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Author |
Peris, J.B.; Davis, P.; Cuevas, J.M.; Nebot, M.; Sanjuan, R. |
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Title |
Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1 |
Type |
Journal Article |
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Year |
2010 |
Publication |
Genetics |
Abbreviated Journal |
Genetics |
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Volume |
185 |
Issue |
2 |
Pages |
603-U308 |
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Abstract |
Empirical knowledge of the fitness effects of mutations is important for understanding many evolutionary processes, yet this knowledge is often hampered by several sources of measurement error and bias. Most of these problems can be solved using site-directed mutagenesis to engineer single mutations, an approach particularly suited for viruses due to their small genomes. Here, we used this technique to measure the fitness effect of 100 single-nucleotide substitutions in the bacteriophage f1, a filamentous single-strand DNA virus. We found that approximately one-fifth of all mutations are lethal. Viable ones reduced fitness by 11% on average and were accurately described by a log-normal distribution. More than 90% of synonymous substitutions were selectively neutral, while those affecting intergenic regions reduced fitness by 14% on average. Mutations leading to amino acid substitutions had an overall mean deleterious effect of 37%, which increased to 45% for those changing the amino acid polarity. Interestingly, mutations affecting early steps of the infection cycle tended to be more deleterious than those affecting late steps. Finally, we observed at least two beneficial mutations. Our results confirm that high mutational sensitivity is a general property of viruses with small genomes, including RNA and single-strand DNA viruses infecting animals, plants, and bacteria. |
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Address |
[Peris, Joan B.; Davis, Paulina; Cuevas, Jose M.; Sanjuan, Rafael] Univ Valencia, Inst Cavanilles Biodiversitat & Biol Evolut, Valencia 46980, Spain, Email: rafael.sanjuan@uv.es |
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Genetics Soc Am |
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English |
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0016-6731 |
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Notes |
ISI:000281905200017 |
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no |
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Is ISI |
yes |
International Collaboration  |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
383 |
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Author |
Mateo, D.; Barranco, M.; Navarro, J. |
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Title |
Elementary excitations in superfluid He-3-He-4 mixtures |
Type |
Journal Article |
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Year |
2010 |
Publication |
Physical Review B |
Abbreviated Journal |
Phys. Rev. B |
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Volume |
82 |
Issue |
13 |
Pages |
134529 - 13pp |
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Abstract |
We have studied the dynamic structure function of superfluid He-3-He-4 mixtures at zero temperature as a function of pressure and He-3 concentration. Results obtained in the full random-phase approximation (RPA) plus density-functional theory and in a generalized Landau-Pomeranchuk approach are presented and compared with experiment. Analytic expressions for several sum rules of the dynamic structure functions have been determined, and have been used to obtain average energies of the collective excitations. In the RPA approach, the dispersion relation of the collective modes shows typical features of level repulsion between zero-soundlike and phonon-rotonlike excitations. The structure of the coupled RPA equations for the mixture leads in a natural way to the hybridization of the collective modes. The mixed He-3-He-4 dynamic structure function quenches the zero-soundlike mode before it crosses the phonon-roton branch, causing that the former mode only appears with enough strength after the crossing. |
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Address |
[Mateo, David; Barranco, Manuel] Univ Barcelona, Fac Fis, Dept ECM, E-08028 Barcelona, Spain |
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Amer Physical Soc |
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English |
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1098-0121 |
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Notes |
ISI:000283291200005 |
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no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
354 |
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Author |
Noguera, S.; Vento, V. |
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Title |
The pion transition form factor and the pion distribution amplitude |
Type |
Journal Article |
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Year |
2010 |
Publication |
European Physical Journal A |
Abbreviated Journal |
Eur. Phys. J. A |
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Volume |
46 |
Issue |
2 |
Pages |
197-205 |
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Abstract |
Recent BaBar data on the pion transition form factor, whose Q(2)-dependence is much steeper then predicted by asymptotic Quantum Chromodynamics (QCD), have caused a renewed interest in its theoretical description. We present here a formalism based on a model-independent description for low photon virtuality and a high photon virtuality description based on QCD, which match at a scale Q(0). The high photon virtuality description incorporates a flat pion distribution amplitude, phi(x) = 1, at the matching scale Q(0) and QCD evolution from Q(0) to Q > Q(0). The flat pion distribution is connected, through soft pion theorems and chiral symmetry, to the pion valence parton distribution at the same low scale Q(0). The procedure leads to a good description of the data, and by incorporating additional twist-three effects, to an excellent description of the data. |
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Address |
[Noguera, S.] Univ Valencia, Dept Fis Teor, CSIC, E-46100 Valencia, Spain, Email: Santiago.Noguera@uv.es |
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Springer |
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English |
