A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments

The computational study of chemical reactions in complex, wet environments is critical for applications in many fields. It is often essential to study chemical reactions in the presence of applied electrochemical potentials, taking into account the non-trivial electrostatic screening coming from the solvent and the electrolytes. As a consequence the electrostatic potential has to be found by solving the generalized Poisson and the Poisson-Boltzmann equation for neutral and ionic solutions, respectively. In the present work solvers for both problems have been developed. A preconditioned conjugate gradient method has been implemented to the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of a ordinary Poisson equation solver. In addition, a self-consistent procedure enables us to solve the non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy and parallel efficiency, and allow for the treatment of different boundary conditions, as for example surface systems. The solver has been integrated into the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be released as an independent program, suitable for integration in other codes

Non-collinear magnetic ordering in compressed FePd3_3 ordered alloy: a first principles study

By means of ab initio calculations based on the density functional theory we investigated magnetic phase diagram of ordered FePd$_3$ alloy as a function of external pressure. Considering several magnetic configurations we concluded that the system under pressure has a tendency to non-collinear spin alignment. Analysis of the Heisenberg exchange parameters $J_{ij}$ revealed strong dependence of iron-iron magnetic couplings on polarization of Pd atoms. To take into account the latter effect we built an extended Heisenberg model with higher order (biquadratic) terms. Minimizing the energy of this Hamiltonian, fully parameterized using the results of ab initio calculations, we found a candidate for a ground state of compressed FePd$_3$, which can be seen as two interpenetrating "triple-Q" phases.Comment: 8 pages, 8 figure

Myrtucommulone from Myrtus communis exhibits potent anti-inflammatory effectiveness in vivo.

Myrtucommulone a nonprenylated acylphloroglucinol contained in the leaves of myrtle (Myrtus communis), has been reported to suppress the biosynthesis of eicosanoids by inhibition of 5-lipoxygenase and cyclooxygenase-1 in vitro and to inhibit the release of elastase and the formation of reactive oxygen species in activated polymorphonuclear leukocytes. Here, in view of the ability of MC to suppress typical proinflammatory cellular responses in vitro, we have investigated the effects of MC in in vivo models of inflammation. MC was administered to mice intraperitoneally, and paw edema and pleurisy were induced by the subplantar and intrapleural injection of carrageenan, respectively. MC (0.5, 1.5, and 4.5 mg/kg i.p.) reduced the development of mouse carrageenan-induced paw edema in a dose-dependent manner. Moreover, MC (4.5 mg/kg i.p. 30 min before and after carrageenan) exerted anti-inflammatory effects in the pleurisy model. In particular, 4 h after carrageenan injection in the pleurisy model, MC reduced: 1) the exudate volume and leukocyte numbers; 2) lung injury (histological analysis) and neutrophil infiltration (myeloperoxidase activity); 3) the lung intercellular adhesion molecule-1 and P-selectin immunohistochemical localization; 4) the cytokine levels (tumor necrosis factor-α and interleukin-1 β in the pleural exudate and their immunohistochemical localization in the lung; 5) the leukotriene B 4, but not prostaglandin E2, levels in the pleural exudates; and 6) lung peroxidation (thiobarbituric acid-reactant substance) and nitrotyrosine and poly (ADP-ribose) immunostaining. In conclusion, our results demonstrate that MC exerts potent anti-inflammatory effects in vivo and offer a novel therapeutic approach for the management of acute inflammation. Copyright © 2009 by The American Society for Pharmacology and Experimental Therapeutics

Norm-conserving pseudopotentials with chemical accuracy compared to all-electron calculations

By adding a non-linear core correction to the well established Dual Space Gaussian type pseudopotentials for the chemical elements up to the third period, we construct improved pseudopotentials for the Perdew Burke Ernzerhof (PBE) functional and demonstrate that they exhibit excellent accuracy. Our benchmarks for the G2-1 test set show average atomization energy errors of only half a kcal/mol. The pseudopotentials also remain highly reliable for high pressure phases of crystalline solids. When supplemented by empirical dispersion corrections the average error in the interaction energy between molecules is also about half a kcal/mol. The accuracy that can be obtained by these pseudopotentials in combination with a systematic basis set is well superior to the accuracy that can be obtained by commonly used medium size Gaussian basis sets in all-electron calculations.Comment: 11 pages, 10 figure

Systematic analysis of SNR in bipartite Ghost Imaging with classical and quantum light

We present a complete and exhaustive theory of signal-to-noise-ratio in bipartite ghost imaging with classical (thermal) and quantum (twin beams) light. The theory is compared with experiment for both twin beams and thermal light in a certain regime of interest

Optimal Control of Superconducting N-level quantum systems

We consider a current-biased dc SQUID in the presence of an applied time-dependent bias current or magnetic flux. The phase dynamics of such a Josephson device is equivalent to that of a quantum particle trapped in a $1-$D anharmonic potential, subject to external time-dependent control fields, {\it i.e.} a driven multilevel quantum system. The problem of finding the required time-dependent control field that will steer the system from a given initial state to a desired final state at a specified final time is formulated in the framework of optimal control theory. Using the spectral filter technique, we show that the selected optimal field which induces a coherent population transfer between quantum states is represented by a carrier signal having a constant frequency but which is time-varied both in amplitude and phase. The sensitivity of the optimal solution to parameter perturbations is also addressed

