Long term temperature stability of thermal cycler developed using low profile microprocessor cooler

International Journal of Electrical and Computer Engineering (IJECE)
Vol. 13, No. 1, February 2023, pp. 278~287
ISSN: 2088-8708, DOI: 10.11591/ijece.v13i1.pp278-287  278
Journal homepage: http://ijece.iaescore.com
Long term temperature stability of thermal cycler developed
using low profile microprocessor cooler
Setyawan Purnomo Sakti1,2
, Adin Okta Triqadafi1
, Aldi Dwi Putra1
, Triswantoro Putro1,2
,
Dewi Anggraeni1,2
1
Department of Physics, Brawijaya University, Malang, Indonesia
2
Sensor Technology Laboratory, Brawijaya University, Malang, Indonesia
Article Info ABSTRACT
Article history:
Received Jan 22, 2022
Revised Jul 17, 2022
Accepted Aug 13, 2022
Developing a low-cost thermal cycler for a polymerase chain reaction (PCR)
is becoming interested in the pandemic era caused by viruses. PCR is the
standard gold for the diagnostic. However, in a low-income country, the
availability of the device is limited. In this work, the development of a
thermal cycler uses electronic modules available in the market. The central
part is thermoelectric for heating and cooling, an embedded system to
control, and a low-profile cooling fan. The system temperature control used
a combination of feedforward, bang-bang, and proportional-integral-
derivative (PID) control. The control parameter of the PID was successfully
obtained by using Chien servo tuning. The feedforward and bang-bang
control are used to optimize the cooling cycle and minimize the rise time.
The system shows a well-suited temperature accuracy at the denaturation,
annealing, and extension temperature with a temperature deviation of less
than 0.5 °C. System performance is maintained even though the system has
been running non-stop for 24 hours. The low-profile cooling fan, which is
usually used for CPU cooling, shows good results in maintaining
temperature stability.
Keywords:
Bang-bang
Proportional integral derivative
Temperature stability
Thermal cycler
Thermoelectric
This is an open access article under the CC BY-SA license.
Corresponding Author:
Setyawan Purnomo Sakti
Department of Physics, Brawijaya University
Jl. Veteran, Malang 65145, Indonesia
Email: sakti@ub.ac.id
1. INTRODUCTION
In the Covid-19 pandemic, many low-income countries lack the polymerase chain reaction (PCR)
machine or thermal cycler to detect the virus. There is a wide range of PCR machines or thermal cyclers
available in the market [1]–[3], portable PCR with battery-operated [4]; even a mini thermal cycler is also
available [5], [6]. Thermal cycler becomes an attractive tool during the Covid-19 pandemic and in the study
of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The mini thermal cycler, which is considered
low cost, limits the cycling speed due to using hardware with a passive cooling mechanism for the cooling
process. Although some work is reported on the development of the thermal cycler [7]–[10], the simplicity of the
design using a limited budget may open a wider possibility for the development and usage of the thermal cycler.
In the market, thermal cyclers are widely available. However, it is still interesting to explore and
develop a simple, low-cost system that can be developed with a limited budget but with good performance.
The heater, cooler, and control system are essential aspects of optimizing for a rapid temperature gradient and
good temperature stability. From the conceptual design, the temperature of the DNA sample to be amplified
in the PCR tube needs to be put at a specific temperature to enable DNA denaturation, primer annealing, and
primer extension condition [11]. At the first cycle, the temperature is raised from the initial state to

