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Dynamic Visualization of Lignocellulose

Integration of computer simulation with neutron scattering to examine the structure of lignocellulose.

Loukas Petridis, Sai Venkatesh Pingali, Derya Vural, Riddhi Shah, Daisuke Sawada, Yunqiao Pu, Volker Urban, Barbara R. Evans, Hugh M. O’Neill, Art Ragauskas, Paul Langan, Jeremy C. Smith, Brian H. Davison

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Project Goals

Lignocellulose enzymatic degradation

Lignocellulosic biomass is recalcitrant to deconstruction and saccharification due to its fundamental molecular architecture and multicomponent laminate composition. A fundamental understanding of the structural changes and associations that occur at the molecular level during biosynthesis, deconstruction, and hydrolysis of biomass is essential for improving processing and conversion methods for lignocellulose-based fuels production. The objective of this research is to develop and demonstrate a combined neutron scattering and computer simulation technology for multiple-length scale, real-time imaging of biomass during pretreatment and enzymatic hydrolysis.



     SANS revealed an increase of the cross-sectional radius of the crystalline cellulose fibril in switchgrass lignocellulose resulting from dilute acid pretreatment. Supporting evidence for the increase in cellulose crystallinity was obtained by NMR. This important finding is counterintuitive given the prevailing paradigm that crystal packing contributes to recalcitrance while pretreatment increases digestibility. We confirmed that our pretreatment experiments indeed increase enzymatic saccharification. Concurrent with the observed re-annealing of cellulose our studies also show removal of hemicellulose and redistribution of lignin into aggregates with Rg~ 135 Å. It is possible that an increase in recalcitrance due to increased crystallinity is outweighed by a reduction in recalcitrance due to increased accessibility of enzymes to cellulose Together these results help close an important knowledge gap about the structural consequences of pretreatment. The degree of crystallinity by itself is a poor indicator for enzymatic digestibility; removal of hemicelluloses and lignin from the native lignocellulose composite morphology appear to be the determining factors for increasing biomass digestibility. This is an important insight because it suggests the possibility of optimizing the dilute acid pretreatment process to tune the balance of these counter effects to maximize digestibility.


   Through technical innovation the molecular dynamics (MD) simulation codes for lignocellulosic biomass were scaled to petascale supercomputers. By combining SANS and MD, softwood lignin aggregates were shown to possess a highly folded and self-similar surface fractal dimension that is invariant under change of scale from ~1–1000 Å. The MD, revealed extensive water penetration of the aggregates and heterogeneous chain dynamics corresponding to a rigid core with a fluid surface.


    MD simulations demonstrate that lignin transitions from glassy, compact to mobile, extended states with increasing temperature at T≥1500C i.e., above typical pretreatment temperatures. The low-temperature collapse of lignin is thermodynamically driven by an increase in translational entropy and density fluctuations of those water molecules removed from the hydration shell. Thus, the results distinguish lignin’s collapse from enthalpy driven coil-globule transitions observed for other polymers and provide a thermodynamic role of hydration water density fluctuations in driving general hydrophobic polymer collapse (Petridis et al., 2011).


    SANS experiments demonstrated that, at the pH of optimal activity (pH 4.2), the solution conformation of cellobiohydrolase I (Cel7A) transitions from a compact structure at neutral pH to a more flexible structure. The catalytic core adopts a structure in which the compact packing typical of a fully folded polypeptide chain is disrupted (Pingali et al., 2011).




Research Highlights

Silane functionalization of silicon cantilevers with chip holder demonstrated for chemical force imaging of switchgrass

Switchgrass Produced with 34% D/H Substitution by Hydroponic Cultivation for Neutron Scattering Experiments

Integration of Powder Diffraction and Simulation Required for Accurate Determination of Cellulose Crystallinity

Five Papers in Cellulose Showcase Power of Neutron Scattering

Neutrons and Simulation Reveal Coupling of Dynamical and Mechanical Properties of Cellulose

BER Biofuels SFA: Patent Issued for "High-Throughput Reproducible Cantilever Functionalization"

Neutrons Probe Common Processes Responsible for Structural Changes during Biomass Pretreatment

Morphological Changes in Cellulose and Lignin Components of Biomass Occur at Different Stages during Steam Pretreatment

Effect of Deuteration on the Structure of Bacterial Cellulose

High-Performance MD Simulation of Lignin Aggregation on Cellulose Shows Stronger binding to Crystalline Regions

Effect of Amines on Disruption of Cellulose

Neutron Technologies for Bioenergy Research

Complex Molecular Architectures of Lignin Measured via Neutron Scattering

Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics




33. G. Bali, X. Meng, J.I. Deneff, Q. Sun, A.J. Ragauskas,; “The Effect of Alkaline Pretreatment Methods on Cellulose Structure and Accessibility in Milled Populus””, Chem. Sus. Chem., 8(2), 275-279 (2015)

