Lattice boltzmann-based approaches for pore-scale reactive transport

Reviews in Mineralogy and Geochemistry

Volumn 80, Issue 1, 2015, Pages 393-431

  Yoon, Hongkyu ^a   Kang, Qinjun ^b   Valocchi, Albert J ^c  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c United States of America   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84945246238     PISSN: 15296466     EISSN: None     Source Type: Book Series    
DOI: 10.2138/rmg.2015.80.12     Document Type: Article

References (209)

1. Adkins JP, Tanner RS, Udegbunam EO, McInerney MJ, Knapp RM (1992) Microbially enahanced oil recovery from unconsolidated limestone cores. Geomicrobiol J 10:77-86
2. Alpkvist E, Klapper I (2007) A multidimensional multispecies continuum model for heterogeneous biofilm development. Bull Math Biol 69:765-789
3. Altman SJ, Aminzadeh B, Balhoff MT, Bennett PC, Bryant SL, Cardenas MB, Chaudhary K, Cygan RT, Deng W, Dewers T, DiCarlo DA, Eichhubl P, Hesse MA, Huh C, Matteo EN, Mehmani Y, Tenney CM, Yoon H (2014) Chemical and hydrodynamic mechanisms for long-term geological carbon storage. J Phys Chem C 118:15103-15113
4. Andrä H, Combaret N, Dvorkin J, Glatt E, Han J, Kabel M, Keehm Y, Krzikalla F, Lee M, Madonna C, Marsh M, Mukerjic T, Saenger EH, Sain R, Saxena N, Ricker S, Wiegmann A, Zhan X (2013a) Digital rock physics benchmarks-Part I: Imaging and segmentation. Comput Geosci 50:25-32
5. Andrä H, Combaret N, Dvorkin J, Glatt E, Han J, Kabel M, Keehm Y, Krzikalla F, Lee M, Madonna C, Marsh M, Mukerjic T, Saenger EH, Sain R, Saxena N, Ricker S, Wiegmann A, Zhan X (2013b) Digital rock physics benchmarks-Part II: Computing effective properties. Comput Geosci 50:33-43
6. Arns CH, Knackstedt MA, Pinczewski WV, Garboczi EJ (2002) Computation of linear elastic properties from microtomographic images: methodology and agreement between theory and experiment. Geophys 67:1395-1405
7. Arns CH, Knackstedt MA, Mecke KR (2009) Boolean reconstructions of complex materials: Integral geometric approach. Phys Rev E 80:051303
8. Baldessari F (2008) Electrokinetics in nanochannels - Part I. Electric double layer overlap and channel-to-well equilibrium. J Colloid Interfac Sci 325:526-538
9. Bancroft WD (1926) Applied Colloid Chemistry General Theory. McGraw-Hill, New York
10. Battiato I, Tartakovsky DM, Tartakovsky AM, Scheibe TD (2011) Hybrid models of reactive transport in porous and fractured media. Adv Water Resour 37:1140-1150
11. Bhatnagar PL, Gross EP, Krook M (1954) A model for collision processes in gases. I. small amplitude processes in charged and neutral one-component systems. Phys Rev 94:511-525
12. Bilger N, Auslender F, Bornert M, Michel JC, Moulinec H, Suquet P, Zaoui A (2005) Effect of a nonuniform distribution of voids on the plastic response of voided materials: a computational and statistical analysis. Int J Solids Struct 42:517-538
13. Boek ES, Zacharoudiou I, Gray F, Shah SMK, Crawshaw J, Yang J (2014) Multiphase flow and reactive transport at the pore scale using lattice-Boltzmann computer simulations. SPE-170941-MS, SPE Annual Technical Conference and Exhibition, Society of Petroleum Engineers
14. Bottero S, Storck T, Heimovaara TJ, van Loosdrecht MCM, Enzien MV, Picioreanu C (2013) Biofilm development and the dynamics of preferential flow paths in porous media. Biofouling 29:1069-1086
15. Bouzidi MH, Firdaouss M, Lallemand P (2001) Momentum transfer of a Boltzmann-lattice fluid with boundaries. Phys Fluids (1994-present) 13:3452-3459
16. 3 precipitation during subsurface reactive transport in a homogeneous silicon-etched pore network. Geochim Cosmochim Acta 135:321-335
17. Breyers J (1988) Modeling biofilm accumulation. In: Physiology Models in Microbiology. Bazin MJ, Prosser JI (eds) CRC Press, Boca Raton FL, p 109-144
18. Chen LQ (2002) Phase-filed models for microstructures evolution. Ann Rev Mater Res 32:113-140
19. Chen S, Doolen G (1998) Lattice Boltzmann method for fluid flows. Ann Rev Fluid Mech 30:329-364
20. Chen S, He X, Luo LS (2007) Lattice Boltzmann models for multiphase flows. In: Computational Methods for Multiphase Flow. Prosperetti A, Tryggvason G (eds) Cambridge University Press, p 157-192, http://dx.doi.org/10.1017/CBO9780511607486.007
21. Chen L, Kang Q, He YL, Tao WQ (2012) Mesoscopic study of the effect of gel concentration and material on the formation of precipitation patterns. Langmuir 28:11745-11754
22. Chen L, He YL, Kang Q, Tao WQ (2013a) Coupled numerical approach combining finite volume and lattice Boltzmann methods for multi-scale multi-physicochemical processes. J Comput Phys 255:83-105
