971 resultados para MOUFANG LOOPS
Resumo:
The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include alpha-helices, beta-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 angstrom. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-beta class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving beta-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare beta-turns of type I' and II' are also identified as preferred sites for insertions.
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Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the er effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.
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The exoloops of glycoprotein hormone receptors (GpHRs) transduce the signal generated by the ligand-ectodomain interactions to the transmembrane helices either through direct hormonal contact and/or by modulating the interdomain interactions between the hinge region (HinR) and the transmembrane domain (TMD). The ligand-induced conformational alterations in the HinRs and the interhelical loops of luteinizing hormone receptor/follicle stimulating hormone receptor/thyroid stimulating hormone receptor were mapped using exoloop-specific antibodies generated against a mini-TMD protein designed to mimic the native exoloop conformations that were created by joining the thyroid stimulating hormone receptor exoloops constrained through helical tethers and library-derived linkers. The antibody against the mini-TMD specifically recognized all three GpHRs and inhibited the basal and hormone-stimulated cAMP production without affecting hormone binding. Interestingly, binding of the antibody to all three receptors was abolished by prior incubation of the receptors with the respective hormones, suggesting that the exoloops are buried in the hormone-receptor complexes. The antibody also suppressed the high basal activities of gain-of-function mutations in the HinRs, exoloops, and TMDs such as those involved in precocious puberty and thyroid toxic adenomas. Using the antibody and point/deletion/chimeric receptor mutants, we demonstrate that changes in the HinR-exoloop interactions play an important role in receptor activation. Computational analysis suggests that the mini-TMD antibodies act by conformationally locking the transmembrane helices by means of restraining the exoloops and the juxta-membrane regions. Using GpHRs as a model, we describe a novel computational approach of generating soluble TMD mimics that can be used to explain the role of exoloops during receptor activation and their interplay with TMDs.
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Most Java programmers would agree that Java is a language that promotes a philosophy of “create and go forth”. By design, temporary objects are meant to be created on the heap, possibly used and then abandoned to be collected by the garbage collector. Excessive generation of temporary objects is termed “object churn” and is a form of software bloat that often leads to performance and memory problems. To mitigate this problem, many compiler optimizations aim at identifying objects that may be allocated on the stack. However, most such optimizations miss large opportunities for memory reuse when dealing with objects inside loops or when dealing with container objects. In this paper, we describe a novel algorithm that detects bloat caused by the creation of temporary container and String objects within a loop. Our analysis determines which objects created within a loop can be reused. Then we describe a source-to-source transformation that efficiently reuses such objects. Empirical evaluation indicates that our solution can reduce upto 40% of temporary object allocations in large programs, resulting in a performance improvement that can be as high as a 20% reduction in the run time, specifically when a program has a high churn rate or when the program is memory intensive and needs to run the GC often.
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Nonlinear dielectric response of BaBi4Ti4O15 ceramics synthesized via the conventional solid-state reaction route has been monitored over a wide range of electric field strengths (E-0 = 0.5 - 5 kV/cm). Dielectric permittivity was found to increase linearly within the range of applied field. Rayleigh relations were employed to interpret the nonlinear dielectric response and the contribution of irreversible domain wall motion to the macroscopic permittivity was separated. The values of room temperature Rayleigh dielectric coefficient (alpha) and relative initial permittivity (epsilon'(init)) were found to be 2.28 +/- 0.02 cm/kV and 146.10 +/- 0.07, respectively. A reasonable agreement between the simulated and measured polarization-electric field (P-E) hysteresis loops was observed at an applied electric field of 5 kV/cm.
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Three samples of multiwall carbon nanotubes (MWCNT) TF200, TF150 and TF100, where T and F stand for toluene and ferrocene respectively, and numeral denotes the amount (mg) of ferrocene] filled with iron-nanoparticles (Fe-NPs) of different aspect ratios are grown by chemical vapor deposition of toluene-ferrocene mixture. Energy dispersive X-ray analysis shows a systematic variation in the intensities of peak corresponding to Fe, indicating that Fe is present in different amounts in the three MWCNT samples. The lengths of Fe-NPs lie in the range of 200-250; 80-120; and 30-40 nm for TF200, TF150 and TF100, respectively, as estimated statistically from transmission electron microscopy micrographs. However, the diameter of the encapsulated Fe-NPs does not vary significantly for different samples and is 20-30 nm for all samples. Hysteresis loop measurements on these MWCNT samples were done at 10, 150 and 300 K up to an applied field of 1.5 T. At 10 K, values of coercivity are 2584, 2315, and 2251 Oe for TF200, TF150 and TF100 respectively. This is attributed to the strong shape anisotropy of the Fe-NPs and significant dipolar interactions between them. Further, M-H loops reveal that saturation magnetization of TF200 is almost four times that of TF100 at all temperatures.
