Chemical environment code and measure of molecular similarity

A new scheme for the code of chemical environments of compounds is described in this paper, and three molecular similarity methods have been used to select nearest neighbors from four different types of probe compounds. One of the methods is based on the C-13 NMR spectra. The second method is based on the code of chemical environments and molecular topological index A(x). The third approach, i.e. the Tanimoto coefficient, is also based on the code of chemical environments, but not to use the topological index. Five nearest neighbors for each probe compound using these three molecular similarity methods were determined and taken from the database of 7309 structures. The results indicate that the scheme of the chemical environment code and the method for similarity measure of intermolecules suggested in this study are reasonable. (C) 1998 Published by Elsevier Science Ltd. All rights reserved.

Code for chemical environment and computation of molecular similarity

A new code for chemical environment and an empirical mathematical pattern Sa(m) on computation of molecular similarity were suggested. Seven molecules which referred to as the probe compounds and the nearest neighbors of each probe structure were determined by the methods of Sa(m) and Tanimoto, The results show an intuitive notion of chemical similarity.

Molecular identification of 16 Porphyra lines using sequence-related amplified polymorphism markers

Sequence-related amplified polymorphism (SRAP) is a novel molecular marker technique designed to amplify open reading frames (ORFs). The SRAP analytic system was set up and applied to Porphyra germplasm identification in this study for the first time. Sixteen Porphyra lines were screened by SRAP technique with 30 primer combinations. In the analysis, 14 primer combinations produced stable and reproducible amplification patterns in three repetitive experiments. Among the total 533 amplified fragments, 522 (98%) were polymorphic, with an average of 38 fragments for each primer combination, ranging in size from 50 to 500 bp. The 533 fragments were visually scored one by one and then used to develop a dendrogram with Unweighted Pair-Group Method Arithmetic Average (UPGMA), and the 16 Porphyra lines were divided into two major groups at the 0.68 similarity level. From the total 533 fragments, I I amplified by two primer combinations, ME1/EM1 and ME4/EM6, were used to develop the DNA fingerprints of the 16 Porphyra lines. The DNA fingerprints were then converted into binary codes, with I and 0 representing presence and absence of the corresponding amplified fragment, respectively. In the DNA fingerprints, each of the 16 Porphyra lines has its unique binary code and can be easily distinguished from the others. This is the first report on the development of SRAP technique and its utilization in germplasm identification of seaweeds. The results demonstrated that SRAP is a simple, stable, polymorphic and reproducible molecular marker technique for the classification and identification of Porphyra lines. (c) 2007 Elsevier B.V. All rights reserved.

A set of polymorphic microsatellite loci for the bay scallop, Argopecten irradians

The method of creating enriched microsatellite libraries can supply an abundant source of microsatellite sequences at a considerably reduced cost. Here we report the development of 15 polymorphic microsatellite loci from the bay scallop, Argopecten irradians, using enrichment protocol. Polymorphism was assessed in a sample of hatchery population (n = 38) revealing three to seven alleles per locus. The expected and observed heterozygosities ranged from 0.198 to 0.813 and from 0.083 to 0.833, respectively. These markers will be useful for genetic variation monitoring and parentage analysis.

数控自动编程专家系统

本文简要地介绍了数控自动编程专家系统.其中包括:专家系统知识表示的形式;分层次的黑板结构;前向推理求解策略和相应的解释功能;系统针对不同类型的曲线组合,采用不同的独立的知识源(KS)进行处理.由于在知识的处理上采用编码技术,在前向推理求解策略中使用启发信息和“剪技”技术,提高了系统的时空效率.系统中的规划程序能自动规划切削路径.输出供数控车床使用的 NC 代码,并可在显示屏上进行图形显示和切削仿真.目前原型系统已经在 IBM-PC 和 Sun3/60计算机上利用FORTRAN 语言实现.

