http://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&feed=atom&action=historyDNA Melting Part 1: Measuring Temperature and Fluorescence - Revision history2024-03-29T05:28:55ZRevision history for this page on the wikiMediaWiki 1.22.3http://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=34914&oldid=prevJuliesutton: /* Wire the Peltier device and test it */2017-04-19T17:49:39Z<p><span dir="auto"><span class="autocomment">Wire the Peltier device and test it</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Diablotek switching power supply.jpg|thumb|right|Diablotek switching power supply (inside east cabinet) provides power to the Peltier devices.]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[Image:Diablotek switching power supply.jpg|thumb|right|Diablotek switching power supply (inside east cabinet) provides power to the Peltier devices.]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Heating and cooling the sample with a Peltier device requires a lot of current. In part 1 of the lab, you will hook the Peltier device (also called a thermoelectric cooler, or TEC) directly its own power supply. When you turn the power supply on, the sample will heat up. After you turn the supply off, the sample will return to room temperature by radiation, conduction, and convection &mdash; all that heat stuff. This is a pretty crude way to control the sample temperature. We'll come up with something better in part 2.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Heating and cooling the sample with a Peltier device requires a lot of current. In part 1 of the lab, you will hook the Peltier device (also called a thermoelectric cooler, or TEC) directly <ins class="diffchange diffchange-inline">to </ins>its own power supply. When you turn the power supply on, the sample will heat up. After you turn the supply off, the sample will return to room temperature by radiation, conduction, and convection &mdash; all that heat stuff. This is a pretty crude way to control the sample temperature. We'll come up with something better in part 2.</div></td></tr>
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</table>Juliesuttonhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=34905&oldid=prevJosephinebagnall: /* Measure temperature */2017-04-13T21:00:40Z<p><span dir="auto"><span class="autocomment">Measure temperature</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* What is the temperature, based on your measured voltage and how does it compare with the clock on the wall (or some better measure)?</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* What is the temperature, based on your measured voltage and how does it compare with the clock on the wall (or some better measure)?</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* How is the temperature calculation affected by a 1% change in the 15 V input voltage? In other words, if you assume the same measured voltage across the RTD, but have a 1% change in the input voltage, how much does your calculated temperature change?</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* How is the temperature calculation affected by a 1% change in the 15 V input voltage? In other words, if you assume the same measured voltage across the RTD, but have a 1% change in the input voltage, how much does your calculated temperature change? <ins class="diffchange diffchange-inline">Note the importance of keeping track of your input voltage.</ins></div></td></tr>
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</table>Josephinebagnallhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=34904&oldid=prevJosephinebagnall: /* Measure temperature */2017-04-13T20:58:50Z<p><span dir="auto"><span class="autocomment">Measure temperature</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* What is the temperature, based on your measured voltage and how does it compare with the clock on the wall (or some better measure)?</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* What is the temperature, based on your measured voltage and how does it compare with the clock on the wall (or some better measure)?</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* How is the temperature calculation affected by a 1% change in the 15 V input voltage?</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* How is the temperature calculation affected by a 1% change in the 15 V input voltage<ins class="diffchange diffchange-inline">? In other words, if you assume the same measured voltage across the RTD, but have a 1% change in the input voltage, how much does your calculated temperature change</ins>?</div></td></tr>
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</table>Josephinebagnallhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=34903&oldid=prevJosephinebagnall: /* Overview of part 1 */2017-04-13T20:50:57Z<p><span dir="auto"><span class="autocomment">Overview of part 1</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>When you get it all put together, the instrument will produce two voltages: one related to the sample temperature and another that depends on the amount of fluorescence coming out of the sample. The goal of part 1 is to produce at least one reasonable quality melting curve. This involves recording the temperature and fluorescence voltage as you heat a sample of DNA + dye from room temperature to about 95&deg;C and then let it cool back down. Computer software for recording the voltages has already been written for you. After you have a melting curve, you will use nonlinear regression to fit thermodynamic parameters to your data and do a little planning for part 2 of this lab. You will probably notice some shortcomings your instrument as you work. Don't worry about that &mdash; in part 2, you will make many improvements to your machine that will make it [https://youtu.be/3rQEbQJx5Bo sing like Elvis].