Axial and pseudoscalar current correlators and their couplings to eta and etaprime mesons

Correlators of singlet and octet axial currents, as well as anomaly and pseudoscalar densities have been studied using QCD sum rules. Several of these sum rules are used to determine the couplings f^8_eta, f^0_eta, f^8_etaprime and f^0_etaprime. We find mutually consistent values which are also in agreement with phenomenological values obtained from data on various decay and production rates. While most of the sum rules studied by us are independent of the contributions of direct instantons and screening correction, the singlet-singlet current correlator and the anomaly-anomaly correlator improve by their inclusion.Comment: 31 pages, 11 figure

Combining stochastic and deterministic approaches within high efficiency molecular simulations

Generalized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). While conventional hybrid Monte Carlo methods completely re-sample particle's velocities between MD trajectories, our method suggests a partial velocity update procedure which keeps a part of the dynamic information throughout the simulation. We use shadow (modified) Hamiltonians, the asymptotic expansions in powers of the discretization parameter corresponding to timestep, which are conserved by symplectic integrators to higher accuracy than true Hamiltonians. We present the implementation of this method into the highly efficient MD code GROMACS and demonstrate its performance and accuracy on computationally expensive systems like proteins in comparison with the molecular dynamics techniques already available in GROMACS. We take advantage of the state-of-the-art algorithms adopted in the code, leading to an optimal implementation of the method. Our implementation introduces virtually no overhead and can accurately recreate complex biological processes, including rare event dynamics, saving much computational time compared with the conventional simulation methods

Chemical-garden formation, morphology, and composition. I. Effect of the nature of the cations

We have grown chemical gardens in different sodium silicate solutions from several metal-ion salts-calcium chloride, manganese chloride, cobalt chloride, and nickel sulfate-with cations from period 4 of the periodic table. We have studied their formation process using photography, examined the morphologies produced using scanning electron microscopy (SEM), and analyzed chemical compositions using X-ray powder diffraction (XRD) and energy dispersive X-ray analysis (EDX) to understand better the physical and chemical processes involved in the chemical-garden reaction. We have identified different growth regimes in these salts that are dependent on the concentration of silicate solution and the nature of the cations involved

Assessment of van der Waals inclusive density functional theory methods for layered electroactive materials

Computational-driven materials discovery requires efficient and accurate methods. Density functional theory (DFT) meets these two requirements for many classes of materials. However, DFT-based methods have limitations. One significant shortcoming is the inadequate treatment of weak van der Waals (vdW) interactions, which are crucial for layered materials. Here we assess the performance of various vdW-inclusive DFT approaches for predicting the structure and voltage of layered electroactive materials for Li-ion batteries, considering a set of 20 different compounds. We find that the so-called optB86b-vdW density functional improves the agreement with experimental data, closely followed by the latest generation of dispersion correction methods. These approaches yield average relative errors for the structural parameters smaller than 3 %. The average deviations for redox potentials are below 0.15 V. Looking ahead, this study identifies accurate methods for Li-ion vdW bound systems, providing enhanced predictive power to DFT-assisted design for developing new types of electroactive materials in general.MINECO MTM2013-46553-C3-1-P MINECO ENE2016-81020-

Constant pressure hybrid Monte Carlo simulations in GROMACS

Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines Andersen barostat with GSHMC to enable molecular simulations in the environment natural for biological applications, namely, at constant pressure and constant temperature. Generalized Hybrid Monte Carlo methods are designed to maintain constant temperature and volume and extending their functionality to preserving pressure is not trivial. The theoretical formulation of NPT-GSHMC was previously introduced. Our main contribution is the implementation of this methodology in the GROMACS molecular simulation package and the evaluation of properties of NPT-GSHMC, such as accuracy, performance, effectiveness for real physical systems in comparison with well-established molecular simulation techniques. Benchmarking tests are presented and the obtained preliminary results are promising. For the first time, the generalized hybrid Monte Carlo simulations at constant pressure are available within the popular open source molecular dynamics software package

Chemical-garden formation, morphology, and composition. II. Chemical gardens in microgravity

