Wajid Khan
Introduction
Polymerase chain reaction (PCR) is a laboratory technique used to make multiple copies of a segment of DNA. PCR is very precise and can be used to amplify, or copy, a specific DNA target from a mixture of DNA molecules. A PCR reaction consists of three steps: denaturation, annealing, and extension. This is how a basic PCR reaction works: First, two short DNA sequences called primers are designed to bind to the start (3�) and end (5�) of the DNA target. The primer nucleic acid sequences are chosen to flank the target region, so that on amplification the target is increased. Then, to perform PCR, the DNA template that contains the target is added to a tube that contains primers, free nucleotides (adenine, guanine, cysteine, thymine), also known as deoxyribonucleotides (dNTPs), and an enzyme called DNA polymerase. This mixture is placed in a PCR machine. The PCR machine increases and decreases the temperature of the sample in automatic, programmed steps. Initially, the mixture is heated (eg, 95�C) to denature, or separate, the double-stranded DNA template into single strands. The mixture is then cooled (eg, 60-65�C) so that the primers anneal (bind) to the DNA template. At this point, the temperature is increased to approximately 72�C to optimize DNA polymerase, catalyzing the addition of nucleotides to synthesize new strands of DNA starting from the primers (extension). At the end of the first cycle, each double-stranded DNA molecule consists of one new and one old DNA strand. PCR then continues with additional cycles that repeat the aforementioned steps. The newly synthesized DNA segments serve as templates in later cycles, which allow the DNA target to be exponentially amplified millions of times.Our Final design will be like:.
Our purpose is to design a machine which follows a series of cycles to achieve the required result. PCR is a common tool used in medical and biological research labs. It is used in the early stages of processing DNA for sequencing, for detecting the presence or absence of a gene to help identify pathogens during infection, and when generating forensic DNA profiles from tiny samples of DNA.The most important parameter of PCR machine is temperature, because for a thermocycle you need to maintain some special ranges.
Importance
The polymerase chain reaction is often considered as one of the most important scientific advances in the field of molecular biology. With this revolutionary yet inexpensive biochemical technology, it's possible to generate millions of DNA copies from a single strand of DNA.
1. Faster Results
2. Shorter Time to Optimal Therapy
3. Improve Treatment Decisions
4. Avoid Unnecessary Antibiotics
5. Support Antimicrobial Stewardship Efforts
6. Reduce Unnecessary Testing
7. Reduce Healthcare Costs
Teamwork
Me Uzam Haider with my team member Wajid Khan will design this PCR. We know that there will comes many difficulties but we will overcome all of them with the teamwork.
High Level Design
Given below in the detail information of the components along with their snaps.
- The Cooling Fan
- Heat Sink
- Sample Holder
- DC Power Supply
- Vnh2sp30 motor driver Monster Shield
- Peltier Modules
- Nokia 5110
Deligation of Tasks
| Task | Name |
|---|---|
| Literature review | Combined |
| PCB Software Design | Uzam Haider |
| PCB Soldering | Combined |
| Ardunio Programming | Combined |
| Components Assembly | Combined |
| Documentation | Wajid Khan |
| Programming logic | Uzam Haider |
| Sensors Installment | Uzam Haider |
| Components Design and Arrangement | Combined |
| PCB Debugging | Combined |
Intellectual Properties and Ethics Considerations
The sites and the sources which we visited are given
Visit Integrated DNA Technologies.net!
There are many websites of whom we go through and we had collected many things from many of them to build up this major one thing. We appreciated the work of each and regret to mention all of them!
Good Things we Took From Referees
1. For the use of Nokia 5110 we took help regarding of the libraries used in our Code. We used Adafruit_GFX.h and Adafruit_PCD8544.h libraries
. These libraries helped us in making the object of our LCD. Also we were helped related to the pins of CLK and BLK of LCD.
As these pins play a major role in the beauty and moving of your bits and nits of data.
2. First we thought that giving only volatage and current is enough to derive the peltiers, but we were wrong. After telling by Prof. Dr Sir Asim and
by doing some research we came up on this spot that "Allowing peltiers to derive withing allowed range as described in the datasheet and only
certain required voltage and current is the only right choice." Otherwise... you know what I means!
