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Title: Coarse-grained simulation of cellulose Iβ with application to long fibrils

Authors:
;
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Center for Lignocellulose Structure and Formation (CLSF)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1385102
DOE Contract Number:  
SC0001090
Resource Type:
Journal Article
Journal Name:
Cellulose
Additional Journal Information:
Journal Volume: 22; Journal Issue: 1; Related Information: CLSF partners with Pennsylvania State University (lead); North Carolina State University; University of Rhode Island; Virginia Tech University; Journal ID: ISSN 0969-0239
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
biofuels (including algae and biomass), bio-inspired, membrane, carbon sequestration, materials and chemistry by design, synthesis (self-assembly)

Citation Formats

Fan, Bingxin, and Maranas, Janna K. Coarse-grained simulation of cellulose Iβ with application to long fibrils. United States: N. p., 2014. Web. doi:10.1007/s10570-014-0481-2.
Fan, Bingxin, & Maranas, Janna K. Coarse-grained simulation of cellulose Iβ with application to long fibrils. United States. doi:10.1007/s10570-014-0481-2.
Fan, Bingxin, and Maranas, Janna K. Thu . "Coarse-grained simulation of cellulose Iβ with application to long fibrils". United States. doi:10.1007/s10570-014-0481-2.
@article{osti_1385102,
title = {Coarse-grained simulation of cellulose Iβ with application to long fibrils},
author = {Fan, Bingxin and Maranas, Janna K.},
abstractNote = {},
doi = {10.1007/s10570-014-0481-2},
journal = {Cellulose},
issn = {0969-0239},
number = 1,
volume = 22,
place = {United States},
year = {2014},
month = {10}
}

Works referenced in this record:

Multiscale Coarse-Graining of Monosaccharides
journal, October 2007

  • Liu, Pu; Izvekov, Sergei; Voth, Gregory. A.
  • The Journal of Physical Chemistry B, Vol. 111, Issue 39
  • DOI: 10.1021/jp0721494

Microfibril diameter in celery collenchyma cellulose: X-ray scattering and NMR evidence
journal, March 2007


Coarse-Grain Model for Glucose, Cellobiose, and Cellotetraose in Water
journal, June 2011

  • Hynninen, Antti-Pekka; Matthews, James F.; Beckham, Gregg T.
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 7
  • DOI: 10.1021/ct200092t

Determination of the leveling-off degree of polymerization of cotton and rayon
journal, June 1953


A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
journal, July 2011

  • Srinivas, Goundla; Cheng, Xiaolin; Smith, Jeremy C.
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 8
  • DOI: 10.1021/ct200181t

M3B:  A Coarse Grain Force Field for Molecular Simulations of Malto-Oligosaccharides and Their Water Mixtures
journal, January 2004

  • Molinero, Valeria; Goddard, William A.
  • The Journal of Physical Chemistry B, Vol. 108, Issue 4
  • DOI: 10.1021/jp0354752

Dynamics of Cellulose−Water Interfaces:  NMR Spin−Lattice Relaxation Times Calculated from Atomistic Computer Simulations
journal, March 2008

  • Bergenstråhle, Malin; Wohlert, Jakob; Larsson, Per Tomas
  • The Journal of Physical Chemistry B, Vol. 112, Issue 9
  • DOI: 10.1021/jp074641t

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations
journal, April 2011

  • Paavilainen, Sami; Róg, Tomasz; Vattulainen, Ilpo
  • The Journal of Physical Chemistry B, Vol. 115, Issue 14
  • DOI: 10.1021/jp111459b

Comparison of Cellulose Iβ Simulations with Three Carbohydrate Force Fields
journal, January 2012

  • Matthews, James F.; Beckham, Gregg T.; Bergenstråhle-Wohlert, Malin
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 2
  • DOI: 10.1021/ct2007692

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
journal, March 1977

  • Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
  • Journal of Computational Physics, Vol. 23, Issue 3
  • DOI: 10.1016/0021-9991(77)90098-5

