Table of contents

Welcome to CCP2012, held next to the K computer site in Kobe and in Japan's best season. The Conference on Computational Physics (CCP) is organized annually under the auspices of Commission 20 of the IUPAP (International Union of Pure and Applied Physics).

This is the first time it has been held in Japan. I was asked to be the chairman about two and half years ago and when I accepted the request I decided to make the conference very unique and different from the traditional style of CCP. I was not satisfied when I attended big conferences where the parallel sessions are classified with the name of the research field. These days we have many opportunities to attend domestic and international conferences, where it is possible to listen to many talks on the same topics. If the topics are very new, then the conference is very useful for my research. However, I wanted to have a conference where I could listen to a variety of topics carried out with the same method.

Computational science is very unique and it is easy to organize a new type of conference with the classification in the horizontal direction of the matrix made of the names of research fields and the name of numerical methods. You may be able to list the names of methods easily; finite difference, Monte Carlo, particle, molecular dynamics and so on. I was dissatisfied to find that most conferences focus solely on research fields and the method that brings to the scientific research is not highlighted as much. I wanted to listen to topics from fundamental physics to industrial science in a systematic way.

In order to create such a conference, a small number of experts is not enough, so I asked for the help of more than 100 Japanese computer scientists, in a variety of fields.

We called this group the Japan Advisory Board (JAB). I asked them to recommend a member of the International Advisory Board (IAB). Then, we could start making the list of plenary and invited speakers. This was almost the end of March last year.

CCP2012 is organized also to celebrate the shared use of the K computer and we selected a venue next to it. Its use is of course open to the public and started on 28 September, one month earlier than had been scheduled. I hope you also enjoy the guided tour of the K computer.

Throughout CCP2012, I hope new collaborations start among scientists in different fields. It would be also my great pleasure if such an inter-disciplinary conference encouraged young scientists (with their fresh energy and skills) to challenge new topics in different fields, particularly emerging ones like bio-computing, industrial applications, social sciences and so on.

Finally, allow me to express my sincere thanks to all members of the local organizing committee (LOC). Twenty scientists from three universities and one institute voluntarily worked very hard to prepare CCP2012.

Hideaki Takabe (Aki)The Chairman, CCP2012

The PDF contains the speech of journalist Atsuko Tsuji (Asahi Shimbun) with the title 'Requests and expectations for computational science' and the record of the following discussion on: 'Will computational science be able to provide answers to important problems of human society?'

The PDF contains a summary of the organization of the conference.

All papers published in this volume of Journal of Physics: Conference Series have been peer reviewed through processes administered by the proceedings Editors. Reviews were conducted by expert referees to the professional and scientific standards expected of a proceedings journal published by IOP Publishing.

Broadband emission from relativistic outflows (jets) of active galactic nuclei (AGN) and gamma-ray bursts (GRBs) contains valuable information about the nature of the jet itself and about the central engine which launches it. Using special relativistic hydrodynamics and magnetohydrodynamics simulations we study the dynamics of the jet and its interaction with the surrounding medium. The observational signature of the simulated jets is computed using a radiative transfer code developed specifically for the purpose of computing multi-wavelength, time-dependent, non-thermal emission from astrophysical plasmas. We present results of a series of long-term projects devoted to understanding the dynamics and emission of jets in parsec-scale AGN jets, blazars and the afterglow phase of the GRBs.

Brown recently introduced a covariant formulation of the BSSN equations which is well suited for curvilinear coordinate systems. This is particularly desirable as many astrophysical phenomena are symmetric with respect to the rotation axis or are such that curvilinear coordinates adapt better to their geometry. We show results from a newly developed numerical code solving the BSSN equations in spherical symmetry and the general relativistic hydrodynamic equations written in flux-conservative form. A key feature of the code is that uses a second-order partially implicit Runge-Kutta method to integrate the evolution equations, and does not need a regularization algorithm at the origin. We discuss a number of tests to assess the accuracy, numerical stability and expected convergence of the code.

In this paper, a symmetry-preserving remapping algorithm for vectors respecting their local bounds by components and in magnitude is presented. First, description of the Vector Image Polygon (VIP) limiter for a piece-wise linear velocity reconstruction is presented. Numerical fluxes obtained from this reconstruction lead to symmetry- and bounds- preserving remap of momentum for staggered Arbitrary Lagrangian-Eulerian (ALE) hydrodynamical methods. A novel bounds definition for vectors and corresponding modification of the VIP limiter is introduced, which fixes undershoots in a radial velocity component for polar meshes. Comparison with standard scalar-based limiters is given. Cyclic remapping is performed to numerically verify properties of the methods.

Using a fluid-orbit coupling simulator, we numerically solve the three-dimensional Navier-Stokes equations with exchanging information of six-degree-of-freedom reactions for predicting impulsive flight motions of a laser propulsion vehicle driven by blast waves. By feedback of angular and translational velocities into the flowfield, pressure and viscous drags induced by the unsteady vehicle motion are introduced to provide precise motion analysis. In the impulsive-motion estimation of the laser-boosted vehicle, restoring forces and moments are underestimated if the vehicle motion effect is modeled using aerodynamic coefficients of steady flow. Also, a simple model using impulse data examined by experiments for predicting the impulsive motion is compared with our coupling approach which can reproduce instantaneous acceleration resulting from the interaction between the vehicle and the blast wave. Velocity overshoot is generated by evaluating sharp thrust through the coupling calculation, and the flight height becomes 6% larger than conventional prediction using the impulse data.

Space plasma is a collisionless, multi-scale, and highly nonlinear medium. There are various types of self-consistent computer simulations that treat space plasma according to various approximations. We develop numerical schemes for solving the Vlasov (collisionless Boltzmann) equation, which is the first-principle kinetic equation for collisionless plasma. The weak-scaling benchmark test shows that our parallel Vlasov code achieves a high performance and a high scalability. Currently, we use more than 1000 cores for parallel computations and apply the present parallel Vlasov code to various cross-scale processes in space plasma, such as a global simulation on the interaction between solar/stellar wind and magnetospheres of astronomical objects.

We present a numerical model based on finite differences to solve the problem of chemical impurity migration within a multilayer spherical system. Migration here means diffusion of chemical species in conditions of concentration partitioning at layer interfaces due to different solubilities of the migrant in different layers. We detail here the numerical model and discuss the results of its implementation. To validate the method we compare it with cases where an analytic solution exists. We also present an application of our model to a practical problem in which we compute the migration of caprolactam from the packaging multilayer foil into the food.

The effects of polymer additives on the behavior of the kinetic energy spectrum in isotropic decaying turbulence were numerically investigated by hybrid Eulerian-Lagrangian simulations making full use of large-scale parallel computation. The kinetic energy spectrum was found to obey the power-law E(k) ~ k^−α in the range below the Kolmogorov length l_K when the turbulence decayed. The exponent α satisfied 4 < α < 5 and decreased with the increase in the Weissenberg number W_i. The value of α obtained by the largest W_i run was close to the values obtained in previous experimental and numerical studies on elastic turbulence, which is characterized by a larger W_i and a Reynolds number of less than unity. The relationship between the results of the present study and the results obtained for elastic turbulence is also discussed.

We conducted a comparative study among the Bi-CG family with incomplete LU factorization employed for solving diffusion-type radiative transfer equation in radiation hydrodynamics (RHD) simulations for laser-produced plasmas. The result suggests that Bi-CGSTAB is the most suitable method thanks to its high convergence stability and low computational cost. RHD simulations were performed for Rayleigh–Taylor instability experiments of an inertial confinement fusion target. We found that higher harmonics of static pressure perturbation become important at an intermediate wavelength.

Expansion dynamics of plume after irradiation of the target material is essential to prepare nanoparticles by pulsed laser ablation and it can be modified by collision of two plumes. In the present paper, effect of head-on collision on the expansion dynamics is discussed by numerical simulation based on the fluid dynamics and compared with the experimental results of plume emission. Suppression of plumes by collision with counter plume observed by experiment is reproduced by numerical simulation. Results of the numerical calculation indicate that shockwave induced by the irradiation of the opposite target suppress vapor expansion. The vapors do not mix around the center of the targets when the two targets are irradiated simultaneously and unstable flow is seen when delay between laser pulses was applied for irradiation of two targets. The results of the numerical simulation suggest that formation of combined and alloy nanoparticles are expected for former and latter cases.

