Sample records for accurate computational approach

  1. A simplified approach to characterizing a kilovoltage source spectrum for accurate dose computation.

    PubMed

    Poirier, Yannick; Kouznetsov, Alexei; Tambasco, Mauro

    2012-06-01

    %. The HVL and kVp are sufficient for characterizing a kV x-ray source spectrum for accurate dose computation. As these parameters can be easily and accurately measured, they provide for a clinically feasible approach to characterizing a kV energy spectrum to be used for patient specific x-ray dose computations. Furthermore, these results provide experimental validation of our novel hybrid dose computation algorithm. © 2012 American Association of Physicists in Medicine.

  2. A new approach to compute accurate velocity of meteors

    NASA Astrophysics Data System (ADS)

    Egal, Auriane; Gural, Peter; Vaubaillon, Jeremie; Colas, Francois; Thuillot, William

    2016-10-01

    The CABERNET project was designed to push the limits of meteoroid orbit measurements by improving the determination of the meteors' velocities. Indeed, despite of the development of the cameras networks dedicated to the observation of meteors, there is still an important discrepancy between the measured orbits of meteoroids computed and the theoretical results. The gap between the observed and theoretic semi-major axis of the orbits is especially significant; an accurate determination of the orbits of meteoroids therefore largely depends on the computation of the pre-atmospheric velocities. It is then imperative to dig out how to increase the precision of the measurements of the velocity.In this work, we perform an analysis of different methods currently used to compute the velocities and trajectories of the meteors. They are based on the intersecting planes method developed by Ceplecha (1987), the least squares method of Borovicka (1990), and the multi-parameter fitting (MPF) method published by Gural (2012).In order to objectively compare the performances of these techniques, we have simulated realistic meteors ('fakeors') reproducing the different error measurements of many cameras networks. Some fakeors are built following the propagation models studied by Gural (2012), and others created by numerical integrations using the Borovicka et al. 2007 model. Different optimization techniques have also been investigated in order to pick the most suitable one to solve the MPF, and the influence of the geometry of the trajectory on the result is also presented.We will present here the results of an improved implementation of the multi-parameter fitting that allow an accurate orbit computation of meteors with CABERNET. The comparison of different velocities computation seems to show that if the MPF is by far the best method to solve the trajectory and the velocity of a meteor, the ill-conditioning of the costs functions used can lead to large estimate errors for noisy

  3. Accurate atom-mapping computation for biochemical reactions.

    PubMed

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  4. A streamline splitting pore-network approach for computationally inexpensive and accurate simulation of transport in porous media

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mehmani, Yashar; Oostrom, Martinus; Balhoff, Matthew

    2014-03-20

    Several approaches have been developed in the literature for solving flow and transport at the pore-scale. Some authors use a direct modeling approach where the fundamental flow and transport equations are solved on the actual pore-space geometry. Such direct modeling, while very accurate, comes at a great computational cost. Network models are computationally more efficient because the pore-space morphology is approximated. Typically, a mixed cell method (MCM) is employed for solving the flow and transport system which assumes pore-level perfect mixing. This assumption is invalid at moderate to high Peclet regimes. In this work, a novel Eulerian perspective on modelingmore » flow and transport at the pore-scale is developed. The new streamline splitting method (SSM) allows for circumventing the pore-level perfect mixing assumption, while maintaining the computational efficiency of pore-network models. SSM was verified with direct simulations and excellent matches were obtained against micromodel experiments across a wide range of pore-structure and fluid-flow parameters. The increase in the computational cost from MCM to SSM is shown to be minimal, while the accuracy of SSM is much higher than that of MCM and comparable to direct modeling approaches. Therefore, SSM can be regarded as an appropriate balance between incorporating detailed physics and controlling computational cost. The truly predictive capability of the model allows for the study of pore-level interactions of fluid flow and transport in different porous materials. In this paper, we apply SSM and MCM to study the effects of pore-level mixing on transverse dispersion in 3D disordered granular media.« less

  5. Automated Development of Accurate Algorithms and Efficient Codes for Computational Aeroacoustics

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.; Dyson, Rodger W.

    1999-01-01

    The simulation of sound generation and propagation in three space dimensions with realistic aircraft components is a very large time dependent computation with fine details. Simulations in open domains with embedded objects require accurate and robust algorithms for propagation, for artificial inflow and outflow boundaries, and for the definition of geometrically complex objects. The development, implementation, and validation of methods for solving these demanding problems is being done to support the NASA pillar goals for reducing aircraft noise levels. Our goal is to provide algorithms which are sufficiently accurate and efficient to produce usable results rapidly enough to allow design engineers to study the effects on sound levels of design changes in propulsion systems, and in the integration of propulsion systems with airframes. There is a lack of design tools for these purposes at this time. Our technical approach to this problem combines the development of new, algorithms with the use of Mathematica and Unix utilities to automate the algorithm development, code implementation, and validation. We use explicit methods to ensure effective implementation by domain decomposition for SPMD parallel computing. There are several orders of magnitude difference in the computational efficiencies of the algorithms which we have considered. We currently have new artificial inflow and outflow boundary conditions that are stable, accurate, and unobtrusive, with implementations that match the accuracy and efficiency of the propagation methods. The artificial numerical boundary treatments have been proven to have solutions which converge to the full open domain problems, so that the error from the boundary treatments can be driven as low as is required. The purpose of this paper is to briefly present a method for developing highly accurate algorithms for computational aeroacoustics, the use of computer automation in this process, and a brief survey of the algorithms that

  6. An Accurate and Computationally Efficient Model for Membrane-Type Circular-Symmetric Micro-Hotplates

    PubMed Central

    Khan, Usman; Falconi, Christian

    2014-01-01

    Ideally, the design of high-performance micro-hotplates would require a large number of simulations because of the existence of many important design parameters as well as the possibly crucial effects of both spread and drift. However, the computational cost of FEM simulations, which are the only available tool for accurately predicting the temperature in micro-hotplates, is very high. As a result, micro-hotplate designers generally have no effective simulation-tools for the optimization. In order to circumvent these issues, here, we propose a model for practical circular-symmetric micro-hot-plates which takes advantage of modified Bessel functions, computationally efficient matrix-approach for considering the relevant boundary conditions, Taylor linearization for modeling the Joule heating and radiation losses, and external-region-segmentation strategy in order to accurately take into account radiation losses in the entire micro-hotplate. The proposed model is almost as accurate as FEM simulations and two to three orders of magnitude more computationally efficient (e.g., 45 s versus more than 8 h). The residual errors, which are mainly associated to the undesired heating in the electrical contacts, are small (e.g., few degrees Celsius for an 800 °C operating temperature) and, for important analyses, almost constant. Therefore, we also introduce a computationally-easy single-FEM-compensation strategy in order to reduce the residual errors to about 1 °C. As illustrative examples of the power of our approach, we report the systematic investigation of a spread in the membrane thermal conductivity and of combined variations of both ambient and bulk temperatures. Our model enables a much faster characterization of micro-hotplates and, thus, a much more effective optimization prior to fabrication. PMID:24763214

  7. Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

    PubMed Central

    Reaz, Rezwana; Bayzid, Md. Shamsuzzoha; Rahman, M. Sohel

    2014-01-01

    Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets. PMID:25117474

  8. Accurate analytical modeling of junctionless DG-MOSFET by green's function approach

    NASA Astrophysics Data System (ADS)

    Nandi, Ashutosh; Pandey, Nilesh

    2017-11-01

    An accurate analytical model of Junctionless double gate MOSFET (JL-DG-MOSFET) in the subthreshold regime of operation is developed in this work using green's function approach. The approach considers 2-D mixed boundary conditions and multi-zone techniques to provide an exact analytical solution to 2-D Poisson's equation. The Fourier coefficients are calculated correctly to derive the potential equations that are further used to model the channel current and subthreshold slope of the device. The threshold voltage roll-off is computed from parallel shifts of Ids-Vgs curves between the long channel and short-channel devices. It is observed that the green's function approach of solving 2-D Poisson's equation in both oxide and silicon region can accurately predict channel potential, subthreshold current (Isub), threshold voltage (Vt) roll-off and subthreshold slope (SS) of both long & short channel devices designed with different doping concentrations and higher as well as lower tsi/tox ratio. All the analytical model results are verified through comparisons with TCAD Sentaurus simulation results. It is observed that the model matches quite well with TCAD device simulations.

  9. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.

    PubMed

    Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L

    2016-01-01

    Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples. © 2016 Elsevier Inc. All rights reserved.

  10. Accurate computation of gravitational field of a tesseroid

    NASA Astrophysics Data System (ADS)

    Fukushima, Toshio

    2018-02-01

    We developed an accurate method to compute the gravitational field of a tesseroid. The method numerically integrates a surface integral representation of the gravitational potential of the tesseroid by conditionally splitting its line integration intervals and by using the double exponential quadrature rule. Then, it evaluates the gravitational acceleration vector and the gravity gradient tensor by numerically differentiating the numerically integrated potential. The numerical differentiation is conducted by appropriately switching the central and the single-sided second-order difference formulas with a suitable choice of the test argument displacement. If necessary, the new method is extended to the case of a general tesseroid with the variable density profile, the variable surface height functions, and/or the variable intervals in longitude or in latitude. The new method is capable of computing the gravitational field of the tesseroid independently on the location of the evaluation point, namely whether outside, near the surface of, on the surface of, or inside the tesseroid. The achievable precision is 14-15 digits for the potential, 9-11 digits for the acceleration vector, and 6-8 digits for the gradient tensor in the double precision environment. The correct digits are roughly doubled if employing the quadruple precision computation. The new method provides a reliable procedure to compute the topographic gravitational field, especially that near, on, and below the surface. Also, it could potentially serve as a sure reference to complement and elaborate the existing approaches using the Gauss-Legendre quadrature or other standard methods of numerical integration.

  11. Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tong, Dudu; Yang, Sichun; Lu, Lanyuan

    2016-06-20

    Structure modellingviasmall-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested againstmore » other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by theqrange of the SAXS data) become necessary for effective structure modelling.« less

  12. Computer-assisted adjuncts for aneurysmal morphologic assessment: toward more precise and accurate approaches

    NASA Astrophysics Data System (ADS)

    Rajabzadeh-Oghaz, Hamidreza; Varble, Nicole; Davies, Jason M.; Mowla, Ashkan; Shakir, Hakeem J.; Sonig, Ashish; Shallwani, Hussain; Snyder, Kenneth V.; Levy, Elad I.; Siddiqui, Adnan H.; Meng, Hui

    2017-03-01

    Neurosurgeons currently base most of their treatment decisions for intracranial aneurysms (IAs) on morphological measurements made manually from 2D angiographic images. These measurements tend to be inaccurate because 2D measurements cannot capture the complex geometry of IAs and because manual measurements are variable depending on the clinician's experience and opinion. Incorrect morphological measurements may lead to inappropriate treatment strategies. In order to improve the accuracy and consistency of morphological analysis of IAs, we have developed an image-based computational tool, AView. In this study, we quantified the accuracy of computer-assisted adjuncts of AView for aneurysmal morphologic assessment by performing measurement on spheres of known size and anatomical IA models. AView has an average morphological error of 0.56% in size and 2.1% in volume measurement. We also investigate the clinical utility of this tool on a retrospective clinical dataset and compare size and neck diameter measurement between 2D manual and 3D computer-assisted measurement. The average error was 22% and 30% in the manual measurement of size and aneurysm neck diameter, respectively. Inaccuracies due to manual measurements could therefore lead to wrong treatment decisions in 44% and inappropriate treatment strategies in 33% of the IAs. Furthermore, computer-assisted analysis of IAs improves the consistency in measurement among clinicians by 62% in size and 82% in neck diameter measurement. We conclude that AView dramatically improves accuracy for morphological analysis. These results illustrate the necessity of a computer-assisted approach for the morphological analysis of IAs.

  13. Computer-based personality judgments are more accurate than those made by humans.

    PubMed

    Youyou, Wu; Kosinski, Michal; Stillwell, David

    2015-01-27

    Judging others' personalities is an essential skill in successful social living, as personality is a key driver behind people's interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants' Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy.

  14. New approach based on tetrahedral-mesh geometry for accurate 4D Monte Carlo patient-dose calculation

    NASA Astrophysics Data System (ADS)

    Han, Min Cheol; Yeom, Yeon Soo; Kim, Chan Hyeong; Kim, Seonghoon; Sohn, Jason W.

    2015-02-01

    In the present study, to achieve accurate 4D Monte Carlo dose calculation in radiation therapy, we devised a new approach that combines (1) modeling of the patient body using tetrahedral-mesh geometry based on the patient’s 4D CT data, (2) continuous movement/deformation of the tetrahedral patient model by interpolation of deformation vector fields acquired through deformable image registration, and (3) direct transportation of radiation particles during the movement and deformation of the tetrahedral patient model. The results of our feasibility study show that it is certainly possible to construct 4D patient models (= phantoms) with sufficient accuracy using the tetrahedral-mesh geometry and to directly transport radiation particles during continuous movement and deformation of the tetrahedral patient model. This new approach not only produces more accurate dose distribution in the patient but also replaces the current practice of using multiple 3D voxel phantoms and combining multiple dose distributions after Monte Carlo simulations. For routine clinical application of our new approach, the use of fast automatic segmentation algorithms is a must. In order to achieve, simultaneously, both dose accuracy and computation speed, the number of tetrahedrons for the lungs should be optimized. Although the current computation speed of our new 4D Monte Carlo simulation approach is slow (i.e. ~40 times slower than that of the conventional dose accumulation approach), this problem is resolvable by developing, in Geant4, a dedicated navigation class optimized for particle transportation in tetrahedral-mesh geometry.

  15. An accurate computational method for the diffusion regime verification

    NASA Astrophysics Data System (ADS)

    Zhokh, Alexey A.; Strizhak, Peter E.

    2018-04-01

    The diffusion regime (sub-diffusive, standard, or super-diffusive) is defined by the order of the derivative in the corresponding transport equation. We develop an accurate computational method for the direct estimation of the diffusion regime. The method is based on the derivative order estimation using the asymptotic analytic solutions of the diffusion equation with the integer order and the time-fractional derivatives. The robustness and the computational cheapness of the proposed method are verified using the experimental methane and methyl alcohol transport kinetics through the catalyst pellet.

