Difference between revisions of "Team:UMaryland/Design"

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Background</b>

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Background</b>

<p>Our first design for a DIY PCR machine was modeled after a more conventional PCR machine. This first prototype relied on two Peltier units stacked on top of each other to heat a customized aluminum block that held the PCR tubes. In order for the system to have feedback, we embedded a temperature sensor in the aluminum block to measure the temperature of the PCR tube wells. The sensor then reported back to an Arduino UNO, which then regulated the energy flow to the Peltier units, thereby regulating the temperature of the block and tubes. However, after much testing, this design proved to be unoriginal, expensive, and inefficient. While the conventionality of the design itself did not pose an issue, we realized that the parts used to assemble it were not as well-known or easily accessible to the general public, which we felt would take away from the possible applications of this machine. In addition, although the price of this first prototype was relatively inexpensive in contrast to laboratory grade PCR machines, the price still ranged in the hundreds of dollars. Finally, the greatest issue with our design was the inefficiency of the hardware; we found that the Peltier units were not able to quickly cycle through the desired temperatures, causing the unit to take 5 to 10 minutes just to rise up to 95℃. After considering all of these factors, we began a redesign of our machine to better suit the needs of the DIY market.</p>

<p>Our first design for a DIY PCR machine was modeled after a more conventional PCR machine. This first prototype relied on two Peltier units stacked on top of each other to heat a customized aluminum block that held the PCR tubes. In order for the system to have feedback, we embedded a temperature sensor in the aluminum block to measure the temperature of the PCR tube wells. The sensor then reported back to an Arduino UNO, which then regulated the energy flow to the Peltier units, thereby regulating the temperature of the block and tubes. However, after much testing, this design proved to be unoriginal, expensive, and inefficient. While the conventionality of the design itself did not pose an issue, we realized that the parts used to assemble it were not as well-known or easily accessible to the general public, which we felt would take away from the possible applications of this machine. In addition, although the price of this first prototype was relatively inexpensive in contrast to laboratory grade PCR machines, the price still ranged in the hundreds of dollars. Finally, the greatest issue with our design was the inefficiency of the hardware; we found that the Peltier units were not able to quickly cycle through the desired temperatures, causing the unit to take 5 to 10 minutes just to rise up to 95℃. After considering all of these factors, we began a redesign of our machine to better suit the needs of the DIY market.</p>

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<p> The idea for our current thermocycler design first came into form when we found that our original prototype was not ramping up to the desired temperatures fast enough. We thus looked into other options such as the heating element in a hair dryer. We found that the hair dryer was able to reach very high temperatures—much higher than the desired maximum of 95℃ for PCR—in a matter of seconds. We then made a decision to suspend construction on the Peltier-centered thermocycler in order to see how successful we could be with making a rapid PCR machine out of a hair dryer. Before this decision, we took into consideration the danger of working with a hair dryer, failure due to uncertainty that the machine could be effectively controlled, and, on top of that, having less time to work on it. Nevertheless, we took the risk.</br><i>Please continue on to see the design of our machine.</i>  

<p> The idea for our current thermocycler design first came into form when we found that our original prototype was not ramping up to the desired temperatures fast enough. We thus looked into other options such as the heating element in a hair dryer. We found that the hair dryer was able to reach very high temperatures—much higher than the desired maximum of 95℃ for PCR—in a matter of seconds. We then made a decision to suspend construction on the Peltier-centered thermocycler in order to see how successful we could be with making a rapid PCR machine out of a hair dryer. Before this decision, we took into consideration the danger of working with a hair dryer, failure due to uncertainty that the machine could be effectively controlled, and, on top of that, having less time to work on it. Nevertheless, we took the risk.</br><i>Please continue on to see the design of our machine.</i>  

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Another consequence of expensive conventional thermocycling is the financial difficulty of bringing these machines into the classroom. PCR is an extremely important topic in biotechnology, but it is typically also one that requires one to "see it to believe it." However, schools often cannot afford to purchase thermocyclers due to their high cost. By manufacturing a cheap, DIY thermocycler that can be assembled at a low cost, we can help bring this technology into schools that would otherwise be unable to afford it.

