Numerical solution of eigenvalue problems for Hamiltonian systems

This paper discusses the numerical solution of eigenvalue problems for Hamiltonian systems of ordinary differential equations. Two new codes are presented which incorporate the algorithms described here; to the best of the author’s knowledge, these are the first codes capable of solving numerically such general eigenvalue problems. One of these implements a new new method of solving a differential equation whose solution is a unitary matrix. Both codes are fully documented and are written inPfort-verifiedFortran 77, and will be available in netlib/aicm/sl11f and netlib/aicm/sl12f.     

Software Cold Test Simulation of Coupled Cavity Slow-Wave Structure in Millimeter Wave TWT

In this paper, the software cold-test simulation method to obtain RF dispersion, interaction impedance by MAFIA software is discussed considering effect of the conducting barrel in the millimeter-wave TWT. The dispersion simulation result is obtained more consistent with experiment data than the method that ignoring effect of the conducting barrel. By changing the structure parameter, high frequency characteristic will be affected. The change relationship of high frequency characteristic with structure parameter is obtained. The different calculation methods of the interaction impedance are discussed. These results are received and are consistent with experiment data.     

线性二次型最优控制的并行算法和软件

构造了线性二次型最优控制的并行算法，介绍了这个并行算法在武汉大学“ＷＵＤＰ９１”并行分布式处理系统上试算的数值应用软件的框图．本软件适用于既定动态系统的平衡问题．对于经济系统，可通过政策控制变量来调节和改善其状态和响应．对于自治系统可找出最优控制使得消耗函数达到最小值．通过对一系列例子进行试算，结果证实，所构造的并行算法和相应的数值软件是有效的，其加速比约为７．     

气-固流化床反应器内双流体力学模型及其验证 Ⅱ.单组分两维射流床内流场特性分析

由以质量、动量和能量三大守恒定律为基础的湍流两相流理论出发,建立了描述气固流化床内两相流动的数学模型;在微型计算机上编写了相应的数值计算和图形处理程序;为了验证模型的可靠性,本文着手模拟与分析了单组分颗粒体系两维射流流化床内气、固相速度场、空隙度和压力场随时间、空间变化规律;得到了与前人实验结果相吻合的结论。     

Improved accuracy of quantitative XPS analysis using predetermined spectrometer transmission functions with UNIFIT 2004

The accuracy of quantitative XPS analysis can be improved using predetermined transmission functions. Two different calibration methods are used for estimating the transmission function T(E) of a photoelectron spectrometer, applying a survey spectra approach (SSA) and a quantified peak‐area approach (QPA) to minimize the quantification error. For the SSA method, Au, Ag and Cu spectra measured with the Metrology Spectrometer II have been used. The new QPA method was built up from Au 4f, Au 4d, Au 4p_3/2, Ag 3d, Ag 3p_3/2, Cu 3p, Cu 2p_3/2, Ge 3p and Ge 2p_3/2 standard peak areas, applying adequate ionization cross‐sections and mean free path lengths for different pass energies (10 and 50 eV), lens modes (large area, large area XL, small area 150) and x‐ray sources (Al/Mg Twin and Al Mono). In the energy range 200–1500 eV a transmission function T(E) = a₀ + b₁E (where a₀, b₁ and b₂ are variable parameters) was found to give an appropriate approximation for eight tested spectrometer settings, implementing the largest changes in the case of pass energy variations. Determination and application of the transmission functions were integrated in the XPS analysis software (UNIFIT 2004) and tested by means of an Ni90Cr10 alloy. The results demonstrate the practicability of the SSA and QPA methods, giving decreased errors of <8% in comparison with errors up to 38% obtained using Wagner's sensitivity factors. Copyright © 2005 John Wiley & Sons, Ltd.     