  16. Computer-based personality judgments are more accurate than those made by humans

    PubMed Central

    Youyou, Wu; Kosinski, Michal; Stillwell, David

    2015-01-01

    Judging others’ personalities is an essential skill in successful social living, as personality is a key driver behind people’s interactions, behaviors, and emotions. Although accurate personality judgments stem from social-cognitive skills, developments in machine learning show that computer models can also make valid judgments. This study compares the accuracy of human and computer-based personality judgments, using a sample of 86,220 volunteers who completed a 100-item personality questionnaire. We show that (i) computer predictions based on a generic digital footprint (Facebook Likes) are more accurate (r = 0.56) than those made by the participants’ Facebook friends using a personality questionnaire (r = 0.49); (ii) computer models show higher interjudge agreement; and (iii) computer personality judgments have higher external validity when predicting life outcomes such as substance use, political attitudes, and physical health; for some outcomes, they even outperform the self-rated personality scores. Computers outpacing humans in personality judgment presents significant opportunities and challenges in the areas of psychological assessment, marketing, and privacy. PMID:25583507

  17. Fast and accurate computation of projected two-point functions

    NASA Astrophysics Data System (ADS)

    Grasshorn Gebhardt, Henry S.; Jeong, Donghui

    2018-01-01

    We present the two-point function from the fast and accurate spherical Bessel transformation (2-FAST) algorithmOur code is available at https://github.com/hsgg/twoFAST. for a fast and accurate computation of integrals involving one or two spherical Bessel functions. These types of integrals occur when projecting the galaxy power spectrum P (k ) onto the configuration space, ξℓν(r ), or spherical harmonic space, Cℓ(χ ,χ'). First, we employ the FFTLog transformation of the power spectrum to divide the calculation into P (k )-dependent coefficients and P (k )-independent integrations of basis functions multiplied by spherical Bessel functions. We find analytical expressions for the latter integrals in terms of special functions, for which recursion provides a fast and accurate evaluation. The algorithm, therefore, circumvents direct integration of highly oscillating spherical Bessel functions.

  18. Petascale self-consistent electromagnetic computations using scalable and accurate algorithms for complex structures

    NASA Astrophysics Data System (ADS)

    Cary, John R.; Abell, D.; Amundson, J.; Bruhwiler, D. L.; Busby, R.; Carlsson, J. A.; Dimitrov, D. A.; Kashdan, E.; Messmer, P.; Nieter, C.; Smithe, D. N.; Spentzouris, P.; Stoltz, P.; Trines, R. M.; Wang, H.; Werner, G. R.

    2006-09-01

    As the size and cost of particle accelerators escalate, high-performance computing plays an increasingly important role; optimization through accurate, detailed computermodeling increases performance and reduces costs. But consequently, computer simulations face enormous challenges. Early approximation methods, such as expansions in distance from the design orbit, were unable to supply detailed accurate results, such as in the computation of wake fields in complex cavities. Since the advent of message-passing supercomputers with thousands of processors, earlier approximations are no longer necessary, and it is now possible to compute wake fields, the effects of dampers, and self-consistent dynamics in cavities accurately. In this environment, the focus has shifted towards the development and implementation of algorithms that scale to large numbers of processors. So-called charge-conserving algorithms evolve the electromagnetic fields without the need for any global solves (which are difficult to scale up to many processors). Using cut-cell (or embedded) boundaries, these algorithms can simulate the fields in complex accelerator cavities with curved walls. New implicit algorithms, which are stable for any time-step, conserve charge as well, allowing faster simulation of structures with details small compared to the characteristic wavelength. These algorithmic and computational advances have been implemented in the VORPAL7 Framework, a flexible, object-oriented, massively parallel computational application that allows run-time assembly of algorithms and objects, thus composing an application on the fly.

  19. Microarray-based cancer prediction using soft computing approach.

    PubMed

    Wang, Xiaosheng; Gotoh, Osamu

    2009-05-26

    One of the difficulties in using gene expression profiles to predict cancer is how to effectively select a few informative genes to construct accurate prediction models from thousands or ten thousands of genes. We screen highly discriminative genes and gene pairs to create simple prediction models involved in single genes or gene pairs on the basis of soft computing approach and rough set theory. Accurate cancerous prediction is obtained when we apply the simple prediction models for four cancerous gene expression datasets: CNS tumor, colon tumor, lung cancer and DLBCL. Some genes closely correlated with the pathogenesis of specific or general cancers are identified. In contrast with other models, our models are simple, effective and robust. Meanwhile, our models are interpretable for they are based on decision rules. Our results demonstrate that very simple models may perform well on cancerous molecular prediction and important gene markers of cancer can be detected if the gene selection approach is chosen reasonably.

  20. Beyond mean-field approximations for accurate and computationally efficient models of on-lattice chemical kinetics

    NASA Astrophysics Data System (ADS)

    Pineda, M.; Stamatakis, M.

    2017-07-01

    Modeling the kinetics of surface catalyzed reactions is essential for the design of reactors and chemical processes. The majority of microkinetic models employ mean-field approximations, which lead to an approximate description of catalytic kinetics by assuming spatially uncorrelated adsorbates. On the other hand, kinetic Monte Carlo (KMC) methods provide a discrete-space continuous-time stochastic formulation that enables an accurate treatment of spatial correlations in the adlayer, but at a significant computation cost. In this work, we use the so-called cluster mean-field approach to develop higher order approximations that systematically increase the accuracy of kinetic models by treating spatial correlations at a progressively higher level of detail. We further demonstrate our approach on a reduced model for NO oxidation incorporating first nearest-neighbor lateral interactions and construct a sequence of approximations of increasingly higher accuracy, which we compare with KMC and mean-field. The latter is found to perform rather poorly, overestimating the turnover frequency by several orders of magnitude for this system. On the other hand, our approximations, while more computationally intense than the traditional mean-field treatment, still achieve tremendous computational savings compared to KMC simulations, thereby opening the way for employing them in multiscale modeling frameworks.

  1. RICO: A NEW APPROACH FOR FAST AND ACCURATE REPRESENTATION OF THE COSMOLOGICAL RECOMBINATION HISTORY

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fendt, W. A.; Wandelt, B. D.; Chluba, J.

    2009-04-15

    We present RICO, a code designed to compute the ionization fraction of the universe during the epoch of hydrogen and helium recombination with an unprecedented combination of speed and accuracy. This is accomplished by training the machine learning code PICO on the calculations of a multilevel cosmological recombination code which self-consistently includes several physical processes that were neglected previously. After training, RICO is used to fit the free electron fraction as a function of the cosmological parameters. While, for example, at low redshifts (z {approx}< 900), much of the net change in the ionization fraction can be captured by loweringmore » the hydrogen fudge factor in RECFAST by about 3%, RICO provides a means of effectively using the accurate ionization history of the full recombination code in the standard cosmological parameter estimation framework without the need to add new or refined fudge factors or functions to a simple recombination model. Within the new approach presented here, it is easy to update RICO whenever a more accurate full recombination code becomes available. Once trained, RICO computes the cosmological ionization history with negligible fitting error in {approx}10 ms, a speedup of at least 10{sup 6} over the full recombination code that was used here. Also RICO is able to reproduce the ionization history of the full code to a level well below 0.1%, thereby ensuring that the theoretical power spectra of cosmic microwave background (CMB) fluctuations can be computed to sufficient accuracy and speed for analysis from upcoming CMB experiments like Planck. Furthermore, it will enable cross-checking different recombination codes across cosmological parameter space, a comparison that will be very important in order to assure the accurate interpretation of future CMB data.« less

  2. Creation of Anatomically Accurate Computer-Aided Design (CAD) Solid Models from Medical Images

    NASA Technical Reports Server (NTRS)

    Stewart, John E.; Graham, R. Scott; Samareh, Jamshid A.; Oberlander, Eric J.; Broaddus, William C.

    1999-01-01

    Most surgical instrumentation and implants used in the world today are designed with sophisticated Computer-Aided Design (CAD)/Computer-Aided Manufacturing (CAM) software. This software automates the mechanical development of a product from its conceptual design through manufacturing. CAD software also provides a means of manipulating solid models prior to Finite Element Modeling (FEM). Few surgical products are designed in conjunction with accurate CAD models of human anatomy because of the difficulty with which these models are created. We have developed a novel technique that creates anatomically accurate, patient specific CAD solids from medical images in a matter of minutes.

  3. Improved patient size estimates for accurate dose calculations in abdomen computed tomography

    NASA Astrophysics Data System (ADS)

    Lee, Chang-Lae

    2017-07-01

    The radiation dose of CT (computed tomography) is generally represented by the CTDI (CT dose index). CTDI, however, does not accurately predict the actual patient doses for different human body sizes because it relies on a cylinder-shaped head (diameter : 16 cm) and body (diameter : 32 cm) phantom. The purpose of this study was to eliminate the drawbacks of the conventional CTDI and to provide more accurate radiation dose information. Projection radiographs were obtained from water cylinder phantoms of various sizes, and the sizes of the water cylinder phantoms were calculated and verified using attenuation profiles. The effective diameter was also calculated using the attenuation of the abdominal projection radiographs of 10 patients. When the results of the attenuation-based method and the geometry-based method shown were compared with the results of the reconstructed-axial-CT-image-based method, the effective diameter of the attenuation-based method was found to be similar to the effective diameter of the reconstructed-axial-CT-image-based method, with a difference of less than 3.8%, but the geometry-based method showed a difference of less than 11.4%. This paper proposes a new method of accurately computing the radiation dose of CT based on the patient sizes. This method computes and provides the exact patient dose before the CT scan, and can therefore be effectively used for imaging and dose control.

  4. Accurate computation of survival statistics in genome-wide studies.

    PubMed

    Vandin, Fabio; Papoutsaki, Alexandra; Raphael, Benjamin J; Upfal, Eli

    2015-05-01

    A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations.

  5. Accurate Computation of Survival Statistics in Genome-Wide Studies

    PubMed Central

    Vandin, Fabio; Papoutsaki, Alexandra; Raphael, Benjamin J.; Upfal, Eli

    2015-01-01

    A key challenge in genomics is to identify genetic variants that distinguish patients with different survival time following diagnosis or treatment. While the log-rank test is widely used for this purpose, nearly all implementations of the log-rank test rely on an asymptotic approximation that is not appropriate in many genomics applications. This is because: the two populations determined by a genetic variant may have very different sizes; and the evaluation of many possible variants demands highly accurate computation of very small p-values. We demonstrate this problem for cancer genomics data where the standard log-rank test leads to many false positive associations between somatic mutations and survival time. We develop and analyze a novel algorithm, Exact Log-rank Test (ExaLT), that accurately computes the p-value of the log-rank statistic under an exact distribution that is appropriate for any size populations. We demonstrate the advantages of ExaLT on data from published cancer genomics studies, finding significant differences from the reported p-values. We analyze somatic mutations in six cancer types from The Cancer Genome Atlas (TCGA), finding mutations with known association to survival as well as several novel associations. In contrast, standard implementations of the log-rank test report dozens-hundreds of likely false positive associations as more significant than these known associations. PMID:25950620

  6. Development of highly accurate approximate scheme for computing the charge transfer integral

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pershin, Anton; Szalay, Péter G.

    The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, itmore » was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the “exact” scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the “exact” calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.« less

  7. Vision drives accurate approach behavior during prey capture in laboratory mice

    PubMed Central

    Hoy, Jennifer L.; Yavorska, Iryna; Wehr, Michael; Niell, Cristopher M.

    2016-01-01

    Summary The ability to genetically identify and manipulate neural circuits in the mouse is rapidly advancing our understanding of visual processing in the mammalian brain [1,2]. However, studies investigating the circuitry that underlies complex ethologically-relevant visual behaviors in the mouse have been primarily restricted to fear responses [3–5]. Here, we show that a laboratory strain of mouse (Mus musculus, C57BL/6J) robustly pursues, captures and consumes live insect prey, and that vision is necessary for mice to perform the accurate orienting and approach behaviors leading to capture. Specifically, we differentially perturbed visual or auditory input in mice and determined that visual input is required for accurate approach, allowing maintenance of bearing to within 11 degrees of the target on average during pursuit. While mice were able to capture prey without vision, the accuracy of their approaches and capture rate dramatically declined. To better explore the contribution of vision to this behavior, we developed a simple assay that isolated visual cues and simplified analysis of the visually guided approach. Together, our results demonstrate that laboratory mice are capable of exhibiting dynamic and accurate visually-guided approach behaviors, and provide a means to estimate the visual features that drive behavior within an ethological context. PMID:27773567

  8. Computational approaches to computational aero-acoustics

    NASA Technical Reports Server (NTRS)

    Hardin, Jay C.

    1996-01-01

    The various techniques by which the goal of computational aeroacoustics (the calculation and noise prediction of a fluctuating fluid flow) may be achieved are reviewed. The governing equations for compressible fluid flow are presented. The direct numerical simulation approach is shown to be computationally intensive for high Reynolds number viscous flows. Therefore, other approaches, such as the acoustic analogy, vortex models and various perturbation techniques that aim to break the analysis into a viscous part and an acoustic part are presented. The choice of the approach is shown to be problem dependent.

  9. An Accurate and Dynamic Computer Graphics Muscle Model

    NASA Technical Reports Server (NTRS)

    Levine, David Asher

    1997-01-01

    A computer based musculo-skeletal model was developed at the University in the departments of Mechanical and Biomedical Engineering. This model accurately represents human shoulder kinematics. The result of this model is the graphical display of bones moving through an appropriate range of motion based on inputs of EMGs and external forces. The need existed to incorporate a geometric muscle model in the larger musculo-skeletal model. Previous muscle models did not accurately represent muscle geometries, nor did they account for the kinematics of tendons. This thesis covers the creation of a new muscle model for use in the above musculo-skeletal model. This muscle model was based on anatomical data from the Visible Human Project (VHP) cadaver study. Two-dimensional digital images from the VHP were analyzed and reconstructed to recreate the three-dimensional muscle geometries. The recreated geometries were smoothed, reduced, and sliced to form data files defining the surfaces of each muscle. The muscle modeling function opened these files during run-time and recreated the muscle surface. The modeling function applied constant volume limitations to the muscle and constant geometry limitations to the tendons.

