![]() Quickplot(sim.time, sim.vRTD, "Simulated RTD Voltage vs. Sim.vRTD = vPower * (sim.rRTD / (rOther + sim.rRTD)) # V across RTD = total voltage * (RTD / (other+RTD)). Simulates RTD voltage (proportional to temp) vs. Time",ĭef simRTD(sim, addNoise=True, plot=True): Quickplot(sim.time, sim.temp, "Simulated Temperature vs. Heating = sim.heatingRate * sim.heatingTime + sim.coolTempĬooling = sim.coolingRate * sim.coolingTime + sim.hotTempĬooling = ((sim.hotTemp - sim.coolTemp) * numpy.exp(olingTime / coolingConst)) + sim.coolTemp Simulating forced heating and forced passive cooling Sim.heatingDuration + sim.coolingDuration,Īccepts a simulated experiment and calculates its temperature over time, Sim.coolingTime = numpy.array(numpy.arange(0.0, Sim.heatingTime = numpy.array(numpy.arange(0.0, Sim.coolingDuration = 900.0 #15 min to cool (would really take a bit longer) ![]() Sim.coolingDuration = (sim.coolTemp - sim.hotTemp) / sim.coolingRate Sim.coolingRate = -0.5 #degrees per second Sim.heatingDuration = (sim.hotTemp - sim.coolTemp) / sim.heatingRate Sim.heatingRate = 0.5 #degrees per second Returns a simulated experimental run, from which we'll produce Quickplot(ideal.temp, ideal.dsDnaFraction, Ideal.dsDnaFraction = DnaFraction(ncentration, ideal.temp, Returns an ideal/theoretical DNA melting experiment. "Temperature (K)", "Delta dsDNA Fraction") Quickplot(expt.dTemp, -1 * expt.diffDsDnaFraction, Takes an Experiment and calculates a differentiated melting curve.Įxpt.diffDsDnaFraction = numpy.diff(expt.dsDnaFraction) Whose values come from averaging each two adjacent values in the input. Returns a new numpy array, 1 element shorter than the input array, T can be a single value or a numpy.array of values.ĬtKeq = Ct * numpy.exp(DeltaS/R - DeltaH/(R*T))į = (1 + CtKeq - numpy.sqrt(1 + 2*CtKeq)) / CtKeq The appropriate value for the optional gas constant parameter. Temperature, entropy of annealing, and enthalpy of annealing.ĭefault units are mole, calorie, kelvin. Of two complementary ssDNA oligos, as a function of total , Returns the fraction of dsDNA in a solution containing equal concentrations Wrapper function for making a simple plot using matplotlib.pyplotĮmpty class definition - works like a struct in C or Matlab.ĭef DnaFraction(Ct, T, DeltaS, DeltaH, R=1.987): # v1.3 changed format of output to match actual LabView VI outputĭef quickplot(xvector, yvector, title, xlabel, ylabel): # v1.2 including option for forced cooling instead of passive cooling # v1.1 including forced heating and option to plot melting curve at end It differs slightly from the Matlab writeup, which was back when forced heating and cooling didn't exist and there was only passive cooling.Īlso, now it optionally plots the melting curve (in addition to fluorescence signal vs. This code models forced heating followed by either forced or passive cooling. Should I write a version that waits until the end and plots everything all at once? Has the same issue of plots appearing sequentially and the script not proceeding until the plot window is dismissed. ![]() ![]() (These packages are already installed on the lab computers.) ![]() In addition to Python, you will need to have installed the packages numpy, scipy, and matplotlib. Hi! I work, even though there's no writeup!įor now, you can copy and run the Python script, and follow along with the explanatory writeup from the Matlab version while it runs. ![]()
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