Cube Method Research Articles

Framework for simulation of natural convection in practical applications

Natural convection is commonly used as a means of heat transfer in many practical products because it is highly cost-effective. The development of simulation tools for this type of application is generally accompanied by several critical issues, including high-temperature differences, rapid turnaround demand, and complex geometries. Under conditions of natural convection with high-temperature differences, the density of the medium is variable but the flow speed is low. Therefore, a compressible solver, i.e., Roe scheme developed by P.L. Roe in 1981, must be combined with a preconditioning method that can make the Roe scheme available at low speeds to allow the above situation to be addressed. The building cube method is adopted to make our method suitable for massive parallelization systems, which can reduce the calculation and turnaround times immensely. An immersed boundary method for compressible flows combined with a fast, easy to implement, and robust interpolation method is developed to handle flows with complex immersed geometries. The results show that the program described here is suitable for application to product design and analysis because of its wide applicability to natural convection with high-temperature differences, its capacity to handle complex geometries, and its feasibility for use in massive parallelization systems.

Octree-based Multiple-material Parallel Unstructured Mesh Generation Method for Seismic Response Analysis of Soil-Structure Systems

We developed an unstructured finite element mesh generation method capable of modeling multiple-material complex geometry problems for large-scale seismic analysis of soil-structure systems. We used an octree structure to decompose the target domain into small subdomains and use the multiple material marching cubes method for robust and parallel tetrahedralization of each subdomain. By using the developed method on a 32 core shared memory machine, we could generate a 594,168,792 tetrahedral element soil-structure model of a power plant in 13h 01min. The validity of the generated model was confirmed by conducting a seismic response analysis on 2,304 compute nodes of the K computer at RIKEN. Although the model contains a small approximation in geometry (half of the minimum octree size) at present, we can expect fast and high quality meshing of large-scale models by making geometry correction in the future, which is expected to help improve the seismic safety of important structures and complex urban systems.

Segmentation of Liver from Abdomen CT images and 3D Visualization

Segmentation of liver is the initial and fundamental step for the diagnosis of liver disease, 3-D volume construction and volume measurement. However, segmentation of liver is a challenging task due to it’s inter and intra intensity and texture similarities among other organs present in CT abdominal images. A semiautomatic method has been proposed to segment the liver portion from CT abdominal images and their three dimensional volume construction by (i)Noise removal using median filter,(ii)Segmentation of liver portion based on active contour method using sparse field method and(iii)liver volume construction using marching cube method. Evaluation of proposed method is carried out on clinically acquired CT images and effectiveness of algorithm is evaluated by comparing manually segmented liver portion marked by radiologist with proposed method

Echocardiographic measurement of left atrial volume: Does the method matter?

Four two-dimensional echocardiographic methods (cube, ellipsoid, Simpson's and area-length) can be used to assess left atrial volume (LAV). To compare absolute LAV measurements and evaluate agreement regarding the semiquantitative assessment of degree of left atrial (LA) enlargement, between methods. We prospectively measured LAV in 51 healthy volunteers using the four methods, and defined thresholds for moderate (mean+2 standard deviations [SDs]) and severe (mean+4 SDs) LA enlargement for each method. In 372 patients referred for echocardiography, we compared absolute LAV measurements and agreement between methods. LAV was significantly different between methods in the healthy volunteer group (11 ± 4, 17 ± 3, 26 ± 6 and 28 ± 7 mL/m(2), respectively; P<0.0001), resulting in different thresholds for moderate and severe LA enlargement. LAV was also significantly different in the 372 patients (30 ± 20, 47 ± 27, 61 ± 34 and 65 ± 36 mL/m(2), respectively; P<0.0001). Agreement regarding degree of LA enlargement (none, moderate, severe), using the area-length method as reference, was modest with the cube method (kappa=0.41), correct with the ellipsoid method (kappa=0.60) and excellent with Simpson's method (kappa=0.83). The choice of the method had a major effect on assessment of degree of LA enlargement. Our results suggest that the cube and ellipsoid methods, which significantly underestimated LAV and provided modest agreement, should be disregarded. In contrast, Simpson's method and the area-length method were slightly different, but showed close agreement, and should be preferred, using dedicated thresholds (50 and 56 mL/m(2) respectively).