23. Chen L, Kang Q, Robinson BA, He YL, Tao WQ (2013b) Pore-scale modeling of multiphase reactive transport with phase transitions and dissolution-precipitation processes in closed systems. Phys Rev E 87:043306
24. Chen L, Kang Q, Carey B, Tao WQ (2014a) Pore-scale study of diffusion-reaction processes involving dissolution and precipitation using the lattice Boltzmann method. Int J Heat Mass Transf 75:483-496
25. Chen L, Kang Q, Viswanathan HS, Tao WQ (2014b) Pore-scale study of dissolution-induced changes in hydrologic properties of rocks with binary minerals. Water Resour Res 50:9343-9365, doi:10.1002/2014WR015646
26. Chou L, Garrels RM, Wollast R (1989) Comparative study of the kinetics and mechanisms of dissolution of carbonate minerals. Chem Geol 78:269-282
27. Chu J, Engquist B, Prodanovic M, Tsai R (2013) A multiscale method coupling network and continuum models in porous media II-Single- and two-phase flows. In: Advances in Applied Mathematics, Modeling, and Computational Science. Melnik R, Kotsireas IS (eds) Springer US, p 161-185
28. Cirpka OA, Valocchi AJ (2007) Two-dimensional concentration distribution for mixing-controlled bioreactive transport in steady state. Adv Water Resour 30:1668-1679
29. Coker DA, Torquato S, Dunsmuir JH (1996) Morphology and physical properties of Fontainebleau sandstone via a tomographic analysis. J Geophys Res: Solid Earth (1978-2012) 101(B8):17497-17506
30. Coles ME, Hazlett RD, Spanne P, Soll WE, Muegge EL, Jones KW (1998) Pore level imaging of fluid transport using synchrotron X-ray microtomography. J Petrol Sci Eng 19:55-63
31. d'Humières D, Ginzburg I, Krafczyk M, Lallemand P, Luo LS (2002) Multiple-relaxation-time lattice Boltzmann models in three dimensions. Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences 360:437-451
32. Davery ME, Gevertz D, Wood WA, Clark JB, Jenneman GE (1998) Microbial selective plugging of sandstone through stimulation of indigenous bacteria in a hypersaline oil reservoir. Geomicrobiol J 15:335-352
33. Davidson SM, Yoon H, Martinez MJ (2012) Pore scale analysis of the impact of mixing-induced reaction on viscosity variations. Adv Water Resour 38:70-80
34. Dawson SP, Chen S, Doolen GD (1993) Lattice Boltzmann computations for reaction-diffusion equations. J Chem Phys 98:1514-1523
35. DeJong J, Fritzges M, Nüsslein K (2006) Microbially induced cementation to control sand response to undrained shear. J Geotech Geoenv Eng 132:1381-1392
36. Deng W, Cardenas MB, Kirk MF, Altman SJ, Bennett PC (2013) Effect of Permeable Biofilm on Micro- And Macro-Scale Flow and Transport in Bioclogged Pores. Env Sci Techol 47:11092-11098
37. DOE (2007) Basic Research Needs for Geosciences: Facilitating 21st Century Energy Systems. A report from the Workshop Sponsored by the US Department of Energy, Office of Basic Energy Sciences, Bethesda, MA, Feb. 21-23, 2007
38. DOE (2012) From Quanta to the Continuum: Opportunities for Mesoscale Science. A report from the Basic Energy Sciences Advisory Committee, US Department of Energy, Office of Basic Energy Sciences, September, 2012
39. Dupin HJ, Kitanidis PK, McCarty PL (2001) Pore-scale modeling of biological clogging due to aggregate expansion: A material mechanics approach. Water Resour Res 37:2965-2979
40. El Mountassir G, Lunn RJ, Moir H, MacLachlan E (2014) Hydrodynamic coupling in microbially mediated fracture mineralization: Formation of self-organized groundwater flow channels. Water Resour Res 50:1-16, doi:10.1002/2013WR013578
41. Emmanuel S, Berkowitz B (2005) Mixing-induced precipitation and porosity evolution in porous media. Adv Water Resour 28:337-344
42. Fang Y, Scheibe TD, Mahadevan R, Garg S, Long PE, Lovley DR (2011) Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model. J Contam Hydrol 122:96-103
43. Fanizza MF, Yoon H, Zhang C, Oostrom M, Wietsma TW, Hess NJ, Bowden ME, Strathmann TJ, Finneran KT, Werth CJ (2013) Pore-scale evaluation of uranyl phosphate precipitation in a model groundwater system. Water Resour Res 49:874-890
44. 2 saturated water flow in 3D realistic geometry: Principles and first results. Chem Geol 265:171-180
45. Fredrich JT, Menendez B, Wong TF (1995) Imaging the pore structure of geomaterials. Science 268(5208):276-279
46. Fredrich JT, DiGiovanni AA, Noble DR (2006) Predicting macroscopic transport properties using microscopic image data. J Geophys Res 111:B03201, doi: 10.1029/2005JB003774