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Edition |
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ISSN |
1434-6001 |
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Conference |
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Notes |
ISI:000284869600005 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
312 |
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Author |
Girones, Z.; Marchetti, A.; Mena, O.; Pena-Garay, C.; Rius, N. |
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Title |
Cosmological data analysis of f(R) gravity models |
Type |
Journal Article |
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Year |
2010 |
Publication |
Journal of Cosmology and Astroparticle Physics |
Abbreviated Journal |
J. Cosmol. Astropart. Phys. |
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Volume |
11 |
Issue |
11 |
Pages |
004 - 18pp |
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Keywords |
modified gravity; cosmological parameters from LSS |
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Abstract |
A class of well-behaved modified gravity models with long enough matter domination epoch and a late-time accelerated expansion is confronted with SNIa, CMB, SDSS, BAO and H(z) galaxy ages data, as well as current measurements of the linear growth of structure. We show that the combination of geometrical probes and growth data exploited here allows to rule out f(R) gravity models, in particular, the logarithmic of curvature model. We also apply solar system tests to the models in agreement with the cosmological data. We find that the exponential of the inverse of the curvature model satisfies all the observational tests considered and we derive the allowed range of parameters. Current data still allows for small deviations of Einstein gravity. Future, high precision growth data, in combination with expansion history data, will be able to distinguish tiny modifications of standard gravity from the Lambda CDM model. |
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Address |
[Girones, Z.; Marchetti, A.; Mena, O.; Pena-Garay, C.; Rius, N.] Univ Valencia, CSIC, IFIC, Dept Fis Teor, Valencia 46071, Spain, Email: girones@ific.uv.es |
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Publisher |
Iop Publishing Ltd |
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English |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1475-7516 |
ISBN |
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Medium |
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Area |
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Expedition |
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Conference |
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Notes |
ISI:000284825100004 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
315 |
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Author |
Oliver, J.F.; Rafecas, M. |
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Title |
Improving the singles rate method for modeling accidental coincidences in high-resolution PET |
Type |
Journal Article |
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Year |
2010 |
Publication |
Physics in Medicine and Biology |
Abbreviated Journal |
Phys. Med. Biol. |
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Volume |
55 |
Issue |
22 |
Pages |
6951-6971 |
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Abstract |
Random coincidences ('randoms') are one of the main sources of image degradation in PET imaging. In order to correct for this effect, an accurate method to estimate the contribution of random events is necessary. This aspect becomes especially relevant for high-resolution PET scanners where the highest image quality is sought and accurate quantitative analysis is undertaken. One common approach to estimate randoms is the so-called singles rate method (SR) widely used because of its good statistical properties. SR is based on the measurement of the singles rate in each detector element. However, recent studies suggest that SR systematically overestimates the correct random rate. This overestimation can be particularly marked for low energy thresholds, below 250 keV used in some applications and could entail a significant image degradation. In this work, we investigate the performance of SR as a function of the activity, geometry of the source and energy acceptance window used. We also investigate the performance of an alternative method, which we call 'singles trues' (ST) that improves SR by properly modeling the presence of true coincidences in the sample. Nevertheless, in any real data acquisition the knowledge of which singles are members of a true coincidence is lost. Therefore, we propose an iterative method, STi, that provides an estimation based on ST but which only requires the knowledge of measurable quantities: prompts and singles. Due to inter-crystal scatter, for wide energy windows ST only partially corrects SR overestimations. While SR deviations are in the range 86-300% (depending on the source geometry), the ST deviations are systematically smaller and contained in the range 4-60%. STi fails to reproduce the ST results, although for not too high activities the deviation with respect to ST is only a few percent. For conventional energy windows, i.e. those without inter-crystal scatter, the ST method corrects the SR overestimations, and deviations from the true random rate are of the order of 1% or less. In addition, in the case of conventional energy window STi results reproduce ST results and therefore the former can be used to obtain the true random rate. |
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Address |
[Oliver, Josep F.; Rafecas, Magdalena] Univ Valencia, CSIC, Inst Fis Corpuscular, IFIC, E-46003 Valencia, Spain, Email: josep.f.oliver@uv.es |
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Publisher |
Iop Publishing Ltd |
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Language |
English |
Summary Language |
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ISSN |
0031-9155 |
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Conference |
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Notes |
ISI:000283789700025 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
344 |
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Author |
Aguiar, P.; Rafecas, M.; Ortuño, J.E.; Kontaxakis, G.; Santos, A.; Pavia, J.; Rosetti, M. |
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Title |
Geometrical and Monte Carlo projectors in 3D PET reconstruction |
