Nonextensive statistical mechanics applied to protein folding problem: kinetics aspects

A reduced (stereo-chemical) model is employed to study kinetic aspects of globular protein folding process, by Monte Carlo simulation. Nonextensive statistical approach is used: transition probability p i j between configurations i &#8594; j is given by p i j =[1 +(1 - q)&#916;Gi j/kB T ]1/(1-q), where q is the nonextensive (Tsallis) parameter. The system model consists of a chain of 27 beads immerse in its solvent; the beads represent the sequence of amino acids along the chain by means of a 10-letter stereo-chemical alphabet; a syntax (rule) to design the amino acid sequence for any given 3D structure is embedded in the model. The study focuses mainly kinetic aspects of the folding problem related with the protein folding time, represented in this work by the concept of first passage time (FPT). Many distinct proteins, whose native structures are represented here by compact self avoiding (CSA) configurations, were employed in our analysis, although our results are presented exclusively for one representative protein, for which a rich statistics was achieved. Our results reveal that there is a specific combinations of value for the nonextensive parameter q and temperature T, which gives the smallest estimated folding characteristic time (t). Additionally, for q = 1.1, (t) stays almost invariable in the range 0.9 < T < 1.3, slightly oscillating about its average value <img border=0 width=32 height=32 src="../../../../../../../img/revistas/bjp/v39n2a/a16txt01.gif" align=absmiddle > or = 27 ±&#963;, where &#963; = 2 is the standard deviation. This behavior is explained by comparing the distribution of the folding times for the Boltzmann statistics (q &#8594; 1), with respect to the nonextensive statistics for q = 1.1, which shows that the effect of the nonextensive parameter q is to cut off the larger folding times present in the original (q &#8594; 1) distribution. The distribution of natural logarithm of the folding times for Boltzmann statistics is a triple peaked Gaussian, while, for q = 1.1 (Tsallis), it is a double peaked Gaussian, suggesting that a log-normal process with two characteristic times replaced the original process with three characteristic times. Finally we comment on the physical meaning of the present results, as well its significance in the near future works

The effect of local thermal fluctuations on the folding kinetics: a study from the perspective of the nonextensive statistical mechanics

Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process with two consecutive and independent stages, namely the search mechanism and the overall productive stabilization; ($ii$) the folding kinetics results from a mechanism as fast as can be; and ($iii$) at nanoscale dimensions, local thermal fluctuations may have important role on the folding kinetics. Here the first stage of folding process (search mechanism) is focused exclusively. The effects and consequences of local thermal fluctuations on the configurational kinetics, treated here in the context of non extensive statistical mechanics, is analyzed in detail through the dependence of the characteristic time of folding ($\tau$) on the temperature $T$ and on the nonextensive parameter $q$.The model used consists of effective residues forming a chain of 27 beads, which occupy different sites of a $3-$D infinite lattice, representing a single protein chain in solution. The configurational evolution, treated by Monte Carlo simulation, is driven mainly by the change in free energy of transfer between consecutive configurations. ...Comment: 19 pages, 3 figures, 1 tabl

Ativação alcalina de cinzas volantes utilizando solução combinada de NaOH e Ca(OH)2

