PHYS521. Biological Physics.

Midterm Exam #1
October 7, 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 Suppose that you purify a viral DNA sample consisting of double-stranded DNA molecules of length 50000 base pairs suspended in salt solution. Using light scattering, you find that each molecule is a blob of diameter 2 m. Your lab partner prepares a DNA sample, in the same buffer solution, from some other organism; her DNA molecules are hundred times longer. How big are the blobs in her sample? Solution: The size of the blob is proportional to a square root of N, the number of monomers. If N is increased 100 times without changing any other conditions, the size of the blob increases 10 times. The answer is 20 m. Problem 2 Consider a random walk in which, at each time step, the particle has a 50% chance of moving a distance d + a to the right or a distance d a to the left (assume d > a). After a large number of steps N, what is the mean position? What is the variance of this position? Solution: The total displacement X is a sum of displacements on each step: X = x1 + x 2 + x 3 + + x N Each xi is a random variable that takes a positive value of d + a with probability 50%, or a negative value of a d with 50% probability. All xi have the same properties with <x> = a and <(x-<x>)2> = <(x-a)2>= d 2. Therefore <X> = N<x> = Na Next we get <(X Na)2> = N <(x-<x>)2> = N d 2 And so var[ X ] = d N Problem 3 (a) Suppose that a one-dimensional random walker takes steps of length L = 1 m, but sometimes it takes no step at all. Thus, suppose that the probabilities for the three kinds of transitions are P-L = 1/3, P0 = 1/3, and P+L = 1/3. Find the mean and the variance of the displacement after N steps.

(b) This time, repeat with P-L = 1/3, P0 = 1/6, and P+L =1/2. What is the big qualitative difference between the cases (a) and (b)? Solution: (a) One can represent the total displacement as a sum of elementary displacements X = x1 + x2 + x3 + xN In this section <x> = 0, <(x - <x>)2> = <x2> = (2/3)L2. Using the fact that all xi are independent, we get in the usual manner <X> = 0 <X 2> = (2N/3)L2 2N var[ X ] = L 3 (b) The difference between this and previous sections is that the average value of elementary displacement is nonzero. Here <x> = L/6, and L L L L ( x x ) 2 = ( x ) 2 = P L ( L ) 2 + P0 (0 ) 2 + P+ L ( L ) 2 = 6 6 6 6 1 49 1 1 1 25 2 29 2 = + + L L = 36 3 36 6 36 2 36 Therefore X = NL 6 29 N 0.9 L N 6

var[ X ] = L

Problem 4 (a) Suppose that a membrane consists of two types of lipids, A and B. The A-lipids assemble in large patches that make up a fraction f of the total membrane area (the rest of the area is composed of B lipids). Molecule X has a permeability PA and PB through A and B respectively. Find the expression for the permeability PAB of the composite membrane. (b) Two membranes A and B have permeabilities PA and PB, respectively. They are joined together to form a single, two-layered membrane. Derive an expression for the permeability of the two-layer membrane PAB , in terms of PA and PB.

Solution: (a) The jump of the concentration is the same on the patches of A and B lipid membranes. The total flux is the sum of the fluxes through the A and B I = (PA f + P B (1 f ) )Ac from this expression we can immediately find P = PA f + P B (1 f )

(b) Here the membranes are in series, so the current through both of them is the same. The concentration jump on each membrane is smaller than the total jump, which is equal to the sum of the two. We have j = PA c A = PB cB c A + cB = c Solving for j and a function of c, we find PP j = A B c PA + PB Thus PP P= A B PA + PB