Abraham, F.F., Broughton, J.Q., Bernstein, N., and Kaxiras, E. (1998) Spanning the length scales in dynamic simulation. Computers in Physics 12: 538-546. Abraham, F.F. (2000) Dynamically spanning the length scales from the quantum to the continuum. International Journal of Modern Physics C 11: 1135-1148. Acharya, R.C., van der Zee, S., and Leijnse, A. (2004) Porosity-permeability properties generated with a new 2-parameter 3D hydraulic pore-network model for consolidated and unconsolidated porous media. Advances in Water Resources 27: 707-723. Ahmed, U., Crary, S.F., and Coates, G.R. (1991) Permeability Estimation - the Various Sources and Their Interrelationships. Journal of Petroleum Technology 43: 578-587. Alexander, F.J., Garcia, A.L., and Tartakovsky, D.M. (2002) Algorithm refinement for stochastic partial differential equations. I. Linear diffusion. Journal of Computational Physics 182: 47-66. Alexander, F.J., Garcia, A.L., and Tartakovsky, D.M. (2005) Algorithm refinement for stochastic partial differential equations: II. Correlated systems. Journal of Computational Physics 207: 769-787. Alexander, F.J., Tartakovsky, D.M., and Garcia, A.L. (2005) Noise in algorithm refinement methods. Computing in Science & Engineering 7: 32-38. Alexander, F.J., Tartakovsky, D.M., and Garcia, A.L. (2005) Noise in algorithm refinement methods. Computing in Science & Engineering 7: 32-38. Allan, B.A., Armstrong, R., Bernholdt, D.E., Bertrand, F., Chiu, K., Dahlgren, T.L. et al. (2006) A component architecture for high-performance scientific computing. International Journal of High Performance Computing Applications 20: 163-202. Alvarado, V., Davis, H.T., and Scriven, L.E. (1997) Effects of pore-level reaction on dispersion In porous media. Chemical Engineering Science 52: 2865-2881. Appelo, C.A.J., and Postma, D. (1999) Variable dispersivity in a column experiment containing MnO2 and FeOOH-coated sand. Journal of Contaminant Hydrology 40: 95-106. Appold, M.S., and Garven, G. (2000) Reactive flow models of ore formation in the Southeast Missouri district. Economic Geology and the Bulletin of the Society of Economic Geologists 95: 1605-1626. Araque-Martinez, A., and Lake, L.W. (2001) A simplified approach to geochemical modeling and its effect on mineral precipitation. Spe Journal 6: 98-107. Arbogast, T., Pencheva, G., Wheeler, M.F., and Yotov, I. (2007) A multiscale mortar mixed finite element method. Multiscale Modeling & Simulation 6: 319-346. Arnon, S., Adar, E., Ronen, Z., Yakirevich, A., and Nativ, R. (2005) Impact of microbial activity on the hydraulic properties of fractured chalk. Journal of Contaminant Hydrology 76: 315-336. Attaway, S.W., Heinstein, M.W., and Swegle, J.W. (1994) Coupling of Smooth Particle Hydrodynamics with the Finite-Element Method. Nuclear Engineering and Design 150: 199-205. Attinger, S., Micha, J.D., and Kinzelbach, W. (2003) Multiscale modeling of nonlinearly adsorbing solute transport. Multiscale Modeling & Simulation 1: 408-431. Attinger, S., Dentz, M., and Kinzelbach, W. (2004) Exact transverse macro dispersion coefficients for transport in heterogeneous porous media. Stochastic Environmental Research and Risk Assessment 18: 9-15. Ayati, B.P., and Klapper, I. (2007) A multiscale model of biofilm as a senscence-structured fluid. Multiscale Modeling & Simulation 6: 347-365. Balhoff, M.T., Thompson, K.E., and Hjortso, M. (2007) Coupling pore-scale networks to continuum-scale models of porous media. Computers & Geosciences 33: 393-410. Ball, L.D., Corbett, P.W.M., Jensen, J.L., and Lewis, J.J.M. (1997) The role of geology in the behavior and choice of permeability predictors. Spe Formation Evaluation 12: 32-39. Beard, D.C., and Weyl, P.K. (1973) Influence of Texture on Porosity and Permeability of Unconsolidated Sand. American Association of Petroleum Geologists Bulletin 57: 349-369. Belytschko, T., and Xiao, S.P. (2003) Coupling methods for continuum model with molecular model. International Journal for Multiscale Computational Engineering 1: 115-126. Benekos, I.D., Cirpka, O.A., and Kitanidis, P.K. (2006) Experimental determination of transverse dispersivity in a helix and a cochlea. Water Resources Research 42. Bergdorf, M., Cottet, G.H., and Koumoutsakos, P. (2005) Multilevel adaptive particle methods for convection-diffusion equations. Multiscale Modeling & Simulation 4: 328-357. Bernholdt, D.E. (2007) Special issue: Component and framework technology in high-performance and scientific computing. Concurrency and Computation-Practice & Experience 19: 571-572. Borisova, E.A., and Adler, P.M. (2005) Deposition in porous media and clogging on the field scale. Physical Review E 71. Bothe, D., Sternich, C., and Warnecke, H.J. (2006) Fluid mixing in a T-shaped micro-mixer. Chemical Engineering Science 61: 2950-2958. Braack, M., and Ern, A. (2003) A posteriori control of modeling errors and discretization errors. Multiscale Modeling & Simulation 1: 221-238. Braack, M., and Ern, A. (2004) Coupling multimodelling with local mesh