Accuracy control in ultra-large-scale electronic structure calculation

Numerical aspects are investigated in ultra-large-scale electronic structure calculation. Accuracy control methods in process (molecular-dynamics) calculation are focused. Flexible control methods are proposed so as to control variational freedoms, automatically at each time step, within the framework of generalized Wannier state theory. The method is demonstrated in silicon cleavage simulation with 10^2-10^5 atoms. The idea is of general importance among process calculations and is also used in Krylov subspace theory, another large-scale-calculation theory.Comment: 8 pages, 3 figures. To appear in J.Phys. Condens. Matter. A preprint PDF file in better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses/index_e.htm

Million-atom molecular dynamics simulation by order-N electronic structure theory and parallel computation

Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for silicon nanocrystals of more than millions atoms with the transferable tight-binding Hamiltonian. The efficiency of parallelism is perfect, 98.8 %, and the method is the most suitable to parallel computation. The elapse time for a system of $2\times 10^6$ atoms is 3.0 minutes by a computer system of 64 processors of SGI Origin 3800. The calculated results are in good agreement with the results of the exact diagonalization, with an error of 2 % for the lattice constant and errors less than 10 % for elastic constants.Comment: 5 pages, 3 figure

Large-scale electronic structure theory for simulating nanostructure process

Fundamental theories and practical methods for large-scale electronic structure calculations are given, in which the computational cost is proportional to the system size. Accuracy controlling methods for microscopic freedoms are focused on two practical solver methods, Krylov-subspace method and generalized-Wannier-state method. A general theory called the 'multi-solver' scheme is also formulated, as a hybrid between different solver methods. Practical examples are carried out in several insulating and metallic systems with 10^3-10^5 atoms. All the theories provide general guiding principles of constructing an optimal calculation for simulating nanostructure processes, since a nanostructured system consists of several competitive regions, such as bulk and surface regions, and the simulation is designed to reproduce the competition with an optimal computational cost.Comment: 19 pages, 6 figures. To appear in J. Phys. Cond. Matt. A preprint PDF file in better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses/index_e.htm

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

Linear Algebraic Calculation of Green's function for Large-Scale Electronic Structure Theory

A linear algebraic method named the shifted conjugate-orthogonal-conjugate-gradient method is introduced for large-scale electronic structure calculation. The method gives an iterative solver algorithm of the Green's function and the density matrix without calculating eigenstates.The problem is reduced to independent linear equations at many energy points and the calculation is actually carried out only for a single energy point. The method is robust against the round-off error and the calculation can reach the machine accuracy. With the observation of residual vectors, the accuracy can be controlled, microscopically, independently for each element of the Green's function, and dynamically, at each step in dynamical simulations. The method is applied to both semiconductor and metal.Comment: 10 pages, 9 figures. To appear in Phys. Rev. B. A PDF file with better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses

Nemo: a computational tool for analyzing nematode locomotion

The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.Comment: 12 pages, 2 figures. accepted by BMC Neuroscience 2007, 8:8

Resolving the Hard X-ray Emission of GX 5-1 with INTEGRAL

We present the study of one year of INTEGRAL data on the neutron star low mass X-ray binary GX 5-1. Thanks to the excellent angular resolution and sensitivity of INTEGRAL, we are able to obtain a high quality spectrum of GX 5-1 from ~5 keV to ~100 keV, for the first time without contamination from the nearby black hole candidate GRS 1758-258 above 20 keV. During our observations, GX 5-1 is mostly found in the horizontal and normal branch of its hardness intensity diagram. A clear hard X-ray emission is observed above ~30 keV which exceeds the exponential cut-off spectrum expected from lower energies. This spectral flattening may have the same origin of the hard components observed in other Z sources as it shares the property of being characteristic to the horizontal branch. The hard excess is explained by introducing Compton up-scattering of soft photons from the neutron star surface due to a thin hot plasma expected in the boundary layer. The spectral changes of GX 5-1 downward along the "Z" pattern in the hardness intensity diagram can be well described in terms of monotonical decrease of the neutron star surface temperature. This may be a consequence of the gradual expansion of the boundary layer as the mass accretion rate increases.Comment: 10 pages, 17 figures, accepted for publication in A&

Cerebral blood flow and behavioural effects of caffeine in habitual and non-habitual consumers of caffeine: A near infrared spectroscopy study

Caffeine has been shown to modulate cerebral blood flow, with little evidence of tolerance to these effects following habitual use. However, previous studies have focused on caffeine levels much higher than those found in dietary servings and have compared high caffeine consumers with low consumers rather than 'non-consumers'. The current placebo-controlled double-blind, balanced-crossover study employed near infrared spectroscopy to monitor pre-frontal cerebral-haemodynamics at rest and during completion of tasks that activate the pre-frontal cortex. Twenty healthy young habitual and non-habitual consumers of caffeine received 75mg caffeine or placebo. Caffeine significantly decreased cerebral blood flow but this was subject to a significant interaction with consumption status, with no significant effect being shown in habitual consumers and an exaggerated effect in non-habitual consumers. These findings suggest that caffeine, at levels typically found in a single dietary serving, is able to modulate cerebral blood flow but these effects are subject to tolerance

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes

A vertical diatomic artificial molecule in the intermediate coupling regime in a parallel and perpendicular magnetic field

We present experimental results for the ground state electrochemical potentials of a few electron semiconductor artificial molecule made by vertically coupling two quantum dots, in the intermediate coupling regime, in perpendicular and parallel magnetic fields up to 5 T. We perform a quantitative analysis based on local-spin density functional theory. The agreement between theoretical and experimental results is good, and the phase transitions are well reproduced.Comment: Typeset using Revtex, 13 pages and 8 Postscript figure