Computer Simulation of

Lignocellulosic Biomass

Loukas Petridis

UT/ORNL Center for Molecular Biophysics

Oak Ridge National Laboratory

1 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name

Cellulosic Ethanol Production

Ligocellulosic Biomass

Pre-treatment

Cellulose

Hemicellulose

Lignin

Enzymatic Hydrolysis

bottleneck: biomass recalcitrance

Fermentation

2 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name

Physical Origins of Recalcitrance

cellulose

lignin

hemi-

cellulose

Collapse of lignin

Enzyme:lignin interaction (Structure of lignin aggregates)

Lignin:cellulose association

enzymes

pretreatment

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Petascale Molecular Dynamics Simulation

Comparison to Experiments

Physical Insights

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Petridis et al JACS 133 20277 (2011)

Temperature Dependence of Lignin

New: lignin aggregation

during heating

heating cool-down

Old: lignin aggregation

during cool-down

160°C

DOE

INCITE

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• Enthalpy

• ΔH ≈ +200 kJ/mol Unfavorable

Collapse Driven by Removal of

Entropically Unfavorable Water

Molecules from Lignin Surface to Bulk

ΔG=ΔH-TΔS collapsed

extended

• Lignin configurational entropy

• -TΔSconf≈ +10 kJ/mol Unfavorable

• Hydration water translational &

rotational entropy

• -TΔSt+r ≈ -100 kJ/mol Favorable

• Hydration water compressibility

• -TΔSfluc ≈ -300 kJ/mol Favorable

Petridis et al JACS 133 20277 (2011)

Why Does Lignin Collapse at Room Temp?

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Lignin surface is “wet” at room T,

more hydrophobic at high T

ρhydr= 0.98ρbulk

ρhydr= 0.90ρbulk Hyd

rop

ho

bic

ity

lignin dimmer

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Are Lignin Aggregates Spheres?

Biomass Pretreatment

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I(Q)Qds6

ds=2.62±0.02

sdrrN

)(

Small-Angle

Neutron Scattering

Molecular Dynamics

Simulation

ds=2.65±0.01

Petridis et al., Phys. Rev. E 83 061911 (2011)

r

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Shape of Surface Invariant Under Change of Scale

Sim: 1Å Sim&Exp:

10Å

Exp:

100Å

Petridis et al., Phys. Rev. E 83 061911 (2011)

Surface Morphology Impacts Enzyme Inhibition

Enzyme:lignin

interaction

distribution

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Petridis et al., Phys. Rev. E 83 061911 (2011)

rigid sphere

SANS

MD

Highly folded

surface

Water

penetration

Rigid core

Fluid surface

Are Lignin Aggregates Solid Spheres?

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DOE INCITE: Lignocellulose Simulation

(30M cpu hours)

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Lignin Aggregation & Precipitation on Cellulose

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Interface Interaction

Energy Density

(kJ/mol/nm2)

lignin:

crystalline cellulose

-49±2

lignin:

noncrystalline cellulose

-50±2

water :

crystalline cellulose

-94±2

water :

non-crystalline cellulose

-107±2

Solvent-Driven Preferential Association of Lignin

with Crystalline Cellulose

Interface Interaction

Energy Density

(kJ/mol/nm2)

lignin:

crystalline cellulose

-49±2

lignin:

non-crystalline cellulose

-50±2

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10PF (CPU)

Petascale

Multiscale Structure and Dynamics

0.1 nm

1 nm

100 nm

1μm

1 fs 1 ps 1 ns 1 μs

domain

motions local

diffusion active site

Complexes

membranes

vibrations

Cluster

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CPU Strong Scaling

~ 100M atoms

24M-atom capability-class

simulation of enzyme binding

to pretreated lignocellulose

~ 24M atoms

Roland Schulz

~1500 atoms/core

16 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name

GPU Scaling

CPU 5 years ago

CPU&GPU 3 years

from now (?)

Roland Schulz

Szilard Pall

Berk Hess

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Exascale

GPU

10PF

Petascale

Outlook

0.1 nm

1 nm

100 nm

1μm

1 fs 1 ps 1 ns 1 μs

domain

motions local

diffusion active site

Complexes

membranes

vibrations

living cell

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Acknowledgements

Funding

DOE Office of Biological and Environmental

Research

Computational Resources

National Center for Computational Sciences

DOE INCITE award from DOE Office of Science

Graphics: T. Splettstoesser and M. Matheson

Venki Pingali

Volker Urban

William Heller

Hugh O’Neill

Barbara Evans

Paul Langan

Brian Davison

Marcus Foston

Art Ragauskas

Jeremy

Smith

Roland

Schulz

Benjamin

Lindner