Dynamic simulation of lipid bilayers

What is a biological membrane?
Why are such molecules simulated?
Views of a membrane simulation
What are the limits of the model?

Why are we doing molecular simulations?

General reasons for simulations in chemistry are the following:

• Study of atomistic details rarely available with measurements

• Avoiding experimental difficulties. One may think of experiments even not realizable. Computer models are able to deal with immense pressure or temperature which we will never receive in our laboratories.

• Comparison of computed model results with measured experiments. This is a very usefull scientific control and it joins theory with practice.

For membrane simulations, particularly the first and the third point are worth to be mentioned.

Membrane Simulations

Membranes are very expendable in molecular simulations. This is due to the very large amount of molecules interacting with each other. Not all that there are so many molecules, the species in and out of the membrane may be very different.

• Main problem:
  The amount of particles is so large that we can never handle them even with the best computers!
• Solution:
  Only a small piece of the membrane is simulated.

* Building a membrane-model for simulation:



1) Set up membrane molecules. 2) Surround them with water and salts.

* Movies of a membrane simulation:

Membrane at 25 centigrade	Membrane at 125 centigrade
Click on the image to select the movie and then click once more to start it

Limits of the simulation

• Number of particles:
  Increases the number of particles (Number of atoms) appr. 25'000, the simulation will be hard to compute. It will need months or years to calculate only a view millionth of a second (=nanoseconds).
  For a complete spherical membrane (vesicle) this unfortunately is true.
  

• Classical (molecular) dynamics is chemically spoken non-reactive:
  The enlisted molecules will never modify.

• Conclusion:
  The limits are well known: we mainly concentrate on the mobility of the molecules. The membrane can be compared with either a crystall or a fluid depending on temperature.

Membranes should never be considered as rigid blocks (have a look at the movies).

Go back to the main page.
Go to the van Gunsteren's group home page.
Go to the NMR group's home page.

Alexandre Bonvin und Lukas Schuler, 29-Sept-97