Symposium on Mechanics in Biology and Medicine
This symposium will be part of the 2007 ASME Applied Mechanics and Materials Conference, to be held in the University of Texas in Austin, in June 3-6, 2007.
biomechanics
A molecular dynamics-decorated finite element framework for simulating the mechanical behaviors of biomolecules
Our 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
use NMA to get the elastic properties of loop
(originally written by Yuye Tang)
A key procedure of the molecular-dynamics decorated finite element method (MDeFEM) is to determine the effective properties of components of a macromolecule. Here I illustrate how could one use the NMA computed from MD to estimate the elastic properties of loops in mechanosensitive channels, which is related with my research.
Lectureships at Cambridge University
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Applications are invited from suitably qualified candidates for three University Lectureships. They should have a proven record of scholarship in experimental and/or theoretical research involving Engineering Materials, Solid Mechanics, Mechanics of Biological Materials or Computational Mechanics. The lecturers will be expected to contribute directly to the research and teaching of the Mechanics, Materials and Design Division of the Engineering Department. This Division enjoys an international reputation for high-quality, innovative research in materials design and characterisation, including novel micro-architectured materials, bulk high-temperature superconducting materials, and increasingly in biological materials.
The posts will involve contributing to the teaching of the undergraduate course in Engineering, leading to the BA and MEng degrees. The successful candidates will take up the appointments 1 October 2006 or as soon as possible thereafter. The appointment will be for 5 years in the first instance with the possibility of reappointment to the retiring age subject to satisfactory performance. The current pensionable scale of stipends is in the range of ยฃ25,565-ยฃ39,303 per annum.
Further particulars and an application form may be obtained from the Personnel Office, Department of Engineering, Trumpington Street, Cambridge CB2 1PZ, UK (tel +44 (0) 1223 332615, fax +44 (0) 1223 766364, email personnel-appointments [at] eng.cam.ac.uk).
Applications should be sent to this address no later than by Friday 9 June 2006 and include a completed form, a curriculum vitae, a list of publications, and a one-page statement of research interests and future plans. Informal enquiries may be made to Professor Norman Fleck (telephone +44 (0)1223 332650 or email mj [at] eng.cam.ac.uk). The University is committed to equality of opportunity