Modulation of the self-assembled structure of biomolecules

Coarse grained molecular dynamics simulation

Baohua Ji*, Yonggang Huang

*Corresponding author for this work

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The mechanisms governing the self-assembled structure of biomolecules (single chain and bundle of chains) are studied with an AB copolymer model via the coarse grained molecular dynamics simulations. Non-local hydrophobic interaction is found to play a critical role in the pattern formation of the assembled structure of polymer chains. We show that the polymer structure could be controlled by adjusting the balance between local (short range) and non-local (long range) hydrophobic interaction which are influenced by various factors such as the sequences, chain length, stiffness, confinement, and the topology of polymers. In addition, the competition between the intrachain hydrophobic interaction and interchain hydrophobic interaction determines the structural transition of the chain bundles. This work may provide important insights into the fundamental physics in the structure control and the self-assembly of biomolecules for various practical applications.

Original languageEnglish (US)
Pages (from-to)109-119
Number of pages11
JournalMCB Molecular and Cellular Biomechanics
Volume3
Issue number3
StatePublished - Sep 1 2006

Fingerprint

Molecular Dynamics Simulation
Hydrophobic and Hydrophilic Interactions
Polymers
Physics

Keywords

  • Biomolecules
  • Coarse grained modeling
  • Molecular dynamics simulation
  • Self-assembly
  • Structure control

ASJC Scopus subject areas

  • Biophysics
  • Molecular Medicine
  • Molecular Biology
  • Cell Biology

Cite this

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abstract = "The mechanisms governing the self-assembled structure of biomolecules (single chain and bundle of chains) are studied with an AB copolymer model via the coarse grained molecular dynamics simulations. Non-local hydrophobic interaction is found to play a critical role in the pattern formation of the assembled structure of polymer chains. We show that the polymer structure could be controlled by adjusting the balance between local (short range) and non-local (long range) hydrophobic interaction which are influenced by various factors such as the sequences, chain length, stiffness, confinement, and the topology of polymers. In addition, the competition between the intrachain hydrophobic interaction and interchain hydrophobic interaction determines the structural transition of the chain bundles. This work may provide important insights into the fundamental physics in the structure control and the self-assembly of biomolecules for various practical applications.",
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Modulation of the self-assembled structure of biomolecules : Coarse grained molecular dynamics simulation. / Ji, Baohua; Huang, Yonggang.

In: MCB Molecular and Cellular Biomechanics, Vol. 3, No. 3, 01.09.2006, p. 109-119.

Research output: Contribution to journalArticle

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AU - Huang, Yonggang

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AB - The mechanisms governing the self-assembled structure of biomolecules (single chain and bundle of chains) are studied with an AB copolymer model via the coarse grained molecular dynamics simulations. Non-local hydrophobic interaction is found to play a critical role in the pattern formation of the assembled structure of polymer chains. We show that the polymer structure could be controlled by adjusting the balance between local (short range) and non-local (long range) hydrophobic interaction which are influenced by various factors such as the sequences, chain length, stiffness, confinement, and the topology of polymers. In addition, the competition between the intrachain hydrophobic interaction and interchain hydrophobic interaction determines the structural transition of the chain bundles. This work may provide important insights into the fundamental physics in the structure control and the self-assembly of biomolecules for various practical applications.

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