Coarse-Grained Molecular Dynamics
Problem of Scale
One of the main unresolved problems in biological science is the time-scale and length-scale gap between computational and experimental methods of studying biological systems. Chemical and mechanical processes on an atomic level form the basis of all phenomena in living systems. The experimental non-invasive observation of such dynamic processes would be greatly beneficial for understanding how life works; however, usually experimental techniques do not achieve a resolution better than ms-&mus in time and a minimum of 100 nm in length. On the other hand, there are the theoretical and computational methods, in particular molecular modeling, that enable the description of biological systems with all-atom detail; however up to now these approaches have been practically limited to simulation times and system sizes less than 100 ns and 10 nm, respectively. A possible way to extend molecular modeling and bridge it with experimental techniques is to do coarse-graining: to represent a system by a reduced (in comparison with an all-atom description) number of degrees of freedom. Due to the reduction in the degrees of freedom and elimination of fine interaction details, the simulation of a coarse-grained (CG) system requires less resources and goes faster than for the same system in all-atom representation. As a result, an increase of orders of magnitude in the simulated time and length scales can be achieved.
Residue-Based Coarse Graining: a Coarse-Grained Lipid-Protein Model
Shape-Based Coarse Graining: an Approach to Model Large Macromolecular Assemblies
Publications
Coarse grained protein-lipid model with application to lipoprotein particles. Amy Y. Shih, Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten. Journal of Physical Chemistry B, 110:3674-3684, 2006.
The role of molecular modeling in bionanotechnology. Deyu Lu, Aleksei Aksimentiev, Amy Y. Shih, Eduardo Cruz-Chu, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Physical Biology, 3:S40-S53, 2006.
Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations. Amy Y. Shih, Peter L. Freddolino, Anton Arkhipov, and Klaus Schulten. Journal of Structural Biology, 157:579-592, 2007.
Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum. Anton Arkhipov, Peter L. Freddolino, Katsumi Imada, Keiichi Namba, and Klaus Schulten. Biophysical Journal, 91:4589-4597, 2006.
Stability and dynamics of virus capsids described by coarse-grained modeling. Anton Arkhipov, Peter L. Freddolino, and Klaus Schulten. Structure, 14:1767-1777, 2006.
Investigators
Collaborators
- Siewert J. Marrink - University of Groningen (The Netherlands)
Related TCB Group Projects
Page created and maintained by Anton Arkhipov.