Hierarchical simulator of biofilm growth and dynamics in granular porous materials

Bailey, 1986 Barrett, 1994 Baveye, 1989, An evaluation of mathematical models of the transport of biologically reacting solutes in saturated soils and aquifers, Water Resour Res, 25, 1413, 10.1029/WR025i006p01413 Bourchtein, 2002, Numerical simulation of incompressible flows through granular porous media, Appl Numer Math, 40, 291, 10.1016/S0168-9274(01)00072-1 Bouwer, 2000, Biofilms in porous media, 123 Brinkman, 1947, A calculation of the viscous force exerted by a flowing fluid on a dense swarm of particles, Appl Sci Res, A1, 27 Bryers, 2000, Biofilm formation and persistence, 45 Burganos, 1992, Creeping flow around and through a permeable sphere moving with constant velocity towards a solid wall – a revision, Chem Eng Commun, 117, 85, 10.1080/00986449208936058 Burganos, 1992, Three-dimensional trajectory analysis and network simulation of deep bed filtration, J Colloid Interf Sci, 148, 167, 10.1016/0021-9797(92)90125-6 Burganos, 1995, Monte Carlo network simulation of horizontal, upflow and downflow depth filtration, AIChE J, 41, 272, 10.1002/aic.690410210 Burganos, 2001, Simulation of the dynamics of depth filtration of non-Brownian particles, AIChE J, 47, 880, 10.1002/aic.690470411 Characklis, 1990, Biofilm processes, 195 Chopp, 2003, The dependence of quorum sensing on the depth of a growing biofilm, Bull Math Biol, 65, 1053, 10.1016/S0092-8240(03)00057-0 Choy, 1999 Cogan, 2004, The role of biofilm matrix in structural development, Math Med Biol, 21, 147, 10.1093/imammb/21.2.147 Costerton, 1994, Biofilms, the customized microniche, J Bacteriol, 176, 2137, 10.1128/jb.176.8.2137-2142.1994 Cunningham, 1991, Influence of biofilm accumulation on porous media hydrodynamics, Environ Sci Technol, 25, 1305, 10.1021/es00019a013 Cushman, 1997 Dogan, 2004, High pressure inactivation kinetics of Listeria monocytogenes inactivation in broth, milk, and peach and orange juices, J Food Eng, 62, 47, 10.1016/S0260-8774(03)00170-5 Dupin, 2000, Impact of colony morphologies and disinfection on biological clogging in porous media, Environ Sci Technol, 34, 1513, 10.1021/es990452f Dupin, 2001, Pore-scale modeling of biological clogging due to aggregate expansion: a material mechanics approach, Water Resour Res, 37, 2965, 10.1029/2001WR000306 Dupin, 2001, Simulations of two-dimensional modeling of biomass aggregate growth in network models, Water Resour Res, 37, 2981, 10.1029/2001WR000310 Eberl, 2001, A new deterministic spatio-temporal continuum model for biofilm development, J Theor Med, 3, 161, 10.1080/10273660108833072 Fletcher, 1996, vol. 2 Ginn, 2002, Processes in microbial transport in the natural subsurface, Adv Water Resour, 25, 1017, 10.1016/S0309-1708(02)00046-5 Goyeau, 2003, Momentum transport at a fluid-porous interface, Int J Heat Mass Transfer, 46, 4071, 10.1016/S0017-9310(03)00241-2 Horn, 2003, Simulation of growth and detachment in biofilm systems under defined hydrodynamic conditions, Biotechnol Bioeng, 81, 607, 10.1002/bit.10503 Jackson, 1986, The permeability of fibrous porous media, Can J Chem Eng, 64, 364, 10.1002/cjce.5450640302 Kapellos GE, Alexiou TS, Pavlou S, Payatakes AC. Hierarchical modeling approach for the prediction of effective hydraulic permeability and diffusion coefficient in biofilms. In: Proceedings of the international conference biofilms 2004: structure and activity of biofilms, Las Vegas (NV, USA), 2004. p. 255–60. Kildsgaard, 2001, Numerical analysis of biological clogging in two-dimensional sand box experiments, J Contam Hydrol, 50, 261, 10.1016/S0169-7722(01)00109-7 Kreft, 2004, Biofilms promote altruism, Microbiol-SGM, 150, 2751, 10.1099/mic.0.26829-0 Laspidou, 2004, Modeling the development of biofilm density including active bacteria, inert biomass, and extracellular polymeric substances, Water Res, 38, 3349, 10.1016/j.watres.2004.04.037 Laspidou, 2004, Evaluating trends in biofilm density using the UMCCA model, Water Res, 38, 3362, 10.1016/j.watres.2004.04.051 Lawrence, 1991, Optical sectioning of microbial biofilms, J Bacteriol, 173, 6558, 10.1128/jb.173.20.6558-6567.1991 Lazarova, 2000, Innovative biofilm treatment technologies for water and wastewater treatment, 159 Lewandowski, 1993, NMR and microelectrode studies of hydrodynamics and kinetics in biofilms, Biotechnol Prog, 9, 40, 10.1021/bp00019a006 McCarty, 1981, Trace organics in groundwater, Environ Sci Technol, 15, 40, 10.1021/es00083a003 McKee, 2004, Recent advances in the marker and cell method, Arch Comput Method E, 11, 107, 10.1007/BF02905936 Michalopoulou, 1993, Hydrodynamic interactions of two permeable particles moving slowly along their centerline, Chem Eng Sci, 48, 2889, 10.1016/0009-2509(93)80035-O Miller, 2001, Quorum sensing in bacteria, Annu Rev Microbiol, 55, 165, 10.1146/annurev.micro.55.1.165 Molz, 1986, Simulation of microbial growth