Stochastic model of lignocellulosic material saccharification

PLoS Comput Biol. 2021 Sep 13;17(9):e1009262. doi: 10.1371/journal.pcbi.1009262. eCollection 2021 Sep.


The processing of agricultural wastes towards extraction of renewable resources is recently being considered as a promising alternative to conventional biofuel production. The degradation of agricultural residues is a complex chemical process that is currently time intensive and costly. Various pre-treatment methods are being investigated to determine the subsequent modification of the material and the main obstacles in increasing the enzymatic saccharification. In this study, we present a computational model that complements the experimental approaches. We decipher how the three-dimensional structure of the substrate impacts the saccharification dynamics. We model a cell wall microfibril composed of cellulose and surrounded by hemicellulose and lignin, with various relative abundances and arrangements. This substrate is subjected to digestion by different cocktails of well characterized enzymes. The saccharification dynamics is simulated in silico using a stochastic procedure based on a Gillespie algorithm. As we additionally implement a fitting procedure that optimizes the parameters of the simulation runs, we are able to reproduce experimental saccharification time courses for corn stover. Our model highlights the synergistic action of enzymes, and confirms the linear decrease of sugar conversion when either lignin content or crystallinity of the substrate increases. Importantly, we show that considering the crystallinity of cellulose in addition to the substrate composition is essential to interpret experimental saccharification data. Finally, our findings support the hypothesis of xylan being partially crystalline.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Wall / chemistry
  • Cellulose / chemistry
  • Computational Chemistry / methods
  • Crystallization
  • Lignin / chemistry*
  • Molecular Structure
  • Stochastic Processes*
  • Sugars / chemistry*
  • Zea mays / chemistry


  • Sugars
  • lignocellulose
  • Cellulose
  • Lignin

Grants and funding

To complete this work the position of E.B. was funded by the Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC 2048/1, Project ID: 390686111. To complete this work the position of A.R. was funded by the Federal Ministry of Education and Research of Germany in the framework of CornWall (Project Number 031B0193A). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.