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PHYS521. Biological Physics.

Midterm Exam #2
November 18, 2010 Each problem is graded out of 10 points. It is enough to solve two problems to get full credit for the exam. If you solve more problems, you will have extra credit. Please give understandable explanations. No partial credit will be given for wrong results without explanations. Problem 1 A muscle fiber is placed in an apparatus that periodically stretches it. That is, the fibers length is forced to change in time as x(t ) x0 A sin(t ) . The force exerted back on the apparatus by the fiber is then also periodic function of time. For small amplitude A, it is a wave with a phase shift f (t ) [ f 0 B sin(t )] . Here A and B are positive constants. If the phase shift is greater than zero, we say that the displacement lags the force. (a. 5 points) Work out the rate at which the apparatus does work on the fiber (i.e., the power). Find the average of this rate over one full cycle. (b. 5 points) The figure shows two curves. One gives the phase shift for a living muscle fiber; the other curve is for a dead fiber. Which is which? Which unusual feature of one of the curves tells you the answer?

Problem 2 Suppose a certain protein is able to slide along DNA: For example, imagine that there is a hole in the protein, and that DNA threads through the hole. Such a picture could model the idea that a regulatory protein moves along the DNA of a bacterium without leaving it, searching for a specific site.

The protein diffuses along the DNA with a one-dimensional diffusion constant D = 10 nm2/ms. (a. 5 points) Suppose that you can follow the position of the protein along the DNA but that your resolution is only to within one basepair (0.34 nm). What is the probability that after a time t = 50ms the protein is exactly 100 basepairs (to within your experimental resolution) from where it started? (b. 5 points) What is the probability that after a time interval t the protein has diffused a distance greater than 2 basepairs from its starting point. Assume that DNA is infinite in both directions. Problem 3 This problem considers the same protein on a DNA as the previous Problem 2. Suppose that the protein can also bind to DNA. When the protein is unbound, it diffuses along the DNA with a diffusion coefficient D. When the protein is bound, it is stationary. The difference between the energy of the bound and unbound states is E Eunbound Ebound . The protein and DNA are inside an organism at temperature T. Letting x denote the distance along the DNA, find the mean square displacement of the protein x 2 as a function of time t. (You do not have to calculate the numbers in this problem.) Hint: find the time the protein spends in the unbound state and calculate how far it will diffuse during this time. Problem 4 Two weights are connected by a thread going over a weightless pulley as shown in the Figure. The weight with mass M is in a viscous liquid. The weight with mass m is in the air. If the weights are released, the one with mass M goes down. The volume of the larger weight is V and the density of the liquid is . The friction coefficient of the larger weight is . Assume that the motion happens with low Reynolds number and find the speed of the larger weight (2 points). Find the total kinetic energy (2 point). Suppose the larger weight goes down by a distance h. Find the amount of heat generated by the friction (6 points).

Problem 5 A student makes a bet with a professor. The professor can choose three secret positive, two-digit numbers X, Y and Z (e.g. 12, 37, 81). The student then gives the professor three numbers a, b and c of his own choice. The professor should compute the sum

S aX bY cZ ,
and tell it to the student. The student claims that from knowing just one number S he can find all three secret numbers X, Y and Z. If he wins, the professor takes him for a free lunch. If he fails, his grade for the class is going to be F. How can the student survive?

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