Seismic waves radiated from an earthquake propagate in the Earth and the ground shaking is felt and recorded at (or near) the ground surface. Understanding the wave propagation with respect to the Earth's structure and the earthquake mechanisms is one of the main objectives of seismology, and predicting the strong ground shaking for moderate and large earthquakes is essential for quantitative seismic hazard assessment. The finite difference scheme for solving the wave propagation problem in elastic (sometimes anelastic) media has been more widely used since the 1970s than any other numerical methods, because of its simple formulation and implementation, and its easy scalability to large computations. This paper briefly overviews the advances in finite difference simulations, focusing particularly on earthquake mechanics and the resultant wave radiation in the near field. As the finite difference formulation is simple (interpolation is smooth), an easy coupling with other approaches is one of its advantages. A coupling with a boundary integral equation method (BIEM) allows us to simulate complex earthquake source processes.

A finite difference time domain method based on regular Yee's algorithm in an orthogonal coordinate system is utilized to calculate the band structure of a two-dimensional square-lattice photonic crystal comprising dielectric cylinders in air background and to simulate the image formation of mentioned structure incorporating the perfectly matched layer boundary condition. By analyzing the photonic band diagram of this system, we find that the frequency region of effective negative refraction exists in the second band in near-infrared domain. In this case, electromagnetic wave propagates with a negative phase velocity and the evanescent waves can be supported to perform higher image resolution.

Large-scale faint structure detected by the recent observations in the halo of the Andromeda galaxy (M31) provides an attractive window to explore the structure of outer cold dark matter (CDM) halo in M31. Using an N-body simulation of the interaction between an accreting satellite galaxy and M31, we investigate the mass-density profile of the CDM halo. We find the sufficient condition of the outer density profile of CDM halo in M31 to reproduce the Andromeda giant stream and the shells at the east and west sides of M31. The result indicates that the density profile of the outer dark matter halo of M31 is a steeper than the prediction of the theory of the structure formation based on the CDM model.

In the hierarchical structure formation scenario, galaxies have experienced many mergers with less massive galaxies and have grown larger and larger. On the other hand, the observations indicate that almost all galaxies have a central massive black hole (MBH) whose mass is ~ 10⁻³ of its spheroidal component. Consequently, MBHs of satellite galaxies are expected to be moving in the halo of their host galaxy after a galaxy collision, although we have not found such MBHs yet. We investigate the current-plausible position of an MBH of the infalling galaxy in the halo of the Andromeda galaxy (M31). Many substructures are found in the M31 halo, and some of them are shown to be remnants of a minor merger about 1 Gyr ago based on theoretical studies using N-body simulations. We calculate possible orbits of the MBH within the progenitor dwarf galaxy using N-body simulations. Our results show that the MBH is within the halo, about 30 kpc away from the center of M31.

In addition, further simulations are necessary to restrict the area in which the MBH exists, and hence to determine the observational field for the future observational detection. The most uncertainty of the current MBH position is caused by uncertainty about the infalling orbit of the progenitor dwarf galaxy. Therefore, we have performed a large (a few 10⁴ realizations) set of parameter study to constrain the orbit in the six-dimensional phase space. For such purpose, we have already investigated in detail a few ten thousand orbit models using HA-PACS, a recently installed GPU cluster in University of Tsukuba.

The discrepancy in the mass-density profile of dark matter halos between simulations and observations, the core-cusp problem, is a long-standing open question in the standard paradigm of cold dark matter cosmology. Here, we study the dynamical response of dark matter halos to oscillations of the galactic potential which are induced by a cycle of gas expansion and contraction in galaxies driven by supernova feedback. We developed a fast tree-code for PC clusters with GPU which displays high performance and high scalability. We perform large scale N-body simulations to follow the dynamical evolution of dark matter halos under the effect of oscillating gravitational potential. Furthermore, we compare the results of simulations with an analytical model of the resonance between particles and density waves to understand the physical mechanism of the cusp-core transition.

In this paper we address the problem of identifying and exploiting techniques that optimize the performance of large scale scientific codes on many-core processors. We consider as a test-bed a state-of-the-art Lattice Boltzmann (LB) model, that accurately reproduces the thermo-hydrodynamics of a 2D-fluid obeying the equations of state of a perfect gas. The regular structure of Lattice Boltzmann algorithms makes it relatively easy to identify a large degree of available parallelism; the challenge is that of mapping this parallelism onto processors whose architecture is becoming more and more complex, both in terms of an increasing number of independent cores and – within each core – of vector instructions on longer and longer data words. We take as an example the Intel Sandy Bridge micro-architecture, that supports AVX instructions operating on 256-bit vectors; we address the problem of efficiently implementing the key computational kernels of LB codes – streaming and collision – on this family of processors; we introduce several successive optimization steps and quantitatively assess the impact of each of them on performance. Our final result is a production-ready code already in use for large scale simulations of the Rayleigh-Taylor instability. We analyze both raw performance and scaling figures, and compare with GPU-based implementations of similar codes.

A new simulation scheme has been developed to investigate high-energy plasma phenomena including pair production and Bremsstrahlung in a high-Z nuclear field. The simulation scheme consists of (1) a Particle-in-Cell scheme for relativistic plasma dynamics, (2) a conservative semi-Lagrangian scheme for hard photon transport and (3) a Monte-Carlo scheme for the considered QED reactions. The developed scheme is applied to a test simulation relevant to recent experiments of positron production from a thin gold target irradiated by a high intensity laser. The simulation results successfully show a basic process leading to the positron ejection from the target. The process involves electron acceleration due to laser-plasma interaction at the target front, hard photon emission and pair production inside the target, and electrostatic positron acceleration at the target rear side.

By performing full Particle-In-Cell simulations, we examined the transient response of electrons released for the charge neutralization of a local ion beam emitted from an ion engine which is one of the electric propulsion systems. In the vicinity of the engine, the mixing process of electrons in the ion beam region is not so obvious because of large difference of dynamics between electrons and ions. A heavy ion beam emitted from a spacecraft propagates away from the engine and forms a positive potential region with respect to the background. Meanwhile electrons emitted for a neutralizer located near the ion engine are electrically attracted or accelerated to the core of the ion beam. Some electrons with the energy lower than the ion beam potential are trapped in the beam region and move along with the ion beam propagation with a multi-streaming structure in the beam potential region. Since the locations of the neutralizer and the ion beam exit are different, the above-mentioned bouncing motion of electrons is also observed in the direction of the beam diameter.

Massively parallel computations (MP-CAFEE) ware developed to calculate absolute binding free energies of small molecules bound to a protein by all-atom molecular dynamics. It uses the nonequilibrium work measurement and Bennett acceptance ratio methods to calculate the free energy difference between the bound and unbound states. The FUJI force field was developed in order to assign force field parameters to arbitrary organic molecules in a unified manner including proteins and nucleic acids. Its dihedral parameters agree with the torsion energy profiles calculated by high-level ab initio molecular orbital theory for the model systems of protein backbone. Comparing with various force fields it agrees well with recent observations by vibrational spectroscopy on Ramachandran angle's population of alanine dipeptide in water. MP-CAFEE with FUJI force field has an efficient parallel algorithm and enough accuracy for computer aided drug design.

The procedures of performing first-principles electronic structure calculation using the Korringa-Kohn-Rostoker (KKR) and the screened KKR methods are reviewed with an emphasis put on their numerical efficiency. It is shown that an iterative matrix inversion combined with a suitable preconditioning greatly improves the computational time of screened KKR method. The method is well parallelized and also has an O(N) scaling property.

The transcorrelated (TC) method is one of the wave-function-based methods used for first-principles electronic structure calculations, and in terms of the computational cost is applicable to solid-state calculation. In this method, a many-body wave function of electrons is approximated as a product of the Jastrow factor and the Slater determinant, and the first-principles Hamiltonian is similarity-transformed by the Jastrow factor. The Schrödinger equation is rewritten as an eigenvalue problem for this similarity-transformed Hamiltonian, from which one obtains a self-consistent field (SCF) equation for optimizing one-electron orbitals in the Slater determinant at low computational cost. In contrast, optimization of the Jastrow factor is computationally much more expensive and has not been performed for solid-state calculation of the TC method before. In this study, we develop a new method for optimizing the Jastrow factor at a reasonable computational cost using the random-phase approximation (RPA) and pseudo-variance minimization. We apply this method to some simple solids, and find that the band gap of a wide-band-gap insulator is much improved by RPA.

