Descripción: We propose a new class of density functionals for liquid 3He based on the Aziz helium-helium interaction screened at short distances by the microscopically calculated two-body distribution function g(r). Our aim is to reduce to a minumum the unavoidable phenomenological ingredients inherent to any density functional approach. Results for the homogeneous liquid and droplets are presented and discussed. © 2006 American Institute of Physics.

Descripción: A recently reported symmetry breaking of density profiles of fluid argon confined by two parallel solid walls of carbon dioxide is studied. The calculations are performed in the framework of a nonlocal density functional theory. It is shown that the existence of such asymmetrical solutions is restricted to a special choice for the adsorption potential, where the attraction of the solid-fluid interaction is reduced by the introduction of a hard-wall repulsion. The behavior as a function of the slit's width is also discussed. All the results are placed in the context of the current knowledge on this matter. © 2008 American Institute of Physics.

Descripción: We have employed the Douglas-Kroll-Hess approximation to derive the perturbative Hamiltonians involved in the calculation of NMR spin-spin couplings in molecules containing heavy elements. We have applied this two-component quasirelativistic approach using finite perturbation theory in combination with a generalized Kohn-Sham code that includes the spin-orbit interaction self-consistently and works with Hartree-Fock and both pure and hybrid density functionals. We present numerical results for one-bond spin-spin couplings in the series of tetrahydrides C H4, Si H4, Ge H4, and Sn H4. Our two-component Hartree-Fock results are in good agreement with four-component Dirac-Hartree-Fock calculations, although a density-functional treatment better reproduces the available experimental data. © 2005 American Institute of Physics.

Descripción: In this paper we propose a functional of the many-body cumulant of the second-order reduced density matrix within the spin-free formalism of quantum chemistry which quantifies the idea of electron correlation and allows one to detect spin entanglement. Its properties are rigorously stated and discussed for spin-adapted pure states. Numerical determinations are performed for both equilibrium conformations and dissociation processes in molecular systems. © 2010 American Institute of Physics.

Descripción: Sviluppo e Studi Superior! in Sardegna (CRS4). The geometries, interaction energies, and harmonic vibrational frequencies of water clusters (with up to 8 molecules) have been studied using density functional theory (DFT) at the gradient corrected level. The water monomer and water dimer calculations have been used as benchmarks to investigate different choices for basis sets and density functionals. Our results for larger clusters agree with both available high-level ab initio calculations and experimental information. The calculations of the vibrational frequencies and IR absorption intensities for the larger clusters, for which no other reliable quantum-chemical calculation is available, are presented to facilitate the frequency assignment of experimental spectra.

Descripción: The confinement of Ar in planar slits of two identical parallel semi-infinite walls of alkali metals, alkaline-earth metal Mg, and CO 2 is investigated within the framework of the density functional theory. It is assumed that (1) the fluid atoms interact via a recently proposed effective attractive pair potential with strength, εff, which reproduces the experimental data of the surface tension of the liquid-vapor interface at the bulk coexistence curve, and (2) the adsorption on the walls is described by ab initio potentials characterized by a well depth, Wsf. In this way the systems were studied in the framework of a realistic approach. We found that for small coverages, the slit is always filled by forming two symmetric vapor films, one at each wall. For increasing coverage the behavior depends on the ratio Wsf/εff and the temperature T. In the case of alkali metals, we found at the triple point, Tt, of the adsorbate a regime of average density ρ*av in which the ground state exhibits asymmetric density profiles, leading to the so-called spontaneous symmetry breaking (SSB) effect. The SSB appears at an average density ρ*sb1 and disappears at a higher average density ρ*sb2 . When T is increased, the range of densities ρ*sb1≤ρ*av≤ ρ* sb2 diminishes and eventually the SSB disappears at a critical temperature, Tsb, which coincides with the critical prewetting temperature Tcpw observed in the adsorption on a single wall. For T>Tcpw the slit is filled symmetrically up to the phase transition to capillary condensation. All these features are examined as a function of the strength of the substrate and the width of the slit. Furthermore, no SSB effect was found for Mg and CO2. © 2010 American Institute of Physics.

Descripción: Background: Functional genetic markers have important implications for genetic analysis by providing direct estimation of functional diversity. Although high throughput sequencing techniques for functional diversity analysis are being developed nowadays, the use of already well established variable markers present in candidate genes is still an interesting alternative for mapping purposes and functional diversity studies. SSR markers are routinely used in most plant and animal breeding programs for many species including Eucalyptus. SSR markers derived from candidate genes (SSR-CG) can be used effectively in co-segregation studies and marker-assisted diversity management. Results: In the present study, eight new non reported SSRs were identified in seven candidate genes for wood properties in Eucalyptus globulus: cinnamoyl CoA reductase (CCR), homocysteine S-methyltransferase (HMT), shikimate kinase (SK), xyloglucan endotransglycosylase 2 (XTH2), cellulose synthase 3 (CesA3), glutathione S-transferase (GST) and the transcription factor LIM1. Microsatellites were located in promoters, introns and exons, being most of them CT dinucleotide repeats. Genetic diversity of these eight CG-derived SSR-markers was explored in 54 unrelated genotypes. Except for XTH2, high levels of polymorphism were detected: 93 alleles (mean of 13.1 sd 1.6 alleles per locus), a mean effective number of alleles (Ne) of 5.4 (sd 1.6), polymorphic information content values (PIC) from 0.617 to 0.855 and probability of Identity (PI) ranging from 0.030 to 0.151. Conclusions: This is the first report on the identification, characterization and diversity analysis of microsatellite markers located inside wood quality candidate genes (CG) from Eucalyptus globulus. This set of markers is then appropriate for characterizing genetic variation, with potential usefulness for quantitative trait loci (QTL) mapping in different eucalypts genetic pedigrees and other applications such as fingerprinting and marker assisted diversity management. © 2012 by Pontificia Universidad Católica de Valparaíso, Chile.

