Raman scattering from fractals. Simulation on large structures by the method of moments

We have employed the method of spectral moments to study the density of vibrational states and the Raman coupling coefficient of large 2- and 3- dimensional percolators at threshold and at higher concentration. We first discuss the over-and under-flow problems of the procedure which arise when -like in the present case- it is necessary to calculate a few thousand moments. Then we report on the numerical results; these show that different scattering mechanisms, all {\it a priori} equally probable in real systems, produce largely different coupling coefficients with different frequency dependence. Our results are compared with existing scaling theories of Raman scattering. The situation that emerges is complex; on the one hand, there is indication that the existing theory is not satisfactory; on the other hand, the simulations above threshold show that in this case the coupling coefficients have very little resemblance, if any, with the same quantities at threshold.Comment: 26 pages, RevTex, 8 figures available on reques

Irreversible reorganization in a supercooled liquid originates from localised soft modes

The transition of a fluid to a rigid glass upon cooling is a common route of transformation from liquid to solid that embodies the most poorly understood features of both phases1,2,3. From the liquid perspective, the puzzle is to understand stress relaxation in the disordered state. From the perspective of solids, the challenge is to extend our description of structure and its mechanical consequences to materials without long range order. Using computer simulations, we show that the localized low frequency normal modes of a configuration in a supercooled liquid are causally correlated to the irreversible structural reorganization of the particles within that configuration. We also demonstrate that the spatial distribution of these soft local modes can persist in spite of significant particle reorganization. The consequence of these two results is that it is now feasible to construct a theory of relaxation length scales in glass-forming liquids without recourse to dynamics and to explicitly relate molecular properties to their collective relaxation.Comment: Published online: 20 July 2008 | doi:10.1038/nphys1025 Available from http://www.nature.com/nphys/journal/v4/n9/abs/nphys1025.htm

Continuum limit of amorphous elastic bodies: A finite-size study of low frequency harmonic vibrations

The approach of the elastic continuum limit in small amorphous bodies formed by weakly polydisperse Lennard-Jones beads is investigated in a systematic finite-size study. We show that classical continuum elasticity breaks down when the wavelength of the sollicitation is smaller than a characteristic length of approximately 30 molecular sizes. Due to this surprisingly large effect ensembles containing up to N=40,000 particles have been required in two dimensions to yield a convincing match with the classical continuum predictions for the eigenfrequency spectrum of disk-shaped aggregates and periodic bulk systems. The existence of an effective length scale \xi is confirmed by the analysis of the (non-gaussian) noisy part of the low frequency vibrational eigenmodes. Moreover, we relate it to the {\em non-affine} part of the displacement fields under imposed elongation and shear. Similar correlations (vortices) are indeed observed on distances up to \xi~30 particle sizes.Comment: 28 pages, 13 figures, 3 table

The evolution of vibrational excitations in glassy systems

The equations of the mode-coupling theory (MCT) for ideal liquid-glass transitions are used for a discussion of the evolution of the density-fluctuation spectra of glass-forming systems for frequencies within the dynamical window between the band of high-frequency motion and the band of low-frequency-structural-relaxation processes. It is shown that the strong interaction between density fluctuations with microscopic wave length and the arrested glass structure causes an anomalous-oscillation peak, which exhibits the properties of the so-called boson peak. It produces an elastic modulus which governs the hybridization of density fluctuations of mesoscopic wave length with the boson-peak oscillations. This leads to the existence of high-frequency sound with properties as found by X-ray-scattering spectroscopy of glasses and glassy liquids. The results of the theory are demonstrated for a model of the hard-sphere system. It is also derived that certain schematic MCT models, whose spectra for the stiff-glass states can be expressed by elementary formulas, provide reasonable approximations for the solutions of the general MCT equations.Comment: 50 pages, 17 postscript files including 18 figures, to be published in Phys. Rev.

Water Dynamics at Protein Interfaces: Ultrafast Optical Kerr Effect Study

The behavior of water molecules surrounding a protein can have an important bearing on its structure and function. Consequently, a great deal of attention has been focused on changes in the relaxation dynamics of water when it is located at the protein surface. Here we use the ultrafast optical Kerr effect to study the H-bond structure and dynamics of aqueous solutions of proteins. Measurements are made for three proteins as a function of concentration. We find that the water dynamics in the first solvation layer of the proteins are slowed by up to a factor of 8 in comparison to those in bulk water. The most marked slowdown was observed for the most hydrophilic protein studied, bovine serum albumin, whereas the most hydrophobic protein, trypsin, had a slightly smaller effect. The terahertz Raman spectra of these protein solutions resemble those of pure water up to 5 wt % of protein, above which a new feature appears at 80 cm–1, which is assigned to a bending of the protein amide chain

K13 blocks KSHV lytic replication and deregulates vIL6 nad hIL6 expression: A model of lytic replication induced clonal selection in viral oncogenesis

Background. Accumulating evidence suggests that dysregulated expression of lytic genes plays an important role in KSHV (Kaposi's sarcoma associated herpesvirus) tumorigenesis. However, the molecular events leading to the dysregulation of KSHV lytic gene expression program are incompletely understood. Methodoloxy/Principal Findings. We have studied the effect of KSHV-encoded latent protein vFLIP K13, a potent activator of the NF-κB pathway, on lytic reactivation of the virus. We demonstrate that K13 antagonizes RTA, the KSHV lytic-regulator, and effectively blocks the expression of lytic proteins, production of infectious virions and death of the infected cells. Induction of lytic replication selects for clones with increased K13 expression and NF-κB activity, while siRNA-mediated silencing of K13 induces the expression of lytic genes. However, the suppressive effect of K13 on RTA-induced lytic genes is not uniform and it falls to block RTA-induced viral IL6 secretion and cooperates with RTA to enhance cellular IL-6 production, thereby dysregulating the lytic gene expression program. Conclusions/Significance. Our results support a model in which ongoing KSHV, lytic replication selects for clones with progressively higher levels of K13 expression and NF-κB activity, which in turn drive KSHV tumorigenesis by not only directly stimulating cellular survival and proliferation, but also indirectly by dysregulating the viral lytic gene program and allowing non-lytic production of growth-promoting viral and cellular genes. Lytic Replication-Induced Clonal Selection (LyRICS) may represent a general mechanism in viral oncogenesis. 2007 Zhao et al

A laser spectrometry technique for the determination of aerosol characteristics Preliminary checks of the system and first results obtained

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Simulated performances of a single particle laser light scattering analyzer

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