High-temperature cuprate superconductors have been known to exhibit significant pressure effects. In order to fathom the origin of why and how T_c is affected by pressure, we have recently studied the pressure effects on T_c adopting a model that contains two copper d-orbitals derived from first-principles band calculations, where the d_z² orbital is considered on top of the usually considered d_x²-y² orbital. In that paper, we have identified two origins for the T_c enhancement under hydrostatic pressure: (i) while at ambient pressure the smaller the hybridization of other orbital components the higher the T_c, an application of pressure acts to reduce the multiorbital mixing on the Fermi surface, which we call the orbital distillation effect, and (ii) the increase of the band width with pressure also contributes to the enhancement. In the present paper, we further elaborate the two points. As for point (i), while the reduction of the apical oxygen height under pressure tends to increase the d_z² mixture, hence to lower T_c, here we show that this effect is strongly reduced in bi-layer materials due to the pyramidal coordination of oxygen atoms. As for point (ii), we show that the enhancement of T_c due to the increase in the band width is caused by the effect that the many-body renormalization arising from the self-energy is reduced.

The dissociation reaction of ethylene molecules on the Ni cluster surface is investigated by ab initio molecular dynamics simulations. We observe that hydrogen atoms are generated from ethylene molecules at a rate of about 20 ps⁻¹. The activation energy for the dissociation of a hydrogen atom is estimated to be about 0.52 eV, which corresponds to a rate of only about 0.1 ps⁻¹. We find that the adsorption energy of an ethylene molecule on the Ni cluster is more than 1.5 eV, which is three times greater than the activation energy for the hydrogen dissociation. It is, therefore, suggested that the adsorption energy is responsible for the increase of the rate of the dissociation reaction. Based on these results, we discuss the microscopic process of the reaction of ethylene molecules on the Ni cluster in detail.

In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett.482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.

The shape transition of micelles in an amphiphilic solution is studied by a molecular dynamics simulation of coarse-grained rigid amphiphilic molecules with explicit solvent molecules. Our simulations show that the micellar shape changes from a disc into a cylinder, and then into a sphere as the hydrophilic interaction increases. We find that the potential energy decreases monotonically even during the micellar shape transition as the hydrophilic interaction increases. In contrast, it is ascertained that there exists a wide coexistence region in the intensity of the hydrophilic interaction between a cylinder and a sphere.

The network structures fluctuating in space and time are studied in glass-forming liquids of silica (SiO₂) and silicate (Mg₂SiO₄), by carrying out molecular dynamics (MD) simulations and then applying the graph theoretical algorithm of a "pebble game". The pebble game algorithm was developed in Thorpe and coworkers' studies on the percolation of rigidity to form amorphous solids and, although its exactness is proved only in two dimensions, it has been demonstrated to apply to three-dimensional networks. In liquid silica and silicates, the network connections are extended with amounts of network-forming Si, O atoms, and infinitely-percolating clusters emerge over an extensive range of compositions. The search along a network for free "pebbles", attached virtually to the constituent atoms to represent their degrees of freedom of motions, shows that one infinitely-percolating cluster contains some rigid clusters. These rigid clusters in liquid states fluctuate in space and time because of the alteration of connections at high temperatures, in contrast to those solidified below glass transition temperatures, and these fluctuations are responsible for the slow structural relaxations. The pebble game analyses thus give insights into the internal structures in infinitely-spanning networks, beyond surveys by the conventional theory of percolation, and reveal the behaviors of rigid clusters playing the dominant role in the slow structural relaxations in glass-forming liquids. We discuss these results especially by taking focus on varieties in network structures, such as the composition-dependent degrees of connectivity and structural transformation under high pressures.

We perform isothermal Brownian-type molecular dynamics simulations with the Gupta potential for bimetallic cluster Ag₁₇Cu₂ from T=0 to 1500K, across the temperature range associated with the melting behaviour determined by the specific heat of the cluster. We also use the instantaneous normal mode (INM) analysis to dissect dynamics of the cluster. In terms of the projected density of states of the vibrational INMs, we propose a new order parameter that specifically describes the melting behaviour of the cluster. The calculated result of our order parameter is consistent with the information inferred from the specific heat data.

We describe molecular dynamics particle simulations with particles that have internal structure and/or undergo reactions. These calculations give an atomic-scale description of hot plasma based on well-established microphysics and test kinetic theories used to calculate energy exchange and transport in plasma hydrodynamic simulations. The computer experiments can be given detailed diagnostics, without the usual limits of resolution of Laboratory equipment. Typical applications are non-equilibrium atomic kinetics for emission or absorption of X-ray laser radiation by solid targets and/or atomic-scale simulation of hot plasma with fusion reactions, as in inertial fusion ignition experiments.

CAMDAS is a conformational search program, through which high temperature molecular dynamics (MD) calculations are carried out. In this study, the conformational search ability of CAMDAS was evaluated using structurally known 281 protein-ligand complexes as a test set. For the test, the influences of initial settings and initial conformations on search results were validated. By using the CAMDAS program, reasonable conformations whose root mean square deviations (RMSDs) in comparison with crystal structures were less than 2.0 Å could be obtained from 96% of the test set even though the worst initial settings were used. The success rate was comparable to those of OMEGA, and the errors of CAMDAS were less than those of OMEGA. Based on the results obtained using CAMDAS, the worst RMSD was around 2.5 Å, although the worst value obtained was around 4.0 Å using OMEGA. The results indicated that CAMDAS is a robust and versatile conformational search method and that it can be used for a wide variety of small molecules. In addition, the accuracy of a conformational search in relation to this study was improved by longer MD calculations and multiple MD simulations.

Photoexcited dynamics of electrons and holes in semiconductor quantum dots (QD), including phonon-induced relaxation, multiple exciton generation, and recombination (MEG and MER), were simulated by combining ab initio time-dependent density functional theory and non-adiabatic (NA) molecular dynamics. These nonequilibrium phenomena govern the optical properties and photoexcited dynamics of QDs, determining the branching between electronic processes and thermal energy losses. Our approach accounts for QD size and shape as well as defects, core-shell distribution, surface ligands and charge trapping, which significantly influence the properties of photoexcited QDs. The method creates an explicit time-domain representation of photoinduced processes and describes various kinetic regimes owing to the non-perturbative treatment of NA couplings in the quantum dynamics. QDs of different sizes and materials, with and without ligands, are considered. The simulations provide direct evidence that the high-frequency ligand modes on the QD surface play a pivotal role in the electron-phonon relaxation, MEG, and MER. The insights reported here suggest novel routes for controlling the photoinduced processes in semiconductor QDs and lead to new design principles for increasing efficiencies of photovoltaic devices.

In the present paper, a numerical method for a semi-classical instanton method was examined. We implemented the instanton approach using discretized path integrals. The computational accuracy of the method is controlled by the following two parameters: the imaginary time duration (τ) and the time increment (Δτ), which represents the discretized path integral. To obtain accurate results, a long τ must be used in combination with a short Δτ; however, because the computational cost is virtually proportional to τ/Δτ, the instanton calculations were computationally expensive under these conditions. In the present study, we propose a method that reduces the computational cost and represents long τ instanton trajectories by employing an extended instanton trajectory from calculations based on a short τ. We applied the method to calculate tunnel splitting in a HO₂ hydrogen transfer reaction using the double many-body extension IV potential as a validation.

The hard-disk problem, the statics and the dynamics of equal two-dimensional hard spheres in a periodic box, has had a profound influence on statistical and computational physics. Markov-chain Monte Carlo and molecular dynamics were first discussed for this model. Here we reformulate hard-disk Monte Carlo algorithms in terms of another classic problem, namely the sampling from a polytope. Local Markov-chain Monte Carlo, as proposed by Metropolis et al. in 1953, appears as a sequence of random walks in high-dimensional polytopes, while the moves of the more powerful event-chain algorithm correspond to molecular dynamics evolution. We determine the convergence properties of Monte Carlo methods in a special invariant polytope associated with hard-disk configurations, and the implications for convergence of hard-disk sampling. Finally, we discuss parallelization strategies for event-chain Monte Carlo and present results for a multicore implementation.