Resumo:
The paper reports exchange-spring soft and hard ferrite nanocomposites synthesized by chemical co-precipitation with or without the application of ultrasonic vibration. The composites contained BaFe12O19 as the hard phase and CoFe2O4/MgFe2O4 as the soft phase. X-ray diffraction patterns of the samples in the optimum calcined condition indicated the presence of soft ferrites as face-centred cubic (fcc) and hard ferrites as hexagonal close packed (hcp) structure respectively. Temperature dependence of magnetization in the range of 20-700 degrees C demonstrated distinct presence of soft and hard ferrites as magnetic phases which are characterized by wide difference in magnetic anisotropy and coercivity. Exchange-spring mechanism led these nanocomposite systems to exchange-coupled, which ultimately produced convex hysteresis loops characteristic of a single-phase permanent magnet. Fairly high value of coercivity and maximum energy product were observed for the samples in the optimum calcined conditions with a maximum applied field of 1600 kA/m (2 T).
Resumo:
Phase-locked loops (PLLs) are necessary in applications which require grid synchronization. Presence of unbalance or harmonics in the grid voltage creates errors in the estimated frequency and angle of a PLL. The error in estimated angle has the effect of distorting the unit vectors generated by the PLL. In this paper, analytical expressions are derived which determine the error in the phase angle estimated by a PLL when there is unbalance and harmonics in the grid voltage. By using the derived expressions, the total harmonic distortion (THD) and the fundamental phase error of the unit vectors can be determined for a given PLL topology and a given level of unbalance and distortion in the grid voltage. The accuracy of the results obtained from the analytical expressions is validated with the simulation and experimental results for synchronous reference frame PLL (SRF-PLL). Based on these expressions, a new tuning method for the SRF-PLL is proposed which quantifies the tradeoff between the unit vector THD and the bandwidth of the SRF-PLL. Using this method, the exact value of the bandwidth of the SRF-PLL can be obtained for a given worst case grid voltage unbalance and distortion to have an acceptable level of unit vector THD. The tuning method for SRF-PLL is also validated experimentally.
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The effect of annealing on structural defects and d(0) ferromagnetism in SnO2 nanoparticles prepared by solution combustion method is investigated. The as-synthesized SnO2 nanoparticles were annealed at 400-800 degrees C for 2 h, in ambient conditions. The crystallinity, size, and morphology of the samples were studied using x-ray diffraction and transmission electron microscopy studies. The annealing results in grain growth due to coarsening as well as reduction in oxygen vacancies as confirmed by Raman spectroscopy, photoluminescence spectroscopy, and x-ray photoelectron spectroscopy. All the as synthesized and annealed samples exhibit room temperature ferromagnetism (RTFM) with distinct hysteresis loops and the saturation magnetization as high as similar to 0.02 emu/g in as-synthesized samples. However, the saturation magnetization is drastically reduced with increasing annealing temperature. Further the presence of singly charged oxygen vacancies (V-o(-) signal at g-value 1.99) is confirmed by electron paramagnetic resonance studies, which also diminish with increasing annealing temperature. The observed diminishing RTFM and simultaneous evidences of diminishing O vacancies clearly indicate that RTFM is driven by defects in oxide lattice and confirms primary role of oxygen vacancies in inducing ferromagnetic ordering in metal oxide semiconductors. The study also provides improved fundamental understanding regarding the ambiguity in the origin of intrinsic RTFM in semiconducting metal oxides and projects their technological application in the field of spintronics. (C) 2013 AIP Publishing LLC.
Resumo:
Mn0.4Zn0.6Fe2O4 powders were prepared by microwave hydrothermal method. The powders were characterized by X-ray diffraction, transmission electron microscope. The powders were sintered at different temperatures 400, 500, 600, 700, 800 and 900 degrees C/30 min using microwave sintering method. The grain size was estimated by scanning electron microscope. The room temperature dielectric and magnetic properties were studied in the frequency range (100 kHz-1.8 GHz). The magnetization properties were measured upto 1.5 T. The acoustic emission has been measured along the hysteresis loops from 80 K to Curie temperature. It is found that the magneto-acoustic emission (MAE) activity along hysteresis loop is proportional to the hysteresis losses during the same loop. This law has been verified on series of polycrystalline ferrites and found that the law is valid whatever the composition, the grain size and temperature. It is also found that the domain wall creation/or annihilation processes are the origin of the MAE. (C) 2013 Published by Elsevier Ltd.
Resumo:
Boron oxide (B2O3) addition to pre-reacted K0.5Na0.5NbO3 (KNN) powders facilitated swift densification at relatively low sintering temperatures which was believed to be a key to minimize potassium and sodium loss. The base KNN powder was synthesized via solid-state reaction route. The different amounts (0.1-1 wt%) of B2O3 were-added, and ceramics were sintered at different temperatures and durations to optimize the amount of B2O3 needed to obtain KNN pellets with highest possible density and grain size. The 0.1 wt% B2O3-added KNN ceramics sintered at 1,100 A degrees C for 1 h exhibited higher density (97 %). Scanning electron microscopy studies confirmed an increase in average grain size with increasing B2O3 content at appropriate temperature of sintering and duration. The B2O3-added KNN ceramics exhibited improved dielectric and piezoelectric properties at room temperature. For instance, 0.1 wt% B2O3-added KNN ceramic exhibited d (33) value of 116 pC/N which is much higher than that of pure KNN ceramics. Interestingly, all the B2O3-added (0.1-1 wt%) KNN ceramics exhibited polarization-electric field (P vs. E) hysteresis loops at room temperature. The remnant polarization (P (r)) and coercive field (E (c)) values are dependent on the B2O3 content and crystallite size.
