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Search Results: 1 - 10 of 328323 matches for " Jose L. F. Abascal "
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Homogeneous bubble nucleation in water at negative pressure: A Voronoi polyhedra analysis
Jose L. F. Abascal,Miguel A. Gonzalez,Juan L. Aragones,C. Valeriani
Physics , 2013, DOI: 10.1063/1.4790797
Abstract: We investigate vapor bubble nucleation in metastable TIP4P/2005 water at negative pressure via the Mean First Passage Time (MFPT) method using the volume of the largest bubble as a local order parameter. We identify the bubbles in the system by means of a Voronoi-based analysis of the Molecular Dynamics trajectories. By comparing the features of the tessellation of liquid water at ambient conditions to those of the same system with an empty cavity we are able to discriminate vapor (or interfacial) molecules from the bulk ones. This information is used to follow the time evolution of the largest bubble until the system cavitates at 280 K above and below the spinodal line. At the pressure above the spinodal line, the MFPT curve shows the expected shape for a moderately metastable liquid from which we estimate the bubble nucleation rate and the size of the critical cluster. The nucleation rate estimated using Classical Nucleation Theory turns out to be about 8 order of magnitude lower than the one we compute by means of MFPT. The behavior at the pressure below the spinodal line, where the liquid is thermodynamically unstable, is remarkably different, the MFPT curve being a monotonous function without any inflection point.
The range of meta stability of ice-water melting for two simple models of water
Carl McBride,Carlos Vega,Eduardo Sanz,Luis G. MacDowell,Jose L. F. Abascal
Physics , 2009, DOI: 10.1080/00268970412331293820
Abstract: A number of crystal structures of water have been `superheated' in Monte Carlo simulations. Two well known models for water were considered; namely the TIP4P model and the SPC/E model. By comparing the fluid-solid coexistence temperature to the temperature at which the solid becomes mechanically unstable and melts it is possible to determine the typical range of temperatures over which is possible to superheat the ice phases in conventional simulation studies. It is found that the ice phases can be superheated to approximately 90K beyond the fluid-solid coexistence temperature. Beyond this limit they spontaneously melt. This limit appears to depend weakly both on the type of ice phase considered and on the chosen model. Obviously only rigorous free energy calculations can determine the equilibrium fluid-solid coexistence of a model. However, a "rule of thumb" is that, by subtracting 90K from the mechanically stability limit of the the ice phase one is provided with a first guess as to the equilibrium fluid-solid coexistence temperature.
Anomalies in water as obtained from computer simulations of the TIP4P/2005 model: density maxima, and density, isothermal compressibility and heat capacity minima
Helena L. Pi,Juan L. Aragones,Carlos Vega,Eva G. Noya,Jose L. F. Abascal,Miguel A. Gonzalez,Carl McBride
Physics , 2009, DOI: 10.1080/00268970902784926
Abstract: The so-called thermodynamic anomalies of water form an integral part of the peculiar behaviour of this both important and ubiquitous molecule. In this paper our aim is to establish whether the recently proposed TIP4P/2005 model is capable of reproducing a number of these anomalies. Using molecular dynamics simulations we investigate both the maximum in density and the minimum in the isothermal compressibility along a number of isobars. It is shown that the model correctly describes the decrease in the temperature of the density maximum with increasing pressure. At atmospheric pressure the model exhibits an additional minimum in density at a temperature of about 200K, in good agreement with recent experimental work on super-cooled confined water. The model also presents a minimum in the isothermal compressibility close to 310K. We have also investigated the atmospheric pressure isobar for three other water models; the SPC/E and TIP4P models also present a minimum in the isothermal compressibility, although at a considerably lower temperature than the experimental one. For the temperature range considered no such minimum is found for the TIP5P model.
Anomalies in bulk supercooled water at negative pressure
Ga?l Pallares,Mouna El Mekki Azouzi,Miguel Angel Gonzalez,Juan Luis Aragones,Jose Luis F. Abascal,Chantal Valeriani,Frédéric Caupin
Physics , 2013, DOI: 10.1073/pnas.1323366111
Abstract: Water is the most familiar liquid, and arguably the most complex. Anomalies of supercooled water have been measured during decades, and competing interpretations proposed. Yet, a decisive experiment remains elusive, because of unavoidable crystallization into ice. We investigate the state of water that is both supercooled and under mechanical tension, or negative pressure. Liquids under negative pressure can be found in plants or fluid inclusions in minerals. Using such water inclusions in quartz, we report the first measurements on doubly metastable water down to $-15^\circ\mathrm{C}$ and around $-100\,\mathrm{MPa}$. We observe sound velocity anomalies that can be reproduced quantitatively with molecular dynamics simulations. These results rule out one proposed scenario for water anomalies, and put further constraints on the remaining ones.