二氧化碳在孔隙咸水层中多相流动数值模拟研究

There has been a growing concern about the use of fossil fuels and its adverse effects on the atmospheric greenhouse and ecological environment. A reduction in the release rate of CO2 into the atmosphere poses a major challenge to the land ecology of China. The most promising way of achieving CO2 reduction is to dispose of CO2 in deep saline aquifers. Deep aquifers have a large potential for CO2 sequestration in geological medium in terms of volume and duration. Through the numerical simulation of multiphase flow in a porous media, the transformation and motion of CO2 in saline aquifers has been implemented under various temperature and hydrostatic pressure conditions, which plays an important role to the assessment of the reliability and safety of CO2 geological storage. As expected, the calculated results can provide meaningful and scientific information for management purposes. The key problem to the numerical simulation of multiphase flow in a porous media is to accurately capture the mass interface and to deal with the geological heterogeneity. In this study, the updated CE/SE (Space and time conservation element and solution element) method has been proposed, and the Hybrid Particle Level Set method (HPLS) has extended for multiphase flows in porous medium, which can accurately trace the transformation of the mass interface. The benchmark problems have been applied to evaluate and validate the proposed method. In this study, the reliability of CO2 storage in saline aquifers in Daqingzi oil field in Sunlong basin has been discussed. The simulation code developed in this study takes into account the state for CO2 covering the triple point temperature and pressure to the supercritical region. The geological heterogeneity has been implemented, using the well known geostatistical model (GSLIB) on the base of the hard data. The 2D and 3D model have been set up to simulate the CO2 multiphase flow in the porous saline aquifer, applying the CE/SE method and the HPLS method .The main contents and results are summarized as followings. (1) The 2D CE/SE method with first and second –order accuracy has been extended to simulate the multiphase flow in porous medium, which takes into account the contribution of source and sink in the momentum equation. The 3D CE/SE method with the first accuracy has been deduced. The accuracy and efficiency of the proposed CE/SE method have been investigated, using the benchmark problems. (2) The hybrid particle level set method has been made appropriate and extended for capturing the mass interface of multiphase flows in porous media, and the numerical method for level set function calculated has been formulated. (3) The closed equations for multiphase flow in porous medium has been developed, adept to both the Darcy flow and non-Darcy flow, getting over the limitation of Reynolds number to the calculation. It is found that Darcy number has a decisive influence on pressure as well as velocity given the Darcy number. (4) The new Euler scheme for numerical simulations of multiphase flows in porous medium has been proposed, which is efficient and can accurately capture the mass interface. The artificial compressibility method has been used to couple the velocities and pressure. It is found that the Darcy number has determinant effects on the numerical convergence and stability. In terms of the different Darcy numbers, the coefficient of artificial compressibility and the time step have been obtained. (5) The time scale of the critical instability for critical CO2 in the saline aquifer has been found, which is comparable with that of completely CO2 dissolved saline aquifer. (6) The concept model for CO2 multiphase flows in the saline aquifer has been configured, based on the temperature, pressure, porosity as well as permeability of the field site .Numerical simulation of CO2 hydrodynamic trapping in saline aquifers has been performed, applying the proposed CE/SE method. The state for CO2 has been employed to take into account realistic reservoir conditions for CO2 geological sequestration. The geological heterogeneity has been sufficiently treated , using the geostatistical model. (7) It is found that the Rayleigh-Taylor instability phenomenon, which is associated with the penetration of saline fluid into CO2 fluid in the direction of gravity, has been observed in CO2 multiphase flows in the saline aquifer. Development of a mushroom-type spike is a strong indication of the formation of Kelvin-Helmholtz instability due to the developed short wavelength perturbations present along the interface and parallel to the bulk flow. Additional key findings: the geological heterogeneity can distort the flow convection. The ascending of CO2 can induce the persistent flow cycling effects. The results show that boundary conditions of the field site have determinant effects on the transformation and motion of CO2 in saline aquifers. It is confirmed that the proposed method and numerical model has the reliability to simulate the process of the hydrodynamic trapping, which is the controlling mechanism for the initial period of CO2 storage at time scale of 100 years.

Rapid identification of pathogenic bacteria by capillary electrophoretic analysis of rRNA genes

Molecular diagnosis is playing an increasingly important role in the rapid detection and identification of pathogenic organisms in clinical samples. The genetic variation of ribosomal genes in bacteria offers an alternative to culturing for the detection and identification of these organisms. Here 16S rRNA and 16S-23S rRNA spacer region genes were chosen as the amplified targets for single-strand conformation polymorphism (SSCP) and restriction fragment length polymorphism (RFLP) capillary electrophoresis analysis and bacterial identification. The multiple fluorescence based SSCP method for the 16S rRNA gene and the RFLP method for the 16S-23S rRNA spacer region gene were developed and applied to the identification of pathogenic bacteria in clinical samples, in which home-made short-chained linear polyacrylamide (LPA) was used as a sieving matrix; a higher sieving capability and shorter analysis time were achieved than with a commercial sieving matrix because of the simplified template preparation procedure. A set of 270 pathogenic bacteria representing 34 species in 14 genera were analyzed, and a total of 34 unique SSCP patterns representing 34 different pathogenic bacterial species were determined. Based on the use of machine code to represent peak patterns developed in this paper, the identification of bacterial species becomes much easier.