Resumo:
Structural dynamics, dielectric permittivity and ferroelectric properties in poly(vinylidene fluoride) (PVDF)/poly(methyl methacrylate) (PMMA) (PVDF/PMMA) blends with respect to crystalline morphology was systematically investigated in presence of amine functionalized MWNTs (NH2-MWNTs) using dielectric spectroscopy. The crystalline morphology and the crystallization driven demixing in the blends was assessed by light microscopy (LM), wide angle X-ray diffraction (WXRD) and, in situ, by shear rheology. The crystal nucleation activity of PVDF was greatly induced by NH2-MWNTs, which also showed two distinct structural relaxations in dielectric loss owing to mobility confinement of PVDF chains and smaller cooperative lengths. The presence of crystal-amorphous interphase was supported by the presence of interfacial polarization at lower frequencies in the dielectric loss spectra. On contrary, the control blends showed a single broad relaxation at higher frequency due to defective crystal nuclei. This was further supported by monitoring the dielectric relaxations during isothermal crystallization of PVDF in the blends. These observations were addressed with respect to the spherulite sizes which were observed to be larger in case of blends with NH2-MWNTs. Higher dielectric permittivity with minimal losses was also observed in blends with NH2-MWNTs as compared to neat PVDF. Polarization obtained using P-E (polarization-electric field) hysteresis loops was higher in case of blends with NH2-MWNTs in contrast to control blends and PVDF. These observations were corroborated with the charge trapped at the crystal-amorphous interphase and larger crystal sizes in the blends with NH2-MWNTs. The microstructure and localization of MWNTs were assessed using SEM.
Resumo:
Rheological behavior of semi-solid slurries forms the backbone of semi-solid processing of metallic alloys. In particular, the effects of several process and metallurgical parameters such as shear rate, shear time, temperature, rest time and size, distribution and morphology of the primary phase on the viscosity of the slurry needs in-depth characterization. In the present work, rheological behaviour of the semisolid aluminium alloy (A356) slurry is investigated by using a high temperature Searle type Rheometer using concentric cylinders. Three different types of experiment are carried out: isothermal test, continuous cooling test and steady state test. Continuous decrease in viscosity is observed with increasing shear rate at a fixed temperature (isothermal test). It is also found that the viscosity increases with decreasing temperature for a particular shear rate due to increasing solid fraction (continuous cooling test). Thixotropic nature of the slurry is confirmed from the hysteresis loops obtained during experimentation. Time dependence of slurry viscosity has been evaluated from the steady state tests. After a longer shearing time under isothermal conditions the starting dendritic structure of the said alloy is transformed into globular grains due to abrasion, agglomeration, welding and ripening.
Resumo:
Phase-locked loops (PLLs) are necessary in grid connected systems to obtain information about the frequency, amplitude and phase of the grid voltage. In stationary reference frame control, the unit vectors of PLLs are used for reference generation. It is important that the PLL performance is not affected significantly when grid voltage undergoes amplitude and frequency variations. In this paper, a novel design for the popular single-phase PLL topology, namely the second-order generalized integrator (SOGI) based PLL is proposed which achieves minimum settling time during grid voltage amplitude and frequency variations. The proposed design achieves a settling time of less than 27.7 ms. This design also ensures that the unit vectors generated by this PLL have a steady state THD of less than 1% during frequency variations of the grid voltage. The design of the SOGI-PLL based on the theoretical analysis is validated by experimental results.
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A new partial integrated guidance and control design approach is proposed in this paper, which combines the benefits of both integrated guidance and control as well as the conventional guidance and control design philosophies. The proposed technique essentially operates in a two-loop structure. In the outer loop, an optimal guidance problem is formulated considering the nonlinear six degrees-of-freedom equation of motion of the interceptor. From this loop, the required pitch and yaw rates are generated by solving a nonlinear suboptimal guidance formulation in a computationally efficient manner while simultaneously assuring roll stabilization. Next, the inner loop tracks these outer loop body rate commands. This manipulation of the six degrees-of-freedom dynamics in both loops preserves the inherent time scale separation property between the translational and rotational dynamics, while retaining the philosophy of integrated guidance and control design as well. Because of this, the tuning process is quite straightforward and nontedious as well. Extensive six degrees-of-freedom simulations studies have been carried out, considering three-dimensional engagement geometry, to demonstrate the effectiveness of the proposed new design approach engaging high-speed ballistic targets. A variety of comparison studies have also been carried out to demonstrate the effectiveness of the proposed approach.