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>When you get it all put together, the instrument will produce two voltages: one related to the sample temperature and another that depends on the amount of fluorescence coming out of the sample. The goal of part 1 is to produce at least one reasonable quality melting curve. This involves recording the temperature and fluorescence voltage as you heat a sample of DNA + dye from room temperature to about 95&deg;C and then let it cool back down. Computer software for recording the voltages has already been written for you. After you have a melting curve, you will use nonlinear regression to fit thermodynamic parameters to your data and do a little planning for part 2 of this lab. You will probably notice some shortcomings your instrument as you work. Don't worry about that &mdash; in part 2, you will make many improvements to your machine that will make it [https://youtu.be/3rQEbQJx5Bo sing like Elvis].</div></td></tr>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>There are instructions below for assembling your DNA melter<del class="diffchange diffchange-inline">. An example instrument is also available in the lab for your perusal. Feel free to inspect the example, but PLEASE DO NOT TAKE IT APART. The example is configured for part 2 of the lab, so you might notice a few differences between what you build and the example</del>.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>There are instructions below for assembling your DNA melter.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Before you get started in the lab &hellip;==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Before you get started in the lab &hellip;==</div></td></tr>
</table>Josephinebagnallhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=34890&oldid=prevJosephinebagnall: /* Build the transimpedance amplifier */2017-04-13T18:38:49Z<p><span dir="auto"><span class="autocomment">Build the transimpedance amplifier</span></span></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#** Connect the blue bus bars on either side of the amplifiers to ground.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#** Connect the blue bus bars on either side of the amplifiers to ground.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Use short wires to connect the power pins of the op amps to the correct power supplies. Double check your connections &mdash; there is no faster way to ruin an op amp than to wire the power backwards.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Use short wires to connect the power pins of the op amps to the correct power supplies. Double check your connections &mdash; there is no faster way to ruin an op amp than to wire the power backwards.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>#* Add the bypass capacitors (the blue ones in the above image) to your circuit to reduce noise from the power supply. Do this by straddling a capacitor between the +15 V supply (pin 7) to ground, and another capacitor between the -15 V (pin 4) <del class="diffchange diffchange-inline">supply </del>to ground. Be sure to note the polarity of your capacitor (the black stripe should go toward the more negative potential) otherwise you might get an unwanted explosion.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>#* Add the bypass capacitors (the blue ones in the above image) to your circuit to reduce noise from the power supply. Do this by straddling a capacitor between the +15 V supply (pin 7) to ground, and another capacitor between the -15 V <ins class="diffchange diffchange-inline">supply </ins>(pin 4) to ground. Be sure to note the polarity of your capacitor (the black stripe should go toward the more negative potential) otherwise you might get an unwanted explosion.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Build the transimpedance amplifier circuit with the component values you selected. [[Image: LF411.jpg|thumb|right|LF411 op amp pin configuration]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Build the transimpedance amplifier circuit with the component values you selected. [[Image: LF411.jpg|thumb|right|LF411 op amp pin configuration]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Use a SMA to BNC adapter; BNC cable; and BNC to wire adapter to connect the photodiode terminals to the electronic breadboard.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Use a SMA to BNC adapter; BNC cable; and BNC to wire adapter to connect the photodiode terminals to the electronic breadboard.</div></td></tr>
</table>Josephinebagnallhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=34889&oldid=prevJosephinebagnall: /* Build the transimpedance amplifier */2017-04-13T18:38:02Z<p><span dir="auto"><span class="autocomment">Build the transimpedance amplifier</span></span></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 18:38, 13 April 2017</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#** Connect the blue bus bars on either side of the amplifiers to ground.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#** Connect the blue bus bars on either side of the amplifiers to ground.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Use short wires to connect the power pins of the op amps to the correct power supplies. Double check your connections &mdash; there is no faster way to ruin an op amp than to wire the power backwards.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Use short wires to connect the power pins of the op amps to the correct power supplies. Double check your connections &mdash; there is no faster way to ruin an op amp than to wire the power backwards.