47. Fu LM, Lin JY, Yang RJ (2003) Analysis of electroosmotic flow with step change in zeta potential. J Colloid Interfac Sci 258:266-275
48. Gao J, Xing H, Rudolph V, Li Q, Golding SD (2015) Parallel lattice Boltzmann computing and applications in core sample feature evaluation. Transp Porous Media 107:65-77
49. Gelb J, Gu A, Fong T, Hunter L, Lau SH, Yun W (2011) A closer look at shale: Representative elementary volume analysis with laboratory 3D X-Ray computed microtomography and nanotomography. SCA2011-58. The International Symposium of the Society of Core Analysts, Austin, Texas, USA, September 18-21, 2011
50. Ginzburg I, d'Humières D (2003) Multireflection boundary conditions for lattice Boltzmann models. Phys Rev E 68:066614
51. Golfier F, Wood BD, Orgogozo L, Quintard M, Buès M (2009) Biofilms in porous media: Development of macroscopic transport equations via volume averaging with closure for local mass equilibrium conditions. Adv Water Resour 32:463-485
52. Groen D, Hetherington J, Carver HB, Nash RW, Bernabeu MO, Coveney PV (2013) Analysing and modelling the performance of the HemeLB lattice-Boltzmann simulation environment. J Comput Sci 4:412-422
53. Gualda GA, Baker DR, Polacci M (2010) Introduction: Advances in 3D imaging and analysis of geomaterials. Geosphere 6:468-469
54. Guo ZL, Zhao TS, Shi Y (2005) A lattice Boltzmann algorithm for electro-osmotic flows in microfluidic devices. J Chem Phys 122:144907
55. Harvey RW, Garabedian SP (1991) Use of colloid filtration theory in modeling movement of bacteria through a contaminated sandy aquifer. Environ Sci Technol 25:178-185
56. He X, Li N (2000) Lattice Boltzmann simulation of electrochemical systems. Comput Phys Commun 129:158-166
57. He X, Zou Q, Luo LS, Dembo M (1997) Analytic solutions of simple flows and analysis of nonslip boundary conditions for the lattice Boltzmann BGK model. J Stat Phys 87:115-136
58. Hilpert M (2005) Lattice-Boltzmann model for bacterial chemotaxis. J Math Biol 51:302-332
59. Hilpert M (2011) Determination of dimensional flow fields in hydrogeological settings via the MRT lattice-Boltzmann method. Water Resour Res 47:W09508, doi:10.1029/2010WR010016
60. Hiorth A, Jettestuen E, Cathles L, Madland M (2013) Precipitation, dissolution, and ion exchange processes coupled with a lattice Boltzmann advection diffusion solver. Geochim Cosmochim Acta 104:99-110
61. Holst M, Baker N, Wang F (2000) Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. J Comput Chem 21:1319-1342
62. Huber C, Parmigiani A, Chopard B, Manga M, Bachmann O (2008) Lattice Boltzmann model for melting with natural convection. Int J Heat Fluid Fl 29:1469-1480
63. Huber C, Shafei B, Parmigiani A (2014) A new pore-scale model for linear and non-linear heterogeneous dissolution and precipitation. Geochim Cosmochim Acta 124:109-130
64. IWA Task Group on Biofilm Modeling (2006) Mathematical Modeling of Biofilms. IWA Publishing, Hove, UK
65. Jiang F, Tsuji T (2014) Changes in pore geometry and relative permeability caused by carbonate precipitation in porous media. Phys Rev E 90:053306
66. Joshi AS, Sun Y (2009) Multiphase lattice Boltzmann method for particle suspensions. Phys Rev E 79:066703
67. Kang QJ, Lichtner PC (2013) A lattice Boltzmann method for coupled fluid flow, solute transport, and chemical reaction. In: Progress in Computational Physics. Ehrhardt M (ed) Bentham Science Publishers
68. Kang S, Suh YK (2006) Unsteady electroosmotic channel flows with the nonoverlapped and overlapped electric double layers. J Mech Sci Technol 20:2250-2264
69. Kang QJ, Zhang DX, Chen S Y, He XY (2002) Lattice Boltzmann simulation of chemical dissolution in porous media. Phys Rev E 65:036318
70. Kang Q, Zhang D, Chen S (2003) Simulation of dissolution and precipitation in porous media. J Geophys Res 108(B10):2505
71. Kang Q, Zhang D, Lichtner PC, Tsimpanogiannis IN (2004) Lattice Boltzmann model for crystal growth from supersaturated solution. Geophys Res Lett 31:L21604
72. Kang QJ, Lichtner PC, Zhang DX (2006) Lattice Boltzmann pore-scale model for multicomponent reactive transport in porous media. J Geophys Res-Solid Earth 111:B05203, doi:10.1029/2005JB003951
73. Kang Q, Lichtner PC, Zhang D (2007) An improved lattice Boltzmann model for multicomponent reactive transport in porous media at the pore scale. Water Resour Res 43:W12S14
74. 2 sequestration. Transp Porous Media 82:197-213
75. Kang Q, Chen L, Valocchi AJ, Viswanathan HS (2014) Pore-scale study of dissolution-induced changes in permeability and porosity of porous media. J Hydrol 517:1049-1055
