Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

The wave model of mesothermal plasma near wakes and Korteweg-de Vries equation

The stationary two-dimensional (x, z) near wakes behind a flat-based projectile which moves at a constant mesothermal speed (V∞) along a z-axis in a rarefied, fully ionized, plasma is studied using the wave model previously proposed by one of the authors (VCL). One-fluid theory is used to depict the free expansion of ambient plasma into the vacuum produced behind a fast-moving projectile. This nonstationary, one-dimensional (x, t) flow which is approximated by the K-dV equation can be transformed, through substitution, t=z/V∞, into a stationary two-dimensional (x, z) near wake flow seen by an observer moving with the body velocity (V∞). The initial value problem of the K-dV equation in (x, t) variables is solved by a specially devised numerical method. Comparisons of the present numerical solution for the asymptotically small and large times with available analytical solutions are made and found in satisfactory agreements.

Parallel optical negabinary arithmetic based on logic operations

On the basis of signed-digit negabinary representation, parallel two-step addition and one-step subtraction can be performed for arbitrary-length negabinary operands.; The arithmetic is realized by signed logic operations and optically implemented by spatial encoding and decoding techniques. The proposed algorithm and optical system are simple, reliable, and practicable, and they have the property of parallel processing of two-dimensional data. This leads to an efficient design for the optical arithmetic and logic unit. (C) 1997 Optical Society of America.

Compact parallel optical modified-signed-digit arithmetic-logic array processor with electron-trapping device

A compact two-step modified-signed-digit arithmetic-logic array processor is proposed. When the reference digits are programmed, both addition and subtraction can be performed by the same binary logic operations regardless of the sign of the input digits. The optical implementation and experimental demonstration with an electron-trapping device are shown. Each digit is encoded by a single pixel, and no polarization is included. Any combinational logic can be easily performed without optoelectronic and electro-optic conversions of the intermediate results. The system is compact, general purpose, simple to align, and has a high signal-to-noise ratio. (C) 1999 Optical Society of America.

Two-step digit-set-restricted modified signed-digit addition-subtraction algorithm and its optoelectronic implementation

A novel, to our knowledge, two-step digit-set-restricted modified signed-digit (MSD) addition-subtraction algorithm is proposed. With the introduction of the reference digits, the operand words are mapped into an intermediate carry word with all digits restricted to the set {(1) over bar, 0} and an intermediate sum word with all digits restricted to the set {0, 1}, which can be summed to form the final result without carry generation. The operation can be performed in parallel by use of binary logic. An optical system that utilizes an electron-trapping device is suggested for accomplishing the required binary logic operations. By programming of the illumination of data arrays, any complex logic operations of multiple variables can be realized without additional temporal latency of the intermediate results. This technique has a high space-bandwidth product and signal-to-noise ratio. The main structure can be stacked to construct a compact optoelectronic MSD adder-subtracter. (C) 1999 Optical Society of America.

One-step digit-set-restricted modified signed-digit adder using an incoherent correlator based on a shared content-addressable memory

An efficient one-step digit-set-restricted modified signed-digit (MSD) adder based on symbolic substitution is presented. In this technique, carry propagation is avoided by introducing reference digits to restrict the intermediate carry and sum digits to {1,0} and {0,1}, respectively. The proposed technique requires significantly fewer minterms and simplifies system complexity compared to the reported one-step MSD addition techniques. An incoherent correlator based on an optoelectronic shared content-addressable memory processor is suggested to perform the addition operation. In this technique, only one set of minterms needs to be stored, independent of the operand length. (C) 2002 society or Photo-Optical Instrumentation Engineers.

Efficient two-step digit-set-restricted modified signed-digit algorithm based on optoelectronic shared content-addressable memory

A two-step digit-set-restricted modified signed-digit (MSD) adder based on symbolic substitution is presented. In the proposed addition algorithm, carry propagation is avoided by using reference digits to restrict the intermediate MSD carry and sum digits into {(1) over bar ,0} and {0, 1}, respectively. The algorithm requires only 12 minterms to generate the final results, and no complementarity operations for nonzero outputs are involved, which simplifies the system complexity significantly. An optoelectronic shared content-addressable memory based on an incoherent correlator is used for experimental demonstration. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