INFLUENCE OF VARIOGRAM PARAMETERS ON THE ACCURACY OF CREATION OF THREE-DIMENSIONAL GEOLOGICAL MODELS

Examine the influence of errors on nugget effect in the variogram in the process of three-dimensional geological modeling. Created experimental model that demonstrates this process. Proposed method of creation cubes of parameters, that consider of nugget effect and reducing the level of errors.

Distributed Multipolar Expansion Approach to Calculation of Excitation Energy Transfer Couplings

We propose a new approach for estimating the electrostatic part of the excitation energy transfer (EET) coupling between electronically excited chromophores based on the transition density-derived cumulative atomic multipole moments (TrCAMM). In this approach, the transition potential of a chromophore is expressed in terms of truncated distributed multipolar expansion and analytical formulas for the TrCAMMs are derived. The accuracy and computational feasibility of the proposed approach is tested against the exact Coulombic couplings, and various multipole expansion truncation schemes are analyzed. The results of preliminary calculations show that the TrCAMM approach is capable of reproducing the exact Coulombic EET couplings accurately and efficiently and is superior to other widely used schemes: the transition charges from electrostatic potential (TrESP) and the transition density cube (TDC) method.

Efficient pathways of excitation energy transfer from delocalized S2 excitons in the peridinin-chlorophyll a-protein complex.

Excitation energy transfer (EET) in peridinin-chlorophyll-protein (PCP) complexes is dominated by the S1 → Qy pathway, but the high efficiencies cannot be solely explained by this one pathway. We postulate that EET from peridinin S2 excitons may also be important. We use complete active space configuration interaction calculations and the transition density cube method to calculate Coulombic couplings between peridinin and chlorophyll a in the PCP complex of the dinoflagellate Amphidinium carterae and compare monomeric and dimeric delocalized peridinin S2 excited states. Our calculations show that the S2 → Qy EET pathway from peridinin to chlorophyll a is the dominant energy transfer pathway from the S2 excited state in PCP, with several values in the sub-picosecond range. This result suggests that the S2 → Qy EET pathway may be responsible for the reported chlorophyll a bleaching signature seen in experiment at around 200 fs, and not the S2 → Qx pathway as previously suggested.

Design of an XY-theta platform held by a planar manipulator with four revolute joints and evaluation of its precision performances

SUMMARYThis paper is about the precision performance evaluation of an XY-theta platform, with a patented kinematic design. Indeed, this platform is held by a serial redundant robot arm actuated with four revolute joints. The platform offers a wide 300 × 300 mm workspace, whereas the whole mechanism is extremely compact. Any workpiece on the platform can be positioned under a vertical axis to be grasped or manufactured in a two-step approach: in a coarse positioning mode, the four revolute joints are controlled to position and orientate the workpiece with a position error of less than 10 μm; in a fine positioning mode, two revolute joints are mechanically blocked while two others are controlled to reduce the final error to below 2 μm. The mechanism design and the choice of the blocked and moving joints are optimized to enhance the positioning performances in the two-step positioning method. In this paper, the platform positioning repeatability and its spatial resolution are characterized with the help of a camera. The advantage of this method is that it avoids any mechanical contact and can be implemented easily. Then, these results are compared to our previous precision performance evaluation obtained with the stationary cube method. Finally, the positioning repeatability is estimated at 6.5 μm in the coarse positioning mode and 1.4 μm in the fine positioning mode. Between the coarse and fine mode, the repeatability is thus improved by the factor of four, as predicted by the theory.