32. I. Lee, B. Evans, G. Bali, M. Foston, A.J. Ragauskas,; “Silicon cantilever functionalization for cellulose-specific chemical force imaging of switchgrass””, Analytical Methods, 7, 4541 (2015)

31. B. Evans, G. Bali, M. Foston, A.J. Ragauskas, H.M. O'Neil, R. Shah, J. McGaughey, D. Reeves, C.S. Rempe, B.H. Davison ; “Production of deuterated switchgrass by hydroponic cultivation”, Planta 242(1), 215 - 222 (2015)

30. B. Lindner, L. Petridis, P. Langan and J. C. Smith; “Cellulose Crystallinity and Powder Diffraction Diagrams”, Biopolymers 203, 67-73 (2015)

29. L. Petridis, H. M. O’Neill, M. Johnsen, B. Fan, R. Schulz, E. Mamontov, J. Maranas, P. Langan and J.C. Smith “Hydration Control of the Mechanical and Dynamical Properties of CelluloseBiomacromolecules 15, 4152–59 (2014).

28. L. Hong, L. Petridis and J. C. Smith; “Biomolecular Structure and Dynamics: The View from Simulation”, Israel Journal of Chemistry 54, 1264-1273 (2014)

27. Q. Sun, M. Foston, D. Sawada, S.V. Pingali, H.M. O’Neill, H. Li, C.E. Wyman, P. Langan, Y. Pu and A.J. Ragauskas, "Comparison of Changes in Cellulose Ultrastructure During Different Pretreatments of Poplar”, Cellulose 21, 2419-31 (2014).

26. D. Sawada, L. Hanson, M. Wada, Y. Nishiyama and P. Langan, “The Initial Structure of Cellulose During Ammonia Pretreatment”, Cellulose 21:1117-1126, (2014).

25. A.J. Ragauskas, G.T. Beckham, M.J. Biddy, R. Chandra, F. Chen, M.F. Davis, B.H. Davison, R.A. Dixon, P. Gilna, M. Keller, P. Langan, A.K. Naskar, J. N. Saddler, T. J. Tschaplinski, G.A. Tuskan and C.E. Wyman, “Lignin Valorization in the Biorefinery”, Science 16, 709 (2014).

24. E. M. Alekozai, P. K. Ghattyvenkatakrishna, E. C. Uberbacher, M. F. Crowley, J. C. Smith and X. Cheng,“Simulation Analysis of the Cellulase Cel7A Carbohydrate Binding Module on the Surface of the Cellulose Iβ”, Cellulose 21(2): 951–971 (2014).

23. D. Sawada, Y. Ogawa, S. Kimura, Y. Nishiyama, P. Langan, and M. Wada, “Solid-Solvent Molecular Interactions Observed in Crystal Structures of Beta-Chitin Complexes”, Cellulose 21(2):1007-1014 (2014).

22. J. He, S.V. Pingali, S.P.S. Chundawat, A. Pack, A. D. Jones, P. Langan, B.H. Davison, V. Urban, B. Evans and H. O’Neill, “Controlled Incorporation of Deuterium into Bacterial Cellulose”, Cellulose 21(2), 927–936 (2014).

21. Y. Nishiyama, P. Langan, H. O'Neill, S.V. Pingali and S. Harton, “Structural Coarsening of Aspen Wood by Hydrothermal Pretreatment Monitored by Small- and Wide-Angle Scattering of X-ray and Neutrons on Oriented Specimens”, Cellulose 21(2), 1015–1024 (2014).

20. S. V. Pingali, H. M. O’Neill, L. He, Y. Nishiyama, Y. Melnichenko, V. S. Urban, L. Petridis, B. Davison, and P. Langan, “Morphological Changes in the Cellulose and Lignin Components of Biomass Occur at Different Stages During Steam Pretreatment”, Cellulose 21(2), 873–878 (2014).

19. H. Wang, G. Gurau, S. V. Pingali, H. O'Neill, B. Evans, V. Urban, W. Heller, and R. Rogers, “Physical Insight into Switchgrass Dissolution in the Ionic Liquid 1-Ethyl-3-Methylimidazolium Acetate”, ACS Sustainable Chemistry & Engineering (April 13, 2014) 1264–1269 (2014).

18. B. Evans, G. Bali, D. Reeves, H. O'Neill, Q. Sun, R. Shah, and A. Ragauskas, A., “Effect of D2O on Growth Properties and Chemical Structure of Annual Ryegrass (Lolium multiflorum)”, Journal of Agricultural and Food Chemistry 62(12), 2592–2604 (2014).