Efficient two-step digit-set-restricted modified signed-digit algorithm based on optoelectronic shared content-addressable memory

A two-step digit-set-restricted modified signed-digit (MSD) adder based on symbolic substitution is presented. In the proposed addition algorithm, carry propagation is avoided by using reference digits to restrict the intermediate MSD carry and sum digits into {(1) over bar ,0} and {0, 1}, respectively. The algorithm requires only 12 minterms to generate the final results, and no complementarity operations for nonzero outputs are involved, which simplifies the system complexity significantly. An optoelectronic shared content-addressable memory based on an incoherent correlator is used for experimental demonstration. (c) 2005 Society of Photo-Optical Instrumentation Engineers.

BaF2替代BaO对钡镓锗酸盐玻璃光学性质的影响

在摩尔分数组成x(BaO),r(Ga2O),r(GeO2)为0．20，0．15,0．65的玻璃中，分别以摩尔分数0．05，0．10．0．15和0．20的BaF2替代BaO,研究了氟化物对玻璃折射率和光吸收性质的影响。结果表明，在玻璃中加入氟化物．玻璃折射率和色散降低，玻璃的紫外吸收边向短波侧迁移，而红外吸收边无明显变化。不含氟化物的氧化物玻璃中含有大量的OH基．这些OH基在2．24μm、2．97μm和4．23μm附近引起光吸收．在含氟化物的玻璃中，2．24μm的吸收峰消失，而2．97μm和4．23μm附近

SiO2 对Bi2O3-B2O3 玻璃体系光学、热学及结构的 影响

Glasses with compositions 50Bi2O3-xB2O3- (50-x)SiO2(x=0, 10, 20, 30, 40, 50) in mol% have been prepared by using a normal melt-quench technique. The effect of SiO2 addition on thermal stability, optical properties and structural characteristic on Bi2O3-B2O3 glass were systematically investigated by using XRD, DTA, ultraviolet-visible transmittance spectra, midinfrared transmittance spectra and Raman spectra. The experimental results demonstrate that, with the addition of SiO2, thermal stability of glass samples has been obviously improved. Once the amount of SiO2 is too much, the glass samples tend to be phase seperation which results in the decrease of thermal stability. With increasing SiO2 content, the UV cutoff edge firstly shifts to short-wave band and then shifts to long-wave band, and the transmittance of mid-infrared has been greatly improved. With substitution of SiO2 for B2O3, the [BO3] triangles and [BO4] tetrahedral groups are gradually replaced by [SiO4]. [BiO6] octahedral and [SiO4] tetrahedral units are connected forming a vibrational mode of Bi-O-Si. The physical chemistry and optical performance of Bi2O3-B2O3 glass were greatly improved by addition of SiO2.

Host dependent frequency upconversion of Er3+-doped oxyfluoride germanate glass

Er3+-doped oxyfluoride germanate glasses have been synthesized by the conventional melting and quenching method. The Judd-Ofelt intensity parameters were calculated based on the Judd-Ofelt theory and absorption spectra measurements. With the substitution of PbF2 for PbO, the Omega(2) parameter decreases, while the Omega(6) parameter increases. These change trends indicate that fluoride anions come to coordinate erbium cations and the covalency of the Er-O bond decreases. Structural and thermal stability properties were obtained by Raman spectra and differential thermal analysis, indicating that PbF2 plays an important role in the formation of glass network and has an important influence on the maximum phonon energy and thermal stability of host glasses. Intense green and red emissions centered at 525, 546, and 657 nm, corresponding to the transitions H-2(11/2) -> I-4(15/2), S-4(3/2) -> I-4(15/2), and F-4(9/2) -> I-4(15/2), respectively, were simultaneously observed at room temperature. With increasing PbF2 content, the intensity of red (657nm) emissions increases significantly, while that of the green (525 and 546nm) emission increases slightly. The results indicate that PbF, has more influence on the red (657nm) emission than the green (525 and 546nm) emissions in oxyfluoride germanate glasses. The possible upconversion luminescence mechanisms have also been estimated and discussed. (c) 2005 Elsevier B.V. All rights reserved.

