development of multiplexed microcontroller...
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DEVELOPMENT OF MULTIPLEXED MICROCONTROLLER BASED SYSTEM
FOR MICROBIOREACTOR
AHMAD YASER AL-HADDAD
A project report submitted in partial fulfillment of the
requirements for the award of the degree of
Master of Engineering (Electrical- Mechatronics & Automatic Control)
Faculty of Electrical Engineering
Universiti Teknologi Malaysia
JANUARY 2013
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I dedicate this to the revolts of Syria, to my parents, who have been supportive
throughout my life, to my grandparents, to my sisters, to my brothers, to all my
teachers who have inspired me a lot.
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ACKNOWLEDGEMENT
First and foremost, I would like to thank the almighty ALLAH (SWT) for
giving me the strength in doing and completing this project.
My sincere appreciation also goes to my supervisors Dr. Abdul Rashid Husain
and Dr. Muhd Nazrul Hisham for their continued guidance, support and
encouragement to ensure this work is a success. My earnest appreciation also goes to
all my colleagues for helping me in achieving this project.
I shall forever be grateful to my family for their belief in me and for their
unending support, financially; morally, spiritually and emotionally. Finally I would
like to express my sincere gratitude to my sister Hadia for her assistance and support.
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ABSTRACT
Bioreactor is a device that widely used in fermentation process. Bench scale
bioreactor and shake flask are the most used devices to optimize such process. Due to
their high running cost and the high amount of labour required, new and better
alternative way must be found to carry on the optimization process. In the most recent
years, scientists have been working on smaller bioreactor of volume less than 1
millilitre and became known as microbioreactor. This device and due to its small
volume size should bring more benefits and potential to optimization process in
fermentation. Since microbioreactor stills in development phase, researches till date
are trying to come with ideas and designs to be adopted later as acceptable industry
standard. In the literature, there have been many designs attempts to create a platform
to support one or more microbioreactors. Many of these attempts have achieved great
results with comparable performance to that of bench scale bioreactor. Most the
previous designs are made with the usage of data acquisition card from National
instrument. The trend toward NI DAQ is due to the simplicity in programming
environment, being user friendly and many other features. Biochemical engineers
could settle for alternative and cheaper way, if they are willing to give up some of the
convenient and features provided by NI DAQ. In this project, this alternative method
is being investigated, tested and used. The goal is to use microcontroller as DAQ to
provide controlling, data logging and monitoring of temperature and speed control for
microbioreactor. This setup will be totally microcontroller based and using dedicated
electronic circuit to achieve the objectives. The results for temperature and agitation
control that have been obtained are satisfactory and now this setup is ready to be used
on actual microbioreactor.
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ABSTRAK
Bioreaktor adalah alat yang digunakan secara meluas dalam proses penapaian.
Bioreaktor skala jenis duduk dan kelalang digunakan secara meluas bagi tujuan
pengoptimuman. Disebabkan kos pengoperasian dan jumlah tenaga kerja yang ramai
diperlukan, kaedah alternative yang baru dan lebih baik diperlukan. Sejak beberapa
tahun kebelakangan ini, saintis telah meneruskan kajian mereka menggunakan
isipadu kurang dari 1 milimeter dan dikenali sebagai microbioreaktor. Peranti ini dan
disebabkan oleh julat kerja yang kecil, ia sepatutnya memberikan kelebihan dan
keupayaan tinggi untuk proses pengoptimuman dalam proses penapaian.
Memandangkan proses mikrobioreaktor masih dalam fasa pembangunan, para
penyelidik masih mengkaji idea-idea dan rekabentuk-rekabentuk yang baru untuk
diadoptasi kemudiannya agar selari dengan standard industri. Dalam kajian yang
dilakukan, terdapat banyak kajian rekabentuk dilakukan bagi tujuan untuk membina
satu platform untuk menyokong satu atau lebih mikrobioreaktor. Kebanyakkan hasil
kajian ini telah mencapai keputusan yang memberangsangkan jika dibandingkan
dengan bioreactor skala jenis duduk. Kebanyakkan rekabentuk-rekabentuk asal dibina
dengan menggunakan kad perolehan data (DAQ) dari National Semiconductor (NI).
Trend masa kini ke arah penggunaan kad DAQ adalah disebabkan oleh mudahnya
pengaturcaraan, mudah diguna, dan ciri-ciri yang lain-lain. Jurutera biokimia
memiliki alternatif dan kaedah yang murah, sekiranya mereka sanggup
mengorbankan kemudahan dan ciri-ciri yang disediakan oleh NI DAQ. Dalam projek
ini, kaedah alternatif ini dikaji, diuji, dan digunakan. Matlamatnya adalah untuk
menggunakan mikropengawal sebagai DAQ untuk membekalkan kawalan, perekodan
data, dan pemantauan suhu dan kawalan kelajuan untuk mikrobioreaktor. Persediaan
ini adalah berdasarkan mikropengawal sepenuhnya dan menggunakan litar elektronik
untuk mencapai objektifnya. Keputusan bagi kawalan suhu dan pergolakan yang
diperolehi adalah memuaskan dan persediakan ini adalah siap dan boleh digunapakai.
