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Solution of the Skyrme-Hartree-Fock-Bogolyubov equations in the Cartesian deformed harmonic-oscillator basis. (VII) HFODD (v2.49t): a new version of the program
N. Schunck,J. Dobaczewski,J. McDonnell,W. Satula,J. A. Sheikh,A. Staszczak,M. Stoitsov,P. Toivanen
Physics , 2011, DOI: 10.1016/j.cpc.2011.08.013
Abstract: We describe the new version (v2.49t) of the code HFODD which solves the nuclear Skyrme Hartree-Fock (HF) or Skyrme Hartree-Fock-Bogolyubov (HFB) problem by using the Cartesian deformed harmonic-oscillator basis. In the new version, we have implemented the following physics features: (i) the isospin mixing and projection, (ii) the finite temperature formalism for the HFB and HF+BCS methods, (iii) the Lipkin translational energy correction method, (iv) the calculation of the shell correction. A number of specific numerical methods have also been implemented in order to deal with large-scale multi-constraint calculations and hardware limitations: (i) the two-basis method for the HFB method, (ii) the Augmented Lagrangian Method (ALM) for multi-constraint calculations, (iii) the linear constraint method based on the approximation of the RPA matrix for multi-constraint calculations, (iv) an interface with the axial and parity-conserving Skyrme-HFB code HFBTHO, (v) the mixing of the HF or HFB matrix elements instead of the HF fields. Special care has been paid to using the code on massively parallel leadership class computers. For this purpose, the following features are now available with this version: (i) the Message Passing Interface (MPI) framework, (ii) scalable input data routines, (iii) multi-threading via OpenMP pragmas, (iv) parallel diagonalization of the HFB matrix in the simplex breaking case using the ScaLAPACK library. Finally, several little significant errors of the previous published version were corrected.
Search for correlation effects in linear chains of trapped ions
C. J. S. Donald,D. M. Lucas,P. A. Barton,M. J. McDonnell,J. P. Stacey,D. A. Stevens,D. N. Stacey,A. M. Steane
Physics , 2000, DOI: 10.1209/epl/i2000-00506-9
Abstract: We report a precise search for correlation effects in linear chains of 2 and 3 trapped Ca+ ions. Unexplained correlations in photon emission times within a linear chain of trapped ions have been reported, which, if genuine, cast doubt on the potential of an ion trap to realize quantum information processing. We observe quantum jumps from the metastable 3d 2D_{5/2} level for several hours, searching for correlations between the decay times of the different ions. We find no evidence for correlations: the number of quantum jumps with separations of less than 10 ms is consistent with statistics to within errors of 0.05%; the lifetime of the metastable level derived from the data is consistent with that derived from independent single-ion data at the level of the experimental errors 1%; and no rank correlations between the decay times were found with sensitivity to rank correlation coefficients at the level of |R| = 0.024.
Isotope-selective photo-ionization for calcium ion trapping
D. M. Lucas,A. Ramos,J. P. Home,M. J. McDonnell,S. Nakayama,J. -P. Stacey,S. C. Webster,D. N. Stacey,A. M. Steane
Physics , 2003, DOI: 10.1103/PhysRevA.69.012711
Abstract: We present studies of resonance-enhanced photo-ionization for isotope-selective loading of Ca+ into a Paul trap. The 4s^2 ^1S_0 <-> 4s4p ^1P_1 transition of neutral calcium is driven by a 423nm laser and the atoms are photo-ionized by a second laser at 389nm. Isotope-selectivity is achieved by using crossed atomic and laser beams to reduce the Doppler width significantly below the isotope shifts in the 423nm transition. The loading rate of ions into the trap is studied under a range of experimental parameters for the abundant isotope 40Ca+. Using the fluorescence of the atomic beam at 423nm as a measure of the Ca number density, we estimate a lower limit for the absolute photo-ionization cross-section. We achieve loading and laser-cooling of all the naturally occurring isotopes, without the need for enriched sources. Laser-heating/cooling is observed to enhance the isotope-selectivity. In the case of the rare species 43Ca+ and 46Ca+, which have not previously been laser-cooled, the loading is not fully isotope-selective but we show that pure crystals of 43Ca+ may nevertheless be obtained. We find that for loading 40Ca+ the 389nm laser may be replaced by an incoherent source.
