Large scale ab initio calculations based on three levels of parallelization

We suggest and implement a parallelization scheme based on an efficient multiband eigenvalue solver, called the locally optimal block preconditioned conjugate gradient LOBPCG method, and using an optimized three-dimensional (3D) fast Fourier transform (FFT) in the ab initio}plane-wave code ABINIT. In addition to the standard data partitioning over processors corresponding to different k-points, we introduce data partitioning with respect to blocks of bands as well as spatial partitioning in the Fourier space of coefficients over the plane waves basis set used in ABINIT. This k-points-multiband-FFT parallelization avoids any collective communications on the whole set of processors relying instead on one-dimensional communications only. For a single k-point, super-linear scaling is achieved for up to 100 processors due to an extensive use of hardware optimized BLAS, LAPACK, and SCALAPACK routines, mainly in the LOBPCG routine. We observe good performance up to 200 processors. With 10 k-points our three-way data partitioning results in linear scaling up to 1000 processors for a practical system used for testing.Comment: 8 pages, 5 figures. Accepted to Computational Material Scienc

First-principles study of the polar O-terminated ZnO surface in thermodynamic equilibrium with oxygen and hydrogen

Using density-functional theory in combination with a thermodynamic formalism we calculate the relative stability of various structural models of the polar O-terminated (000-1)-O surface of ZnO. Model surfaces with different concentrations of oxygen vacancies and hydrogen adatoms are considered. Assuming that the surfaces are in thermodynamic equilibrium with an O2 and H2 gas phase we determine a phase diagram of the lowest-energy surface structures. For a wide range of temperatures and pressures we find that hydrogen will be adsorbed at the surface, preferentially with a coverage of 1/2 monolayer. At high temperatures and low pressures the hydrogen can be removed and a structure with 1/4 of the surface oxygen atoms missing becomes the most stable one. The clean, defect-free surface can only exist in an oxygen-rich environment with a very low hydrogen partial pressure. However, since we find that the dissociative adsorption of molecular hydrogen and water (if also the Zn-terminated surface is present) is energetically very preferable, it is very unlikely that a clean, defect-free (000-1)-O surface can be observed in experiment.Comment: 10 pages, 4 postscript figures. Uses REVTEX and epsf macro

Осложнения COVID-19-ассоциированной пневмонии: тромбоз ветвей легочных артерий (клинический случай)

The article presents a rare case of thrombosis of the pulmonary arteries branches, which developed in a patient two months after infection with the SARS-CoV-2 virus, that caused bilateral polysegmental pneumonia. The thrombosis was suspected because of a high plasma D-dimer level. Contrast-enhanced chest CT was performed to make a definitive diagnosis. The absence of blood clots in the veins of the lower extremities and pelvis allowed us to conclude that the patient did not have thromboembolism, but rather a pulmonary thrombosis in situ. Such possible causes of venousthromboembolic complications as tumors, systemic diseases of the connective tissue, and antiphospholipid syndrome were excluded based on negative tests for tumor and autoimmune diseases markers. The long-stay in the hospital was associated with the inability of the patient to maintain the normal level of blood oxygen saturation independently due to the large area of the lung damage associated with COVID-19 pneumonia and ischemia caused by thrombosis of the branches of the pulmonary arteries.Представлен редкий случай тромбоза ветвей (ТВ) легочных артерий (ЛА), развившийся у пациента через 2 мес. после инфицирования вирусом SARS-CoV-2, вызвавшим двустороннюю полисегментарную пневмонию. Диагноз тромбоз верифицирован при проведении компьютерной томографии органов грудной клетки с контрастным усилением. Предиктором тромбоза являлся повышенный уровень плазменной концентрации D-димера. Ввиду отсутствия тромбов в венах нижних конечностей и таза сделано заключение, что у пациента не тромбоэмболия, а именно ТВ ЛА in situ. На основании отрицательных тестов на онкомаркеры и маркеры аутоиммунных заболеваний исключены такие возможные причины венозно-тромбоэмболических осложнений, как опухоли, системные заболевания соединительной ткани и антифосфолипидный синдром. Длительное пребывание пациента в стационаре было связано с невозможностью самостоятельно поддерживать нормальный уровень сатурации крови кислородом из-за большой площади поражения легких и ишемии легочной ткани, обусловленной ТВ ЛА

Electron Beam-Induced Writing of Nanoscale Iron Wires on a Functional Metal Oxide

Electron beam-induced surface activation (EBISA) has been used to grow wires of iron on rutile TiO2(110)-(1 × 1) in ultrahigh vacuum. The wires have a width down to ∼20 nm and hence have potential utility as interconnects on this dielectric substrate. Wire formation was achieved using an electron beam from a scanning electron microscope to activate the surface, which was subsequently exposed to Fe(CO)5. On the basis of scanning tunneling microscopy and Auger electron spectroscopy measurements, the activation mechanism involves electron beam-induced surface reduction and restructuring

The pH Response and Sensing Mechanism of n-Type ZnO/Electrolyte Interfaces

Ever since the discovery of the pH-sensing properties of ZnO crystals, researchers have been exploring their potential in electrochemical applications. The recent expansion and availability of chemical modification methods has made it possible to generate a new class of electrochemically active ZnO nanorods. This reduction in size of ZnO (to a nanocrystalline form) using new growth techniques is essentially an example of the nanotechnology fabrication principle. The availability of these ZnO nanorods opens up an entire new and exciting research direction in the field of electrochemical sensing. This review covers the latest advances and mechanism of pH-sensing using ZnO nanorods, with an emphasis on the nano-interface mechanism. We discuss methods for calculating the effect of surface states on pH-sensing at a ZnO/electrolyte interface. All of these current research topics aim to explain the mechanism of pH-sensing using a ZnO bulk- or nano-scale single crystal. An important goal of these investigations is the translation of these nanotechnology-modified nanorods into potential novel applications

Polarity in ZnO nanowires: A critical issue for piezotronic and piezoelectric devices

The polar and piezoelectric nature of the wurtzite structure of ZnO nanowires with a high aspect ratio at nanoscale dimensions is of high interest for piezotronic and piezoelectric devices, but a number of issues related to polarity are still open and deserve a particular attention. In this context, chemical bath deposition offers a unique opportunity to select the O- or Zn-polarity of the resultant nanowires and is further compatible with the fabrication processes of flexible devices. The control and use of the polarity in ZnO nanowires grown by chemical bath deposition opens a new way to greatly enhance the performance of the related piezotronic and piezoelectric devices. However, polarity as an additional tunable parameter should be considered with care because it has a strong influence on many processes and properties. The present review is intended to report the most important consequences related to the polarity in ZnO nanowires for piezotronic and piezoelectric devices. After introducing the basic principles involving crystal polarity in ZnO, a special emphasis is placed on the effects of polarity on the nucleation and growth mechanisms of ZnO nanowires using chemical bath deposition, defect incorporation and doping, electrical contacts and device properties