Krylov Subspace Method for Molecular Dynamics Simulation based on Large-Scale Electronic Structure Theory

For large scale electronic structure calculation, the Krylov subspace method is introduced to calculate the one-body density matrix instead of the eigenstates of given Hamiltonian. This method provides an efficient way to extract the essential character of the Hamiltonian within a limited number of basis set. Its validation is confirmed by the convergence property of the density matrix within the subspace. The following quantities are calculated; energy, force, density of states, and energy spectrum. Molecular dynamics simulation of Si(001) surface reconstruction is examined as an example, and the results reproduce the mechanism of asymmetric surface dimer.Comment: 7 pages, 3 figures; corrected typos; to be published in Journal of the Phys. Soc. of Japa

Dynamical brittle fractures of nanocrystalline silicon using large-scale electronic structure calculations

A hybrid scheme between large-scale electronic structure calculations is developed and applied to nanocrystalline silicon with more than 10$^5$ atoms. Dynamical fracture processes are simulated under external loads in the [001] direction. We shows that the fracture propagates anisotropically on the (001) plane and reconstructed surfaces appear with asymmetric dimers. Step structures are formed in larger systems, which is understood as the beginning of a crossover between nanoscale and macroscale samples.Comment: 10 pages, 4 figure

A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys

Defining cellular and molecular identities within the kidney is necessary to understand its organization and function in health and disease. Here we demonstrate a reproducible method with minimal artifacts for single-nucleus Droplet-based RNA sequencing (snDrop-Seq) that we use to resolve thirty distinct cell populations in human adult kidney. We define molecular transition states along more than ten nephron segments spanning two major kidney regions. We further delineate cell type-specific expression of genes associated with chronic kidney disease, diabetes and hypertension, providing insight into possible targeted therapies. This includes expression of a hypertension-associated mechano-sensory ion channel in mesangial cells, and identification of proximal tubule cell populations defined by pathogenic expression signatures. Our fully optimized, quality-controlled transcriptomic profiling pipeline constitutes a tool for the generation of healthy and diseased molecular atlases applicable to clinical samples

ASCA Observations of Soft X-Ray Transients in Quiescence: X1608-52 and Cen X-4

We observed soft X-ray transients, X1608-52 and Cen X-4, in quiescence with ASCA at X-ray luminosities on the order of 10^(32- 33) erg s^(-1).The energy spectra were rather soft for both sources. Blackbody fits to the data required characteristic temperatures of 0.2-0.3 keV and emission regions of ~10 km^2. A conspicuous hard tail remained after fitting Cen X-4 with a blackbody curve. An extremely soft spectrum in quiescence seems to be a common property of soft X-ray transients

Timesaving Double-Grid Method for Real-Space Electronic-Structure Calculations

We present a simple and efficient technique in ab initio electronic-structure calculation utilizing real-space double-grid with a high density of grid points in the vicinity of nuclei. This technique promises to greatly reduce the overhead for performing the integrals that involves non-local parts of pseudopotentials, with keeping a high degree of accuracy. Our procedure gives rise to no Pulay forces, unlike other real-space methods using adaptive coordinates. Moreover, we demonstrate the potential power of the method by calculating several properties of atoms and molecules.Comment: 4 pages, 5 figure

Elaboration and characterization of Fe1–xO thin films sputter deposited from magnetite target

Majority of the authors report elaboration of iron oxide thin films by reactive magnetron sputtering from an iron target with Ar–O2 gas mixture. Instead of using the reactive sputtering of a metallic target we report here the preparation of Fe1–xOthin films, directly sputtered froma magnetite target in a pure argon gas flow with a bias power applied. This oxide is generally obtained at very low partial oxygen pressure and high temperature.We showed that bias sputtering which can be controlled very easily can lead to reducing conditions during deposition of oxide thin film on simple glass substrates. The proportion of wustite was directly adjusted bymodifying the power of the substrate polarization. Atomic force microscopy was used to observe these nanostructured layers. Mössbauer measurements and electrical properties versus bias polarization and annealing temperature are also reported

Why Canonical Disks Cannot Produce Advection Dominated Flows

Using simple arguments we show that the canonical thin keplerian accretion disks cannot smoothly match any plain advection dominated flow (ADAF) model. By 'plain' ADAF model we mean the ones with zero cooling. The existence of sonic points in exact solutions is critical and imposes constraints that cannot be surpassed adopting 'reasonable' physical conditions at the hypothetical match point. Only the occurrence of new critical physical phenomena may produce a transition. We propose that exact advection models are a class of solutions which don't necessarily involve the standard thin cool disks and suggest a different scenario in which good ADAF solutions could eventually occur.Comment: 12 pages, 2 figures, Accepted for publication in Ap.J. Letter

One-way multigrid method in electronic structure calculations

We propose a simple and efficient one-way multigrid method for self-consistent electronic structure calculations based on iterative diagonalization. Total energy calculations are performed on several different levels of grids starting from the coarsest grid, with wave functions transferred to each finer level. The only changes compared to a single grid calculation are interpolation and orthonormalization steps outside the original total energy calculation and required only for transferring between grids. This feature results in a minimal amount of code change, and enables us to employ a sophisticated interpolation method and noninteger ratio of grid spacings. Calculations employing a preconditioned conjugate gradient method are presented for two examples, a quantum dot and a charged molecular system. Use of three grid levels with grid spacings 2h, 1.5h, and h decreases the computer time by about a factor of 5 compared to single level calculations.Comment: 10 pages, 2 figures, to appear in Phys. Rev. B, Rapid Communication