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Title: Coarse-grained molecular dynamics simulations of α-1,3-glucan

Abstract

In this work we present a coarse-grained model for α-1,3-glucan that captures hydrogen bonding directionality and polysaccharide monomer structure.

Authors:
ORCiD logo [1];  [1];  [2];  [2];  [3]; ORCiD logo [4]
+ Show Author Affiliations
  1. Dept. of Chemical and Biomolecular Engineering, University of Delaware, Newark, USA
  2. Biomaterials, DuPont Industrial Biosciences, DowDuPont Specialty Products Division, Wilmington, USA
  3. Science and Innovation, DuPont Specialty Products, DowDuPont Specialty Products Division, Wilmington, USA
  4. Dept. of Chemical and Biomolecular Engineering, University of Delaware, Newark, USA, Dept. of Materials Science and Engineering, University of Delaware
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1514756
Grant/Contract Number:  
SC0017753
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Soft Matter
Additional Journal Information:
Journal Name: Soft Matter Journal Volume: 15 Journal Issue: 23; Journal ID: ISSN 1744-683X
Publisher:
Royal Society of Chemistry (RSC)
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Beltran-Villegas, Daniel J., Intriago, Daniel, Kim, Kyle H. C., Behabtu, Natnael, Londono, J. David, and Jayaraman, Arthi. Coarse-grained molecular dynamics simulations of α-1,3-glucan. United Kingdom: N. p., 2019. Web. doi:10.1039/C9SM00580C.
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Beltran-Villegas, Daniel J., Intriago, Daniel, Kim, Kyle H. C., Behabtu, Natnael, Londono, J. David, & Jayaraman, Arthi. Coarse-grained molecular dynamics simulations of α-1,3-glucan. United Kingdom. doi:https://doi.org/10.1039/C9SM00580C
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Beltran-Villegas, Daniel J., Intriago, Daniel, Kim, Kyle H. C., Behabtu, Natnael, Londono, J. David, and Jayaraman, Arthi. Wed . "Coarse-grained molecular dynamics simulations of α-1,3-glucan". United Kingdom. doi:https://doi.org/10.1039/C9SM00580C.
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@article{osti_1514756,
title = {Coarse-grained molecular dynamics simulations of α-1,3-glucan},
author = {Beltran-Villegas, Daniel J. and Intriago, Daniel and Kim, Kyle H. C. and Behabtu, Natnael and Londono, J. David and Jayaraman, Arthi},
abstractNote = {In this work we present a coarse-grained model for α-1,3-glucan that captures hydrogen bonding directionality and polysaccharide monomer structure.},
doi = {10.1039/C9SM00580C},
journal = {Soft Matter},
number = 23,
volume = 15,
place = {United Kingdom},
year = {2019},
month = {6}
}
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Journal Article:
Free Publicly Available Full Text
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DOI: https://doi.org/10.1039/C9SM00580C
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Works referenced in this record:

Application of molecular dynamics simulation in food carbohydrate research—a review
journal, October 2015

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

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

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

High-temperature molecular dynamics simulation of cellobiose and maltose
journal, May 2015

  • Murillo, Jessica D.; Moffet, Melissa; Biernacki, Joseph J.
  • AIChE Journal, Vol. 61, Issue 8
  • DOI: 10.1002/aic.14854

A coarse-grained model for β-d-glucose based on force matching
journal, March 2012

  • Markutsya, Sergiy; Kholod, Yana A.; Devarajan, Ajitha
  • Theoretical Chemistry Accounts, Vol. 131, Issue 3
  • DOI: 10.1007/s00214-012-1162-6

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

Hydrogen Bonding
journal, October 1971

Development of a Coarse-Grained Model of Collagen-Like Peptide (CLP) for Studies of CLP Triple Helix Melting
journal, February 2018

  • Condon, Joshua E.; Jayaraman, Arthi
  • The Journal of Physical Chemistry B, Vol. 122, Issue 6
  • DOI: 10.1021/acs.jpcb.7b10916

Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse‐grained molecular simulation study
journal, January 2019

  • Prhashanna, Ammu; Jayaraman, Arthi
  • Journal of Polymer Science Part B: Polymer Physics, Vol. 57, Issue 18
  • DOI: 10.1002/polb.24780

Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids
journal, June 1971

  • Weeks, John D.; Chandler, David; Andersen, Hans C.
  • The Journal of Chemical Physics, Vol. 54, Issue 12
  • DOI: 10.1063/1.1674820

Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance
journal, September 2011

  • Cho, Hyung Min; Gross, Adam S.; Chu, Jhih-Wei
  • Journal of the American Chemical Society, Vol. 133, Issue 35
  • DOI: 10.1021/ja2046155

Integrated Modeling Program, Applied Chemical Theory (IMPACT)
journal, January 2005

  • Banks, Jay L.; Beard, Hege S.; Cao, Yixiang
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20292

Molecular and crystal structure of the regenerated form of (1→3)-α-d-glucan
journal, February 1981

  • Ogawa, Kozo; Okamura, Keizo; Sarko, Anatole
  • International Journal of Biological Macromolecules, Vol. 3, Issue 1
  • DOI: 10.1016/0141-8130(81)90021-0

