Modeling Framework for Control of Bacterial Nitrification in Aquaponics-Inspired Hydroponic System

153 Pages·2014·12.79 MB·English

by  Clayton R. Thurmer

MODELING FRAMEWORK FOR CONTROL OF BACTERIAL
NITRIFICATION IN AQUAPONICS-INSPIRED
HYDROPONIC SYSTEM
by
Clayton R. Thurmer
(cid:13)c Copyright by Clayton R. Thurmer, 2014
All Rights Reserved
A thesis submitted to the Faculty and the Board of Trustees of the Colorado School of
Mines in partial fulfillment of the requirements for the degree of Master of Science (Electrical
Engineering).
Golden, Colorado
Date
Signed:
Clayton R. Thurmer
Signed:
Dr. Kevin L. Moore
Thesis Advisor
Golden, Colorado
Date
Signed:
Dr. Randy Haupt
Professor and Head
Department of Electrical Engineering and Computer Science
ii
ABSTRACT
Aquaponics is an agriculture technique that combines recirculating aquaculture systems
(fish farming) with hydroponics (growing plants without soil) in an integrated system. The
elegant principle behind aquaponics is that fish waste is used to fertilize plants while plants
are used to filter toxins from the fish water. Both fish and plant crops may be harvested for
food. This concept relies on nitrifying bacteria to convert Nitrogen from toxic to beneficial
forms. The apparent trade-offs between energy and water used in aquaponic systems ver-
sus other horticulture and aquaculture techniques is not well understood and has motivated
the development in this thesis of a system-level model of aquaponic systems with emphasis
on defining input streams used, such as: energy, water, and chemical additives; and output
streams produced, such as: fish and plant mass. Input streams were identified as the control
effort needed to maintain acceptable conditions. An analysis framework was devised using
the costs (or values) of input and output streams identified in the model. A long-term goal
is to use this framework to increase system efficiency. A lab was designed to provide prelim-
inary experimentation. Observation of lab start-up has informed experimental procedures
including the chemical simulation of aquatic life. The affects of water temperature set-point
changes over steady state operation were investigated experimentally by growing Mesclun
cultures from seed to harvest at 80◦ F and 70◦ F. Results show that the 70◦ F set-point
resulted in a more efficient system than the 80◦ F system due to decreased energy and water
use even though plant biomass was also decreased. Nitrification rates were increased at 70◦
F versus 80◦ F as measured by the increased use of chemical additives and is attributed to
an increase in measured dissolved Oxygen at 70◦ F. These results provide useful information
for future aquaponic system efficiency studies.
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TABLE OF CONTENTS
ABSTRACT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iii
LIST OF FIGURES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
LIST OF TABLES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xii
LIST OF SYMBOLS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
LIST OF ABBREVIATIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xviii
ACKNOWLEDGMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xx
CHAPTER 1 INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.2 Research Objectives and Scope . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2.1 Initial Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2.2 Challenges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.2.3 Modified Objectives . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 Background and Literature Review . . . . . . . . . . . . . . . . . . . . . . 4
1.3.1 Aquaponics Case Studies . . . . . . . . . . . . . . . . . . . . . . 4
1.3.1.1 Red Rocks Community College . . . . . . . . . . . . . . 4
1.3.1.2 GrowHaus . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3.2 Modeling for Control of Aquaponics Systems . . . . . . . . . . . 5
1.3.3 Analysis Framework . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.4 Summary of Thesis Results and Contributions . . . . . . . . . . . . . . . . 6
1.4.1 Nitrifying Hydroponics Model . . . . . . . . . . . . . . . . . . . . 6
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1.4.2 Analysis Framework . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.4.3 Experimental Results . . . . . . . . . . . . . . . . . . . . . . . 10
1.5 Thesis Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
CHAPTER 2 AQUAPONIC SYSTEMS MODELING . . . . . . . . . . . . . . . . . . 12
2.1 Biological . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1.1 Plants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1.1.1 Nutrients . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.1.1.2 Photosynthetically Active Radiation . . . . . . . . . . 14
2.1.1.3 Photosynthesis and Cellular Respiration . . . . . . . . 14
2.1.1.4 Nitrogen Assimilation . . . . . . . . . . . . . . . . . . 15
2.1.1.5 Environmental Parameters . . . . . . . . . . . . . . . 16
2.1.1.6 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.1.2 Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.2 Chemical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.2.1 pH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.2.2 Simulated Aquatic Life . . . . . . . . . . . . . . . . . . . . . . 21
2.3 Thermal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.4 Fluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
2.4.1 Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.4.2 Water Temperature . . . . . . . . . . . . . . . . . . . . . . . . 25
2.4.3 Aeration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.5 Control Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.6 Abstract Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
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CHAPTER 3 LAB DESIGN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.1 Physical Plant . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
3.2 Species Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
3.3 Actuators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.3.1 Thermal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.3.1.1 Light . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.3.1.2 Fan . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.3.2 Fluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
