Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

PMMA with Long-Persistent Phosphors and Its Behavior of Luminescence

A new kind of rare earth material with high efficient long-persistent phosphors, such as SrAl2O4: Eu, Dy, has been developed in recent years. The PMMA with long-persistent phosphors is typical one of applications for the phosphors. In this work, we try to probe into the affection of the manufacture process on the PMMA with long-persistent phosphors, to analyze its performance, and its luminescence behavior, especially to study the self-excitation of the PMMA with long-persistent phosphors.

Effect of Surface Condition of Electrode on the Surface Melting of Material by Laser-Guided Micro-Arc Discharge

This paper studies the surface melting in the atmosphere by YAG laser-guided micro-arc discharge. In three kinds of surface conditions (free, oiled, and polyethylene covered), we try to control the diameter and the power density of discharge pit. It is found that the power density of 3 x 10(6) W/cm(2) of discharge pit on the oiled surface is moderate to form the melted layer thicker than that of the others, adapting to strengthen the surface of material, and the power density of 1.07 x 10(7) W/cm(2) of discharge pit on the polyethylene-covered surface is highest to form the deepest discharge pit among them, adapting to remove the material.

A new method of studying the dynamical behavior of the sine-gordon equation

We try to connect the theory of infinite dimensional dynamical systems and nonlinear dynamical methods. The sine-Gordon equation is used to illustrate our method of discussing the dynamical behaviour of infinite dimensional systems. The results agree with those of Bishop and Flesch [SLAM J. Math. Anal. 21 (1990) 1511].

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

The near wall velocity measurements in microchannels with different diameter particles by microPIV/PTV. 8th International symposium on PIV

In near wall measurements with microPIV/PTV, whether seeding particles can be effectively used to detect local fluid velocity is a crucial problem. This talk presents our recent measurements in microchannels [1][2]. Based on measured velocity profiles with 200nm and 50nm in pure water, we found that the measured velocity profiles are agreed with the theoretical values in the middle of channel, but large deviations between measured data and theoretical prediction appear close to wall (0.25mm try to analysis the influence of focal plane thickness and particle concentration distribution near wall on the velocity deviation appeared in shear flows.

沙冬青抗冻组份的分离纯化和afp基因克隆的尝试

本文用三种方法分离纯化沙冬青（Ammopiptanthus mongolicus）叶片抗冻蛋白质。从70%硫酸铵沉淀后的上清液中得到了一种碱性的小分子物质，UiS，具有较高的溶解度( 260 mg/ml)和较强的降低溶液冰点的能力（200 mg/ml，冰点小于-20℃）：从10%硫酸铵和26%氯化铵共沉淀物中分离到一种抗冻蛋白-B3，B3分子量为39.8 kDa，热滞活性为0.45℃(10 mg/ml)：从沙冬青叶片热稳定蛋白质中用双向电泳一电泳回收法分离到afp,其分子量为40 kDa,pl为9.0。热滞活性为0.9℃(20 mg/ml)，和其他抗冻蛋白质进行比较，没有发现相同的类型。afp和uis在叶片含量都很高，可能是沙冬青抗冻生理过程中两种主要物质，它们对于沙冬青抵御-20℃左右的冷冻温度具有重要的意义。afp N端序列为SDDL SFTF NKFV PCQT DILF，据此合成了六段5’引物和一段3’引物，用RT - PCR方法从叶片中扩增出一段200 bp左右的片段。

Sleeping sites of black-and-white snub-nosed monkeys (Rhinopithecus bieti) at Baima Snow Mountain, China

Data on sleeping sites of a group of black-and-white snub-nosed monkeys Rhinopithecus bieti (Colobinae, Primates) were collected between April-July and September-December 2001 to try to determine the factors affecting site selection at Nanren (99 degrees

Defects around self-organized InAs quantum dots measured by slow positron beam

Self-organized InAs quantum dots (QDs) have been fabricated by molecular beam epitaxy. The authors try to use a slow positron beam to detect defects in and around self-organized QDs, and point defects are observed in GaAs cap layer above QDs. For the self-organized InAs QDs without strain-reducing layer, it is free of defects. However, by introducing a strain-reducing layer, the density of point defects around larger sized InAs QDs increased. The above results suggest that low energy positron beam measurements may be a good approach to detect depth profiles of defects in QD materials. (c) 2007 American Institute of Physics.

SOC dynamic power management using artificial neural network

Dynamic Power Management (DPM) is a technique to reduce power consumption of electronic system by selectively shutting down idle components. In this article we try to introduce back propagation network and radial basis network into the research of the system-level power management policies. We proposed two PM policies-Back propagation Power Management (BPPM) and Radial Basis Function Power Management (RBFPM) which are based on Artificial Neural Networks (ANN). Our experiments show that the two power management policies greatly lowered the system-level power consumption and have higher performance than traditional Power Management(PM) techniques-BPPM is 1.09-competitive and RBFPM is 1.08-competitive vs. 1.79, 1.45, 1.18-competitive separately for traditional timeout PM, adaptive predictive PM and stochastic PM.

