In many geotechnical systems, it is not uncommon to observe failure in zones of high localized strain called shear bands. The existing models predict the existence and the extent of these localizations, but provide little insight into the micromechanics within the shear bands. This research captures and compares the variation in microstructure both inside and outside of shear bands that formed in physical laboratory plane strain and companion numerical two-dimensional discrete element method (DEM) biaxial compression experiments. Unsheared and sheared laboratory specimens of Ottawa 20-30 sand of varying dilatancy were solidified using a two-stage resin impregnation procedure. The solidified specimens were sectioned and the resulting surfaces were prepared for microstructure observation using optical bright-field microscopy and stereological analysis. Statistical properties of microstructural parameters for sub-regions in a grid pattern and along predefined inclined zones were determined. Similar measurements were performed on 2D DEM simulation specimens at varying strain levels to characterize the evolution of microstructure with increasing strain. The results showed how differences evolved in the mean, standard deviation, and entropy of void distributions with increasing global strain levels. The results indicate how disorder increases and that the material within the shear band does not adhere to the classical concept of critical state, but reaches a terminal void ratio that is largely a function of initial void ratio. Furthermore, there appears to be a transition zone between the far field and the fully formed shear block, as opposed to an abrupt delineation as is traditionally inferred. Copyright © 2010 John Wiley & Sons, Ltd.
jueves, 28 de enero de 2010
Multiscale investigation of shear bands in sand: Physical and numerical experiments
In many geotechnical systems, it is not uncommon to observe failure in zones of high localized strain called shear bands. The existing models predict the existence and the extent of these localizations, but provide little insight into the micromechanics within the shear bands. This research captures and compares the variation in microstructure both inside and outside of shear bands that formed in physical laboratory plane strain and companion numerical two-dimensional discrete element method (DEM) biaxial compression experiments. Unsheared and sheared laboratory specimens of Ottawa 20-30 sand of varying dilatancy were solidified using a two-stage resin impregnation procedure. The solidified specimens were sectioned and the resulting surfaces were prepared for microstructure observation using optical bright-field microscopy and stereological analysis. Statistical properties of microstructural parameters for sub-regions in a grid pattern and along predefined inclined zones were determined. Similar measurements were performed on 2D DEM simulation specimens at varying strain levels to characterize the evolution of microstructure with increasing strain. The results showed how differences evolved in the mean, standard deviation, and entropy of void distributions with increasing global strain levels. The results indicate how disorder increases and that the material within the shear band does not adhere to the classical concept of critical state, but reaches a terminal void ratio that is largely a function of initial void ratio. Furthermore, there appears to be a transition zone between the far field and the fully formed shear block, as opposed to an abrupt delineation as is traditionally inferred. Copyright © 2010 John Wiley & Sons, Ltd.
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus
The M2 protein of the influenza A virus is activated by low endosomal pH and performs the essential function of proton transfer into the viral interior. The resulting decrease in pH within the virion is essential for the uncoating and further replication of the viral genetic material. The x-ray crystal [Stouffer AL, et al. (2008) Nature 451:596–599] and solution NMR [Schnell JR, Chou JJ (2008) Nature 451:591–595] structures of the transmembrane region of the M2 homo-tetrameric bundle both revealed pores with narrow constrictions at one end, leaving a question as to how protons enter the channel. His-37, which is essential for proton-gating and selective conduction of protons, lies in the pore of the crystallographic and NMR structures. Here, we explore the different protonation states of the His-37 residues of the M2 bundle in a bilayer using molecular dynamics (MD) simulations. When the His-37 residues are neutral, the protein prefers an Openout-Closedin conformation in which the channel is open to the environment on the outside of the virus but closed to the interior environment of the virus. Diffusion of protons into the channel from the outside of the virus and protonation of His-37 residues in the tetramer stabilizes an oppositely gated Closedout-Openin conformation. Thus, protons might be conducted through a transporter-like mechanism, in which the protein alternates between Openout-Closedin and Closedout-Openin conformations, and His-37 is protonated/deprotonated during each turnover. The transporter-like mechanism is consistent with the known properties of the M2 bundle, including its relatively low rate of proton flux and its strong rectifying behavior.
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