Stimulated by the recent interest in graphene, the elastic behavior of crystalline membranes continues to be under debate. In their flat phase, one observes scaling of the correlation functions of in-plane and out-of-plane deformations u(x) and f(x) at long wavelengths with respect to a given reference plane governed by a single universal exponent η. The purpose of the present article is to explain the ideas and techniques underlying our Fourier Monte Carlo simulation approach to the numerical determination of η in much greater detail than was possible in a recent letter that is currently under review. Our simulations are based on an effective Hamiltonian first derived by Nelson and Peliti formulated exclusively in terms of the Fourier amplitudes (q) of the field f(x), and we calculate the out-of-plane correlation function ⟨|(q)|²⟩ = (q) and their related mean squared displacement ⟨(Δf)²⟩. The key to the progress reported in this work is the observation that on tuning the Monte Carlo acceptance rates separately for each wave vector, we are able to eliminate critical slowing down and thus achieve unprecedented statistical accuracy. A finite size scaling analysis for ⟨(Δf)²⟩ gives η = 0.795(10). In the alternative approach, where we study the scaling of (q), we observe an unexpected anisotropic finite size effect at small wave vectors which hampers a similarly accurate numerical analysis.

The Rayleigh hypothesis is the assumption that the field in the region above (below) a rough surface can be expressed as a weighted sum of upwards (downwards) propagating scattered (transmitted) modes, and that these expressions can be used to satisfy the boundary conditions on the fields at the surface. This hypothesis is expected to be valid for surfaces of sufficiently small slopes. For one-dimensional sinusoidal surfaces, the region of validity is known analytically, while for randomly rough surfaces in one and two dimensions, the limits of validity of the Rayleigh hypothesis are not known. In this paper, we perform a numerical study of the validity of the Rayleigh hypothesis for two-dimensionally rough metal and perfectly conducting surfaces by considering the conservation of energy. It is found for a perfect electric conductor that the region of validity is defined by the ratio of the root-mean-square roughness, δ, over the correlation length, α, being less than about 0.2, while for silver we find δ/α ≲ 0.08 for an incident wavelength λ = 457.9 nm. Limitations in our simulations made us unable to check the Rayleigh hypothesis for roughness where δ ≳ 0.13λ.

An intrinsically disordered protein is one that does not spontaneously fold in physiological conditions but only folds when it binds to a target protein. Computer simulation of this coupled folding and binding is one of the central subjects of computational biophysics. Computing the free energy landscape is helpful in understanding coupled folding and binding. For this reason, we developed an Ising-like protein model and a multicanonical simulation in an energy-entropy space. The calculated free energy landscape indicates that coupled folding and binding induces rapid structural switching of the bound target protein.

In this paper, we investigate the stochastic properties and fractal behavior of Si and porous silicon (PS) rough surfaces to characterize the complexity of their morphology. To this end, height fluctuations of these rough surfaces are determined by Atomic Force Microscopy (AFM) and then roughness and correlation length of the surfaces are calculated. The generalized Hurst exponent, h(q) and singularity spectrum, f(α) are obtained by using two dimensional MF-DFA method for both rough surfaces; Our results show that both mentioned surfaces are multifractal and have different scaling exponents. To investigate the reason of the observed multifractality behavior, we determine height distribution, skewness and kurtosis measures and show that the deviation from the Gaussian distribution for the height fluctuations of the surfaces can be a reason for the observed multifractality behavior.

We carried out Monte Carlo simulation of In_0.53Ga_0.47As/strained-InAs/In_0.53Ga_0.47As composite channel high electron mobility transistors (HEMTs) considering strain and quantum confinement effects in very thin InAs layer. We calculated the unstrained and the strained band structures of InAs. We also considered the self-consistent analysis of 2-dimensional electron gas (2DEG) by solving Schrödinger and Poisson equations. With considering the effect of 2DEG, the drain-source current I_ds decreases. However, the negative threshold voltage shift due to the short-channel effects is not affected by considering 2DEG. The threshold voltage shift occurs in the region L_g/d < ~5 (L_g: gate length, d: sum of the barrier and channel layer thicknesses). We also obtained the cutoff frequency f_T values. At a gate length L_g of 20 nm, the calculated f_T values were 943 GHz without 2DEG and 813 GHz with 2DEG. The trend of the f_T values with L_g reflects that of the electron velocities mainly. The present simulation results indicate that the record f_T might be obtained by reducing L_g to around 20 nm for In_0.53Ga_0.47As/strained-InAs/In_0.53Ga_0.47As channel HEMTs.

Nano-porous polymers of intrinsic microporosity, PIM, have exhibited excellent permeability and selectivity characteristics that could be utilized in an environmentally friendly gas separation process. A full understanding of the mechanism through which these membranes effectively and selectively allow for the permeation of specific gases will lead to further development of these membranes. Three factors obviously influenced the conformational behavior of these polymers, which are the presence of electronegative atoms, the presence of non-linearity in the polymeric backbones (backbone kinks) and the presence of bulky side groups on the polymeric chains. The dipole moment increased sharply with the presence of backbone kinks more than any other factor. Replacing the fluorine atoms with bulky alkyl groups didn't influence the dipole moment greatly indicating that the size of the side chains had much less dramatic influence on the dipole moment than having a bent backbone. Similarly, the presence of the backbone kinks in the polymeric chains influenced the polymeric chains to assume less extended configuration causing the torsional angles around the interconnecting bonds unable to cross the high potential energy barriers. The presence of the bulky side groups also caused the energy barriers of the cis-configurations to increase dramatically, which prevented the polymeric segments from experiencing full rotation about the connecting bonds. For these polymers, it was clear that the fully extended configurations are the preferred configurations in the absence of strong electronegative atoms, backbones kinks or bulky side groups. The addition of any of these factors to the polymeric structures resulted in the polymeric chains being forced to assume less extended configurations. Rather interestingly, the length or bulkiness of the side groups didn't affect the end-to-end distance distribution to a great deal since the presence of quite large bulky side chain such as the pentyl group has caused the polymeric chains to revert back to the fully extended configurations possibly due to the quite high potential energy barriers that the chains have to cross to reach the less extended configurational states.

2D lattice neutral models in ecology are studied using general-purpose computing on graphic processing units (GPGPU). Processing times of GPGPU and CPU simulations are compared for various system sizes and it is found out that the larger the system size, the faster the GPGPU version, and the efficiency of GPGPU is maximally 263 times higher. Ecological significance of the GPGPU simulations and the lattice neutral model is also reported.

We develop statistical enumeration methods for self-avoiding walks using a powerful sampling technique called the multicanonical Monte Carlo method. Using these methods, we estimate the numbers of the two dimensional N-step self-avoiding walks up to N = 256 with statistical errors. The developed methods are based on statistical mechanical models of paths which include self-avoiding walks. The criterion for selecting a suitable model for enumerating self-avoiding walks is whether or not the configuration space of the model includes a set for which the number of the elements can be exactly counted. We call this set a scale fixing set. We selected the following two models which satisfy the criterion: the Gō model for lattice proteins and the Domb-Joyce model for generalized random walks. There is a contrast between these two models in the structures of the configuration space. The configuration space of the Gō model is defined as the universal set of self-avoiding walks, and the set of the ground state conformation provides a scale fixing set. On the other hand, the configuration space of the Domb-Joyce model is defined as the universal set of random walks which can be used as a scale fixing set, and the set of the ground state conformation is the same as the universal set of self-avoiding walks. From the perspective of enumeration performance, we conclude that the Domb-Joyce model is the better of the two. The reason for the performance difference is partly explained by the existence of the first-order phase transition of the Gō model.

We use the GARCH model with a fat-tailed error distribution described by a rational function and apply it to stock price data on the Tokyo Stock Exchange. To determine the model parameters we perform Bayesian inference to the model. Bayesian inference is implemented by the Metropolis-Hastings algorithm with an adaptive multi-dimensional Student's t-proposal density. In order to compare our model with the GARCH model with the standard normal errors, we calculate the information criteria AIC and DIC, and find that both criteria favor the GARCH model with a rational error distribution. We also calculate the accuracy of the volatility by using the realized volatility and find that a good accuracy is obtained for the GARCH model with a rational error distribution. Thus we conclude that the GARCH model with a rational error distribution is superior to the GARCH model with the normal errors and it can be used as an alternative GARCH model to those with other fat-tailed distributions.