Why are coarse-grained force fields too fast? A look at dynamics of four coarse-grained polymers
journal, January 2011

  • Depa, Praveen; Chen, Chunxia; Maranas, Janna K.
  • The Journal of Chemical Physics, Vol. 134, Issue 1
  • DOI: 10.1063/1.3513365

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995


Comparison of simple potential functions for simulating liquid water
journal, July 1983

  • Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
  • The Journal of Chemical Physics, Vol. 79, Issue 2
  • DOI: 10.1063/1.445869

The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008

  • Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier
  • Journal of Chemical Theory and Computation, Vol. 4, Issue 5
  • DOI: 10.1021/ct700324x

A Revised Architecture of Primary Cell Walls Based on Biomechanical Changes Induced by Substrate-Specific Endoglucanases
journal, February 2012


Structure of Cellulose Microfibrils in Primary Cell Walls from Collenchyma
journal, November 2012

  • Thomas, Lynne H.; Forsyth, V. Trevor; Šturcová, Adriana
  • Plant Physiology, Vol. 161, Issue 1
  • DOI: 10.1104/pp.112.206359

The Path Forward for Biofuels and Biomaterials
journal, January 2006

  • Ragauskas, Arthur J.; Williams, Charlotte K.; Davison, Brian H.
  • Science, Vol. 311, Issue 5760, p. 484-489
  • DOI: 10.1126/science.1114736

Solid-State 13C NMR Investigation of Molecular Ordering in the Cellulose of Apple Cell Walls
journal, July 1994

  • Newman, Roger H.; Ha, Marie-Ann; Melton, Laurence D.
  • Journal of Agricultural and Food Chemistry, Vol. 42, Issue 7
  • DOI: 10.1021/jf00043a002

Estimation of the lateral dimensions of cellulose crystallites using NMR signal strengths
journal, October 1999


Additive empirical force field for hexopyranose monosaccharides
journal, November 2008

  • Guvench, Olgun; Greene, Shannon N.; Kamath, Ganesh
  • Journal of Computational Chemistry, Vol. 29, Issue 15
  • DOI: 10.1002/jcc.21004

Nanostructure of cellulose microfibrils in spruce wood
journal, November 2011

  • Fernandes, A. N.; Thomas, L. H.; Altaner, C. M.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 47
  • DOI: 10.1073/pnas.1108942108

Martini Coarse-Grained Force Field: Extension to Carbohydrates
journal, October 2009

  • López, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 12
  • DOI: 10.1021/ct900313w

Exploring the utility of coarse-grained water models for computational studies of interfacial systems
journal, August 2010


Native Cellulose: A Composite of Two Distinct Crystalline Forms
journal, January 1984


A Coarse-Grained Model for Molecular Dynamics Simulations of Native Cellulose
journal, January 2011

  • Wohlert, Jakob; Berglund, Lars A.
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 3
  • DOI: 10.1021/ct100489z

Periodic Disorder along Ramie Cellulose Microfibrils
journal, July 2003

  • Nishiyama, Yoshiharu; Kim, Ung-Jin; Kim, Dae-Young
  • Biomacromolecules, Vol. 4, Issue 4
  • DOI: 10.1021/bm025772x

The Hydrogen Bond in the Solid State
journal, January 2002


Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993

  • Darden, Tom; York, Darrin; Pedersen, Lee
  • The Journal of Chemical Physics, Vol. 98, Issue 12
  • DOI: 10.1063/1.464397

Coarse Grained Protein−Lipid Model with Application to Lipoprotein Particles
journal, March 2006

  • Shih, Amy Y.; Arkhipov, Anton; Freddolino, Peter L.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 8
  • DOI: 10.1021/jp0550816

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
journal, July 1983

  • Brooks, Bernard R.; Bruccoleri, Robert E.; Olafson, Barry D.
  • Journal of Computational Chemistry, Vol. 4, Issue 2
  • DOI: 10.1002/jcc.540040211

