Structural analysis of human CCR2b and primate CCR2b by molecular modeling and molecular dynamics simulation

CCR2b, a chemokine receptor for MCP-1, -2, -3, -4, plays an important role in a variety of diseases involving infection, inflammation, and/or injury, as well as being a coreceptor for HIV-1 infection. Two models of human CCR2b (hCCR2b) were generated by h

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Structural selectivity of aromatic diamidines

Competition dialysis was used to study the interactions of 13 substituted aromatic diamidine compounds with 13 nucleic acid structures and sequences. The results show a striking selectivity of these compounds for the triplex structure poly dA:(poly dT)(2), a novel aspect of their interaction with nucleic acids not previously described. The triplex selectivity of selected compounds was confirmed by thermal denaturation studies. Triplex selectivity was found to be modulated by the location of amidine substiuents on the core phenyl-furan-phenyl ring scaffold. Molecular models were constructed to rationalize the triplex selectivity of DB359, the most selective compound in the series. Its triplex selectivity was found to arise from optimal ring stacking on base triplets, along with proper positioning of its amidine substituents to occupy the minor and the major-minor grooves of the triplex. New insights into the molecular recognition of nucleic acid structures emerged from these studies, adding to the list of available design principles for selectively targeting DNA and RNA.

Stochastic Structural Model of Rock and Soil Aggregates by Continuum-Based Discrete Element Method

This paper first presents a stochastic structural model to describe the random geometrical features of rock and soil aggregates. The stochastic structural model uses mixture ratio, rock size and rock shape to construct the microstructures of aggregates,and introduces two types of structural elements (block element and jointed element) and three types of material elements (rock element, soil element, and weaker jointed element)for this microstructure. Then, continuum-based discrete element method is used to study the deformation and failure mechanism of rock and soil aggregate through a series of loading tests. It is found that the stress-strain curve of rock and soil aggregates is nonlinear, and the failure is usually initialized from weaker jointed elements. Finally, some factors such as mixture ratio, rock size and rock shape are studied in detail. The numerical results are in good agreement with in situ test. Therefore, current model is effective for simulating the mechanical behaviors of rock and soil aggregates.

Long-range automaton models of earthquakes: Power-law accelerations, correlation evolution, and mode-switching

We introduce a conceptual model for the in-plane physics of an earthquake fault. The model employs cellular automaton techniques to simulate tectonic loading, earthquake rupture, and strain redistribution. The impact of a hypothetical crustal elastodynamic Green's function is approximated by a long-range strain redistribution law with a r(-p) dependance. We investigate the influence of the effective elastodynamic interaction range upon the dynamical behaviour of the model by conducting experiments with different values of the exponent (p). The results indicate that this model has two distinct, stable modes of behaviour. The first mode produces a characteristic earthquake distribution with moderate to large events preceeded by an interval of time in which the rate of energy release accelerates. A correlation function analysis reveals that accelerating sequences are associated with a systematic, global evolution of strain energy correlations within the system. The second stable mode produces Gutenberg-Richter statistics, with near-linear energy release and no significant global correlation evolution. A model with effectively short-range interactions preferentially displays Gutenberg-Richter behaviour. However, models with long-range interactions appear to switch between the characteristic and GR modes. As the range of elastodynamic interactions is increased, characteristic behaviour begins to dominate GR behaviour. These models demonstrate that evolution of strain energy correlations may occur within systems with a fixed elastodynamic interaction range. Supposing that similar mode-switching dynamical behaviour occurs within earthquake faults then intermediate-term forecasting of large earthquakes may be feasible for some earthquakes but not for others, in alignment with certain empirical seismological observations. Further numerical investigation of dynamical models of this type may lead to advances in earthquake forecasting research and theoretical seismology.

Sample-specific behavior in failure models of disordered medial

The concept ''sample-specific'' is suggested to describe the behavior of disordered media close to macroscopic failure. it is pointed out that the transition from universal scaling to sample-specific behavior may be a common phenomenon in failure models of disordered media. The dynamical evolution plays an important role in the transition.