Int J Elec & Comp Eng ISSN: 2088-8708 
Long term temperature stability of thermal cycler developed using low … (Setyawan Purnomo Sakti)
279
denaturation temperature, followed by a temperature change at annealing and extension. The temperature is
maintained for a certain period (dwelling time) in each step. The denaturation, annealing, and extension cycle
is repeated up to 40 cycles. After the extension, the temperature is pulled down to room temperature or low
temperature (close to 0 C) for further process. The denaturation temperature is around 92 °C, annealing at
around 55 °C, and primer extension at 72 °C.
Temperature control in the heating and cooling process at this time can be done in several ways.
Thermoelectric is the most widely used method because it conveniently controls the heating and cooling
process temperature using a single system [12]–[15]. The direction of the current flow to the thermoelectric
changes the thermoelectric element as a heater or cooler. Those make the electrical and mechanical design easier.
In general, the heating process does not cause many problems. However, the heat removal system
requires attention to achieve a faster cooling process. A cooling system such as an aluminum block and a
cooling fan with fins is commonly used. The cooling system selection is based on the given constraints. The
selection of the system cooling system with an aluminum fin and fan has been used widely for a microprocessor
cooler in a personal computer. The reliability and durability of such a cooler are proven [16], [17].
Operating a thermal cylinder during heating and cooling requires energy channeled to the
thermoelectric and other electronic systems. Heat removal to the surrounding area is required to avoid the
increasing temperature of the system. If the heat dissipation system to the environment does not work well,
then continuous use for a long time will cause problems in the performance of the thermal cycler system.
The proportional integral derivative controller (PID) has been widely used because of its simplicity
and effectiveness [18]. The PID controller is commonly used to control temperature, flow, level, pressure,
and speed [15], [19]–[24]. Furthermore, the determination of the three parameters 𝐾𝑝, 𝐾𝑖, and 𝐾𝑑 has been
well developed, hence, it is easy to be implemented and tuned to obtain the best parameter related to the
controlled plant. Some common methods are Ziegler–Nichols, Cohen-Conn, Relay method, and Chien-Hrones-
Reswick method [25]–[28], PID and bang-bang control together have been used and show a better response
compared to the PID only [29]–[31]. Feedforward and PID also show a better result than PID only [32].
This paper combines a control method using PID with feedforward and bang-bang control to
increase the system's response speed. The control system is implemented in the Raspberry Pi. The use of the
low-profile central processing units (CPU) cooler makes the system compact and light. The Chien servo
method is the tuning method to determine the PID parameters used. This method was chosen as the target
temperature conditions in the thermal cycler system change according to the cycle. With the design of the
casing and the placement of the sub-components of the thermal cycler, it is expected that heat dissipation will
not affect the performance of the thermal cycler system. The developed system was tested to work 24 hours to
see the operating performance.
2. METHOD
The thermal cycler system and its control system can be developed from scratch. It requires a
detailed circuit design and time for the electronic design and fabrication process. We develop the system by
utilizing the available electronic system modules in this work. So, the development concept is a modular
concept from available modules in the market. There is no need to design a low-level electronic circuit. The
functional block of the system is realized with the available electronic module. For the cooling system, a low-
profile cooling fan (cooler), commonly used for cooling a CPU, is used for compactness and durability.
Using available electronic modules in the market, we reduce the design step on the electronic circuit
and lower production time and the entry barrier for developing the system. The selection also minimizes the
skill for fine soldering or the use of any soldering station. The user with experience in microelectronics and
control may improve the system's performance by using a more complex control algorithm and minimizing
the electronic system by changing the electronic board into a single board containing the microcontroller,
H-bridge, and metal oxide semiconductor field effect transistor (MOSFET) circuit.
The thermal cycler consists of a heating and cooling system implemented using a thermoelectric and
electronic control system to perform the temperature cycle. The heating-cooling system consists of an
aluminum block for placing the PCR tube, thermoelectric, and cooler. The cooler consists of a cooper block,
heat pipe, fan, and aluminum fin. The heating-cooling system configuration is presented in Figure 1. Figure 1(a)
shows the photograph of the heating cooling system and the figurative block diagram in Figure 1(b). The PCR
tube (0.1 mL) is placed on the aluminum block. Under the aluminum block is thermoelectric and placed on
top of the copper base of the cooler.
We developed a mini compact thermal cycler using an available electronic module that could be
quickly developed in the laboratory without any complex electronic circuit design detail. We developed the
system using the widely available electronic module to perform the required function. The system consists of
an embedded system (Raspberry Pi) as the core of the control system, switching power supply (12 V, 10 A),
buck converter steps down module for 5 V supply, H-bridge to control the thermoelectric cooling and heating