  10. A Unified Methodology for Computing Accurate Quaternion Color Moments and Moment Invariants.

    PubMed

    Karakasis, Evangelos G; Papakostas, George A; Koulouriotis, Dimitrios E; Tourassis, Vassilios D

    2014-02-01

    In this paper, a general framework for computing accurate quaternion color moments and their corresponding invariants is proposed. The proposed unified scheme arose by studying the characteristics of different orthogonal polynomials. These polynomials are used as kernels in order to form moments, the invariants of which can easily be derived. The resulted scheme permits the usage of any polynomial-like kernel in a unified and consistent way. The resulted moments and moment invariants demonstrate robustness to noisy conditions and high discriminative power. Additionally, in the case of continuous moments, accurate computations take place to avoid approximation errors. Based on this general methodology, the quaternion Tchebichef, Krawtchouk, Dual Hahn, Legendre, orthogonal Fourier-Mellin, pseudo Zernike and Zernike color moments, and their corresponding invariants are introduced. A selected paradigm presents the reconstruction capability of each moment family, whereas proper classification scenarios evaluate the performance of color moment invariants.

  11. An accurate model for the computation of the dose of protons in water.

    PubMed

    Embriaco, A; Bellinzona, V E; Fontana, A; Rotondi, A

    2017-06-01

    The accurate and fast calculation of the dose in proton radiation therapy is an essential ingredient for successful treatments. We propose a novel approach with a minimal number of parameters. The approach is based on the exact calculation of the electromagnetic part of the interaction, namely the Molière theory of the multiple Coulomb scattering for the transversal 1D projection and the Bethe-Bloch formula for the longitudinal stopping power profile, including a gaussian energy straggling. To this e.m. contribution the nuclear proton-nucleus interaction is added with a simple two-parameter model. Then, the non gaussian lateral profile is used to calculate the radial dose distribution with a method that assumes the cylindrical symmetry of the distribution. The results, obtained with a fast C++ based computational code called MONET (MOdel of ioN dosE for Therapy), are in very good agreement with the FLUKA MC code, within a few percent in the worst case. This study provides a new tool for fast dose calculation or verification, possibly for clinical use. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  12. Computational approaches to predict bacteriophage–host relationships

    PubMed Central

    Edwards, Robert A.; McNair, Katelyn; Faust, Karoline; Raes, Jeroen; Dutilh, Bas E.

    2015-01-01

    Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. PMID:26657537

  13. Accurate Bit Error Rate Calculation for Asynchronous Chaos-Based DS-CDMA over Multipath Channel

    NASA Astrophysics Data System (ADS)

    Kaddoum, Georges; Roviras, Daniel; Chargé, Pascal; Fournier-Prunaret, Daniele

    2009-12-01

    An accurate approach to compute the bit error rate expression for multiuser chaosbased DS-CDMA system is presented in this paper. For more realistic communication system a slow fading multipath channel is considered. A simple RAKE receiver structure is considered. Based on the bit energy distribution, this approach compared to others computation methods existing in literature gives accurate results with low computation charge. Perfect estimation of the channel coefficients with the associated delays and chaos synchronization is assumed. The bit error rate is derived in terms of the bit energy distribution, the number of paths, the noise variance, and the number of users. Results are illustrated by theoretical calculations and numerical simulations which point out the accuracy of our approach.

  14. Multislice Computed Tomography Accurately Detects Stenosis in Coronary Artery Bypass Conduits

    PubMed Central

    Duran, Cihan; Sagbas, Ertan; Caynak, Baris; Sanisoglu, Ilhan; Akpinar, Belhhan; Gulbaran, Murat

    2007-01-01

    The aim of this study was to evaluate the accuracy of multislice computed tomography in detecting graft stenosis or occlusion after coronary artery bypass grafting, using coronary angiography as the standard. From January 2005 through May 2006, 25 patients (19 men and 6 women; mean age, 54 ± 11.3 years) underwent diagnostic investigation of their bypass grafts by multislice computed tomography within 1 month of coronary angiography. The mean time elapsed after coronary artery bypass grafting was 6.2 years. In these 25 patients, we examined 65 bypass conduits (24 arterial and 41 venous) and 171 graft segments (the shaft, proximal anastomosis, and distal anastomosis). Compared with coronary angiography, the segment-based sensitivity, specificity, and positive and negative predictive values of multislice computed tomography in the evaluation of stenosis were 89%, 100%, 100%, and 99%, respectively. The patency rate for multislice compu-ted tomography was 85% (55/65: 3 arterial and 7 venous grafts were occluded), with 100% sensitivity and specificity. From these data, we conclude that multislice computed tomography can accurately evaluate the patency and stenosis of bypass grafts during outpatient follow-up. PMID:17948078

  15. An approach for accurate simulation of liquid mixing in a T-shaped micromixer.

    PubMed

    Matsunaga, Takuya; Lee, Ho-Joon; Nishino, Koichi

    2013-04-21

    In this paper, we propose a new computational method for efficient evaluation of the fluid mixing behaviour in a T-shaped micromixer with a rectangular cross section at high Schmidt number under steady state conditions. Our approach enables a low-cost high-quality simulation based on tracking of fluid particles for convective fluid mixing and posterior solving of a model of the species equation for molecular diffusion. The examined parameter range is Re = 1.33 × 10(-2) to 240 at Sc = 3600. The proposed method is shown to simulate well the mixing quality even in the engulfment regime, where the ordinary grid-based simulation is not able to obtain accurate solutions with affordable mesh sizes due to the numerical diffusion at high Sc. The obtained results agree well with a backward random-walk Monte Carlo simulation, by which the accuracy of the proposed method is verified. For further investigation of the characteristics of the proposed method, the Sc dependency is examined in a wide range of Sc from 10 to 3600 at Re = 200. The study reveals that the model discrepancy error emerges more significantly in the concentration distribution at lower Sc, while the resulting mixing quality is accurate over the entire range.

  16. A simple, stable, and accurate linear tetrahedral finite element for transient, nearly, and fully incompressible solid dynamics: A dynamic variational multiscale approach [A simple, stable, and accurate tetrahedral finite element for transient, nearly incompressible, linear and nonlinear elasticity: A dynamic variational multiscale approach

    DOE PAGES

    Scovazzi, Guglielmo; Carnes, Brian; Zeng, Xianyi; ...

    2015-11-12

    Here, we propose a new approach for the stabilization of linear tetrahedral finite elements in the case of nearly incompressible transient solid dynamics computations. Our method is based on a mixed formulation, in which the momentum equation is complemented by a rate equation for the evolution of the pressure field, approximated with piece-wise linear, continuous finite element functions. The pressure equation is stabilized to prevent spurious pressure oscillations in computations. Incidentally, it is also shown that many stabilized methods previously developed for the static case do not generalize easily to transient dynamics. Extensive tests in the context of linear andmore » nonlinear elasticity are used to corroborate the claim that the proposed method is robust, stable, and accurate.« less

  17. A simple, stable, and accurate linear tetrahedral finite element for transient, nearly, and fully incompressible solid dynamics: A dynamic variational multiscale approach [A simple, stable, and accurate tetrahedral finite element for transient, nearly incompressible, linear and nonlinear elasticity: A dynamic variational multiscale approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Scovazzi, Guglielmo; Carnes, Brian; Zeng, Xianyi

    Here, we propose a new approach for the stabilization of linear tetrahedral finite elements in the case of nearly incompressible transient solid dynamics computations. Our method is based on a mixed formulation, in which the momentum equation is complemented by a rate equation for the evolution of the pressure field, approximated with piece-wise linear, continuous finite element functions. The pressure equation is stabilized to prevent spurious pressure oscillations in computations. Incidentally, it is also shown that many stabilized methods previously developed for the static case do not generalize easily to transient dynamics. Extensive tests in the context of linear andmore » nonlinear elasticity are used to corroborate the claim that the proposed method is robust, stable, and accurate.« less

  18. Time accurate application of the MacCormack 2-4 scheme on massively parallel computers

    NASA Technical Reports Server (NTRS)

    Hudson, Dale A.; Long, Lyle N.

    1995-01-01

    Many recent computational efforts in turbulence and acoustics research have used higher order numerical algorithms. One popular method has been the explicit MacCormack 2-4 scheme. The MacCormack 2-4 scheme is second order accurate in time and fourth order accurate in space, and is stable for CFL's below 2/3. Current research has shown that the method can give accurate results but does exhibit significant Gibbs phenomena at sharp discontinuities. The impact of adding Jameson type second, third, and fourth order artificial viscosity was examined here. Category 2 problems, the nonlinear traveling wave and the Riemann problem, were computed using a CFL number of 0.25. This research has found that dispersion errors can be significantly reduced or nearly eliminated by using a combination of second and third order terms in the damping. Use of second and fourth order terms reduced the magnitude of dispersion errors but not as effectively as the second and third order combination. The program was coded using Thinking Machine's CM Fortran, a variant of Fortran 90/High Performance Fortran, and was executed on a 2K CM-200. Simple extrapolation boundary conditions were used for both problems.

  19. Parallel Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC Simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Candel, A.; Kabel, A.; Lee, L.

    Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell)more » approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.« less

  20. Using an In-House Approach to Computer-Assisted Design and Computer-Aided Manufacturing Reconstruction of the Maxilla.

    PubMed

    Numajiri, Toshiaki; Morita, Daiki; Nakamura, Hiroko; Tsujiko, Shoko; Yamochi, Ryo; Sowa, Yoshihiro; Toyoda, Kenichiro; Tsujikawa, Takahiro; Arai, Akihito; Yasuda, Makoto; Hirano, Shigeru

    2018-06-01

    Computer-assisted design (CAD) and computer-aided manufacturing (CAM) techniques are in widespread use for maxillofacial reconstruction. However, CAD/CAM surgical guides are commercially available only in limited areas. To use this technology in areas where these commercial guides are not available, the authors developed a CAD/CAM technique in which all processes are performed by the surgeon (in-house approach). The authors describe their experience and the characteristics of their in-house CAD/CAM reconstruction of the maxilla. This was a retrospective study of maxillary reconstruction with a free osteocutaneous flap. Free CAD software was used for virtual surgery and to design the cutting guides (maxilla and fibula), which were printed by a 3-dimensional printer. After the model surgery and pre-bending of the titanium plates, the actual reconstructions were performed. The authors compared the clinical information, preoperative plan, and postoperative reconstruction data. The reconstruction was judged as accurate if more than 80% of the reconstructed points were within a deviation of 2 mm. Although on-site adjustment was necessary in particular cases, all 4 reconstructions were judged as accurate. In total, 3 days were needed before the surgery for planning, printing, and pre-bending of plates. The average ischemic time was 134 minutes (flap suturing and bone fixation, 70 minutes; vascular anastomoses, 64 minutes). The mean deviation after reconstruction was 0.44 mm (standard deviation, 0.97). The deviations were 67.8% for 1 mm, 93.8% for 2 mm, and 98.6% for 3 mm. The disadvantages of the regular use of CAD/CAM reconstruction are the intraoperative changes in defect size and local tissue scarring. Good accuracy was obtained for CAD/CAM-guided reconstructions based on an in-house approach. The theoretical advantage of computer simulation contributes to the accuracy. An in-house approach could be an option for maxillary reconstruction. Copyright © 2017

  1. Third-Order Incremental Dual-Basis Set Zero-Buffer Approach: An Accurate and Efficient Way To Obtain CCSD and CCSD(T) Energies.

    PubMed

    Zhang, Jun; Dolg, Michael

    2013-07-09

    An efficient way to obtain accurate CCSD and CCSD(T) energies for large systems, i.e., the third-order incremental dual-basis set zero-buffer approach (inc3-db-B0), has been developed and tested. This approach combines the powerful incremental scheme with the dual-basis set method, and along with the new proposed K-means clustering (KM) method and zero-buffer (B0) approximation, can obtain very accurate absolute and relative energies efficiently. We tested the approach for 10 systems of different chemical nature, i.e., intermolecular interactions including hydrogen bonding, dispersion interaction, and halogen bonding; an intramolecular rearrangement reaction; aliphatic and conjugated hydrocarbon chains; three compact covalent molecules; and a water cluster. The results show that the errors for relative energies are <1.94 kJ/mol (or 0.46 kcal/mol), for absolute energies of <0.0026 hartree. By parallelization, our approach can be applied to molecules of more than 30 atoms and more than 100 correlated electrons with high-quality basis set such as cc-pVDZ or cc-pVTZ, saving computational cost by a factor of more than 10-20, compared to traditional implementation. The physical reasons of the success of the inc3-db-B0 approach are also analyzed.

  2. Accurate evaluation of exchange fields in finite element micromagnetic solvers

    NASA Astrophysics Data System (ADS)

    Chang, R.; Escobar, M. A.; Li, S.; Lubarda, M. V.; Lomakin, V.

    2012-04-01

    Quadratic basis functions (QBFs) are implemented for solving the Landau-Lifshitz-Gilbert equation via the finite element method. This involves the introduction of a set of special testing functions compatible with the QBFs for evaluating the Laplacian operator. The results by using QBFs are significantly more accurate than those via linear basis functions. QBF approach leads to significantly more accurate results than conventionally used approaches based on linear basis functions. Importantly QBFs allow reducing the error of computing the exchange field by increasing the mesh density for structured and unstructured meshes. Numerical examples demonstrate the feasibility of the method.

  3. Higher-order accurate space-time schemes for computational astrophysics—Part I: finite volume methods

    NASA Astrophysics Data System (ADS)

    Balsara, Dinshaw S.

    2017-12-01

    As computational astrophysics comes under pressure to become a precision science, there is an increasing need to move to high accuracy schemes for computational astrophysics. The algorithmic needs of computational astrophysics are indeed very special. The methods need to be robust and preserve the positivity of density and pressure. Relativistic flows should remain sub-luminal. These requirements place additional pressures on a computational astrophysics code, which are usually not felt by a traditional fluid dynamics code. Hence the need for a specialized review. The focus here is on weighted essentially non-oscillatory (WENO) schemes, discontinuous Galerkin (DG) schemes and PNPM schemes. WENO schemes are higher order extensions of traditional second order finite volume schemes. At third order, they are most similar to piecewise parabolic method schemes, which are also included. DG schemes evolve all the moments of the solution, with the result that they are more accurate than WENO schemes. PNPM schemes occupy a compromise position between WENO and DG schemes. They evolve an Nth order spatial polynomial, while reconstructing higher order terms up to Mth order. As a result, the timestep can be larger. Time-dependent astrophysical codes need to be accurate in space and time with the result that the spatial and temporal accuracies must be matched. This is realized with the help of strong stability preserving Runge-Kutta schemes and ADER (Arbitrary DERivative in space and time) schemes, both of which are also described. The emphasis of this review is on computer-implementable ideas, not necessarily on the underlying theory.