球状蛋白质分子中氨基酸紧密接触对性质的研究

采用CSU软件 (Contactsofstructuralunits) ,对 61种球状蛋白质分子中氨基酸紧密接触对 (Residue residuecontact)进行了研究 .重点研究了不同氨基酸在形成远程紧密接触对 (Long rangecontact)和近程紧密接触对 (Short rangecontact)时的不同能力 .发现氨基酸Leu,Val,Ile,Met,Phe,Tyr,Cys,Trp(疏性氨基酸 ,H)比较容易形成远程紧密接触对 ,氨基酸Glu,Gln ,Asp ,Asn,Lys,Ser,Arg,Pro(亲水氨基酸 ,P)比较难形成远程紧密接触对 ,而氨基酸Ala,Gly,Thr,His(中性氨基酸 ,N)在形成远程紧密接触对时能力一般 .它们平均每个氨基酸可形成 6 0 3 ,3 64和 4 43个远程紧密接触对 .同时它们在形成近程紧密接触对时能力非常接近 ,平均每个氨基酸可形成的近程紧密接触对数目在 2 3 4～ 2 85变化 ,差别非常小 .亲水氨基酸 (P) ,中性氨基酸 (N)和疏水性氨基酸 (H)在蛋白质分子结构稳定性上起着不同的作用     

Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

---

Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.

     

Error estimation in peak‐shape analysis of XPS core‐level spectra using UNIFIT 2003: how significant are the results of peak fits?

An error analysis for numerically evaluating random uncertainties in x‐ray photoelectron spectroscopy has been implemented in version 2003 of the spectra treatment and analysis software UNIFIT in order to improve the understanding of the statistical basis and the reliability of the model parameters for photoelectron spectra. The theoretical basis as well as two approaches to obtain error limits of the fit parameters have been considered. Several test spectra have been analysed and discussed. A representative example has been chosen to demonstrate the relevance of the error estimation for practical surface analysis. Suggestions for the minimization of errors in the peak‐fitting procedures are presented. Copyright © 2004 John Wiley & Sons, Ltd.     

Optimization of a GFAAS method for determination of total inorganic arsenic in drinking water

The new 10 μg l⁻¹ arsenic standard in drinking water has been a spur to the search for reliable routine analytical methods with a limit of detection at the μg l⁻¹ level. These methods also need to be easy to handle due to the routine analyses that are required in drinking water monitoring. Graphite furnace atomic absorption spectrometry (GFAAS) meets these requirements, but the limit of detection is generally too high except for methods using a pre-concentration or separation step. The use of a high-intensity boosted discharge hollow-cathode lamp decreases the baseline noise level and therefore allows a lower limit of detection. The temperature program, chemical matrix modifier and thermal stabilizer additives were optimized for total inorganic arsenic determination with GFAAS, without preliminary treatment. The optimal furnace program was validated with a proprietary software. The limit of detection was 0.26 μg As l⁻¹ for a sample volume of 16 μl corresponding to 4.2 pg As. This attractive technique is rapid as 20 samples can be analysed per hour. This method was validated with arsenic reference solutions. Its applicability was verified with artificial and natural groundwaters. Recoveries from 91 to 105% with relative standard deviation <5% can be easily achieved. The effect of interfering anions and cations commonly found in groundwater was studied. Only phosphates and silicates (respectively at 4 and 20 mg l⁻¹) lead to significant interferences in the determination of total inorganic arsenic at 4 μg l⁻¹.     

The index of ideality of correlation: improvement of models for toxicity to algae

Toxicity to algae is important characteristic of substances from ecologic point of view. The CORAL software (http://www.insilico.eu/coral) gives possibility to build up model of toxicity to algae using data on the molecular architecture and experimental toxicity, without additional data on physicochemical and/or biochemical parameters. Considerable improvement of the model is observed in the case of using the index of ideality of correlation (IIC) in the role of additional criterion of predictive potential. The IIC is calculated with using of the correlation coefficient between experimental and calculated values of endpoint for the calibration set, with taking into account the positive and negative dispersions between experimental and calculated values. The best model calculated with use the IIC is characterized (the validation set) by n?=?50, r²?=?0.947, RMSE?=?0.401 whereas, model calculated without use the IIC is characterized by n?=?50, r²?=?0.805, and RMSE?=?0.539. The suggested models are built up in accordance to five OECD principles.