Descripción: Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis, J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2 -water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. © 2009 American Institute of Physics.

Descripción: In the frame of finite range density functional (FRDF) theory, we review the systematics of energetic features of 4HeN clusters doped with atomic or molecular impurities, as well as the instability scenario of their collective motions. It is shown that for drops up to N = 500, the predictions of FRDF theory are coincident with those arising from microscopic many-body calculations that employ variational or diffusion Monte Carlo methods. For larger drops, the present description predicts a smooth approach to zero of the collective energies, a scenario that appears to support the most recent experimental data and microscopic calculations that demonstrate that the impurity is located within the bulk of the drop. © 1997 American Institute of Physics.

Descripción: The set of 1:1 and 2:1 complexes of XOOX′ (X, X′ H, CH 3) with lithium cation has been studied to determine if they are suitable candidates for chiral discrimination in an isotropic medium via nuclear magnetic resonance spectroscopy. Conventional nuclear magnetic resonance is unable to distinguish between enantiomers in the absence of a chiral solvent. The criterion for experimental detection is valuated by the isotropic part of nuclear shielding polarisability tensors, related to a pseudoscalar of opposite sign for two enantiomers. The study includes calculations at coupled Hartree-Fock and density functional theory schemes for 17O nucleus in each compound. Additional calculations for 1H are also included for some compounds. A huge static homogeneous electric field, perpendicular to the magnetic field of the spectromer, as big as ≈1.7 108 V m -1 should be applied to observe a shift of ≈1 ppm for 17O magnetic shielding in the proposed set of complexes. © 2011 American Institute of Physics.

Descripción: Adsorption on single planar walls and filling of slits with identical planar walls are investigated in the frame of the density functional theory. In this sort of slits the external potential is symmetric with respect to its central plane. Calculations were carried out by applying both the canonical and grand canonical ensembles (CE and GCE, respectively). The behavior is analyzed by varying the strength of the adsorbate-substrate attraction, the temperature T, and the coverage Results obtained for physisorption of Xe on alkaline surfaces are reported in the present work. Prewetting (PW) lines and wetting temperatures, T w, are determined from the analysis of adsorption on single walls. The filling of slits is analyzed for temperatures T T w. It is found that whenever for a given Xe-substrate combination the adsorption on a single wall exhibits a first-order wetting transition then asymmetric profiles that break the left-right symmetry of the external potential appear in the filling of an equivalent slit. These spontaneously symmetry breaking (SSB) solutions occur in a restricted range of with a T-dependent width. In the case of closed slits analyzed in the CE scheme, the obtained asymmetric profiles exhibit lower Helmholtz free energies than the symmetric species and, therefore, could be stabilized in this geometry. For open slits, the GCE scheme yields all the symmetric and SSB states in the corresponding convex regimes of the free energy. It is shown that both the CE and the GCE frames yield three coexistent states, two symmetric and one asymmetric twofold degenerate. Both a PW line and the related SSB effect terminate at the same temperature. For rather strongly attractive surfaces reentrant SSB states are found at a fixed value of T. © Copyright 2011 Author(s).

Descripción: A simple model, previously used to explore wetting transitions, is evaluated for the case of a slab geometry in which adsorption occurs between two semi-infinite solids, with parallel faces separated by a distance L. The model yields a universal description of possible wetting and capillary condensation (CC) transitions. The system’s thermodynamic behavior is predicted from the values of two dimensionless parameters: [Formula Presented] (the reduced gas-surface interaction strength, a function of temperature) and [Formula Presented] (the reduced separation). If [Formula Presented] negligible adsorption occurs at all pressures below saturated vapor pressure (SVP). For somewhat larger values of [Formula Presented] CC occurs for sufficiently small [Formula Presented] close to SVP. For very large values of [Formula Presented] an additional prewetting transition (formation of a film) is predicted for large [Formula Presented] this is accompanied by a CC transition close to SVP. The model is generally consistent with limited results of density-functional calculations for the He liquids at zero temperature. © 1999 The American Physical Society.

