Reduced parabolic model for radical addition reactions

The transition state of addition of free radicals and atoms to multiple bonds is considered as a result of intersecting of two parabolic potential curves. One of them characterizes the stretching vibration of the attacked multiple bond, and another curve characterizes the stretching vibration of the bond formed in the transition state. The force constant of the latter is calculated by an empirical equation that correlates the force constant with the bond dissociation energy. In the framework of this model, the thermally neutral activation energy (E _e0) and the elongation of the attacked and formed bonds (r _e) in the transition state were calculated from the experimental data (activation energy (E _e) and enthalpy of reaction (H _e)) for the addition of an H atom and methyl, alkoxyl, aminyl, triethylsilyl, and peroxyl radicals to the C=C bond and the addition of H and CH₃ to the C=O and CC bonds. Analysis of the data obtained showed that E _e0 depends linearly on the |H _e| + E_e sum, i.e., E_e0/kJ mol^–1 = 14.2 + 0.61 · (E_e – H _e), and the bond elongation in the transition state for addition of the most part of radicals to ethylene and acetylene vary within (0.65–0.87)·10_–10 m. The factors affecting the activation energy of the radical addition reactions are discussed.Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1542–August, 2004.     

Consequences of sample size, variable selection, and model validation and optimisation, for predicting classification ability from analytical data

This article discusses problems of validating classification models especially in datasets where sample sizes are small and the number of variables is large. It describes the use of percentage correctly classified (%CC) as an indicator for success of a classification model. For small datasets, %CC should not be used uncritically and its interpretation depends on sample size. It illustrates the use of a common classification method, discriminant partial least squares (D-PLS) on a randomly generated dataset of 200 samples and 200 variables.

An aim of the classifier is to determine whether the null hypothesis (there is no distinction between two classes) can be rejected. Autoprediction gives an 84.5% CC. It is shown that, if there is variable selection, it must be performed independently on the training set to obtain a CC close to 50% on the test set; otherwise, over-optimistic and false conclusions can be reached about the ability to classify samples into groups.

Finally, two aims of determining the quality of a model are frequently confused, namely optimisation (often used to determine the most appropriate number of components in a model) and independent validation; to overcome this, the data should be split into three groups.

There are often difficulties with model building if validation and optimisation have been done on different groups of samples, especially using iterative methods, each group being modelled using properties, such as a different number of components or different variables.     

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiements showed that the elongation temperature of 50 °C and the Mg²⁺ concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.     

桑蚕种良卵率调查中样本间卵粒数的偏差控制方法

桑蚕种良卵率是蚕种质量检验的重要指标,控制样本间卵粒数的偏差是保证良卵率准确性的关键。通过对桑蚕卵粒重的调查分析,得出其分布服从正态分布。若从一批蚕种中抽取1g卵作为样本,则来自同一总体的2个样本的卵粒数之差不超过16粒,其置信概率为95%;当置信概率取99%时,两个样本的卵粒数之差不超过21粒。文章为蚕业生产提供了一种实用的克卵粒数偏差控制方法。     

Elongation method with intermediate mechanical and electrostatic embedding for geometry optimizations of polymers

The elongation method with intermediate mechanical and electrostatic embedding (ELG-IMEE) is proposed. The electrostatic embedding uses atomic charges generated by a charge sensitivity analysis (CSA) method and parameterized for three different population analyses, namely, the Merz–Singh–Kollman scheme, the charge model 5, and the atomic polar tensor. The obtained CSA models were tested on two model systems. Test calculations show that the electrostatic embedding provides several times of decrease in the difference of energies of testing and reference calculations in comparison with the conventional elongation approach (ELG). The mechanical embedding is implemented in a combination of the conventional elongation method and the ONIOM approach. Moreover, it was demonstrated that the geometry optimization with the ELG-IMEE reduces the errors in the optimized structures by about one order in root-mean-square deviation, when compared to ELG.     

Real-Time Detection of Polymerase Activity Using Supercritical Angle Fluorescence

We investigated the incorporation efficiencies of different fluorescently labelled dNTPs with polymerases by complementary strand synthesis. For this reason single stranded DNA was immobilized on a coverslip and the increase of fluorescence due to the synthesis of the corresponding strand with tagged dNTPs was detected with a supercritical angle fluorescence biosensor in real-time. By comparison of the observed signal intensities it was possible to conclude that the system Cy5-dCTP-Klenow (exonuclease free) fragment gives the best incorporation yield of the investigated enzymes and dNTPs.     

Effect of the Mixture Composition on Shear and Extensional Rheology of Recycled PET and ABS Nanocomposites

Summary: Recycled PET as well as ABS - organomodified montmorillonite nanocomposites were prepared via melt compounding in a counter-rotating twin screw extruder. The topological changes in polymer matrices as dependency on clay modification have been evaluated from dynamic experiments in the shear flow using low amplitude oscillatory measurements. Flow characteristics of all studied organoclay nanocomposites showed shear-thinning behavior at low frequencies. Filling of PET with some organoclays led to degradation reactions, which were reflected by lower magnitudes of viscosity and storage modulus in the range of higher frequencies as compared to unfilled polymer matrix. On the contrary, no degradation during the processing of different organoclays with recycled ABS has been observed.     

Skilled workforce scheduling in Service Centres

The Skilled Workforce Project Scheduling Problem (SWPSP) is a complex problem of task scheduling and resource assignment that comes up in the daily management of many company Service Centres (SC). The SWPSP considers many real characteristics faced daily by the SC: client-company service quality agreements that establish maximum dates for the beginning and the end of tasks with penalties for delays, criticality levels indicating the client-priority in processing each task, generalized precedence relationships that can produce cycle structures, time period and percentage time lags and variable task durations depending on the worker executing the task. Furthermore, the SC workforce is made up of specialist workers characterised by efficiency levels showing their efficiency and speed executing the several types of tasks. Each worker has his or her own timetable.     

Rolling of a Rigid Cylinder over a Half-Plane with Initial Stresses (Harmonic and Bartenev–Khazanovich Potentials)

An asymmetric quasistationary problem for a prestressed half-plane with harmonic and Bartenev–Khazanovich potentials is solved based of the linearized theory of elasticity. The Mehler–Fock integral transform is used to solve the differential equations that describe the stress–strain state of the half-plane. The dependences of the normal and tangential stresses and stress intensity factors on the elongation are plotted     

Contact Stress Distribution Under a Rigid Cylinder Rolling Over a Prestressed Strip

A nonsymmetric quasistationary problem for a strip with initial stresses is solved under the linearized theory of elasticity for harmonic and Bartenev–Khazanovich potentials. The Hankel integral transform is used to solve the differential equations that describe the stress–strain state of the strip. The dependences of the normal and tangential stresses and stress intensity factors on the elongation are plotted