Increase In Computational Efficiency Research Articles

Modeling watershed rainfall–runoff relations using impervious surface-area data with high spatial resolution

A distributed object-based rainfall–runoff simulation (DORS) model with incorporation of detailed impervious surface-area (ISA) data, derived from digital true-color orthophotography data with high spatial resolution, was developed. This physically based model simulates hydrologic processes of precipitation interception, infiltration, runoff, evapotranspiration, change of soil moisture, change of water-table depth, runoff routing, groundwater routing, and channel-flow routing. The modeling processes take objects based on land-cover types as fundamental spatial units in order to reduce data volume, increase computational efficiency, strengthen representation of watersheds, and utilize the data in variable scales. US Geological Survey stream-gaging data were used to validate the temporal variation of simulated discharge within two watersheds in Rhode Island State. The ratio of absolute error to the mean and the Nash coefficient in the validation period are 7.2% and 0.90 for the first watershed, and 8.0% and 0.77 for the second watershed, respectively. The results indicate that the DORS model is able to capture the relationship between rainfall and runoff in the study area, and that it is applicable in the further study of ISA impacts on the water cycle and associated pollution problems. The results also demonstrate that the performance of the hydrologic simulation is improved with ISA data with high spatial resolution.

Systematic coarse-graining of a multicomponent lipid bilayer.

A solvent-free coarse-grained model for a 1:1 mixed dioleoylphosphatidylcholine (DOPC) and a dioleoylphospatidylethanolamine (DOPE) bilayer is developed using the multiscale coarse-graining (MS-CG) approach. B-spline basis functions are implemented instead of the original cubic spline basis functions in the MS-CG method. The new B-spline basis functions are able to dramatically reduce memory requirements and increase computational efficiency of the MS-CG calculation. Various structural properties from the CG simulations are compared with their corresponding all-atom counterpart in order to validate the CG model. The resulting CG structural properties agree well with atomistic results, which shows that the MS-CG force field can reasonably approximate the many-body potential of mean force in the coarse-grained coordinates. Fast lipid lateral diffusion in the CG simulations, as a result of smoother free energy landscape, makes the study of phase behavior of the binary mixture possible. Small clusters of distinct lipid composition are identified by analyzing the DOPC/DOPE lipid lateral distribution, indicating a nonuniform distribution for the mixed bilayer. The results of lipid phase behavior are compared to experimental results, and connections between the experimental and simulation conclusions are discussed.

Non-Equilibrium Molecular Dynamics Simulation of Nanojet Injection with Adaptive-Spatial Decomposition Parallel Algorithm

An Adaptive-Spatial Decomposition parallel algorithm was developed to increase computation efficiency for molecular dynamics simulations of nano-fluids. Injection of a liquid argon jet with a scale of 17.6 molecular diameters was investigated. A solid annular platinum injector was also solved simultaneously with the liquid injectant by adopting a solid modeling technique which incorporates phantom atoms. The viscous heat was naturally discharged through the solids so the liquid boiling problem was avoided with no separate use of temperature controlling methods. Parametric investigations of injection speed, wall temperature, and injector length were made. A sudden pressure drop at the orifice exit causes flash boiling of the liquid departing the nozzle exit with strong evaporation on the surface of the liquids, while rendering a slender jet. The elevation of the injection speed and the wall temperature causes an activation of the surface evaporation concurrent with reduction in the jet breakup length and the drop size.

VEAL

Performance improvement solely through transistor scaling is becoming more and more difficult, thus it is increasingly common to see domain specific accelerators used in conjunction with general purpose processors to achieve future performance goals. There is a serious drawback to accelerators, though: binary compatibility. An application compiled to utilize an accelerator cannot run on a processor without that accelerator, and applications that do not utilize an accelerator will never use it. To overcome this problem, we propose decoupling the instruction set architecture from the underlying accelerators. Computation to be accelerated is expressed using a processor’s baseline instruction set, and light-weight dynamic translation maps the representation to whatever accelerators are available in the system. In this paper, we describe the changes to a compilation framework and processor system needed to support this abstraction for an important set of accelerator designs that support innermost loops. In this analysis, we investigate the dynamic overheads associated with abstraction as well as the static/dynamic tradeoffs to improve the dynamic mapping of loop-nests. As part of the exploration, we also provide a quantitative analysis of the hardware characteristics of effective loop accelerators. We conclude that using a hybrid static-dynamic compilation approach to map computation on to loop-level accelerators is an practical way to increase computation efficiency, without the overheads associated with instruction set modification.

