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One way to mathematically model the flexibility of a polymer is to consider it to be a series of rigid segments that are freely jointed together. This means that each segment is free to angle and rotate relative to its adjacent neighboring segments. The length of each segment is the persistence length of the polymer. In reality the molecule may not be a chain of freely jointed rigid segments, but this model often works well to predict properties of polymers that result from flexibility. In this way we can mathematically describe the flexibility of DNA and other biopolymers without the need to measure flexibility directly. The freely jointed chain model allows us to calculate the root mean square end-to-end distance. Each segment is treated as a vector pointing to the next segment. The sum of all of these vectors is a single vector pointing from one end of the chain to the other. Figure 10-18 illustrates this. We can calculate this single end-to-end vector for all possible conformations of the freely jointed chain. We would like to get some average value for this end-to-end vector, as a way of characterizing the set of all possible conformations of the chain. If we consider all possible conformations, the set of all possible end-to-end vectors will include vectors in all different directions. Adding up these vectors will result in some of the vectors canceling each other out (because they point in opposite directions). The average vector will then be zero. We solve this problem by squaring the end-to-end vector. Multiplying vectors together converts them to scalars, so each squared vector is a scalar. We then sum all of the squared end-to-end vectors and take the mean (average) of the squares. The square root converts the units from distance squared back into a simple distance. This root mean square (RMS) end-to-end distance gives us one measure of the compactness of the polymer. It turns out that for a freely jointed chain of N segments, each of length L, the RMS distance is equal to the square root of the number of segments times the length of each segment.
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8. Click OK to close the calibration dialog, and then click OK again to close the
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