 ISSN: 2088-8708
Int J Elec & Comp Eng, Vol. 13, No. 1, February 2023: 278-287
280
direction, N-type MOSFET board for fan controller, thermoelectric, negative temperature coefficient (NTC)
sensor, low profile cooling fan (cooler), analog digital converter (ADC) module, and voltage level shifter.
The system's body was developed using acrylonitrile butadiene styrene (ABS) material made using a 3D
printer, 8 mm acrylic parts cut using laser cutting, and the thermal block was made from aluminum 6061. The
3D design of the system is presented in Figure 2. The block diagram of the system is presented in Figure 3.
Where:
(1) Aluminum block
(2) Thermoelectric
(3) Cooler cooper based
(4) Heat-pipe
(5) Fan
(6) Aluminum fin of the cooler
(a) (b)
Figure 1. Heating-cooling system configuration (a) photo and (b) the block diagram
Where:
(1) Aluminum block for tube,
(2) The low-profile CPU cooler
(3) Raspberry Pi
(4) H-bridge
(5) Power supply
Figure 2. 3D design of the thermal cycler system
Figure 3. System block diagram
Changes in the target temperature and changes from the initial conditions to the target temperature
in the temperature change cycle in the thermal cycler require attention in the design of the control system.
Rapid temperature changes, small overshot, and demands for stability at high target temperatures require
implementing a good control system. For this purpose, the control system design is implemented using a PID
system combined with on-off control bang-bang (BB) and feedforward, as shown in Figure . The feedforward

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is used to minimize disturbance. The bang-bang control is intended to speed up the cooling and heating at the
beginning of the target temperature change. It is a priory knowledge that the target temperature changes
abruptly. With the ease of implementation in the device, each control system has a role in optimizing changes-
temperature and temperature stability at the desired state. The PID control parameter values, namely Kp, Ki, and
Kd, are determined according to the specified temperature range using the tuning method.
Figure 4. Control system block diagram
With the control parameters obtained from the tuning process, the temperature control process
follows the flow chart in Figure 5. The target temperature (TTarget) is set as required in each part of the
temperature cycle. The aluminum block temperature (TAl) is compared to TTarget. If the difference exceeds the
threshold, heating and cooling are carried out with bang-bang control through a 100% PWM duty cycle. If
the temperature difference is smaller than the threshold, the control uses PID with the appropriate parameters.
The PID control works until the end of the dwelling time in each cycle step. This process is executed for each
part of the target temperature cycle.
Figure 5. Control system flowchart

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3. RESULT AND DISCUSSION
In this study, thermoelectric temperature control is carried out through a pulse-width modulation
(PWM) pulse duty cycle to flow current to the thermoelectric through the H-bridge. PWM working frequency
is 25 KHz. On average, the longer the duty cycle, the greater the current flowing into the thermoelectric for
heating or cooling. At 100% duty cycle, thermoelectric works with maximum power.
In the control design, as shown in Figure , the feedforward control works at the beginning of the
process and during the cooling process, namely, to control the thermal temperature of the aluminum block
from room temperature to the denaturation temperature (round 94 °C). The use of feedforward is intended to
reach the target temperature quickly. After the system is in the temperature cycle, the bang-bang control (BB)
and PID work in the denaturation-annealing-extension control system. These methods are effective methods
primarily to design a mono variable control. However, during the tuning process for the cooling stage from
denaturation to annealing temperature, the PID control showed an error of more than 0.5 °C. By introducing
the BB and feedforward, the response faster reaches the target temperature and has a less steady-state error.
The feedforward control value is determined by making a relationship between the duty cycle and
the temperature achieved. Based on the test results, the magnitude of the Tdisturbance value of the system is
34.207. The duty cycle can be calculated using (1).
% 𝑑𝑢𝑡𝑦 𝑐𝑦𝑐𝑙𝑒 =
𝑇𝑠𝑡𝑒𝑎𝑑𝑦−𝑇𝑑𝑖𝑠𝑡𝑢𝑟𝑏𝑎𝑛𝑐𝑒
1.7254
(1)
The BB control works at the beginning when the target temperature changes until the temperature is
less than the threshold. The thermoelectric is controlled with a 100% duty cycle to heat or cool the aluminum
block when the BB is working. Compared to a pure PID control which is not working at full 100% duty
cycle. Heating occurs when the temperature changes from annealing to extension and extension to
denaturation. The cooling process is carried out when changing from denaturation to annealing temperature.
When the thermal block temperature approaches the target temperature, i.e., the temperature
difference is less than the threshold, the control is transferred to the PID control. The PID control parameters
are determined based on the desired target temperature conditions. For this purpose, parameters were
determined using Chien-servo tuning with bump tests for various low-duty cycles. The temperature change of
the aluminum block at a given duty cycle is presented in Figure 6.
Figure 6. Temperature change at bump test to determine the PID parameters
The determination of PID control parameters is based on the equation in Table 1. The PID
parameters for each temperature condition are obtained in Table 2 using the bump-test as presented in
Figure 6. The proportional, derivative, and integral control parameter values are slightly different at different
temperature setpoints. These different PID parameter values are used by storing the parameters in a look-up
table in the Raspberry PI implementation for control. The system control parameters are implemented in the
program on the Raspberry Pi with the system algorithm, as shown in Figure 5. The threshold value in control
is set at 2 °C.