A spin model is used for simulations of financial markets. To determine return volatility in the spin financial market we use the GARCH model often used for volatility estimation in empirical finance. We apply the Bayesian inference performed by the Markov Chain Monte Carlo method to the parameter estimation of the GARCH model. It is found that volatility determined by the GARCH model exhibits "volatility clustering" also observed in the real financial markets. Using volatility determined by the GARCH model we examine the mixture-of-distribution hypothesis (MDH) suggested for the asset return dynamics. We find that the returns standardized by volatility are approximately standard normal random variables. Moreover we find that the absolute standardized returns show no significant autocorrelation. These findings are consistent with the view of the MDH for the return dynamics.

An overview is given on present lattice field theory computations. We demonstrate the progress obtained in the field due to algorithmic, conceptual and supercomputer advances. We discuss as particular examples Higgs boson mass bounds in lattice Higgs-Yukawa models and the baryon spectrum, the anomalous magnetic moment of the muon and nuclear physics for lattice QCD. We emphasize a number of major challenges lattice field theory is still facing and estimate the computational cost for simulations at physical values of the pion mass.

In this project we initiate an investigation of the applicability of Quasi-Monte Carlo methods to lattice field theories in order to improve the asymptotic error behavior of observables for such theories. In most cases the error of an observable calculated by averaging over random observations generated from an ordinary Monte Carlo simulation behaves like N^−1/2, where N is the number of observations. By means of Quasi-Monte Carlo methods it is possible to improve this behavior for certain problems to up to N⁻¹. We adapted and applied this approach to simple systems like the quantum harmonic and anharmonic oscillator and verified an improved error scaling.

Quantum Chromodynamics (QCD) is the fundamental theory for the interaction between quarks and gluons. It manifests as the short-range strong interaction inside the nucleus and plays an important role in the evolution of the early universe, from the quark-gluon phase to the hadron phase. To solve QCD is a grand challenge, since it requires very large-scale numerical simulations of the discretized action of QCD on the 4-dimensional space-time lattice. Moreover, since quarks are relativistic fermions, the fifth dimension is introduced so that massless quarks with exact chiral symmetry can be realized at finite lattice spacing, on the boundaries of the fifth dimension, the so-called domain-wall fermion (DWF). In this work, I discuss how to simulate lattice QCD with DWF so that the chiral symmetry can be preserved optimally with a finite extent in the fifth dimension. I also outline the simulations which have been performed by the TWQCD Collaboration and present some recent physical results.

The half-filled Hubbard model on the honeycomb lattice is investigated by numerically exact large-scale quantum Monte Carlo simulations for lattice sizes up to 2592 sites. By performing careful finite-size scaling for the spin-spin correlation functions, calculated with a high degree of accuracy, we find that the ground state is antiferromagnetically long-range ordered at U/t = 4, where U is the on-site Hubbard interaction and t is the nearest neighbor hopping. Our result is in sharp contrast to a recent report [Meng et al., Nature 464, 847 (2010)], where instead strong evidence of spin liquid behavior is found.

We revisit the accuracy of the variational Monte Carlo (VMC) method by taking an example of ground state properties for the one-dimensional Hubbard model. We start from the variational wave functions with the Gutzwiller and long-range Jastrow factor introduced by Capello et al. [Phys. Rev. B 72, 085121 (2005)] and further improve it by considering several quantum-number projections and a generalized one-body wave function. We find that the quantum spin projection and total momentum projection greatly improve the accuracy of the ground state energy within 0.5% error, for both small and large systems at half filling. Besides, the momentum distribution function n(k) at quarter filling calculated up to 196 sites allows us direct estimate of the critical exponents of the charge correlations from the power-law behavior of n(k) near the Fermi wave vector. Estimated critical exponents well reproduce those predicted by the Tomonaga-Luttinger theory.

To examine the insulating mechanism of a novel 5d-electron system Sr₂IrO₄, we study the ground state properties of a three-orbital Hubbard model using a variational Monte Carlo method. We find that the insulating state in the ground state phase diagram shows crossover behavior from a weakly-correlated to a strongly-correlated antiferromagnetic state. This crossover is characterized by the different mechanisms of the insulating state, i.e., changing from an interaction-energy driven insulator to a band-energy driven insulator with increasing the interaction. We discuss that Sr₂IrO₄ is located around this crossover region and displays an anomalous behavior.

Bose-Fermi mixtures with attractive Bose-Fermi interactions in one-dimensional optical lattices are studied by using Quantum Monte Carlo simulations of an extended Bose-Fermi Hubbard model. We first derived the extended Hubbard model with the hopping terms of each species modified to include interaction effects. Bosonic Mott transition induced by introducing fermions into bosons is demonstrated by the simulations.

Models of fermions interacting with classical degrees of freedom are applied to a large variety of systems in condensed matter physics. For this class of models, Weiße [Phys. Rev. Lett. 102, 150604 (2009)] has recently proposed a very efficient numerical method, called O(N) Green-Function-Based Monte Carlo (GFMC) method, where a kernel polynomial expansion technique is used to avoid the full numerical diagonalization of the fermion Hamiltonian matrix of size N, which usually costs O(N³) computational complexity. Motivated by this background, in this paper we apply the GFMC method to the double exchange model in three spatial dimensions. We mainly focus on the implementation of GFMC method using both MPI on a CPU-based cluster and Nvidia's Compute Unified Device Architecture (CUDA) programming techniques on a GPU-based (Graphics Processing Unit based) cluster. The time complexity of the algorithm and the parallel implementation details on the clusters are discussed. We also show the performance scaling for increasing Hamiltonian matrix size and increasing number of nodes, respectively. The performance evaluation indicates that for a 32³ Hamiltonian a single GPU shows higher performance equivalent to more than 30 CPU cores parallelized using MPI.

The wave function of ⁸Be, which is obtained from the Monte Carlo shell model (MCSM), is discussed. A method to define an intrinsic state in the MCSM is proposed. The appearance of two-α-cluster structures in ⁸Be is demonstrated.

High-energy physics data analysis relies heavily on the comparison between experimental and simulated data as stressed lately by the Higgs search at LHC and the recent identification of a Higgs-like new boson. The first link in the full simulation chain is the event generation both for background and for expected signals. Nowadays event generators are based on the automatic computation of matrix element or amplitude for each process of interest.

Moreover, recent analysis techniques based on the matrix element likelihood method assign probabilities for every event to belong to any of a given set of possible processes. This method originally used for the top mass measurement, although computing intensive, has shown its efficiency at LHC to extract the new boson signal from the background.

Serving both needs, the automatic calculation of matrix element is therefore more than ever of prime importance for particle physics. Initiated in the 80's, the techniques have matured for the lowest order calculations (tree-level), but become complex and CPU time consuming when higher order calculations involving loop diagrams are necessary like for QCD processes at LHC. New calculation techniques for next-to-leading order (NLO) have surfaced making possible the generation of processes with many final state particles (up to 6). If NLO calculations are in many cases under control, although not yet fully automatic, even higher precision calculations involving processes at 2-loops or more remain a big challenge.

After a short introduction to particle physics and to the related theoretical framework, we will review some of the computing techniques that have been developed to make these calculations automatic. The main available packages and some of the most important applications for simulation and data analysis, in particular at LHC will also be summarized (see CCP2012 slides [1]).

The present status of the development of our code, QEDynamics, is reported. In this code, the time evolution simulation is carried out for Heisenberg operators based on quantum electrodynamics in a manner of quantum field theory. For this simulation, the treatment of the photon is important, particularly infrared and ultra-violet photons. As a result, renormalization is one of essential ingredients, since quantum field theory is adopted.

In order to investigate conductive properties of the system composed of a channel molecule and electrodes, a coupled perturbed Hartree-Fock method for non-Hermitian perturbation Hamiltonians is derived. A non-Hermitian perturbation Hamiltonian which describes interactions between the channel molecule and an electrode is given to represent inflow and outflow at the interface. The effects of electrodes includes the states of the density of state of the channel molecule and the statistical distribution of electrons in electrodes. Benzenedithiol and dihydro-benzenedithiol are studied in this paper, and the first order perturbations of molecular orbital energies of them are obtained.

We carried out a simulation of heavy ion collision using a time-dependent density functional theory. We call it the canonical-basis time-dependent Hartree-Fock-Bogoliubov theory (Cb-TDHFB) which can describe nuclear dynamics in three-dimensional coordinate space, treating nuclear pairing correlation. We simulate ²⁰O+²⁰O collision using the Cb-TDHFB with a contact-type pairing functional, and show the behavior of gap energy which is decreasing and vibrating while colliding.

