(731a) Restraint-Free Coarse-Grain Modeling of a Crystalline Cellulose Fibril Based on Force Matching
- Conference: AIChE Annual Meeting
- Year: 2014
- Proceeding: 2014 AIChE Annual Meeting
- Group: Computational Molecular Science and Engineering Forum
- Time: Thursday, November 20, 2014 - 3:15pm-3:35pm
As a major component of ligno-cellulosic biomass, crystalline cellulose fibrils are resistant to hydrolysis (biomass recalcitrance) and this is a bottle neck for any process that hopes to decompose cellulosic feedstocks into glucose that can later be converted to bio-fuels. To design efficient processes to degrade the biomass, it is important to understand the molecular forces that bind the cellulosic units. Coarse-grained simulations are useful to explore the residue scale motions in large molecules for long periods of time. The multi-scale coarse-graining (MS-CG) method based on force matching is used to derive effective coarse-grained forces from all-atom molecular dynamics trajectories to model a crystalline cellulose fibril. Unlike for many coarse-graining methods, the force matching method systematically optimizes coarse-grained forces from all-atom simulation trajectories without fitting them to a predetermined analytical function. Two restraint-free coarse-grained mapping schemes with two and eight unique coarse-grain bead types are evaluated and tested against the same all-atom reference system. For the performance analysis of coarse-grained models such properties as crystalline lattice parameters, radial distribution functions, and root mean square fluctuations and displacements are compared. The choice of coarse-grained mapping scheme significantly influences the performance of the coarse-grained molecular dynamics simulation in predicting the properties computed for the reference all-atom crystalline cellulose. A rationale strategy for designing two-type and eight-type coarse-grained mapping schemes in a crystalline cellulose fibril is developed and presented. Using this approach, both CG mapping schemes predicted the sheet structure of a cellulose fibril well, while only eight-type CG model is capable to accurately represent the intersheet ordering and therefore a complete crystalline structure for a crystalline cellulose fibril.