How many variables do we need to describe macromolecular motion? The answer depends on the time and length scale of interest.
By analyzing the geometry of the space defined by long molecular dynamics trajectories of
macromolecular systems, we find that different regions of the configurational space have
different local intrinsic dimension
and local spatial scale.
When this local heterogeneity is taken into account, it is possible to define
diffusion maps that yield
global reaction coordinates for the system and associated
low–dimensional nonlinear projections of the configurational space, to describe the
slowest motions. This low–dimensional representation of the system on the long timescale
is able to accurately reproduce certain statistics of the dynamics, such as reaction rates
between semi–stable configurations. The methods proposed hold promise for larger and
more complex molecules.
More details can be found in the following articles:
Rohrdanz, M.A., Zheng, W., Maggioni, M. and Clementi, C.
Journal of Chemical Physics, 134(12), 124116 (2011)
Zheng, W., Rohrdanz, M.A., Maggioni, M. and Clementi, C.
Journal of Chemical Physics 134(14), 144108 (2011)
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