%0 Journal Article %1 doi:10.1021/jp0721494 %A Liu, Pu %A Izvekov, Sergei %A Voth, Gregory. A. %D 2007 %J The Journal of Physical Chemistry B %K Glycans %N 39 %P 11566-11575 %R 10.1021/jp0721494 %T Multiscale Coarse-Graining of Monosaccharides %U http://pubs.acs.org/doi/abs/10.1021/jp0721494 %V 111 %X A systematic multiscale coarse-graining (MS-CG) algorithm is applied to build coarse-grained models for monosaccharides in aqueous solution. The methodology is demonstrated for the example of α-d-glucopyranose. The nonbonded interactions are directly derived from the force-matching approach, whereas the bonded interactions are obtained through Boltzmann statistical analyses of the underlying atomistic trajectory. The MS-CG model is shown to reproduce many structural and thermodynamic properties in the constant NPT ensemble. Although the model is derived at a single temperature, pressure, and concentration, it is shown to be reasonably transferable to other thermodynamic states. In this model, long-range interactions are effectively mapped into short-range forces with a moderate cutoff and are evaluated by table look-up. As a result, molecular dynamics employing the MS-CG model is ∼3 orders of magnitude more efficient than its atomistic counterpart. Consequently, the model is particularly suitable for simulating carbohydrate systems at large length and long time scales. Results for an α-(1→4)-d-glucan with 14 glucose units are also presented, demonstrating that the MS-CG algorithm is also applicable to the coarse-graining of other saccharide systems.

@article{doi:10.1021/jp0721494, abstract = { A systematic multiscale coarse-graining (MS-CG) algorithm is applied to build coarse-grained models for monosaccharides in aqueous solution. The methodology is demonstrated for the example of α-d-glucopyranose. The nonbonded interactions are directly derived from the force-matching approach, whereas the bonded interactions are obtained through Boltzmann statistical analyses of the underlying atomistic trajectory. The MS-CG model is shown to reproduce many structural and thermodynamic properties in the constant NPT ensemble. Although the model is derived at a single temperature, pressure, and concentration, it is shown to be reasonably transferable to other thermodynamic states. In this model, long-range interactions are effectively mapped into short-range forces with a moderate cutoff and are evaluated by table look-up. As a result, molecular dynamics employing the MS-CG model is ∼3 orders of magnitude more efficient than its atomistic counterpart. Consequently, the model is particularly suitable for simulating carbohydrate systems at large length and long time scales. Results for an α-(1→4)-d-glucan with 14 glucose units are also presented, demonstrating that the MS-CG algorithm is also applicable to the coarse-graining of other saccharide systems. }, added-at = {2012-04-23T12:57:18.000+0200}, author = {Liu, Pu and Izvekov, Sergei and Voth, Gregory. A.}, biburl = {https://www.bibsonomy.org/bibtex/2af194bddec98ab8c67ec387745c0aa33/claudia89}, description = {Multiscale Coarse-Graining of Monosaccharides - The Journal of Physical Chemistry B (ACS Publications)}, doi = {10.1021/jp0721494}, eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp0721494}, interhash = {762dd91b42be829671d3cc3c07faebe4}, intrahash = {af194bddec98ab8c67ec387745c0aa33}, journal = {The Journal of Physical Chemistry B}, keywords = {Glycans}, number = 39, pages = {11566-11575}, timestamp = {2012-04-26T11:57:34.000+0200}, title = {Multiscale Coarse-Graining of Monosaccharides}, url = {http://pubs.acs.org/doi/abs/10.1021/jp0721494}, volume = 111, year = 2007 }