Global energy matching method for atomistic-to-continuum modeling of self-assembling biopolymer aggregates

Lei Zhang, Leonid Berlyand, Maxim V. Fedorov, Houman Owhadi

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

This paper studies mathematical models of biopolymer supramolecular aggregates that are formed by the self-assembly of single monomers. We develop a new multiscale numerical approach to model the structural properties of such aggregates. This theoretical approach establishes micro-macro relations between the geometrical and mechanical properties of the monomers and supramolecular aggregates. Most atomistic-to-continuum methods are constrained by a crystalline order or a periodic setting and therefore cannot be directly applied to modeling of soft matter. By contrast, the energy matching method developed in this paper does not require crystalline order and, therefore, can be applied to general microstructures with strongly variable spatial correlations. In this paper we use this method to compute the shape and the bending stiffness of their supramolecular aggregates from known chiral and amphiphilic properties of the short chain peptide monomers. Numerical implementation of our approach demonstrates consistency with results obtained by molecular dynamics simulations.

LanguageEnglish
Pages1958-1980
Number of pages23
JournalMultiscale Modeling and Simulation: A SIAM Interdisciplinary Journal
Volume8
Issue number5
DOIs
Publication statusPublished - 2010

Fingerprint

continuum modeling
Biopolymers
biopolymers
assembling
Continuum
monomers
Monomers
Energy
Modeling
modeling
energy
Crystalline materials
Self-assembly
Spatial Correlation
Peptides
peptide
Structural Properties
Self assembly
Molecular Dynamics Simulation
Mechanical Properties

Keywords

  • atomistic-to-continuum
  • self-assembly
  • biopolymer aggregates
  • multiscale
  • cauchy-born rule
  • peptides
  • molecular dynamics
  • nanotubes
  • lattice

Cite this

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title = "Global energy matching method for atomistic-to-continuum modeling of self-assembling biopolymer aggregates",
abstract = "This paper studies mathematical models of biopolymer supramolecular aggregates that are formed by the self-assembly of single monomers. We develop a new multiscale numerical approach to model the structural properties of such aggregates. This theoretical approach establishes micro-macro relations between the geometrical and mechanical properties of the monomers and supramolecular aggregates. Most atomistic-to-continuum methods are constrained by a crystalline order or a periodic setting and therefore cannot be directly applied to modeling of soft matter. By contrast, the energy matching method developed in this paper does not require crystalline order and, therefore, can be applied to general microstructures with strongly variable spatial correlations. In this paper we use this method to compute the shape and the bending stiffness of their supramolecular aggregates from known chiral and amphiphilic properties of the short chain peptide monomers. Numerical implementation of our approach demonstrates consistency with results obtained by molecular dynamics simulations.",
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Global energy matching method for atomistic-to-continuum modeling of self-assembling biopolymer aggregates. / Zhang, Lei; Berlyand, Leonid; Fedorov, Maxim V.; Owhadi, Houman.

In: Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal , Vol. 8, No. 5, 2010, p. 1958-1980.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Global energy matching method for atomistic-to-continuum modeling of self-assembling biopolymer aggregates

AU - Zhang, Lei

AU - Berlyand, Leonid

AU - Fedorov, Maxim V.

AU - Owhadi, Houman

PY - 2010

Y1 - 2010

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AB - This paper studies mathematical models of biopolymer supramolecular aggregates that are formed by the self-assembly of single monomers. We develop a new multiscale numerical approach to model the structural properties of such aggregates. This theoretical approach establishes micro-macro relations between the geometrical and mechanical properties of the monomers and supramolecular aggregates. Most atomistic-to-continuum methods are constrained by a crystalline order or a periodic setting and therefore cannot be directly applied to modeling of soft matter. By contrast, the energy matching method developed in this paper does not require crystalline order and, therefore, can be applied to general microstructures with strongly variable spatial correlations. In this paper we use this method to compute the shape and the bending stiffness of their supramolecular aggregates from known chiral and amphiphilic properties of the short chain peptide monomers. Numerical implementation of our approach demonstrates consistency with results obtained by molecular dynamics simulations.

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KW - peptides

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KW - nanotubes

KW - lattice

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