Biomass Depolymerization projects

Molecular Mechanisms of the Enzymatic Decomposition of Cellulose Microfibrils

This project is developing mechanistic knowledge of elementary steps in the enzymatic decomposition of cellulosic materials. The team is modeling and simulating, in silico, the structural deformation of a cellulose microfibril by mechanical and thermophysical means; the cleavage of β-1,4-glycosidic bonds on the surfaces of a microfibril by cellulases; and the detachment of broken glucose chains from the microfibril into solution. Their effort will be joined with other UC Berkeley researchers who will employ complementary computational methodologies and stimulation strategies in analyzing the effects of ionic liquids (IL) on cellulosic materials.

project Highlights

2012 Highlights

This project has two complementary aspects: (1) analysis of how the reported cellulose solvents deconstruct the crystalline network in the material, and (2) elucidation of the physical parameters that limit the enzyme kinetics of cellulose decomposition. In the former, we have completed the study on the lithium chloride (LiCl) in N,N-dimethylacetamide (DMA) system that dissolves cellulose up to 10-15 wt %. We showed that the ionic species have preferential couplings with cellulose in DMA but not in water. Therefore, solvent-mediated interactions can be a useful knob for designing pretreatment solvent systems for softening biomass. This work has just been accepted for publication in the Journal of Physical Chemistry B.


In the second area, we have finished the development of a staggered lattice enzyme model (SLATE) to perform spatially resolved simulation of enzymatic cellulose decomposition. A key finding is that the activities of desorption and decomplexation for removing the jammed configurations of cellulases are essential to reach the optimal apparent rate of substrate conversion. Currently, we are writing a paper based on these findings. In the future, we will generalize this model to analyze the molecular origin of synergy between different enzymes in cellulose decomposition.

2011 Highlights

Chu’s lab developed a mechanistic understanding of in silico screening of pretreatment solvent to soften the recalcitrance of cellulose. They resolved the molecular driving forces provided by an ionic liquid, 1-Butyl-3-Methylimidazolim Chloride  (BmimCl), to deconstruct/dissolve crystalline cellulose. In addition, they characterized the interaction sites of BmimCl cations and anions with cellulose and connected the structure fluctuations of cellulase enzymes with a correlation in multiple sequence alignment, identifying useful mutation sites for protein engineering.

2010 Highlights

In 2010, the team developed atomic models of cellulose microfibrils and simulation protocols for characterizing the interaction network in cellulose. Chu’s lab found that intersheet interactions and small-scale hydrophobicity were essential causes of cellulose recalcitrance.  They developed simulation models for computing the free-energy profiles of cellulose deconstruction, and then, based on that information, analyzed the molecular forces provided by ionic liquid for dissolving cellulose. Chu’s group showed that cation-mediated interactions depend on the structures of cellulose, but anion-mediated interactions do not.



Published in 2012

Entropy of Cellulose Dissolution in Water and in the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride, Adam Gross, Alexis T. Bell, Jhih-Wei Chu, Physical Chemistry Chemical Physics, doi: 10.1039/C2CP40417F, March 27, 2012


Degree of Polymerization of Glucan Chains Shapes the Structure Fluctuations and Melting Thermodynamics of a Cellulose Microfibril, Rakwoo Chang, Adam Gross, and Jhih-Wei Chu, Journal of Physical Chemistry B 116, 8074–8083.


Preferential Interactions Between Lithium Chloride and Glucan Chains in N,N-Dimethylacetamide Drive Cellulose Dissolution, Adam Gross, Alexis T. Bell, and Jhih-Wei Chu, Journal of Physical Chemistry B (in press).

Published in 2011

The Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride, Adam Gross, Alexis Bell, Jhih-Wei Chu, Journal of Physical Chemistry, doi: 10.1021/jp202415v, September 28, 2011.


Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance, Hyung Min Cho, Adam Gross, Jhih-Wei Chu, Journal of the American Chemical Society, doi: 10.1021/ja2046155, July 28, 2011.


"Fluctuograms" Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution, Jordi Silvestre-Ryan, Yuchin Lin, Jhih-Wei Chu, PLOS Computational Biology, 7(3): e1002023. doi:10.1371/journal.pcbi.1002023, March 24, 2011.

Published in 2010

On the Molecular Origins of Biomass Recalcitrance: The Interaction Network and Solvation Structures of Cellulose Microfibrils, Adam Gross, Jhih-Wei Chu, The Journal of Physical Chemistry B, 114(42), pps. 13333-13341, Sept. 30, 2010.



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