Descripción: Fil:Ison, M.J. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.

Descripción: The dynamics of open balloons in an atmosphere may be studied with a body-fluid coupled model. A numerical approach is required to solve the corresponding equation set. Solutions under different conditions are obtained here for the vertical and one horizontal direction. Relevant dynamical features during ascent, flotation, and descent depend on balloon thermodynamics, wind, air small-scale turbulence, and perturbations to the background atmosphere. After analysis of the results it is found that approximate analytical solutions may be found in certain cases. The effect of nonlinear drag on balloon oscillation period and damping near flotation is evaluated. © 2003 American Institute of Physics.

Descripción: Using methods of non-equilibrium thermodynamics that extend and generalize the MHD energy principle of Bernstein et al. (1958, Proc. Roy. Soc. A, 244, 17) we develop a formalism in order to analyze the stability properties of prominence models considered as dissipative states i.e. states far form thermodynamic equilibrium. As an example, the criterion is applied to the Kippenhahn-Schlüter model (hereafter K-S) considering the addition of dissipative terms in the coupled system of equations: the balance of energy equation and the equation of motion. We show from this application, that periods corresponding to typical oscillations of the chromosphere and photosphere (3 and 5 min respectively), that were reported as observations of the prominence structure, can be explained as internal modes of the prominence itself. This is an alternative explanation to the one that supposes that the source of these perturbations are the cold foot chromospheric and photospheric basis.

Descripción: In this work we studied the effect of NaCl on the thermodynamic and dynamic properties of supercooled water, for salt concentrations between 0.19 and 1.33mol kg-1, using molecular dynamic simulations for TIP5PE water model and ion parameters specially designed to be used in combination with this potential. We studied the isobaric heat capacity (Cp) temperature dependence and observed a maximum in Cp, occurring at Tm, that moves to lower temperature values with increasing salt concentration. Many characteristic changes were observed at scaled temperature TTm ∼ 0.96, namely a minimum in the density of the system, a reduction of the slope of the number of hydrogen bonds vs. temperature, and a crossover from Vogel-Tamman-Fulcher to Arrhenius dynamics. Finally, at low temperatures we observed that water dynamics become heterogeneous with an apparently common relationship between the fraction of immobile molecules and T/Tm for all studied systems. © 2011 American Institute of Physics.

Descripción: Aims. We study the modes and stability of non-isothermal coronal loop models with different intensity values of the equilibrium magnetic field. Methods. We use an energy principle obtained via non-equilibrium thermodynamic arguments. The principle is expressed in terms of Hermitian operators and allow to consider together the coupled system of equations: the balance of energy equation and the equation of motion. Results. We determine modes characterized as long - wavelength disturbances that are present in inhomogeneous media. This character of the system introduces additional difficulties for the stability analysis because the inhomogeneous nature of the medium determines the structure of the disturbance, which is no longer sinusoidal. Moreover, another complication is that we obtain a continuous spectrum of stable modes in addition to the discrete one. Conclusions. We obtain a unique unstable mode with a characteristic time that is comparable with the characteristic life-time observed for loops. The feasibility of wave-based and flow-based models is examined. © ESO 2006.

Descripción: Natural protein domains must be sufficiently stable to fold but often need to be locally unstable to function. Overall, strong energetic conflicts are minimized in native states satisfying the principle of minimal frustration. Local violations of this principle open up possibilities to form the complex multifunnel energy landscapes needed for large-scale conformational changes. We survey the local frustration patterns of allosteric domains and show that the regions that reconfigure are often enriched in patches of highly frustrated interactions, consistent both with the idea that these locally frustrated regions may act as specific hinges or that proteins may "crack" in these locations. On the other hand, the symmetry of multimeric protein assemblies allows near degeneracy by reconfiguring while maintaining minimally frustrated interactions. We also anecdotally examine some specific examples of complex conformational changes and speculate on the role of frustration in the kinetics of allosteric change.

Descripción: 1. 1. The effects of light and porphyrins on the activity of red cell uroporphyrinogen decarboxylase were studied. 2. 2. Photoinactivation of uroporphyrinogen decarboxylase was dependent on uroporphyrin concentration, irradiation time and temperature. Using 40 W/m2 of UV light intensity, 40-45% decreased activity was produced with 200 μM uroporphyrin I, at 37°C and after 2 hr of illumination. 3. 3. It has been demonstrated that porphyrins photoinactivate uroporphyrinogen decarboxylase and a mechanism for this action in relation to skin lesions is proposed. © 1986.

