Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

A study of the cambial zone and conductive phloem of common beech (Fagus sylvatica L.) using an image analysis method. I. Influence of tree age on the structure

Quantification is a major problem when using histology to study the influence of ecological factors on tree structure. This paper presents a method to prepare and to analyse transverse sections of cambial zone and of conductive phloem in bark samples. The following paper (II) presents the automated measurement procedure. Part I here describes and discusses the preparation method, and the influence of tree age on the observed structure. Highly contrasted images of samples extracted at breast height during dormancy were analysed with an automatic image analyser. Between three young (38 years) and three old (147 years) trees, age-related differences were identified by size and shape parameters, at both cell and tissue levels. In the cambial zone, older trees had larger and more rectangular fusiform initials. In the phloem, sieve tubes were also larger, but their shape did not change and the area for sap conduction was similar in both categories. Nevertheless, alterations were limited, and demanded statistical analysis to be identified and ascertained. The physiological implications of the structural changes are discussed.

Impact of regeneration method on stand structure prior to first thinning

Summary

Capital Structure and Firm Growth: R&D Intensive Companies

The purpose of this study is to examine and explain firm`s growth impact on capital structure decision-making in research and development intensive companies. Many studies claim that R&D has a pivotal impact on capital structure decisions, but corporate finance theories have often failed to explain these observed patterns. As sales growth is an important concept and objective for R&D firms, it is logical to assume that it plays a vital role in capital structure decisions. This study applies nomothetic research approach. The theoretical part employs a formal conceptual analysis in order to develop the propositions that are tested with empirical data. The empirical part consists of the analysis of three companies; the data is obtained from the annual reports over the period 2003 – 2008. The companies operate in IT- or ICT-industry and are publicly listed. The method for analyzing the case data is based on the financial indicators, which are obtained from the financials of the case companies. These economic indicators describe the capital structure and the financial decision-making of the firms. The method relates to the quantitative studies. Yet, this study extends the analysis beyond the indicators. Specifically, this study addresses the question of what is behind the economic indicators, therefore combining aspects of quantitative and qualitative analysis. The firms examined in this study seem to prefer internal finance during growth. However, external finance seems to be a catalyst for sales growth. Firms strongly prefer equity financing. In growth, the use of equity per capital either increases or stays in a constant level. Over the period 2003 – 2008, the firms were often associated to equity related transactions and short-term debt. Short-term debt was used as a substitute of long-term debt and equity. The case firms also adjusted their capital structure – these adjustments were carried out with short-term debt or equity. The case data also provides implications for the growth signal theory that was developed in this study. Based on the econometric indicators, arguments can be made that equity investors are `attracted` to growing R&D firms. This is because growth helps investors perceive the true type of firm. The findings of this study are best explained by the trade-off theory and the pecking order theory. These corporate finance theories are considered as mainstream. Little support can be found to the implications of the signaling theory and market timing theory.

A benchmark method for global optimization problems in structure determination from powder diffraction data

Quasi-Newton-Raphson minimization and conjugate gradient minimization have been used to solve the crystal structures of famotidine form B and capsaicin from X-ray powder diffraction data and characterize the chi(2) agreement surfaces. One million quasi-Newton-Raphson minimizations found the famotidine global minimum with a frequency of ca 1 in 5000 and the capsaicin global minimum with a frequency of ca 1 in 10 000. These results, which are corroborated by conjugate gradient minimization, demonstrate the existence of numerous pathways from some of the highest points on these chi(2) agreement surfaces to the respective global minima, which are passable using only downhill moves. This important observation has significant ramifications for the development of improved structure determination algorithms.

Automated tertiary structure prediction with accurate local model quality assessment using the IntFOLD-TS method

The IntFOLD-TS method was developed according to the guiding principle that the model quality assessment would be the most critical stage for our template based modelling pipeline. Thus, the IntFOLD-TS method firstly generates numerous alternative models, using in-house versions of several different sequence-structure alignment methods, which are then ranked in terms of global quality using our top performing quality assessment method – ModFOLDclust2. In addition to the predicted global quality scores, the predictions of local errors are also provided in the resulting coordinate files, using scores that represent the predicted deviation of each residue in the model from the equivalent residue in the native structure. The IntFOLD-TS method was found to generate high quality 3D models for many of the CASP9 targets, whilst also providing highly accurate predictions of their per-residue errors. This important information may help to make the 3D models that are produced by the IntFOLD-TS method more useful for guiding future experimental work

Calculating Flash Point Numbers from Molecular Structure: An Improved Method for Predicting the Flash Points of Acyclic Alkanes

We report a novel method for calculating flash points of acyclic alkanes from flash point numbers, N(FP), which can be calculated from experimental or calculated boiling point numbers (Y(BP)) with the equation N(FP) = 1.020Y(BP) - 1.083 Flash points (FP) are then determined from the relationship FP(K) = 23.369N(FP)(2/3) + 20.010N(FP)(1/3) + 31.901 For it data set of 102 linear and branched alkanes, the correlation of literature and predicted flash points has R(2) = 0.985 and an average absolute deviation of 3.38 K. N(FP) values can also be estimated directly from molecular structure to produce an even closer correspondence of literature and predicted FP values. Furthermore, N(FP) values provide a new method to evaluate the reliability of literature flash point data.

