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Mathematical Modeling of Biofilms

Mathematical Modeling of Biofilms

(2006)

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Book Details

Abstract

Over 90% of bacterial biomass exists in the form of biofilms. The ability of bacteria to attach to surfaces and to form biofilms often is an important competitive advantage for them over bacteria growing in suspension. Some biofilms are "good" in natural and engineered systems; they are responsible for nutrient cycling in nature and are used to purify waters in engineering processes. Other biofilms are "bad" when they cause fouling and infections of humans and plants. Whether we want to promote good biofilms or eliminate bad biofilms, we need to understand how they work and what works to control them. Mathematical Modeling of Biofilms provides guidelines for the selection and use of mathematical models of biofilms. The whole range of existing models - from simple analytical expressions to complex numerical models - is covered. The application of the models for the solution of typical problems is demonstrated, and the performance of the models is tested in comparative studies. With the dramatic evolution of the computational capacity still going on, modeling tools for research and practice will become more and more significant in the next few years. This report provides the foundation to understand the models and to select the most appropriate one for a given use. Mathematical Modeling of Biofilms gives a state-of-the-art overview that is especially valuable for educating students, new biofilm researchers, and design engineers. Through a series of three benchmark problems, the report demonstrates how to use the different models and indicates when simple or highly complex models are most appropriate. This is the first report to give a quantitative comparison of existing biofilm models.               The report supports model-based design of biofilm reactors.               The report can be used as basis for teaching biofilm-system modeling.               The report provides the foundation for researchers seeking to use biofilm modeling or to develop new biofilm models.   Scientific and Technical Report No.18

Table of Contents

Section Title Page Action Price
Contents 6
Overview 12
WHAT IS A BIOFILM 12
WHAT IS A MODEL? 12
MODEL SELECTION 13
BIOFILM MODELS 16
BENCHMARK PROBLEMS 19
1.0 INTRODUCTION 22
WHAT IS A BIOFILM? 22
GOOD AND BAD BIOFILMS 23
WHAT IS A MODEL? 25
THE RESEARCH CONTEXT FOR BIOFILM MODELING 26
A BRIEF OVERVIEW OF BIOFILM MODELS 27
GOALS FOR BIOFILM MODELING 28
THE IWA TASK GROUP ON BIOFILM MODELING 29
OVERVIEW OF THIS REPORT 29
Guidance for model selection 29
Biofilm models considered by the Task Group 30
Benchmark problems 31
2.0 MODEL SELECTION 32
BIOFILM FEATURES RELEVANT TO MODELING 32
COMPARTMENTS 33
The biofilm 33
The bulk liquid 36
The mass-transfer boundary layer 37
The substratum 38
The gas phase 38
COMPONENTS 38
Dissolved components 38
Particulate components 41
PROCESSES AND MASS BALANCES 42
Transformation processes 43
Transport processes 46
Transfer processes 47
MODEL PARAMETERS 50
Significance of model-parameter definitions 50
Significance of model parameter units 51
Significance of environmental conditions 52
Plausibility of parameter values 53
Sensitivity of model parameters 53
System-specific parameters 54
GUIDANCE FOR MODEL SELECTION 54
Overview of the models 55
Modeling objectives and user capability 56
Time scale 58
Macro versus micro scales 59
Substrate removal 59
Biomass accumulation, production, and loss 60
Spatial profiles of dissolved components 62
Spatial distribution of particulate components 62
Physical structure of the biofilm 62
3.0 BIOFILM MODELS 63
MASS BALANCES IN BIOFILM MODELS 63
Microscopic (local or differential) mass balances 64
General differential mass balances 64
Particular forms of differential mass balances 65
Macroscopic (global or integral) mass balances 67
General integral mass balances 67
Particular forms of the integral mass balance 69
Relationships among the various models 70
ANALYTICAL MODELS (A) 73
Features 73
Definitions and equations 74
Mass balances for substrate in the bulk liquid 74
Mass balances for substrate in the biofilm 74
Mass balances for biomass 76
Mathematical treatment 76
One biological conversion process 76
Two or more biological conversion processes & biofilm architecture 77
Kinetics for multiple limiting substrates 77
Solving the problem with a simple spreadsheet 77
Applications 78
Numerical versus analytical solutions 78
Describing an existing reactor system 78
Designing a biofilm reactor 80
PSEUDO-ANALYTICAL MODELS (PA) 80
Features of the basic pseudo-analytical model 80
Adapting the pseudo-analytical model for multiple species 82
The multi-species models 82
Multi-species applications 86
Standard condition 86
High influent N:COD 86
Low influent N:COD 87
High detachment rate 87
Oxygen Flux 88
Interfacial Concentrations and Biofilm Deepness 88
Summary for multi-species PA models 89
NUMERICAL ONE-DIMENSIONAL DYNAMIC MODEL (N1) 89
Features 90
Definitions and equations 92
Mathematical treatment with AQUASIM 94
Applications 95
Substrate removal 95
Biofilm growth, microbial composition and detachment 96
Pseudo 2d modeling of plug flow 98
Pseudo 3d modeling 98
NUMERICAL ONE-DIMENSIONAL STEADY STATE MODEL (N1s) 100
Features 100
Definitions and equations 101
Software Implementation 101
MULTI-DIMENSIONAL NUMERICAL MODELS (N2 and N3) 102
General features 102
Model classifications 103
Definitions 103
Representation of dissolved components 103
Representation of particulate components 104
Summary of multidimensional models used 106
2d and 3d models with discrete biomass and solutes in continuum space (N2a, N2b, N3a, N3b, N3c) 107
Features 107
Definitions and equations 108
Biofilm system definition 108
Mass balances for dissolved components 110
Momentum and mass balances for the liquid flow 113
Mass balances for particulate components 114
Solution methods 116
The overall solution approach 116
Solution methods for particular parts of the model 117
Software implementation 118
2d models with discrete biomass and discrete solutes (the Cellular Automata models N2c, N2d, N2e, N2f) 119
Discretization of the physical domain 119
Definition of substrate and microbial particles 120
Discretization of Monod-type substrate-utilization kinetics 120
Stochastic representation of microbial growth, inactivation, and endogenous respiration 120
Simulation of microbial dynamics within the biofilm (N2f) 121
Simulation of advective flux (N2d, N2e) 121
Applications 122
Formation of biofilm structure and activity in relation with the environment 122
Biomass accumulation in biofilm 122
Substrate uptake and mass transport in biofilm systems 123
Biofilm structure 125
Model comparison with experimental data 127
Interactions in multispecies biofilms 128
Multispecies nitrifying biofilm 128
Multispecies methanogenic biofilm 129
Competition between internal storage compound producer and EPS producing bacteria 131
4.0 BENCHMARK PROBLEMS 133
INTRODUCTION 133
BENCHMARK 1: SINGLE-SPECIES, FLAT BIOFILM 134
Definition of the system to be modeled 134
Nomenclature 183
References 189