refinement for the numerical computation of laminar flames. Combustion Theory and Modelling 8: 771-788. Braatz, R.D., He, Y., and Alkire, R.C. (2005) Guidelines for the Design of Multiscale Simulation Codes. In 2005 AIChE Annual Meeting. Cincinnati, Ohio. Brown, K., Attaway, S., Plimpton, S., and Hendrickson, B. (2000) Parallel strategies for crash and impact simulations. Computer Methods in Applied Mechanics and Engineering 184: 375-390. Bryant, S., Cade, C., and Mellor, D. (1993) Permeability Prediction from Geologic Models. Aapg Bulletin-American Association of Petroleum Geologists 77: 1338-1350. Bryant, S.L., King, P.R., and Mellor, D.W. (1993) Network Model Evaluation of Permeability and Spatial Correlation in a Real Random Sphere Packing. Transport in Porous Media 11: 53-70. Budd, D.A. (2002) The relative roles of compaction and early cementation in the destruction of permeability in carbonate grainstones: a case study from the Paleogene of west-central Florida, USA. Journal of Sedimentary Research 72: 116-128. Canals, M., and Meunier, J.D. (1995) A Model for Porosity Reduction in Quartzite Reservoirs by Quartz Cementation. Geochimica Et Cosmochimica Acta 59: 699-709. Cao, J., and Kitanidis, P.K. (1998) Pore-scale dilution of conservative solutes: An example. Water Resources Research 34: 1941-1949. Chai, L.H. (2005) Recent progress of multiscale science. Progress in Chemistry 17: 186-191. Charrier, P., and Dubroca, B. (2003) Asymptotic transport models for heat and mass transfer in reactive porous media. Multiscale Modeling & Simulation 2: 124-157. Chen, W., and Ortoleva, P. (1990) Reaction Front Fingering in Carbonate-Cemented Sandstones. Earth-Science Reviews 29: 183-198. Chen, J.S., and Liu, C.W. (2002) Numerical simulation of the evolution of aquifer porosity and species concentrations during reactive transport. Computers & Geosciences 28: 485-499. Chen, J.S., and Liu, C.W. (2004) Interaction of reactive fronts during transport in a homogeneous porous medium with initial small non-uniformity. Journal of Contaminant Hydrology 72: 47-66. Chen, S.Q., E, W.N., and Shu, C.W. (2005) The heterogeneous multiscale method based on the discontinuous Galerkin method for hyperbolic and parabolic problems. Multiscale Modeling & Simulation 3: 871-894. Choly, N., Lu, G., E, W., and Kaxiras, E. (2005) Multiscale simulations in simple metals: A density-functional-based methodology. Physical Review B 71. Chu, M., Kitanidis, P.K., and McCarty, P.L. (2005) Modeling microbial reactions at the plume fringe subject to transverse mixing in porous media: When can the rates of microbial reaction be assumed to be instantaneous? Water Resources Research 41. Cirpka, O.A., Frind, E.O., and Helmig, R. (1999) Numerical simulation of biodegradation controlled by transverse mixing. Journal of Contaminant Hydrology 40: 159-182. Cirpka, O.A., and Kitanidis, P.K. (2000) Characterization of mixing and dilution in heterogeneous aquifers by means of local temporal moments. Water Resources Research 36: 1221-1236. Cirpka, O.A., and Kitanidis, P.K. (2001) Theoretical basis for the measurement of local transverse dispersion in isotropic porous media. Water Resources Research 37: 243-252. Cirpka, O.A., and Kitanidis, P.K. (2002) Numerical evaluation of solute dispersion and dilution in unsaturated heterogeneous media. Water Resources Research 38. Cirpka, O.A. (2005) Effects of sorption on transverse mixing in transient flows. Journal of Contaminant Hydrology 78: 207-229. Cirpka, O.A., Olsson, A., Ju, Q.S., Rahman, M.A., and Grathwohl, P. (2006) Determination of transverse dispersion coefficients from reactive plume lengths. Ground Water 44: 212-221. Cola, B.A., Schaffer, D.K., Fisher, T.S., and Stremler, M.A. (2006) A pulsed source-sink fluid mixing device. Journal of Microelectromechanical Systems 15: 259-266. Colon, C.F.J., Oelkers, E.H., and Schott, J. (2004) Experimental investigation of the effect of dissolution on sandstone permeability, porosity, and reactive surface area. Geochimica Et Cosmochimica Acta 68: 805-817. Csanyi, G., Albaret, T., Moras, G., Payne, M.C., and De Vita, A. (2005) Multiscale hybrid simulation methods for material systems. Journal of Physics-Condensed Matter 17: R691-R703. Curtin, W.A., and Miller, R.E. (2003) Atomistic/continuum coupling in computational materials science. Modelling and Simulation in Materials Science and Engineering 11: R33-R68. Cushman, J.H., Bennethum, L.S., and Hu, B.X. (2002) A primer on upscaling tools for porous media. Advances in Water Resources 25: 1043-1067. Dai, Z.X., and Samper, J. (2004) Inverse problem of multicomponent reactive chemical transport in porous media: Formulation and applications. Water Resources Research 40. Darhuber, A.A., Chen, J.Z., Davis, J.M., and Troian, S.M. (2004) A study of mixing in thermocapillary flows on micropatterned surfaces. Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences 362: 1037-1058. Davis, J.M., Roy, N.D., Mozley, P.S., and Hall, J.S. (2006) The effect of carbonate cementation on permeability heterogeneity in fluvial aquifers: An outcrop analog study. Sedimentary Geology 184: 267-280. De Fabritiis, G.D., Coveney, P.V., and Flekkoy, E.G. (2002) Multiscale dissipative particle dynamics. Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences 360: 317-331. De Fabritiis, G., Delgado-Buscalioni, R., and Coveney, P.V. (2006) Multiscale modeling of liquids with molecular specificity. Physical Review Letters 97. De Vuyst, T., Vignjevic, R., and Campbell, J.C. (2005) Coupling between meshless and finite element methods. International Journal of Impact Engineering 31: 1054-1064. deMello, A.J. (2006) Control and detection of chemical reactions in microfluidic systems. Nature 442: 394-402. Diedericks, G.P.J., and Duplessis, J.P. (1995) On Tortuosity and Areosity Tensors for Porous-Media. Transport in Porous Media 20: 265-279. Dillon, C.G., Worden, R.H., and Barclay, S.A. (2004) Simulations of the effects of diagenesis on the evolution of sandstone porosity. Journal of Sedimentary Research 74: 877-888. Dubois, P.F. (2005) Maintaining correctness in scientific programs. Computing in Science & Engineering 7: 80-85. Dutton, S.P., White, C.D., Willis, B.J., and Novakovic, D. (2002) Calcite cement distribution and its effect on fluid flow in a deltaic sandstone, Frontier Formation, Wyoming. Aapg Bulletin 86: 2007-2021. Dzwinel, W., Yuen, D.A., and Boryczko, K. (2006) Bridging diverse physical scales with the discrete-particle paradigm in modeling colloidal dynamics with mesoscopic features. Chemical Engineering Science 61: 2169-2185. E, W.N., and Huang, Z.Y. (2001) Matching conditions in atomistic-continuum modeling of materials. Physical Review Letters 8713. E, W., and Huang, Z.Y. (2002) A dynamic atomistic-continuum method for the simulation of crystalline materials. Journal of Computational Physics 182: 234-261. E, W., Engquist, B., and Huang, Z.Y. (2003) Heterogeneous multiscale method: A general methodology for multiscale modeling. Physical Review B 67. E, W.N., and Ming, P.B. (2004) Analysis of multiscale methods. Journal of Computational Mathematics 22: 210-219. E, W., Liu, D., and Vanden-Eijnden, E. (2005) Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. Journal of Chemical Physics 123. E, W., Engquist, B., Li, X.T., Ren, W.Q., and Vanden-Eijnden, E. (2007) Heterogeneous multiscale methods: A review. Communications in Computational Physics 2: 367-450. Efendiev, Y., and Durlofsky, L.J. (2003) A generalized convection-diffusion model for subgrid transport in porous media. Multiscale Modeling & Simulation 1: 504-526. Emmanuel, S., and Berkowitz, B. (2005) Mixing-induced precipitation and porosity evolution in porous media. Advances in Water Resources 28: 337-344. Fabriol, R., Sauty, J.P., and Ouzounian, G. (1993) Coupling Geochemistry with a Particle Tracking Transport Model. Journal of Contaminant Hydrology 13: 117-129. Fernandez-Mendez, S., Bonet, J., and Huerta, A. (2005) Continuous blending of SPH with finite elements. Computers & Structures 83: 1448-1458. Flekkoy, E.G., Feder, J., and Wagner, G. (2001) Coupling particles and fields in a diffusive hybrid model. Physical Review E 64: 066302. Freedman, V.L., Saripalli, K.P., and Meyer, P.D. (2003) Influence of mineral precipitation and dissolution on hydrologic properties of porous media in static and dynamic systems. Applied Geochemistry 18: 589-606. Fyta, M.G., Melchionna, S., Kaxiras, E., and Succi, S. (2006) Multiscale coupling of molecular dynamics and hydrodynamics: Application to DNA translocation through a nanopore. Multiscale Modeling & Simulation 5: 1156-1173. Garcia, A.L., Bell, J.B., Crutchfield, W.Y., and Alder, B.J. (1999) Adaptive mesh and algorithm refinement using direct simulation Monte Carlo. Journal of Computational Physics 154: 134-155. Goldenfeld, N., Chan, P.Y., and Veysey, J. (2006) Dynamics of precipitation pattern formation at geothermal hot springs. Physical Review Letters 96. Gouze, P., and Coudrain-Ribstein, A. (2002) Chemical reactions and porosity changes during sedimentary diagenesis. Applied Geochemistry 17: 39-47. Gu, Y.T., and Zhang, L.C. (2006) A concurrent multiscale method based on the meshfree method and molecular dynamics analysis. Multiscale Modeling & Simulation 5: 1128-1155. Hadjiconstantinou, N.G., and Patera, A.T. (1997) Heterogeneous atomistic-continuum representations for dense fluid systems. International Journal of Modern Physics C 8: 967-976. Hadjiconstantinou, N.G. (2004) Combining atomistic and continuum simulations of contact-line motion. Physical Review E 69. Haszeldine, R.S., Macaulay, C.I., Marchand, A., Wilkinson, M., Graham, C.M., Cavanagh, A. et al. (2000) Sandstone cementation and fluids in hydrocarbon basins. Journal of Geochemical Exploration 69: 195-200. Hornung, R.D., Wissink, A.M., and Kohn, S.R. (2006) Managing complex data and geometry in parallel structured AMR applications. Engineering with Computers 22: 181-195. Huerta, A., Fernandez-Mendez, S., and Liu, W.K. (2004) A comparison of two