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">#* Add the bypass capacitors (the blue ones in the above image) to your circuit to reduce noise from the power supply. Do this by straddling a capacitor between the +15 V supply (pin 7) to ground, and another capacitor between the -15 V (pin 4) supply to ground. Be sure to note the polarity of your capacitor (the black stripe should go toward the more negative potential) otherwise you might get an unwanted explosion.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Build the transimpedance amplifier circuit with the component values you selected. [[Image: LF411.jpg|thumb|right|LF411 op amp pin configuration]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Build the transimpedance amplifier circuit with the component values you selected. [[Image: LF411.jpg|thumb|right|LF411 op amp pin configuration]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Use a SMA to BNC adapter; BNC cable; and BNC to wire adapter to connect the photodiode terminals to the electronic breadboard.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div># Use a SMA to BNC adapter; BNC cable; and BNC to wire adapter to connect the photodiode terminals to the electronic breadboard.</div></td></tr>
</table>Josephinebagnallhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=34858&oldid=prevJuliesutton: /* Transimpedance amplifier */2017-04-11T14:50:50Z<p><span dir="auto"><span class="autocomment">Transimpedance amplifier</span></span></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 14:50, 11 April 2017</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===Transimpedance amplifier===</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>===Transimpedance amplifier===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:Transimpedance amplifier part 1.png|thumb|right|400px|Two-stage transimpedance amplifier for converting photocurrent to voltage.]]</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>[[File:Transimpedance amplifier part 1.png|thumb|right|400px|Two-stage transimpedance amplifier for converting photocurrent to voltage.]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Fluorescent light from the sample falls on the photodiode and produces a photocurrent. The amount of current depends on the irradiance of the sample and the light collection efficiency of your optical system (and probably some other stuff). In most instruments, the photocurrent is around a microamp, but this number can vary up or down by a few orders of magnitude depending on the details of your optics. This small current must be amplified to a level where it can be easily measured. The voltage measurement range of the data acquisition system is &plusmn;10 V. It makes sense to shoot for an output voltage that fills most of the range of the data acquisition system. The <del class="diffchange diffchange-inline">following questions will guide you in select components for </del>the two-stage <del class="diffchange diffchange-inline">op amp circuit to convert </del>the photodiode current to a voltage.  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Fluorescent light from the sample falls on the photodiode and produces a photocurrent. The amount of current depends on the irradiance of the sample and the light collection efficiency of your optical system (and probably some other stuff). In most instruments, the photocurrent is around a microamp, but this number can vary up or down by a few orders of magnitude depending on the details of your optics. This small current must be amplified to a level where it can be easily measured. The voltage measurement range of the data acquisition system is &plusmn;10 V. It makes sense to shoot for an output voltage that fills most of the range of the data acquisition system. The <ins class="diffchange diffchange-inline">circuit shown to </ins>the <ins class="diffchange diffchange-inline">right is a </ins>two-stage <ins class="diffchange diffchange-inline">amplifier which converts </ins>the photodiode current to a voltage<ins class="diffchange diffchange-inline">, and amplifies this voltage.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins class="diffchange diffchange-inline">Before you build the circuit, you will need to choose values for the resistors and capacitors to get the right amount of gain and an appropriate cutoff frequency. The following questions will guide you in selecting these components (note that these questions are very similar to PSet 3)</ins>.  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><ol type = "1"></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div><ol type = "1"></div></td></tr>
</table>Juliesuttonhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=33662&oldid=prevKatherine Whang: /* Measure temperature */2017-01-17T18:54:29Z<p><span dir="auto"><span class="autocomment">Measure temperature</span></span></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 18:54, 17 January 2017</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Make note of the actual supply voltage measured by your DMM.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Make note of the actual supply voltage measured by your DMM.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Measure the voltage across the RTD using the DMM.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* Measure the voltage across the RTD using the DMM.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># You may mount your electronic breadboard to your optical breadboard using the CL5 clamps, along with some screws and washers.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># You may mount your electronic breadboard to your optical breadboard using the CL5 clamps, along with some screws and washers<ins class="diffchange diffchange-inline">, as shown in right image</ins>. <ins class="diffchange diffchange-inline">[[Image: CL5clamp.JPG|thumb|right|Clamp usage]]</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Find an equation for the voltage across the RTD as a function of temperature. What voltage do you expect given an input voltage of 15 V with the RTD at room temperature?</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* Find an equation for the voltage across the RTD as a function of temperature. What voltage do you expect given an input voltage of 15 V with the RTD at room temperature?</div></td></tr>
