Lignin-KMC: A Toolkit for Simulating Lignin Biosynthesis

Joshua Vermaas, Gregg Beckham, Michael Orella, Terry Gani, Michael Stone, Eric Anderson, Fikile Brushett, Yuriy Roman-Leshkov

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33 Scopus Citations


Lignin is an abundant biopolymer of phenylpropanoid monomers that is critical for plant structure and function. Based on the abundance of lignin in the biosphere and interest in lignin valorization, a more comprehensive understanding of lignin biosynthesis is imperative. Here, we present an open-source software toolkit, Lignin-KMC, that combines kinetic Monte Carlo and first-principles calculations of radical coupling events to model lignin biosynthesis in silico. Lignification is simulated using the Gillespie algorithm with rates derived from density functional theory calculations of individual fragment couplings. Using this approach, we confirm experimental findings regarding the impact of lignification conditions on the polymer structure such as (1) the positive correlation between sinapyl alcohol fraction and depolymerization yield and (2) the primarily benzodioxane linked structure of C-lignin. Additionally, we identify the in planta monolignol supply rate as a possible control mechanism for lignin biosynthesis based on evolutionary stresses. These examples not only highlight the robustness of our modeling framework but also motivate future studies of new lignin types, unexplored monolignol chemistries, and lignin structure predictions, all with an overarching aim of developing a more comprehensive molecular understanding of native lignin, which, in turn, can advance the biological and chemistry communities interested in this important biopolymer.

Original languageAmerican English
Pages (from-to)18313-18322
Number of pages10
JournalACS Sustainable Chemistry and Engineering
Issue number22
StatePublished - 18 Nov 2019

Bibliographical note

Publisher Copyright:
© 2019 American Chemical Society.

NREL Publication Number

  • NREL/JA-2700-74622


  • kinetic Monte Carlo
  • lignin biosynthesis
  • lignin polymerization
  • lignin structure
  • polymerization
  • radical coupling


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