formulations to blend finite elements and mesh-free methods. Computer Methods in Applied Mechanics and Engineering 193: 1105-1117. Hyman, J.M. (2005) Patch dynamics for multiscale problems. Computing in Science & Engineering 7: 47-53. Ingram, G.D., Cameron, I.T., and Hangos, K.M. (2004) Classification and analysis of integrating frameworks in multiscale modelling. Chemical Engineering Science 59: 2171-2187. Janssen, G.M.C.M., Cirpka, O.A., and van der Zee, S. (2006) Stochastic analysis of nonlinear biodegradation in regimes controlled by both chromatographic and dispersive mixing. Water Resources Research 42. Jendrejack, R.M., de Pablo, J.J., and Graham, M.D. (2002) A method for multiscale simulation of flowing complex fluids. Journal of Non-Newtonian Fluid Mechanics 108: 123-142. Jenny, P., Lee, S.H., and Tchelepi, H.A. (2004) Adaptive multiscale finite-volume method for multiphase flow and transport in porous media. Multiscale Modeling & Simulation 3: 50-64. Johnson, G.R., Stryk, R.A., and Beissel, S.R. (1996) SPH for high velocity impact computations. Computer Methods in Applied Mechanics and Engineering 139: 347-373. Kadowaki, H., and Liu, W.K. (2004) Bridging multi-scale method for localization problems. Computer Methods in Applied Mechanics and Engineering 193: 3267-3302. Kainourgiakis, M.E., Kikkinides, E.S., and Stubos, A.K. (2002) Diffusion and flow in porous domains constructed using process-based and stochastic techniques. Journal of Porous Materials 9: 141-154. Kapoor, V., and Kitanidis, P.K. (1996) Concentration fluctuations and dilution in two-dimensionally periodic heterogeneous porous media. Transport in Porous Media 22: 91-119. Kapoor, V., and Kitanidis, P.K. (1998) Concentration fluctuations and dilution in aquifers. Water Resources Research 34: 1181-1193. Karpov, E.G., Yu, H., Park, H.S., Liu, W.K., Wang, Q.J., and Qian, D. (2006) Multiscale boundary conditions in crystalline solids: Theory and application to nanoindentation. International Journal of Solids and Structures 43: 6359-6379. Kim, J., Schwartz, F.W., Xu, T.F., Choi, H., and Kim, I.S. (2005) Coupled processes of fluid flow, solute transport, and geochemical reactions in reactive barriers. Vadose Zone Journal 3: 867-874. Kitanidis, P.K. (1994) The Concept of the Dilution Index. Water Resources Research 30: 2011-2026. Klein, P.A., and Zimmerman, J.A. (2006) Coupled atomistic-continuum simulations using arbitrary overlapping domains. Journal of Computational Physics 213: 86-116. Knutson, C.E., Werth, C.J., and Valocchi, A.J. (2005) Pore-scale simulation of biomass growth along the transverse mixing zone of a model two-dimensional porous medium. Water Resources Research 41. Knutson, C., Werth, C.J., and Valocchi, A.J. (2006) Comparison of continuum and pore-scale models of nutrient biodegradation under transverse mixing conditions. Advances in Water Resources In press. Kojic, M., Filipovic, N., and Tsuda, A. (2007) A mesoscopic bridging scale method for fluids and coupling dissipative particle dynamics with continuum finite element method. Computer Methods in Applied Mechanics and Engineering 197: 821-833. Kolobov, V.I., Bayyuk, S.A., Arslanbekov, R.R., Aristov, V.V., Frolova, A.A., and Zabelok, S.A. (2005) Construction of a unified continuum/kinetic solver for aerodynamic problems. Journal of Spacecraft and Rockets 42: 598-606. Koltermann, C.E., and Gorelick, S.M. (1995) Fractional packing model for hydraulic conductivity derived from sediment mixtures. Water Resources Research 31: 3283-3297. Koumoutsakos, P. (2005) Multiscale flow simulations using particles. Annual Review of Fluid Mechanics 37: 457-487. Kroger, M., Stankovic, I., and Hess, S. (2003) Towards multiscale modeling of metals via embedded particle computer simulation. Multiscale Modeling & Simulation 1: 25-39. Kuhn, M., and Stofen, H. (2005) A reactive flow model of the geothermal reservoir Waiwera, New Zealand. Hydrogeology Journal 13: 606-626. Le Gallo, Y., Bildstein, O., and Brosse, E. (1998) Coupled reaction-flow modeling of diagenetic changes in reservoir permeability, porosity and mineral compositions. Journal of Hydrology 209: 366-388. Li, J., Liao, D.Y., and Yip, S. (1998) Coupling continuum to molecular-dynamics simulation: Reflecting particle method and the field estimator. Physical Review E 57: 7259-7267. Li, J., Kevrekidis, P.G., Gear, C.W., and Kevrekidis, I.G. (2003) Deciding the nature of the coarse equation through microscopic simulations: The baby-bathwater scheme. Multiscale Modeling & Simulation 1: 391-407. Li, J.H., and Kwauk, M. (2003) Exploring complex systems in chemical engineering - the multi-scale methodology. Chemical Engineering Science 58: 521-535. Liang, Z., Ioannidis, M.A., and Chatzis, I. (2000) Permeability and electrical conductivity of porous media from 3D stochastic replicas of the microstructure. Chemical Engineering Science 55: 5247-5262. Lichtner, P.C. (1988) The Quasi-Stationary State Approximation to Coupled Mass-Transport and Fluid-Rock Interaction in a