</table>Katherine Whanghttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=33654&oldid=prevJuliesutton: /* Build the transimpedance amplifier */2017-01-17T15:26:00Z<p><span dir="auto"><span class="autocomment">Build the transimpedance amplifier</span></span></p>
<table class='diff diff-contentalign-left'>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 15:26, 17 January 2017</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>## Enable the power supply and verify that +15V appears on pin 7 and -15V on pin 4.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>## Enable the power supply and verify that +15V appears on pin 7 and -15V on pin 4.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>## Temporarily disconnect the photodiode from the amplifier input. This will set the input current to zero.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>## Temporarily disconnect the photodiode from the amplifier input. This will set the input current to zero.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>## Measure the voltage on the output pins of both amplifiers (<del class="diffchange diffchange-inline">IC1 and IC2</del>).</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>## Measure the voltage on the output pins of both amplifiers (<ins class="diffchange diffchange-inline">pin 6</ins>).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>##* If the outputs are not close to zero (say, less than a hundred millivolts), there is probably something wrong. Time for some debugging.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>##* If the outputs are not close to zero (say, less than a hundred millivolts), there is probably something wrong. Time for some debugging.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>## Reconnect the photodiode. Hook a voltmeter to the amplifier output.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>## Reconnect the photodiode. Hook a voltmeter to the amplifier output.</div></td></tr>
</table>Juliesuttonhttp://engineerbiology.org/w/index.php?title=DNA_Melting_Part_1:_Measuring_Temperature_and_Fluorescence&diff=33650&oldid=prevKatherine Whang: /* Wire the Peltier device and test it */2017-01-13T21:58:40Z<p><span dir="auto"><span class="autocomment">Wire the Peltier device and test it</span></span></p>
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</tr><tr><td colspan="2" class="diff-lineno">Line 64:</td>
<td colspan="2" class="diff-lineno">Line 64:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Heating and cooling the sample with a Peltier device requires a lot of current. In part 1 of the lab, you will hook the Peltier device (also called a thermoelectric cooler, or TEC) directly its own power supply. When you turn the power supply on, the sample will heat up. After you turn the supply off, the sample will return to room temperature by radiation, conduction, and convection &mdash; all that heat stuff. This is a pretty crude way to control the sample temperature. We'll come up with something better in part 2.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Heating and cooling the sample with a Peltier device requires a lot of current. In part 1 of the lab, you will hook the Peltier device (also called a thermoelectric cooler, or TEC) directly its own power supply. When you turn the power supply on, the sample will heat up. After you turn the supply off, the sample will return to room temperature by radiation, conduction, and convection &mdash; all that heat stuff. This is a pretty crude way to control the sample temperature. We'll come up with something better in part 2.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DNA part 1 TEC hookup.jpg|thumb|right|Power supply connected to Peltier devices.]]</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>[[Image:DNA part 1 TEC hookup.jpg|thumb|right|Power supply connected to Peltier devices <ins class="diffchange diffchange-inline">(TECs)</ins>.]]</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div># Hook up the Peltier devices in series.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div># Hook up the Peltier devices <ins class="diffchange diffchange-inline">(TECs) </ins>in series.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>#* There are two Peltier devices sandwiched between the sample holder and the heat sink.  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>#* There are two Peltier devices <ins class="diffchange diffchange-inline">(TECs) </ins>sandwiched between the sample holder and the heat sink.  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* They must be connected in series.  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* They must be connected in series.  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* The black lead of the top device should be connected to the red lead of the bottom device.  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>#* The black lead of the top device should be connected to the red lead of the bottom device.  </div></td></tr>
</table>Katherine Whang