Due on 11/15/2024

Please review lecture notes and study the relevant chapters of the textbook.
Please clearly explain your answers and the steps by which you arrive your
answers.

1. (15 points) The ideal gas constant R is 8.315 J/mol/K and an estimation of
thermal energy is R times T, where T is temperature. At 300 K, please
calculate the value of thermal energy in the unit of kcal/mol. 1 cal=4.18 J.
Please describe what is a hydrogen bond. The binding energy of forming a
hydrogen bond is 5-10 kcal/mol. Please determine how many times of
thermal energy that a hydrogen bond corresponds to.

2. (20 points) You were given a pair of dices, each has 6 faces and each face
was inscribed an integer from 1 to 6. The dices can be considered fair. You
were asked to through the two dices once and calculate the sum of the two
numbers of the up faces. Please determine the probabilities of obtaining 2,
10, and 18.

3. (30 points) Please consider the formula for computing the population mean
and variance. Z Z <latexit sha1_base64="ieQmiwWEbt6RlywnjtV1S07JRGo=">AAACJHicbVDLSgMxFM34rPVVdekmWIR2YZkpvkAKRTcuK9gHdOqQSdM2NMkMSUamlH6MG3/FjQsfuHDjt5hOu6itBy4czrmXe+/xQ0aVtu1va2l5ZXVtPbWR3tza3tnN7O3XVBBJTKo4YIFs+EgRRgWpaqoZaYSSIO4zUvf7N2O//kikooG414OQtDjqCtqhGGkjeZkrV9EuR15cchkSXUZgLj5xeeTF+YcidGWilVwqNGzHYS7Oz9heJmsX7ARwkThTkgVTVLzMh9sOcMSJ0JghpZqOHerWEElNMSOjtBspEiLcR13SNFQgTlRrmDw5gsdGacNOIE2ZaxJ1dmKIuFID7ptOjnRPzXtj8T+vGenOZWtIRRhpIvBkUSdiUAdwnBhsU0mwZgNDEJbU3ApxD0mEtck1bUJw5l9eJLViwTkvnN2dZsvX0zhS4BAcgRxwwAUog1tQAVWAwRN4AW/g3Xq2Xq1P62vSumRNZw7AH1g/v+Ybo7c=</latexit>

µx = hxi = dxp(x)x x = h(x µx ) 2 i = dxp(x)(x µx ) 2

<latexit sha1_base64="ivhbiixjB0gIIz85JRaXDQKznnM=">AAACDXicbZDLSsNAFIYn9VbrLerSzWAV6qYkIuimUHTjsoK9QBPCZDJth04mYWYiKaEv4MZXceNCEbfu3fk2TtMstPWHgY//nMOc8/sxo1JZ1rdRWlldW98ob1a2tnd298z9g46MEoFJG0csEj0fScIoJ21FFSO9WBAU+ox0/fHNrN59IELSiN+rSUzcEA05HVCMlLY888QJEy9tOAzxISMwhY7IqeFQrmCQxrX0LPXMqlW3csFlsAuogkItz/xygggnIeEKMyRl37Zi5WZIKIoZmVacRJIY4TEakr5GjkIi3Sy/ZgpPtRPAQST00zvk7u+JDIVSTkJfd4ZIjeRibWb+V+snanDlZpTHiSIczz8aJAyqCM6igQEVBCs20YCwoHpXiEdIIKx0gBUdgr148jJ0zuu2VbfvLqrN6yKOMjgCx6AGbHAJmuAWtEAbYPAInsEreDOejBfj3fiYt5aMYuYQ/JHx+QO7n5tS</latexit>