We studied the growth of metal-ion silicate chemical gardens under Earth gravity (1 g) and microgravity (μg) conditions. Identical sets of reaction chambers from an automated system (the Silicate Garden Habitat or SGHab) were used in both cases. The μg experiment was performed on board the International Space Station (ISS) within a temperature-controlled setup that provided still and video images of the experiment downlinked to the ground. Calcium chloride, manganese chloride, cobalt chloride, and nickel sulfate were used as seed salts in sodium silicate solutions of several concentrations. The formation and growth of osmotic envelopes and microtubes was much slower under μg conditions. In 1 g, buoyancy forces caused tubes to grow upward, whereas a random orientation for tube growth was found under μg conditions

Molecular dynamics simulations of iron- and aluminum-loaded serum transferrin: Protonation of tyr188 is necessary to prompt metal release

Serum transferrin (sTf) carries iron in blood serum and delivers it into cells by receptor-mediated endocytosis. The protein can also bind other metals, including aluminum. The crystal structures of the metal-free and metal-loaded protein indicate that the metal release process involves an opening of the protein. In this process, Lys206 and Lys296 lying in the proximity of each other form the dilysine pair or, so-called, dilysine trigger. It was suggested that the conformational change takes place due to variations of the protonation state of the dilysine trigger at the acidic endosomal pH. In 2003, Rinaldo and Field (Biophys. J. 85, 3485-3501) proposed that the dilysine trigger alone can not explain the opening and that the protonation of Tyr188 is required to prompt the conformational change. However, no evidence was supplied to support this hypothesis. Here, we present several 60 ns molecular dynamics simulations considering various protonation states to investigate the complexes formed by sTf with Fe(III) and Al(III). The calculations demonstrate that only in those systems where Tyr188 has been protonated does the protein undergo the conformational change and that the dilysine trigger alone does not lead to the opening. The simulations also indicate that the metal release process is a stepwise mechanism, where the hinge-bending motion is followed by the hinge-twisting step. Therefore, the study demonstrates for the first time that the protonation of Tyr188 is required for the release of metal from the metal loaded sTf and provides valuable information about the whole process

Revealing the Mechanism of Sodium Diffusion in NaxFePO4 Using an Improved Force Field

Olivine NaFePO4 is a promising cathode material for Na-ion batteries. Intermediate phases such as Na0.66FePO4 govern phase stability during intercalation-deintercalation processes, yet little is known about Na+ diffusion in NaxFePO4 (0 < x < 1). Here we use an advanced simulation technique, Randomized Shell Mass Generalized Shadow Hybrid Monte Carlo Method (RSM-GSHMC) in combination with a specifically developed force field for describing NaxFePO4 over the whole range of sodium compositions, to thoroughly examine Na+ diffusion in this material. We reveal a novel mechanism through which Na+/Fe2+ antisite defect formation halts transport of Na+ in the main diffusion direction [010], while simultaneously activating diffusion in the [001] channels. A similar mechanism was reported for Li+ in LiFePO4, suggesting that a transition from one- to two-dimensional diffusion prompted by antisite defect formation is common to olivine structures, in general.MTM2013-46553-C3-1-P ENE2016-81020-R SGI/IZO-SGIker UPV/EHU i2BASQUE academic network Barcelona Supercomputer Cente

Comparación de la estructura y rendimientos ganaderos en sistemas de producción tradicional y ecológico de bovino en Extremadura. Comparison of the structure and livestock yields in traditional production systems and ecological bovine Extremadura

The paper analyzes the structure and performance of beef cattle farms in Extremadura: Conventional (n = 50), Organic with no sales of organic products (n = 37) and Organic farms with sales of organic products (n = 11). Regarding stocking rate levels, no significant differences were observed among groups. By contrast, significant differences among the three types of farms regarding racial structure (p <0.05). Similarly, significant differences were found (p <0.1) in relation to farm's area, cattle's reproductive management and performance. The study highlights the similarity between conventional and organic cattle production in Extremadura. This fact could allow a smooth transition of conventional farms to the organic production model