Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

A simple combinatorial method aiding research on single-walled carbon nanotube growth on substrates

Establishing fabrication methods of carbon nanotubes (CNTs) is essential to realize many applications expected for CNTs. Catalytic growth of CNTs on substrates by chemical vapor deposition (CVD) is promising for direct fabrication of CNT devices, and catalyst nanoparticles play a crucial role in such growth. We have developed a simple method called "combinatorial masked deposition (CMD)", in which catalyst particles of a given series of sizes and compositions are formed on a single substrate by annealing gradient catalyst layers formed by sputtering through a mask. CMD enables preparation of hundreds of catalysts on a wafer, growth of single-walled CNTs (SWCNTs), and evaluation of SWCNT diameter distributions by automated Raman mapping in a single day. CMD helps determinations of the CVD and catalyst windows realizing millimeter-tall SWCNT forest growth in 10 min, and of growth curves for a series of catalysts in a single measurement when combined with realtime monitoring. A catalyst library prepared using CMD yields various CNTs, ranging from individuals, networks, spikes, and to forests of both SWCNTs and multi-walled CNTs, and thus can be used to efficiently evaluate self-organized CNT field emitters, for example. The CMD method is simple yet effective for research of CNT growth methods. © 2010 The Japan Society of Applied Physics.

SIMPLE REMESHING SCHEME FOR THE FINITE ELEMENT BASED SIMULATION OF DOPANT DIFFUSION IN SILICON.

Process simulation programs are valuable in generating accurate impurity profiles. Apart from accuracy the programs should also be efficient so as not to consume vast computer memory. This is especially true for devices and circuits of VLSI complexity. In this paper a remeshing scheme to make the finite element based solution of the non-linear diffusion equation more efficient is proposed. A remeshing scheme based on comparing the concentration values of adjacent node was then implemented and found to remove the problems of oscillation.

A simple prediction model for asphalt surface texture incorporating mix gradation and air voids

This paper presents the results of a preliminary study that seeks to show how asphalt grading and air voids are related to the texture depth of asphalt. The fiftieth percentile particle size (D50) is shown to be a good predictor of texture depth measurements from a collected database of field and laboratory studies. The D50 is used to normalise collected texture data and this 'relative texture' is shown to correlate with air voids. Regression analyses confirm that air voids should be included along with a measure of gradation in the interpretation of asphalt surface texture.The derived formulae are used to develop correlation charts.

Highly chiral-selective growth of single-walled carbon nanotubes with a simple monometallic Co catalyst

We report on the growth of single-walled carbon nanotubes from a monometallic Co catalyst on an oxidized Si wafer support by the most simple growth recipe (vacuum annealing, growth by undiluted C 2H 2). Nevertheless, multiwavelength Raman spectroscopy and transmission electron spectroscopy show a remarkable selectivity for chiral indices and thus, e.g., high abundance with a single chirality representing 58% of all semiconducting tubes. In situ x-ray photoelectron spectroscopy monitors the catalyst chemistry during carbon nanotube growth and shows interfacial Co-Si interactions that may help to stabilize the nanoparticle/nanotube diameter. We outline a two-mechanism model explaining the selective growth. © 2012 American Physical Society.

SiGMa: Simple Greedy Matching for Aligning Large Knowledge Bases

The Internet has enabled the creation of a growing number of large-scale knowledge bases in a variety of domains containing complementary information. Tools for automatically aligning these knowledge bases would make it possible to unify many sources of structured knowledge and answer complex queries. However, the efficient alignment of large-scale knowledge bases still poses a considerable challenge. Here, we present Simple Greedy Matching (SiGMa), a simple algorithm for aligning knowledge bases with millions of entities and facts. SiGMa is an iterative propagation algorithm which leverages both the structural information from the relationship graph as well as flexible similarity measures between entity properties in a greedy local search, thus making it scalable. Despite its greedy nature, our experiments indicate that SiGMa can efficiently match some of the world's largest knowledge bases with high precision. We provide additional experiments on benchmark datasets which demonstrate that SiGMa can outperform state-of-the-art approaches both in accuracy and efficiency.

线粒体D-loop序列变异与东方鲀属鱼类系统发育

东方鲀属的红鳍东方鲀(Takifugu rubripes)是后基因组时代的一种重要模式生物。本研究中,利用东方鲀属11种鱼类(18尾)的D-loop基因序列,对东方鲀属鱼类的系统发育关系进行研究。经序列比对排定后,分析中D-loop序列有841个位点,其中395个位点为可变位点,267个位点为系统发育信息位点。分别采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯方法构建了分子系统树。研究结果表明:(1)东方鲀属鱼类为一单系类群;(2)由横纹东方鲀(T. oblongus)和铅点东方鲀(T

A simple bioconjugate attachment protocol for use in single molecule force spectroscopy experiments based on mixed self-assembled monolayers.

Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin.

A family of simple benzene 1,3,5-tricarboxamide (BTA) aromatic carboxylic acid hydrogels.

We present the characterisation of a hydrogel forming family of benzene 1,3,5-tricarboxamide (BTA) aromatic carboxylic acid derivatives. The simple, easy to synthesise compounds presented here exhibit consistent gel formation at low concentrations through the use of a pH trigger.