Coarse-grained

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Definition

A coarse-grained description or model does not take into account every detail but rather averages it out. [1] Unlike fine-grained models, a coarse-grained model will not include details at the atomic-level scale. [2] "Coarse-graining" arises from the idea of using simplified descriptions by reducing large numbers of degrees of freedom into a few.

Examples

In molecular dynamics of proteins within cells, protein-protein interactions occur on the timescale of microseconds to milliseconds and involve much greater length-scales than atomic-level simulations. The number of degrees of freedom is at least one order of magnitude and the timescale four to six orders of magnitude higher then all-atom simulations. [3] Thus, it is advantageous to use coarse-grained models in order to simulate larger systems. However, the difficulty of achieving accurate simulations increases as more and more specific interactions must be taken into account with a reduced number of degrees of freedom. In elastic network models, the proteins are simulated by a network of beads. One or more beads correspond to one amino acid and each bead is said to be connected to other beads by elastic springs. The figure below provides an example of the complexity of these elastic network models.

The figure represents bead models, the number of parameters that are used, which methods are used to solve these models, and some applications.

References

[1] R. Jones, "Soft Condensed Matter," Oxford University Press Inc., New York (2002)

[2] http://en.wikipedia.org/wiki/Granularity

[3] Coarse-grained models for proteins. Tozzini, V. Current opinion in structural biology 2005, 15:144-150.