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

Large scale simulation of quantum-mechanical molecular dynamics for nano-polycrystalline diamond

Quantum-mechanical molecular-dynamics simulations are carried out to explore possible precursor states of nano-polycrystalline diamond, a novel ultra-hard material produced directly from graphite. Large-scale simulation with 10^5 atoms is realized by using the ' order-N' simulation code 'ELSES' (http://www.elses.jp). The simulation starts with a diamond structure that contains initial structural defects and results in a mixture of graphite(sp^2)-like and diamond(sp^3)-like regions as nano-meter-scale domains. We speculate that the domains are metastable and are possible candidates of the precursor structures.Comment: 4 pages 2 figures. A PDF file in better graphics is available at http://www.elses.jp

Neurohormonal modulation of the Limulus heart: amine actions on neuromuscular transmission and cardiac muscle

The responses of Limulus cardiac neuromuscular junctions and cardiac muscle cells to four endogenous amines were determined in order to identify the cellular targets underlying amine modulation of heartbeat amplitude. The amines increased the amplitude of the Limulus heartbeat, with dopamine (DA) being more potent than octopamine, epinephrine or norepinephrine. The effect of DA on heartbeat amplitude was not blocked by phentolamine. DA enhanced the contractility of deganglionated heart muscle, with time course and dose-dependence similar to its effect on the intact heart. The amines also enhanced neuromuscular transmission, with time course and dose-dependence similar to their effects upon the intact heart. The amplitude of unitary excitatory junction potentials (EJPs) and frequency of miniature excitatory junction potentials (mEJPs) were increased by DA, while mEJP amplitude was unchanged. Thus DA, and probably the other amines, had a presynaptic effect. Combined actions upon cardiac muscle and cardiac neuromuscular transmission account for the ability of these amines to increase the amplitude of the Limulus heartbeat

The eye tracks the aesthetic appeal of sentences

Abstract Eye-tracking parameters (fixation and pupillary responses) have been shown to be modulated by the aesthetic perception and evaluation of visual and auditory artworks (e.g., paintings, music). The present study investigated whether similar effects can be found in visual text processing. Participants read four groups of short sentences in which a key predictor of aesthetic liking, i.e., familiarity, was systematically modified to four degrees. Across all four groups, the sentences moreover varied with regard to featuring or not featuring meter. During reading, pupil sizes and eye movements were recorded. Aesthetic ratings of all sentences were collected afterwards, and the relationships between the ratings, levels of familiarity, meter, and eye-tracking datasets were tested. The results showed that the rating scores were interactively modulated by both familiarity-driven and meter-driven fluency. Using factor analysis, we extracted two key factors of the aesthetic appeal of the texts: an affective and a cognitive factor. The cognitive factor comprised the rating items “succinctness” and “familiarity,” whereas the affective factor reflected the ratings for “beauty” and “liking.” A higher cognitive factor predicted shorter dwelling time. Moreover, the two factors modulated the pupillary data antagonistically: A higher affective factor predicted larger pupil dilations, whereas a higher cognitive factor predicted smaller pupil dilations. The study shows a possible application of the eye-tracking method for capturing aesthetically evaluative dimensions of processing sentences

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

Very early responses to colour stimuli detected in prestriate visual cortex by magnetoencephalography (MEG)

Our previous studies with the visual motion and form systems show that visual stimuli belonging to these categories trigger much earlier latency responses from the visual cortex than previously supposed and that the source of the earliest signals can be located in either the prestriate cortex or in both the striate (V1) and prestriate cortex. This is consistent with the known anatomical connections since, in addition to the classical retino-geniculo-striate cortex input to the prestriate visual areas, there are direct anatomical inputs from both the lateral geniculate nucleus and the pulvinar that reach the prestriate visual cortex without passing through striate cortex. In pursuing our studies, we thought it especially interesting to study another cardinal visual attribute, namely colour, to learn whether colour stimuli also provoke very early responses, at less than 50 ms from visual cortex. To address the question, we asked participants to view stimuli that changed in colour and used magneto-encephalography to detect very early responses (< 50 ms) in the occipital visual cortex. Our results show that coloured stimuli also provoke an early cortical response (M30), with an average peak time at 31.7 ms, thus bringing the colour system into line with the visual motion and form systems. We conclude that colour signals reach visual cortex, including prestriate visual cortex, earlier than previously supposed

Development of simulation package 'ELSES' for extra-large-scale electronic-structure calculation

An early-stage version of simulation package ' ELSES' (Extra-Large-Scale Electronic-Structure calculation) is developed for electronic structure and dynamics of large systems, particularly, nm-scale or 10nm-scale systems (www.elses.jp). Input and output files are written in the Extensible Markup Language (XML) style for general users. Related pre-/post-simulation tools are also available. Practical work flow and example are described. A test calculation of GaAs bulk system is shown to demonstrate that the present code can handle systems with more than one atom species. Several future aspects are also discussed.Comment: 7 Pages, 4 figures. A PDF file in better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses/index_e.htm