  4. Accurate paleointensities - the multi-method approach

    NASA Astrophysics Data System (ADS)

    de Groot, Lennart

    2016-04-01

    The accuracy of models describing rapid changes in the geomagnetic field over the past millennia critically depends on the availability of reliable paleointensity estimates. Over the past decade methods to derive paleointensities from lavas (the only recorder of the geomagnetic field that is available all over the globe and through geologic times) have seen significant improvements and various alternative techniques were proposed. The 'classical' Thellier-style approach was optimized and selection criteria were defined in the 'Standard Paleointensity Definitions' (Paterson et al, 2014). The Multispecimen approach was validated and the importance of additional tests and criteria to assess Multispecimen results must be emphasized. Recently, a non-heating, relative paleointensity technique was proposed -the pseudo-Thellier protocol- which shows great potential in both accuracy and efficiency, but currently lacks a solid theoretical underpinning. Here I present work using all three of the aforementioned paleointensity methods on suites of young lavas taken from the volcanic islands of Hawaii, La Palma, Gran Canaria, Tenerife, and Terceira. Many of the sampled cooling units are <100 years old, the actual field strength at the time of cooling is therefore reasonably well known. Rather intuitively, flows that produce coherent results from two or more different paleointensity methods yield the most accurate estimates of the paleofield. Furthermore, the results for some flows pass the selection criteria for one method, but fail in other techniques. Scrutinizing and combing all acceptable results yielded reliable paleointensity estimates for 60-70% of all sampled cooling units - an exceptionally high success rate. This 'multi-method paleointensity approach' therefore has high potential to provide the much-needed paleointensities to improve geomagnetic field models for the Holocene.

  5. Computing 3-D steady supersonic flow via a new Lagrangian approach

    NASA Technical Reports Server (NTRS)

    Loh, C. Y.; Liou, M.-S.

    1993-01-01

    The new Lagrangian method introduced by Loh and Hui (1990) is extended for 3-D steady supersonic flow computation. Details of the conservation form, the implementation of the local Riemann solver, and the Godunov and the high resolution TVD schemes are presented. The new approach is robust yet accurate, capable of handling complicated geometry and reactions between discontinuous waves. It keeps all the advantages claimed in the 2-D method of Loh and Hui, e.g., crisp resolution for a slip surface (contact discontinuity) and automatic grid generation along the stream.

  6. Fast and accurate computation of system matrix for area integral model-based algebraic reconstruction technique

    NASA Astrophysics Data System (ADS)

    Zhang, Shunli; Zhang, Dinghua; Gong, Hao; Ghasemalizadeh, Omid; Wang, Ge; Cao, Guohua

    2014-11-01

    Iterative algorithms, such as the algebraic reconstruction technique (ART), are popular for image reconstruction. For iterative reconstruction, the area integral model (AIM) is more accurate for better reconstruction quality than the line integral model (LIM). However, the computation of the system matrix for AIM is more complex and time-consuming than that for LIM. Here, we propose a fast and accurate method to compute the system matrix for AIM. First, we calculate the intersection of each boundary line of a narrow fan-beam with pixels in a recursive and efficient manner. Then, by grouping the beam-pixel intersection area into six types according to the slopes of the two boundary lines, we analytically compute the intersection area of the narrow fan-beam with the pixels in a simple algebraic fashion. Overall, experimental results show that our method is about three times faster than the Siddon algorithm and about two times faster than the distance-driven model (DDM) in computation of the system matrix. The reconstruction speed of our AIM-based ART is also faster than the LIM-based ART that uses the Siddon algorithm and DDM-based ART, for one iteration. The fast reconstruction speed of our method was accomplished without compromising the image quality.

  7. Accurate complex scaling of three dimensional numerical potentials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cerioni, Alessandro; Genovese, Luigi; Duchemin, Ivan

    2013-05-28

    The complex scaling method, which consists in continuing spatial coordinates into the complex plane, is a well-established method that allows to compute resonant eigenfunctions of the time-independent Schroedinger operator. Whenever it is desirable to apply the complex scaling to investigate resonances in physical systems defined on numerical discrete grids, the most direct approach relies on the application of a similarity transformation to the original, unscaled Hamiltonian. We show that such an approach can be conveniently implemented in the Daubechies wavelet basis set, featuring a very promising level of generality, high accuracy, and no need for artificial convergence parameters. Complex scalingmore » of three dimensional numerical potentials can be efficiently and accurately performed. By carrying out an illustrative resonant state computation in the case of a one-dimensional model potential, we then show that our wavelet-based approach may disclose new exciting opportunities in the field of computational non-Hermitian quantum mechanics.« less

  8. A Computational Approach to Evaluate the Androgenic Affinity of Iprodione, Procymidone, Vinclozolin and Their Metabolites

    PubMed Central

    Fumagalli, Amos; Parravicini, Chiara; Marinovich, Marina; Eberini, Ivano

    2014-01-01

    Our research is aimed at devising and assessing a computational approach to evaluate the affinity of endocrine active substances (EASs) and their metabolites towards the ligand binding domain (LBD) of the androgen receptor (AR) in three distantly related species: human, rat, and zebrafish. We computed the affinity for all the selected molecules following a computational approach based on molecular modelling and docking. Three different classes of molecules with well-known endocrine activity (iprodione, procymidone, vinclozolin, and a selection of their metabolites) were evaluated. Our approach was demonstrated useful as the first step of chemical safety evaluation since ligand-target interaction is a necessary condition for exerting any biological effect. Moreover, a different sensitivity concerning AR LBD was computed for the tested species (rat being the least sensitive of the three). This evidence suggests that, in order not to over−/under-estimate the risks connected with the use of a chemical entity, further in vitro and/or in vivo tests should be carried out only after an accurate evaluation of the most suitable cellular system or animal species. The introduction of in silico approaches to evaluate hazard can accelerate discovery and innovation with a lower economic effort than with a fully wet strategy. PMID:25111804

  9. A computational approach to evaluate the androgenic affinity of iprodione, procymidone, vinclozolin and their metabolites.

    PubMed

    Galli, Corrado Lodovico; Sensi, Cristina; Fumagalli, Amos; Parravicini, Chiara; Marinovich, Marina; Eberini, Ivano

    2014-01-01

    Our research is aimed at devising and assessing a computational approach to evaluate the affinity of endocrine active substances (EASs) and their metabolites towards the ligand binding domain (LBD) of the androgen receptor (AR) in three distantly related species: human, rat, and zebrafish. We computed the affinity for all the selected molecules following a computational approach based on molecular modelling and docking. Three different classes of molecules with well-known endocrine activity (iprodione, procymidone, vinclozolin, and a selection of their metabolites) were evaluated. Our approach was demonstrated useful as the first step of chemical safety evaluation since ligand-target interaction is a necessary condition for exerting any biological effect. Moreover, a different sensitivity concerning AR LBD was computed for the tested species (rat being the least sensitive of the three). This evidence suggests that, in order not to over-/under-estimate the risks connected with the use of a chemical entity, further in vitro and/or in vivo tests should be carried out only after an accurate evaluation of the most suitable cellular system or animal species. The introduction of in silico approaches to evaluate hazard can accelerate discovery and innovation with a lower economic effort than with a fully wet strategy.

  10. A computational language approach to modeling prose recall in schizophrenia

    PubMed Central

    Rosenstein, Mark; Diaz-Asper, Catherine; Foltz, Peter W.; Elvevåg, Brita

    2014-01-01

    Many cortical disorders are associated with memory problems. In schizophrenia, verbal memory deficits are a hallmark feature. However, the exact nature of this deficit remains elusive. Modeling aspects of language features used in memory recall have the potential to provide means for measuring these verbal processes. We employ computational language approaches to assess time-varying semantic and sequential properties of prose recall at various retrieval intervals (immediate, 30 min and 24 h later) in patients with schizophrenia, unaffected siblings and healthy unrelated control participants. First, we model the recall data to quantify the degradation of performance with increasing retrieval interval and the effect of diagnosis (i.e., group membership) on performance. Next we model the human scoring of recall performance using an n-gram language sequence technique, and then with a semantic feature based on Latent Semantic Analysis. These models show that automated analyses of the recalls can produce scores that accurately mimic human scoring. The final analysis addresses the validity of this approach by ascertaining the ability to predict group membership from models built on the two classes of language features. Taken individually, the semantic feature is most predictive, while a model combining the features improves accuracy of group membership prediction slightly above the semantic feature alone as well as over the human rating approach. We discuss the implications for cognitive neuroscience of such a computational approach in exploring the mechanisms of prose recall. PMID:24709122

  11. Accurate structure, thermodynamics and spectroscopy of medium-sized radicals by hybrid Coupled Cluster/Density Functional Theory approaches: the case of phenyl radical

    PubMed Central

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina

    2015-01-01

    The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956

  12. Computer-Assisted Drug Formulation Design: Novel Approach in Drug Delivery.

    PubMed

    Metwally, Abdelkader A; Hathout, Rania M

    2015-08-03

    We hypothesize that, by using several chemo/bio informatics tools and statistical computational methods, we can study and then predict the behavior of several drugs in model nanoparticulate lipid and polymeric systems. Accordingly, two different matrices comprising tripalmitin, a core component of solid lipid nanoparticles (SLN), and PLGA were first modeled using molecular dynamics simulation, and then the interaction of drugs with these systems was studied by means of computing the free energy of binding using the molecular docking technique. These binding energies were hence correlated with the loadings of these drugs in the nanoparticles obtained experimentally from the available literature. The obtained relations were verified experimentally in our laboratory using curcumin as a model drug. Artificial neural networks were then used to establish the effect of the drugs' molecular descriptors on the binding energies and hence on the drug loading. The results showed that the used soft computing methods can provide an accurate method for in silico prediction of drug loading in tripalmitin-based and PLGA nanoparticulate systems. These results have the prospective of being applied to other nano drug-carrier systems, and this integrated statistical and chemo/bio informatics approach offers a new toolbox to the formulation science by proposing what we present as computer-assisted drug formulation design (CADFD).

  13. Research on the Rapid and Accurate Positioning and Orientation Approach for Land Missile-Launching Vehicle

    PubMed Central

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-01-01

    Getting a land vehicle’s accurate position, azimuth and attitude rapidly is significant for vehicle based weapons’ combat effectiveness. In this paper, a new approach to acquire vehicle’s accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle’s accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm’s iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system’s working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249

  14. Research on the rapid and accurate positioning and orientation approach for land missile-launching vehicle.

    PubMed

    Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao

    2015-10-20

    Getting a land vehicle's accurate position, azimuth and attitude rapidly is significant for vehicle based weapons' combat effectiveness. In this paper, a new approach to acquire vehicle's accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle's accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm's iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system's working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min.

  15. Accurate traveltime computation in complex anisotropic media with discontinuous Galerkin method

    NASA Astrophysics Data System (ADS)

    Le Bouteiller, P.; Benjemaa, M.; Métivier, L.; Virieux, J.

    2017-12-01

    Travel time computation is of major interest for a large range of geophysical applications, among which source localization and characterization, phase identification, data windowing and tomography, from decametric scale up to global Earth scale.Ray-tracing tools, being essentially 1D Lagrangian integration along a path, have been used for their efficiency but present some drawbacks, such as a rather difficult control of the medium sampling. Moreover, they do not provide answers in shadow zones. Eikonal solvers, based on an Eulerian approach, have attracted attention in seismology with the pioneering work of Vidale (1988), while such approach has been proposed earlier by Riznichenko (1946). They have been used now for first-arrival travel-time tomography at various scales (Podvin & Lecomte (1991). The framework for solving this non-linear partial differential equation is now well understood and various finite-difference approaches have been proposed, essentially for smooth media. We propose a novel finite element approach which builds a precise solution for strongly heterogeneous anisotropic medium (still in the limit of Eikonal validity). The discontinuous Galerkin method we have developed allows local refinement of the mesh and local high orders of interpolation inside elements. High precision of the travel times and its spatial derivatives is obtained through this formulation. This finite element method also honors boundary conditions, such as complex topographies and absorbing boundaries for mimicking an infinite medium. Applications from travel-time tomography, slope tomography are expected, but also for migration and take-off angles estimation, thanks to the accuracy obtained when computing first-arrival times.References:Podvin, P. and Lecomte, I., 1991. Finite difference computation of traveltimes in very contrasted velocity model: a massively parallel approach and its associated tools, Geophys. J. Int., 105, 271-284.Riznichenko, Y., 1946. Geometrical

  16. A sparse matrix-vector multiplication based algorithm for accurate density matrix computations on systems of millions of atoms

    NASA Astrophysics Data System (ADS)

    Ghale, Purnima; Johnson, Harley T.

    2018-06-01

    We present an efficient sparse matrix-vector (SpMV) based method to compute the density matrix P from a given Hamiltonian in electronic structure computations. Our method is a hybrid approach based on Chebyshev-Jackson approximation theory and matrix purification methods like the second order spectral projection purification (SP2). Recent methods to compute the density matrix scale as O(N) in the number of floating point operations but are accompanied by large memory and communication overhead, and they are based on iterative use of the sparse matrix-matrix multiplication kernel (SpGEMM), which is known to be computationally irregular. In addition to irregularity in the sparse Hamiltonian H, the nonzero structure of intermediate estimates of P depends on products of H and evolves over the course of computation. On the other hand, an expansion of the density matrix P in terms of Chebyshev polynomials is straightforward and SpMV based; however, the resulting density matrix may not satisfy the required constraints exactly. In this paper, we analyze the strengths and weaknesses of the Chebyshev-Jackson polynomials and the second order spectral projection purification (SP2) method, and propose to combine them so that the accurate density matrix can be computed using the SpMV computational kernel only, and without having to store the density matrix P. Our method accomplishes these objectives by using the Chebyshev polynomial estimate as the initial guess for SP2, which is followed by using sparse matrix-vector multiplications (SpMVs) to replicate the behavior of the SP2 algorithm for purification. We demonstrate the method on a tight-binding model system of an oxide material containing more than 3 million atoms. In addition, we also present the predicted behavior of our method when applied to near-metallic Hamiltonians with a wide energy spectrum.