Porous-Medium. Geochimica Et Cosmochimica Acta 52: 143-165. Lichtner, P.C., and Carey, J.W. (2006) Incorporating solid solutions in reactive transport equations using a kinetic discrete-composition approach. Geochimica Et Cosmochimica Acta 70: 1356-1378. Lin, Y.P., and Singer, P.C. (2005) Effects of seed material and solution composition on calcite precipitation. Geochimica Et Cosmochimica Acta 69: 4495-4504. Lin, Y.P., Singer, P.C., and Aiken, G.R. (2005) Inhibition of calcite precipitation by natural organic material: Kinetics, mechanism, and thermodynamics. Environmental Science & Technology 39: 6420-6428. Lipatov, A.S., Motschmann, U., and Bagdonat, T. (2002) 3D hybrid simulations of the interaction of the solar wind with a weak comet. Planetary and Space Science 50: 403-411. Liu, W.K., Karpov, E.G., Zhang, S., and Park, H.S. (2004) An introduction to computational nanomechanics and materials. Computer Methods in Applied Mechanics and Engineering 193: 1529-1578. Liu, W.K., Park, H.S., Qian, D., Karpov, E.G., Kadowaki, H., and Wagner, G.J. (2006) Bridging scale methods for nanomechanics and materials. Computer Methods in Applied Mechanics and Engineering 195: 1407-1421. Magan, R.V., and Sureshkumar, R. (2004) A multiscale-linking algorithm for the simulation of irreversible deposition. Multiscale Modeling & Simulation 2: 475-500. Magan, R.V., and Sureshkumar, R. (2006) Multiscale-linking simulation of irreversible colloidal deposition in the presence of DLVO interactions. Journal of Colloid and Interface Science 297: 389-406. Mahadevan, R., Bond, D.R., Butler, J.E., Esteve-Nunez, A., Coppi, M.V., Palsson, B.O. et al. (2006) Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Applied and Environmental Microbiology 72: 1558-1568. Martin, D.F., Colella, P., Anghel, M., and Alexander, F.J. (2005) Adaptive mesh refinement for multiscale nonequilibrium physics. Computing in Science & Engineering 7: 24-31. Martys, N.S., and Hagedorn, J.G. (2002) Multiscale modeling of fluid transport in heterogeneous materials using discrete Boltzmann methods. Materials and Structures 35: 650-658. Meile, C., and Tuncay, K. (2006) Scale dependence of reaction rates in porous media. Advances in Water Resources 29: 62-71. Mhadeshwar, A.B., and Vlachos, D.G. (2005) Hierarchical, multiscale surface reaction mechanism development: CO and H-2 oxidation, water-gas shift, and preferential oxidation of CO on Rh. Journal of Catalysis 234: 48-63. Michopoulos, J.G., Farhat, C., and Fish, J. (2005) Modeling and simulation of multiphysics systems. Journal of Computing and Information Science in Engineering 5: 198-213. Ming, P.B., and Zhang, P.W. (2006) Analysis of the heterogeneous multiscale method for parabolic homogenization problems. Mathematics of Computation 76: 153-177. Molinero, J., and Samper, J. (2006) Large-scale modeling of reactive solute transport in fracture zones of granitic bedrocks. Journal of Contaminant Hydrology 82: 293-318. Moro, E. (2004) Hybrid method for simulating front propagation in reaction-diffusion systems. Physical Review E 69. Morris, J.P., Fox, P.J., and Zhu, Y. (1997) Modeling low Reynolds number incompressible flows using SPH. Journal of Computational Physics 136: 214-226. Nambi, I.M., Werth, C.J., Sanford, R.A., and Valocchi, A.J. (2003) Pore-scale analysis of anaerobic halorespiring bacterial growth along the transverse mixing zone of an etched silicon pore network. Environmental Science & Technology 37: 5617-5624. Nie, X.B., Chen, S.Y., E, W.N., and Robbins, M.O. (2004) A continuum and molecular dynamics hybrid method for micro- and nano-fluid flow. Journal of Fluid Mechanics 500: 55-64. Niessner, J., and Helmig, R. (2006) Multi-scale modelling of two-phase-two-component processes in heterogeneous porous media. Numerical Linear Algebra with Applications 13: 699-715. Nourtier-Mazauric, E., Guy, B., Fritz, B., Brosse, E., Garcia, G., and Clement, A. (2005) Modelling the dissolution/precipitation of ideal solid solutions. Oil & Gas Science and Technology-Revue De L Institut Francais Du Petrole 60: 401-415. O'Connell, S.T., and Thompson, P.A. (1995) Molecular dynamics-continuum hybrid computations: A tool for studying complex fluid flows. Physical Review E 52: R5792-R5795. Oden, J.T., and Vemaganti, K. (1999) Adaptive hierarchical modeling of heterogeneous structures. Physica D 133: 404-415. Oden, J.T., Vemaganti, K., and Moes, N. (1999) Hierarchical modeling of heterogeneous solids. Computer Methods in Applied Mechanics and Engineering 172: 3-25. Oden, J.T., and Vemaganti, K.S. (2000) Estimation of local modeling error and goal-oriented adaptive modeling of heterogeneous materials I. Error estimates and adaptive algorithms. Journal of Computational Physics 164: 22-47. Oden, J.T., Prudhomme, S., Hammerand, D.C., and Kuczma, M.S. (2001) Modeling error and adaptivity in nonlinear continuum mechanics. Computer Methods in Applied Mechanics and Engineering 190: 6663-6684. Oden, J.T., and Prudhomme, S. (2002) Estimation of modeling error in computational