What results or insights were obtained using molecular modelling that could not be obtained using current experimental methods

1)With
regard to classical Molecular Dynamics Simulations, describe

a.the
main energy functions employed to model interactions between atoms and

b.the
general simulation method for generating molecular motions (~600 words, 10 marks)

2)Is
the classical MD simulation method described in the Weeks 2 and 3 lectures suitable
for studying chemical reactions at the atomic scale? Why or why not? If not, very briefly(in 1-2 sentences) describe
an alternative method that could model chemical reactions. (~200 words, 5 marks)

3)Briefly
describe ONE recent application (published after 2011) of molecular dynamics
simulation in biology that was not covered in lectures. In particular, answer
the following as appropriate:

a.Summarise
the aims, methods and findings of the study

b.What
results or insights were obtained using molecular modelling that could not be obtained using current
experimental methods? Alternatively, how could the modelling results be tested
experimentally?

c.How
would you improve the model(s) employed in the study?

Hint:
Use “Web of Science”, Scopus and other literature search databases and search
for keywords such as “proteins and molecular dynamics”. Remember to reference
your source/s. (~600 words, 15 marks)