Automatic atom type and bond type perception in molecular mechanical calculations
journal, October 2006

  • Wang, Junmei; Wang, Wei; Kollman, Peter A.
  • Journal of Molecular Graphics and Modelling, Vol. 25, Issue 2
  • DOI: 10.1016/j.jmgm.2005.12.005

GROMACS 3.0: a package for molecular simulation and trajectory analysis
journal, August 2001

  • Lindahl, Erik; Hess, Berk; van der Spoel, David
  • Journal of Molecular Modeling, Vol. 7, Issue 8
  • DOI: 10.1007/s008940100045

X-Ray diffraction data for (1→3)-α-d-glucan
journal, October 1979

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

Polymorphism in crystalline (1→3)-α-d-glucan from fungal cell-walls
journal, June 1979

Atomistic molecular dynamics simulations on the interaction of TEMPO-oxidized cellulose nanofibrils in water
journal, September 2016

Polysaccharide–Protein Complexes in a Coarse-Grained Model
journal, August 2015

  • Poma, Adolfo B.; Chwastyk, Mateusz; Cieplak, Marek
  • The Journal of Physical Chemistry B, Vol. 119, Issue 36
  • DOI: 10.1021/acs.jpcb.5b06141

Chemical and structural similarities in wall polysaccharides of some Penicillium, Eupenicillium and Aspergillus species
journal, January 1992

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
journal, September 2015

Effects of Polymer Conjugation on Hybridization Thermodynamics of Oligonucleic Acids
journal, September 2016

  • Ghobadi, Ahmadreza F.; Jayaraman, Arthi
  • The Journal of Physical Chemistry B, Vol. 120, Issue 36
  • DOI: 10.1021/acs.jpcb.6b06970

Evaluation of coarse-grained mapping schemes for polysaccharide chains in cellulose
journal, June 2013

  • Markutsya, Sergiy; Devarajan, Ajitha; Baluyut, John Y.
  • The Journal of Chemical Physics, Vol. 138, Issue 21
  • DOI: 10.1063/1.4808025

Development and testing of a general amber force field
journal, January 2004

  • Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
  • Journal of Computational Chemistry, Vol. 25, Issue 9
  • DOI: 10.1002/jcc.20035

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

Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
journal, January 2000

PITOMBA: Parameter Interface for Oligosaccharide Molecules Based on Atoms
journal, October 2014

  • Rusu, Victor H.; Baron, Riccardo; Lins, Roberto D.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 11
  • DOI: 10.1021/ct500455u

Conformational and Dynamical Properties of Disaccharides in Water: a Molecular Dynamics Study
journal, June 2006

Procedure for Transferable Coarse-Grained Models of Aqueous Polysaccharides
journal, December 2016

  • Sauter, Jörg; Grafmüller, Andrea
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 1
  • DOI: 10.1021/acs.jctc.6b00613

Polysaccharide aggregation as a potential sink of marine dissolved organic carbon
journal, April 2004

  • Engel, Anja; Thoms, Silke; Riebesell, Ulf
  • Nature, Vol. 428, Issue 6986
  • DOI: 10.1038/nature02453

Biodegradable and Bio-Based Polymers: Future Prospects of Eco-Friendly Plastics
journal, January 2015

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

Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids
journal, January 2017

  • Poma, Adolfo B.; Chwastyk, Mateusz; Cieplak, Marek
  • Phys. Chem. Chem. Phys., Vol. 19, Issue 41
  • DOI: 10.1039/C7CP05269C

Function and Biosynthesis of Cell Wall α-1,3-Glucan in Fungi
journal, November 2017

  • Yoshimi, Akira; Miyazawa, Ken; Abe, Keietsu
  • Journal of Fungi, Vol. 3, Issue 4
  • DOI: 10.3390/jof3040063

Crystalline Features of Streptococcal (l→3)- α -D-Glucans of Human Saliva
journal, January 1994

  • Ogawa, Kozo; Yui, Toshifumi; Okamura, Keizo
  • Bioscience, Biotechnology, and Biochemistry, Vol. 58, Issue 7
  • DOI: 10.1271/bbb.58.1326

Molecular modeling tools to characterize the structure and complexation behavior of carbohydrates
journal, June 2016

A Systematic Coarse-Grained Model for Methylcellulose Polymers: Spontaneous Ring Formation at Elevated Temperature
journal, February 2016

Characterization of crystalline linear (1 → 3)-α-d-glucan synthesized in vitro
journal, December 2017

Modeling of negative Poisson’s ratio (auxetic) crystalline cellulose Iβ
journal, September 2016

A new all-atom force field for crystalline cellulose I
journal, January 2000

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

Fast Monte Carlo algorithm for site or bond percolation
journal, June 2001

Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects
journal, August 2010

Force fields and scoring functions for carbohydrate simulation
journal, January 2015

Chemical characterization of a water insoluble (1→3)-α-d-glucan from an alkaline extract of Aspergillus wentii
journal, January 2013

The missing term in effective pair potentials
journal, November 1987

  • Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P.
  • The Journal of Physical Chemistry, Vol. 91, Issue 24
  • DOI: 10.1021/j100308a038
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