(a) Please show that the variance is the difference between the average of
squared x and the square of the averaged x.
(b) Please show the following result when the two random variables are
independent, the variance of their difference is: x1 x2 = x1 + x2
<latexit sha1_base64="x+CrRyst+M1QsY1JF4YoWsch0Vk=">AAACE3icbVDLSsNAFJ3UV62vqEs3g0UQxZIUXxuh6MZlBfuANoTJdNIOnUzCzERaQv7Bjb/ixoUibt2482+ctgFr64ELZ865l7n3eBGjUlnWt5FbWFxaXsmvFtbWNza3zO2dugxjgUkNhywUTQ9JwignNUUVI81IEBR4jDS8/s3IbzwQIWnI79UwIk6Aupz6FCOlJdc8akvaDZCbDFz7ZOCW06spIT3+fZRT1yxaJWsMOE/sjBRBhqprfrU7IY4DwhVmSMqWbUXKSZBQFDOSFtqxJBHCfdQlLU05Coh0kvFNKTzQSgf6odDFFRyr0xMJCqQcBp7uDJDqyVlvJP7ntWLlXzoJ5VGsCMeTj/yYQRXCUUCwQwXBig01QVhQvSvEPSQQVjrGgg7Bnj15ntTLJfu8dHZ3WqxcZ3HkwR7YB4fABhegAm5BFdQABo/gGbyCN+PJeDHejY9Ja87IZnbBHxifPyrrnlw=</latexit>

(c) If x1 = x2 = , please evaluate the population mean and variance of

<latexit sha1_base64="wJCy9+YbU4E6DhcrjTl0XqhJ9i0=">AAACCXicbVDLSgMxFL1TX7W+Rl26CRbBVZkpvjZC0Y3LCvYB7TBk0rQNzWSGJCOWoVs3/oobF4q49Q/c+Tem7eCj9UDg3HPu5eaeIOZMacf5tHILi0vLK/nVwtr6xuaWvb1TV1EiCa2RiEeyGWBFORO0ppnmtBlLisOA00YwuBz7jVsqFYvEjR7G1AtxT7AuI1gbybdRW7FeiP30zndH5z9F+buwi07JmQDNEzcjRchQ9e2PdiciSUiFJhwr1XKdWHsplpoRTkeFdqJojMkA92jLUIFDqrx0cskIHRilg7qRNE9oNFF/T6Q4VGoYBqYzxLqvZr2x+J/XSnT3zEuZiBNNBZku6iYc6QiNY0EdJinRfGgIJpKZvyLSxxITbcIrmBDc2ZPnSb1cck9Kx9dHxcpFFkce9mAfDsGFU6jAFVShBgTu4RGe4cV6sJ6sV+tt2pqzspld+APr/QvfBpp1</latexit>

1
<latexit sha1_base64="DeEe7GQhIc08Aww4/frFx+rCwaE=">AAACBXicbVDLSsNAFJ3UV62vqEtdDBahIpSk+NoIRTcuK9gHNCFMppN26GQSZibSErJx46+4caGIW//BnX/jtM1CqwcuHM65l3vv8WNGpbKsL6OwsLi0vFJcLa2tb2xumds7LRklApMmjlgkOj6ShFFOmooqRjqxICj0GWn7w+uJ374nQtKI36lxTNwQ9TkNKEZKS5657/hIpKPs0gkEwqmdpbWsMvLs45FXO/LMslW1poB/iZ2TMsjR8MxPpxfhJCRcYYak7NpWrNwUCUUxI1nJSSSJER6iPulqylFIpJtOv8jgoVZ6MIiELq7gVP05kaJQynHo684QqYGc9ybif143UcGFm1IeJ4pwPFsUJAyqCE4igT0qCFZsrAnCgupbIR4gHYfSwZV0CPb8y39Jq1a1z6qntyfl+lUeRxHsgQNQATY4B3VwAxqgCTB4AE/gBbwaj8az8Wa8z1oLRj6zC37B+PgGcUGX4w==</latexit>

x̄ = (x1 + x2 )
2

4. (20 points) The mean of a random variable x1 is 5.0 and its standard
deviation is 2.0. The mean of a random variable x2 is 8.0 and its standard
deviation is also 2.0. Please determine the mean and standard deviation of
r=x1/x2.

5. (25 points) The probability of having sequence a and b aligned for an

evolutionary model and a random model is qab and papb, respectively. The
two quantities are related as qab= papbexp(sab), where sab is the substitution
matrix component. Using the attached substitution matrix to calculate the
odds-ratio of the evolutionary and random model of the following sequence
pairs: (a) ape and ade (b) cca and ywc.