# Low-Cost Temperature Logger for a Polymerase Chain Reaction Thermal Cyler
## 1 Introduction  
Polymerase chain reaction (PCR), a method of amplifying segments or parts of DNA with a thermal cycler, is the most potent technology in molecular biology which is employed in various biochemical analysis, clinical laboratories, and basic research areas [1; 2; 3; 4; 5]. The efficiency or amplification results are very sensitive to the reaction conditions due to the exponential DNA amplification during the reaction [6; 7; 8]. Therefore, the reagent used or the performance of the thermal cycler to control and maintain the chamber temperature greatly influences the reproducibility or inter-laboratory variability. To obtain globally reliable PCR results, the PCR thermal cycler must be stable in temperature control and maintenance, and the inter-laboratory temperature variation should be reduced by temperature calibration [6; 7; 8; 9]. To measure the temperature of the well within a thermal cycler, a temperature probe and data logger are required [6; 8; 9; 10; 11]. The probe with a temperature sensor should be designed to provide tight thermal-coupling with the well of the aluminum block, and the logger should read and store the temperature of the sensor. In a common research laboratory, the temperature is read through a high-cost data acquisition system and a probe composed of a reagent container with a thermocoupleis inserted [6; 8; 9; 10]. A PCR tube made of polypropylene is adapted as the reagent container which is susceptible to wear out over the course of time and therefore is not permanently reusable, and should be built anew for every test. However, employing a high-cost acquisition system to read the probe sensor has disadvantages regarding portability and cost. The temperature sensing probe is usually designed for repetitive use in a commercial thermal cycler temperature verification system [12; 13; 14; 15; 16]. Currently, the provider of a thermal cycler offers periodic validation services with a large scale thermal cycler temperature logger [17; 18]. However, this service is not readily available to users who want to immediately measure and calibrate the temperature when the PCR amplification results seem to be off. Therefore, the users commonly employ a general temperature logger and a hand-made probe to serve that purpose. Many companies also provide hand-held type thermal cycler checkers for this purpose [14; 15]. They commonly embed both of the temperature reading logic in a portable system and graphical user interface (GUI) with an LCD screen [12; 13; 14; 15; 16]. However, providing GUI with a LCD screen increases the system size and its production and maintenance cost. Owing to the recent portability enhancement of standard computing devices, including PCs and smart devices, it is more beneficial to perform the user interaction such as saving the log information with the standard computing devices [19; 20; 21; 22]. If a user adopts a standard computing device as a host system, it is possible to reduce the system cost drastically by using a low cost microcontroller only to interface the probe sensor. The maintenance cost can also be reduced by leaving complex tasks to the host PC and simplifying the embedded firmware. Although a thermocouple is mainly adopted in temperature sensing and calibration, the negative temperature coefficient (NTC) thermistor is more advantageous in cases where the temperature range is limited such as in the PCR thermal cycler. In addition, an NTC thermistor which is a lower cost temperature sensor providing highest sensitivity at a narrow temperature range, can also contribute to decreasing the system cost. The existing portable thermal cycler validation systems provide an accuracy of 0.1 \({}^{\circ}\)C and the drift of 0.1 \({}^{\circ}\)C/year which are acceptable in the PCR application [14; 15; 23]. The calibration of the systems is required for them to be regularly authenticated by an official certification authority for traceability.