An adaptive octree finite element method for PDEs posed on surfaces

Abstract The paper develops a finite element method for partial differential equations posed on hypersurfaces in R N , N = 2 , 3 . The method uses traces of bulk finite element functions on a surface embedded in a volumetric domain. The bulk finite element space is defined on an octree grid which is locally refined or coarsened depending on error indicators and estimated values of the surface curvatures. The cartesian structure of the bulk mesh leads to easy and efficient adaptation process, while the trace finite element method makes fitting the mesh to the surface unnecessary. The number of degrees of freedom involved in computations is consistent with the two-dimension nature of surface PDEs. No parametrization of the surface is required; it can be given implicitly by a level set function. In practice, a variant of the marching cubes method is used to recover the surface with the second order accuracy. We prove the optimal order of accuracy for the trace finite element method in H 1 and L 2 surface norms for a problem with smooth solution and quasi-uniform mesh refinement. Experiments with less regular problems demonstrate optimal convergence with respect to the number of degrees of freedom, if grid adaptation is based on an appropriate error indicator. The paper shows results of numerical experiments for a variety of geometries and problems, including advection–diffusion equations on surfaces. Analysis and numerical results of the paper suggest that combination of cartesian adaptive meshes and the unfitted (trace) finite elements provide simple, efficient, and reliable tool for numerical treatment of PDEs posed on surfaces.

FPGA-based Custom Computing Architecture for Large-Scale Fluid Simulation with Building Cube Method

We are designing a custom computing machine for large-scale flui simulation with the building-cube method (BCM). In BCM, parallel computation is performed with cubes, each of which is an orthogonal grid with a f xed resolution of cells. Although BCM is advantageous in balancing loads with cubes, it also has a problem of efficien y and scalability for comptuting with general-purpose supercomputers due to insufficien memory bandwidth and communication overhead of an interconnection network. In this paper, we present a custom computing architecture for FPGA-based scalable BCM computation with a dedicated network, called an accelerator domain network (ADN). We design a cube engine which allows bandwidth-efficien computation of cubes based on streamed stencil computation of the fractional-step method. Through prototype implementation, we evaluate the potential performance of the architecture. For ALTERA Stratix V 28nm FPGA, we estimate that a single FPGA has the peak performance of 107 GFlop/s in a single precision.

Virtual Reality Haptic Simulation of Root Canal Therapy

Here we report a haptic virtual reality simulator for root canal treatment (endodontic procedures). A virtual jaw model was extracted from CT data of a live patient and the volumetric data obtained were visualized using a Marching Cubes algorithm. Collision detection and collision response algorithms were developed using a voxel-based approach. Removal of bone was visualized using a modified real-time Marching Cubes method and deformation of the K-files in the internal surface of tooth canal was simulated haptically and graphically using OpenGL and HDAPI of OpenHaptics Libraries. Using a haptic robot (Omni Phantom) the user can burr the enamel and dentin until reaching the pulp chamber and then the internal surface of a root canal can be cleaned using a simulated K-file.

Excitation Energy Transfer in the Peridinin-Chlorophyll a-Protein Complex Modeled Using Configuration Interaction

We modeled excitation energy transfer (EET) in the peridinin-chlorophyll a-protein (PCP) complex of dinoflagellate Amphidinium carterae to determine which pathways contribute dominantly to the high efficiency of this process. We used complete active space configuration interaction (CAS-CI) to calculate electronic structure properties of the peridinin (PID) and chlorophyll a (CLA) pigments in PCP and the transition density cube (TDC) method to calculate Coulombic couplings between energy transfer donors and acceptors. Our calculations show that the S1 → Qy EET pathway from peridinin to chlorophyll a is the dominant energy transfer pathway in PCP, with two sets of interactions-between PID612 and CLA601 and between PID622 and CLA602-contributing most strongly. EET lifetimes for these two interactions were calculated to be 2.66 and 2.90, with quantum efficiencies of 85.75 and 84.65%, respectively. The calculated Coulombic couplings for EET between two peridinin molecules in the strongly allowed S2 excited states are extremely large and suggest excitonic coupling between pairs of peridinin S2 states. This methodology is also broadly applicable to the study of EET in other photosynthetic complexes and/or organic photovoltaics, where both single and double excitations are present and donor and acceptor molecules are tightly packed.