Another consequence of expensive conventional thermocycling is the financial difficulty of bringing these machines into the classroom. PCR is an extremely important topic in biotechnology, but it is typically also one that requires one to "see it to believe it." However, schools often cannot afford to purchase thermocyclers due to their high cost. By manufacturing a cheap, DIY thermocycler that can be assembled at a low cost, we can help bring this technology into schools that would otherwise be unable to afford it.

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<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>UMD DIY PCR</b>

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>UMD DIY PCR</b>

<p>Our first design for a DIY PCR machine was modeled after a more conventional PCR machine design. This first prototype consisted of two Peltier units stacked on top of each other that would then heat a customized aluminum block that sat on top of the two units and held the PCR tubes. In order for the system to have feedback, we embedded a temperature sensor in the aluminum block to measure the temperature of the PCR tube wells. The sensor then reported back to an Arduino UNO, which then regulated the energy flow to the Peltier units, thereby regulating the temperature of the block and tubes. However, after much testing, this design proved to be unoriginal, expensive, and inefficient. While the conventionality of the design itself did not pose an issue, we realized that the parts used to assemble it were not as well-known or easily accessible to the general public, which we felt would take away from the possible applications of this machine. In addition, although the price of this first prototype was relatively inexpensive in contrast to laboratory grade PCR machines, the price still ranged in the hundreds of dollars. Finally, the greatest issue with our design was the inefficiency of the hardware; we found that the Peltier units were not able to quickly cycle through the desired temperatures, causing the unit to take 5 to 10 minutes just to rise up to 95℃. After considering all of these factors, we began a redesign of our machine to better suit the needs of the DIY market.</p>

<p>Our first design for a DIY PCR machine was modeled after a more conventional PCR machine design. This first prototype consisted of two Peltier units stacked on top of each other that would then heat a customized aluminum block that sat on top of the two units and held the PCR tubes. In order for the system to have feedback, we embedded a temperature sensor in the aluminum block to measure the temperature of the PCR tube wells. The sensor then reported back to an Arduino UNO, which then regulated the energy flow to the Peltier units, thereby regulating the temperature of the block and tubes. However, after much testing, this design proved to be unoriginal, expensive, and inefficient. While the conventionality of the design itself did not pose an issue, we realized that the parts used to assemble it were not as well-known or easily accessible to the general public, which we felt would take away from the possible applications of this machine. In addition, although the price of this first prototype was relatively inexpensive in contrast to laboratory grade PCR machines, the price still ranged in the hundreds of dollars. Finally, the greatest issue with our design was the inefficiency of the hardware; we found that the Peltier units were not able to quickly cycle through the desired temperatures, causing the unit to take 5 to 10 minutes just to rise up to 95℃. After considering all of these factors, we began a redesign of our machine to better suit the needs of the DIY market.</p>

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<p> The idea for our current thermocycler design first came into form when we found that our original prototype was not ramping up to the desired temperatures fast enough. We thus looked into other options such as the heating element in a hair dryer. We found that the hair dryer was able to reach very high temperatures—much higher than the desired maximum of 95℃ for PCR—in a matter of seconds. We then made a decision to suspend construction on the Peltier-centered thermocycler in order to see how successful we could be with making a rapid PCR machine out of a hair dryer. Before this decision, we took into consideration the danger of working with a hair dryer, failure due to uncertainty that the machine could be effectively controlled, and, on top of that, having less time to work on it.

<p> The idea for our current thermocycler design first came into form when we found that our original prototype was not ramping up to the desired temperatures fast enough. We thus looked into other options such as the heating element in a hair dryer. We found that the hair dryer was able to reach very high temperatures—much higher than the desired maximum of 95℃ for PCR—in a matter of seconds. We then made a decision to suspend construction on the Peltier-centered thermocycler in order to see how successful we could be with making a rapid PCR machine out of a hair dryer. Before this decision, we took into consideration the danger of working with a hair dryer, failure due to uncertainty that the machine could be effectively controlled, and, on top of that, having less time to work on it.