Structure and microstructure of PbTiO3 thin films obtained from hybrid chemical method

PbTiO3 thin films were deposited on Si(100) via hybrid chemical method and crystallized between 400 and 700 degreesC to study the effect of the crystallization kinetics on structure and microstructure of these materials. X-ray diffraction (XRD) technique was used to study the structure of the crystallized films. In the temperature range investigated, the lattice strain (c/a) presented a maximum value (c/a = 1.056) for film crystallized at 600 degreesC for I h. Atomic force microscopy (AFM) was used in investigation of the microstructure of the films. The rms roughness of the films linearly increases with temperature and ranged from 1.25 to 9.04 nm while the grain sizes ranged from 130.6 to 213.6 nm. Greater grain size was observed for film crystallized at 600 degreesC for 1 h. (C) 2002 Elsevier B.V. S.A. All rights reserved.

Quantitative structural analysis of the transition from LT-LixCoO2 to HT-LixCoO2 using the rietveld method: correlation between structure and electrochemical performance

A quantitative phase analysis was made of LiXCoO2 powders obtained by two distinct chemical methodologies at different temperatures (from 400 to 700degreesC). A phase analysis was made using Rietveld refinements based on X-ray diffraction data, considering the LiXCoO2 powders as a multiphase system that simultaneously contained two main phases with distinct, layered and spinel-type structures. The sults showed the coexistence of both structures in LiXCoO2 obtained at low temperature (400 and 500degreesC), although only the layered structure was detected at higher temperatures (600 and 700degreesC, regardless of the chemical powder process employed. The electrochemical performance, evaluated mainly by the cycling reversibility of LiXCoO2 in the form of cathode insertion electrodes, revealed that there is a close correlation between structural features and the electrochemical response, with one of the redox processes (3.3 v/3.9 v) associated only with the presence of the spinel-type structure. (C) 2003 Elsevier B.V. All rights reserved.

Relationship between Crystal Shape, Photoluminescence, and Local Structure in SrTiO3 Synthesized by Microwave-Assisted Hydrothermal Method

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Quantitative structural analysis of the transition from LT-Li xCoO2 to HT-LixCoO2 using the rietveld method: Correlation between structure and electrochemical performance

A quantitative phase analysis was made of LixCoO2 powders obtained by two distinct chemical methodologies at different temperatures (from 400 to 700°C). A phase analysis was made using Rietveld refinements based on X-ray diffraction data, considering the Li xCoO2 powders as a multiphase system that simultaneously contained two main phases with distinct, layered and spinel-type structures. The results showed the coexistence of both structures in LixCoO 2 obtained at low temperature (400 and 500°C), although only the layered structure was detected at higher temperatures (600 and 700°C), regardless of the chemical powder process employed. The electrochemical performance, evaluated mainly by the cycling reversibility of Li xCoO2 in the form of cathode insertion electrodes, revealed that there is a close correlation between structural features and the electrochemical response, with one of the redox processes (3.3 v/3.9 v) associated only with the presence of the spinel-type structure. © 2003 Elsevier B.V. All rights reserved.

Electronic structure and magnetic properties of FeWO 4 nanocrystals synthesized by the microwave-hydrothermal method

This communication reports that FeWO 4 nanocrystals were successfully synthesized by the microwave-hydrothermal method at 443 K for 1 h. The structure and shape of these nanocrystals were characterized by X-ray diffraction, Rietveld refinement, and transmission electron microscopy. The experimental results and first principles calculations were combined to explain the electronic structure and magnetic properties. Experimental data were obtained by magnetization measurements for different applied magnetic fields. Theoretical calculations revealed that magnetic properties of FeWO 4 nanocrystals can be assigned to two magnetic orderings with parallel or antiparallel spins in adjacent chains. These factors are crucial to understanding of competition between ferro- and antiferromagnetic behavior. © 2012 Elsevier Inc.

Structure and photocatalytic properties of Nb-doped Bi12TiO20 prepared by the oxidant peroxide method (OPM)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)