UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309, USA.
Biomacromolecules. 2012 Sep 10;13(9):2634-44. doi: 10.1021/bm300460f. Epub 2012 Aug 31.
A molecular level understanding of the structure, dynamics and mechanics of cellulose fibers can aid in understanding the recalcitrance of biomass to hydrolysis in cellulosic biofuel production. Here, a residue-scale REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-grained force field was derived from all-atom molecular dynamics (MD) simulations of the crystalline Iβ cellulose fibril. REACH maps the atomistic covariance matrix onto coarse-grained elastic force constants. The REACH force field was found to reproduce the positional fluctuations and low-frequency vibrational spectra from the all-atom model, allowing elastic properties of the cellulose fibril to be characterized using the coarse-grained force field with a speedup of >20 relative to atomistic MD on systems of the same size. The calculated longitudinal/transversal Young's modulus and the velocity of sound are in agreement with experiment. The persistence length of a 36-chain cellulose microcrystal was estimated to be ~380 μm. Finally, the normal-mode analysis with the REACH force field suggests that intrinsic dynamics might facilitate the deconstruction of the cellulose fibril from the hydrophobic surface.
从纤维素纤维的结构、动力学和力学的分子水平理解，可以帮助我们理解生物质在纤维素生物燃料生产中对水解的抗性。在这里，从晶态 Iβ纤维素原纤维的全原子分子动力学 (MD) 模拟中，推导出了一种残基尺度的 REACH（通过协方差 Hessian 的真实扩展算法）粗粒化力场。REACH 将原子协方差矩阵映射到粗粒化弹性力常数上。发现 REACH 力场再现了全原子模型的位置波动和低频振动谱，从而可以使用粗粒化力场来表征纤维素原纤维的弹性性质，与相同大小的原子 MD 相比，速度提高了>20。计算得到的纵向/横向杨氏模量和声速与实验相符。36 链纤维素微晶的持久长度估计约为 380 μm。最后，REACH 力场的正则模态分析表明，固有动力学可能有助于纤维素原纤维从疏水面解构成。
