Multiscale Approach to Biomolecular Interactions: From Molecular Dynamics to Brownian Dynamics Simulation of Chromatin Components
A major challenge in the simulation of
biomolecular interactions is to find ways of transferring the information
obtained from atomic-detail molecular dynamics (MD) simulations, which can be
performed on time-scales up to ~10-9-10-7 s and for studying
conformational changes on the ~10-10-10-9 m
length scale, to models that can be used to understand biological processes
occurring on longer length-and/or time-scales (e.g. 10-9-10-6 m and
up to 10-3-1
s). This strategy is of particular importance for understanding the dynamic
organization of the genome in the cell nucleus, where it is known that
phenomena occurring on the local atomic scale (e.g. protein and DNA
modifications) can influence global genome organization.
To access long spatial and temporal
scales, we will use MD simulations to derive simplified parameterized
descriptions of the dynamics and interactions in chromatin, which can
then be
used in ‘higher order’ models, in particular in Brownian Dynamics (BD).
The multiscale simulation techniques developed will allow a
transformation from the all-atom to a more coarse-grained
representation, thus
permitting access to the much longer time and length scales necessary.