Este trabalho teve como objetivo avaliar o comportamento da resistência à compressão, ao longo do tempo, em amostras de argamassas à base de cinzas volantes álcali-ativadas. Como ativador alcalino foi utilizada uma solução combinada de NaOH e Ca(OH)2. A cura das amostras foi realizada de duas formas distintas. Na primeira, as amostras foram mantidas em estufa à 70°C/12 hs e à temperatura constante de 22°C em sala climatizada até a idade de ensaio. Apesar de serem obtidas resistências da ordem de 20 MPa nas primeiras 24 hs, houve decréscimo da resistência a partir da idade de 7 dias. Verificado esse comportamento, um segundo método de cura foi adotado. Para isso, o traço utilizado para o preparo de novas argamassas foi o mesmo adotado no método anterior. Porém, foram submetidas à temperatura constante de 70°C até a idade de ensaio. Nesse caso, as amostras apresentaram decréscimo mais acentuado da resistência em menor espaço de tempo, quando comparado às amostras curadas no primeiro método. Como estudos complementares foram realizadas análises microestruturais da CV antes e depois da ativação, utilizando o MEV/EDS.The main objective of this work was to evaluate the development of the compressive strength, along time, in alkali-activated fly ash mortars. As alkaline activator a combined solution of NaOH and Ca(OH)2 was used. The cure of the samples was carried through two distinct forms. In the first one, samples were kept in oven at 70°C during the first 12 hours and at constant room temperature of 22°C afterwards, until the age of testing. Compressive strength of 20 MPa magnitude were achieved during the first 24 hours, however it started to decrease after the age of 7 days. Considering this behaviour, second method of curing was adopted for the same mixing proportions. However, mortar samples were kept in oven at 70°C until the age of testing. In this case, compressive strength results decreased more significantly and at earlier ages, when compared with the results of samples cured using the first method. As complementary to understand the decreasing in compressive strength, microstructural analyses of the fly ash, before and after the activation, have been carried out, using the SEM/EDS

Cinzas volantes álcali-ativadas com solução combinada de NaOH e Ca(OH)2

Este trabalho teve como objetivo avaliar o comportamento da resistência à compressão, ao longo do tempo, em amostras de argamassas à base de cinzas volantes álcali-ativadas. Como ativador alcalino foi utilizada uma solução combinada de NaOH e Ca(OH)2. A cura das amostras foi realizada de duas formas distintas. Na primeira, as amostras foram mantidas em estufa à 70°C/12 h e à temperatura constante de 22°C em sala climatizada até a idade de ensaio. Apesar de serem obtidas resistências da ordem de 20 MPa nas primeiras 24 h, houve decréscimo da resistência a partir da idade de 7 dias. Verificado esse comportamento, um segundo método de cura foi adotado. Para isso, o traço utilizado para o preparo de novas argamassas foi o mesmo adotado no método anterior. Porém, foram submetidas à temperatura constante de 70°C até a idade de ensaio. Nesse caso, as amostras apresentaram decréscimo mais acentuado da resistência em menor espaço de tempo, quando comparado às amostras curadas no primeiro método. Como estudos complementares foram realizadas análises microestruturais da CV antes e depois da álcali-ativação, utilizando o MEV/EDS. Nas imagens microestruturais foi possível identificar três morfologias distintas nas pastas álcali-ativadas: uma composta de regiões com aspecto denso; outra apresentando partículas de cinzas volantes parcialmente solubilizadas; e outra mostrando a formação de produtos em forma de cristais aciculares. Porém, apenas o uso do MEV/EDS não foi suficiente para que se pudesse entender o mecanismo de reação deletéria provocada entre os ativadores alcalinos e a cinza volante. Portanto, trabalhos futuros deverão contemplar o uso de ferramentas auxiliares às adotadas nesse trabalho com o objetivo de esclarecer tal mecanismo deletério.The main objective of this work was to evaluate over time the development of the compressive strength of alkali-activated fly ash mortars. A combined solution of NaOH and Ca(OH)2 was used as alkaline activator. The curing of the samples was carried out in two distinct ways. In the first one, samples were kept at 70°C during the first 12 hours after mixing and at 22°C afterwards, until the age of testing. Although compressive strengths of about 20 MPa were achieved during the first 24 hours, the strength started to decrease after 7 days. Considering this behaviour, a second method of curing was adopted. The mix proportions were the same as before, however the mortar samples were kept in an oven at 70°C until the age of testing. In this case, the compressive strength values decreased more significantly and in a shorter period of time, as compared to the results obtained for samples cured using the first method. Complementary studies were performed in order to better understand the observed reduction in compressive strength. Microstructural analyses of the fly ash, before and after the alkali-activation, have been carried out using Scanning Electron Microscopy (SEM) and Energy-Dispersive Spectroscopy (EDS). It was possible to identify three different morphologies in the alkali-activated pastes: one composed by regions with dense aspect; other showing partially solubilised particles of fly ash; and a third showing the formation of products with a needle-like shape. The information provided by the SEM/EDS experiments was not enough to enable the complete understanding of the mechanism of the deleterious reaction that took place among the alkaline activators and the fly ash. Therefore, future studies should address this question by using additional analysis tools in order to clarify this deleterious mechanism