A New Simplified Selection Algorithm of the Guide Star Catalogue for a Star Sensor

A guide star catalogue characterised by fewer guide stars, uniform distribution and high completeness is conducive to the improvement of star pattern identification and star tracking efficiency, and it has become an important study objective. A screening method, which takes “quasi-uniform distribution” of space solid angles as the principle and the size of the space solid angle corresponding to 4°×4° on the equator as the reference and divided the whole celestial sphere into 2,664 sub-blocks in sequence, is proposed in this paper. Based on this method, a “quasi-uniform” guide star catalogue with 2,937 guide stars was obtained. According to our ergodic statistical analysis of the whole celestial sphere, in a 12°×12° field of view, after the space solid angle method was used to divide the celestial sphere, the probability of emergence of three guide stars was 99·9% or above, while the number of guide stars decreased by 12·6% compared to the inscribed cube method. It can be concluded that when the completeness is equal, the space solid angle method is superior to the inscribed cube method in both capacity and distribution uniformity.

Novel Technique for Hepatic Fiducial Marker Placement for Stereotactic Body Radiation Therapy

To report experience with fiducial marker insertion and describe an advantageous, novel technique for fiducial placement in the liver for stereotactic body radiation therapy with respiratory tracking. We implanted 1444 fiducials (single: 834; linked: 610) in 328 patients with 424 hepatic lesions. Two methods of implantation were compared: the standard method (631 single fiducials) performed on 153 patients from May 2007 to May 2010, and the cube method (813 fiducials: 610 linked/203 single) applied to 175 patients from April 2010 to March 2013. The standard method involved implanting a single marker at a time. The novel technique entailed implanting 2 pairs of linked markers when possible in a way to occupy the perpendicular edges of a cube containing the tumor inside. Mean duration of the cube method was shorter than the standard method (46 vs 61 minutes; P<.0001). Median numbers of skin and subcapsular entries were significantly smaller with the cube method (2 vs 4, P<.0001, and 2 vs 4, P<.0001, respectively). The rate of overall complications (total, major, and minor) was significantly lower in the cube method group compared with the standard method group (5.7% vs 13.7%; P=.013). Major complications occurred while using single markers only. The success rate was 98.9% for the cube method and 99.3% for the standard method. We propose a new technique of hepatic fiducial implantation that makes use of linked fiducials and involves fewer skin entries and shorter time of implantation. The technique is less complication-prone and is migration-resistant.

SU-E-T-154: Establishment and Implement of 3D Image Guided Brachytherapy Planning System

Purpose: Cannot observe the dose intuitionally is a limitation of the existing 2D pre-implantation dose planning. Meanwhile, a navigation module is essential to improve the accuracy and efficiency of the implantation. Hence a 3D Image Guided Brachytherapy Planning System conducting dose planning and intra-operative navigation based on 3D multi-organs reconstruction is developed. Methods: Multi-organs including the tumor are reconstructed in one sweep of all the segmented images using the multiorgans reconstruction method. The reconstructed organs group establishs a three-dimensional visualized operative environment. The 3D dose maps of the three-dimentional conformal localized dose planning are calculated with Monte Carlo method while the corresponding isodose lines and isodose surfaces are displayed in a stereo view. The real-time intra-operative navigation is based on an electromagnetic tracking system (ETS) and the fusion between MRI and ultrasound images. Applying Least Square Method, the coordinate registration between 3D models and patient is realized by the ETS which is calibrated by a laser tracker. The system is validated by working on eight patients with prostate cancer. The navigation has passed the precision measurement in the laboratory. Results: The traditional marching cubes (MC) method reconstructs one organ at one time and assembles them together. Compared to MC, presentedmore » multi-organs reconstruction method has superiorities in reserving the integrality and connectivity of reconstructed organs. The 3D conformal localized dose planning, realizing the 'exfoliation display' of different isodose surfaces, helps make sure the dose distribution has encompassed the nidus and avoid the injury of healthy tissues. During the navigation, surgeons could observe the coordinate of instruments real-timely employing the ETS. After the calibration, accuracy error of the needle position is less than 2.5mm according to the experiments. Conclusion: The speed and quality of 3D reconstruction, the efficiency in dose planning and accuracy in navigation all can be improved simultaneously.« less

水面の品質と計算速度のための流体シミュレーションと可視化

A mesh-free method MPS is implemented for fluid simulation. A Marching Cubes method is applied to obtain the free surface of the fluid which is represented by particles. We used a cubic spline instead of the weight function to map particle data into the scalar field in 3D space. The method shows smoothness in surface representation. Then we give a CUDA implementation of both the simulation part and the rendering part, and for performance consideration, a novel method for neighbor particle searching is given. We finally get a near real-time outcome running at a frame rate of 30fps.

