Persistent confusion of total entropy and chemical system entropy in chemical thermodynamics.

The change in free energy with temperature at constant pressure of a chemical reaction is determined by the sum (dS) of changes in entropy of the system of reagents, dS(i), and the additional entropy change of the surroundings, dS(H), that results from the enthalpy change, W. A faulty identification of the total entropy change on reaction with dS(i) has been responsible for the attribution of general validity to the expressions (d deltaG/dT)p = -deltaS(i) and d(deltaG/T)/d(1/T)= deltaH, which are found in most textbooks and in innumerable papers.

Least activation path for protein folding: investigation of staphylococcal nuclease folding by stopped-flow circular dichroism.

Is the pathway of protein folding determined by the relative stability of folding intermediates, or by the relative height of the activation barriers leading to these intermediates? This is a fundamental question for resolving the Levinthal paradox, which stated that protein folding by a random search mechanism would require a time too long to be plausible. To answer this question, we have studied the guanidinium chloride (GdmCl)-induced folding/unfolding of staphylococcal nuclease [(SNase, formerly EC 3.1.4.7; now called microbial nuclease or endonuclease, EC 3.1.31.1] by stopped-flow circular dichroism (CD) and differential scanning microcalorimetry (DSC). The data show that while the equilibrium transition is a quasi-two-state process, kinetics in the 2-ms to 500-s time range are triphasic. Data support the sequential mechanism for SNase folding: U3 <--> U2 <--> U1 <--> N0, where U1, U2, and U3 are substates of the unfolded protein and N0 is the native state. Analysis of the relative population of the U1, U2, and U3 species in 2.0 M GdmCl gives delta-G values for the U3 --> U2 reaction of +0.1 kcal/mol and for the U2 --> U1 reaction of -0.49 kcal/mol. The delta-G value for the U1 --> N0 reaction is calculated to be -4.5 kcal/mol from DSC data. The activation energy, enthalpy, and entropy for each kinetic step are also determined. These results allow us to make the following four conclusions. (i) Although the U1, U2, and U3 states are nearly isoenergetic, no random walk occurs among them during the folding. The pathway of folding is unique and sequential. In other words, the relative stability of the folding intermediates does not dictate the folding pathway. Instead, the folding is a descent toward the global free-energy minimum of the native state via the least activation path in the vast energy landscape. Barrier avoidance leads the way, and barrier height limits the rate. Thus, the Levinthal paradox is not applicable to the protein-folding problem. (ii) The main folding reaction (U1 --> N0), in which the peptide chain acquires most of its free energy (via van der Waals' contacts, hydrogen bonding, and electrostatic interactions), is a highly concerted process. These energy-acquiring events take place in a single kinetic phase. (iii) U1 appears to be a compact unfolded species; the rate of conversion of U2 to U1 depends on the viscosity of solution. (iv) All four relaxation times reported here depend on GdmCl concentrations: it is likely that none involve the cis/trans isomerization of prolines. Finally, a mechanism is presented in which formation of sheet-like chain conformations and a hydrophobic condensation event precede the main-chain folding reaction.

Simple model of protein folding kinetics.

A simple model of the kinetics of protein folding is presented. The reaction coordinate is the "correctness" of a configuration compared with the native state. The model has a gap in the energy spectrum, a large configurational entropy, a free energy barrier between folded and partially folded states, and a good thermodynamic folding transition. Folding kinetics is described by a master equation. The folding time is estimated by means of a local thermodynamic equilibrium assumption and then is calculated both numerically and analytically by solving the master equation. The folding time has a maximum near the folding transition temperature and can have a minimum at a lower temperature.

Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.

A Monte Carlo simulation method for globular proteins, called extended-scaled-collective-variable (ESCV) Monte Carlo, is proposed. This method combines two Monte Carlo algorithms known as entropy-sampling and scaled-collective-variable algorithms. Entropy-sampling Monte Carlo is able to sample a large configurational space even in a disordered system that has a large number of potential barriers. In contrast, scaled-collective-variable Monte Carlo provides an efficient sampling for a system whose dynamics is highly cooperative. Because a globular protein is a disordered system whose dynamics is characterized by collective motions, a combination of these two algorithms could provide an optimal Monte Carlo simulation for a globular protein. As a test case, we have carried out an ESCV Monte Carlo simulation for a cell adhesive Arg-Gly-Asp-containing peptide, Lys-Arg-Cys-Arg-Gly-Asp-Cys-Met-Asp, and determined the conformational distribution at 300 K. The peptide contains a disulfide bridge between the two cysteine residues. This bond mimics the strong geometrical constraints that result from a protein's globular nature and give rise to highly cooperative dynamics. Computation results show that the ESCV Monte Carlo was not trapped at any local minimum and that the canonical distribution was correctly determined.