Room-temperature ferromagnetism in zinc-blende and deformed CrAs thin films

We try to clarify the controversy about the origin of room-temperature ferromagnetism in a CrAs compound. Two kinds of CrAs thin films were grown on GaAs by molecular-beam epitaxy. Structural analyses confirm that the as-grown CrAs film is a pure zinc-blende phase. Magnetic measurements suggest that room-temperature ferromagnetism exists in zinc-blende CrAs. In contrast, the CrAs film turns into a mixture of zinc-blende and deformed CrAs after annealing. A ferromagnetic signal measured at room temperature demonstrates that zinc-blende CrAs remains room-temperature ferromagnetism even when it is partly deformed into a non-zinc-blende phase. (c) 2006 American Institute of Physics.

Dynamic power management approaches based on neural network

Dynamic Power Management (DPM) is a technique to reduce power consumption of electronic system. by selectively shutting down idle components. In this article we try to introduce back propagation network and radial basis network into the research of the system-level policies. We proposed two PAY policies-Back propagation Power Management (BPPM) and Radial Basis Function Power management (RBFPM) which are based on Artificial Neural Networks (ANN). Our experiments show that the two power management policies greatly lowered the system-level power consumption and have higher performance than traditional Power Management(PM) techniques-BPPM is 1.09-competitive and RBFPM is 1.08-competitive vs. 1.79,145,1.18-competitive separately for traditional timeout PM, adaptive predictive PM and stochastic PM.

SOC dynamic power management using artificial neural network

Dynamic Power Management (DPM) is a technique to reduce power consumption of electronic system by selectively shutting down idle components. In this article we try to introduce back propagation network and radial basis network into the research of the system-level power management policies. We proposed two PM policies-Back propagation Power Management (BPPM) and Radial Basis Function Power Management (RBFPM) which are based on Artificial Neural Networks (ANN). Our experiments show that the two power management policies greatly lowered the system-level power consumption and have higher performance than traditional Power Management(PM) techniques-BPPM is 1.09-competitive and RBFPM is 1.08-competitive vs. 1.79 . 1.45 . 1.18-competitive separately for traditional timeout PM . adaptive predictive PM and stochastic PM.

Visible vertical cavity surface emitting laser

We have designed and fabricated the visible vertical-cavity surface-emitting lasers (VCSEL's) by using metalorganic vapor phase epitaxy (MOVPE). We use the 8 lambda optical cavities with 3 quantum wells in AlGaInP/AlGaAs red VCSEL's to reduce the drift leakage current and enhance the model gain in AlGaInP active region. The structure has a p-type stack with 36 DBR pairs on the top and an n-type with 55-1/2 pairs on the bottom. Using micro-area reflectance spectrum, we try to get a better concordance between the center wavelength of DBR and the emitting wavelength of the active region. We used a component graded layer of 0.05 lambda thick (x = 0.5 similar to 0.9) at the p-type DBR AlGaAs/AlAs interface to reduce the resistance of p-type DBR. We use selective oxidation to define the current injection path. Because the oxidation rate of a thick layer is faster than a thinner one, we grown a thick AlAs layer close to the active region. In this way, we got a smaller active region for efficient confinement of injected carriers (the aperture area is 3 x 3 mu m) to reduce the threshold and, at the same time, a bigger conductive area in the DBR layers to reduce the resistance. We employ Zn doping on the p-side of the junction to improve hole injection and control the Zn dopant diffusion to get proper p-i-n junction. At room temperature, pulse operation of the laser has been achieved with the low threshold current of 0.8mA; the wavelength is about 670nm.

Substitution Matrices of Residue Triplets Derived from Protein Blocks.

In protein sequence alignment, residue similarity is usually evaluated by substitution matrix, which scores all possible exchanges of one amino acid with another. Several matrices are widely used in sequence alignment, including PAM matrices derived from homologous sequence and BLOSUM matrices derived from aligned segments of BLOCKS. However, most matrices have not addressed the high-order residue-residue interactions that are vital to the bioproperties of protein.With consideration for the inherent correlation in residue triplet, we present a new scoring scheme for sequence alignment. Protein sequence is treated as overlapping and successive 3-residue segments. Two edge residues of a triplet are clustered into hydrophobic or polar categories, respectively. Protein sequence is then rewritten into triplet sequence with 2 · 20 · 2 = 80 alphabets. Using a traditional approach, we construct a new scoring scheme named TLESUMhp (TripLEt SUbstitution Matrices with hydropobic and polar information) for pairwise substitution of triplets, which characterizes the similarity of residue triplets. The applications of this matrix led to marked improvements in multiple sequence alignment and in searching structurally alike residue segments. The reason for the occurrence of the ‘‘twilight zone,’’ i.e., structure explosion of lowidentity sequences, is also discussed.