3. One of the last major thing that must need to be sorted was our Motor Driver. Which in our case is not a simple motor driver but a Monter Shield
named by sparkfun is VNH2SP30. It is highly durable, sustainable and comes up with thermal breakdown feauture. The mistake we were doing was that
we thought that giving only supply voltage to the Motor driver is enough to run the Shield, but again after doing research we came up with this solution
that giving +5V to the IC's of the Shield must to derive the Motor driver to play in the field.
Gantt Chart
We implemented our work in the form of gantt chart. You can go through our work.
You can read thoroughly by clicking on below PCR Gantt Chart
Design
The Design process has several layers to it. Electrical Design, Software Design, Final Hardware Assembly Which are elaborated below.Electrical Circuit
Here is our elcetrical circuit of PCR. For the demonstration purpose we used arduio uno sheild. Bill of material is mentioned above. Our fulfill operation of PCR is very much dependent on exact proposed values of components. The values of components was set up after plenty of hit and trail method.
How Things Work
First our PCR will be turn On. Our LCD shows the Menu to the User. The User set it's required parameters. When the process starts the peltiers will heat the sample block. All the process now dependds upon the values of thermister. When the thermister value reaches the desired temperature value as set by the user, the arduino then tell the motor driver to reverse the polarity of the peltiers. Now the peltiers cool the sample block. The same process repeats depending upon the number of cycles as set by the user.
PCB Layout
Here is the Schematic of PCR in eagle software.
Here is the Board of PCR in eagle software.
A fresh-baked PCB ready to boost up the line.
Bootloading
A bootloader helps to load the operating system or runtime environment to add programs to memory and provide access for components. It is needed to run the startup process, initialize the hardware, and pass control to the kernel, which initializes the operating system. One of the big features of the ATmega32u4 is that is has a built-in USB interface. This means that it�s super simple to program (just connect a USB cable and you�re good to go). Now in order to upload Arduino sketches to it, We first had to burn the Arduino bootloader to it. We burn the bootloader to the Atmega32u4 and then we upload the testing arduino code on it. We set the port to the Arduino leonardo. Within minutes it showed the results.
Take a look on the Boot loading of our Atmega38u4
After the job of several hours we got a fully solded PCB
TroubleShooting Of PCB
A 2 layer PCB
Because of one capacitor our PCB was not responing right. To check a two layer PCB you have to make sure the connectivity is perfect from both sides. So, after replacing the right component our PCB was reponding. Also make sure that the VCC and GND lines must not short with each other, and always check your and PCB connectivity well before powering, otherwise you have to start from the beginning.
Software Development
Our Program logic is based on the given mechanism
Design of finished Product
Here is the final design of our Product. A crystal cut and a real- commercial type design. Where you can see the lcd tilted. Specially designed for the special people. Where you can find of this type?
We had designed our PCR enclosure in Solidworks and the remaining work was being done by the Printer.
CAD Design
We had implemented our PCR Hardware design in the Solidworks. In Assembly we had made two parts an Upper one and a lower one. Our design come up with an attach and a detach technique with witch user can easily open up the PCR whenever want.
The Following is the lowe part of our PCR machine.
Results
Further Materials:
Here are some of the links in case if you want to do reserach furtherrelated to PCR and it's Modern applications.
Open PCR
from the Instructables
Updated Version to qPCR
A journal to read
From the Industrial View
Conclusion:
After completing this project, One thing that we learned so far is that "Project Management is the end goal". From Imagination to reality, from initial trials to the ending is a journey that teaches us a lot of things. We learned many fruitful skills from this project. First Analyzing real time problems in Arduino and how to write code in Arduino. Secondly, we learned how to design a PCB in CAD (Eagle). Actually before making a PCB we always thought that it is too easy to make it but one thing that we learn is that you only know the real depth of an Ocean when you dive into it. Selection of Components is the real part. Sometimes even one wrong capacitor can make you driven hard. Datasheet help you in many ways. Whatever component you use, it comes with datasheet with each minor details. As in our case, we don't know of Thermister, Peltiers and Motor Driver, that how much they consume current and what are the requirements of true measures to get the results. After studying we come to know that what the true value of resistors that are being use with the thermister. We also faced a alot of problems in the initial attempt of our PCB. As because of one capacitor, our board was not getting on the right spot. After doing testing again and agian we finally come to that point where our Board was ready to hand shake with us.
Bill Of Materials
Appendix
Here is our downloadable stuff
Click on the thumbnails to download the files:
PCB files
Ardunio File
.jpg)
Enclosure File
