doi: 10. 5194/bg-10-1323-2013.
16. Konopka, A.: Ecology, microbial. In: Moselio, S. (ed.) Encyclopedia of Microbiology, 3rd edn, pp. 91-106. Academic Press, Oxford (2009).
17. Lee, I.-B., Bitog, J. P. P., Hong, S.-W., Seo, I.-H., Kwon, K.-S., Bartzanas, T., Kacira, M.: The past, present and future of CFD for agro-environmental applications. Comput. Electron. Agric. 93, 168-183 (2013). doi: 10. 1016/j. compag. 2012. 09. 006.
18. Lehmann, J., Solomon, D., Kinyangi, J., Dathe, L., Wirick, S., Jacobsen, C.: Spatial complexity of soil organic matter forms at nanometre scales. Nat. Geosci. 1(4), 238-242 (2008).
19. Logtenberg, S. A., Dixon, A. G.: Computational fluid dynamics studies of the effects of temperature-dependent physical properties on fixed-bed heat transfer. Ind. Eng. Chem. Res. 37(3), 739-747 (1998). doi: 10. 1021/ie970382q.
20. Molins, S., Trebotich, D., Steefel, C. I.: An investigation of the effect of pore scale flow on average geochemical reaction rates using direct numerical simulation. Water Resour. Res. 48, W03527 (2012). doi: 10. 1029/2011wr011404.
21. Morais, A. F., Seybold, H., Herrmann, H. J., Andrade, J. S.: Non-Newtonian fluid flow through three-dimensional disordered porous media. Phys. Rev. Lett. 103(19), 194502 (2009). doi: 10. 1103/PhysRevLett. 103. 194502.
22. MPI-Forum: MPI: A Message-Passing Interface Standard. Version 2. 2. http://www. mpi-forum. org (2009).
23. Nieplocha, J., Harrison, R., Littlefield, R.: Global arrays: a nonuniform memory access programming model for high-performance computers. J. Supercomput. 10(2), 169-189 (1996). doi: 10. 1007/BF00130708.
24. Nieplocha, J., Palmer, B., Tipparaju, V., Krishnan, M., Trease, H., Apra, E.: Advances, applications and performance of the global arrays shared memory programming toolkit. Int. J. High Perform. Comput. Appl. 20(2), 203-231 (2006). doi: 10. 1177/1094342006064503.
25. Nijemeisland, M., Dixon, A. G.: CFD study of fluid flow and wall heat transfer in a fixed bed of spheres. Aiche J. 50(5), 906-921 (2004). doi: 10. 1002/aic. 10089.
26. Nunan, N., Ritz, K., Rivers, M., Feeney, D. S., Young, I. M.: Investigating microbial micro-habitat structure using X-ray computed tomography. Geoderma 133, 398-407 (2006).
27. Nunan, N., Wu, K., Young, I. M., Crawford, J. W., Ritz, K.: In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil. Microb. Ecol. 44(4), 296-305 (2002).
28. Or, D., Smets, B. F., Wraith, J. M., Dechesne, A., Friedman, S. P.: Physical constraints affecting bacterial habitats and activity in unsaturated porous media-a review. Adv. Water Resour. 30, 1505-1527 (2007).
29. Patankar, S. V.: Numerical Heat Transfer and Fluid Flow. Hemisphere/McGraw-Hill, New York (1980).
30. Peth, S., Horn, R., Beckmann, F., Donath, T., Fischer, J., Smucker, A. J. M.: Three-dimensional quantification of intra-aggregate pore-space features using synchrotron-radiation-based microtomography. Soil Sci. Soc. Am. J. 72(4), 897-907 (2008). doi: 10. 2136/sssaj2007. 0130.
31. Porporato, A., D'Odorico, P., Laio, F., Rodriguez-Iturbe, I.: Hydrologic controls on soil carbon and nitrogen cycles. I. Modeling scheme. Adv. Water Resour. 26(1), 45-58 (2003).
32. Prosser, J. I., Bohannan, B. J. M., Curtis, T. P., Ellis, R. J., Firestone, M. K., Freckleton, R. P., Green, J. L., Green, L. E., Killham, K., Lennon, J. J., Osborn, A. M., Solan, M., van der Gast, C. J., Young, J. P. W.: The role of ecological theory in microbial ecology. Nat. Rev. Microbiol. 5(5), 384-392 (2007). doi: 10. 1038/nrmicro1643.
33. Raeini, A. Q., Blunt, M. J., Bijeljic, B.: Modelling two-phase flow in porous media at the pore scale using the volume-of-fluid method. J. Comput. Phys. 231, 5653-5668 (2012).
34. Ranjard, L., Richaume, A. S.: Quantitative and qualitative microscale distribution of bacteria in soil. Res. Microbiol. 152(8), 707-716 (2001).
35. Resat, H., Bailey, V., McCue, L. A., Konopka, A.: Modeling microbial dynamics in heterogeneous environments: growth on soil carbon sources. Microb. Ecol. 63(4), 883-897 (2012). doi: 10. 1007/s00248-011-9965-x.
