Inferring a weighted elastic network from partial unfolding with coarse-grained simulations

A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental C coordinates, and they only take the pairs of C atoms within a given cutoff distance r(c) into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two C atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures. Proteins 2014; 82:119-129. (c) 2013 Wiley Periodicals, Inc.

Economic analysis of cucumber and lettuce intercropping under greenhouse in the winter-spring

A análise econômica complementa a avaliação da eficiência dos cultivos consorciados, considerando além da produção física das culturas, o preço dos produtos segundo sua classificação qualitativa e época do ano. Avaliou-se economicamente consórcios de alface crespa e pepino, em duas populações de plantas, no inverno-primavera, em casa de vegetação, em Jaboticabal, SP, Brasil. Foram calculados o custo operacional total (COT), a receita bruta (RB) e o lucro operacional (LO) das culturas do pepino e alface em monocultura e em consórcio. A mão-de-obra foi a componente com maior participação no COT das culturas em consórcio e monocultura. Maiores RB e LO foram observadas nos cultivos consorciados estabelecidos com o transplante da alface e do pepino no mesmo dia, independente da densidade populacional. Considerando-se o lucro operacional e o índice de uso eficiente da área, recomenda-se o cultivo consorciado com transplante da alface até 10 dias após o transplante (DAT) do pepino, com duas linhas, e ao 0 DAT do pepino cultivado com uma linha no canteiro

On the dynamic behaviour of a mass supported by a parallel combination of a spring and an elastically connected damper

This paper presents a consistent and concise analysis of the free and forced vibration of a mass supported by a parallel combination of a spring and an elastically supported damper (a Zener model). The results are presented in a compact form and the physical behaviour of the system is emphasised. This system is very similar to the conventional single-degree-of freedom system (sdof)-(Voigt model), but the dynamics can be quite different depending on the system parameters. The usefulness of the additional spring in series with the damper is investigated, and optimum damping values for the system subject to different types of excitation are determined and compared.There are three roots to the characteristic equation for the Zener model; two are complex conjugates and the third is purely real. It is shown that it is not possible to achieve critical damping of the complex roots unless the additional stiffness is at least eight times that of the main spring. For a harmonically excited system, there are some possible advantages in using the additional spring when the transmitted force to the base is of interest, but when the displacement response of the system is of interest then the benefits are marginal. It is shown that the additional spring affords no advantages when the system is excited by white noise. (c) 2007 Elsevier Ltd. All rights reserved.

Vibration Attenuation in Rotating Machines Using Smart Spring Mechanism

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effect of eFSH on ovarian cyclicity and embryo production of mares in spring transitional phase

The use of equine FSH (eFSH) for inducing follicular development and ovulation in transitional mares was evaluated. Twenty-seven mares, from 3 to 15 years of age, were examined during the months of August and September 2004, in Brazil. Ultrasound evaluations were performed during 2 weeks before the start of the experiment to confirm transitional characteristics (no follicles larger than 25 mm and no corpus luteum [CL] present). After this period, as the mares obtained a follicle of at least 25 mm, they were assigned to one of two groups: (1) control group, untreated; (2) treated with 12.5 mg eFSH, 2 times per day, until at least half of all follicles larger than 30 mm had reached 35 mm. Follicular activity of all mares was monitored. When most of the follicles from treated mares and a single follicle from control mares acquired a preovulatory size ( : 35 mm), 2,500 IU human chorionic gonadotropin (hCG) was administered IV to induce ovulation. After hCG administration, the mares were inseminated with fresh semen every other day until ovulation. Ultrasound examinations continued until detection of the last ovulation, and embryo recovery was performed 7 to 8 days after ovulation. The mares of the treated group reached the first preovulatoiy follicle (4.1 +/- 1.0 vs 14.9 +/- 10.8 days) and ovulated before untreated mares (6.6 +/- 1.2 vs 18.0 +/- 11.1 days; P <.05). All mares were treated with prostaglandin F-2 alpha (PGF(2 alpha)), on the day of embryo flushing. Three superovulated mares did not cycle immediately after PGF(2 alpha), treatment, and consequently had a longer interovulatory interval (22.4 vs 10.9 days, P < 0.05). The mean period of treatment was 4.79 1.07 days and 85.71% of mares had multiple ovulations. The number of ovulations (5.6 vs 1.0) and embryos (2.0 vs 0.7) per mare were higher (P < 0.05) for treated mares than control mares. In conclusion, treatment with eFSH was effective in hastening the onset of the breeding season, inducing multiple ovulations, and increasing embryo production in transitional mares. This is the first report showing the use of FSH treatment to recover embryos from the first cycle of the year.

