Homeworks are due at the beginning of class one week after
they are
posted. Solutions will be posted two days after the homeworks
are
submitted, and homeworks will be returned a week after they are
submitted.
Late
policy: NO late homeworks will be accepted (late means anytime after
class starts the day the homework is due) unless you have a
mindblowingly good excuse - this means a note from someone like a
doctor or a Dean. Rob does not grant extensions.
Collaboration
policy: you may discuss the homework with others, but your explanations
and derivations must be your own. Your logic and the significance of
your results should also be explained.
HW1
(due
1/14),
solutions
Reading
for referee report
ATP pdb file, B-DNA pdb file,
phosphatidylcholine
pdb file, GFP
pdb file, chlorophyll
pdb file
LB and
minimal media recipes, from the APh 162 website
Papers:
van
de Meene A.M.L., Hohmann-Marriott, M.F., Vermaas W.F.J., and Robertson
R.W. (2006) The three-dimensional structure of the
cyanobacterium
Synechocystis
sp. PCC 6803. Arch.
Microbiol 184: 259-270.
Mitra
K., Belandia I.U., Taguchi T., Warren G., and Engelman D.M. (2004)
Modulation of the bilayer thickness of exoytic pathway membranes by
membrane proteins rather than cholesterol. PNAS 101 (12): 4083-4088.
- Table 1 of this paper provides the protein:lipid mass ratios in a
number of different biologically interesting membranes.
Takamori et
al. (2006) Molecular anatomy of a trafficking organelle. Cell
127: 831-846. - Figure 4 of this paper illustrates the true
crowded nature of biological membranes.
HW2
(due
1/21),
solutions
Reading for referee report:
preface
to Cell Biology by the Numbers, vignettes
HW3
(due 1/28),
solutions
The data you
need for problem 1.
HW4
(due 2/12
at 5 pm),
solutions
Please note that the Sourjik+Berg and Bray papers referenced in problem
3 are posted
on the
syllabus page under Lecture 5.
Sample
simulation code to help you with the last problem.
The paper referenced in
problem
4:
Rosenfeld
N., Young J.W., Alon U., Swain P.S., and Elowtiz M.B. (2005)
Gene
regulation at the single-cell level. Science, 307: 1962-1965.
HW5
(due 2/26 at 5 pm),
solutions
Paper
for the last problem: Elowitz M.B. and Leibler S. (2000) A synthetic
oscillatory network of transcriptional regulators. Nature 403: 335-338.
The corrected figure
for the last problem.
Code
to help you solve ODE's and plot figures in Matlab.
HW6 (due 3/5 at 5 pm)