  17. Finding accurate frontiers: A knowledge-intensive approach to relational learning

    NASA Technical Reports Server (NTRS)

    Pazzani, Michael; Brunk, Clifford

    1994-01-01

    An approach to analytic learning is described that searches for accurate entailments of a Horn Clause domain theory. A hill-climbing search, guided by an information based evaluation function, is performed by applying a set of operators that derive frontiers from domain theories. The analytic learning system is one component of a multi-strategy relational learning system. We compare the accuracy of concepts learned with this analytic strategy to concepts learned with an analytic strategy that operationalizes the domain theory.

  18. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching.

    PubMed

    Huynh, Linh; Tagkopoulos, Ilias

    2015-08-21

    In computer-aided biological design, the trifecta of characterized part libraries, accurate models and optimal design parameters is crucial for producing reliable designs. As the number of parts and model complexity increase, however, it becomes exponentially more difficult for any optimization method to search the solution space, hence creating a trade-off that hampers efficient design. To address this issue, we present a hierarchical computer-aided design architecture that uses a two-step approach for biological design. First, a simple model of low computational complexity is used to predict circuit behavior and assess candidate circuit branches through branch-and-bound methods. Then, a complex, nonlinear circuit model is used for a fine-grained search of the reduced solution space, thus achieving more accurate results. Evaluation with a benchmark of 11 circuits and a library of 102 experimental designs with known characterization parameters demonstrates a speed-up of 3 orders of magnitude when compared to other design methods that provide optimality guarantees.

  19. Cognitive Approaches for Medicine in Cloud Computing.

    PubMed

    Ogiela, Urszula; Takizawa, Makoto; Ogiela, Lidia

    2018-03-03

    This paper will present the application potential of the cognitive approach to data interpretation, with special reference to medical areas. The possibilities of using the meaning approach to data description and analysis will be proposed for data analysis tasks in Cloud Computing. The methods of cognitive data management in Cloud Computing are aimed to support the processes of protecting data against unauthorised takeover and they serve to enhance the data management processes. The accomplishment of the proposed tasks will be the definition of algorithms for the execution of meaning data interpretation processes in safe Cloud Computing. • We proposed a cognitive methods for data description. • Proposed a techniques for secure data in Cloud Computing. • Application of cognitive approaches for medicine was described.

  20. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

    PubMed Central

    Boitard, Simon; Rodríguez, Willy; Jay, Flora; Mona, Stefano; Austerlitz, Frédéric

    2016-01-01

    Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey), PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles. PMID:26943927

  1. Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

    NASA Technical Reports Server (NTRS)

    Chaderjian, Neal M.

    1991-01-01

    Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

  2. Accurate and efficient calculation of response times for groundwater flow

    NASA Astrophysics Data System (ADS)

    Carr, Elliot J.; Simpson, Matthew J.

    2018-03-01

    We study measures of the amount of time required for transient flow in heterogeneous porous media to effectively reach steady state, also known as the response time. Here, we develop a new approach that extends the concept of mean action time. Previous applications of the theory of mean action time to estimate the response time use the first two central moments of the probability density function associated with the transition from the initial condition, at t = 0, to the steady state condition that arises in the long time limit, as t → ∞ . This previous approach leads to a computationally convenient estimation of the response time, but the accuracy can be poor. Here, we outline a powerful extension using the first k raw moments, showing how to produce an extremely accurate estimate by making use of asymptotic properties of the cumulative distribution function. Results are validated using an existing laboratory-scale data set describing flow in a homogeneous porous medium. In addition, we demonstrate how the results also apply to flow in heterogeneous porous media. Overall, the new method is: (i) extremely accurate; and (ii) computationally inexpensive. In fact, the computational cost of the new method is orders of magnitude less than the computational effort required to study the response time by solving the transient flow equation. Furthermore, the approach provides a rigorous mathematical connection with the heuristic argument that the response time for flow in a homogeneous porous medium is proportional to L2 / D , where L is a relevant length scale, and D is the aquifer diffusivity. Here, we extend such heuristic arguments by providing a clear mathematical definition of the proportionality constant.

  3. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    PubMed

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  4. Probabilistic techniques for obtaining accurate patient counts in Clinical Data Warehouses

    PubMed Central

    Myers, Risa B.; Herskovic, Jorge R.

    2011-01-01

    Proposal and execution of clinical trials, computation of quality measures and discovery of correlation between medical phenomena are all applications where an accurate count of patients is needed. However, existing sources of this type of patient information, including Clinical Data Warehouses (CDW) may be incomplete or inaccurate. This research explores applying probabilistic techniques, supported by the MayBMS probabilistic database, to obtain accurate patient counts from a clinical data warehouse containing synthetic patient data. We present a synthetic clinical data warehouse (CDW), and populate it with simulated data using a custom patient data generation engine. We then implement, evaluate and compare different techniques for obtaining patients counts. We model billing as a test for the presence of a condition. We compute billing’s sensitivity and specificity both by conducting a “Simulated Expert Review” where a representative sample of records are reviewed and labeled by experts, and by obtaining the ground truth for every record. We compute the posterior probability of a patient having a condition through a “Bayesian Chain”, using Bayes’ Theorem to calculate the probability of a patient having a condition after each visit. The second method is a “one-shot” approach that computes the probability of a patient having a condition based on whether the patient is ever billed for the condition Our results demonstrate the utility of probabilistic approaches, which improve on the accuracy of raw counts. In particular, the simulated review paired with a single application of Bayes’ Theorem produces the best results, with an average error rate of 2.1% compared to 43.7% for the straightforward billing counts. Overall, this research demonstrates that Bayesian probabilistic approaches improve patient counts on simulated patient populations. We believe that total patient counts based on billing data are one of the many possible applications of our

  5. Kinetic approach to degradation mechanisms in polymer solar cells and their accurate lifetime predictions

    NASA Astrophysics Data System (ADS)

    Arshad, Muhammad Azeem; Maaroufi, AbdelKrim

    2018-07-01

    A beginning has been made in the present study regarding the accurate lifetime predictions of polymer solar cells. Certain reservations about the conventionally employed temperature accelerated lifetime measurements test for its unworthiness of predicting reliable lifetimes of polymer solar cells are brought into light. Critical issues concerning the accelerated lifetime testing include, assuming reaction mechanism instead of determining it, and relying solely on the temperature acceleration of a single property of material. An advanced approach comprising a set of theoretical models to estimate the accurate lifetimes of polymer solar cells is therefore suggested in order to suitably alternate the accelerated lifetime testing. This approach takes into account systematic kinetic modeling of various possible polymer degradation mechanisms under natural weathering conditions. The proposed kinetic approach is substantiated by its applications on experimental aging data-sets of polymer solar materials/solar cells including, P3HT polymer film, bulk heterojunction (MDMO-PPV:PCBM) and dye-sensitized solar cells. Based on the suggested approach, an efficacious lifetime determination formula for polymer solar cells is derived and tested on dye-sensitized solar cells. Some important merits of the proposed method are also pointed out and its prospective applications are discussed.

  6. An accurate, compact and computationally efficient representation of orbitals for quantum Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Luo, Ye; Esler, Kenneth; Kent, Paul; Shulenburger, Luke

    Quantum Monte Carlo (QMC) calculations of giant molecules, surface and defect properties of solids have been feasible recently due to drastically expanding computational resources. However, with the most computationally efficient basis set, B-splines, these calculations are severely restricted by the memory capacity of compute nodes. The B-spline coefficients are shared on a node but not distributed among nodes, to ensure fast evaluation. A hybrid representation which incorporates atomic orbitals near the ions and B-spline ones in the interstitial regions offers a more accurate and less memory demanding description of the orbitals because they are naturally more atomic like near ions and much smoother in between, thus allowing coarser B-spline grids. We will demonstrate the advantage of hybrid representation over pure B-spline and Gaussian basis sets and also show significant speed-up like computing the non-local pseudopotentials with our new scheme. Moreover, we discuss a new algorithm for atomic orbital initialization which used to require an extra workflow step taking a few days. With this work, the highly efficient hybrid representation paves the way to simulate large size even in-homogeneous systems using QMC. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Computational Materials Sciences Program.

  7. Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

    NASA Astrophysics Data System (ADS)

    Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

    2008-05-01

    Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

  8. Catalyzing Novel Approaches to Rapid, Accurate, and Affordable Early Cancer Detection.

    PubMed

    Dhar, Asif; Meagher, Beth; Ryscavage, Andrew

    Inspired by the Cancer Moonshot, a dedicated team of professionals worked with leaders across the cancer ecosystem to look for an opportunity to radically reduce cancer mortality globally by focusing on early cancer detection. After an initial survey of cancer innovation, progress, and pitfalls, the team believed that if new rapid, affordable, and accurate early detection solutions were appropriately brought to market, it would be possible to intervene earlier when cancer is most treatable.An extensive process began, informed by dozens of experts in the cancer ecosystem. The Cancer XPRIZE team designed a prize competition where "the winning team will develop a means to rapidly, accurately, and affordably screen for early cancers where intervention can reduce human suffering."The following outlines the Cancer XPRIZE's experience using a powerful approach-the radical prize design-to catch more cancers in time to make a difference saving lives, dollars, and suffering.

  9. Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts.

    PubMed

    Tackenberg, Michael C; Jones, Jeff R; Page, Terry L; Hughey, Jacob J

    2018-06-01

    Estimations of period and phase are essential in circadian biology. While many techniques exist for estimating period, comparatively few methods are available for estimating phase. Current approaches to analyzing phase often vary between studies and are sensitive to coincident changes in period and the stage of the circadian cycle at which the stimulus occurs. Here we propose a new technique, tau-independent phase analysis (TIPA), for quantifying phase shifts in multiple types of circadian time-course data. Through comprehensive simulations, we show that TIPA is both more accurate and more precise than the standard actogram approach. TIPA is computationally simple and therefore will enable accurate and reproducible quantification of phase shifts across multiple subfields of chronobiology.

  10. A flexible and accurate digital volume correlation method applicable to high-resolution volumetric images

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo

    2017-10-01

    Digital volume correlation (DVC) is a powerful technique for quantifying interior deformation within solid opaque materials and biological tissues. In the last two decades, great efforts have been made to improve the accuracy and efficiency of the DVC algorithm. However, there is still a lack of a flexible, robust and accurate version that can be efficiently implemented in personal computers with limited RAM. This paper proposes an advanced DVC method that can realize accurate full-field internal deformation measurement applicable to high-resolution volume images with up to billions of voxels. Specifically, a novel layer-wise reliability-guided displacement tracking strategy combined with dynamic data management is presented to guide the DVC computation from slice to slice. The displacements at specified calculation points in each layer are computed using the advanced 3D inverse-compositional Gauss-Newton algorithm with the complete initial guess of the deformation vector accurately predicted from the computed calculation points. Since only limited slices of interest in the reference and deformed volume images rather than the whole volume images are required, the DVC calculation can thus be efficiently implemented on personal computers. The flexibility, accuracy and efficiency of the presented DVC approach are demonstrated by analyzing computer-simulated and experimentally obtained high-resolution volume images.

  11. Spatial adaption procedures on unstructured meshes for accurate unsteady aerodynamic flow computation

    NASA Technical Reports Server (NTRS)

    Rausch, Russ D.; Batina, John T.; Yang, Henry T. Y.

    1991-01-01

    Spatial adaption procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaption procedures were developed and implemented within a two-dimensional unstructured-grid upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in a high gradient region or the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational costs. A detailed description is given of the enrichment and coarsening procedures and comparisons with alternative results and experimental data are presented to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady transonic results, obtained using spatial adaption for the NACA 0012 airfoil, are shown to be of high spatial accuracy, primarily in that the shock waves are very sharply captured. The results were obtained with a computational savings of a factor of approximately fifty-three for a steady case and as much as twenty-five for the unsteady cases.

  12. Spatial adaption procedures on unstructured meshes for accurate unsteady aerodynamic flow computation

    NASA Technical Reports Server (NTRS)

    Rausch, Russ D.; Yang, Henry T. Y.; Batina, John T.

    1991-01-01

    Spatial adaption procedures for the accurate and efficient solution of steady and unsteady inviscid flow problems are described. The adaption procedures were developed and implemented within a two-dimensional unstructured-grid upwind-type Euler code. These procedures involve mesh enrichment and mesh coarsening to either add points in high gradient regions of the flow or remove points where they are not needed, respectively, to produce solutions of high spatial accuracy at minimal computational cost. The paper gives a detailed description of the enrichment and coarsening procedures and presents comparisons with alternative results and experimental data to provide an assessment of the accuracy and efficiency of the capability. Steady and unsteady transonic results, obtained using spatial adaption for the NACA 0012 airfoil, are shown to be of high spatial accuracy, primarily in that the shock waves are very sharply captured. The results were obtained with a computational savings of a factor of approximately fifty-three for a steady case and as much as twenty-five for the unsteady cases.

  13. A hybrid approach for nonlinear computational aeroacoustics predictions

    NASA Astrophysics Data System (ADS)

    Sassanis, Vasileios; Sescu, Adrian; Collins, Eric M.; Harris, Robert E.; Luke, Edward A.

    2017-01-01

    In many aeroacoustics applications involving nonlinear waves and obstructions in the far-field, approaches based on the classical acoustic analogy theory or the linearised Euler equations are unable to fully characterise the acoustic field. Therefore, computational aeroacoustics hybrid methods that incorporate nonlinear wave propagation have to be constructed. In this study, a hybrid approach coupling Navier-Stokes equations in the acoustic source region with nonlinear Euler equations in the acoustic propagation region is introduced and tested. The full Navier-Stokes equations are solved in the source region to identify the acoustic sources. The flow variables of interest are then transferred from the source region to the acoustic propagation region, where the full nonlinear Euler equations with source terms are solved. The transition between the two regions is made through a buffer zone where the flow variables are penalised via a source term added to the Euler equations. Tests were conducted on simple acoustic and vorticity disturbances, two-dimensional jets (Mach 0.9 and 2), and a three-dimensional jet (Mach 1.5), impinging on a wall. The method is proven to be effective and accurate in predicting sound pressure levels associated with the propagation of linear and nonlinear waves in the near- and far-field regions.

  14. Numerically accurate computational techniques for optimal estimator analyses of multi-parameter models

    NASA Astrophysics Data System (ADS)

    Berger, Lukas; Kleinheinz, Konstantin; Attili, Antonio; Bisetti, Fabrizio; Pitsch, Heinz; Mueller, Michael E.