Investigation of the H tau tau and Hbb coupling constants for a scalar (Pseudoscalar) higgs Boson at a future linear electron-positron collider

The possibility of setting constraints on the Couplings of a scalar (pseudoscalar) Higgs boson to the tau lepton and the b quark in the reactions e(+)e(-)-->v (v) over bar tau(+)tau(-) and e(+)e(-)-->v (v) over barb (b) over bar at a future linear electron-positron collider of total energy roots = 500 GeV is studied. The admixture of a new hypothetical pseudoscalar state of the Higgs boson in the Hf (f) over bar vertex is parametrized in the form (mf/v)(a+igamma(5)b). on the basis of an analysis of differential distributions for the processes under study, it is shown that data from the future linear collider TESLA will make it possible to constrain the parameters a and b as -0.32 less than or equal to Deltaa less than or equal to 0.24 and -0.73 less than or equal to b less than or equal to 0.73 in the case of the reaction e(+)e(-)-->v (v) over bar tau(+)tau(-) and as -0.026 less than or equal to Deltaa less than or equal to 0.027 and -0.23 less than or equal to b less than or equal to 0.23 in the case of the reaction e(+)e(-) --> v (v) over barb (b) over bar. It is emphasized that the contribution of the fusion Subprocess WW --> H in the channel involving an electron neutrino is of particular importance, since this contribution enhances the sensitivity of data to the parameters being analyzed. (C) 2004 MAIK Nauka/Inierperiodica.

Hydrochemical evaluation of different spring waters for bottling

This investigation was carried out within the Parana sedimentary basin in São Paulo and Mato Grosso do Sul States, Brazil, and involved the sampling of different spring water samples with the purpose of evaluating their quality for bottling Several methods were utilized for acquiring the hydrochemical data, such as methyl orange end-point titration, potentiometry, ion selective electrodes, spectrophotometry, atomic absorption spectrophotometry and inductively coupled plasma spectrometry The results obtained for the analyzed samples were compared with the guideline values established by the São Paulo State and Brazilian Health Ministry legislations for defining the potable water standards The Brazilian Code for Mineral Waters that was established by Register 7841 published on 8 August 1945 was also taken into account for verifying if the spring waters are mineralized The hydrochemical data allowed the identification of anthropogenic and geogenic inputs of some constituents in most of the samples, which affected the water quality and did not allow them to be utilized for commercial purposes (bottling) The waters of these springs can only become appropriate for human consumption after previous chemical treatment

A Contribution to the Estimation of Binary Halide and Pseudo-Halide Equilibrium Constants using a Linear Extrapolation Methodology

The molar single ion activity coefficient (y(F)) of fluoride ions was determined at 25 degrees C and ionic strengths between 0.100 and 3.00 mol L(-1) NaClO(4) using an ion-selective electrode. The activity coefficient dependency on ionic strength was determined to be Phi(F) = log y(F) = 0.2315I-0.041I(2). The function Phi(F)(I), combined with functions obtained in previous work for copper (Phi(Cu)) and hydrogen (Phi(H)), allowed us to make the estimation of the stoichiometric and thermodynamic protonation constants of some halides and pseudo-halides as well as the formation constants of some pseudo-halides and fluoride 1:1 bivalent cation complexes. The calculation procedure proposed in this paper is consistent with critically-selected experimental data. It was demonstrated that it is possible to use Phi(F)(I) for predicting the thermodynamic equilibrium parameters independently of Pearson's hardness of acids and bases.

