Paper Citing NAMD - Abstract
Castro-Roman, Francisco
Dynamic structure of lipid membranes: Lamellar diffraction in concert with molecular dynamics simulations
ADVANCED SUMMER SCHOOL IN PHYSICS 2007: FRONTIERS IN CONTEMPORARY PHYSICS, 960:107-112, 2007
Biological cells have a barrier that separates their content from the environment and regulates the transport of molecules and signals into and out of the cells. The structural basis of this envelope, known as the cell membrane, consists of a double layer of phospholipids of similar to 50 angstrom of thickness. These membranes, which are also present in the organelles as their barriers, are fluid and show a rapid lateral diffusion of its components, i.e. lipids, cholesterol and proteins. In the direction of the bilayer normal, on the other hand, the atoms are inherently delocalized because of the thermal motion they experience. Atom distributions along the bilayer normal are rather wide (similar to 5 to 10 angstrom). Due to these thermal fluctuations, x-ray and neutron diffraction experiments are able to provide structural information only in the direction of the bilayer normal (1D structure information). On the other hand, Molecular Dynamics (MD) simulations produce dynamic and structural information inherently in three dimensions (3D). However, the precision of MD simulations is uncertain in many cases. A possible way to overcome the limitations of each of these techniques is to combine them to obtain 3D dynamic membrane structures, validated experimentally. We will present and discuss the results of using this strategy.
