Open Access

ARTICLE

Modulation of the Self-assembled Structure of Biomolecules: Coarse Grained Molecular Dynamics Simulation

Baohua Ji^*, Yonggang Huang^†

* Department of Engineering Mechanics, Tsinghua University, Beijing 100084, P. R. China
† Department of Mechanical and Industrial Engineering, University of Illinois, Urbana, IL61801, USA

Molecular & Cellular Biomechanics 2006, 3(3), 109-120. https://doi.org/10.3970/mcb.2006.003.109

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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Keywords

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