The impact of a future solar minimum on climate change projections in the Northern Hemisphere

Solar variability represents a source of uncertainty in the future forcings used in climate model simulations. Current knowledge indicates that a descent of solar activity into an extended minimum state is a possible scenario. With aid of experiments from a state-of-the-art Earth system model, we investigate the impact of a future solar minimum on Northern Hemisphere climate change projections. This scenario is constructed from recent 11 year solar-cycle minima of the solar spectral irradiance, and is therefore more conservative than the 'grand' minima employed in some previous modeling studies. Despite the small reduction in total solar irradiance (0.36 W m^-2), relatively large responses emerge in the winter Northern Hemisphere, with a reduction in regional-scale projected warming by up to 40%. To identify the origin of the enhanced regional signals, we assess the role of the different mechanisms by performing additional experiments forced only by irradiance changes at different wavelengths of the solar spectrum. We find that a reduction in visible irradiance drives changes in the stationary wave pattern of the North Pacific and sea-ice cover. A decrease in UV irradiance leads to smaller surface signals, although its regional effects are not negligible. These results point to a distinct but additive role of UV and visible irradiance in the Earth's climate, and stress the need to account for solar forcing as a source of uncertainty in regional scale projections.

Simultaneous optical and X-ray observations of flares and rotational modulation on the RS CVn binary HR 1099 (V711 Tau) from the MUSICOS 1998 campaign

We present simultaneous and continuous observations of the Hα, Hβ, He I D_3, Na I D_1,D_2 doublet and the Ca II H&K lines for the RS CVn system HR 1099. The spectroscopic observations were obtained during the MUSICOS 1998 campaign involving several observatories and instruments, both echelle and long-slit spectrographs. During this campaign, HR 1099 was observed almost continuously for more than 8 orbits of 2^d.8. Two large optical flares were observed, both showing an increase in the emission of Hα, Ca II H K, Hβ and He I D_3 and a strong filling-in of the Na I D_1, D_2 doublet. Contemporary photometric observations were carried out with the robotic telescopes APT-80 of Catania and Phoenix-25 of Fairborn Observatories. Maps of the distribution of the spotted regions on the photosphere of the binary components were derived using the Maximum Entropy and Tikhonov photometric regularization criteria. Rotational modulation was observed in Hα and He I D_3 in anti-correlation with the photometric light curves. Both flares occurred at the same binary phase (0.85), suggesting that these events took place in the same active region. Simultaneous X-ray observations, performed by ASM on board RXTE, show several flare-like events, some of which correlate well with the observed optical flares. Rotational modulation in the X-ray light curve has been detected with minimum flux when the less active G5 V star was in front. A possible periodicity in the X-ray flare-like events was also found.

Entropy production and thermodynamic power of the squeezed thermal reservoir

We analyze the entropy production and the maximal extractable work from a squeezed thermal reservoir. The nonequilibrium quantum nature of the reservoir induces an entropy transfer with a coherent contribution while modifying its thermal part, allowing work extraction from a single reservoir, as well as great improvements in power and efficiency for quantum heat engines. Introducing a modified quantum Otto cycle, our approach fully characterizes operational regimes forbidden in the standard case, such as refrigeration and work extraction at the same time, accompanied by efficiencies equal to unity.

Diversity for Texts Builds in Language L(MT): Indexes Based in Theory of Information

If one has a distribution of words (SLUNs or CLUNS) in a text written in language L(MT), and is adjusted one of the mathematical expressions of distribution that exists in the mathematical literature, some parameter of the elected expression it can be considered as a measure of the diversity. But because the adjustment is not always perfect as usual measure; it is preferable to select an index that doesn't postulate a regularity of distribution expressible for a simple formula. The problem can be approachable statistically, without having special interest for the organization of the text. It can serve as index any monotonous function that has a minimum value when all their elements belong to the same class, that is to say, all the individuals belong to oneself symbol, and a maximum value when each element belongs to a different class, that is to say, each individual is of a different symbol. It should also gather certain conditions like they are: to be not very sensitive to the extension of the text and being invariant to certain number of operations of selection in the text. These operations can be theoretically random. The expressions that offer more advantages are those coming from the theory of the information of Shannon-Weaver. Based on them, the authors develop a theoretical study for indexes of diversity to be applied in texts built in modeling language L(MT), although anything impedes that they can be applied to texts written in natural languages.

Políticas europeas para la competitividad, salarios mìnimos y tutela del poder adquisitivo de las retribuciones en Italia tras el acuerdo de noviembre de 2012 [European Policies for competitiveness, minimum wages and purchasing power protection in Italy after the November 2012 agreement]. WP C.S.D.L.E. “Massimo D’Antona”.INT – 99/2013

On the floor of the Global Wage Report 2012/2013 by ILO, entitled Wages and equitable growth, the A. thinks that the wage regulation has to take into account competitiveness without compressing global aggregate demand. Therefore, International and European rules are necessary to avoid the spiral towards the wages dampen, which is bad for the economic development. The rules in action at the different levels are inadequate. The A. proposes an interpretation of Article 153 and Article 155 TFEU that is more suitable for a European regulation promoting better minimum wages and more coherent with the current legal framework of the right to pay, which can be considered, even if partially, as a social right.