Effect of Gypsum on the Early Hydration of Cubic and Na-Doped Orthorhombic Tricalcium Aluminate

The tricalcium aluminate (C3A) and sulfate content in cement influence the hydration chemistry, setting time and rheology of cement paste, mortar and concrete. Here, in situ experiments are performed to better understand the effect of gypsum on the early hydration of cubic (cub-)C3A and Na-doped orthorhombic (orth-)C3A. The isothermal calorimetry data show that the solid-phase assemblage produced by the hydration of C3A is greatly modified as a function of its crystal structure type and gypsum content, the latter of which induces non-linear changes in the heat release rate. These data are consistent with the in situ X-ray diffraction results, which show that a higher gypsum content accelerates the consumption of orth-C3A and the subsequent precipitation of ettringite, which is contrary to the cub-C3A system where gypsum retarded the hydration rate. These in situ results provide new insight into the relationship between the chemistry and early-age properties of cub- and orth-C3A hydration and corroborate the reported ex situ findings of these systems

Real-Time High-Resolution X-ray Imaging and Nuclear Magnetic Resonance Study of the Hydration of Pure and Na-Doped C 3

This study details the differences in real-time hydration between pure tricalcium aluminate (cubic C{sub 3}A or 3CaO {center_dot} Al{sub 2}O{sub 3}) and Na-doped tricalcium aluminate (orthorhombic C{sub 3}A or Na{sub 2}Ca{sub 8}Al{sub 6}O{sub 18}), in aqueous solutions containing sulfate ions. Pure phases were synthesized in the laboratory to develop an independent benchmark for the reactions, meaning that their reactions during hydration in a simulated early age cement pore solution (saturated with respect to gypsum and lime) were able to be isolated. Because the rate of this reaction is extremely rapid, most microscopy methods are not adequate to study the early phases of the reactions in the early stages. Here, a high-resolution full-field soft X-ray imaging technique operating in the X-ray water window, combined with solution analysis by {sup 27}Al nuclear magnetic resonance (NMR) spectroscopy, was used to capture information regarding the mechanism of C{sub 3}A hydration during the early stages. There are differences in the hydration mechanism between the two types of C{sub 3}A, which are also dependent on the concentration of sulfate ions in the solution. The reactions with cubic C{sub 3}A (pure) seem to be more influenced by higher concentrations of sulfate ions, forming smaller ettringite needles at a slower pace than the orthorhombic C{sub 3}A (Na-doped) sample. The rate of release of aluminate species into the solution phase is also accelerated by Na doping

Desenvolvimento inicial do milho e atributos químicos do solo em função de diferentes doses de silicato de cálcio

Calcium silicate applied to the soil has an effect on plant nutrition since it is a source of silicon, calcium and magnesium. With the aim to evaluate the effect of doses of calcium silicate on soil chemical properties and on early development of corn, an experiment was conducted in a greenhouse, in pots containing eutroferric Oxisol, testing five rates of calcium silicate (0, 1.2; 2.4; 4.8 and 9.6 t ha-1) with four replications in a randomized complete block design. The levels of N, P, K, Ca and Mg in the plant shoot were evaluated, and, at the end of the experiment, shoot dry weight and plant height as well as Ca and Mg, and soil pH were also estimated. Shoot dry matter and plant height were not affected by fertilization with calcium silicate. The application of calcium silicate provided soil amendment, increasing the availability of calcium and magnesium, in addition to increasing the levels of N, K, Ca and Mg in the shoots of corn.O silicato de c&aacute;lcio, quando aplicado ao solo, tem efeito sobre a nutri&ccedil;&atilde;o das plantas, uma vez que &eacute; fonte de sil&iacute;cio, c&aacute;lcio e magn&eacute;sio. Com o objetivo de avaliar o efeito de doses de silicato de c&aacute;lcio sobre atributos qu&iacute;micos do solo e o desenvolvimento inicial da cultura do milho, realizou-se um experimento em casa de vegeta&ccedil;&atilde;o, em vasos com Latossolo Vermelho eutrof&eacute;rrico &ndash; LVef, para testar cinco doses de silicato de c&aacute;lcio (0; 1,2; 2,4; 4,8 e 9,6 t ha-1) com quatro repeti&ccedil;&otilde;es em, delineamento experimental de blocos casualizados. Foram avaliados os teores N, P, K, Ca e Mg da parte a&eacute;rea, e, ao final do experimento, a massa da mat&eacute;ria seca da parte a&eacute;rea e altura de plantas, bem como os teores de Ca e Mg e pH do solo. A mat&eacute;ria seca da parte a&eacute;rea e altura de plantas n&atilde;o foram influenciadas pela aduba&ccedil;&atilde;o com silicato de c&aacute;lcio. A aplica&ccedil;&atilde;o de silicato de c&aacute;lcio promoveu uma a&ccedil;&atilde;o corretiva no solo, com aumento da disponibilidade de c&aacute;lcio e magn&eacute;sio, al&eacute;m de promover incremento dos teores de N, K, Ca e Mg na parte a&eacute;rea da cultura do milho

