NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations

We present a benchmark of the density functional linear response calculation of NMR shieldings within the Gauge-Including Projector-Augmented-Wave method against all-electron Augmented-Plane-Wave$+$local-orbital and uncontracted Gaussian basis set results for NMR shieldings in molecular and solid state systems. In general, excellent agreement between the aforementioned methods is obtained. Scalar relativistic effects are shown to be quite large for nuclei in molecules in the deshielded limit. The small component makes up a substantial part of the relativistic corrections.Comment: 3 figures, supplementary material include

The shortcomings of semi-local and hybrid functionals: what we can learn from surface science studies

A study of the adsorption of CO on late 4d and $5d$ transition metal (111) surfaces (Ru, Rh, Pd, Ag, Os, Ir, and Pt) considering atop and hollow site adsorption is presented. The applied functionals include the gradient corrected PBE and BLYP functional, and the corresponding hybrid Hartree-Fock density functionals HSE and B3LYP. We find that PBE based hybrid functionals (specifically HSE) yield, with the exception of Pt, the correct site order on all considered metals, but they also considerably overestimate the adsorption energies compared to experiment. On the other hand, the semi-local BLYP functional and the corresponding hybrid functional B3LYP yield very satisfactory adsorption energies and the correct adsorption site for all surfaces. We are thus faced with a Procrustean problem: the B3LYP and BLYP functionals seem to be the overall best choice for describing adsorption on metal surfaces, but they simultaneously fail to account well for the properties of the metal, vastly overestimating the equilibrium volume and underestimating the atomization energies. Setting out from these observations, general conclusions are drawn on the relative merits and drawbacks of various semi-local and hybrid functionals. The discussion includes a revised version of the PBE functional specifically optimized for bulk properties and surface energies (PBEsol), a revised version of the PBE functional specifically optimized to predict accurate adsorption energies (rPBE), as well as the aforementioned BLYP functional. We conclude that no semi-local functional is capable to describe all aspects properly, and including non-local exchange also only improves some, but worsens other properties.Comment: 12 pages, 6 figures; to be published in New Journal of Physic

Maximally localized Wannier functions in LaMnO3 within PBE+U, hybrid functionals, and partially self-consistent GW: an efficient route to construct ab-initio tight-binding parameters for e_g perovskites

Using the newly developed VASP2WANNIER90 interface we have constructed maximally localized Wannier functions (MLWFs) for the e_g states of the prototypical Jahn-Teller magnetic perovskite LaMnO3 at different levels of approximation for the exchange-correlation kernel. These include conventional density functional theory (DFT) with and without additional on-site Hubbard U term, hybrid-DFT, and partially self-consistent GW. By suitably mapping the MLWFs onto an effective e_g tight-binding (TB) Hamiltonian we have computed a complete set of TB parameters which should serve as guidance for more elaborate treatments of correlation effects in effective Hamiltonian-based approaches. The method-dependent changes of the calculated TB parameters and their interplay with the electron-electron (el-el) interaction term are discussed and interpreted. We discuss two alternative model parameterizations: one in which the effects of the el-el interaction are implicitly incorporated in the otherwise "noninteracting" TB parameters, and a second where we include an explicit mean-field el-el interaction term in the TB Hamiltonian. Both models yield a set of tabulated TB parameters which provide the band dispersion in excellent agreement with the underlying ab initio and MLWF bands.Comment: 30 pages, 7 figure

A method for mechanical generation of radio frequency fields in nuclear magnetic resonance force microscopy

We present an innovative method for magnetic resonance force microscopy (MRFM) with ultra-low dissipation, by using the higher modes of the mechanical detector as radio frequency (rf) source. This method allows MRFM on samples without the need to be close to an rf source. Furthermore, since rf sources require currents that give dissipation, our method enables nuclear magnetic resonance experiments at ultra-low temperatures. Removing the need for an on-chip rf source is an important step towards a MRFM which can be widely used in condensed matter physics.Comment: 7 pages, 5 figures, to be submitted to Physical Review Applie

Coxsackie and adenovirus receptor is a modifier of cardiac conduction and arrhythmia vulnerability in the setting of myocardial ischemia.