76. Karniadakis G, Beskok A, Aluru N (2005) Microflows and Nanoflows: Fundamentals and Simulation. Springer, New York.
77. Keehm Y, Mukerji T, Nur A (2004) Permeability prediction from thin sections: 3D reconstruction and Lattice-Boltzmann flow simulation. Geophys Res Lett 31:L04606, doi:10.1029/2003GL018761
78. Kelemen PB, Whitehead JA, Aharonov E, Jordahl KA (1995) Experiments on flow focusing in soluble porous media, with applications to melt extraction from the mantle. J Geophys Res: Solid Earth 100(B1):475-496
79. 2-saturated brine flow in sandstone aquifers. Water Resourc Res 47:W01505, doi:10.1029/2010WR009472
80. Kingdon RD, Schofield P (1992) A reaction-flow lattice Boltzmann model. J Phys A 25:L907-L910
81. Kirk MF, Santillan EF, McGrath LK, Altman SJ (2012) Variation in hydraulic conductivity with decreasing pH in a biologically-clogged porous medium. Int J Greenhouse Gas Control 11:133-140
82. Klapper I, Dockery J (2010) Mathematical description of microbial biofilms. SIAM Review 52:221-265
83. Knutson CE, Werth CJ, Valocchi AJ (2005) Pore-scale simulation of biomass growth along the transverse mixing zone of a model two-dimensional porous medium. Water Resour Res 41:W07007, doi:10.1029/2004WR003459
84. Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (2001) Individual-based modelling of biofilms. Microbiol 147:2897-2912
85. Kusy K, Ford RM (2007) Monte Carlo simulations derived from direct observations of individual bacteria inform macroscopic migration models at granular porous media interfaces. Env Sci Tech 41:6403-6409
86. Ladd AJ (1994) Numerical simulations of particulate suspensions via a discretized Boltzmann equation. Part 1. Theoretical foundation. J Fluid Mech 271:285-309
87. 2 mineralization. Chem Geol 318-319:113-125
88. Lasaga AC (1981) Transition state theory. Rev Mineral 8:135-168
89. Lasaga A (1998) Kinetic Theory in the Earth Sciences. Princeton Series in Geochemistry. Princeton University Press
90. Lattice Boltzmann methods (2015, February 14). In Wikipedia, The Free Encyclopedia. http://en. wikipedia.org/w/index.php?title=Lattice-Boltzmann-methods&oldid=647112117
91. Levich VG (1962) Physico-Chemical Hydrodynamics. Prentice-Hall, New York
92. Li DQ (2001) Electro-viscous effects on pressure-driven liquid flow in microchannels. Colloids and Surfaces A-Physicochemical and Engineering Aspects 195:35-57
93. Li DQ (2004) Electrokinetics in Microfluidics. Academic, Oxford
94. Li L, Peters CA, Celia MA (2006) Upscaling geochemical reaction rates using pore-scale network modeling. Adv Water Res 29:1351-1370
95. Li L, Peters CA, Celia MA (2007) Reply to "Comment on upscaling geochemical reaction rates using porescale network modeling" by Lichtner PC and Kang Q. Adv Water Resour 30:691-695
96. Li X, Huang H, Meakin P (2008) Level set simulation of coupled advection-diffusion and pore structure evolution due to mineral precipitation in porous media. Water Resour Res 44:W12407
97. Lichtner PC (1985) Continuum model for simultaneous chemical reactions and mass transport in hydrothemal systems. Geochim Cosmochim Acta 49:779-800
98. Lichtner PC (1996) Continuum formulation of multicomponent-multiphase reactive transport. Rev Mineral 34:1-81
99. Lichtner PC and Kang Q (2007) Comment on: "Upscaling geochemical reaction rates using pore-scale network modeling" by Li, Peters and Celia. Adv Water Resour 30:686-690
100. Lichtner PC, Hammond GE, Lu C, Karra S, Bisht G, Andre B, Mills RT, Kumar J (2014) PFLOTRAN User Manual
101. Lindley B, Wang Q, Zhang T (2012) Multicomponent hydrodynamic model for heterogeneous biofilms: Twodimensional numerical simulations of growth and interaction with flows. Phys Rev E 85:031908
102. LinkMasliyah JH (2006). Electrokinetic and Colloid Transport Phenomena. Wiley-Interscience, Hoboken
103. Liu J, Pancera S, Boyko V, Shukla A, Narayanan T, Huber K (2010) Evaluation of the particle growth of amorphous calcium carbonate in water by means of the Porod Invariant from SAXS. Langmuir 26:17405-17412
104. Liu C, Shang J, Zachara JM (2011) Multispecies diffusion models: A study of uranyl species diffusion. Water Resour Res 47:W12514, doi: 10.1029/2011WR010575
105. Lu G, DePaolo DJ, Kang Q, Zhang D (2009) Lattice Boltzmann simulation of snow crystal growth in clouds. J Geophys Res: Atmospheres 114:D07305