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TABLE OF CONTENTS
CHAPTER TITLE PAGE
DECLARATION ii
DEDICATION iii
ACKNOWLEDGMENT iv
ABSTRACT v
ABSTRAK vi
TABLE OF CONTENTS vii
LIST OF TABLES x
LIST OF FIGURES xi
LIST OF ABBREVIATIONS xiv
LIST OF SYMBOLS xv
1 INTRODUCTION
1.1 Introduction 1
1.2 Problem Statement 3
1.3 Project Objectives 5
1.4 Scope of the Project 5
1.5 Summary of the Chapter 6
2 LITERATURE REVIEW
2.1 Devices used in microbial cultivation 7
2.1.1 Bench scale Bioreactor 7
2.1.2 Shake flask culture 9
2.1.3 Microbioreactor 12
2.1.4 Comparison 14
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2.2 Considerations in microbioreactor design 17
2.2.1 Fabrication materials 17
2.2.2 Mixing 18
2.2.3 Temperature 19
2.2.4 pH 21
2.2.5 Evaporation 22
2.3 Previous works on microbioreactor 23
2.3.1 Development of a single-use microbioreactor by
D. Schäpper el. al (2010) 23
2.3.2 Development of a multiplexed microbioreactor
system by Szita N el. al (2005) 28
2.4 Summary of the Chapter 33
3 DESIGN AND DEVELOPMENT
3.1 Introduction 34
3.2 Hardware development 35
3.2.1 Temperature Measurement 35
3.2.1.1 The LM35 35
3.2.1.2 The PT100 37
3.2.2 Speed Measurement 46
3.2.3 Actuators 52
3.2.3.1 Motor 52
3.2.3.2 Heater 53
3.2.4 DAQ 55
3.3 Software Development 56
3.3.1 Arduino Software 56
3.3.2 GUI 57
3.3.2.1 Setting up the interface 58
3.3.2.2 Extra Considerations 60
3.3.2.3 Simple Example 64
3.3.3 PI Controller 65
3.3.4 PCB design 66
3.4 Summary of the Chapter 68
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4 RESULTS AND DISCUSSION
4.1 Introduction 69
4.2 First phase 70
4.2.1 Hardware 70
4.2.2 Temperature control 71
4.2.3 Speed control 73
4.3 Second phase 75
4.3.1 Hardware 75
4.3.2 Temperature control 77
4.3.3 Speed control 78
4.4 LabView GUI 82
4.5 Summary of the Chapter 87
5 CONCLUSION AND FUTURE PLAN
5.1 Conclusion 88
5.2 Future plan 89
REFERENCES 90
Appendix A 93
x
LIST OF TABLES
TABLE NO. TITLE PAGE
2.1 Comparison 15
3.1 PT100 Chart of values 38
3.2 PI parameters 65
4.1 Testing PI parameters 79
xi
LIST OF FIGURES
FIGURE NO TITLE PAGE
1.1 New Brunswick bioreactor 3
1.2 Prototype microbioreactor with 100 μl working volume 3
2.1 Bench scale bioreactor 9
2.2 Shake flask 10
2.3 Shake flask shaker 10
2.4 Shake flask culture 11
2.5 Controlled environment chamber 12
2.6 Microbioreactor platform at UTM 13
2.7 The microbioreactor mechanical design 13
2.8 Mixing scheme through the mounting of stirrer bar on a revolting
central shaft 19
2.9 The PT100 Temperature sensor 20
2.10 Photo of the complete microbioreactor seen from the bottom 24
2.11 Sketch of both main reactor layers as seen from below 24
2.12 Mixing in the microbioreactor at 500rpm 26
2.13 Temperature response at different set points 27
2.14 Displaying set points and the measured values of pH 28
2.15 The reactor design 29
2.16 Photograph of the multiplexed microbioreactor system 29
2.17a Parallel fermentations of E. coli 31
2.17b Parallel fermentations of E. coli 31
2.18 Comparison with bench scale bioreactor 32
3.1 LM35 terminal connections 35
3.2 Circuit schematic of the LM35 followed by the amplifier 36
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3.3 PT100 37
3.4 Transmitter 39
3.5 Wheatstone bridge 39
3.6 Difference amplifier 41
3.7 Non-inverting operational amplifier 42
3.8 Low-Pass filter 43
3.9 Conditioning circuit for the PT00 44
3.10 Simulation of PT100 circuit in Protus 45
3.11 Hall-effect sensor 46
3.12 Terminal connections 46
3.13 ATMEGA328P Pins mapping 47
3.14 Complete Circuitry for speed measurement 48
3.15 Flow chart for speed measurement 50
3.16 Stages of development 53
3.17 Control circuit 54
3.18 Arduino mega 2560 55
3.19 Arduino IDE 56
3.20 Firmware for Arduino 59
3.21 Arduino Functions in LabView 59
3.22 Init VI 61
3.23 Init Front Panel 61
3.24 Init Block Diagram 62
3.25 Example 64
3.26 First Design 66
3.27a Second design main board 67
3.27b Expansion to the second design 68
4.1 Hardware of the first stage 70