Water quality in a reservoir used for carp production
V. Martínez,F. Abascal,M. V. Esteller,L. Bibiano
Geofísica internacional , 2002,
Abstract: Guadalupe Reservoir, on the San Cayetano river, feeds into the Lerma river about 18 km north of Toluca in the State of Mexico, Mexico. On August 9, 1995, more than 6000 Israeli carp (Cyprinus carpio v. specularis and rubrofruscus) died within a week in this reservoir. We investigated the cause of the fish mortality and we determined whether the reservoir could be used again for carp culture. Five days after the accident the residual chlorine was 4 times higher than the maximum permissible amount. Ammonia nitrogen, biochemical oxygen demand (BOD) and chemical oxygen demand (COD) were also above the recommended levels. Six months later, the amount of some contaminants in the water, such as chlorine, were back to normal ranges of water quality criteria for aquaculture. Ammonia, BOD and COD concentrations were lower to those found in the previous analyses but remained higher than the recommended levels. Most probably, residual chlorine was the cause of carp mortality as the chlorine level was very high when the fishes died.
What ice can teach us about water interactions: a critical comparison of the performance of different water models
C. Vega,J. L. F. Abascal,M. M. Conde,J. L. Aragones
Physics , 2009, DOI: 10.1039/b805531a
Abstract: The performance of several popular water models (TIP3P, TIP4P, TIP5P and TIP4P/2005) is analysed. For that purpose the predictions for ten different properties of water are investigated, namely: 1. vapour-liquid equilibria (VLE) and critical temperature; 2. surface tension; 3. densities of the different solid structures of water (ices); 4. phase diagram; 5. melting point properties; 6. maximum in density at room pressure and thermal coefficients $\alpha$ and $\kappa_T$; 7. structure of liquid water and ice; 8. equation of state at high pressures; 9. diffusion coefficient; 10. dielectric constant. For each property, the performance of each model is analysed in detail with a critical discussion of the possible reason of the success or failure of the model. A final judgement on the quality of these models is provided. TIP4P/2005 provides the best description of almost all properties of the list, with the only exception of the dielectric constant. In the second position, TIP5P and TIP4P yield an overall similar performance, and the last place with the poorest description of the water properties is provided by TIP3P. The ideas leading to the proposal and design of the TIP4P/2005 are also discussed in detail. TIP4P/2005 is probably close to the best description of water that can be achieved with a non polarizable model described by a single Lennard-Jones (LJ) site and three charges.
Determination of phase diagrams via computer simulation: Methodology and applications to water, electrolytes and proteins
C. Vega,E. Sanz,J. L. F. Abascal,E. G. Noya
Physics , 2009, DOI: 10.1088/0953-8984/20/15/153101
Abstract: In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and Einstein molecule methods are described in detail. It is shown that for the hard spheres solid both methods yield the same results and that free energies of solid phases present noticeable finite size effects. Finite size corrections can be introduced, although in an approximate way, to correct for the dependence of the free energy on the size of the system. The computation of free energies of solid phases can be extended to molecular fluids. The procedure to compute free energies of solid phases of water (ices Ih, II, III, IV, V, VI, VII, VIII, IX, XI and XII) using the SPC/E and TIP4P models will be described.Other methods to estimate the melting point of a solid, as the direct fluid-solid coexistence or simulations of the free surface of the solid will be discussed. It will be shown that the melting points of ice Ih for several water models, obtained from these two methods and from free energy calculations agree within statistical uncertainty. Phase diagram calculations can help to improve potential models of molecular fluids; for water, the TIP4P/2005 model can be regarded as an improved version of TIP4P. We will also review some recent work on the phase diagram of the simplest ionic model, the restricted primitive model. Although originally devised to describe ionic liquids, the model is becoming quite popular to describe charged colloids. Besides the possibility of obtaining fluid-solid equilibria for simple protein models will be discussed. In these primitive models, the protein is described by a spherical potential with certain anisotropic bonding sites.