106. Luan HB, Xu H, Chen L, Sun DL, Tao WQ (2010) Numerical illustrations of the coupling between the lattice Boltzmann method and finite-type macro-numerical methods. Numerical Heat Transfer, Part B: Fundamentals 57(2):147-171, doi: 10.1080/15421400903579929
107. Luan HB, Xu H, Chen L, Sun DL, He YL, Tao WQ (2011) Evaluation of the coupling scheme of FVM and LBM for fluid flows around complex geometries. Int J Heat Mass Transf 54:1975-1985
108. Luo H, Quintard M, Debenest G, Laouafa F (2012) Properties of a diffuse interface model based on a porous medium theory for solid-liquid dissolution problems. Comput Geosci 16:913-932
109. Martin D, Dodds K, Butler IB, Ngwenya BT (2013) Carbonate precipitation under pressure for bioengineering in the anaerobic subsurface via denitrification. Env Sci Techol 47:8692-8699, doi: 10.1021/es401270q
110. Martys NS, Chen H (1996) Simulation of multicomponent fluids in complex three-dimensional geometries by the lattice Boltzmann method. Phys Rev E 53:743
111. Meakin P, Tartakovsky AM. (2009) Modeling and simulation of pore-scale multiphase fluid flow and reactive transport in fractured and porous media. Rev Geophys 47:RG3002, doi: 10.1029/2008RG000263
112. Miller W, Succi S, Mansutti D (2001) Lattice Boltzmann model for anisotropic liquid-solid phase transition. Phys Rev Letters 86:3578-3581
113. Mohamad AA (2011) Lattice Boltzmann Method - Fundamentals and Engineering Applications with Computer Codes. Springer-Verlag, London
114. Molins S, Trebotich D, Steefel CI, Shen C (2012) An investigation of the effect of pore scale flow on average geochemical reaction rates using direct numerical simulation. Water Resour Res 48:W03527, doi:10.1029/2011WR011404
115. Molins S, Trebotich D, Yang L, Ajo-Franklin JB, Ligocki TJ, Shen C, Steefel CI (2014) Pore-scale controls on calcite dissolution rates from flow-through laboratory and numerical experiments. Environ Sci Technol 48:7453-7460
116. Mozley PS, Davis JM (2005) Internal structure and mode of growth of elongate calcite concretions: Evidence for small-scale, microbially induced, chemical heterogeneity in groundwater. Geol Soc Am Bull 117:1400-1412
117. Nambi IM, Werth CJ, Sanford RA, Valocchi AJ (2003) Pore-Scale Analysis of Anaerobic Halorespiring Bacterial Growth along the Transverse Mixing Zone of an Etched Silicon Pore Network. Env Sci Techol 37:5617-5624
118. Navarre-Sitchler A, Brantley S (2007) Basalt weathering across scales. Earth Planet Sci Lett 261:321-334
119. Navarre-Sitchler A, Steefel CI, Yang L, Tomutsa L, Brantley SL (2009) Evolution of porosity and diffusivity associated with chemical weathering of a basalt clast. J Geophys Res 114:F02016, doi:10.1029/2008JF001060
120. Nemati M, Voordouw G (2003) Modification of porous media permeability, using calcium carbonate produced enzymatically in situ. Enzyme Microbiol Technol 33:635-642
121. Noguera DP, Pizarro G, Stahl DA, Rittmann BE (1999) Simulation of multispecies biofilm development in three dimensions. Water Sci Technol 39:123-130
122. Ogino T, Suzuki T, Sawada K (1987) The formation and transformation mechanism of calcium carbonate in water. Geochim Cosmochim Acta 51:2757-2767
123. Oostrom M, Mehmani Y, Romero-Gomez P, Tang Y, Liu H, Yoon H, Kang Q et al. (2014) Pore-scale and continuum simulations of solute transport micromodel benchmark experiments. Comput Geosci, doi: 10.1007/s10596-014-9424-0
124. Pan C, Luo LS, Miller CT (2006) An evaluation of lattice Boltzmann schemes for porous medium flow simulation. Comput Fluids 35:898-909
125. Parkhurst DL, Appelo CAJ (2013) Description of input and examples for PHREEQC Version 3-A computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations. U. S. Geological Survey Techniques and Methods, Book 6, http://pubs.usgs.gov/tm/06/a43
126. Parmigiani A, Huber C, Bachmann O, Chopard B (2011) Pore scale mass and reactant transport in multiphase porous media flows. J Fluid Mech 686:40-76
127. Patel RA, Perko J, Jacques D, De Schutter G, Van Breugel K, Ye G (2014) A versatile pore-scale multicomponent reactive transport approach based on lattice Boltzmann method: Application to portlandite dissolution. Phys Chem Earth, Parts A/B/C 70:127-137