Biphoton compression in standard optical fiber: exact numerical calculation

Generation of two-photon wavepackets, produced by spontaneous parametric down conversion in crystals with linearly chirped quasi-phase matching grating, is analyzed. Although being spectrally broad, two-photon wavepackets produced this way are not Fourier transform limited. In the paper we discuss the temporal compression of the wavepackets, exploiting the insertion of a standard optical fiber in the path of one of the two photons. The effect is analyzed by means of full numerical calculation and the exact dispersion dependencies in both the crystal and the fiber are considered. The study opens the way to the practical realization of this idea.Comment: 10 pages, 16 figure

How glassy are neural networks?

In this paper we continue our investigation on the high storage regime of a neural network with Gaussian patterns. Through an exact mapping between its partition function and one of a bipartite spin glass (whose parties consist of Ising and Gaussian spins respectively), we give a complete control of the whole annealed region. The strategy explored is based on an interpolation between the bipartite system and two independent spin glasses built respectively by dichotomic and Gaussian spins: Critical line, behavior of the principal thermodynamic observables and their fluctuations as well as overlap fluctuations are obtained and discussed. Then, we move further, extending such an equivalence beyond the critical line, to explore the broken ergodicity phase under the assumption of replica symmetry and we show that the quenched free energy of this (analogical) Hopfield model can be described as a linear combination of the two quenched spin-glass free energies even in the replica symmetric framework

Intrinsic noise-induced phase transitions: beyond the noise interpretation

We discuss intrinsic noise effects in stochastic multiplicative-noise partial differential equations, which are qualitatively independent of the noise interpretation (Ito vs. Stratonovich), in particular in the context of noise-induced ordering phase transitions. We study a model which, contrary to all cases known so far, exhibits such ordering transitions when the noise is interpreted not only according to Stratonovich, but also to Ito. The main feature of this model is the absence of a linear instability at the transition point. The dynamical properties of the resulting noise-induced growth processes are studied and compared in the two interpretations and with a reference Ginzburg-Landau type model. A detailed discussion of new numerical algorithms used in both interpretations is also presented.Comment: 9 pages, 8 figures, to be published in Phys. Rev.

Antibody response to pneumococcal and influenza vaccination in patients with rheumatoid arthritis receiving abatacept

Background Patients with rheumatoid arthritis (RA), including those treated with biologics, are at increased risk of some vaccine-preventable infections. We evaluated the antibody response to standard 23-valent pneumococcal polysaccharide vaccine (PPSV23) and the 2011–2012 trivalent seasonal influenza vaccine in adults with RA receiving subcutaneous (SC) abatacept and background disease-modifying anti-rheumatic drugs (DMARDs). Methods Two multicenter, open-label sub-studies enrolled patients from the ACQUIRE (pneumococcal and influenza) and ATTUNE (pneumococcal) studies at any point during their SC abatacept treatment cycle following completion of ≥3 months’ SC abatacept. All patients received fixed-dose abatacept 125 mg/week with background DMARDs. A pre-vaccination blood sample was taken, and after 28 ± 3 days a final post- vaccination sample was collected. The primary endpoint was the proportion of patients achieving an immunologic response to the vaccine at Day 28 among patients without a protective antibody level to the vaccine antigens at baseline (pneumococcal: defined as ≥2-fold increase in post-vaccination titers to ≥3 of 5 antigens and protective antibody level of ≥1.6 μg/mL to ≥3 of 5 antigens; influenza: defined as ≥4-fold increase in post-vaccination titers to ≥2 of 3 antigens and protective antibody level of ≥1:40 to ≥2 of 3 antigens). Safety and tolerability were evaluated throughout the sub-studies. Results Pre- and post-vaccination titers were available for 113/125 and 186/191 enrolled patients receiving the PPSV23 and influenza vaccine, respectively. Among vaccinated patients, 47/113 pneumococcal and 121/186 influenza patients were without protective antibody levels at baseline. Among patients with available data, 73.9 % (34/46) and 61.3 % (73/119) met the primary endpoint and achieved an immunologic response to PPSV23 or influenza vaccine, respectively. In patients with pre- and post-vaccination data available, 83.9 % in the pneumococcal study demonstrated protective antibody levels with PPSV23 (titer ≥1.6 μg/mL to ≥3 of 5 antigens), and 81.2 % in the influenza study achieved protective antibody levels (titer ≥1:40 to ≥2 of 3 antigens) at Day 28 post-vaccination. Vaccines were well tolerated with SC abatacept with background DMARDs. Conclusions In these sub-studies, patients with RA receiving SC abatacept and background DMARDs were able to mount an appropriate immune response to pneumococcal and influenza vaccines. Trial registration NCT00559585 (registered 15 November 2007) and NCT00663702 (registered 18 April 2008)