Descripción: We assessed the intracellular association states of the Parkinson's disease related protein α-synuclein (AS) in living cells by transfection with a functional recombinant mutant protein (AS-C4) bearing a tetracysteine tag binding the fluorogenic biarsenical ligands FlAsH and ReAsH, The aggregation states of AS-C4 were assessed by in situ microscopy of molecular translational mobility with FRAP (fluorescence recovery after photobleaching) and of local molecular density with confocal fluorescence anisotropy (CFA). FRAP recovery was quantitative and rapid in regions of free protein, whereas AS in larger aggregates was>80% immobile. A small 16% recovery characterized by an apparent diffusion constant of 0.03-0.04 μm 2/s was attributed to the dynamics of smaller, associated forms of AS-C4 and the exchange of mobile species with the larger immobile aggregates. By CFA, the larger aggregates exhibited high brightness and very low anisotropy, consistent with homoFRET between closely packed AS, for which a Förster distance (R o) of 5.3 nm was calculated. Other bright regions had high anisotropy values, close to that of monomeric AS, and indicative of membrane-associated protein with both low mobility and low degree of association. The anisotropy-fluorescence intensity correlations also revealed regions of free protein or of small aggregates, undetectable by conventional fluorescence imaging alone. The combined strategy (FRAP+CFA) provides a highly sensitive means for elucidating both the dynamics and structural features of protein aggregates and other intracellular complexes in living cells, and can be extended to other amyloid systems and to drug screening protocols. © 2011 Roberti et al.

Descripción: Energetics, structural features, polarity, and melting transitions in water clusters containing up to eight molecules were studied using ab initio methods and empirical force field models. Our quantum approach was based on density functional theory performed at the generalized gradient approximation level. For the specific case of (H2O)6, we selected five conformers of similar energy with different geometries and dipolar moments. For these cases, the cyclic arrangement was found to be the only nonpolar aggregate. For (H2O)8, the most stable structures corresponded to nonpolar, cubic-like, D2d and S4 conformers. Higher energy aggregates exhibit a large spectrum in their polarities. The static polarizability was found to be proportional to the size of the aggregates and presents a weak dependence with the number of hydrogen bonds. In order to examine the influence of thermal fluctuations on the aggregates, we have performed a series of classical molecular dynamics experiments from low temperature up to the melting transition using two different effective pseudopotentials: the TIP4P and MCY models. Minimum energy structures for both classical potentials were found to reproduce reasonably well the results obtained using ab initio methods. Isomerization and phase transitions were monitored by following changes in dipole moments, number of hydrogen bonds and Lindemann's parameter. For (H2O)6 and (H2O)8, the melting transitions were found at Tm≈50 and 160 K, respectively; for both aggregates, we observed premelting transitions between well differentiated conformers as well. © 1999 American Institute of Physics.

Descripción: Background: Human spermatozoa decondense in vitro upon exposure to heparin and glutathione. Glutathione is also the disulfide bond reducer in vivo, and heparan sulfate, a functional analogue of heparin, has been proposed as the protamine acceptor. The aim of this study was to evaluate the decondensing ability of chemically modified heparins and different glycosaminoglycans (GAGs) on isolated sperm nuclei in vitro, and to analyse the possible role of different GAGs as protamine acceptors. Methods: Capacitated spermatozoa and isolated sperm nuclei from normospermic semen samples were decondensed in the presence of heparin (or its equivalent) and glutathione. After fixation with glutaraldehyde, the percentage of decondensed spermatozoa and nuclei was determined under phase-contrast. Proteins were extracted from sperm nuclei previously incubated in the presence of gluhathione and different GAGs by incubation with urea-β-meracptoethanol-NaCl, and analysed by acid polyacrylamide gel electrophoresis. Results: The ability of desulfated heparins and other GAGs to decondense isolated nuclei mirrored exactly the decondensation of capacitated spermatozoa, the only difference being the level of maximum decondensation achieved. Heparan sulfate and heparin, but not other GAGs, were able to release protamines from sperm chromatin. Conclusions: Heparan sulfate could be functioning as protamine acceptor in vivo during human sperm nuclear decondensation. © The Author 2005. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved.

Descripción: A novel method for simulating the statistical mechanics of molecular systems in which both nuclear and electronic degrees of freedom are treated quantum mechanically is presented. The scheme combines a path integral description of the nuclear variables with a first-principles adiabatic description of the electronic structure. The electronic problem is solved for the ground state within a density functional approach, with the electronic orbitals expanded in a localized (Gaussian) basis set. The discretized path integral is computed by a METROPOLIS Monte Carlo sampling technique on the normal modes of the isomorphic ring polymer. An effective short-time action correct to order τ4 is used. The validity and performance of the method are tested by studying two small lithium clusters, namely Li4 and Li5+. Structural and electronic properties computed within this fully quantum-mechanical scheme are presented and compared to those obtained within the classical nuclei approximation. Quantum delocalization effects turn out to be significant as shown by the fact that quantum simulation results at 50 K approximately correspond to those of classical simulations carried out at 150 K. The scaling factor depends, however, on the specific physical property, thus evidencing the different character of quantum and thermal correlations. Tunneling turns out to be irrelevant in the temperature range investigated (50-200 K). © 1998 American Institute of Physics.