    2018-05-01

    Modelling unclosed terms in partial differential equations typically involves two steps: First, a set of known quantities needs to be specified as input parameters for a model, and second, a specific functional form needs to be defined to model the unclosed terms by the input parameters. Both steps involve a certain modelling error, with the former known as the irreducible error and the latter referred to as the functional error. Typically, only the total modelling error, which is the sum of functional and irreducible error, is assessed, but the concept of the optimal estimator enables the separate analysis of the total and the irreducible errors, yielding a systematic modelling error decomposition. In this work, attention is paid to the techniques themselves required for the practical computation of irreducible errors. Typically, histograms are used for optimal estimator analyses, but this technique is found to add a non-negligible spurious contribution to the irreducible error if models with multiple input parameters are assessed. Thus, the error decomposition of an optimal estimator analysis becomes inaccurate, and misleading conclusions concerning modelling errors may be drawn. In this work, numerically accurate techniques for optimal estimator analyses are identified and a suitable evaluation of irreducible errors is presented. Four different computational techniques are considered: a histogram technique, artificial neural networks, multivariate adaptive regression splines, and an additive model based on a kernel method. For multiple input parameter models, only artificial neural networks and multivariate adaptive regression splines are found to yield satisfactorily accurate results. Beyond a certain number of input parameters, the assessment of models in an optimal estimator analysis even becomes practically infeasible if histograms are used. The optimal estimator analysis in this paper is applied to modelling the filtered soot intermittency in large eddy

  15. Funnel metadynamics as accurate binding free-energy method

    PubMed Central

    Limongelli, Vittorio; Bonomi, Massimiliano; Parrinello, Michele

    2013-01-01

    A detailed description of the events ruling ligand/protein interaction and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have developed a metadynamics-based approach, named funnel metadynamics, that allows the ligand to enhance the sampling of the target binding sites and its solvated states. This method leads to an efficient characterization of the binding free-energy surface and an accurate calculation of the absolute protein–ligand binding free energy. We illustrate our protocol in two systems, benzamidine/trypsin and SC-558/cyclooxygenase 2. In both cases, the X-ray conformation has been found as the lowest free-energy pose, and the computed protein–ligand binding free energy in good agreement with experiments. Furthermore, funnel metadynamics unveils important information about the binding process, such as the presence of alternative binding modes and the role of waters. The results achieved at an affordable computational cost make funnel metadynamics a valuable method for drug discovery and for dealing with a variety of problems in chemistry, physics, and material science. PMID:23553839

  16. Computational Approach for Developing Blood Pump

    NASA Technical Reports Server (NTRS)

    Kwak, Dochan

    2002-01-01

    This viewgraph presentation provides an overview of the computational approach to developing a ventricular assist device (VAD) which utilizes NASA aerospace technology. The VAD is used as a temporary support to sick ventricles for those who suffer from late stage congestive heart failure (CHF). The need for donor hearts is much greater than their availability, and the VAD is seen as a bridge-to-transplant. The computational issues confronting the design of a more advanced, reliable VAD include the modelling of viscous incompressible flow. A computational approach provides the possibility of quantifying the flow characteristics, which is especially valuable for analyzing compact design with highly sensitive operating conditions. Computational fluid dynamics (CFD) and rocket engine technology has been applied to modify the design of a VAD which enabled human transplantation. The computing requirement for this project is still large, however, and the unsteady analysis of the entire system from natural heart to aorta involves several hundred revolutions of the impeller. Further study is needed to assess the impact of mechanical VADs on the human body

  17. Cloud computing approaches for prediction of ligand binding poses and pathways.

    PubMed

    Lawrenz, Morgan; Shukla, Diwakar; Pande, Vijay S

    2015-01-22

    We describe an innovative protocol for ab initio prediction of ligand crystallographic binding poses and highly effective analysis of large datasets generated for protein-ligand dynamics. We include a procedure for setup and performance of distributed molecular dynamics simulations on cloud computing architectures, a model for efficient analysis of simulation data, and a metric for evaluation of model convergence. We give accurate binding pose predictions for five ligands ranging in affinity from 7 nM to > 200 μM for the immunophilin protein FKBP12, for expedited results in cases where experimental structures are difficult to produce. Our approach goes beyond single, low energy ligand poses to give quantitative kinetic information that can inform protein engineering and ligand design.

  18. The NASA MERIT program - Developing new concepts for accurate flight planning

    NASA Technical Reports Server (NTRS)

    Steinberg, R.

    1982-01-01

    It is noted that the rising cost of aviation fuel has necessitated the development of a new approach to upper air forecasting for flight planning. It is shown that the spatial resolution of the present weather forecast models used in fully automated computer flight planning is an important accuracy-limiting factor, and it is proposed that man be put back into the system, although not in the way he has been used in the past. A new approach is proposed which uses the application of man-computer interactive display techniques to upper air forecasting to retain the fine scale features of the atmosphere inherent in the present data base in order to provide a more accurate and cost effective flight plan. It is pointed out that, as a result of NASA research, the hardware required for this approach already exists.

  19. Accurate modeling of defects in graphene transport calculations

    NASA Astrophysics Data System (ADS)

    Linhart, Lukas; Burgdörfer, Joachim; Libisch, Florian

    2018-01-01

    We present an approach for embedding defect structures modeled by density functional theory into large-scale tight-binding simulations. We extract local tight-binding parameters for the vicinity of the defect site using Wannier functions. In the transition region between the bulk lattice and the defect the tight-binding parameters are continuously adjusted to approach the bulk limit far away from the defect. This embedding approach allows for an accurate high-level treatment of the defect orbitals using as many as ten nearest neighbors while keeping a small number of nearest neighbors in the bulk to render the overall computational cost reasonable. As an example of our approach, we consider an extended graphene lattice decorated with Stone-Wales defects, flower defects, double vacancies, or silicon substitutes. We predict distinct scattering patterns mirroring the defect symmetries and magnitude that should be experimentally accessible.

  20. Automated particle correspondence and accurate tilt-axis detection in tilted-image pairs

    DOE PAGES

    Shatsky, Maxim; Arbelaez, Pablo; Han, Bong-Gyoon; ...

    2014-07-01

    Tilted electron microscope images are routinely collected for an ab initio structure reconstruction as a part of the Random Conical Tilt (RCT) or Orthogonal Tilt Reconstruction (OTR) methods, as well as for various applications using the "free-hand" procedure. These procedures all require identification of particle pairs in two corresponding images as well as accurate estimation of the tilt-axis used to rotate the electron microscope (EM) grid. Here we present a computational approach, PCT (particle correspondence from tilted pairs), based on tilt-invariant context and projection matching that addresses both problems. The method benefits from treating the two problems as a singlemore » optimization task. It automatically finds corresponding particle pairs and accurately computes tilt-axis direction even in the cases when EM grid is not perfectly planar.« less

  1. Toward Accurate and Quantitative Comparative Metagenomics

    PubMed Central

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  2. FASTSIM2: a second-order accurate frictional rolling contact algorithm

    NASA Astrophysics Data System (ADS)

    Vollebregt, E. A. H.; Wilders, P.

    2011-01-01

    In this paper we consider the frictional (tangential) steady rolling contact problem. We confine ourselves to the simplified theory, instead of using full elastostatic theory, in order to be able to compute results fast, as needed for on-line application in vehicle system dynamics simulation packages. The FASTSIM algorithm is the leading technology in this field and is employed in all dominant railway vehicle system dynamics packages (VSD) in the world. The main contribution of this paper is a new version "FASTSIM2" of the FASTSIM algorithm, which is second-order accurate. This is relevant for VSD, because with the new algorithm 16 times less grid points are required for sufficiently accurate computations of the contact forces. The approach is based on new insights in the characteristics of the rolling contact problem when using the simplified theory, and on taking precise care of the contact conditions in the numerical integration scheme employed.

  3. A compositional approach to building applications in a computational environment

    NASA Astrophysics Data System (ADS)

    Roslovtsev, V. V.; Shumsky, L. D.; Wolfengagen, V. E.

    2014-04-01

    The paper presents an approach to creating an applicative computational environment to feature computational processes and data decomposition, and a compositional approach to application building. The approach in question is based on the notion of combinator - both in systems with variable binding (such as λ-calculi) and those allowing programming without variables (combinatory logic style). We present a computation decomposition technique based on objects' structural decomposition, with the focus on computation decomposition. The computational environment's architecture is based on a network with nodes playing several roles simultaneously.

  4. Simple but accurate GCM-free approach for quantifying anthropogenic climate change

    NASA Astrophysics Data System (ADS)

    Lovejoy, S.

    2014-12-01

    We are so used to analysing the climate with the help of giant computer models (GCM's) that it is easy to get the impression that they are indispensable. Yet anthropogenic warming is so large (roughly 0.9oC) that it turns out that it is straightforward to quantify it with more empirically based methodologies that can be readily understood by the layperson. The key is to use the CO2 forcing as a linear surrogate for all the anthropogenic effects from 1880 to the present (implicitly including all effects due to Greenhouse Gases, aerosols and land use changes). To a good approximation, double the economic activity, double the effects. The relationship between the forcing and global mean temperature is extremely linear as can be seen graphically and understood without fancy statistics, [Lovejoy, 2014a] (see the attached figure and http://www.physics.mcgill.ca/~gang/Lovejoy.htm). To an excellent approximation, the deviations from the linear forcing - temperature relation can be interpreted as the natural variability. For example, this direct - yet accurate approach makes it graphically obvious that the "pause" or "hiatus" in the warming since 1998 is simply a natural cooling event that has roughly offset the anthropogenic warming [Lovejoy, 2014b]. Rather than trying to prove that the warming is anthropogenic, with a little extra work (and some nonlinear geophysics theory and pre-industrial multiproxies) we can disprove the competing theory that it is natural. This approach leads to the estimate that the probability of the industrial scale warming being a giant natural fluctuation is ≈0.1%: it can be dismissed. This destroys the last climate skeptic argument - that the models are wrong and the warming is natural. It finally allows for a closure of the debate. In this talk we argue that this new, direct, simple, intuitive approach provides an indispensable tool for communicating - and convincing - the public of both the reality and the amplitude of anthropogenic warming

  5. Machine learning and computer vision approaches for phenotypic profiling

    PubMed Central

    Morris, Quaid

    2017-01-01

    With recent advances in high-throughput, automated microscopy, there has been an increased demand for effective computational strategies to analyze large-scale, image-based data. To this end, computer vision approaches have been applied to cell segmentation and feature extraction, whereas machine-learning approaches have been developed to aid in phenotypic classification and clustering of data acquired from biological images. Here, we provide an overview of the commonly used computer vision and machine-learning methods for generating and categorizing phenotypic profiles, highlighting the general biological utility of each approach. PMID:27940887

  6. Machine learning and computer vision approaches for phenotypic profiling.

    PubMed

    Grys, Ben T; Lo, Dara S; Sahin, Nil; Kraus, Oren Z; Morris, Quaid; Boone, Charles; Andrews, Brenda J

    2017-01-02

    With recent advances in high-throughput, automated microscopy, there has been an increased demand for effective computational strategies to analyze large-scale, image-based data. To this end, computer vision approaches have been applied to cell segmentation and feature extraction, whereas machine-learning approaches have been developed to aid in phenotypic classification and clustering of data acquired from biological images. Here, we provide an overview of the commonly used computer vision and machine-learning methods for generating and categorizing phenotypic profiles, highlighting the general biological utility of each approach. © 2017 Grys et al.

  7. Accurate Arabic Script Language/Dialect Classification

    DTIC Science & Technology

    2014-01-01

    Army Research Laboratory Accurate Arabic Script Language/Dialect Classification by Stephen C. Tratz ARL-TR-6761 January 2014 Approved for public...1197 ARL-TR-6761 January 2014 Accurate Arabic Script Language/Dialect Classification Stephen C. Tratz Computational and Information Sciences...Include area code) Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 January 2014 Final Accurate Arabic Script Language/Dialect Classification

  8. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Computer Page: Computer Studies for All--A Wider Approach

    ERIC Educational Resources Information Center

    Edens, A. J.

    1975-01-01

    An approach to teaching children aged 12 through 14 a substantial course about computers is described. Topics covered include simple algorithms, information and communication, man-machine communication, the concept of a system, the definition of a system, and the use of files. (SD)

  10. Demystifying the GMAT: Computer-Based Testing Terms

    ERIC Educational Resources Information Center

    Rudner, Lawrence M.

    2012-01-01

    Computer-based testing can be a powerful means to make all aspects of test administration not only faster and more efficient, but also more accurate and more secure. While the Graduate Management Admission Test (GMAT) exam is a computer adaptive test, there are other approaches. This installment presents a primer of computer-based testing terms.

  11. Enabling high grayscale resolution displays and accurate response time measurements on conventional computers.

    PubMed

    Li, Xiangrui; Lu, Zhong-Lin

    2012-02-29

    Display systems based on conventional computer graphics cards are capable of generating images with 8-bit gray level resolution. However, most experiments in vision research require displays with more than 12 bits of luminance resolution. Several solutions are available. Bit++ (1) and DataPixx (2) use the Digital Visual Interface (DVI) output from graphics cards and high resolution (14 or 16-bit) digital-to-analog converters to drive analog display devices. The VideoSwitcher (3) described here combines analog video signals from the red and blue channels of graphics cards with different weights using a passive resister network (4) and an active circuit to deliver identical video signals to the three channels of color monitors. The method provides an inexpensive way to enable high-resolution monochromatic displays using conventional graphics cards and analog monitors. It can also provide trigger signals that can be used to mark stimulus onsets, making it easy to synchronize visual displays with physiological recordings or response time measurements. Although computer keyboards and mice are frequently used in measuring response times (RT), the accuracy of these measurements is quite low. The RTbox is a specialized hardware and software solution for accurate RT measurements. Connected to the host computer through a USB connection, the driver of the RTbox is compatible with all conventional operating systems. It uses a microprocessor and high-resolution clock to record the identities and timing of button events, which are buffered until the host computer retrieves them. The recorded button events are not affected by potential timing uncertainties or biases associated with data transmission and processing in the host computer. The asynchronous storage greatly simplifies the design of user programs. Several methods are available to synchronize the clocks of the RTbox and the host computer. The RTbox can also receive external triggers and be used to measure RT with respect

  12. Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory.

    PubMed

    Cao, Xiaofang; Rong, Chunying; Zhong, Aiguo; Lu, Tian; Liu, Shubin

    2018-01-15

    Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. Application of the accurate mass and time tag approach in studies of the human blood lipidome

    PubMed Central

    Ding, Jie; Sorensen, Christina M.; Jaitly, Navdeep; Jiang, Hongliang; Orton, Daniel J.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Richard D.; Metz, Thomas O.