Structural change of laser-irradiated Ge2Sb2Te5 films studied by electrical property measurement

Sheet resistance of laser-irradiated Ge2Sb2Te5 thin films prepared by magnetron sputtering was measured by the four-point probe method. With increasing laser power the sheet resistance undergoes an abrupt drop from 10(7) to 10(3) Omega/square at about 580 mW. The abrupt drop in resistance is due to the structural change from amorphous to crystalline state as revealed by X-ray diffraction (XRD) study of the samples around the abrupt change point. Crystallized dots were also formed in the amorphous Ge2Sb2Te5 films by focused short pulse laser-irradiated, the resistivities at the crystallized dots and the non-crystallized area are 3.375 x 10(-3) and 2.725 Omega m, sheet resistance is 3.37 x 10(4) and 2.725 x 10(7) Omega/square respectively, deduced from the I-V Curves that is obtained by conductive atomic force microscope (C-AFM). (C) 2008 Elsevier B.V. All rights reserved.

Structural role of fluoride in aluminophosphate sol-gel glasses: High-resolution double-resonance NMR studies

The local structure of Na-Al-P-O-F glasses, prepared by a novel sol-gel route, was extensively investigated by advanced solid-state NMR techniques. Al-21{F-19} rotational echo double resonance (REDOR) results indicate that the F incorporated into aluminophosphate glass is preferentially bonded to octahedral Al units and results in a significant increase in the concentration of six-coordinated aluminum. The extent of Al-F and Al-O-P connectivities are quantified consistently by analyzing Al-27{P-31} and Al-21{F-19} REDOR NMR data. Two distinct types of fluorine species were identified and characterized by various F-19{Al-27}, F-19{Na-23}, and F-19{P-31} double resonance experiments, which were able to support peak assignments to bridging (Al-F-Al, -140 ppm) and terminal (Al-F, -170 ppm) units. On the basis of the detailed quantitative dipole-dipole coupling information obtained, a comprehensive structural model for these glasses is presented, detailing the structural speciation as a function of composition.

Structural Integration of Tellurium Oxide into Mixed-Network-Former Glasses: Connectivity Distribution in the System NaPO3–TeO2

FSodium phosphate tellurite glasses in the system (NaPO3)(x)(TeO2)(1-x) were prepared and structurally characterized by thermal analysis, vibrational spectroscopy, X-ray photoelectron spectroscopy (XPS) and a variety of complementary solid-state nuclear magnetic resonance (NMR) techniques. Unlike the situation in other mixed-network-former glasses, the interaction between the two network formers tellurium oxide and phosphorus oxide produces no new structural units, and no sharing of the network modifier Na2O takes place. The glass structure can be regarded as a network of interlinked metaphosphate-type P(2) tetrahedral and TeO4/2 antiprismotic units. The combined interpretation of the O 1s XPS data and the P-31 solid-state NMR spectra presents clear quantitative evidence for a nonstatistical connectivity distribution. Rather the formation of homootomic P-O-P and Te-O-Te linkages is favored over mixed P-O-Te connectivities. As a consequence of this chemical segregation effect, the spatial sodium distribution is not random, as also indicated by a detailed analysis of P-31/No-23 rotational echo double-resonance (REDOR) experiments. ACHTUNGTRENUNG(TeO2)1 x were prepared and structurally characterized by thermal analysis,vibrat ional spectroscopy,X-ray photoelectron spectroscopy (XPS) and a variety of complementary solid-state nuclear magnetic resonance (NMR) techniques. Unlike the situation in other mixed-network-former glasses,the interaction between the two network formers tellurium oxide and phosphorus oxide produces no new structural units,and no sharing of the network modifier Na2O takes place. The glass structure can be regarded as a network of interlinked metaphosphate-type P(2) tetrahedral and TeO4/2 antiprismatic units. The combined interpretation of the O 1s XPS data and the 31P solid-state NMR spectra presents clear quantitative evidence for a nonstatistical connectivity distribution. Rather,the formation of homoatomic P O P and Te O Te linkages is favored over mixed P O Te connectivities. As a consequence of this chemical segregation effect,the spatial sodium distribution is not random,as also indicated by a detailed analysis of 31P/23Na rotational echo double-resonance (REDOR) experiments.