Quantum mechanics/molecular mechanics (QM/MM) methods have grown to be a standard tool for chemical reactions in biological systems. Still, the remaining problem is that the MM point charges induce artificial polarizations in QM regions, spoiling the quality of the QM calculations. Thus, how to determine boundaries between QM and MM regions is an essential issue for QM/MM calculations. Recently, we proposed the use of a linear response function as an indicator to examine the validity of the replacement of QM peripheral ligands with MM point charges. In this study, we examine the glutathione molecule, for which protonation models have been proposed so far. The calculated results are discussed in relation to the QM/MM modeling of this system.

To check the validity of the recently proposed kinetic energy (KE) functional of the pair density (PD) functional theory, we perform the numerical calculation for the neutral Ne atom. This is the first computational trial for the PD functional theory which includes the KE functional that is approximately derived on the basis of the rigorous expression with the coupling-constant integration. In this work we adopt the correlated Thomas-Fermi functional as the approximate KE functional. Although it is shown that non-negligible errors exist in the resulting PD, the present results will be useful as reference data in cases of developing further the approximate KE functional.

We have performed structural relaxation and calculated binding energy of protein-ligand complex systems, FK506 binding protein (FKBP) and some ligand molecules, using a large-scale density functional theory (DFT) code CONQUEST. Detailed comparison of the calculated binding energies of FKBP with various ligand molecules is reported including the effects of the full geometry relaxation.

The phosphate diester is a basic structure in DNA and RNA. The mechanism of phosphate diester hydrolysis is important for understanding the decomposition reactions of nucleic acids. In this study, we have explored the reaction pathway of alkaline hydrolysis of dimethyl phosphate, which is the simplest phosphate diester, with a hydroxide ion. Since the conformations of the intermediates and transition states reportedly influence the reaction mechanism of transacylation of methyl acetate with methoxide, we considered the conformational preferences on the alkaline hydrolysis of dimethyl phosphate, by using the most stable conformer as a reactant. Upon the reaction with hydroxide, a concerted reaction pathway was obtained in the gas phase, whereas a stepwise reaction pathway was obtained in water. As compared to the earlier study, our computation shows more stable conformations in the hydrolysis reactions than the previous study.

The effect of the adsorption of catalytic metal atoms on tensile strength and structural deformation of graphene is examined using the density functional theory. In the case when a line of Ni atoms is adsorbed at hollow sites aligned along zigzag direction of the honeycomb structure, the tensile strength against the uniaxial strain in armchair direction is calculated to be 82.64 GPa, which is 21% smaller than that of the pristine graphene. The reduction of the tensile strength monotonically depends on the line density of Ni. It is predicted that if the stress reaches the tensile strength, the system will undergo a stress-induced structural transformation that involves the breaking of C-C bond adjacent to Ni atoms, the formation of Ni-C bonds and a resultant jump in the strain.

Residual defects after growth of semiconductors crystals is a hot issue to be solved for manufacturing new efficient electronic or optic devices. These defects can be conveniently observed using birefringence optical microscopy for extended defects that will create a local strain field which in turn can cause a nominally isotropic optical material to become anisotropic and induce birefringence. In order to perform a quantitative analysis, the knowledge of the photoelastic constants (P_ij) of the material that measure the strength of the change of the refractive index under application of strains or stresses is necessary. As an experimental determination of the whole set of constants is not always possible, a theoretical evaluation can be of valuable interest. In this work, we propose ab-initio calculations by the WIEN2k program of the optical properties of the zinc blende silicon carbide polytype with a self-consistent scheme by solving the Kohn-Sham equations using a full potential linearized augmented plane waves (FPLAPW) method in the framework of the density functional theory (DFT) along with the generalized gradient approximation (GGA) pseudo-potentials. A combination of specific compressive and tensile strains is applied to the two atoms unit cell and the tensor containing each specific combination of the P_ij constants is extracted.

The orthosilicate systems Li₂MSiO₄ (M = Fe, Mn, Co and Ni) are recently believed to be a promising alternative to the olivine phosphates. In this paper, we present an interpretation of the diffusion mechanism for polaron-Li vacancy complexes in Li₂NiSiO₄ based on the hybrid functional method HSE06. A comparison between the results obtained by GGA+U and HSE06 methods is carried out. The results confirm that the HSE06 method succeeds in describing the polaron localization in Li₂NiSiO₄. A polaron-Li vacancy complex model (V. A. Dinh et al., Appl. Phys. Express, 5, 045801 (2012)) is used to handle the explanation of the diffusion mechanism in this material. Four elementary diffusion processes for the polaron-Li vacancy complex are investigated and the preferable diffusion pathways are constructed by combining the possible elementary processes. It is found that the Li diffusion may proceed along the two preferable pathways in the [100] and [001] directions with the activation barriers of 1.17 and 0.96 eV, respectively. Furthermore, the accompanied migration of polaron can enhance the diffusion rate of Li ion in Li₂NiSiO₄.

A density functional calculation is performed to investigate optical properties of blue silicate phosphor, BaCa₂MgSi₂O₈:Eu (BCMS:Eu). The optical absorption and emission processes are discussed based on electronic band structures and density of states. Our calculation indicates that hybridization of the wave function plays an important role for nonradiative migration of electrons and holes. Our results also explain adequately the luminescence feature of BCMS which exhibits two components of blue emission from Eu ion substituted for Ba and Ca site. In addition, it is shown that the structural relaxation around Eu ion does work effectively to describe appropriately the difference of crystal field strength between Ba and Ca sites in BCMS host.

The atomic nucleus is a self-bound system of strongly interacting nucleons. In No-Core Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions (Configurations), and the many-body Schrödinger equation becomes a large sparse matrix problem. The challenge is to reach numerical convergence to within quantified numerical uncertainties for physical observables using finite truncations of the infinite-dimensional basis space. We discuss strategies for constructing and solving the resulting large sparse matrices for a set of low-lying eigenvalues and eigenvectors on current multicore computer architectures. Several of these strategies have been implemented in the code MFDn, a hybrid MPI/OpenMP Fortran code for ab initio nuclear structure calculations that scales well to over 200,000 cores. We discuss how the similarity renormalization group can be used to improve the numerical convergence. We present results for excitation energies and other selected observables for ⁸Be and ¹²C using realistic 2- and 3-body forces obtained from chiral perturbation theory. Finally, we demonstrate that collective phenomena such as rotational band structures can emerge from these microscopic calculations.

The time-dependent matrix-product-state (TDMPS) simulation method has been used for numerically simulating quantum computing for a decade. We introduce our C++ library ZKCM_QC developed for multiprecision TDMPS simulations of quantum circuits. Besides its practical usability, the library is useful for evaluation of the method itself. With the library, we can capture two types of numerical errors in the TDMPS simulations: one due to rounding errors caused by the shortage in mantissa portions of floating-point numbers; the other due to truncations of nonnegligible Schmidt coefficients and their corresponding Schmidt vectors. We numerically analyze these errors in TDMPS simulations of quantum computing.

Open quantum systems (OQS), extended in space (halo nuclei) or even unbound, differ from closed quantum systems (CQS), for which the methods of standard shell model (SM) [1] can be utilized in order to expand their wave function in a configuration interaction framework. Configuration interaction methods based on the use of Berggren bases [2], comprising bound, resonant and scattering states, which have the ability to generate the very long range asymptotic behavior of OQSs, are used instead for that matter. This demands the introduction of new computational techniques, including the optimization and discretization of the Berggren basis [3], the development of an algorithm to efficiently calculate their two-body matrix elements [4], and an overall optimization of memory storage absent from SM, where, for instance, all data related to proton and neutron spaces only can be precalculated and stored [1]. In order to diagonalize the very large induced matrices, the Density Matrix Renormalization Group (DMRG) method [5] extended to OQSs has been developed [6, 7]. A renormalization procedure which generates more and more correlated many-body basis states iteratively is used therein, so that the Hamiltonian matrix to diagonalize is very small compared to that occurring with a many-body basis of independent particles [6, 7]. Parallelization of presented methods will also be discussed.