Spatiotemporal variability and long-term trends of ocean acidification in the California Current System
C. Hauri, N. Gruber, M. Vogt, S. C. Doney, R. A. Feely, Z. Lachkar, A. Leinweber, A. M. P. McDonnell, M. Munnich,G.-K. Plattner
Biogeosciences (BG) & Discussions (BGD) , 2013,
Abstract: Due to seasonal upwelling, the upper ocean waters of the California Current System (CCS) have a naturally low pH and aragonite saturation state (Ωarag), making this region particularly prone to the effects of ocean acidification. Here, we use the Regional Oceanic Modeling System (ROMS) to conduct preindustrial and transient (1995–2050) simulations of ocean biogeochemistry in the CCS. The transient simulations were forced with increasing atmospheric pCO2 and increasing oceanic dissolved inorganic carbon concentrations at the lateral boundaries, as projected by the NCAR CSM 1.4 model for the IPCC SRES A2 scenario. Our results show a large seasonal variability in pH (range of ~ 0.14) and Ωarag (~ 0.2) for the nearshore areas (50 km from shore). This variability is created by the interplay of physical and biogeochemical processes. Despite this large variability, we find that present-day pH and Ωarag have already moved outside of their simulated preindustrial variability envelopes (defined by ±1 temporal standard deviation) due to the rapidly increasing concentrations of atmospheric CO2. The nearshore surface pH of the northern and central CCS are simulated to move outside of their present-day variability envelopes by the mid-2040s and late 2030s, respectively. This transition may occur even earlier for nearshore surface Ωarag, which is projected to depart from its present-day variability envelope by the early- to mid-2030s. The aragonite saturation horizon of the central CCS is projected to shoal into the upper 75 m within the next 25 yr, causing near-permanent undersaturation in subsurface waters. Due to the model's overestimation of Ωarag, this transition may occur even earlier than simulated by the model. Overall, our study shows that the CCS joins the Arctic and Southern oceans as one of only a few known ocean regions presently approaching the dual threshold of widespread and near-permanent undersaturation with respect to aragonite and a departure from its variability envelope. In these regions, organisms may be forced to rapidly adjust to conditions that are both inherently chemically challenging and also substantially different from past conditions.
A long-lived memory qubit on a low-decoherence quantum bus
D. M. Lucas,B. C. Keitch,J. P. Home,G. Imreh,M. J. McDonnell,D. N. Stacey,D. J. Szwer,A. M. Steane
Physics , 2007,
Abstract: We demonstrate long-lived coherence in internal hyperfine states of a single \Ca{43} trapped-ion qubit $[T_2=1.2(2)\s]$, and in external motional states of a single \Ca{40} trapped-ion qubit $[T_2'=0.18(4)\s]$, in the same apparatus. The motional decoherence rate is consistent with the heating rate, which was measured to be 3(1) quanta/sec. Long coherence times in the external motional states are essential for performing high-fidelity quantum logic gates between trapped-ion qubits. The internal-state $T_2$ time that we observe in \Ca{43}, which has not previously been used as a trapped-ion qubit, is about one thousand times longer than that of physical qubits based on \Ca{40} ions. Using a single spin-echo pulse to ``re-phase'' the internal state, we can detect no decoherence after 1\s, implying an effective coherence time $T_2^{\mbox{\tiny SE}} \gtish 45\s$. This compares with timescales in this trap for single-qubit operations of \ish 1\us, and for two-qubit operations of \ish 10\us.
Memory coherence of a sympathetically cooled trapped-ion qubit
J. P. Home,M. J. McDonnell,D. J. Szwer,B. C. Keitch,D. M. Lucas,D. N. Stacey,A. M. Steane
Physics , 2008, DOI: 10.1103/PhysRevA.79.050305
Abstract: We demonstrate sympathetic cooling of a 43Ca+ trapped-ion "memory" qubit by a 40Ca+ "coolant" ion near the ground state of both axial motional modes, whilst maintaining coherence of the qubit. This is an essential ingredient in trapped-ion quantum computers. The isotope shifts are sufficient to suppress decoherence and phase shifts of the memory qubit due to the cooling light which illuminates both ions. We measure the qubit coherence during 10 cycles of sideband cooling, finding a coherence loss of 3.3% per cooling cycle. The natural limit of the method is O(0.01%) infidelity per cooling cycle.
Nuclear Energy Density Optimization: UNEDF2
M. Kortelainen,J. McDonnell,W. Nazarewicz,E. Olsen,P. -G. Reinhard,J. Sarich,N. Schunck,S. M. Wild,D. Davesne,J. Erler,A. Pastore
Physics , 2014,
Abstract: The parameters of the UNEDF2 nuclear energy density functional (EDF) model were obtained in an optimization to experimental data consisting of nuclear binding energies, proton radii, odd-even mass staggering data, fission-isomer excitation energies, and single particle energies. In addition to parameter optimization, sensitivity analysis was done to obtain parameter uncertainties and correlations. The resulting UNEDF2 is an all-around EDF. However, the sensitivity analysis also demonstrated that the limits of current Skyrme-like EDFs have been reached and that novel approaches are called for.
