computer simulation of lignocellulosic biomass - gtc...
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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
3 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
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
5 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
• 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
10 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
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?
11 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
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
14 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
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
15 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
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
17 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
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
18 Managed by UT-Battelle for the U.S. Department of Energy Presentation_name
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