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<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Design</b>

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Design</b>

<p> We began by working out how to wire the hairdryer so that we could regulate the heating unit and the fan separately.  

<p> We began by working out how to wire the hairdryer so that we could regulate the heating unit and the fan separately.  

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<img src="https://static.igem.org/mediawiki/2015/d/dc/UMD_PCR_hardware3.jpg">

<img src="https://static.igem.org/mediawiki/2015/d/dc/UMD_PCR_hardware3.jpg">

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<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Hardware</b>

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Hardware</b>

<p>The working internals of our PCR machine are comprised of hairdryer elements. With the exception of the hairdryers outer housing, the thermal fuse and bimetallic circuit breaker all other working components remain intact. The thermal fuse and bimetallic circuit breaker were shorted using copper wire in order to reach temperatures up to 95 within our machine. The outer plastic housing of the hairdryer was also removed to enable our machine to stand upright and fit PCR tubes. The hairdryers heating mechanism which utilizes a bank of nichrome wires and fan that distributes the heat remained untouched. <a href = "https://static.igem.org/mediawiki/2015/2/2f/UMDPCR.pdf">Click here to read about the parts used for our thermocycler</a>.

<p>The working internals of our PCR machine are comprised of hairdryer elements. With the exception of the hairdryers outer housing, the thermal fuse and bimetallic circuit breaker all other working components remain intact. The thermal fuse and bimetallic circuit breaker were shorted using copper wire in order to reach temperatures up to 95 within our machine. The outer plastic housing of the hairdryer was also removed to enable our machine to stand upright and fit PCR tubes. The hairdryers heating mechanism which utilizes a bank of nichrome wires and fan that distributes the heat remained untouched. <a href = "https://static.igem.org/mediawiki/2015/2/2f/UMDPCR.pdf">Click here to read about the parts used for our thermocycler</a>.

<img src="https://static.igem.org/mediawiki/2015/e/e8/IGEMUMDPCR.png" style="width:450px;height:450px;float:left;">

<img src="https://static.igem.org/mediawiki/2015/e/e8/IGEMUMDPCR.png" style="width:450px;height:450px;float:left;">

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<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Problems and Current issues </b>

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Problems and Current issues </b>

<p> We have had one successful amplification with our machine however we understand that repeatability is a vital component of all lab work and currently we are attempting to make our device repeatable. From our early days of testing we found that peltier units were not powerful enough to enable PCR tube to reach 95 degrees. On the other hand, the fan and heating element of a cheap hairdryer provide a control scheme that enables for rapid cycling of temperature. We have found that developing a housing for the PCR tubes and enabling even heat distribution is challenging. We often have found that our temperature sensor and the pcr reaction tube are not at the same temperature and degree of difference is a delta of over 10 degrees Celsius. We are currently working of milling a block of aluminum with better and more consistent heat transfer properties, and modeling the heat transfer within the can. Our ambition is that this will enable better control of temperature within the device.         

<p> We have had one successful amplification with our machine however we understand that repeatability is a vital component of all lab work and currently we are attempting to make our device repeatable. From our early days of testing we found that peltier units were not powerful enough to enable PCR tube to reach 95 degrees. On the other hand, the fan and heating element of a cheap hairdryer provide a control scheme that enables for rapid cycling of temperature. We have found that developing a housing for the PCR tubes and enabling even heat distribution is challenging. We often have found that our temperature sensor and the pcr reaction tube are not at the same temperature and degree of difference is a delta of over 10 degrees Celsius. We are currently working of milling a block of aluminum with better and more consistent heat transfer properties, and modeling the heat transfer within the can. Our ambition is that this will enable better control of temperature within the device.         

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<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>CODE</b></p>

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>CODE</b></p>

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