Nuclear energy density optimization: Shell structure
M. Kortelainen,J. McDonnell,W. Nazarewicz,E. Olsen,P. -G. Reinhard,J. Sarich,N. Schunck,S. M. Wild,D. Davesne,J. Erler,A. Pastore
Physics , 2013, DOI: 10.1103/PhysRevC.89.054314
Abstract: Nuclear density functional theory is the only microscopical theory that can be applied throughout the entire nuclear landscape. Its key ingredient is the energy density functional. In this work, we propose a new parameterization UNEDF2 of the Skyrme energy density functional. The functional optimization is carried out using the POUNDerS optimization algorithm within the framework of the Skyrme Hartree-Fock-Bogoliubov theory. Compared to the previous parameterization UNEDF1, restrictions on the tensor term of the energy density have been lifted, yielding a very general form of the energy density functional up to second order in derivatives of the one-body density matrix. In order to impose constraints on all the parameters of the functional, selected data on single-particle splittings in spherical doubly-magic nuclei have been included into the experimental dataset. The agreement with both bulk and spectroscopic nuclear properties achieved by the resulting UNEDF2 parameterization is comparable with UNEDF1. While there is a small improvement on single-particle spectra and binding energies of closed shell nuclei, the reproduction of fission barriers and fission isomer excitation energies has degraded. As compared to previous UNEDF parameterizations, the parameter confidence interval for UNEDF2 is narrower. In particular, our results overlap well with those obtained in previous systematic studies of the spin-orbit and tensor terms. UNEDF2 can be viewed as an all-around Skyrme EDF that performs reasonably well for both global nuclear properties and shell structure. However, after adding new data aiming to better constrain the nuclear functional, its quality has improved only marginally. These results suggest that the standard Skyrme energy density has reached its limits and significant changes to the form of the functional are needed.
Risk of ESRD and All Cause Mortality in Type 2 Diabetes According to Circulating Levels of FGF-23 and TNFR1
Jung Eun Lee, Tomohito Gohda, William H. Walker, Jan Skupien, Adam M. Smiles, Rita R. Holak, Jackson Jeong, Kevin P. McDonnell, Andrzej S. Krolewski, Monika A. Niewczas
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0058007
Abstract: Introduction Recent studies demonstrated that circulating fibroblast growth factor (FGF)-23 was associated with risk of end stage renal disease (ESRD) and mortality. This study aims to examine whether the predictive effect of FGF-23 is independent from circulating levels of tumor necrosis factor receptor 1 (TNFR1), a strong predictor of ESRD in Type 2 diabetes (T2D). Methods We studied 380 patients with T2D who were followed for 8–12 years and were used previously to examine the effect of TNFR1. Baseline plasma FGF-23 was measured by immunoassay. Results During follow-up, 48 patients (13%) developed ESRD and 83 patients (22%) died without ESRD. In a univariate analysis, baseline circulating levels of FGF-23 and TNFR1 were significantly higher in subjects who subsequently developed ESRD or died without ESRD than in those who remained alive. In a Cox proportional hazard model, baseline concentration of FGF-23 was associated with increased risk of ESRD, however its effect was no longer significant after controlling for TNFR1 and other clinical characteristics (HR 1.3, p = 0.15). The strong effect of circulating level of TNFR1 on risk of ESRD was not changed by including circulating levels of FGF-23 (HR 8.7, p<0.001). In the Cox multivariate model, circulating levels of FGF-23 remained a significant independent predictor of all-cause mortality unrelated to ESRD (HR 1.5, p<0.001). Conclusions We demonstrated that the effect of circulating levels of FGF-23 on the risk of ESRD is accounted for by circulating levels of TNFR1. We confirmed that circulating levels of FGF-23 have an independent effect on all-cause mortality in T2D.
Long-lived mesoscopic entanglement outside the Lamb-Dicke regime
M. J. McDonnell,J. P. Home,D. M. Lucas,G. Imreh,B. C. Keitch,D. J. Szwer,N. R. Thomas,S. C. Webster,D. N. Stacey,A. M. Steane
Physics , 2006, DOI: 10.1103/PhysRevLett.98.063603
Abstract: We create entangled states of the spin and motion of a single $^{40}$Ca$^+$ ion in a linear ion trap. The motional part consists of coherent states of large separation and long coherence time. The states are created by driving the motion using counterpropagating laser beams. We theoretically study and experimentally observe the behaviour outside the Lamb-Dicke regime, where the trajectory in phase space is modified and the coherent states become squeezed. We directly observe the modification of the return time of the trajectory, and infer the squeezing. The mesoscopic entanglement is observed up to $\Delta \alpha = 5.1$ with coherence time 170 microseconds and mean phonon excitation $\nbar = 16$.
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