Descripción: Immune responses are qualitatively and quantitatively influenced by a complex network of receptor-ligand interactions. Among them, the CD137:CD137L pathway is known to modulate innate and adaptive human responses against Mycobacterium tuberculosis. However, the underlying mechanisms of this regulation remain unclear. In this work, we developed a Bayesian Computational Model (BCM) of in vitro CD137 signaling, devised to fit previously gathered experimental data. The BCM is fed with the data and the prior distribution of the model parameters and it returns their posterior distribution and the model evidence, which allows comparing alternative signaling mechanisms. The BCM uses a coupled system of non-linear differential equations to describe the dynamics of Antigen Presenting Cells, Natural Killer and T Cells together with the interpheron (IFN)-γ and tumor necrosis factor (TNF)-α levels in the media culture. Fast and complete mixing of the media is assumed. The prior distribution of the parameters that describe the dynamics of the immunological response was obtained from the literature and theoretical considerations Our BCM applies successively the Levenberg-Marquardt algorithm to find the maximum a posteriori likelihood (MAP); the Metropolis Markov Chain Monte Carlo method to approximate the posterior distribution of the parameters and Thermodynamic Integration to calculate the evidence of alternative hypothesis. Bayes factors provided decisive evidence favoring direct CD137 signaling on T cells. Moreover, the posterior distribution of the parameters that describe the CD137 signaling showed that the regulation of IFN-γ levels is based more on T cells survival than on direct induction. Furthermore, the mechanisms that account for the effect of CD137 signaling on TNF-α production were based on a decrease of TNF-α production by APC and, perhaps, on the increase in APC apoptosis. BCM proved to be a useful tool to gain insight on the mechanisms of CD137 signaling during human response against Mycobacterium tuberculosis. © 2013 Fernández Do Porto et al.

Descripción: The partition function of two hard spheres in a hard-wall pore is studied, appealing to a graph representation. The exact evaluation of the canonical partition function and the one-body distribution function in three different shaped pores are achieved. The analyzed simple geometries are the cuboidal, cylindrical, and ellipsoidal cavities. Results have been compared with two previously studied geometries; the spherical pore and the spherical pore with a hard core. The search of common features in the analytic structure of the partition functions in terms of their length parameters and their volumes, surface area, edges length, and curvatures is addressed too. A general framework for the exact thermodynamic analysis of systems with few and many particles in terms of a set of thermodynamic measures is discussed. We found that an exact thermodynamic description is feasible based on the adoption of an adequate set of measures and the search of the free energy dependence on the adopted measure set. A relation similar to the Laplace equation for the fluid-vapor interface is obtained, which expresses the equilibrium between magnitudes that in extended systems are intensive variables. This exact description is applied to study the thermodynamic behavior of the two hard spheres in a hard-wall pore for the analyzed different geometries. We obtain analytically the external reversible work, the pressure on the wall, the pressure in the homogeneous region, the wall-fluid surface tension, the line tension, and other similar properties. © 2010 American Institute of Physics.

Descripción: Aims. We study the stability and modes of non - isothermal coronal loop models with different intensity values of equilibrium twisted magnetic field.Methods. We use an energy principle obtained by means of non - equilibrium thermodynamic arguments. The principle is expressed in terms of Hermitian operators and enables us to consider the coupled system of equations, the balance of energy equation and the equation of motion, to obtain modes and eigenmodes in a spectrum ranging from short to long-wavelength disturbances without using weak varying approximations of the equilibrium parameters. Long-wavelength perturbations introduce additional difficulties because the inhomogeneous nature of the medium produce disturbances corresponding to continuous intervals of eigenfrequencies, which cannot be considered as purely sinusoidal.Results. We analyze the modification of periods, modes structure, and stability when the helicity, the magnetic field strength, and the radius of the fluxtube are varied. The efficiency of the damping due to the resonant absorption mechanism is analyzed in terms of modes that can either impulsively release or store magnetic energy.Conclusions. We find that the onset of the instability is associated with a critical value of the helicity and the magnetic energy content has a determinant role on the instability of the system with respect to the stabilizing effect of the resonant absorption mechanism. © 2008 ESO.

Descripción: Splitting and apparent splicing of ribosomal RNA, both previously unknown in vertebrates, were found in rodents of the genus Ctenomys. Instead of being formed by a single molecule of 4.4 kb, 28S rRNA is split in two molecules of 2.6 and 1.8 kb. A hidden break, mapping within a 106 bp 'intron' located in the D6 divergent region, is expressed in mature ribosomes of liver, lung, heart and spleen, as well as in primary fibroblast cultures. Testis-specific processing eliminates the intron and concomitantly the break site, producing non-split 28S rRNA molecules exclusively in this organ. The intron is flanked by two 9 bp direct repeats, revealing the acquisition by insertion of a novel rRNA processing strategy in the evolution of higher organisms.

Descripción: The noncovalent complex formed by the association of two fragments of chymotrypsin inhibitor-2 is reversibly denatured by pressure in the absence of chemical denaturants. On pressure release, the complex returned to its original conformation through a biphasic reaction, with first-order rate constants of 0.012 and 0.002 s-1, respectively. The slowest phase arises from an interconversion of the pressure-denatured state, as revealed by double pressure-jump experiments. Below 5 μM, the process was concentration dependent with a second-order rate constant of 1,700 s-1 M-1. Fragment association at atmospheric pressure showed a similar break in the order of the reaction above 5 μM, but both first- and second-order folding/association rates are 2.5 times faster than those for the refolding of the pressure-denatured state. Although the folding rates of the intact protein and the association of the fragments displayed nonlinear Eyring behavior for the temperature dependence, refolding of the pressure-denatured complex showed a linear response. The negligible heat capacity of activation reflects a balance of minimal change in the burial of residues from the pressure-denatured state to the transition state. If we add the higher energy barrier in the refolding of the pressure-denatured state, the rate differences must lie in the structure of this state, which has to undergo a structural rearrangement. This clearly differs from the conformational flexibility of the isolated fragments or the largely unfolded denatured state of the intact protein in acid and provides insight into denatured states of proteins under folding conditions.

