Donut-Shaped Fingerprint In Homologous Polypeptide Relationships-A Topological Feature Related To Pathogenic Structural Changes In Conformational Disease

Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.

Fabrication and characterization of self-doped poly (aniline-co-anthranilic acid) nanorods in bundles

Poly (aniline-co-anthranilic acid) (PANANA) nanorods in bundles was prepared successfully in an alcohol/aqueous media without assistance of an), other kinds of acids. Anthranilic acid played all roles of monomer, acid-media provider, and dopant in the reaction system, and ammonium persulfate (APS) served as the oxidant. The morphologies of PANANA nanorods in bundles were investigated by scanning electron microscopy (SEM). Influences of the monomer molar ratio on the resulting morphology were investigated. Moreover the formation mechanism of the nanostructured copolymer was proposed. FT-IR. UV-vis and X-ray diffraction (XRD) measurements were used to confirm the molecular and electrical structure of the self-doped PANANA. The intrinsic properties, such as conductivity, electrochemical redox activity and room-temperature solubility of the resulting copolymer were explored.

A Crack Perpendicular to the Bimaterial Interface in Finite Solid

The dislocation simulation method is used in this paper to derive the basic equations for a crack perpendicular to the bimaterial interface in a finite solid. The complete solutions to the problem, including the T stress and the stress intensity factors are obtained. The stress field characteristics are investigated in detail. It is found that when the crack is within a weaker material, the stress intensity factor is smaller than that in a homogeneous material and it decreases when the distance between the crack tip and interface decreases. When the crack is within a stiffer material, the stress intensity factor is larger than that in a homogeneous material and it increases when the distance between the crack tip and interface decreases. In both cases, the stress intensity factor will increase when the ratio of the size of a sample to the crack length decreases. A comparison of stress intensity factors between a finite problem and an infinite problem has been given also. The stress distribution ahead of the crack tip, which is near the interface, is shown in details and the T stress effect is considered.

Extending Tsai-Hill and norris criteria to predict cracking direction in orthotropic materials

methods of lifetime measurement are discussed.

An application of adjoint variational method to the capillary instability in liquid

In this paper, applying the direct variational approach of first-order approximation to the capillary instability problem for the eases of rotating liquid column, toroid and films on both sides of cylinder, we have obtained the necessary and sufficient conditions for motion stability of the "cylindrical coreliquid-liquid-cylindrical shell" systems. The results obtained before are found to be special cases of the present investigation. At the same time, we have explained physical essence of rotating instability and settled a few disputes in previous investigations.

A smoothing technique for discrete delta functions with application to immersed boundary method in moving boundary simulations.

The effects of complex boundary conditions on flows are represented by a volume force in the immersed boundary methods. The problem with this representation is that the volume force exhibits non-physical oscillations in moving boundary simulations. A smoothing technique for discrete delta functions has been developed in this paper to suppress the non-physical oscillations in the volume forces. We have found that the non-physical oscillations are mainly due to the fact that the derivatives of the regular discrete delta functions do not satisfy certain moment conditions. It has been shown that the smoothed discrete delta functions constructed in this paper have one-order higher derivative than the regular ones. Moreover, not only the smoothed discrete delta functions satisfy the first two discrete moment conditions, but also their derivatives satisfy one-order higher moment condition than the regular ones. The smoothed discrete delta functions are tested by three test cases: a one-dimensional heat equation with a moving singular force, a two-dimensional flow past an oscillating cylinder, and the vortex-induced vibration of a cylinder. The numerical examples in these cases demonstrate that the smoothed discrete delta functions can effectively suppress the non-physical oscillations in the volume forces and improve the accuracy of the immersed boundary method with direct forcing in moving boundary simulations.