17. P. Langan, L. Petridis, H. M. O’Neill, S.V. Pingali, M. Foston, Y. Nishiyama, R. Schulz, B. Lindner, B.L. Hanson, S. Harton, W.T. Heller, V. Urban, B.R. Evans, S. Gnanakaran, A.J. Ragauskas, J.C. Smith and B.H. Davison, “Common Processes Driving the Thermochemical Pretreatment of Lignocellulosic Biomass”, Green Chemistry 16, 63–68 (2014).

16. B. Lindner, L. Petridis, R. Schulz and J. C. Smith; “Solvent-Driven Preferential Association of Lignin with Crystalline Cellulose Regions in Multimillion Atom Molecular Dynamics Simulation”, Biomacromolecules 14(10), 3390–3398 (2013)

15. D. Sawada, Y. Nishiyama, L. Petridis, R. Parthasarathi, S. Gnanakaran, V. T. Forsyth, M. Wada, P. Langan, “Structure and dynamics of a complex of cellulose with EDA: insights into the action of amines on cellulose”, Cellulose, 20 1563-1571 (2013).

14. G. Bali, M. Foston, B. R. Evans, J. He, A. J. Ragauskas, "The effect of deuteration on the structure of bacterial cellulose”  Carbohydrate Research, 347, 82-88 (2013)

13. P. Langan, B. R. Evans, M. Foston, W. T. Heller, H. M. O’Neill, L. Petridis, S. V. Pingali, A. J. Ragauskas, J. C. Smith,  B. Davison, “Neutron Technologies for Bioenergy Research”  Industrial Biotechnology, 8, 209 (2012)

12. S. E, Harton, S. V., Pingali, G. A. Nunnery, D. A. Baker, S. H. Walker, D. C.  Muddiman, T. Koga, T. G.  Rials, V. S. Urban, and P. Langan (2012) ACS Macro Lett.  1, 568-573, “Evidence for Complex Molecular Architectures for Solvent-Extracted Lignins.

11. Foston, M.B.; McGaughey, J.; O’Neill, H.; Barbara R. Evans, B.R.; Ragauskas, A.J - “Deuterium Incorporation in Biomass Cell Wall Components by NMR Analysis”, Analyst 137, 1090-1093 (2012)

10. Petridis, R. Schulz, J.C. Smith – “Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics", J. Am. Chem. Soc. 133, 20277-20287 (2011)

9. Petridis, S.V. Pingali, V. Urban, W.T. Heller, H.M. O' Neill, M. Foston, A. Ragauskas, and J.C. Smith – Phys. Rev. E83, 061911 (2011), “Self-Similar Multiscale Structure of Lignin Revealed by Neutron Scattering and Molecular Dynamics Simulation.

8. S.V. Pingali, H.M. O'Neill, J. McGaughey, V.S. Urban, C.S. Rempe, L. Petridis, J.C. Smith, B.R. Evans, and W.T. Heller – (2011) J. Biol. Chem.286, 32801-32809, “Small-angle neutron scattering reveals a pH-dependent conformational change in Trichoderma reesei cellobiohydrolase I: Implications for enzymatic activity.”

7. M. Foston, C.A. Hubbel, A.J. Ragauskas – “Cellulose isolation methodology for NMR analysis of cellulose ultrastructure,” Materials 4, 1985-2002 (2011).

6. J.C. Smith, M. Krishnan, L. Petridis, N. Smolin – “Structure and dynamics of biological systems: Integration of Neutron Scattering with Computer Simulation,” Dynamics of Soft Matter (2011)

5. S.V. Pingali, V. Urban, W.T. Heller, J. McGaughey, H.M. O' Neill, M. Foston, D. Myles, A. Ragauskas, B.R. Evans – Biomacromolecules 11, 2329-2335 (2010), “Breakdown of Cell Wall Nanostructure in Dilute Acid Pretreated Biomass."

4. S.V. Pingali, V. Urban, W.T. Heller, J. McGaughey, H.M. O' Neill, M. Foston, D. Myles, A. Ragauskas, B.R. Evans – ActaCryst. D66, 1189-1193 (2010), “SANS Study of Cellulose Extracted from Switchgrass.

3. Foston, M; Ragauskas, AJ, “Changes in lignocellulosic supramolecular and ultrastructure during dilute acid pretreatment of Populus and switchgrass", Biomass & Bioenergy, 34:1885-1895 (2010).

2. Schulz, R.; Lindner, B.; Petridis, L.; Smith, J.C. – J.Chem. Theory Comput.5, 2798–2808 (2009), “Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Computer.”

1. Petridis, L., and Smith, J.C. – J. Comp. Chem. 30(3):457-67 (2009). “A molecular mechanics force field for lignin.”


This research (ORNL Biofuels SFA) is funded by the Genomic Science Program, Office of Biological and Environmental Research, U. S. Department of Energy.

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