The New Brazilian Power Quality Standard and a Low Cost Device Meter  [PDF]
Guilherme P. Colnago, Jose L. F. Vieira, Gilberto C. D. Sousa, Jose R. Macedo Jr.
Energy and Power Engineering (EPE) , 2012, DOI: 10.4236/epe.2012.43020
Abstract: This paper presents an overview about the new Brazilian Power Quality Standard and provides a low cost device PQ meter, developed and implemented to assist the national campaign to assess the Brazilian power quality indices, unknown until now. This work contributes with the search of a low cost devices PQ meter for a cost sensitive market, and introduces the new Brazilian Power Quality Standard to the international community.
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level
Federico Abascal,Iakes Ezkurdia?,Juan Rodriguez-Rivas?,Jose Manuel Rodriguez?,Angela del Pozo?,Jesús Vázquez?,Alfonso Valencia?,Michael L. Tress
PLOS Computational Biology , 2015, DOI: 10.1371/journal.pcbi.1004325
Abstract: Alternative splicing of messenger RNA can generate a wide variety of mature RNA transcripts, and these transcripts may produce protein isoforms with diverse cellular functions. While there is much supporting evidence for the expression of alternative transcripts, the same is not true for the alternatively spliced protein products. Large-scale mass spectroscopy experiments have identified evidence of alternative splicing at the protein level, but with conflicting results. Here we carried out a rigorous analysis of the peptide evidence from eight large-scale proteomics experiments to assess the scale of alternative splicing that is detectable by high-resolution mass spectroscopy. We find fewer splice events than would be expected: we identified peptides for almost 64% of human protein coding genes, but detected just 282 splice events. This data suggests that most genes have a single dominant isoform at the protein level. Many of the alternative isoforms that we could identify were only subtly different from the main splice isoform. Very few of the splice events identified at the protein level disrupted functional domains, in stark contrast to the two thirds of splice events annotated in the human genome that would lead to the loss or damage of functional domains. The most striking result was that more than 20% of the splice isoforms we identified were generated by substituting one homologous exon for another. This is significantly more than would be expected from the frequency of these events in the genome. These homologous exon substitution events were remarkably conserved—all the homologous exons we identified evolved over 460 million years ago—and eight of the fourteen tissue-specific splice isoforms we identified were generated from homologous exons. The combination of proteomics evidence, ancient origin and tissue-specific splicing indicates that isoforms generated from homologous exons may have important cellular roles.
Deformación andina en la cuenca de Choromoro, NO de Tucumán: estilo estructural combinado Andean deformation in the Choromoro Basin, NW Tucuman: mixed structural styles
L. del V. Abascal
Revista de la Asociación Geológica Argentina , 2005,
Abstract: La estructura de la depresión tectónica de Choromoro, situada en la parte norte de la provincia de Tucumán, es el resultado de la compresión cenozoica que imprimió un estilo combinado de deformación, representado por una tectónica que involucra al basamento y otra que afecta sólo a la cobertura sedimentaria. Ambas son sincrónicas y se encuentran superpuestas. El estilo de cobertura o de piel delgada se desarrolla en el interior de la cuenca, asociado a una superficie de despegue situada a una profundidad entre los 2,5 y 3 km, probablemente en pelitas del Subgrupo Balbuena (Formación Lumbrera). La deformación que involucra al basamento ha generado láminas delimitadas por cabalgamientos, despegadas de un substrato profundo a lo largo de una superficie ubicada aproximadamente a 20 km de profundidad. The Choromoro Basin is a tectonic depression in north-western Tucuman Province. Its present structural geometry is the result of Cenozoic compression that yielded a combined deformation style on the Neogene deposits. This structural style is represented by thick- and thin-skinned tectonics, superimposed in time and space. The thin-skinned style developed in the interior of the basin, associated with a detachment surface at a depth of 2.5 to 3 km, probably in shales of the Balbuena Subgroup (Lumbrera Formation). The thickskinned deformation relates to a deep detachment at a depth of about 20 km, incorporating metamorphic basement blocks, bounded by high-angle reverse faults and tilted with the cover strata.
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