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Table 1. PID parameter equation
Kp Ki Kd
𝟎.𝟔𝑻
𝑲𝑳
𝐾𝑝
𝑇
𝐾𝑝 .0.5𝐿
Table 2. PID parameter for temperature target from 45°C to 94°C
Setpoint (°C) Kp Ki Kd
45 33.61163 0.114325 42.01453
49 31.25138 0.119737 39.06422
53 35.95431 0.118271 44.94289
57 31.82256 0.128836 39.77819
61 33.67367 0.126119 42.09209
65 32.11367 0.131613 40.14208
69 29.36100 0.129916 36.70125
72 33.22567 0.127301 41.53208
76 32.43461 0.126698 40.54326
80 22.88167 0.141245 28.60209
83 27.98795 0.130177 34.98494
87 28.84282 0.128190 36.05353
91 26.89011 0.136498 33.61264
94 21.81368 0.131408 27.26710
The temperature cycle change of the system at the start is shown in Figure 7. In the beginning, the
temperature of the aluminum block and the cooler's temperature are at the same temperature of 30 °C. The
initial setting of the target denaturation temperature is set at 94 °C. Thermoelectric works with maximum
power to heat the aluminum block. In this condition, the cooler heat pipe temperature remains at 30 °C.
When the aluminum temperature reaches 94 °C (the first denaturation temperature), the system keeps the
temperature with a temperature fluctuation of less than 0.5 °C. This result is comparable with many
well-known PCR systems [33] and better than the reported proportional controller using liquid cooling [34].
Figure 1. Detail temperature at the first two cycles
After reaching the denaturation temperature, the aluminum temperature is cooled to 54 °C
(annealing temperature). On the graph, the temperature of aluminum is decreasing. Thermoelectric works to
transfer heat from the aluminum and is discharged to the cooler. The discharge causes an increase in
temperature in the heat pipe of the cooler. The heat pipe temperature changes up to a temperature of about
40 °C.
The aluminum block assembly process is carried out by changing the target temperature to 72 °C
(extension temperature) and then to the denaturation temperature (94 °C). In this cycle, the thermoelectric
heat is transferred from the copper block in the cooler to the aluminum. The thermoelectric side in contact
with the copper block is at a low temperature. The cooling process of the cooler can be seen from a decrease
in the temperature of the heat pipe.
In the next cycle, the thermoelectric cools the aluminum. The temperature of aluminum changes
from denaturation (94 °C) to annealing (54 °C). The heat from the aluminum is discharged to the cooler. The
heat pipe temperature of the cooler increased and reached a temperature close to 50 °C. This process is
repeated. When the aluminum is heated, the heat pipe temperature cools down and vice versa.