    2008-01-01

    We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance. PMID:18502191

  14. Computing Optimal Stochastic Portfolio Execution Strategies: A Parametric Approach Using Simulations

    NASA Astrophysics Data System (ADS)

    Moazeni, Somayeh; Coleman, Thomas F.; Li, Yuying

    2010-09-01

    Computing optimal stochastic portfolio execution strategies under appropriate risk consideration presents great computational challenge. We investigate a parametric approach for computing optimal stochastic strategies using Monte Carlo simulations. This approach allows reduction in computational complexity by computing coefficients for a parametric representation of a stochastic dynamic strategy based on static optimization. Using this technique, constraints can be similarly handled using appropriate penalty functions. We illustrate the proposed approach to minimize the expected execution cost and Conditional Value-at-Risk (CVaR).

  15. Role of Soft Computing Approaches in HealthCare Domain: A Mini Review.

    PubMed

    Gambhir, Shalini; Malik, Sanjay Kumar; Kumar, Yugal

    2016-12-01

    In the present era, soft computing approaches play a vital role in solving the different kinds of problems and provide promising solutions. Due to popularity of soft computing approaches, these approaches have also been applied in healthcare data for effectively diagnosing the diseases and obtaining better results in comparison to traditional approaches. Soft computing approaches have the ability to adapt itself according to problem domain. Another aspect is a good balance between exploration and exploitation processes. These aspects make soft computing approaches more powerful, reliable and efficient. The above mentioned characteristics make the soft computing approaches more suitable and competent for health care data. The first objective of this review paper is to identify the various soft computing approaches which are used for diagnosing and predicting the diseases. Second objective is to identify various diseases for which these approaches are applied. Third objective is to categories the soft computing approaches for clinical support system. In literature, it is found that large number of soft computing approaches have been applied for effectively diagnosing and predicting the diseases from healthcare data. Some of these are particle swarm optimization, genetic algorithm, artificial neural network, support vector machine etc. A detailed discussion on these approaches are presented in literature section. This work summarizes various soft computing approaches used in healthcare domain in last one decade. These approaches are categorized in five different categories based on the methodology, these are classification model based system, expert system, fuzzy and neuro fuzzy system, rule based system and case based system. Lot of techniques are discussed in above mentioned categories and all discussed techniques are summarized in the form of tables also. This work also focuses on accuracy rate of soft computing technique and tabular information is provided for

  16. Accurate transport properties for H–CO and H–CO{sub 2}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dagdigian, Paul J., E-mail: pjdagdigian@jhu.edu

    2015-08-07

    Transport properties for collisions of hydrogen atoms with CO and CO{sub 2} have been computed by means of quantum scattering calculations. The carbon oxides are important species in hydrocarbon combustion. The following potential energy surfaces (PES’s) for the interaction of the molecule fixed in its equilibrium geometry were employed: for H–CO, the PES was taken from the work of Song et al. [J. Phys. Chem. A 117, 7571 (2013)], while the PES for H–CO{sub 2} was computed in this study by a restricted coupled cluster method that included single, double, and (perturbatively) triple excitations. The computed transport properties were foundmore » to be significantly different from those computed by the conventional approach that employs isotropic Lennard-Jones (12-6) potentials. The effect of using the presently computed accurate transport properties in 1-dimensional combustion simulations of methane-air flames was investigated.« less

  17. Dynamical Approach Study of Spurious Numerics in Nonlinear Computations

    NASA Technical Reports Server (NTRS)

    Yee, H. C.; Mansour, Nagi (Technical Monitor)

    2002-01-01

    The last two decades have been an era when computation is ahead of analysis and when very large scale practical computations are increasingly used in poorly understood multiscale complex nonlinear physical problems and non-traditional fields. Ensuring a higher level of confidence in the predictability and reliability (PAR) of these numerical simulations could play a major role in furthering the design, understanding, affordability and safety of our next generation air and space transportation systems, and systems for planetary and atmospheric sciences, and in understanding the evolution and origin of life. The need to guarantee PAR becomes acute when computations offer the ONLY way of solving these types of data limited problems. Employing theory from nonlinear dynamical systems, some building blocks to ensure a higher level of confidence in PAR of numerical simulations have been revealed by the author and world expert collaborators in relevant fields. Five building blocks with supporting numerical examples were discussed. The next step is to utilize knowledge gained by including nonlinear dynamics, bifurcation and chaos theories as an integral part of the numerical process. The third step is to design integrated criteria for reliable and accurate algorithms that cater to the different multiscale nonlinear physics. This includes but is not limited to the construction of appropriate adaptive spatial and temporal discretizations that are suitable for the underlying governing equations. In addition, a multiresolution wavelets approach for adaptive numerical dissipation/filter controls for high speed turbulence, acoustics and combustion simulations will be sought. These steps are corner stones for guarding against spurious numerical solutions that are solutions of the discretized counterparts but are not solutions of the underlying governing equations.

  18. Estimation of relative free energies of binding using pre-computed ensembles based on the single-step free energy perturbation and the site-identification by Ligand competitive saturation approaches.

    PubMed

    Raman, E Prabhu; Lakkaraju, Sirish Kaushik; Denny, Rajiah Aldrin; MacKerell, Alexander D

    2017-06-05

    Accurate and rapid estimation of relative binding affinities of ligand-protein complexes is a requirement of computational methods for their effective use in rational ligand design. Of the approaches commonly used, free energy perturbation (FEP) methods are considered one of the most accurate, although they require significant computational resources. Accordingly, it is desirable to have alternative methods of similar accuracy but greater computational efficiency to facilitate ligand design. In the present study relative free energies of binding are estimated for one or two non-hydrogen atom changes in compounds targeting the proteins ACK1 and p38 MAP kinase using three methods. The methods include standard FEP, single-step free energy perturbation (SSFEP) and the site-identification by ligand competitive saturation (SILCS) ligand grid free energy (LGFE) approach. Results show the SSFEP and SILCS LGFE methods to be competitive with or better than the FEP results for the studied systems, with SILCS LGFE giving the best agreement with experimental results. This is supported by additional comparisons with published FEP data on p38 MAP kinase inhibitors. While both the SSFEP and SILCS LGFE approaches require a significant upfront computational investment, they offer a 1000-fold computational savings over FEP for calculating the relative affinities of ligand modifications once those pre-computations are complete. An illustrative example of the potential application of these methods in the context of screening large numbers of transformations is presented. Thus, the SSFEP and SILCS LGFE approaches represent viable alternatives for actively driving ligand design during drug discovery and development. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  19. Computer Series, 101: Accurate Equations of State in Computational Chemistry Projects.

    ERIC Educational Resources Information Center

    Albee, David; Jones, Edward

    1989-01-01

    Discusses the use of computers in chemistry courses at the United States Military Academy. Provides two examples of computer projects: (1) equations of state, and (2) solving for molar volume. Presents BASIC and PASCAL listings for the second project. Lists 10 applications for physical chemistry. (MVL)

  20. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  1. Light Field Imaging Based Accurate Image Specular Highlight Removal

    PubMed Central

    Wang, Haoqian; Xu, Chenxue; Wang, Xingzheng; Zhang, Yongbing; Peng, Bo

    2016-01-01

    Specular reflection removal is indispensable to many computer vision tasks. However, most existing methods fail or degrade in complex real scenarios for their individual drawbacks. Benefiting from the light field imaging technology, this paper proposes a novel and accurate approach to remove specularity and improve image quality. We first capture images with specularity by the light field camera (Lytro ILLUM). After accurately estimating the image depth, a simple and concise threshold strategy is adopted to cluster the specular pixels into “unsaturated” and “saturated” category. Finally, a color variance analysis of multiple views and a local color refinement are individually conducted on the two categories to recover diffuse color information. Experimental evaluation by comparison with existed methods based on our light field dataset together with Stanford light field archive verifies the effectiveness of our proposed algorithm. PMID:27253083

  2. Accurate Time-Dependent Traveling-Wave Tube Model Developed for Computational Bit-Error-Rate Testing

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    2001-01-01

    The phenomenal growth of the satellite communications industry has created a large demand for traveling-wave tubes (TWT's) operating with unprecedented specifications requiring the design and production of many novel devices in record time. To achieve this, the TWT industry heavily relies on computational modeling. However, the TWT industry's computational modeling capabilities need to be improved because there are often discrepancies between measured TWT data and that predicted by conventional two-dimensional helical TWT interaction codes. This limits the analysis and design of novel devices or TWT's with parameters differing from what is conventionally manufactured. In addition, the inaccuracy of current computational tools limits achievable TWT performance because optimized designs require highly accurate models. To address these concerns, a fully three-dimensional, time-dependent, helical TWT interaction model was developed using the electromagnetic particle-in-cell code MAFIA (Solution of MAxwell's equations by the Finite-Integration-Algorithm). The model includes a short section of helical slow-wave circuit with excitation fed by radiofrequency input/output couplers, and an electron beam contained by periodic permanent magnet focusing. A cutaway view of several turns of the three-dimensional helical slow-wave circuit with input/output couplers is shown. This has been shown to be more accurate than conventionally used two-dimensional models. The growth of the communications industry has also imposed a demand for increased data rates for the transmission of large volumes of data. To achieve increased data rates, complex modulation and multiple access techniques are employed requiring minimum distortion of the signal as it is passed through the TWT. Thus, intersymbol interference (ISI) becomes a major consideration, as well as suspected causes such as reflections within the TWT. To experimentally investigate effects of the physical TWT on ISI would be

  3. The DYNAMO Simulation Language--An Alternate Approach to Computer Science Education.

    ERIC Educational Resources Information Center

    Bronson, Richard

    1986-01-01

    Suggests the use of computer simulation of continuous systems as a problem solving approach to computer languages. Outlines the procedures that the system dynamics approach employs in computer simulations. Explains the advantages of the special purpose language, DYNAMO. (ML)

  4. A tale of three bio-inspired computational approaches

    NASA Astrophysics Data System (ADS)

    Schaffer, J. David

    2014-05-01

    I will provide a high level walk-through for three computational approaches derived from Nature. First, evolutionary computation implements what we may call the "mother of all adaptive processes." Some variants on the basic algorithms will be sketched and some lessons I have gleaned from three decades of working with EC will be covered. Then neural networks, computational approaches that have long been studied as possible ways to make "thinking machines", an old dream of man's, and based upon the only known existing example of intelligence. Then, a little overview of attempts to combine these two approaches that some hope will allow us to evolve machines we could never hand-craft. Finally, I will touch on artificial immune systems, Nature's highly sophisticated defense mechanism, that has emerged in two major stages, the innate and the adaptive immune systems. This technology is finding applications in the cyber security world.

  5. Muver, a computational framework for accurately calling accumulated mutations.

    PubMed

    Burkholder, Adam B; Lujan, Scott A; Lavender, Christopher A; Grimm, Sara A; Kunkel, Thomas A; Fargo, David C

    2018-05-09

    Identification of mutations from next-generation sequencing data typically requires a balance between sensitivity and accuracy. This is particularly true of DNA insertions and deletions (indels), that can impart significant phenotypic consequences on cells but are harder to call than substitution mutations from whole genome mutation accumulation experiments. To overcome these difficulties, we present muver, a computational framework that integrates established bioinformatics tools with novel analytical methods to generate mutation calls with the extremely low false positive rates and high sensitivity required for accurate mutation rate determination and comparison. Muver uses statistical comparison of ancestral and descendant allelic frequencies to identify variant loci and assigns genotypes with models that include per-sample assessments of sequencing errors by mutation type and repeat context. Muver identifies maximally parsimonious mutation pathways that connect these genotypes, differentiating potential allelic conversion events and delineating ambiguities in mutation location, type, and size. Benchmarking with a human gold standard father-son pair demonstrates muver's sensitivity and low false positive rates. In DNA mismatch repair (MMR) deficient Saccharomyces cerevisiae, muver detects multi-base deletions in homopolymers longer than the replicative polymerase footprint at rates greater than predicted for sequential single-base deletions, implying a novel multi-repeat-unit slippage mechanism. Benchmarking results demonstrate the high accuracy and sensitivity achieved with muver, particularly for indels, relative to available tools. Applied to an MMR-deficient Saccharomyces cerevisiae system, muver mutation calls facilitate mechanistic insights into DNA replication fidelity.

  6. Predicting Transport of 3,5,6-Trichloro-2-Pyridinol Into Saliva Using a Combination Experimental and Computational Approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, Jordan Ned; Carver, Zana A.; Weber, Thomas J.

    A combination experimental and computational approach was developed to predict chemical transport into saliva. A serous-acinar chemical transport assay was established to measure chemical transport with non-physiological (standard cell culture medium) and physiological (using surrogate plasma and saliva medium) conditions using 3,5,6-trichloro-2-pyridinol (TCPy) a metabolite of the pesticide chlorpyrifos. High levels of TCPy protein binding was observed in cell culture medium and rat plasma resulting in different TCPy transport behaviors in the two experimental conditions. In the non-physiological transport experiment, TCPy reached equilibrium at equivalent concentrations in apical and basolateral chambers. At higher TCPy doses, increased unbound TCPy was observed,more » and TCPy concentrations in apical and basolateral chambers reached equilibrium faster than lower doses, suggesting only unbound TCPy is able to cross the cellular monolayer. In the physiological experiment, TCPy transport was slower than non-physiological conditions, and equilibrium was achieved at different concentrations in apical and basolateral chambers at a comparable ratio (0.034) to what was previously measured in rats dosed with TCPy (saliva:blood ratio: 0.049). A cellular transport computational model was developed based on TCPy protein binding kinetics and accurately simulated all transport experiments using different permeability coefficients for the two experimental conditions (1.4 vs 0.4 cm/hr for non-physiological and physiological experiments, respectively). The computational model was integrated into a physiologically based pharmacokinetic (PBPK) model and accurately predicted TCPy concentrations in saliva of rats dosed with TCPy. Overall, this study demonstrates an approach to predict chemical transport in saliva potentially increasing the utility of salivary biomonitoring in the future.« less

  7. Using a combined computational-experimental approach to predict antibody-specific B cell epitopes.

    PubMed

    Sela-Culang, Inbal; Benhnia, Mohammed Rafii-El-Idrissi; Matho, Michael H; Kaever, Thomas; Maybeno, Matt; Schlossman, Andrew; Nimrod, Guy; Li, Sheng; Xiang, Yan; Zajonc, Dirk; Crotty, Shane; Ofran, Yanay; Peters, Bjoern

    2014-04-08

    Antibody epitope mapping is crucial for understanding B cell-mediated immunity and required for characterizing therapeutic antibodies. In contrast to T cell epitope mapping, no computational tools are in widespread use for prediction of B cell epitopes. Here, we show that, utilizing the sequence of an antibody, it is possible to identify discontinuous epitopes on its cognate antigen. The predictions are based on residue-pairing preferences and other interface characteristics. We combined these antibody-specific predictions with results of cross-blocking experiments that identify groups of antibodies with overlapping epitopes to improve the predictions. We validate the high performance of this approach by mapping the epitopes of a set of antibodies against the previously uncharacterized D8 antigen, using complementary techniques to reduce method-specific biases (X-ray crystallography, peptide ELISA, deuterium exchange, and site-directed mutagenesis). These results suggest that antibody-specific computational predictions and simple cross-blocking experiments allow for accurate prediction of residues in conformational B cell epitopes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Development and Validation of a Fast, Accurate and Cost-Effective Aeroservoelastic Method on Advanced Parallel Computing Systems

    NASA Technical Reports Server (NTRS)

    Goodwin, Sabine A.; Raj, P.