One of the major challenges in nuclear theory is to reproduce and to predict nuclear structure from ab initio calculations with realistic nuclear forces. As the current limitation of direct diagonalization of Hamiltonian matrices by Lanczos iteration method is around the order of matrix dimensionality 10¹⁰ in shell-model calculations, it is difficult to access heavier nuclei beyond the p shell with sufficiently large basis spaces. It is possible to overcome this difficulty by utilizing efficient approximate methods to reproduce full ab initio solutions with good precision and quantified uncertainties. Following the major success of the Monte Carlo shell model (MCSM) with an assumed inert core in the sd- and pf-shell regions and also by recent developments in the MCSM algorithm, the no-core MCSM is expected to be one of the most powerful tools to meet these conditions. We have performed benchmark calculations in the p-shell region. Results of energies are compared with those in the full configuration interaction and no-core full configuration methods. These are found to be consistent with each other within quoted uncertainties when they could be quantified. We also compare and discuss the radial density of the helium-4 ground state extracted from the MCSM and FCI many-body wave functions.

Recent experiments have made it possible to spatially control local two-body interactions between ultracold atoms in inhomogeneous optical lattices. Motivated by this experimental progress, here we study theoretically one-dimensional trapped fermionic optical lattices with spatially modulated on-site interactions. The density matrix renormalization group method is used to examine the ground state phase diagram of a harmonically trapped Hubbard model with spatially alternating on-site repulsive interactions, U₁ and U₂. With varying the strength of the harmonic trapping potential, we find a pair correlated metallic state in the ground state phase diagram, which can be stable only when U₁ ≠ U₂. We discuss the properties of this possibly new state by examining various static physical quantities.

Motivated by recent experiments on Sr₂IrO₄, we study the ground state properties of a two-dimensional three-band Hubbard model with a strong relativistic spin-orbit coupling. Using the exact diagonalization technique, the dynamical magnetic structure factor M(q, ω) is calculated to examine the low-energy magnetic excitations. We find that the low-energy excitations in M(q, ω) are well described by an effective Heisenberg model composed of a local Kramers doublet of an effective total angular momentum J_eff = | − | = 1/2. The antiferromagnetic exchange interaction estimated from M(q, ω) is as large as ~ 80 meV, which is in good quantitative agreement with experiments. To study a possible long-range ordered state in the thermodynamic limit, we use the variational cluster approximation based on the self-energy functional theory, which is parallelized to accelerate the calculations. We find the ground state where the local Kramers doublet is in-plane antiferromagnetic ally ordered.

The technological importance of higher acenes has led to resurgence of interest in synthesizing higher acenes such as octacene, nonacene etc. Recently, Tönshoff and Bettinger [2010 Angew. Chem. Int. Ed.49 4125] have synthesized octacene and nonacene. Motivated by their work, we have performed large-scale calculations of linear optical absorption of octacene and nonacene. Methodology adopted in our work is based upon Pariser-Parr-Pople model (PPP) Hamiltonian, along with large-scale multi-reference singles-doubles configuration interaction (MRSDCI) approach.

Topological polymer networks consist of circular polymers that are topologically linked. Topological networks made of small circular DNA or protein molecules are of great interest in biology and nanotechnology because they are found in living organisms and can be constructed in-vitro. The physical factors that determine the topology of a network as well as the pathways that are followed for its formation remain poorly understood. In our previous work we proposed a novel biophysical/computational approach to model the formation of planar DNA minicircle networks in trypanosomatid parasites. This model suggests that minicircle networks in trypanosomatid parasites emerged from topologically free minicircles upon space confinement through a percolation pathway. Our model however is somewhat idealized because it assumes that the centers of the minicircles in the network are positioned following a regular planar lattice. Here we propose an extension of the model by allowing the centers of the minicircles to be randomly displaced from the vertices of the lattice. We numerically show that networks form following a percolation pathway upon increasing minicircle density. Our model suggests that the critical percolation density increases as D^perc = 0.8357 − 1.4297 exp(0.6439x) with x is the maximum displacement of the centers of the minicircles. Our results therefore show that the plane distribution of minicircles does not dramatically affect the percolation of minicircles and therefore supports they hypothesis that DNA minicircle networks in trypanosomes evolved through a percolation pathway.

Understanding protein folding confined by surfaces is important for both biological sciences and the development of nanomaterials. In this work, we study the properties of a confined HP model protein by three different types of surfaces, namely, surfaces that attract: (a) all monomers; (b) only P monomers; and (c) only H monomers. The thermodynamic and structural quantities, such as the specific heat, number of surface contacts, and number of hydrophobic pairs, are obtained by using Wang-Landau sampling. The conformational "transitions", specifically, the debridging process and hydrophobic core formation, can be identified based on an analysis of these quantities. We found that these transitions take place at different temperatures, and the ground state configurations show variations in structural properties when different surface type is used. These scenarios are confirmed by snapshots of typical states of the systems. From our study, we conclude that the thermodynamics of these transitions and the structural changes depend on the combined actions of both the composition of the H monomers and the P monomers in the HP chain and the surface types.

Mechanisms of interactions among different scale phenomena play important roles for forecasting of weather and climate. Multi-scale Simulator for the Geoenvironment (MSSG), which deals with multi-scale multi-physics phenomena, is a coupled non-hydrostatic atmosphere-ocean model designed to be run efficiently on the Earth Simulator. We present simulation results with the world-highest 1.9km horizontal resolution for the entire globe and regional heavy rain with 1km horizontal resolution and 5m horizontal/vertical resolution for urban area simulation. To gain high performance by exploiting the system capabilities, we propose novel performance evaluation metrics introduced in previous studies that incorporate the effects of the data caching mechanism between CPU and memory. With a useful code optimization guideline based on such metrics, we demonstrate that MSSG can achieve an excellent peak performance ratio of 32.2% on the Earth Simulator with the single-core performance found to be a key to a reduced time-to-solution.

A five-year research project of high performance regional numerical weather prediction is underway as one of the five research fields of the Strategic Programs for Innovative Research (SPIRE). The ultimate goal of the project is to demonstrate feasibility of precise prediction of severe weather phenomena using the K-computer. Three sub-themes of the project are shown with achievements at the present and developments in the near future.

We have devised a general numerical scheme applied to a system of independent, distinguishable, non-interacting particles, to demonstrate in a direct manner the extensive nature of statistical entropy. Working within the microcanonical ensemble, our methods enable one to directly monitor the approach to the thermodynamic limit (N → ∞) in a manner that has not been known before. We show that (s_N − s_∞) → N^−α where s_N is the entropy per particle for N particles and S_∞ is the entropy per particle in the thermodynamic limit. We demonstrate universal behaviour by considering a number of different systems each defined by its unique single-particle spectrum. Various thermodynamic quantities as a function of N may be computed using our methods; in this paper, we focus on the entropy, the chemical potential and the temperature. Our results are applicable to systems of finite size, e.g. nano-particle systems. Furthermore, we demonstrate a new phenomenon, referred to as entropic interference, which manifests as a cancellation of terms in the thermodynamic limit and which results in the additive nature of entropy.

Most modern scientific research problems are complex and interdisciplinary in nature. It is impossible to study such problems in detail without the use of computation in addition to theory and experiment. Although it is widely agreed that students should be introduced to computational methods at the undergraduate level, it remains a challenge to do this in a full traditional undergraduate curriculum. In this paper, we report on a survey that we conducted of undergraduate physics curricula in South Africa to determine the content and the approach taken in the teaching of computational physics. We also considered the pedagogy of computational physics at the postgraduate and research levels at various South African universities, research facilities and institutions. We conclude that the state of computational physics training in South Africa, especially at the undergraduate teaching level, is generally weak and needs to be given more attention at all universities. Failure to do so will impact negatively on the countrys capacity to grow its endeavours generally in the field of computational sciences, with negative impacts on research, and in commerce and industry.

Once upon a time, after making simulations, one had to go to a visualization center with fancy SGI machines to run a GL visualization and make a movie. More recently, OpenGL and its mesa clone have let us create 3D on simple desktops (or laptops), whether or not a Z-buffer card is present. Today, 3D a la Avatar is a commodity technique, presented in cinemas and sold for home TV. However, only a few special research centers have systems large enough for entire classes to view 3D, or special immersive facilities like visualization CAVEs or walls, and not everyone finds 3D immersion easy to view. For maximum physics with minimum effort a 3D system must come to each researcher and student. So how do we create 3D visualization cheaply on every desktop for atomistic simulations? After several months of attempts to select commodity equipment for a whole room system, we selected an approach that goes back a long time, even predating GL. The old concept of anaglyphic stereo relies on two images, slightly displaced, and viewed through colored glasses, or two squares of cellophane from a regular screen/projector or poster. We have added this capability to our AViz atomistic visualization code in its new, 6.1 version, which is RedHat, CentOS and Ubuntu compatible. Examples using data from our own research and that of other groups will be given.