OBJECTIVES: The aim of this study was to investigate the modulatory effect of the coxsackie and adenovirus receptor (CAR) on ventricular conduction and arrhythmia vulnerability in the setting of myocardial ischemia. BACKGROUND: A heritable component in the risk of ventricular fibrillation during myocardial infarction has been well established. A recent genome-wide association study of ventricular fibrillation during acute myocardial infarction led to the identification of a locus on chromosome 21q21 (rs2824292) in the vicinity of the CXADR gene. CXADR encodes the CAR, a cell adhesion molecule predominantly located at the intercalated disks of the cardiomyocyte. METHODS: The correlation between CAR transcript levels and rs2824292 genotype was investigated in human left ventricular samples. Electrophysiological studies and molecular analyses were performed using CAR haploinsufficient (CAR(+/-)) mice. RESULTS: In human left ventricular samples, the risk allele at the chr21q21 genome-wide association study locus was associated with lower CXADR messenger ribonucleic acid levels, suggesting that decreased cardiac levels of CAR predispose to ischemia-induced ventricular fibrillation. Hearts from CAR(+/-) mice displayed slowing of ventricular conduction in addition to an earlier onset of ventricular arrhythmias during the early phase of acute myocardial ischemia after ligation of the left anterior descending artery. Expression and distribution of connexin 43 were unaffected, but CAR(+/-) hearts displayed increased arrhythmia susceptibility on pharmacological electrical uncoupling. Patch-clamp analysis of isolated CAR(+/-) myocytes showed reduced sodium current magnitude specifically at the intercalated disk. Moreover, CAR coprecipitated with NaV1.5 in vitro, suggesting that CAR affects sodium channel function through a physical interaction with NaV1.5. CONCLUSIONS: CAR is a novel modifier of ventricular conduction and arrhythmia vulnerability in the setting of myocardial ischemia. Genetic determinants of arrhythmia susceptibility (such as CAR) may constitute future targets for risk stratification of potentially lethal ventricular arrhythmias in patients with coronary artery disease

The lethal response to Cdk1 inhibition depends on sister chromatid alignment errors generated by KIF4 and isoform 1 of PRC1

Cyclin-dependent kinase 1 (Cdk1) is absolutely essential for cell division. Complete ablation of Cdk1 precludes the entry of G2 phase cells into mitosis, and is early embryonic lethal in mice. Dampening Cdk1 activation, by reducing gene expression or upon treatment with cell-permeable Cdk1 inhibitors, is also detrimental for proliferating cells, but has been associated with defects in mitotic progression, and the formation of aneuploid daughter cells. Here, we used a large-scale RNAi screen to identify the human genes that critically determine the cellular toxicity of Cdk1 inhibition. We show that Cdk1 inhibition leads to fatal sister chromatid alignment errors and mitotic arrest in the spindle checkpoint. These problems start early in mitosis and are alleviated by depletion of isoform 1 of PRC1 (PRC1-1), by gene ablation of its binding partner KIF4, or by abrogation of KIF4 motor activity. Our results show that, normally, Cdk1 activity must rise above the level required for mitotic entry. This prevents KIF4-dependent PRC1-1 translocation to astral microtubule tips and safeguards proper chromosome congression. We conclude that cell death in response to Cdk1 inhibitors directly relates to chromosome alignment defects generated by insufficient repression of PRC1-1 and KIF4 during prometaphase

An introduction to network psychometrics:Relating ising network models to item response theory models

In recent years, network models have been proposed as an alternative representation of psychometric constructs such as depression. In such models, the covariance between observables (e.g., symptoms like depressed mood, feelings of worthlessness, and guilt) is explained in terms of a pattern of causal interactions between these observables, which contrasts with classical interpretations in which the observables are conceptualized as the effects of a reflective latent variable. However, few investigations have been directed at the question how these different models relate to each other. To shed light on this issue, the current paper explores the relation between one of the most important network models—the Ising model from physics—and one of the most important latent variable models—the Item Response Theory (IRT) model from psychometrics. The Ising model describes the interaction between states of particles that are connected in a network, whereas the IRT model describes the probability distribution associated with item responses in a psychometric test as a function of a latent variable. Despite the divergent backgrounds of the models, we show a broad equivalence between them and also illustrate several opportunities that arise from this connection

Accurate screened exchange band structures for transition metal monoxides MnO, FeO, CoO and NiO

We report calculations of the band structures and density of states of the four transition metal monoxides MnO, FeO, CoO and NiO using the hybrid density functional sX-LDA. Late transition metal oxides are prototypical examples of strongly correlated materials, which pose challenges for electronic structure methods. We compare our results with available experimental data and show that our calculations yield accurate predictions for the fundamental band gaps and valence bands of FeO, CoO and NiO. For MnO, the band gaps are underestimated, suggesting additional many-body effects that are not captured by our screened hybrid functional approach.Comment: 9 pages, 3 figures, 3 table