128. Peters C (2009) Accessibilities of reactive minerals in consolidated sedimentary rock: an imaging study of three sandstones. Chem Geol 265:198-208
129. Picioreanu C, van Loosdrecht MCM, Heijnen JJ (1998) Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach. Biotechnol Bioeng 58:101-116
130. Picioreanu C, Van Loosdrecht MCM, Heijnen JJ (2000) Effect of diffusive and convective substrate transport on biofilm structure formation: A two-dimensional modeling study. Biotechnol Bioeng 69:504-515
131. Picioreanu C, van Loosdrecht MCM, Heijnen JJ (2001) Two-dimensional model of biofilm detachment caused by internal stress from liquid flow. Biotechnol Bioeng 72:205-218
132. Picioreanu C, Kreft JU, van Loosdrecht MCM (2004) Particle-based multidimensional multispecies biofilm model. Appl Environ Microbiol 70:3024-3040
133. Pintelon TRR, von der Schulenburg DAG, Johns ML (2009) Towards Optimum Permeability Reduction in Porous Media Using Biofilm Growth Simulations. Biotechnol Bioeng 103:767-779
134. Pintelon TRR, Picioreanu C, van Loosdrecht MCM, Johns ML (2012) The effect of biofilm permeability on bio-clogging of porous media. Biotechnol Bioeng 109:1031-1042
135. 3 formation revealed by cryo-TEM. Science 323:1455-1458
136. Prieto M, Cubillas P, Fernández-Gonzalez Á (2003) Uptake of dissolved Cd by biogenic and abiogenic aragonite: a comparison with sorption onto calcite. Geochim Cosmochim Acta 67:3859-3869
137. Qian YH, Orszag SA (1995) Scalings in diffusion-driven reaction A + B → C: Numerical simulations by lattice BGK models,. J Stat Phys 81:237-253
138. Qu WL, Li DQ (2000) A model for overlapped EDL fields. J Colloid Interfac Sci 224:397-407
139. Raoof A (2011) Reactive/adsorptive transport in (partially-) saturated porous media; from pore scale to core scale. PhD Dissertation, Utrecht University, Utrecht, Netherlands
140. 3 and control of particle formation by polyelectrolytes. Faraday Discussions 136:265-277, doi: 10.1039/B701450C
141. Rittmann BE (1993) The significance of biofilms in porous media. Water Resourc Res 29:2195-2208
142. Rittmann BE, McCarty PL (2001) Environmental Biotechnology. McGraw-Hill, Boston
143. Scheibe TD, Fang Y, Murray CJ, Roden EE, Chen J, Chien YJ, Brooks SC, Hubbard SS (2006) Transport and biogeochemical reaction of metals in a physically and chemically heterogeneous aquifer. Geosphere 2:220-235
144. Scheibe TD, Murphy EM, Chen X, Rice AK, Carroll KC, Palmer BJ, Tartakovsky AM, Battiato I, Wood BD (2015) An analysis platform for multiscale hydrogeologic modeling with emphasis on hybrid multiscale methods. Groundwater 53:38-56
145. Seifert D, Engesgaard P (2007) Use of tracer tests to investigate changes in flow and transport properties due to bioclogging of porous media. J Contam Hydrol 93:58-71
146. Seifert D, Engesgaard P (2012) Sand box experiments with bioclogging of porous media: Hydraulic conductivity reductions. J Contam Hydrol 136-137:1-9
147. Shan X, Chen H (1993) Lattice Boltzmann model for simulating flows with multiple phases and components. Phys Rev E 47:1815
148. Shi Y, Zhao TS, Guo ZL (2008) Lattice Boltzmann simulation of thermal electro-osmotic flows in micro/nanochannels. J Comput Theor Nanosci 5:236-246
149. Smith NS, Notte JA, Steele AV (2014) Advances in source technology for focused ion beam instruments. MRS Bulletin 39:329-335, doi:10.1557/mrs.2014.53
150. Spanne P, Thovert JF, Jacquin CJ, Lindquist WB, Jones KW, Adler PM (1994) Synchrotron computed microtomography of porous media: topology and transports. Phys Rev Letters 73:2001
151. Steefel CI, Lasaga AC (1990) The evolution of dissolution patterns: Permeability change due to coupled flow and reaction. In: Chemical Modeling of Aqueous Systems II. Melchior D and Bassett RL (eds) ACS Symposium Series No. 416, American Chemical Society, Washington, p 212-225
152. Steefel CI, Lasaga AC (1994) A coupled model for transport of multiple chemical species and kinetic precipitation/dissolution reactions with application to reactive flow in single phase hydrothermal systems. Am J Sci 294:529-592
153. Steefel CI, Lichtner PC (1994) Diffusion and reaction in rock matrix bordering a hyperalkaline fluid-filled fracture. Geochim Cosmochim Acta 58:3595-3612
