In order to refine homology models and to simulate models or crystal structures in solution we use molecular dynamics simulations. Molecular dynamics (MD) is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics, giving a view of the motion of the atoms. This picture illustrates how the crystral structure of the TLR3 ectodomain relaxes to a more open conformation in simulation. Changes in diameter were recently shown to be relevant for the initiation of signalling in TLR9 (Latz et al Nature Immunology 2007). Read more.