Subgrid-scale contributions to Lagrangian time correlations in isotropic turbulence

The application of large-eddy simulation (LES) to particle-laden turbulence raises such a fundamental question as whether the LES with a subgrid scale (SGS) model can correctly predict Lagrangian time correlations (LTCs). Most of the currently existing SGS models are constructed based on the energy budget equations. Therefore, they are able to correctly predict energy spectra, but they may not ensure the correct prediction on the LTCs. Previous researches investigated the effect of the SGS modeling on the Eulerian time correlations. This paper is devoted to study the LTCs in LES. A direct numerical simulation (DNS) and the LES with a spectral eddy viscosity model are performed for isotropic turbulence and the LTCs are calculated using the passive vector method. Both a priori and a posteriori tests are carried out. It is observed that the subgrid-scale contributions to the LTCs cannot be simply ignored and the LES overpredicts the LTCs than the DNS. It is concluded from the straining hypothesis that an accurate prediction of enstrophy spectra is most critical to the prediction of the LTCs.

Phase control of switching from positive to negative index material in a four-level atomic system

Electric and magnetic responses of the medium to the probe field are analysed in a four-level loop atomic system by taking into account the relative phase of the applied fields. An interesting phenomenon is found: under suitable conditions, a change of the refractive index from positive to negative can occur by modulating the relative phase of the applied fields. Then the medium can be switched from a positive index material to a negative index material in our scheme. In addition, a negative index material can be realized in different frequency regions by adjusting the relative phase. It may give us a convenient way to obtain the desired material with positive or negative index.

Specklegram in a grapefruit fiber and its response to external mechanical disturbance in a single-multiple-single mode fiber structure

Specklegram in multimode fiber has successfully been used as a sensor for detecting mechanical disturbance. Speckles in a multimode pure silica grapefruit fiber are observed and compared to that of a step-index multimode fiber, showing different features between them. The sensitivities to external disturbance of two kinds of fiber were measured, based on single-multiple-single mode (SMS) fiber structure. Experimental results show that the grapefruit fiber shows higher sensitivity than does the step-index multimode fiber. The transmission spectrum of the grapefruit fiber was measured as well, showing some oscillation features that are significantly different from that of a step-index multimode fiber. The experiments may provide suggestions to understand the mechanisms of light propagation in grapefruit fibers. (D 2008 Optical Society of America.

Infrared-to-visible upconversion emissions in Er3+ doped TeO2-based oxyhalide glasses

The fluorescence and up-conversion spectral properties of Er3+-doped TeO2-ZnO and TeO2-ZnO-PbCl2 glasses suitable for developing optical fiber amplifier and laser have been fabricate and characterized. Strong green (around 527-550 nm) and red (around 661 nm) up-conversion emissions under 977 nm laser diode excitation were investigated, corresponding to H-2(11/2), S-4(3/2), --> I-4(15/2) and F-4(9/2) --> I-4(15/2) transitions of Er3+ ions respectively, have been observed and the involved mechanisms have been explained. The dependence of up-converted fluorescence intensity versus laser power confirm that two-photons contribute to up-conversion of the green-red emissions. The novelty of this kind of optical material has been its ability in resisting devitrification, and its promising optical properties strongly encourage for their further development as the rare-earth doped optical fiber amplifiers and upconversion fiber laser systems.

Infrared to visible upconversion fluorescence in Yb,Tm : YAG single crystal

Absorption spectrum from 400 to 2000 run and upconversion fluorescence spectra under 940 nm pumping of YAG single crystal codoped with 5 at.% Yb3+ and 4 at.% Tm3+ were studied at room temperature. The blue upconversion emission centered at 483 nm corresponds to the transition (1)G(4) -> H-3(6), the emission band around 646 nm corresponds to the transition (1)G(4) -> F-3(4) of Tm3+. Energy transfer from Yb3+ to Tm3+ is mainly nonradiative and the transfer efficiency was experimentally assessed. The line strengths, transition probabilities and radiative lifetimes of (1)G(4) level were calculated by using Judd-Ofelt theory. Gain coefficient calculated from spectra shows that the upconversion corresponding with transitions (1)G(4) -> H-3(6) in YAG doped with Yb3+ and Tm3+ is potentially useful for blue light Output. (c) 2006 Elsevier B.V. All rights reserved.