Structural and up-conversion luminescence properties in Tm (3+)/Yb3+-codoped heavy metal oxide-halide glasses

Tm3+/Yb3+-codoped heavy metal oxide-halide glasses have been synthesized by conventional melting and quenching method. Structural properties were obtained based on the Raman spectra, indicating that halide ion has an important influence on the phonon density and maximum phonon energy of host glasses. Intense blue and weak red emissions centered at 477 and 650 nm, corresponding to the transitions (1)G(4) -> H-3(6) and (1)G(4) -> H-3(4), respectively, were observed at room temperature. The possible up-conversion mechanisms are discussed and estimated. With increasing halide content, the up-conversion luminescence intensity and blue luminescence lifetimes of Tm3+ ion increase notably. Our results show that with the substitution of halide ion for oxygen ion, the decrease of phonon density and maximum phonon energy of host glasses both contribute to the enhanced up-conversion emissions. (c) 2005 Elsevier B.V. All rights reserved.

Effect of CdF2 addition on thermal stability and upconversion luminescence properties in Tm3+-Yb3+ codoped oxyfluoride silicate glasses

Tm3+-Yb3+ codoped oxyfluoride silicate glasses suitable for upconversion laser has been fabricated. In this paper, effect of CdF2 addition on thermal stability and upconversion luminescence properties in Tm3+-Yb3+ codoped oxyfluoride silicate glasses have been systematically investigated. The experimental results indicate that, with the substitution CdF2 for PbF2, the glass thermal stability increases and the UV cutoff edge moves to short-wave band slightly. With increasing CdF2 content, the blue and red upconversion luminescence intensity increases slightly at first, and then increases rapidly. While the near infrared (NIR) upconversion emission intensity increases notably at first and then increases slightly. However, the blue and NIR luminescence intensity are much stronger than that of red, indicating these oxyfluoride silicate glasses are more preferable for blue and NIR emissions than red emission. The possible upconversion mechanisms for the blue, red and NIR fluorescence are also estimated and evaluated. (c) 2006 Elsevier B.V. All rights reserved.

Effect of bismuth oxide introduction on spectroscopic properties of Er3+/Yb3+ co-doped aluminophosphate glasses

The absorption spectra, emission spectra and infrared spectra of Er3+/Yb3+ co-doped xBi(2)O(3)-(65 - x)P2O5-4Yb(2)O(3)-11Al(2)O(3)-5BaO-15Na(2)O were measured and investigated. Spontaneous emission probability, radiative lifetime and branching ratios of Er3+ were calculated according to the Judd-Ofelt theory. The role of substitution of Bi2O3 for P2O5 on luminescence of Er3+/Yb3+ co-doped aluminophosphate glasses has been investigated. The calculated radiative lifetimes (tau(rad)) for I-4(13/2) and I-4(11/2) were decreasing with Bi2O3 content increases, whereas the measured total lifetime (tau(meas)) for I-4(13/2) showed linearly increasing trends. The effect of Bi2O3 introduction on OH- groups was also discussed according to the IR transmittance spectra of glasses. It was found that FWHM of glasses were not affected with the substitution of Bi2O3 for P2O5. The emission spectra intensity increased with Bi2O3 content due to the decreases of phonon energy and OH- content in glasses. (C) 2007 Elsevier B.V. All rights reserved.

Effect of La3+ on microwave dielectric properties of (Pb0.45Ca0.55) (Fe0.5Nb0.5)O-3 ceramics

In this work, microwave dielectric properties of A-site substitution by La3+ in (Pb0.45Ca0.55) (Fe0.5Nb0.5) 03 system were investigated. Microwave dielectric properties of A-site charge unbalance substitution of [(Pb0.45Ca0.55)(1-x) La-x] (Fe0.5Nb0.5)O-3(+) (P45CLFN) were improved because the solid solution of small amount of surplus La3+ with (Pb, Ca)(2+) could eliminate oxygen vacancies, and the formation of secondary phase (pyrochlore) was also caused by surplus La3+. The decreasing of dielectric constant with the increase of La3+ content is due to the formation of pyrochlore. The grain size is changed slightly and Q(f) values (7000 similar to 7300 GHz) are almost unchanged at x = 0.02 similar to 0.10, but the temperature coefficient of resonant frequency (TCF) are increased and changed from negative to positive. TCF is zero at x 0.075 with Q(f) = 7267 GHz and K = 89. TCF of all specimens are within +/- 5 x 10(-6)degrees C-1.