3.3.2.1 Pump . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
3.3.2.2 Water Heater . . . . . . . . . . . . . . . . . . . . . . . 39
3.3.2.3 Aerators . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.4 Sensors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.4.1 Exogenous Inputs . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.4.2 Intermediate Measurements . . . . . . . . . . . . . . . . . . . . 44
3.4.3 Outputs and Control Effort . . . . . . . . . . . . . . . . . . . . 45
3.5 Data Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.6 Hardware Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.7 Integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.8 Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
3.8.1 Physical Plant and Plumbing . . . . . . . . . . . . . . . . . . . 59
3.8.2 Actuators and Control . . . . . . . . . . . . . . . . . . . . . . . 61
3.8.3 Sensors and Integration . . . . . . . . . . . . . . . . . . . . . . 61
3.8.4 Additives and Seeds . . . . . . . . . . . . . . . . . . . . . . . . 62
vi
3.9 Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
3.10 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
CHAPTER 4 START-UP AND NOMINAL OPERATION . . . . . . . . . . . . . . . . 66
4.1 Failed Cycling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
4.2 Water Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
4.3 RRCC Water Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
4.4 Preliminary Plant Culture . . . . . . . . . . . . . . . . . . . . . . . . . . 68
4.5 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
CHAPTER 5 MODEL VERIFICATION AND CONTROL . . . . . . . . . . . . . . . 77
5.1 Control Architecture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
5.2 Biochemical System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
5.2.1 pH Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
5.2.2 Water Level Control . . . . . . . . . . . . . . . . . . . . . . . . 80
5.2.3 Aquatic Life Simulation . . . . . . . . . . . . . . . . . . . . . . 81
5.2.4 Combined Biochemical Model . . . . . . . . . . . . . . . . . . . 82
5.3 Thermal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
5.3.1 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
5.3.2 Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
5.3.3 Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.4 Fluidics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.4.1 Plumbing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.4.2 Water Temperature . . . . . . . . . . . . . . . . . . . . . . . . 92
5.4.3 Aeration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
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5.4.3.1 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
5.4.3.2 Control . . . . . . . . . . . . . . . . . . . . . . . . . . 94
5.4.4 Combined Fluidics Model . . . . . . . . . . . . . . . . . . . . . 97
5.4.5 Design Verification . . . . . . . . . . . . . . . . . . . . . . . . . 97
5.5 Nitrifying Hydroponics Model . . . . . . . . . . . . . . . . . . . . . . . 100
5.6 Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
CHAPTER 6 EXPERIMENT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.2 Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
6.3 Hypothesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
6.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
6.4.1 80 Degree F Culture . . . . . . . . . . . . . . . . . . . . . . . 110
6.4.2 70 Degree F Culture . . . . . . . . . . . . . . . . . . . . . . . 111
6.5 Summary and Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 117
CHAPTER 7 CONCLUSIONS AND FUTURE WORK . . . . . . . . . . . . . . . . 125
7.1 Contributions of the Thesis Work . . . . . . . . . . . . . . . . . . . . . 125
7.2 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
7.3 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
7.4 Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
REFERENCES CITED . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
APPENDIX - SUPPLEMENTAL FILES . . . . . . . . . . . . . . . . . . . . . . . . . 132
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LIST OF FIGURES
Figure 1.1 Layout of the RRCC aquaponics system. . . . . . . . . . . . . . . . . . . . 5
Figure 1.2 Symbolic convention for closed-loop control. . . . . . . . . . . . . . . . . . 7
Figure 1.3 Top-level model of controlled nitrifying hydroponics system. . . . . . . . . . 8
Figure 1.4 Store bought micro-greens. . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Figure 2.1 Block diagram representation of photosynthesis and cellular respiration . 15
Figure 2.2 Block diagram representation of ionic balance in nitrogen assimilation. . . 16
Figure 2.3 Block diagram representation of aquaponic plant life as a MIMO process. . 17
Figure 2.4 Block diagram representation of bacterial nitrification as a MIMO
process. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Figure 2.5 Illustration of the nitrogen cycle process. . . . . . . . . . . . . . . . . . . 24
Figure 2.6 Block diagram representation of the abstract model for a controlled
nitrifying hydroponic system. . . . . . . . . . . . . . . . . . . . . . . . . . 29
Figure 2.7 Simplified block diagram representation of the abstract model for a
controlled nitrifying hydroponic system. . . . . . . . . . . . . . . . . . . . 30
Figure 3.1 Photo of the lab system following the Japan Aquaponics design . . . . . . 33
Figure 3.2 Photo of the complete lab system with select components noted. . . . . . 33
Figure 3.3 Schematic diagram of the lab implementation. . . . . . . . . . . . . . . . 34
Figure 3.4 Impact of the mylar enclosure cnfiguration on measured light and air
temperature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Figure 3.5 Flow rate versus outlet height for AAPW160. . . . . . . . . . . . . . . . . 40
Figure 3.6 Air stone installation in the media bed. . . . . . . . . . . . . . . . . . . . 42
Figure 3.7 Photo of the Arduino data acquisition enclosure. . . . . . . . . . . . . . . 49
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