The equal spacing of N points on a sphere with application to partition-of-unity wave diffraction problems

This paper addresses applications involving the selection of a set of points on a sphere, in which the uniformity of spacing can be of importance in enhancing the computational performance and/or the accuracy of some simulation. For the authors, the motivation for this work arises from the need to specify wave directions in a partition-of-unity approach for numerical analysis of wave diffraction problems. A new spacing method is presented, based on a physical analogy in which an arbitrary number of charged particles are held in static equilibrium on a spherical surface. The new method, referred to in this paper as the Coulomb force method, offers an improvement over simpler methods, e.g., latitude/longitude and discretised cube methods, in terms of both the uniformity of spacing and the arbitrary nature of the number of points N that can be considered. A simple extension to the algorithm allows points to be biased towards a direction of choice. Numerical results of a wave scattering problem solved with a partition-of-unity boundary element method demonstrate the benefits of the algorithm.

Improved Decomposition for a System of Completely Specified Boolean Functions

Functional decomposition is an important and powerful technique in the logic synthesis. The ternary matrix cover approach is one of the existing methods of this type. This method is also used in decomposition of a system of completely specified Boolean functions. Before constructing the desired superposition, it needs to encode a table. There is a trivial encoding method. But to find a better solution, it is important to use a special approach, because the result of the encoding has a direct influence on the obtained functions. In this paper, an efficient algorithm to encode this table is presented. It uses the approach connected with the assembling Boolean hyper cube method. The proposed algorithm is explained in details with an example. The benefits and impacts of the suggested technique are also discussed.

Ab Initio Calculation of Molecular Aggregation Effects: A Coumarin-343 Case Study

We present time-dependent density functional theory (TDDFT) calculations for single and dimerized Coumarin-343 molecules to investigate the quantum mechanical effects of chromophore aggregation in extended systems designed to function as a new generation of sensors and light-harvesting devices. Using the single-chromophore results, we describe the construction of effective Hamiltonians to predict the excitonic properties of aggregate systems. We compare the electronic coupling properties predicted by such effective Hamiltonians to those obtained from TDDFT calculations of dimers and to the coupling predicted by the transition density cube (TDC) method. We determine the accuracy of the dipole-dipole approximation and TDC with respect to the separation distance and orientation of the dimers. In particular, we investigate the effects of including Coulomb coupling terms ignored in the typical tight-binding effective Hamiltonian. We also examine effects of orbital relaxation which cannot be captured by either of these models.

Fuel vertical structure affects fire sustainability and behaviour of prescribed burning in Spartium junceum shrublands

Prescribed burning is increasingly recommended to control encroaching shrublands in the Mediterranean area. The aims of this paper are to analyze the fuel structural characteristics of Spartium junceum and how they influence fire behaviour during prescribed burning. Two winter–spring prescribed burns were conducted in 2009 and 2011. Fuel load and structure of S. junceum shrubs were assessed using the Cube Method, and shrub 3-D models were built using the FIRE PARADOX FUEL MANAGER software. Allometric equations to estimate S. junceum fuel load were developed. During burning, thermocouples measured temperature variations, which were then analyzed relative to fuel characteristics. Fuel load components and distribution were strictly related to shrub height; in tall shrubs, most of the fine fuel was more than 1.5 m aboveground. Due to fuel vertical discontinuity, not all shrubs were burned in the fires, but wind increased fire sustainment and fuel consumption. Maximum temperatures (over 800 °C) and residence times were positively related to fuel load. S. junceum tall shrublands represent high hazard formations due to their elevated fuel load, mostly in fine fuel fractions. Vertical discontinuity among fuel strata limits fire propagation in mild weather conditions. Winter–spring prescribed burning cannot eliminate S. junceum shrublands, but do create shrub cover discontinuity. As S. junceum has fire-adapted morphological traits, a single burn is insufficient to control it.