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Published 2010 | Published
Journal Article Open

Global Energy Matching Method for Atomistic-to-Continuum Modeling of Self-Assembling Biopolymer Aggregates


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.

Additional Information

© 2010 Society for Industrial and Applied Mathematics. Received January 04, 2010. Accepted September 02, 2010. Published online December 07, 2010. This work started while Leonid Berlyand was visiting the Max Planck Institute in Leipzig by invitation of Stefan Müller. He is grateful for the financial support and hospitality received during this visit. Lei Zhang and Maxim Fedorov acknowledge Giovanni Bellesia for the help on atomistic simulations. Part of this work was completed while Lei Zhang and Leonid Berlyand were visiting the Chinese Academy of Sciences. They thank their host, Pingbing Ming, and his institution for the kind invitation and hospitality.

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