154. Steefel C, Lichtner P (1998) Multicomponent reactive transport in discrete fractures: II: Infiltration of hyperalkaline groundwater at Maqarin, Jordan, a natural analogue site. J Hydrol 209:200-224
155. 2 injection and sequestration. Rev Mineral Geochem 77:259-303
156. Stewart TL, Kim DS (2004) Modeling of biomass-plug development and propagation in porous media. Biochem Eng J 17:107-119
157. Stockman HW, Li C, Wilson JL (1997) A lattice-gas and lattice Boltzmann study of mixing at continuous fracture junctions: Importance of boundary conditions. Geophys Res Lett 24:1515-1518
158. Succi S (2001) The Lattice Boltzmann Equation for Fluid Dynamics and Beyond. Oxford University Press, Oxford
159. Sukop M, Thorne DT (2007) Lattice Boltzmann Modeling: An Introduction for Geoscientists and Engineers. Springer, 2nd edition, Heidelberg, Berlin, New York
160. Sullivan SP, Sani FM, Johns ML, Gladden LF (2005) Simulation of packed bed reactors using lattice Boltzmann methods. Chem Eng Sci 60:3405-3418
161. Sullivan SP, Gladden LF, Johns ML (2006) 3D chemical reactor LB simulations. Math Comput Simul 72:206-211
162. Sun D, Zhu M, Pan S, Raabe D (2009) Lattice Boltzmann modeling of dendritic growth in a forced melt convection. Acta Materialia 57:1755-1767
163. Tang Y, Valocchi AJ (2013) An improved cellular automaton method to model multispecies biofilms. Water Research 47:5729-5742
164. Tang Y, Valocchi AJ, Werth CJ, Liu H (2013) An improved pore-scale biofilm model and comparison with a microfluidic flow cell experiment. Water Resour Res 49:8370-8382
165. Tartakovsky AM, Meakin P, Scheibe TD, Wood BD (2007) A smoothed particle hydrodynamics model for reactive transport and mineral precipitation in porous and fractured porous media. Water Resour Res 43(5):W05437, doi:10.1029/2005WR004770
166. Tartakovsky AM, Redden G, Lichtner PC, Scheibe TD, Meakin P (2008) Mixing-induced precipitation: Experimental study and multiscale numerical analysis. Water Resour Res 44:W06S04
167. Tartakovsky AM, Scheibe TD, Meakin P (2009) Pore-scale model for reactive transport and biomass growth. J Porous Media 12:417-434
168. Taylor SW, Jaffé PR (1990) Biofilm growth and the related changes in the physical properties of a porous medium: 1. Experimental investigation. Water Resour Res 26:2153-2159
169. Thullner M, Baveye P (2008) Computational pore network modeling of the influence of biofilm permeability on bioclogging in porous media. Biotechnol Bioeng 99:1337-1351
170. Tomin P, Lunati I (2013) Hybrid Multiscale Finite Volume method for two-phase flow in porous media. J Comput Phys 250:293-307
171. Tong ZX, He YL (2015) A unified coupling scheme between lattice Boltzmann method and finite volume method for unsteady fluid flow and heat transfer. Int J Heat Mass Transf 80:812-824
172. Valocchi AJ (2012) Hydrogeochemical models. In: Delivery and Mixing in the Subsurface: Processes and Design Principles for In Situ Remediation. Kitanidis PK, McCarty PL (eds) Springer, New York, p 77-116
173. Van Cappellen P, Gaillard JF (1996) Biogeochemical dynamics in aquatic sediments. Rev Mineral 34:335-376
174. Vandevivere P, Baveye P (1992) Saturated hydraulic conductivity reduction caused by aerobic bacteria in sand columns. Soil Sci Soc Amer J 56:1-13
175. Varloteaux C, Békri S, Adler PM (2013) Pore network modelling to determine the transport properties in presence of a reactive fluid: From pore to reservoir scale. Adv Water Resour 53:87-100
176. Verberg R, Ladd AJC (2000). Lattice-Boltzmann model with sub-grid-scale boundary conditions. Phys Rev letters 84:2148
177. Verberg R, Ladd AJC (2002) Simulation of chemical erosion in rough fractures. Phys Rev E 65:056311
178. Verhaeghe F, Arnout S, Blanpain B, Wollants P (2006) Lattice-Boltzmann modeling of dissolution phenomena. Phys Rev E 73:036316
179. Vilcáez J, Li L, Wu D, Hubbard SS (2013) Reactive transport modeling of induced selective plugging by Leuconostoc mesenteroides in carbonate formations. Geomicrobiol J 30:813-828
180. von der Schulenburg DAG, Pintelon TRR, Picioreanu C, Van Loosdrecht MCM, Johns ML (2009) Three-dimensional simulations of biofilm growth in porous eedia. AIChE J 55:494-504
181. Wang MR, Kang QJ (2009) Electrokinetic transport in microchannels with random roughness. Anal Chem 81:2953-2961