Addition of urease inhibitor has no effect on ammonia volatilization following soil application of poultry litter or organomineral fertilizer, unlike urea.

Abstract: Quantification of ammonia volatilization after addition of animal residues and nitrogen (N) mineral fertilizers to the soil is important for N management in fertilization programs. The objective of this study was to evaluate the effect of adding a urease inhibitor to N fertilizers to minimize ammonia losses following soil application. The experiment was carried out in a laboratory with samples of a Brazilian Oxisol containing 790 g kg-1 clay and 23 g kg-1 organic matter. Treatments consisted of addition of poultry litter (PL), organic mineral fertilizer (OMF) and urea to the soil, with and without the urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT), plus a control with no fertilizer. We applied the fertilizers over the soil surface, with no soil incorporation, at a rate of 200 mg kg-1 N. Experimental units consisted of PVC tubes with a diameter of 0.15 m, containing 1.0 kg of soil (dry basis). Ammonia volatilization was measured for 56 days following fertilizer application to the soil using sponge discs impregnated with phosphoric acid and glycerin, which were fitted inside the tubes 0.15 m above the soil surface. Ammonia volatilization peaks varied according to the fertilizer, and most of them occurred in the first 15 days following application to the soil. Total ammonia volatilized from the soil treated with PL or OMF had no influence on the urease inhibitor, probably because the losses were small, attaining a maximum of 2.5 and 9 % of the total N applied, respectively. In the treatment that received urea, NBPT delayed the peak of volatilization by three weeks and decreased the loss of ammonia from 22 to 9 % of the N applied. Use of urease inhibitor does not always decrease ammonia volatilization, especially when mixed with fertilizers in which urea is not the only source of N

Bioavailability of phosphorus on highly weathered Oxisoils of the Brazilian Mid-West.

Soils from mid-west Brazil show strong phosphorus (P) fixation, which can reduce the efficiency of P fertilizers. Under this condition, soil competes with the plant for the applied P adsorbing it strongly in its mineral fraction. Nevertheless, in areas where crops are grown and fertilizers are added for many years, soil fertility status has increased over time, making these soils nonresponsive to P. The objective of this study was to evaluate how P availability changes with soil use. Forty soil samples were collected under different types of land use: native forest, pasture, no-tillage, and areas with periodic tillage. P fractionation was performed to determine the amount of P in the organic and inorganic fractions with high, medium, and low lability under each land use. Corn was cultivated in a greenhouse experiment to evaluate P uptake and values correlated with different P fractions. The results showed differences in the P fraction relations among different land uses. Cultivated areas (no tillage and periodic tillage) accumulated greater amounts of P in all fractions than pastures and the native forest. A higher proportion of labile organic P was observed under no tillage than under periodic tillage. NaHCO3 and NaOH 0.1 mol L-1were the most relevant P fractions for shoot P uptake. No tillage promoted the accumulation of available P fractions, suggesting that it is a good management strategy to ensure fertilizer use efficienc