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In this paper, we analyze the nature of stress distribution experienced by large particles in a dense granular media subjected to slow shearing, using the distinct element method. The particles were generated in a three-dimensional cuboidal periodic cell in which a large solid spherical particle was submerged ('submerged particle ') at the center of a bed of monodispersed spherical particles. The granular systems with different size ratio (i.e., the ratio of the diameter of submerged particle to that of the surrounding monodispersed particles) were subjected to quasi-static shearing under constant mean stress condition. The evolution of stress distribution in the submerged particle during shearing was carefully tracked down and presented here. The nature of stress distribution is bifurcated into two components, viz., (i) hydrostatic and (ii) deviatoric components. It has been shown that, for size ratio greater than c.a. 10, the nature of stress distribution in the submerged particle is hydrostatically dominant (increases the 'fluidity'). For smaller size ratios, the nature of stress distribution in the submerged particle is dominantly deviatoric. [DOI: 10.1115/1.1387443]

Author(s): Sara Fernandez-Lopez; Hui-Sun Kim; Ellen C. Choi; Mercedes Delgado; Juan R. Granja [1]; Alisher Khasanov; Karin Kraehenbuehl; Georgina Long; Dana A. Weinberger; Keith M. Wilcoxen; M. Reza Ghadiri (corresponding [...]

It has been possible to design and evaluate a synthetic peptide able to ligate two shorter fragments with considerable efficiency and selectivity. This is the first example of a peptide catalyst with designed substrate binding sites which can substantially speed up a bimolecular reaction.

Experimental evidence shows that the Met -> Nle derivative of the N-terminal domain of the capsid protein cleavage product of the flock house virus efficiently causes the formation of the interdigitated gel phase of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) layers. This is evident in in situ scanning force microscopy of solid supported bilayers and fluorescence spectroscopy of peptide-treated DPPC vesicles. A mechanistic model for the peptide-mediated induction of interdigitation in DPPC bilayers is described.

A study was conducted to clearly characterize some of the structural factors governing the supramolecular organization of the three cyclic peptides belonging to the class of self-assembling peptide nanotubes. The experiment was performed by using grazing incidence X-ray diffraction of Langmuir films of the peptides. Grazing incidence X-ray diffraction and scanning force microscopy were also used to observe the effect of the phospholipid L-alpha-phosphatidic acid dipalmitoyl on the aggregation behavior of two of the peptides.

A porous silicon biosensor using p-type silicon wafers, has been fabricated, and characterized. The transparent porous silicon thin films provided a broad range of pore sizes, and scanning force microscopy and scanning electron microscopy were used to characterize them. The porosity and thickness of the porous layer were determined using reflectance interference spectroscopy and effective medium approximations. The porous silicon matrixes were used in the study of specific protein-ligand binding interactions.

Hollow tubular structures with nanometer-sized interiors or nanotubes are well precedented in both natural and artificial systems. A study was conducted to explore the scope and limitations of a method to promote the biomaterial-based self-assembly of 20 cyclic peptides, which were used to . prepare peptide nanotubes through a selective integration of N-methylated residues, thereby constraining self-assembly to the formation of hydrogen-bonded dimers. The results are discussed.

Research was conducted to examine oriented self-assembly of cyclic peptide nanotubes in lipid membranes. This is the first detailed biophysical investigation of the peptide nanotubes within the context of the lipid film to yield a quantitative estimate of their angle of orientation relative to the lipid bilayer. Results indicate that the orientation of the tubes can be mediated by a supporting environment, implicating biological and nanotechnological applications.

A study was conducted on a new class of self-assembling transmembrane ion channels based on cyclic Beta3-peptides. Liposome-based proton transport assays indicate that Beta3-HTrp residues of channel-forming peptides cyclo[(-Beta3-HTrp)4-] and cyclo[(-Beta3-HTrp-Beta-HLeu)2-] play a key role in solubilizing peptides and allowing their incorporation into lipid membranes. Moreover, the results suggest that the indole NH moiety of Beta3-HTrp may help orient subunits at the lipid-water interface.

An approach based on the self-assembly of flat ring-shaped cyclic peptides into tubular channels in the organosulfur self-assembled monolayers on gold films has proved useful in the design, synthesis and characterization of an unusual diffusion-limited size-selective ion sensor. Grazing angle FTIR spectroscopy has been used to assess the structural properties of monolayer-supported peptide nanotubes. It was also possible to use cyclic voltammetry and impedance spectroscopy to investigate their selective ion transport activities.

A 33-residue synthetic peptide based on the coiled-coil structural motif has been shown to efficiently catalyze the condensation of two shorter peptide fragments with high sequence- and diastereoselectivity. The high sequence- and diastereoselectivity of the 33-residue ligase was indicated by experiments with altered electrophilic and nucleophilic peptide fragments. This research highlights the use of alpha-helical protein-like assemblies in artificial enzyme design.

Thiol additives act as fast catalysts to the formation of polypeptide chains in native chemical ligation. The transthioesterification process has been successfully used to synthesise several peptide-alpha-thioesters such as phospholipase A2. Weakly activated thioesters are manufactured in a chemical reaction using peptide-alpha-thiocarboxylate and an alkyl halide like benzyl bromide. Peptide-alpha-thiocarboxylate activity is regulated using thiol reducing agent.

A 32-residue alpha-helix peptide, is based on the yeast transcription factor GCN4 leucine-zipper domain, is capable of autocatalysis and self-replication. The peptide catalyzes its own synthesis in neutral, dilute aqueous solutions by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments. The peptide's self-replication process exhibits parabolic growth, where the initial rate of product formation correlates with the square-root of initial concentration of the template.

A study has been conducted to describe the peptide self-assembly process by using design principles that are unique for nanotubular structures. The peptide nanotubes were constructed by the self-assembly of flat, ring-shaped peptide subunits that consist of alternating D- and L-amino acid residues. The constructs were held together by intersubunit hydrogen bonds while the crystal structures were held by intertubular hydrophobic packing interactions.