182. Wang MR, Kang QJ (2010) Modeling electrokinetic flows in microchannels using coupled lattice Boltzmann methods. J Comput Phys 229:728-744
183. Wang Q, Zhang T (2010) Review of mathematical models for biofilms. Solid Stat Comm 150:1009-1022
184. Wang JK, Wang M, Li ZX (2006) Lattice Poisson-Boltzmann simulations of electro-osmotic flows in microchannels. J Colloid Interfac Sci 296:729-736
185. Wang D, Summers JL, Gaskell PH (2008) Modelling of electrokinetically driven mixing flow in microchannels with patterned blocks. Comput Math Appl 55:1601-1610
186. Wang M, Kang QJ, Ben-Naim E (2010a) Modeling of electrokinetic transport in silica nanofluidic channels. Anal Chimica Acta 664:158-164
187. Wang M, Kang QJ, Viswanathan H, Robinson BA (2010b) Modeling of electro-osmosis of dilute electrolyte solutions in silica microporous media. J Geophys Res 115:B10205, doi:10.1029/2010JB007460
188. Weimar JR, Boon JP (1996) Nonlinear reactions advected by a flow. Physica A 224:207-215
189. Weinan E, Engquist B, Li X, Ren W, Vanden-Eijnden E (2007). Heterogeneous multiscale methods: a review. Commun Comput Phys 2:367-450
190. Wells JT, Janecky DR, Travis BJ (1991) A lattice gas automata model for heterogeneous chemical reactions at mineral surfaces and in pore networks. Physica D 47:115-123
191. Wildenschild D, Sheppard AP (2013) X-ray imaging and analysis techniques for quantifying pore-scale structure and processes in subsurface porous medium systems. Adv Water Resour 51:217-46
192. Wolf-Gladrow D (2000) Lattice-Gas Cellular Automata and Lattice Boltzmann Models - An Introduction. Springer, Verlag
193. Xu Z, Meakin P, Tartakovsky A, Scheibe T (2011) Dissipative-particle-dynamics model of biofilm growth. Phys Rev E 83:066702
194. Yan GW, Yuan L (2001) A lattice Boltzmann method for the chemical clock in the Belousov-Zhabotinskii reaction. Chin Phys Lett 18:918-920
195. Yang RJ, Fu LM, Hwang CC (2001) Electroosmotic entry flow in a microchannel. J Colloid Interfac Sci 244:173-179
196. Yang X, Liu C, Shang J, Fang Y, Bailey VL (2014a) A Unified multiscale model for pore-scale flow simulations in soils. Soil Sci Soc Am J 78:108-118
197. Yang X, Shi B, Chai Z, Guo Z (2014b) A Coupled Lattice Boltzmann Method to Solve Nernst-Planck Model for Simulating Electro-osmotic Flows. J Sci Comput 61:222-238
198. Yoon H, Valocchi AJ, Werth CJ, Dewers T (2012) Pore-scale simulation of mixing-induced calcium carbonate precipitation and dissolution in a microfluidic pore network. Water Resour Res 48:W02524
199. Yoon H, Dewers T (2013) Nanopore structures, statistically representative elementary volumes, and transport properties of chalk. Geophys Res Lett 40:4294-4298
200. Yoon H, Leibeling S, Zhang C, Müller RH, Werth CJ, Zilles JL (2014) Adaptation of Delftia acidovorans for degradation of 2, 4-dichlorophenoxyacetate in a microfluidic porous medium. Biodegradation 25:595-604
201. Yu D, Ladd AJC (2010) A numerical simulation method for dissolution in porous and fractured media. J Comput Phys 229:6450-6465
202. Yu D, Mei R, Luo L, Shyy W (2003) Viscous flow computations with the method of lattice Boltzmann equation. Prog Aerosp Sci 39:329-367
203. Zarghami A, Maghrebi MJ, Ghasemi J, Ubertini S (2012) Lattice Boltzmann finite volume formulation with improved stability. Comm Comput Phys 12:42
204. Zhang J (2011) Lattice Boltzmann method for microfluidics: models and applications. Microfluid Nanofluid 10:1-28
205. Zhang T, Klapper I (2014) Critical occlusion via biofilm induced calcite precipitation in porous media. New J Phys 16:055009
206. 3 precipitation and permeability reduction in a model subsurface sedimentary system. Environ Sci Technol 44:7833-7838
207. Zhang C, Kang Q, Wang X, Zilles JL, Müller RH, Werth CJ (2010b) Effects of pore-scale heterogeneity and transverse mixing on bacterial growth in porous media. Environ Sci Technol 44:3085-3092, doi: 10.1021/es903396h
208. Zhang T, Shi B, Guo Z, Chai Z, Lu J (2012) General bounce-back scheme for concentration boundary condition in the lattice-Boltzmann method. Phys Rev E 85:016701
209. Zhu H, Carlson HK, Coates JD (2013) Applicability of anaerobic nitrate-dependent Fe (II) oxidation to microbial enhanced oil recovery (MEOR). Environ Sci Technol 47(15):8970-7, doi: 10.1021/es401838b