An improved OPLS-AA force field for carbohydrates
journal, October 2002

  • Kony, D.; Damm, W.; Stoll, S.
  • Journal of Computational Chemistry, Vol. 23, Issue 15
  • DOI: 10.1002/jcc.10139

Coarse-grained normal mode analysis in structural biology
journal, October 2005


Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004

  • Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E.
  • The Journal of Physical Chemistry B, Vol. 108, Issue 2
  • DOI: 10.1021/jp036508g

A Multiscale Coarse-Graining Method for Biomolecular Systems
journal, February 2005

  • Izvekov, Sergei; Voth, Gregory A.
  • The Journal of Physical Chemistry B, Vol. 109, Issue 7
  • DOI: 10.1021/jp044629q

Force Pulling of Single Cellulose Chains at the Crystalline Cellulose−Liquid Interface: A Molecular Dynamics Study
journal, April 2009

  • Bergenstråhle, Malin; Thormann, Esben; Nordgren, Niklas
  • Langmuir, Vol. 25, Issue 8
  • DOI: 10.1021/la803915c

Computer simulation studies of microcrystalline cellulose Iβ
journal, January 2006


Cellulose Microfibril Twist, Mechanics, and Implication for Cellulose Biosynthesis
journal, March 2013

  • Zhao, Zhen; Shklyaev, Oleg E.; Nili, Abdolmajid
  • The Journal of Physical Chemistry A, Vol. 117, Issue 12
  • DOI: 10.1021/jp3089929

The xyloglucan–cellulose assembly at the atomic scale
journal, January 2006

  • Hanus, Jaroslav; Mazeau, Karim
  • Biopolymers, Vol. 82, Issue 1
  • DOI: 10.1002/bip.20460

Extraction of cellulose and preparation of nanocellulose from sisal fibers
journal, August 2007


The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations
journal, July 2007

  • Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
  • The Journal of Physical Chemistry B, Vol. 111, Issue 27
  • DOI: 10.1021/jp071097f

High-Temperature Behavior of Cellulose I
journal, March 2011

  • Matthews, James F.; Bergenstråhle, Malin; Beckham, Gregg T.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 10
  • DOI: 10.1021/jp1106839

REACH Coarse-Grained Simulation of a Cellulose Fiber
journal, August 2012

  • Glass, Dennis C.; Moritsugu, Kei; Cheng, Xiaolin
  • Biomacromolecules, Vol. 13, Issue 9
  • DOI: 10.1021/bm300460f

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses
journal, August 2009

  • Guvench, Olgun; Hatcher, Elizabeth; Venable, Richard M.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 9
  • DOI: 10.1021/ct900242e

Coarse-grained models for proteins
journal, April 2005


The Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface is Altered by Hydrolyzed Glycosidic Bonds
journal, August 2009

  • Bu, Lintao; Beckham, Gregg T.; Crowley, Michael F.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 31
  • DOI: 10.1021/jp904003z

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
journal, August 2003

  • Reith, Dirk; Pütz, Mathias; Müller-Plathe, Florian
  • Journal of Computational Chemistry, Vol. 24, Issue 13
  • DOI: 10.1002/jcc.10307

Dynamics of large proteins through hierarchical levels of coarse-grained structures
journal, November 2001

  • Doruker, Pemra; Jernigan, Robert L.; Bahar, Ivet
  • Journal of Computational Chemistry, Vol. 23, Issue 1
  • DOI: 10.1002/jcc.1160

Crystal Structure and Hydrogen-Bonding System in Cellulose Iβ from Synchrotron X-ray and Neutron Fiber Diffraction
journal, August 2002

  • Nishiyama, Yoshiharu; Langan, Paul; Chanzy, Henri
  • Journal of the American Chemical Society, Vol. 124, Issue 31
  • DOI: 10.1021/ja0257319