A new approach for determining stability constants of metal ion complexes in aquatic systems based on flow injection-ion exchange-flame atomic absorption spectrometry coupling

A method based an ion exchange(IE)-atomic absorption spectrometry(AAS) coupled by flow techniques, allowing the determination of formation constants of, at least, the first species of complex systems, in aqueous solution, was developed.The IE-AAS coupling reduces significantly the number of experimental steps in comparison with IE batch methods, resulting in an important increase in analytical rate. The method is simple both from experimental and computational points of view, making possible its utilization by workers without special expertise in the field of complex equilibria in solution. on the other hand, taking into account mainly the amount of hollow cathode lamps available to date, the developed procedure may be applied, within certain limitations, to the study of many systems whose features prevent the use of traditional approaches.

Density-dependent coupling constants and charge symmetry breaking

The effect of the medium in the coupling constants implicate in a charge symmetry breaking on nuclear interactions. The amount of energy due to this modification can explain the Nolen-Schiffer anomaly.

Huge values of room-temperature dielectric constants in pellets of poly(3-methylthiophene)

Room temperature data of impedance and phase angle in pellets of electrochemically synthesized ClO4- doped poly(3-methylthiophene) (P3MT) were analyzed assuming the sample being represented by a parallel resistor-capacitor (RC) circuit or by a series RC circuit. The last assumption proved to be the correct one, and to confirm it we use the sample as the RC component of a resistor-capacitor-inductor series resonator. We discuss the possibility of this RC series behavior to be due to a charge-density wave characteristic also evidenced from the huge values of the low-frequency dielectric constant of the system.

A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Huckel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Huckel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

Environmental coordination chemistry: Binary systems comprising some bivalent cations and monocarboxylates in aqueous solution. Ionic medium effects on equilibrium constants

The molar single activity coefficients associated with propionate ion (Pr) have been determined at 25 degrees C and ionic strengths comprised between 0.300 and 3.00 M, adjusted with NaClO4, as background electrolyte. The investigation was carried out potentiometrically by using a second class Hg/Hg2Pr2 electrode. It was found that the dependence of propionate activity coefficients as a function of ionic strength (I) can be assessed through the following empirical equation: log y(Pr) = -0.185 I-3/2 + 0.104 I-2. Next, simple equations relating stoichiometric protonation constants of several monocarboxylates and formation constants associated with 1:1 complexes involving some bivalent cations and selected monocarboxylates, in aqueous solution, at 25 degrees C, as a function of ionic strength were derived, allowing the interconversion of parameters from one ionic strength to another, up to I = 3.00 M. In addition, thermodynamic formation constants as well as parameters associated with activity coefficients of the complex species in the equilibria are estimated. The body of results shows that the proposed calculation procedure is very consistent with critically selected experimental data.

Ionic medium effects on equilibrium constants .2. Binary systems comprising some bivalent cations and monocarboxylates in aqueous solution

Simple equations were derived relating stoichiometric protonation constants of several monocarboxylates and formation constants associated with 1:1 complexes involving some bivalent cations and selected monocarboxylates, in aqueous sodium perchlorate media, at 25 degrees C, as a function of ionic strength (I), allowing the interconversion of parameters from one ionic strength to another, up to I = 3.00 M. In addition, thermodynamic formation constants as well as activity coefficients of the species involved in the equilibria were estimated. The results show that the proposed calculation procedure is very consistent with critically selected experimental data.

INFLUENCE OF HIGH MICROWAVE DIELECTRIC-CONSTANTS ON THE LINESHAPE OF CONDUCTION-ELECTRON SPIN-RESONANCE

Some synthetic metals show in addition to good conductivity, high microwave dielectric constants. In this work, it is shown how conduction-electron spin resonance(CESR) lineshape can be affected by these high constants. The conditions for avoiding these effects in the CESR measurements are discussed as well as a method for extracting microwave dielectric constants from CESR lines. (C) 1995 Academic Press, Inc.