Spectroscopic and structural properties of YbF3-doped fluorophosphate glasses

Compositional influences on the spectroscopic properties of Yb3+ and the structural variations with the introduction of YbF3 were studied in fluorophosphate glasses. Emission cross-section (sigma(emi)) and gain coefficient (sigma(emi) x tau(f)) were calculated which exhibit maximum at RF2 = 33 mol%. YbF3 has an important effect on the glass forming ability of fluorophosphate glasses when RF2 is over 36 mol%. The study of Raman spectra showed big differences on the glass structure between non-Yb3+ and Yb3+ -doped glasses. The main building units in Yb3+-doped samples are metaphosphate groups, pyrophosphate groups (P-2(O,F)(7), PO3F), Al[F-6] +Al[O,F](6) and F3Al-O-AlF3 while those of the non-Yb3+-doped glasses are monophosphate group P(O,F)(4), little pyrophosphate group, Al[F-4] + Al[F-6] + Al[O,F](4) + Al[O,F](6) and F3Al-O-AlF3, which means Yb3+ ions contribute to a better glass polymerization and network uniformity. (C) 2004 Elsevier B.V. All rights reserved.

Thermal analyses, spectral characterization and structural interpretation of Yb3+ doped TeO2-ZnO-ZnCl2 glasses

Bulk-lasses have been prepared in the TeO2-ZnO-ZnCl2 systems. Their characteristic temperatures were determined and analyzed. Raman and FT-IR spectra were used to analyze the effect of ZnCl2 on the structure and spectral properties of tellurite glasses and OH- groups in this glass system. The spectroscopic properties including absorption spectra, emission cross-sections and fluorescence lifetimes of Yb3+ in TeO2-ZnO-ZnCl2 were measured and calculated. It is demonstrated that the progressive replacement less than 20 mol% of TeO2 by ZnCl2 improves the thermal stability, removes the OH- groups, turns TeO4 bipyramidal arrangement into TeO3 (and/or TeO3+1) trigonal pyramids structures and results in the decrease of the symmetry of the structure, which increases the emission cross-sections and lifetimes. But when the content of ZnCl2 up to 30 mol%, the glass system becomes more hygroscopic and introduces more OH- groups, which decrease the emission cross-sections and shorten the lifetimes. The results show that the glass system with (TeO2)-Te-69-(ZnO)-Zn-10-20ZnCl(2)-1Yb(2)O(3) is a desirable component for active laser media for high power generation. (c) 2005 Elsevier B.V. All rights reserved.

Effects of PbF2 on the spectroscopic, lasing and structural properties of Yb3+-doped fluorophosphate glass

Effect of PbF2 on Yb3+ -doped fluorophosphate glasses is studied. Results indicate that proper amount of PbF2 has absolute advantages in improving the crystallization stability of fluorophosphate glasses. T, value performs a decreasing and increasing tendency with 25 mol% PbF2 as the turning-point. And the spectroscopic properties such as absorption and emission cross section, effective fluorescence linewidth are apparently enhanced with PbF2 over 25 mol%. Lasing parameters beta, I-sat and I-min increase slightly with the addition of PbF2. Raman analysis proves that over 20 mol% PbF2, destroys the phosphate vibration groups greatly. (c) 2005 Elsevier Ltd. All rights reserved.

Annealing effects on the optical and structural properties of Al2O3/SiO2 films as UV antireflection coatings on 4H-SiC substrates

Al2O3/SiO2 films have been prepared by electron-beam evaporation as ultraviolet (UV) antireflection coatings on 4H-SiC substrates and annealed at different temperatures. The films were characterized by reflection spectra, ellipsometer system, atomic force microscopy (AFM), X-ray diffraction (XRD) and Xray photoelectron spectroscopy (XPS), respectively. As the annealing temperature increased, the minimum reflectance of the films moved to the shorter wavelength for the variation of refractive indices and the reduction of film thicknesses. The surface grains appeared to get larger in size and the root mean square (RMS) roughness of the annealed films increased with the annealing temperature but was less than that of the as-deposited. The Al2O3/SiO2 films maintained amorphous in microstructure with the increase of the temperature. Meanwhile, the transition and diffusion in film component were found in XPS measurement. These results provided the important references for Al2O3/SiO2 films annealed at reasonable temperatures and prepared as fine anti-reflection coatings on 4H-SiC-based UV optoelectronic devices. (c) 2008 Elsevier B.V. All rights reserved.