8.592HST.452J: Statistical Physics in Biology
Assignment # 1
Due: 2/14/05
Probability
1. Open Reading Frames: Assume that the nucleotides A, G, T, C occur with equal
probability (and independently) along a segment of DNA.
(a) From the genetic code calcula
8.592: Statistical Physics in Biology
Assignment # 2
Due: 2/28/05
Sequence Alignment
1. Number of gapped alignments: The following problem is taken from Chapter 2 of Durbin
et. al., which provides the needed background on sequence alignments.
(a) Show tha
8.592: Statistical Physics in Biology
Assignment # 3
Due: 3/7/05
Recursive Schemes
1. Fibonaccis Rabbits: Consider a generalization of Fibonaccis model for rabbit populations, in which some of the rabbits (whether young or adult) die in each generation, a
8.592: Statistical Physics in Biology
Assignment # 4
Due: 3/16/05
Coulomb Interactions
1. Flory Theory: The Coulomb energy of a ball of charge Q and dimension R in d spacial
dimensions scales as
Ec
Q2
.
Rd2
The proportionality coecient depends on the exa
8.592J: Statistical Physics in Biology
Assignment # 5
Due: 4/4/05
Protein Folding
1. Designed Random Energy Model (REM): Consider a protein model in which for a
given sequence and structure, the energy is randomly taken from the Gaussian probability
densi
8.592: Statistical Physics in Biology
Assignment # 6
Due: 4/11/05
Force-Extension Relations for Polymers
1. Linear polymers: Using optical tweezers, it is now possible to pull on the two ends of a
single molecule. (Actually the tweezers pull on latex ball
8.592: Statistical Physics in Biology
Assignment # 7
Due: 4/25/05
Drift, Diusion, and Dynamic Instability
1. Treadmilling Actin: Actin laments are long, asymmetric, polymers involved in a
variety of cellular functions. In some cases the laments are in a d
8.592: Statistical Physics in Biology
Assignment # 8
Due: 5/4/05
ProteinDNA Interactions
1. Weight matrices: You are given a set of binding sites for the E. Coli purine repressor,
P urR (see le purR sites.txt on the assignment page).
(a) Build a weight ma