mechanics. Journal of Computational Physics 182: 496-515. Oden, J.T., Belytschko, T., Babuska, V., and Hughes, T.J.R. (2003) Research directions in computational mechanics. Computer Methods in Applied Mechanics and Engineering 192: 913-922. Oden, J.T., Prudhomme, S., Romkes, A., and Bauman, P.T. (2006) Multiscale modeling of physical phenomena: Adaptive control of models. Siam Journal on Scientific Computing 28: 2359-2389. Oelkers, E.H., Bjorkum, P.A., Walderhaug, O., Nadeau, P.H., and Murphy, W.M. (2000) Making diagenesis obey thermodynamics and kinetics: the case of quartz cementation in sandstones from offshore mid-Norway. Applied Geochemistry 15: 295-309. O'Leary, D.P. (2005) Finite differences and finite elements: Getting to know you. Computing in Science & Engineering 7: 72-75. Oren, P.E., and Bakke, S. (2002) Process based reconstruction of sandstones and prediction of transport properties. Transport in Porous Media 46: 311-343. Ottino, J.M., and Wiggins, S. (2004) Introduction: mixing in microfluidics. Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences 362: 923-935. Panda, M.N., and Lake, L.W. (1994) Estimation of Single-Phase Permeability from Parameters of Particle-Size Distribution. Aapg Bulletin-American Association of Petroleum Geologists 78: 1028-1039. Panda, M.N., and Lake, L.W. (1995) A Physical Model of Cementation and Its Effects on Single-Phase Permeability. Aapg Bulletin-American Association of Petroleum Geologists 79: 431-443. Pannone, M., and Kitanidis, P.K. (1999) Large-time behavior of concentration variance and dilution in heterogeneous formations. Water Resources Research 35: 623-634. Pannone, M., and Kitanidis, P.K. (2004) On the asymptotic behavior of dilution parameters for Gaussian and hole-Gaussian log-conductivity covariance functions. Transport in Porous Media 56: 257-281. Quarteroni, A., and Veneziani, A. (2003) Analysis of a geometrical multiscale model based on the coupling of ODEs and PDEs for blood flow simulations. Multiscale Modeling & Simulation 1: 173-195. Rabczuk, T., and Belytschko, T. (2005) Adaptivity for structured meshfree particle methods in 2D and 3D. International Journal for Numerical Methods in Engineering 63: 1559-1582. Rabczuk, T., Xiao, S.P., and Sauer, A. (2006) Coupling of mesh-free methods with finite elements: basic concepts and test results. Communications in Numerical Methods in Engineering 22: 1031-1065. Rahman, M.A., Jose, S.C., Nowak, W., and Cirpka, O.A. (2005) Experiments on vertical transverse mixing in a large-scale heterogeneous model aquifer. Journal of Contaminant Hydrology 80: 130-148. Raimondeau, S., and Vlachos, D.G. (2002) Recent developments on multiscale, hierarchical modeling of chemical reactors. Chemical Engineering Journal 90: 3-23. Redden, G.D., Fang, Y., Scheibe, T., Tartakovsky, A., Fox, D.T., White, T.A. et al. (2005) Calcium carbonate precipitation along solution-solution interfaces in porous media. . EOS Trans. AGU 86: Abstract B33C-1042. Ren, W.Q., and E, W. (2005) Heterogeneous multiscale method for the modeling of complex fluids and micro-fluidics. Journal of Computational Physics 204: 1-26. Ren, W.Q. (2007) Analytical and numerical study of coupled atomistic-continuum methods for fluids. Journal of Computational Physics 227: 1353-1371. Robinson, B.A., and Viswanathan, H.S. (2003) Application of the theory of micromixing to groundwater reactive transport models. Water Resources Research 39. Romkes, A., Oden, J.T., and Vemaganti, K. (2006) Multi-scale goal-oriented adaptive modeling of random heterogeneous materials. Mechanics of Materials 38: 859-872. Saripalli, K.P., Meyer, P.D., Bacon, D.H., and Freedman, V.L. (2001) Changes in hydrologic properties of aquifer media due to chemical reactions: A review. Critical Reviews in Environmental Science and Technology 31: 311-349. Saripalli, K.P., Serne, R.J., Meyer, P.D., and McGrail, B.P. (2002) Prediction of diffusion coefficients in porous media using tortuosity factors based on interfacial areas. Ground Water 40: 346-352. Saripalli, K.P., Meyer, P.D., Parker, K.E., and Lindberg, M.J. (2005) Effect of chemical reactions on the hydrologic properties of fractured and rubbelized glass media. Applied Geochemistry 20: 1677-1686. Sbalzarini, I.F., Walther, J.H., Polasek, B., Chatelain, P., Bergdorf, M., Hieber, S.E. et al. (2006) A software framework for the portable parallelization of particle-mesh simulations. In Euro-Par 2006 Parallel Processing, pp. 730-739. Scheibe, T.D., and Freyberg, D.L. (1995) Use of sedimentological information for geometric simulation of natural porous media structure. Water Resources Research 31: 3259-3270. Scheibe, T.D., Tartakovsky, A.M., Redden, G., Meakin, P., and Fang, Y. (2006) Pore-scale simulations of reactive transport with smoothed particle hydrodynamics. In Society for Industrial and Applied Mathematics Annual Meeting. Boston, MA. Schuchardt, K., Chin, G.J., Chase, J., Daily, J., and Scheibe, T.D. (2008) Experiences in the design of scientific workflows for subsurface