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Figure 8 shows the temperature cycle for aluminum, the heat pipe, and the temperature target for the
aluminum temperature in the first hour of the thermal cycle. The temperature profile of TAl from each cycle
(denaturation-annealing–extension) in the first hour remains. The heat pipe temperature undergoes an up and
down process following aluminum's heating and cooling cycle. The average heat pipe temperature increased
up to the fifth cycle. In the next cycle, the heat pipe temperature fluctuations were relatively constant. An
equilibrium condition has been reached in heat dissipation by the coolant to the environment. The ramp rates
for heating reach 0.7 °C/second, and cooling is 0.5 °C/second, which is slower than the commercial PCR
[1], [3], [35].
In an entire 24-hour operation, as shown in Figure 9, it can be seen that there is no change in the
temperature cycle in the aluminum or heat pipe. Figure 10 shows the temperature conditions 24 hours after
the thermal cycler runs. There is no change in the temperature profile or the aluminum or heat pipe
temperature value as shown in Figure 8. It shows that the thermal cycler control system's design and the heat
dissipation system to the environment run well.
Figure 8. Thermal cycler temperature in the first hour
Figure 9. Thermal cycler temperature along 24 hours continuous operation
Figure 10. Thermal cycler temperature after 24 hours of continuous operation

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4. CONCLUSION
Electronic modules available in the market to build a thermocycler provide convenience and speed
to realize the system. A good temperature profile and temperature stability are obtained using a combined
control model involving feedforward, bang-bang, and PID. PID control parameters optimized for specific
temperature targets can efficiently be run using the Raspberry Pi embedded system by placing a list of
control parameters in a look-up table. The target temperature, denaturation, annealing, and extension can be
achieved quickly and precisely. The use of coolers by utilizing the low-profile cooling fan shows good
cooling quality. The cooling system's temperature does not change significantly when the thermal cylinder is
run for a full 24 hours. At each temperature of denaturation, annealing, and extension, the temperature
difference between the aluminum block and the target temperature is less than 0.5 °C.
ACKNOWLEDGEMENTS
This work is supported by the Ministry of Research and Technology and the National Research and
Innovation Agency (BRIN) of the Republic of Indonesia under PDUPT Research Grant.
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BIOGRAPHIES OF AUTHORS
Setyawan Purnomo Sakti received the B.Sc. degree in Physics from Gadjah
Mada University, Indonesia, in 1989. He got his M.Eng. degree in Electrical and Electronics
Engineering from University of South Australia in 1994. In 2000, he got his Dr.-Ing. from the
Otto von Guericke Universität, Magdeburg, Germany. Currently, he is a Professor at the
Department of Physics, Brawijaya University. His research interests include sensor
technology, internet of things, medical technology, rapid detection, embedded system,
microcontroller, biosensor, and chemical sensor. He can be contacted at sakti@ub.ac.id.
Adin Okta Triqadafi received a B.Sc. degree in Instrumentation Physics from
Brawijaya University, Indonesia in 2020. He is currently studying for a master's degree in
physics at Brawijaya University, Indonesia. His research interests include sensor technology,
instrumentation systems, microcontrollers, and embedded systems. He can be contacted at
triqadafi@students.ub.ac.id.
Aldi Dwi Putra received a B.Sc. degree in Instrumentation Physics from
Brawijaya University, Indonesia in 2021, Currently, he is an employee in a company engaged
on the Internet of Things end to end, who has the position as a hardware and firmware
engineer. He can be contacted at aldidwiputra9@students.ub.ac.id.

287
Triswantoro Putro received a bachelor's degree in Physics department at Institut
Teknologi Sepuluh November in 2003, then a master's study in the same department in 2011.
He became a lecturer in the instrumentation study program, Physics Department of Brawijaya
University with a research focus on instrumentation of plasma. He can be contacted at
triswantoro@ub.ac.id.
Dewi Anggraeni is a researcher and lecturer at Instrumentation Study Program,
Department of Physics, Faculty of Science, Brawijaya University. She completed her B.S.
degrees from Brawijaya University and M.S. degrees from Double Degree Program between
Brawijaya University (Indonesia) and National Central University (Taiwan). She can be
contacted at dewianggraeni.x@ub.ac.id.

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