36. Resat, H., Brockman, F. J., Konopka, A.: Microbial dynamics in soil aggregates: sensitivity to exo-enzyme production and kinetics under carbon-limited conditions. (2013, submitted).
37. Richmond, M. C., Perkins, W. A., Scheibe, T. D., Lambert, A., Wood, B. D.: Flow and axial dispersion in a sinusoidal-walled tube: effects of inertial and unsteady flows. Adv. Water Resour. (2013). doi: 10. 1016/j. advwatres. 2013. 06. 014.
38. Sammartino, S., Michel, E., Capowiez, Y.: A novel method to visualize and characterize preferential flow in undisturbed soil cores by using multislice helical CT. Vadose Zone J. 11(1) (2012). doi: 10. 2136/vzj2011. 0100.
39. Schlegel, H. G., Jannasch, H. W.: Prokaryotes and their habitats. Prokaryotes 1, 137-184 (2006).
40. Sinsabaugh, R. L., Shah, J. J. F.: Ecoenzymatic stoichiometry and ecological theory. Annu. Rev. Ecol. Evol. Syst. 43, 313-343 (2012). doi: 10. 1146/annurev-ecolsys-071112-124414.
41. Sleutel, S., Cnudde, V., Masschaele, B., Vlassenbroek, J., Dierick, M., van Hoorebeke, L., Jacobs, P., De Neve, S.: Comparison of different nano- and micro-focus X-ray computed tomography set-ups for the visualization of the soil microstructure and soil organic matter. Comput. Geosci. 34(8), 931-938 (2008). doi: 10. 1016/j. cageo. 2007. 10. 006.
42. Strong, D. T., De Wever, H., Merckx, R., Recous, S.: Spatial location of carbon decomposition in the soil pore system. Eur. J. Soil Sci. 55(4), 739-750 (2004). doi: 10. 1111/j. 1365-2389. 2004. 00639. x.
43. Sukop, M. C., Huang, H., Lin, C. L., Deo, M. D., Oh, K., Miller, J. D.: Distribution of multiphase fluids in porous media: comparison between lattice Boltzmann modeling and micro-X-ray tomography. Phys. Rev. E 77(2), 026710 (2008). doi: 10. 1103/PhysRevE. 77. 026710.
44. Tartakovsky, A. M., Redden, G., Lichtner, P. C., Scheibe, T. D., Meakin, P.: Mixing-induced precipitation: experimental study and multiscale numerical analysis. Water Resour. Res. 44(6), W06S04 (2008). doi: 10. 1029/2006WR005725.
45. Tartakovsky, A. M., Scheibe, T. D., Meakin, P.: Pore-scale model for reactive transport and biomass growth. J. Porous Media 12(5), 417-434 (2009).
46. Xia, B., Sun, D. W.: Applications of computational fluid dynamics (CFD) in the food industry: a review. Comput. Electron. Agric. 34(1-3), 5-24 (2002). doi: 10. 1016/s0168-1699(01)00177-6.
47. Yang, X., Scheibe, T. D., Richmond, M. C., Perkins, W. A., Vogt, S. J., Codd, S. L., Seymour, J. D., McKinley, M. I.: Direct Numerical Simulation of Pore-Scale Flow in a Bead Pack: Validation against Magnetic Resonance Imaging Observations. Adv. Water Resour. 54, 228-241 (2013). doi: 10. 1016/j. advwatres. 2013. 01. 009.
48. Yiallourou, T. I., Asboth, L., Kroeger, J.-R., Maintz, D., Bunck, A. C., Stergiopulos, N., Martin, B. A.: Quantitative comparison of 4D MRI flow measurements to 3D computational fluid dynamics simulation of cerebrospinal fluid movement in the spinal subarachnoid space. In: 10th International Workshop on Biomedical Engineering, Kos Island, Greece 2011. IEEE.
49. Young, I. M., Crawford, J. W.: Interactions and self-organization in the soil-microbe complex. Science 304(5677), 1634-1637 (2004).
50. Young, I. M., Crawford, J. W., Nunan, N., Otten, W., Spiers, A.: Microbial distribution in soils: physics and scaling. Adv. Agron. 100(100), 81-121 (2008). doi: 10. 1016/s0065-2113(08)00604-4.
51. Zaretskiy, Y., Geiger, S., Sorbie, K., Forster, M.: Efficient flow and transport simulations in reconstructed 3D pore geometries. Adv. Water Resour. 33(12), 1508-1516 (2010). doi: 10. 1016/j. advwatres. 2010. 08. 008.
52. Zhuang, J., McCarthy, J. F., Perfect, E., Mayer, L. M., Jastrow, J. D.: Soil water hysteresis in water-stable microaggregates as affected by organic matter. Soil Sci. Soc. Am. J. 72(1), 212-220 (2008). doi: 10. 2136/sssaj2007. 0001.