4.2 Temperature control response 71
4.3 Testing condition where the heater placed underneath 71
4.4 Temperature control response 72
4.5 Testing condition where the heaters placed on the side 73
4.6 Speed control response 74
4.7 Main board 75
4.8 Optional expansion 76
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4.9 Temperature control response 77
4.10 Testing condition where the heater placed underneath 77
4.11 Speed control response 78
4.12 Testing condition 78
4.13 Speed control response for set one 79
4.14 Speed control response for set two 80
4.15 Mixing Quality test at 300rpm 81
4.16 Block diagram for temperature control 82
4.17 Front Panel for temperature control 83
4.18 Block diagram for speed control 84
4.19 Front Panel for speed control 85
4.20 Block diagram of the combined GUI 86
4.21 Front panel of the combined GUI 86
4.22 Testing conditions 87
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LIST OF ABBREVIATIONS
DAQ - Data Acquisition Card
DO - Dissolved Oxygen
OD - Optical Density
NI - National Instruments
PID - proportional-integral-derivative
GUI - Graphical User Interface
rpm - revolution per minute
PMMA - polymethylmethacrylate
PDMS - polydimethylsiloxane
RTD - resistance temperature detectors
S/V - surface area to working volume ratio
ISFET - ion-sensitive and field-effect transistor
PWM - Pulse-width modulation
ADC - Analog Digital converter
PCB - printed circuit board
IC - integrated circuit
xv
LIST OF SYMBOLS
mL - millilitre
µL - microlitre
°C - celsius
V - voltage/volts
mV - millivolt
µV - microvolt
A - ampere
mA - milliampere
Ω - ohms
µF - microfarad
Hz - hertz
CHAPTER 1
INTRODUCTION
1.1 Introduction to Bioreactors
A bioreactor as shown in Figure 1.1 is simply a vessel usually cylindrical in
shape that used to carry out fermentation experiments. A bioreactor normally integrated
with tight on line measurements and process control capabilities. These features are
critically important such that fermentation experiments in bioreactor can be performed
under controlled conditions as stated by Bailey el. al (1986). For a standard bioreactor
system, it is norm to have a feedback control loop over physical parameters such as pH,
temperature, agitation, dissolved oxygen concentration and water level.
Fermentation is a process that is widely performed in many sectors such as
biotechnology, food processing, health care, agriculture and environmental management
as stated by Szita N el. al (2005). They are many devices that are in use to optimize such
processes for example bench scale bioreactors or shake flasks. These devices range in
terms of the volume size and capabilities. Bench scale biroeactors normally operated
between working volume of 1 liter and 10 liters where else shake flasks utilized much
lower volume i.e. less than 2 liters. In relative to bench scale bioreactors, shake flasks
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usually do not integrated with sensors and actuators. Mixing is based on shaking
principle and operation is generally limited to batch mode operation only.
In the most recent years, scientists have been attempting to create smaller
bioreactor design that comprises the advantages of both types of experimental tools
(shake flasks and bioreactor) in one small unit named as microbioreactor shown in
Figure 1.2. The drastic reduction in volume’s size to less than 1mL will reduce the cost
dramatically and open the possibilities of running multi microbioreactors simultaneously
(multiplexing) hence increasing the throughput. As stated by D. Schäpper el. al (2009)
microbioreactor would not only reduce the fabrication cost per bioreactor compared to
bench scale, but will also add more advantages such as reduced running cost through the
reduction of substrate required, reduced power requirements, reduced space
requirements especially in parallel operations and finally reducing the effort and labour
required to prepare the bioreactor through the usage of disposable microbioreactors.
