Assignment 7, Part 1: op amp golden rules questions
This is Part 1 of Assignment 7.
Turn in your answers to the following questions 
 Op amp circuits:

Calculate the gain of circuit (a), V_{o} / V_{i}, in terms of the input voltage and the two resistor values.

In the DNA melting lab, fluorescence intensity will be determined by measuring the output current of a photodiode. Schematic (b) shows a circuit called a transimpedance amplifier that converts a current to a voltage.
Derive an expression for the output voltage of the circuit produced by a DC current input at i_{in} (b). (At DC, you can ignore the effect of the capacitor.) Express your answer in the form of a transfer function, V_{out} / i_{in}.  What is the high frequency gain of the transimpedance amplifier shown in Schematic (b)? Remember that a capacitor acts like an open circuit at low frequencies and a short circuit at high frequencies.
 A transimpedance amplifier with a gain of approximately 10^{6} V/A will be required for the DNA melting lab. What value of resistor in the circuit (b) would achieve this gain?

It is undesirable to use the large value of resistor you computed in part A.4. Shown in (c) is another possible implementation of the transimpedance amplifier. Derive an expression for the output voltage of this circuit in terms of the input current and the three resistor values.
 In part A.3., you determined the effect of putting a capacitor across the feedback resistor in a transimpedance amplifier. High gain amplifiers are susceptible to noise coupling from a variety of sources. Since high frequencies are not of interest in the DNA melting lab, it is beneficial to insert a capacitor to reduce the noise. In circuit (c), where would you connect the capacitor and how would you choose its size?
 Now work out the expression for this new circuit's output with respect to the current input for AC signals.

Unfortunately, when the gain of an op amp circuit is very high (i.e. higher than ~10^{6} V/A), we can no longer ignore the nonidealities of the op amp, and the circuit starts to misbehave. If we want to increase the gain beyond this limit, we can add an additional amplification stage to our circuit (Schematic (d)). Solve for the gain, V_{out} / V_{in}, of the circuit in Schematic (d) in terms of the input voltage and the two resistor values, R_{4} and R_{5}.

 Simulating DNA melting lab:
 Using DINAmelt or OligoCalc, find an estimate for ΔH^{0} and ΔS^{0} for the following oligonucleotide sequence: ATC AAG CAG CCA TCG AAA AAA CT. Assume the complementary strand has no mismatches, the sodium concentration is 100 mM, and the total concentration of oligonucleotide strands is 30 μM.

In class, we derived an equation to describe the fraction (f) of doublestranded DNA in solution as a function of temperature (T) in Kelvin as shown below:
$ f = {1 + C_T K_{eq}  \sqrt{(1 + 2C_T K_{eq})} \over C_T K_{eq}} $
C_{T} is the total concentration of oligonucleotide strands (30 μM), and K_{eq} is the equilibrium constant as described by the following equation:
$ K_{eq} = e^{ [{\Delta S^0 \over R}  { \Delta H^0 \over RT }]} $
Using these equations and the values you found in part 1, simulate a DNA melting curve, plotting f vs. T. Feel free to use the MATLAB functions given on the wiki page:
http://measurebiology.org/wiki/DNA_Melting:_Simulating_DNA_Melting__Basics
 Overview
 Part 1: Prelab problems
 Part 2: Build an instrument to measure temperature and fluorescence
 Part 3: Testing and measuring stuff
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