Type |
Journal Article |
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Year |
2010 |
Publication |
Medical Physics |
Abbreviated Journal |
Med. Phys. |
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Volume |
37 |
Issue |
11 |
Pages |
5691-5702 |
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Keywords |
3D PET; iterative reconstruction; list-mode reconstruction; ray-tracing techniques; Monte Carlo simulation; system response matrix |
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Abstract |
Purpose: In the present work, the authors compare geometrical and Monte Carlo projectors in detail. The geometrical projectors considered were the conventional geometrical Siddon ray-tracer (S-RT) and the orthogonal distance-based ray-tracer (OD-RT), based on computing the orthogonal distance from the center of image voxel to the line-of-response. A comparison of these geometrical projectors was performed using different point spread function (PSF) models. The Monte Carlo-based method under consideration involves an extensive model of the system response matrix based on Monte Carlo simulations and is computed off-line and stored on disk. Methods: Comparisons were performed using simulated and experimental data of the commercial small animal PET scanner rPET. Results: The results demonstrate that the orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions yield better images in terms of contrast and spatial resolution than those obtained after using the conventional method and the multiray-based S-RT. Furthermore, the Monte Carlo-based method yields slight improvements in terms of contrast and spatial resolution with respect to these geometrical projectors. Conclusions: The orthogonal distance-based ray-tracer and Siddon ray-tracer using PSF image-space convolutions represent satisfactory alternatives to factorizing the system matrix or to the conventional on-the-fly ray-tracing methods for list-mode reconstruction, where an extensive modeling based on Monte Carlo simulations is unfeasible. |
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Address |
[Aguiar, Pablo] Univ Santiago de Compostela, Dept Fis Particulas, Complexo Hosp Univ Santiago de Compostela, Fdn IDICHUS IDIS, Santiago De Compostela, Spain, Email: pablo.aguiar.fernandez@sergas.es |
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Amer Assoc Physicists Medicine Amer Inst Physics |
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English |
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ISSN |
0094-2405 |
ISBN |
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Notes |
ISI:000283747600015 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
338 |
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Author |
Wagner, C.; Verde, L.; Boubekeur, L. |
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Title |
N-body simulations with generic non-Gaussian initial conditions I: power spectrum and halo mass function |
Type |
Journal Article |
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Year |
2010 |
Publication |
Journal of Cosmology and Astroparticle Physics |
Abbreviated Journal |
J. Cosmol. Astropart. Phys. |
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Volume |
10 |
Issue |
10 |
Pages |
022 - 24pp |
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Keywords |
power spectrum; cosmological simulations; initial conditions and eternal universe; galaxy clusters |
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Abstract |
We address the issue of setting up generic non-Gaussian initial conditions for N-body simulations. We consider inflationary-motivated primordial non-Gaussianity where the perturbations in the Bardeen potential are given by a dominant Gaussian part plus a non-Gaussian part specified by its bispectrum. The approach we explore here is suitable for any bispectrum, i.e. it does not have to be of the so-called separable or factorizable form. The procedure of generating a non-Gaussian field with a given bispectrum (and a given power spectrum for the Gaussian component) is not univocal, and care must be taken so that higher-order corrections do not leave a too large signature on the power spectrum. This is so far a limiting factor of our approach. We then run N-body simulations for the most popular inflationary-motivated non-Gaussian shapes. The halo mass function and the non-linear power spectrum agree with theoretical analytical approximations proposed in the literature, even if they were so far developed and tested only for a particular shape (the local one). We plan to make the simulations outputs available to the community via the non-Gaussian simulations comparison project web site http://icc.ub.edu/similar to liciaverde/NGSCP.html. |
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Address |
[Wagner, Christian; Verde, Licia] Univ Barcelona, ICCUB IEEC, E-08028 Barcelona, Spain, Email: cwagner@icc.ub.edu |
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Publisher |
Iop Publishing Ltd |
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English |
Summary Language |
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Series Editor |
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Abbreviated Series Title |
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ISSN |
1475-7516 |
ISBN |
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Area |
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Conference |
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Notes |
ISI:000283577600013 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
339 |
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Author |
Gamermann, D.; Nieves, J.; Oset, E.; Ruiz Arriola, E. |
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Title |
Couplings in coupled channels versus wave functions: Application to the X(3872) resonance |
Type |
Journal Article |
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Year |
2010 |
Publication |
Physical Review D |
Abbreviated Journal |
Phys. Rev. D |
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Volume |
81 |
Issue |
1 |
Pages |
014029 - 14pp |
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Keywords |
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Abstract |
