LIGNIN-KMC

LIGNIN-KMC simulates lignin biosynthesis using kinetic Monte Carlo methods and first-principles energetics to model stochastic radical coupling, polymer growth, and resulting lignin structures.

Key Features:

• Kinetic Monte Carlo (Gillespie) Simulation: Employs the Gillespie algorithm to simulate the stochastic nature of radical coupling events during lignin formation, capturing probabilistic monomer interactions and polymer growth.
• Graph Representation of Lignin Fragments: Represents lignin fragments as graphs to model and analyze structural outcomes of polymerization events.
• DFT-derived Reaction Rates: Derives rates for fragment couplings from Density Functional Theory (DFT) calculations to ground kinetics in first-principles energetics.
• Monolignol Supply Dynamics Simulation: Simulates varying monolignol supply rates to evaluate their impact on lignification dynamics and depolymerization yields.
• Subunit-specific Energetics and C‑lignin Modeling: Incorporates energetics of specific lignin subunits, including caffeyl alcohol homopolymers, to enable prediction of C-lignin structures.

Scientific Applications:

• Validation of Experimental Observations: Validates experimental findings on how different lignification conditions affect polymer structure.
• Investigation of Monolignol Supply Effects: Explores how varying monolignol supply rates influence lignification and indicates that increased sinapyl alcohol fractions can enhance depolymerization yields upon ether bond cleavage under low supply.
• Prediction of Lignin Structures: Predicts lignin structural outcomes, including C-lignin, by incorporating subunit energetics such as caffeyl alcohol homopolymers.

Methodology:

Uses Density Functional Theory (DFT) to derive coupling rates, applies the Gillespie algorithm for kinetic Monte Carlo simulation of radical coupling events, and employs a graph-based model to represent lignin fragments.