dynamics coupled to nutrient and oxygen transport in porous media, Water Resour Res, 22, 1207, 10.1029/WR022i008p01207 Murphy, 1997, The influence of physical heterogeneity on microbial degradation and distribution in porous media, Water Resour Res, 33, 1087, 10.1029/96WR03851 Murphy, 2000, Modeling microbial processes in porous media, Hydrogeol J, 8, 142, 10.1007/s100409900043 Neale, 1973, Prediction of transport processes within porous media: diffusive flow processes within an homogeneous swarm of spherical particles, AIChE J, 19, 112, 10.1002/aic.690190116 Neale, 1974, Prediction of transport processes within porous media: creeping flow relative to a fixed swarm of spherical particles, AIChE J, 20, 530, 10.1002/aic.690200314 Ochoa-Tapia, 1995, Momentum transfer at the boundary between a porous medium and a homogeneous fluid-I. Theoretical development, Int J Heat Mass Transfer, 38, 2635, 10.1016/0017-9310(94)00346-W Ogston, 1973, On the transport of compact particles through solutions of chain polymers, P Roy Soc Lond A Math Phys Sci, 333, 297, 10.1098/rspa.1973.0064 Ohashi, 1994, Adhesion strength of biofilm developed in an attached growth reactor, Water Sci Technol, 29, 281, 10.2166/wst.1994.0771 Parsek, 2005, Sociomicrobiology: the connections between quorum sensing and biofilms, Trends Microbiol, 13, 27, 10.1016/j.tim.2004.11.007 Paulsen, 1997, Biofilm morphology in porous media, a study with microscopic and image techniques, Water Sci Technol, 36, 1, 10.1016/S0273-1223(97)00317-X Payatakes, 1987, Creeping flow around and through a permeable sphere moving with constant velocity towards a solid wall, Chem Eng Commun, 58, 119, 10.1080/00986448708911963 Picioreanu, 1998, Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach, Biotechnol Bioeng, 58, 101, 10.1002/(SICI)1097-0290(19980405)58:1<101::AID-BIT11>3.0.CO;2-M Rasmussen, 1998, Microelectrode measurements of local mass transport rates in heterogeneous biofilms, Biotechnol Bioeng, 59, 302, 10.1002/(SICI)1097-0290(19980805)59:3<302::AID-BIT6>3.0.CO;2-F Rittmann, 1993, The significance of biofilms in porous media, Water Resour Res, 29, 2195, 10.1029/93WR00611 Rockhold, 2002, Considerations for modeling bacterial-induced changes in hydraulic properties of variably saturated porous media, Adv Water Resour, 25, 477, 10.1016/S0309-1708(02)00023-4 Schäfer, 1998, Simulation of reactive processes related to biodegradation in aquifers 1. Structure of the three-dimensional reactive transport model, J Contam Hydrol, 31, 167, 10.1016/S0169-7722(97)00060-0 Sharp, 1999, Observation of thick biofilm accumulation and structure in porous media and corresponding hydrodynamic and mass transfer effects, Water Sci Technol, 39, 195, 10.1016/S0273-1223(99)00168-7 Sorbie, 1991, Rheological and transport effects in the flow of low-concentration xanthan solution through porous media, J Colloid Interf Sci, 145, 74, 10.1016/0021-9797(91)90100-M Stewart, 2004, Modeling of biomass-plug development and propagation in porous media, Biochem Eng J, 17, 107, 10.1016/S1369-703X(03)00146-3 Suchomel, 1998, Network model of flow, transport and biofilm effects in porous media, Transport Porous Med, 30, 1, 10.1023/A:1006560705680 Suchomel, 1998, Macroscale properties of porous media from a network model of biofilm processes, Transport Porous Med, 31, 39, 10.1023/A:1006506104835 Tanner, 1991, Microbially enhanced oil-recovery from carbonate reservoirs, Geomicrobiol J, 9, 169, 10.1080/01490459109385998 Taylor, 1990, Substrate and biomass transport in a porous medium, Water Resour Res, 26, 2181, 10.1029/WR026i009p02181 Thullner, 2002, Influence of microbial growth on hydraulic properties of pore networks, Transport Porous Med, 49, 99, 10.1023/A:1016030112089 Tyson, 2000, Fractional step methods applied to a chemotaxis model, J Math Biol, 41, 455, 10.1007/s002850000038 Varonos, 1998, Development and assessment of a variable-order non-oscillatory scheme for convection term discretization, Int J Numer Meth Fl, 26, 1, 10.1002/(SICI)1097-0363(19980115)26:1<1::AID-FLD603>3.0.CO;2-N Vayenas, 2002, Visualization experiments of biodegradation in porous media and calculation of the biodegradation rate, Adv Water Resour, 25, 203, 10.1016/S0309-1708(01)00023-9 Wanner, 1995, Modeling biofilm accumulation and mass transport in a porous medium under high substrate loading, Biotechnol Bioeng, 47, 703, 10.1002/bit.260470611 Ward, 2004, Cell-signalling repression in bacterial quorum sensing, Math Med Biol, 21, 169, 10.1093/imammb/21.3.169 Wimpenny, 2000, Heterogeneity in biofilms, FEMS Microbiol Rev, 24, 661, 10.1111/j.1574-6976.2000.tb00565.x Wolfaardt, 1999, Function of EPS, 171 Yang, 1996, Simulation of correlated and uncorrelated packing of random size spheres, Phys Rev E, 53, 1516, 10.1103/PhysRevE.53.1516 Zhang, 1994, Density, porosity and pore structure of biofilms, Water Res, 28, 2267, 10.1016/0043-1354(94)90042-6