sciences. IEEE Transactions on Automation Science and Engineering, In review. Schwartzentruber, T.E., and Boyd, I.D. (2006) A hybrid particle-continuum method applied to shock waves. Journal of Computational Physics 215: 402-416. Seeboonruang, U., and Ginn, T.R. (2006) Upscaling heterogeneity in aquifer reactivity via exposure-time concept: Forward model. Journal of Contaminant Hydrology 84: 127-154. Seeboonruang, U., and Ginn, T.R. (2006) Upscaling heterogeneity in aquifer reactivity via the exposure-time concept: Inverse model. Journal of Contaminant Hydrology 84: 155-177. Setayeshgar, S., Gear, C.W., Othmer, H.G., and Kevrekidis, I.G. (2005) Application of coarse integration to bacterial chemotaxis. Multiscale Modeling & Simulation 4: 307-327. Shalev, E., Lyakhovsky, V., and Yechieli, Y. (2006) Salt dissolution and sinkhole formation along the Dead Sea shore. Journal of Geophysical Research-Solid Earth 111. Sirisup, S., Karniadakis, G.E., Xiu, D.B., and Kevrekidis, I.G. (2005) Equation-free/Galerkin-free POD-assisted computation of incompressible flows. Journal of Computational Physics 207: 568-587. Sorbie, K.S., and Mackay, E.J. (2000) Mixing of injected, connate and aquifer brines in waterflooding and its relevance to oilfield scaling. Journal of Petroleum Science and Engineering 27: 85-106. Spearing, M., and Matthews, G.P. (1991) Modeling Characteristic Properties of Sandstones. Transport in Porous Media 6: 71-90. Suman, R., and Ruth, D. (1993) Formation Factor and Tortuosity of Homogeneous Porous-Media. Transport in Porous Media 12: 185-206. Sun, N.Z. (1999) A finite cell method for simulating the mass transport process in porous media. Water Resources Research 35: 3649-3662. Sun, Q., Boyd, I.D., and Candler, G.V. (2004) A hybrid continuum/particle approach for modeling subsonic, rarefied flows. Journal of Computational Physics 194: 256-277. Sun, Y., and Engquist, B. (2006) Heterogeneous multiscale methods for interface tracking of combustion fronts. Multiscale Modeling & Simulation 5: 532-563. Symeonidis, V., Karniadakis, G.E., and Caswell, B. (2005) A seamless approach to multiscale complex fluid simulation. Computing in Science & Engineering 7: 39-46. Tang, S.Q., Hou, T.Y., and Liu, W.K. (2006) A pseudo-spectral multiscale method: Interfacial conditions and coarse grid equations. Journal of Computational Physics 213: 57-85. Tang, S.Q., Hou, T.Y., and Liu, W.K. (2006) A mathematical framework of the bridging scale method. International Journal for Numerical Methods in Engineering 65: 1688-1713. Tartakovsky, A.M., Meakin, P., and Scheibe, T.D. (2005) Pore-scale smoothed particle hydrodynamics model for reactive transport and mineral precipitation. EOS Trans. AGU 86: Abstract H47A-07. Tartakovsky, A.M., Meakin, P., and Scheibe, T.D. (2005) A smoothed particle hydrodynamics model for reactive transport in porous and fractured media. In Joint International Symposia for Subsurface Microbiology (ISSM 2005) and Environmental Biogeochemistry (ISEB XVII). Jackson, WY. Tartakovsky, A., and Meakin, P. (2005) Modeling of surface tension and contact angles with smoothed particle hydrodynamics. Physical Review E 72. Tartakovsky, A.M., and Meakin, P. (2005) Simulation of unsaturated flow in complex fractures using smoothed particle hydrodynamics. Vadose Zone Journal 4: 848-855. Tartakovsky, A.M., and Meakin, P. (2005) A smoothed particle hydrodynamics model for miscible flow in three-dimensional fractures and the two-dimensional Rayleigh-Taylor instability. Journal of Computational Physics 207: 610-624. Tartakovsky, D.M., and Alexander, F.J. (2005) Multiphysics modeling - Guest editors' introduction. Computing in Science & Engineering 7: 14-15. Tartakovsky, A.M., Scheibe, T.D., Redden, G., Fang, Y., Meakin, P., and Saripalli, K.P. (2006) Smoothed particle hydrodynamics model for pore-scale flow, reactive transport and mineral precipitation. In XVI International Conference on Computational Methods in Water Resources. Binning, P.J., Engesgaard, P.K., Dahle, H.K., Pinder, G.F., and Gray, W.G. (eds). Copenhagne, Denmark. Tartakovsky, A.M., and Meakin, P. (2006) Pore scale modeling of immiscible and miscible fluid flows using smoothed particle hydrodynamics. Advances in Water Resources 29: 1464-1478. Tartakovsky, A.M., Meakin, P., Scheibe, T.D., and Eichler West, R.M. (2007) Simulations of reactive transport and precipitation with smoothed particle hydrodynamics. Journal of Computational Physics 222: 654-672. Tartakovsky, A.M., Meakin, P., Scheibe, T.D., and Wood, B.D. (2007) A smoothed particle hydrodynamics model for reactive transport and mineral precipitation in porous and fractured porous media. Water Resources Research 43. Tartakovsky, A.M., Tartakovsky, D.M., Scheibe, T.D., and Meakin, P. (2008) Hybrid simulations of reaction-diffusion systems in porous media. Siam Journal on Scientific Computing in press. Tartakovsky, A.M., Scheibe, T.D., and Meakin, P. (2008) Pore-scale model for reactive transport and biomass growth. Journal of Porous Media,In