All-electron magnetic response with pseudopotentials: NMR chemical shifts

A theory for the ab initio calculation of all-electron NMR chemical shifts in insulators using pseudopotentials is presented. It is formulated for both finite and infinitely periodic systems and is based on an extension to the Projector Augmented Wave approach of Bloechl [P. E. Bloechl, Phys. Rev. B 50, 17953 (1994)] and the method of Mauri et al [F. Mauri, B.G. Pfrommer, and S.G. Louie, Phys. Rev. Lett. 77, 5300 (1996)]. The theory is successfully validated for molecules by comparison with a selection of quantum chemical results, and in periodic systems by comparison with plane-wave all-electron results for diamond.Comment: 25 pages, 4 tables, submitted to Physical Review

High-order density-matrix perturbation theory

We present a simple formalism for the calculation of the derivatives of the electronic density matrix at any order, within density functional theory. Our approach, contrary to previous ones, is not based on the perturbative expansion of the Kohn-Sham wavefunctions. It has the following advantages: (i) it allows a simple derivation for the expression for the high order derivatives of the density matrix; (ii) in extended insulators, the treatment of uniform-electric-field perturbations and of the polarization derivatives is straightforward.Comment: 4 page

Diagnostic host gene signature for distinguishing enteric fever from other febrile diseases

Misdiagnosis of enteric fever is a major global health problem, resulting in patient mismanagement, antimicrobial misuse and inaccurate disease burden estimates. Applying a machine learning algorithm to host gene expression profiles, we identified a diagnostic signature, which could distinguish culture‐confirmed enteric fever cases from other febrile illnesses (area under receiver operating characteristic curve > 95%). Applying this signature to a culture‐negative suspected enteric fever cohort in Nepal identified a further 12.6% as likely true cases. Our analysis highlights the power of data‐driven approaches to identify host response patterns for the diagnosis of febrile illnesses. Expression signatures were validated using qPCR, highlighting their utility as PCR‐based diagnostics for use in endemic settings

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Inorganic double-helix structures of unusually simple lithium-phosphorus species

Theoretical evidence: The existence of inorganic double-helix structures at the atomic level is theoretically predicted. An unbiased quantum-chemical search for the global minimum structures of Li xP x (x=5-9) species is performed. For the Li 7P 7-Li 9P 9 stoichiometries the global minimum structure has a peculiar double-helix form. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Theoretical and experimental insights into applicability of solid-state 93Nb NMR in catalysis

Ab initio DFT calculations of 93Nb NMR parameters using the NMR-CASTEP code were performed for a series of over fifty individual niobates, and a good agreement has been found with experimental NMR parameters. New experimental and calculated 93Nb NMR data were obtained for several compounds, AlNbO4, VNb9O25, K 8Nb6O19 and Cs3NbO8, which are of particular interest for catalysis. Several interesting trends have been identified between 93Nb NMR parameters and the specifics of niobium site environments in niobates. These trends may serve as useful guidelines in interpreting 93Nb NMR spectra of complex niobium oxide systems, including amorphous samples and niobium-based multicomponent heterogeneous catalysts. Potential applications of 93Nb NMR to study solid polyoxoniobates are discussed. \ua9 2013 The Owner Societies.Peer reviewed: YesNRC publication: Ye

Accurate kinetic energy evaluation in electronic structure calculations with localized functions on real space grids

We present a method for calculating the kinetic energy of localized functions represented on a regular real space grid. This method uses fast Fourier transforms applied to restricted regions commensurate with the simulation cell and is applicable to grids of any symmetry. In the limit of large systems it scales linearly with system size. Comparison with the finite difference approach shows that our method offers significant improvements in accuracy without loss of efficiency

EPR g-tensor of paramagnetic centers in yttria-stabilized zirconia from first-principles calculations.

International audienceIn order to assign the defect responsible for the experimental electron paramagnetic resonance (EPR) signal with trigonal symmetry (T center), we have studied the properties of different paramagnetic centers in yttria-stabilized cubic zirconia by computing the EPR g-tensor from density functional perturbation theory. We have considered reduced vacancy-zirconium complexes and reduced Ti impurities. These first-principles calculations allow us to discard the experimental assignment of the T center to an extrinsic Ti3+ ion nearest neighbor to a single vacancy. Instead, the calculated EPR g tensors of both a Zr3+ or a Ti3+ ion at the center of a divacancy aligned along the directions are compatible with the experimental EPR signal. However, since the EPR signal of the T center is correlated experimentally with an optical absorption band at 370 nm, calculated optical excitations allow us to decide in favor of the Ti3+ divacancy complex