A note on cuts for contingency tables

In this note, we propose a general method to find cuts for a contingency table. Useful cuts are, in many cases, statistics S-sufficient for the nuisance parameter and S-ancillary for the parameter of interest. In general, cuts facilitate a strong form of parameter separation known to be useful for conditional inference [E.L. Lehmann, Testing Statistical Hypotheses, 2nd ed., Springer, New York, 1997, pp. 546–548]. Cuts also achieve significant dimension reduction, hence, increase computational efficiency. This is particularly true for the inference about cross-tabulated data, usually with a large number of parameters. Depending on the parameter of interest, we propose a flexible transformation to reparameterize the discrete multivariate response distribution. Inference on cell probabilities or odds ratios will require different parameterizations. The reparameterized distribution is not sum-symmetric. Thus, the finding in this paper expands the results in Barndorff-Nielsen [O.E. Barndorff-Nielsen, Information and Exponential Families in Statistical Theory, John Wiley, New York, 1978, pp. 202–206].

Semi-automated image processing system for micro- to macro-scale analysis of immunohistopathology: application to ischemic brain tissue

Immunochemical staining techniques are commonly used to assess neuronal, astrocytic and microglial alterations in experimental neuroscience research, and in particular, are applied to tissues from animals subjected to ischemic stroke. Immunoreactivity of brain sections can be measured from digitized immunohistology slides so that quantitative assessment can be carried out by computer-assisted analysis. Conventional methods of analyzing immunohistology are based on image classification techniques applied to a specific anatomic location at high magnification. Such micro-scale localized image analysis limits one for further correlative studies with other imaging modalities on whole brain sections, which are of particular interest in experimental stroke research. This report presents a semi-automated image analysis method that performs convolution-based image classification on micro-scale images, extracts numerical data representing positive immunoreactivity from the processed micro-scale images and creates a corresponding quantitative macro-scale image. The present method utilizes several image-processing techniques to cope with variances in intensity distribution, as well as artifacts caused by light scattering or heterogeneity of antigen expression, which are commonly encountered in immunohistology. Micro-scale images are composed by a tiling function in a mosaic manner. Image classification is accomplished by the K-means clustering method at the relatively low-magnification micro-scale level in order to increase computation efficiency. The quantitative macro-scale image is suitable for correlative analysis with other imaging modalities. This method was applied to different immunostaining antibodies, such as endothelial barrier antigen (EBA), lectin, and glial fibrillary acidic protein (GFAP), on histology slides from animals subjected to middle cerebral artery occlusion by the intraluminal suture method. Reliability tests show that the results obtained from immunostained images at high magnification and relatively low magnification are virtually the same.

Micromachined variable impedance acoustic waveguides for fluid-structure waves

Micromachined fluid filled variable impedance waveguides intended to mimic the mechanics of the passive cochlea have been fabricated and experimentally examined. These devices consist of a fluid filled chamber of dimension 37 mm by 6.25 mm by 0.1 mm fabricated on a pyrex wafer. One side of this chamber is constrained by a 3-cm-long, exponentially tapered, 0.3-μm thick tensioned membrane made of low-pressure chemical vapor deposited (LPCVD) silicon nitride. The membranes vary in width from 170 μm to 1.9 mm, and are fabricated using deep reactive ion etching (DRIE). The devices are filled with silicone oil or de-ionized water. Experimental tests demonstrate acoustically excited traveling fluid-structure waves with wave numbers well below the free-plane wave wave number, and with phase accumulations as high as 25 rad (at 6.5 kHz) in the 3 cm length of the device. Comparison of experimental measurements with both numerical (finite-element) and asymptotic (Liouville–Green) models assist in understanding the results. A thin-layer finite-element approximation is developed to take advantage of the device aspect ratio and increase computational efficiency. Viscous fluid effects are included in the models to accurately capture damping phenomena. [Work supported by ONR and NSF.]