We developed an application launcher called Multiverse for scientific visualizations in a CAVE-type virtual reality (VR) system. Multiverse can be regarded as a type of three-dimensional (3D) desktop environment. In Multiverse, a user in a CAVE room can browse multiple visualization applications with 3D icons and explore movies that float in the air. Touching one of the movies causes "teleportation" into the application's VR space. After analyzing the simulation data using the application, the user can jump back into Multiverse's VR desktop environment in the CAVE.

We propose in this paper a data compression scheme for large-scale particle simulations, which has favorable prospects for scientific visualization of particle systems. Our data compression concepts deal with the data of particle orbits obtained by simulation directly and have the following features: (i) Through control over the compression scheme, the difference between the simulation variables and the reconstructed values for the visualization from the compressed data becomes smaller than a given constant. (ii) The particles in the simulation are regarded as independent particles and the time-series data for each particle is compressed with an independent time-step for the particle. (iii) A particle trajectory is approximated by a polynomial function based on the characteristic motion of the particle. It is reconstructed as a continuous curve through interpolation from the values of the function for intermediate values of the sample data. We name this concept "TOKI (Time-Order Kinetic Irreversible compression)". In this paper, we present an example of an implementation of a data-compression scheme with the above features. Several application results are shown for plasma and galaxy formation simulation data.

By employing the time-dependent Lanczos method, the nonequilibrium process of the half-filled one-dimensional extended Hubbard model under the irradiation of a transient laser pulse is investigated. We show that in the spin-density-wave (SDW) phase, the antiferromagnetic spin correlations are impaired by the photoinduced charge carriers. Near the phase boundary between the SDW and charge-density-wave (CDW) phases, a local enhancement of charge (spin) order that is absent in the original SDW (CDW) phase can be realized with proper laser frequency and strength. The possibility of restoration of spin orders from the CDW phase by optical means is discussed.

A fitting formula for radiative cooling with collisional-radiative population for air plasma flowfield has been developed. Population number densities are calculated from rate equations in order to evaluate the effects of nonequilibrium atomic and molecular processes. Many elementary processes are integrated to be applied to optically-thin plasmas in the number density range of 10¹²/cm³ ≤ N ≤ 10¹⁹/cm³ and the temperature range of 300 K ≤ T ≤ 40,000 K. Our results of the total radiative emissivity calculated from the collisional-radiative population are fitted in terms of temperature and total number density. To validate the analytic fitting formula, numerical simulation of a laser-induced blast wave propagation with the nonequilibrium radiative cooling is conducted and successfully reproduces the shock and plasma wave front time history observed by experiments. In addition, from the comparison between numerical simulations with the radiation cooling effect based on the fitting formula and those with a gray gas radiation model that assumes local thermodynamic equilibrium, we find that the displacement of the plasma front is slightly different due to the deviation of population probabilities. By using the fitting formula, we can easily and more accurately evaluate the radiative cooling effect without solving detailed collisional-radiative rate equations.

The current and future colliders in high-energy physics require theorists to carry out a large scale computation for a precise comparison between experimental results and theoretical ones. In a perturbative approach several methods to evaluate Feynman loop integrals which appear in the theoretical calculation of cross-sections are well established in the one-loop level, however, more studies are necessary for higher-order levels. Direct Computation Method (DCM) is developed to evaluate multi-loop integrals. DCM is based on a combination of multidimensional numerical integration and extrapolation on a sequence of integrals. It is a fully numerical method and is applicable to a wide class of integrals with various physics parameters. The computation time depends on physics parameters and the topology of loop diagrams and it becomes longer for the two-loop integrals. In this paper we present our approach to the acceleration of the two-loop integrals by DCM on multiple GPU boards.

Feynman loop integrals appear in higher order corrections of interaction cross section calculations in perturbative quantum field theory. The integrals are computationally intensive especially in view of singularities which may occur within the integration domain. For the treatment of threshold and infrared singularities we developed techniques using iterated (repeated) adaptive integration and extrapolation. In this paper we describe a shared memory parallelization and its application to one- and two-loop problems, by multi-threading in the outer integrations of the iterated integral. The implementation is layered over OpenMP and retains the adaptive procedure of the sequential method exactly. We give performance results for loop integrals associated with various types of diagrams including one-loop box, pentagon, two-loop self-energy and two-loop vertex diagrams.

Collapse transition of the lattice polymer on a square lattice is studied by calculating the exact partition functions up to chain length 38; they are obtained by enumerating the number of possible conformations for each energy value. We observe that the locus of partition function zeros approaches the positive real axis as the chain length increases, providing evidence of the collapse transition. The crossover exponent and the transition temperature are estimated from the scaling behavior of the first partition function zeros with increasing chain length.

Reconstruction of particle tracks from information collected by position-sensitive detectors is an important procedure in HEP experiments. It is usually controlled by a set of numerical parameters which have to be manually optimized. This paper proposes an automatic approach to this task by utilizing evolutionary algorithm (EA) operating on both real-valued and binary representations. Because of computational complexity of the task a special distributed architecture of the algorithm is proposed, designed to be run in grid environment. It is two-level hierarchical hybrid utilizing asynchronous master-slave EA on the level of clusters and island model EA on the level of the grid. The technical aspects of usage of production grid infrastructure are covered, including communication protocols on both levels. The paper deals also with the problem of heterogeneity of the resources, presenting efficiency tests on a benchmark function. These tests confirm that even relatively small islands (clusters) can be beneficial to the optimization process when connected to the larger ones. Finally a real-life usage example is presented, which is an optimization of track reconstruction in Large Angle Spectrometer of NA-58 COMPASS experiment held at CERN, using a sample of Monte Carlo simulated data. The overall reconstruction efficiency gain, achieved by the proposed method, is more than 4%, compared to the manually optimized parameters.

It is difficult to measure any quantity in plasmas, since the physical quantity is usually measured only under very severe experimental conditions. For instance, it is often observed that the frequency of the wave changes during propagation and also different waves from the incident one are newly stimulated. Therefore, proposed is the most suitable method for computer experiment using technique of signal processing. In plasmas, various phenomena are described by a fluid theory. The fluid theory consists of a system of Maxwell's equations and that of Euler's equations. Applying the technique of wave digital filters (WDF) to these equation systems, the partial differential equations are integrated directly. Considering all physical quantities as currents, a system of partial differential equation systems is transformed into an equivalent Kirchhoff circuit. Wave-flow diagrams corresponding to their Kirchhoff circuits are obtained by the ordinary WDF procedures, which are algorithms themselves for numerical calculations. Therefore, we may safely say that these algorithms construct a computer experimental apparatus, which simulates many plasma experiments concerning propagation properties of plasma waves. Here, we simulate frequency-shift phenomena of some plasma wave by means of the function with respect to spectrum analysis of this apparatus.

We present in this work an algorithm for electrocardiogram (ECG) signal compression aimed to its transmission via telecommunication channel. Basically, the proposed ECG compression algorithm is articulated on the use of wavelet transform, leading to low/high frequency components separation, high order statistics based thresholding, using level adjusted kurtosis value, to denoise the ECG signal, and next a linear predictive coding filter is applied to the wavelet coefficients producing a lower variance signal. This latter one will be coded using the Huffman encoding yielding an optimal coding length in terms of average value of bits per sample. At the receiver end point, with the assumption of an ideal communication channel, the inverse processes are carried out namely the Huffman decoding, inverse linear predictive coding filter and inverse discrete wavelet transform leading to the estimated version of the ECG signal. The proposed ECG compression algorithm is tested upon a set of ECG records extracted from the MIT-BIH Arrhythmia Data Base including different cardiac anomalies as well as the normal ECG signal. The obtained results are evaluated in terms of compression ratio and mean square error which are, respectively, around 1:8 and 7%. Besides the numerical evaluation, the visual perception demonstrates the high quality of ECG signal restitution where the different ECG waves are recovered correctly.