Even though dramatic cost reduction can be obtained using microbioreactors as
previously mentioned, another part of the microbioreactor platform circuit design still
suffering from high cost and still need to be considered. The circuit design includes all
the necessary electrical components that are needed to interface and control the
microbioreactor such as Data Acquisition Card (DAQ), temperature sensor transmitter
and any possible actuators. Most of the work previously performed on microbioreactor
such that by Szita N el. al (2005), M.N.H.Z Alam el. al (2010), D. Schäpper el. al
(2010) and Lee HL el. al (2006) are all made using high end DAQ from National
instrument. The trend toward NI DAQ is due to many features provided and the
convenient when it comes to programming, but that comes with a price. Since many of
the great capabilities and features of NI DAQ are being paid for and not being used,
alternative and cheaper way could be used as replacement if giving up some of the
convenience provided by NI DAQ is not an issue.
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The aim of this project is to present cheaper and effective way with comparable
results to replace the expensive and bulky circuitry that is usually used on
microbioreactor design. Many of the devices around us are being incorporated with low-
cost microcontroller into their circuitry design to perform many tasks effectively. Part of
this project is to introduce the microcontroller into micobioreactor circuit design to
replace the DAQ without dramatic lose in the performance. The microcontroller based
DAQ should handle data logging, controlling and monitoring.
1.2 Problem statement
On line measurements and process automation is a necessity for microbioreactor
operation. In microbioreactor operation, often sensors and actuators from the
microbioreactor system are connected to a data acquisition device for in- and output of
signal during a standard process control routine. The monitoring and process control
tasks in microbioreactor are normally complex as it involves more than one feedback
Figure 1.2 Prototype microbioreactor with
100 μl working volume developed in the
BIOS/Lab-on-a-Chip group
Figure 1.1 New Brunswick bioreactor
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control looping. As reported by Szita N el. al (2005), data such as temperature, dissolved
oxygen, agitation, pH and optical density are typically the measured and controlled
variables in microbioreactor operation. Due to limited knowledge on computer
programming, microbioreactor operators (mostly Biochemical Engineers) would go for a
readily available data acquisition device to execute the above mentioned tasks. One of
the most widely utilized data acquisition devices is the DAQ produced from National
Instruments (NI). As example, NI USB 6343 consisting of 16 number of analog input, 4
number of analog output, and 48 number of digital input/output with 500 kS/s sampling
rate. Despite these distinctive features which obviously can be beneficial for process
automation of microbioreactor operation, there are relatively expensive compared to a
standard microcontroller platform.
Microcontroller based DAQ could be of great replacement to typical DAQ at
much lower cost, provided that some of the convenient and features must be given up.
For example, most of microbioreactor operations are relatively slow and take long time
to respond, thus paying extra money for DAQ to have a very high sampling time isn’t
necessary. Microbioreactor would work perfectly with low sampling time without the
risk of any loses in terms of the performance and the controlling ability. Any typical
microcontroller consists of many digital and analog pins. For example, Mega 2567
consists of 16 analog pins, and 15 PWM pins that can be used as analog outputs and 54
pins of digital input/output. When paired with LabView, Mega 2567 can achieve
sampling rate up to 125 S/s.
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1.3 Project objectives
The main objective of this project is to design a low-cost microcontroller based
platform as data acquisition device for microbioreactor operations.
1.4 Scope of the project
The scope of this project is divided into three main categories. There are as follows:-
a) Microbioreactor design
(i) A simple polymer based microbioreactor design that is cylindrical in
shape will be used.
(ii) Working volume of the microbioreactor is 600microliter.
(iii) The microbioreactor should be integrated with suitable temperature and
agitation (via magnetic stirrer bar) features.
(iv) PT100 temperature sensor will be used for temperature measurement of
the microbioreactor content.
(v) A hall-effect magnetic sensor will be used to measure the rotational speed
of a DC motor used for the agitation control.
(vi) The performance of the temperature and the agitation control will be
evaluated based on the controller accuracy, response time, and settling
time through the set-point tracking experiments.
(vii) A Proportional-Integral-Derivative (PID) control algorithm will be
implemented for the temperature and the agitation control.
(viii) Data on the performance of the temperature and the agitation control of
the microbioreactor will be collected and discussed.
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b) Microcontroller platform
i) Arduino based microcontroller will be used as data acquisition card and it
should handle the controlling, monitoring and data logging.
ii) Another dedicated microcontroller will be used mainly to handle the
speed measurement and to convert rpm measurements into voltage levels
to be read by the Arduino microcontroller
c) Programming for control routines and data logging
i) Programs for control routines and data logging of the microbioreactor
operation will be written by using the GUI LabVIEWTM
(National
Instruments, US) software.
ii) The programs will be implemented by interfacing the microcontroller
platform with the microbioreactor system.
1.5 Summary of the chapter
In this chapter, brief introduction to bioreactor and microbioreactor been
presented. Next, the problem that still exists with the previously proposed designs in the
literature been highlighted. Finally, the steps and measurements taken to overcome them
and they are all presented as scope of this project.
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