We perform an analytical study of the scattering matrix and bound states in problems with many physical coupled channels. We establish the relationship of the couplings of the states to the different channels, obtained from the residues of the scattering matrix at the poles, with the wave functions for the different channels. The couplings basically reflect the value of the wave functions around the origin in coordinate space. In the concrete case of the X(3872) resonance, understood as a bound state of D-0(D) over bar*(0) and D+D*(-) (and c.c. From now on, when we refer to D-0(D) over bar*(0), D+D*(-), or D (D) over bar* we are actually referring to the combination of these states with their complex conjugate in order to form a state with positive C-parity), with the D-0(D) over bar*(0) loosely bound, we find that the couplings to the two channels are essentially equal leading to a state of good isospin I = 0 character. This is in spite of having a probability for finding the D-0(D) over bar*(0) state much larger than for D+D*(-) since the loosely bound channel extends further in space. The analytical results, obtained with exact solutions of the Schrodinger equation for the wave functions, can be useful in general to interpret results found numerically in the study of problems with unitary coupled channels methods. |
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Address |
[Gamermann, D.; Nieves, J.; Oset, E.] Univ Valencia, Ctr Mixto, Inst Fis Corpuscular IFIC, CSIC,Inst Invest Paterna, Valencia 46071, Spain, Email: daniel.gamermann@ific.uv.es |
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Publisher |
Amer Physical Soc |
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English |
Summary Language |
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ISSN |
1550-7998 |
ISBN |
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Conference |
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Notes |
ISI:000284268800001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
329 |
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Author |
Kiesewetter, S.; Vento, V. |
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Title |
eta-eta '-glueball mixing |
Type |
Journal Article |
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Year |
2010 |
Publication |
Physical Review D |
Abbreviated Journal |
Phys. Rev. D |
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Volume |
82 |
Issue |
3 |
Pages |
034003 - 13pp |
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Keywords |
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Abstract |
We have revisited glueball mixing with the pseudoscalar mesons in the MIT bag model scheme. The calculation has been performed in the spherical cavity approximation to the bag using two different fermion propagators, the cavity and the free propagators. We obtain probabilities of mixing for the eta at the level of 0.006%-2.0%, while for the eta' one at the level of 0.6%-40%, depending on the choice of bag radius and, therefore, of the strong coupling constant. Our results differ from previous calculations. The origin of our difference stems from the treatment of the time integrations. The comparison of our calculation with experimental data, which is consistent with small eta – eta' – G mixing, implies that the pseudoscalar glueball is small, R similar to 0.5-0.6 fm and has a large mass, M-G similar to 2000-2500 MeV. |
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Address |
[Kiesewetter, Simon] Univ Valencia, Dept Fis Teor, CSIC, E-46100 Burjassot, Valencia, Spain |
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Publisher |
Amer Physical Soc |
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Language |
English |
Summary Language |
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Abbreviated Series Title |
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ISSN |
1550-7998 |
ISBN |
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Conference |
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Notes |
ISI:000280611800007 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
399 |
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Author |
Gonzalez-Alonso, M.; Pich, A.; Prades, J. |
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Title |
Pinched weights and duality violation in QCD sum rules: A critical analysis |
Type |
Journal Article |
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Year |
2010 |
Publication |
Physical Review D |
Abbreviated Journal |
Phys. Rev. D |
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Volume |
82 |
Issue |
1 |
Pages |
014019 - 7pp |
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Keywords |
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Abstract |
We analyze the so-called pinched weights, that are generally thought to reduce the violation of quarkhadron duality in finite-energy sum rules. After showing how this is not true in general, we explain how to address this question for the left-right correlator and any particular pinched weight, taking advantage of our previous work [1], where the possible high-energy behavior of the left-right spectral function was studied. In particular, we show that the use of pinched weights allows to determine with high accuracy the dimension six and eight contributions in the operator-product expansion, O-6 = (-4.3(-0.7)(+0.9)) x 10(-3) GeV6 and O-8 = (-7.2(-5.3)(+4.2)) x 10(-3) GeV8. |
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Address |
[Gonzalez-Alonso, Martin; Pich, Antonio] Univ Valencia, CSIC, Dept Fis Teor, E-46071 Valencia, Spain |
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Publisher |
Amer Physical Soc |
Place of Publication |
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Editor |
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Language |
English |
Summary Language |
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Original Title |
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Series Editor |
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Abbreviated Series Title |
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Series Volume |
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ISSN |
1550-7998 |
ISBN |
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Medium |
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Area |
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Expedition |
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Conference |
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Notes |
ISI:000280470200001 |
Approved |
no |
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Is ISI |
yes |
International Collaboration |
no |
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Call Number |
IFIC @ elepoucu @ |
Serial |
403 |
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