Problems chemists present to us.

I) (10) Describe the problem the chemist presented to us. In particular, describe the shape of the molecular motor and the main questions
we were asked to answer.
II) (10) Describe the model, a Markov process, for the flipper motion
of a single molecule.
III) (10) Explain how the model can be used to predict the concentrations of molecules in the different states. Explain how this can be
used to validate the model.
IV) (10) Explain the dynamical situation at equilibrium.
V) (10) Describe a simulation of the flipper motion of a single molecule. Explain how the output of a simulation, given by the second
program, of a single molecule relates to the actual motion of the flipper. Include several examples.
VI) (10) What is the problem with the simulations and how can we
solve it? Explain why we have to use statistical methods. Explain with
data/examples: Present the results of the simulations. Explain what
is the time scale to get reasonable results. (The results are tables with
estimated rotational speed for different values of T).
VII) (10) Give the final table of rotational speeds dependent on the
light intensity. Use groups of molecules and simulations of long enough
time. Explain that the size of the groups and the time you use are
suffciently large. What is the influence of the simulation time?
VIII) (10) Give a formula for the speed in terms of the probability
matrix and the equilibrium concentrations. Compare with the results
of the table of question VII).
IX) (10) Discuss the qualitative behavior of the rotation speed in
terms of the light intensity. When is the speed optimal? Hint: give two