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Rui Huang's picture

Modeling Place

Starting from January 2006, my group has been posting in Modeling Place as a blogspot to share research experience and ideas. We will gradually migrate to iMechanica for better publicity and more web functions.

Xi Chen's picture

A molecular dynamics-decorated finite element framework for simulating the mechanical behaviors of biomolecules

Cover of Biophysical JournalOur first paper in biomechanics is featured as the cover of the Biophysical Journal. The paper is attached. Several freelance writers in biophysics have reported this paper in magazines and websites/blogs. This framework is very versatile and powerful, and we are now implementing more details/atomistic features into this phenomenological approach, and the follow-up paper will be submitted soon.

Abstract: The gating pathways of mechanosensitive channels of large conductance (MscL) in two bacteria (Mycobacterium tuberculosis and Escherichia coli) are studied using the finite element method. The phenomenological model treats transmembrane helices as elastic rods and the lipid membrane as an elastic sheet of finite thickness; the model is inspired by the crystal structure of MscL. The interactions between various continuum components are derived from molecular-mechanics energy calculations using the CHARMM all-atom force field. Both bacterial MscLs open fully upon in-plane tension in the membrane and the variation of pore diameter with membrane tension is found to be essentially linear. The estimated gating tension is close to the experimental value. The structural variations along the gating pathway are consistent with previous analyses based on structural models with experimental constraints and biased atomistic molecular-dynamics simulations. Upon membrane bending, neither MscL opens substantially, although there is notable and nonmonotonic variation in the pore radius. This emphasizes that the gating behavior of MscL depends critically on the form of the mechanical perturbation and reinforces the idea that the crucial gating parameter is lateral tension in the membrane rather than the curvature of the

Split singularities and the competition between crack penetration and debond at a bimaterial interface

Zhen Zhang and Zhigang Suo

For a crack impinging upon a bimaterial interface at an angle, the singular stress field is a linear superposition of two modes, usually of unequal exponents, either a pair of complex conjugates, or two unequal real numbers. In the latter case, a stronger and a weaker singularity coexist (known as split singularities). We define a dimensionless parameter, called the local mode mixity, to characterize the proportion of the two modes at the length scale where the processes of fracture occur. We show that the weaker singularity can readily affect whether the crack will penetrate, or debond, the interface.

Teng Li's picture

Review Articles on Flexible Electronics

[img_assist|nid=46|title=|desc=|link=url,|align=right|width=75|height=100]The cover story of the April 2006 issue of Materials Today features Flexible Electronics. This issue also includes two review articles in this emerging field of research. Access to full text articles is free of charge at

Review Article:

Material challenge for flexible organic devices, by Jay Lewis

Review Article:

Organic and polymer transistors for electronics, by Ananth Dodabalapur

Cover Story:

Jet printing flexible displays, by R.A. Street et al.


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