Coarse-grained simulation of cellulose Iβ with application to long fibrils
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Cellulose microfibrils are recalcitrant toward dissolution, thus it is difficult to extract and characterize them without modifying their native state. To study the molecular level behavior of microfibrils over 100 sugar residues, we construct a coarse-grained model of solvated cellulose Iβ microfibril using one bead per sugar residue. We derive the coarse-grained force field from atomistic simulation of a 36 chain, 40-residue microfibril by requiring consistency between the chain configuration, intermolecular packing and hydrogen bonding of the two levels of modeling. Coarse-grained force sites are placed at the geometric center of each glucose ring. Intermolecular van der Waals and hydrogen bonding interactions are added sequentially until the microfibril crystal structure in the atomistic simulation is achieved. This requires hydrogen bond potentials for pairs that hydrogen bond in cellulose Iβ, as well as those that can hydrogen bond in other structures, but not in cellulose Iβ. Microfibrils longer than 100 nm form kinks along their longitudinal direction, with an average periodicity of 70 nm. The behavior of kinked regions is similar with a bending angle of approximately 20°. These kinked regions might be linked to observations of periodic disorder from small angle neutron scattering and acid hydrolysis.
KeywordsCoarse-grained simulation Cellulose Iβ Force field Full-length microfibril
We thank Dr. Zhen Zhao and Dr. Linghao Zhong for providing the atomistic simulation coordinates of the solvated 6 × 6×40 microfibril. This work is supported as part of The Center for Lignocellulose Structure and Formation, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001090. The simulations were performed on high performance computing systems supported and maintained by the Penn State Research Computing and Cyberinfrastructure (RCC).
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