Hybrid Laplace transform finite element method for solving the convection–dispersion problem

It can be very time consuming to use the conventional numerical methods, such as the finite element method, to solve convection–dispersion equations, especially for solutions of large-scale, long-term solute transport in porous media. In addition, the conventional methods are subject to artificial diffusion and oscillation when used to solve convection-dominant solute transport problems. In this paper, a hybrid method of Laplace transform and finite element method is developed to solve one- and two-dimensional convection–dispersion equations. The method is semi-analytical in time through Laplace transform. Then the transformed partial differential equations are solved numerically in the Laplace domain using the finite element method. Finally the nodal concentration values are obtained through a numerical inversion of the finite element solution, using a highly accurate inversion algorithm. The proposed method eliminates time steps in the computation and allows using relatively large grid sizes, which increases computation efficiency dramatically. Numerical results of several examples show that the hybrid method is of high efficiency and accuracy, and capable of eliminating numerical diffusion and oscillation effectively.

Genetic algorithms for optimized re-triangulation in the context of reverse engineering

In reverse engineering, an existing part is first digitized. When a prototype of the digitized data is needed, it can be made by means of rapid prototyping technologies directly from a triangulation of the digitized data without constructing a CAD model. This will be illustrated by the novel method proposed in this article. Firstly, an optimized STL file (the de facto file format for rapid prototyping machines) is constructed directly from digitized part data. In order to reduce storage space and increase computational efficiency for subsequent processes such as slicing, significant data reduction can be achieved by the users’ discretion by deleting triangles in planar and near planar regions. Points around the ‘blank region’ left by deleted triangle are linked through re-triangulation to form triangular facets obeying STL file rules. To obtain optimized re-triangulation result, a genetic algorithm (GA) is developed and implemented. The GA features optimized initial population, constrained crossover operator, constrained mutation operator and multi-objective fitness evaluation function. Finally, experiments on different amount of data reduction over a digitized sample are conducted with satisfactory results.

Data reduction in integrated reverse engineering and rapid prototyping

In reverse engineering, a digitizer usually generates a large cloud of 3D points data, many of which are not necessary for subsequent applications. When a digitized part is to be manufactured by means of rapid prototyping machines, e.g. stereolithography apparatus (SLA) and selective laser sintering equipment (SLS), etc. there is no need to construct the CAD model of the digitized part. This will be described by the proposed novel method which can construct an STL file (the de facto file format for rapid prototyping machines) directly from digitized part data. In order to reduce storage space and increase computational efficiency for subsequent processes, e.g. slicing, data reduction is achieved based on two criteria: One is the desired percentage data reduction; the other is the maximum bounded error.

Solution of the nonlinear transport equation using modified Picard iteration

The transport and fate of reactive chemicals in groundwater is governed by equations which are often difficult to solve due to the nonlinear relationship between the solute concentrations for the liquid and solid phases. The nonlinearity may cause mass balance errors during the numerical simulation in addition to numerical errors for linear transport system. We have generalized the modified Picard iteration algorithm of Celia et al. 5 for unsaturated flow to solve the nonlinear transport equation. Written in a ‘mixed-form’ formulation, the total solute concentration is expanded in a Taylor series with respect to the solution concentration to linearize the transport equation, which is then solved with a conventional finite element method. Numerical results of this mixed-form algorithm are compared with those obtained with the concentration-based scheme using conventional Picard iteration. In general, the new solver resulted in negligible mass balance errors (< ∥10 −8∥%) and required less computational time than the conventional iteration scheme for the test examples, including transport involving highly nonlinear adsorption under steady-state as well as transient flow conditions. In contrast, mass balance errors resulting from the conventional Picard iteration method were higher than 10% for some highly nonlinear problems. Application of the modified Picard iteration scheme to solve the nonlinear transport equation may greatly reduce the mass balance errors and increase computational efficiency.

Earthquake design forces in regular highway bridges

The microcomputer implementation of a recently developed seismic analysis method for ‘regular’ highway bridges is presented. The method was developed by the Applied Technology Council (ATC), and has been adopted by the American Association of State Highway and Transportation Officials (AASHTO) as a guide. The modeling of the three-dimensional behavior and techniques to reduce computer memory requirements and to increase computation efficiency are described in this paper. The limits of the application of the program are established by a sensitivity study of the effect of skew angle and curvature in a two-span bridge. It is shown that skew angles of less than 15 degrees can be ignored without a significant loss of accuracy.