press. Tartakovsky, A.M., Redden, G., Lichtner, P.C., Scheibe, T.D., and Meakin, P. (2008) Mixing-induced precipitation: Experimental study and multiscale numerical analysis. Water Resources Research 44. Tello, J.S., and Curtin, W.A. (2005) A coupled discrete/continuum model for multiscale diffusion. International Journal for Multiscale Computational Engineering 3: 257-265. Thierrin, J., and Kitanidis, P.K. (1994) Solute Dilution at the Borden and Cape-Cod Groundwater Tracer Tests. Water Resources Research 30: 2883-2890. Thullner, M., Mauclaire, L., Schroth, M.H., Kinzelbach, W., and Zeyer, J. (2002) Interaction between water flow and spatial distribution of microbial growth in a two-dimensional flow field in saturated porous media. Journal of Contaminant Hydrology 58: 169-189. To, A.C., and Li, S.F. (2005) Perfectly matched multiscale simulations. Physical Review B 72. Vemaganti, K.S., and Oden, J.T. (2001) Estimation of local modeling error and goal-oriented adaptive modeling of heterogeneous materials Part II: A computational environment for adaptive modeling of heterogeneous elastic solids. Computer Methods in Applied Mechanics and Engineering 190: 6089-6124. Villa, E., Balaeff, A., Mahadevan, L., and Schulten, K. (2004) Multiscale method for simulating protein-DNA complexes. Multiscale Modeling & Simulation 2: 527-553. Vlachos, D.G. (1997) Multiscale integration hybrid algorithms for homogeneous-heterogeneous reactors. Aiche Journal 43: 3031-3041. Vlachos, D.G. (1999) The role of macroscopic transport phenomena in film microstructure during epitaxial growth. Applied Physics Letters 74: 2797-2799. Vlachos, D.G., Mhadeshwar, A.B., and Kaisare, N.S. (2006) Hierarchical multiscale model-based design of experiments, catalysts, and reactors for fuel processing. Computers & Chemical Engineering 30: 1712-1724. Wagner, G.J., and Liu, W.K. (2003) Coupling of atomistic and continuum simulations using a bridging scale decomposition. Journal of Computational Physics 190: 249-274. Wang, C.Y., and Zhang, X. (2006) Multiscale modeling and related hybrid approaches. Current Opinion in Solid State & Materials Science 10: 2-14. Weimar, J.R. (2001) Coupling microscopic and macroscopic cellular automata. Parallel Computing 27: 601-611. Wen, C., and Fish, J. (2006) A generalized space-time mathematical homogenization theory for bridging atomistic and continuum scales. International Journal for Numerical Methods in Engineering 67: 253-271. Werder, T., Walther, J.H., and Koumoutsakos, P. (2005) Hybrid atomistic-continuum method for the simulation of dense fluid flows. Journal of Computational Physics 205: 373-390. Wijesinghe, H.S., Hornung, R.D., Garcia, A.L., and Hadjiconstantinou, N.G. (2004) Three-dimensional hybrid continuum-atomistic simulations for multiscale hydrodynamics. Journal of Fluids Engineering-Transactions of the Asme 126: 768-777. Wijesinghe, H.S., and Hadjiconstantinou, N.G. (2004) A hybrid atomistic-continuum formulation for unsteady, viscous, incompressible flows. Cmes-Computer Modeling in Engineering & Sciences 5: 515-526. Wilson, A.M., Boles, J.R., and Garven, G. (2000) Calcium mass transport and sandstone diagenesis during compaction-driven flow: Stevens Sandstone, San Joaquin basin, California. Geological Society of America Bulletin 112: 845-856. Woo, X.Y., Tan, R.B.H., Chow, P.S., and Braatz, R.D. (2006) Simulation of mixing effects in antisolvent crystallization using a coupled CFD-PDF-PBE approach. Crystal Growth & Design 6: 1291-1303. Xiao, S.P., and Belytschko, T. (2004) A bridging domain method for coupling continua with molecular dynamics. Computer Methods in Applied Mechanics and Engineering 193: 1645-1669. Xiu, D.B., and Kevrekidis, I.G. (2005) Equation-free, multiscale computation for unsteady random diffusion. Multiscale Modeling & Simulation 4: 915-935. Xiu, D.B., Kevrekidis, I.G., and Ghanem, R. (2005) An equation-free, multiscale approach to uncertainty quantification. Computing in Science & Engineering 7: 16-23. Xu, T.F., Sonnenthal, E., and Bodvarsson, G. (2003) A reaction-transport model for calcite precipitation and evaluation of infiltration fluxes in unsaturated fractured rock. Journal of Contaminant Hydrology 64: 113-127. Xu, T.F., Sonnenthal, E., Spycher, N., and Pruess, K. (2006) TOUGHREACT - A simulation program for non-isothermal multiphase reactive geochemical transport in variably saturated geologic media: Applications to geothermal injectivity and CO2 geological sequestration. Computers & Geosciences 32: 145-165. Yeh, G.T., Sun, J.T., Jardine, P.M., Burgos, W.D., Fang, Y.L., Li, M.H., and Siegel, M.D. (2004) HYDROGEOCHEM 5.0: A three-dimensional model of coupled fluid flow, thermal transport and hydrogeochemical transport through variable saturated conditions -- Version 5.0. In. Oak Ridge, TN: Oak Ridge National Laboratory. Zhang, L.T., Wagner, G.J., and Liu, W.K. (2003) Modelling and simulation of fluid structure interaction by meshfree and FEM. Communications in Numerical Methods in Engineering 19: 615-621.