Descripción: The energetic contributions of individual DNA-contacting side chains to specific DNA recognition in the human papillomavirus 16 E2C-DNA complex is small (less than 1.0 kcal mol-1), independent of the physical and chemical nature of the interaction, and is strictly additive. The sum of the individual contributions differs 1.0 kcal mol-1 from the binding energy of the wild-type protein. This difference corresponds to the contribution from the deformability of the DNA, known as "indirect readout." Thus, we can dissect the energetic contribution to DNA binding into 90% direct and 10% indirect readout components. The lack of high energy interactions indicates the absence of "hot spots," such as those found in protein-protein interfaces. These results are compatible with a highly dynamic and "wet" protein-DNA interface, yet highly specific and tight, where individual interactions are constantly being formed and broken. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Descripción: This paper reviews recent progress made in our understanding of the functioning and variability of the South American Monsoon System (SAMS) on time scales varying from synoptic to long-term variability and climate change. The SAMS contains one of the most prominent summertime climate patterns in South America, featuring a strong seasonal variability in a region lying between the Amazon and the La Plata Basin. Much of the recent progress is derived from complementary international programs, such as the Monsoon Experiment South America (MESA), as well as from ongoing international programs such as the Large Scale Biosphere Atmosphere Experiment in the Amazon Basin (LBA) and the La Plata Basin (LPB) Regional Hydroclimate Project, which includes the CLARIS LPB Europe-South America Network for Climate Change Assessment and Impact Studies in La Plata Basin Project. The latter assesses atmosphere-land surface interactions, the role of land use changes and aerosols from biomass burning considered as sources of variability and change in the SAMS functioning, characteristics and behaviour. The SAMS region is particularly susceptible to variations of climate due to the importance of hydroelectricity generation and the agricultural base of local economies. Also addressed in this report are projections of climate change and extremes, which are important for impact and vulnerability assessments. This discussion includes the need to identify and understand important processes that control the monsoonal climate, how these processes may vary and change, and how they may interact with key societal sectors, including water resource management, hydroelectric generation, agriculture, and agribusiness. This paper reports on the major contributions of MESA to the knowledge of characteristics, functioning and variability of the SAMS, and is based on recent studies and publications, and can be considered as an update of a previous review by C. S. Vera et al. (2006a). © 2010 Royal Meteorological Society.

Descripción: Vertical excitation and electron detachment energies associated with the optical absorption of iodide ions dissolved in supercritical ammonia at 420 K have been calculated in two limiting scenarios: as a solvated free I- ion and forming a K+ I- contact ion pair (CIP). The evolution of the transition energies as a result of the gradual building up of the solvation structure was studied for each absorbing species as the solvent's density increased, i.e., changing the N H3 supercritical thermodynamic state. In both cases, if the solvent density is sufficiently high, photon absorption produces a spatially extended electron charge beyond the volume occupied by the solvated solute core; this excited state resembles a typical charge-transfer-to-solvent (CTTS) state. A combination of classical molecular dynamics simulations followed by quantum mechanical calculations for the ground, first-excited, and electron-detached electronic states have been carried out for the system consisting of one donor species (free I- ion or K+ I- CIP) surrounded by ammonia molecules. Vertical excitation and electron detachment energies were obtained by averaging 100 randomly chosen microconfigurations along the molecular dynamics trajectory computed for each thermodynamic condition (fluid density). Short- and long-range contributions of the solvent-donor interaction upon the CTTS states of I- and K+ I- were identified by performing additional electronic structure calculations where only the solvent interaction due to the first neighbor molecules was taken into account. These computations, together with previous experimental evidence that we collected for the system, have been used to analyze the solvent effects on the CTTS transition. In this paper we have established the following: (i) the CTTS electron of free I- ion or K+ I- CIP presents similar features, and it gradually localizes in close proximity of the iodine parent atom when the ammonia density is increased; (ii) for the free I- ion, the short-range solvent interaction contributes to the stabilization of the ground state more than it does for the CTTS excited state, which is evidenced experimentally as a blueshift in the maximum absorption of the CTTS transition when the density is increased; (iii) this effect is less noticeable for the K+ I- ion pair, because in this case a tight solvation structure, formed by four N H3 molecules wedged between the ions, appears at very low density and is very little affected by changes in the density; (iv) the long-range contribution to the solvent stabilization can be neglected for the K+ I- CIP, since the main features of its electronic transition can be explained on the basis of the vicinity of the cation; (v) however, the long-range solvent field contribution is essential for the free I- ion to become an efficient CTTS donor upon photoexcitation, and this establishes a difference in the CTTS behavior of I- in bulk and in clusters. © 2007 American Institute of Physics.