    1999-01-01

    Progress to date towards the development and validation of a fast, accurate and cost-effective aeroelastic method for advanced parallel computing platforms such as the IBM SP2 and the SGI Origin 2000 is presented in this paper. The ENSAERO code, developed at the NASA-Ames Research Center has been selected for this effort. The code allows for the computation of aeroelastic responses by simultaneously integrating the Euler or Navier-Stokes equations and the modal structural equations of motion. To assess the computational performance and accuracy of the ENSAERO code, this paper reports the results of the Navier-Stokes simulations of the transonic flow over a flexible aeroelastic wing body configuration. In addition, a forced harmonic oscillation analysis in the frequency domain and an analysis in the time domain are done on a wing undergoing a rigid pitch and plunge motion. Finally, to demonstrate the ENSAERO flutter-analysis capability, aeroelastic Euler and Navier-Stokes computations on an L-1011 wind tunnel model including pylon, nacelle and empennage are underway. All computational solutions are compared with experimental data to assess the level of accuracy of ENSAERO. As the computations described above are performed, a meticulous log of computational performance in terms of wall clock time, execution speed, memory and disk storage is kept. Code scalability is also demonstrated by studying the impact of varying the number of processors on computational performance on the IBM SP2 and the Origin 2000 systems.

  9. Computational Approaches to Phenotyping

    PubMed Central

    Lussier, Yves A.; Liu, Yang

    2007-01-01

    The recent completion of the Human Genome Project has made possible a high-throughput “systems approach” for accelerating the elucidation of molecular underpinnings of human diseases, and subsequent derivation of molecular-based strategies to more effectively prevent, diagnose, and treat these diseases. Although altered phenotypes are among the most reliable manifestations of altered gene functions, research using systematic analysis of phenotype relationships to study human biology is still in its infancy. This article focuses on the emerging field of high-throughput phenotyping (HTP) phenomics research, which aims to capitalize on novel high-throughput computation and informatics technology developments to derive genomewide molecular networks of genotype–phenotype associations, or “phenomic associations.” The HTP phenomics research field faces the challenge of technological research and development to generate novel tools in computation and informatics that will allow researchers to amass, access, integrate, organize, and manage phenotypic databases across species and enable genomewide analysis to associate phenotypic information with genomic data at different scales of biology. Key state-of-the-art technological advancements critical for HTP phenomics research are covered in this review. In particular, we highlight the power of computational approaches to conduct large-scale phenomics studies. PMID:17202287

  10. Numerical Computation of Sensitivities and the Adjoint Approach

    NASA Technical Reports Server (NTRS)

    Lewis, Robert Michael

    1997-01-01

    We discuss the numerical computation of sensitivities via the adjoint approach in optimization problems governed by differential equations. We focus on the adjoint problem in its weak form. We show how one can avoid some of the problems with the adjoint approach, such as deriving suitable boundary conditions for the adjoint equation. We discuss the convergence of numerical approximations of the costate computed via the weak form of the adjoint problem and show the significance for the discrete adjoint problem.

  11. Progress in fast, accurate multi-scale climate simulations

    DOE PAGES

    Collins, W. D.; Johansen, H.; Evans, K. J.; ...

    2015-06-01

    We present a survey of physical and computational techniques that have the potential to contribute to the next generation of high-fidelity, multi-scale climate simulations. Examples of the climate science problems that can be investigated with more depth with these computational improvements include the capture of remote forcings of localized hydrological extreme events, an accurate representation of cloud features over a range of spatial and temporal scales, and parallel, large ensembles of simulations to more effectively explore model sensitivities and uncertainties. Numerical techniques, such as adaptive mesh refinement, implicit time integration, and separate treatment of fast physical time scales are enablingmore » improved accuracy and fidelity in simulation of dynamics and allowing more complete representations of climate features at the global scale. At the same time, partnerships with computer science teams have focused on taking advantage of evolving computer architectures such as many-core processors and GPUs. As a result, approaches which were previously considered prohibitively costly have become both more efficient and scalable. In combination, progress in these three critical areas is poised to transform climate modeling in the coming decades.« less

  12. Identification of fidgety movements and prediction of CP by the use of computer-based video analysis is more accurate when based on two video recordings.

    PubMed

    Adde, Lars; Helbostad, Jorunn; Jensenius, Alexander R; Langaas, Mette; Støen, Ragnhild

    2013-08-01

    This study evaluates the role of postterm age at assessment and the use of one or two video recordings for the detection of fidgety movements (FMs) and prediction of cerebral palsy (CP) using computer vision software. Recordings between 9 and 17 weeks postterm age from 52 preterm and term infants (24 boys, 28 girls; 26 born preterm) were used. Recordings were analyzed using computer vision software. Movement variables, derived from differences between subsequent video frames, were used for quantitative analysis. Sensitivities, specificities, and area under curve were estimated for the first and second recording, or a mean of both. FMs were classified based on the Prechtl approach of general movement assessment. CP status was reported at 2 years. Nine children developed CP of whom all recordings had absent FMs. The mean variability of the centroid of motion (CSD) from two recordings was more accurate than using only one recording, and identified all children who were diagnosed with CP at 2 years. Age at assessment did not influence the detection of FMs or prediction of CP. The accuracy of computer vision techniques in identifying FMs and predicting CP based on two recordings should be confirmed in future studies.

  13. An implicit higher-order spatially accurate scheme for solving time dependent flows on unstructured meshes

    NASA Astrophysics Data System (ADS)

    Tomaro, Robert F.

    1998-07-01

    The present research is aimed at developing a higher-order, spatially accurate scheme for both steady and unsteady flow simulations using unstructured meshes. The resulting scheme must work on a variety of general problems to ensure the creation of a flexible, reliable and accurate aerodynamic analysis tool. To calculate the flow around complex configurations, unstructured grids and the associated flow solvers have been developed. Efficient simulations require the minimum use of computer memory and computational times. Unstructured flow solvers typically require more computer memory than a structured flow solver due to the indirect addressing of the cells. The approach taken in the present research was to modify an existing three-dimensional unstructured flow solver to first decrease the computational time required for a solution and then to increase the spatial accuracy. The terms required to simulate flow involving non-stationary grids were also implemented. First, an implicit solution algorithm was implemented to replace the existing explicit procedure. Several test cases, including internal and external, inviscid and viscous, two-dimensional, three-dimensional and axi-symmetric problems, were simulated for comparison between the explicit and implicit solution procedures. The increased efficiency and robustness of modified code due to the implicit algorithm was demonstrated. Two unsteady test cases, a plunging airfoil and a wing undergoing bending and torsion, were simulated using the implicit algorithm modified to include the terms required for a moving and/or deforming grid. Secondly, a higher than second-order spatially accurate scheme was developed and implemented into the baseline code. Third- and fourth-order spatially accurate schemes were implemented and tested. The original dissipation was modified to include higher-order terms and modified near shock waves to limit pre- and post-shock oscillations. The unsteady cases were repeated using the higher

  14. A dental vision system for accurate 3D tooth modeling.

    PubMed

    Zhang, Li; Alemzadeh, K

    2006-01-01

    This paper describes an active vision system based reverse engineering approach to extract the three-dimensional (3D) geometric information from dental teeth and transfer this information into Computer-Aided Design/Computer-Aided Manufacture (CAD/CAM) systems to improve the accuracy of 3D teeth models and at the same time improve the quality of the construction units to help patient care. The vision system involves the development of a dental vision rig, edge detection, boundary tracing and fast & accurate 3D modeling from a sequence of sliced silhouettes of physical models. The rig is designed using engineering design methods such as a concept selection matrix and weighted objectives evaluation chart. Reconstruction results and accuracy evaluation are presented on digitizing different teeth models.

  15. A multi-objective optimization approach accurately resolves protein domain architectures

    PubMed Central

    Bernardes, J.S.; Vieira, F.R.J.; Zaverucha, G.; Carbone, A.

    2016-01-01

    Motivation: Given a protein sequence and a number of potential domains matching it, what are the domain content and the most likely domain architecture for the sequence? This problem is of fundamental importance in protein annotation, constituting one of the main steps of all predictive annotation strategies. On the other hand, when potential domains are several and in conflict because of overlapping domain boundaries, finding a solution for the problem might become difficult. An accurate prediction of the domain architecture of a multi-domain protein provides important information for function prediction, comparative genomics and molecular evolution. Results: We developed DAMA (Domain Annotation by a Multi-objective Approach), a novel approach that identifies architectures through a multi-objective optimization algorithm combining scores of domain matches, previously observed multi-domain co-occurrence and domain overlapping. DAMA has been validated on a known benchmark dataset based on CATH structural domain assignments and on the set of Plasmodium falciparum proteins. When compared with existing tools on both datasets, it outperforms all of them. Availability and implementation: DAMA software is implemented in C++ and the source code can be found at http://www.lcqb.upmc.fr/DAMA. Contact: juliana.silva_bernardes@upmc.fr or alessandra.carbone@lip6.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26458889

  16. What is Intrinsic Motivation? A Typology of Computational Approaches

    PubMed Central

    Oudeyer, Pierre-Yves; Kaplan, Frederic

    2007-01-01

    Intrinsic motivation, centrally involved in spontaneous exploration and curiosity, is a crucial concept in developmental psychology. It has been argued to be a crucial mechanism for open-ended cognitive development in humans, and as such has gathered a growing interest from developmental roboticists in the recent years. The goal of this paper is threefold. First, it provides a synthesis of the different approaches of intrinsic motivation in psychology. Second, by interpreting these approaches in a computational reinforcement learning framework, we argue that they are not operational and even sometimes inconsistent. Third, we set the ground for a systematic operational study of intrinsic motivation by presenting a formal typology of possible computational approaches. This typology is partly based on existing computational models, but also presents new ways of conceptualizing intrinsic motivation. We argue that this kind of computational typology might be useful for opening new avenues for research both in psychology and developmental robotics. PMID:18958277

  17. Autonomic Closure for Turbulent Flows Using Approximate Bayesian Computation

    NASA Astrophysics Data System (ADS)

    Doronina, Olga; Christopher, Jason; Hamlington, Peter; Dahm, Werner

    2017-11-01

    Autonomic closure is a new technique for achieving fully adaptive and physically accurate closure of coarse-grained turbulent flow governing equations, such as those solved in large eddy simulations (LES). Although autonomic closure has been shown in recent a priori tests to more accurately represent unclosed terms than do dynamic versions of traditional LES models, the computational cost of the approach makes it challenging to implement for simulations of practical turbulent flows at realistically high Reynolds numbers. The optimization step used in the approach introduces large matrices that must be inverted and is highly memory intensive. In order to reduce memory requirements, here we propose to use approximate Bayesian computation (ABC) in place of the optimization step, thereby yielding a computationally-efficient implementation of autonomic closure that trades memory-intensive for processor-intensive computations. The latter challenge can be overcome as co-processors such as general purpose graphical processing units become increasingly available on current generation petascale and exascale supercomputers. In this work, we outline the formulation of ABC-enabled autonomic closure and present initial results demonstrating the accuracy and computational cost of the approach.

  18. A comparative approach to closed-loop computation.

    PubMed

    Roth, E; Sponberg, S; Cowan, N J

    2014-04-01

    Neural computation is inescapably closed-loop: the nervous system processes sensory signals to shape motor output, and motor output consequently shapes sensory input. Technological advances have enabled neuroscientists to close, open, and alter feedback loops in a wide range of experimental preparations. The experimental capability of manipulating the topology-that is, how information can flow between subsystems-provides new opportunities to understand the mechanisms and computations underlying behavior. These experiments encompass a spectrum of approaches from fully open-loop, restrained preparations to the fully closed-loop character of free behavior. Control theory and system identification provide a clear computational framework for relating these experimental approaches. We describe recent progress and new directions for translating experiments at one level in this spectrum to predictions at another level. Operating across this spectrum can reveal new understanding of how low-level neural mechanisms relate to high-level function during closed-loop behavior. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Allele-sharing models: LOD scores and accurate linkage tests.

    PubMed

    Kong, A; Cox, N J

    1997-11-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested.

  20. Allele-sharing models: LOD scores and accurate linkage tests.

    PubMed Central

    Kong, A; Cox, N J

    1997-01-01

    Starting with a test statistic for linkage analysis based on allele sharing, we propose an associated one-parameter model. Under general missing-data patterns, this model allows exact calculation of likelihood ratios and LOD scores and has been implemented by a simple modification of existing software. Most important, accurate linkage tests can be performed. Using an example, we show that some previously suggested approaches to handling less than perfectly informative data can be unacceptably conservative. Situations in which this model may not perform well are discussed, and an alternative model that requires additional computations is suggested. PMID:9345087

  1. Approaches for the accurate definition of geological time boundaries

    NASA Astrophysics Data System (ADS)

    Schaltegger, Urs; Baresel, Björn; Ovtcharova, Maria; Goudemand, Nicolas; Bucher, Hugo

    2015-04-01

    Which strategies lead to the most precise and accurate date of a given geological boundary? Geological units are usually defined by the occurrence of characteristic taxa and hence boundaries between these geological units correspond to dramatic faunal and/or floral turnovers and they are primarily defined using first or last occurrences of index species, or ideally by the separation interval between two consecutive, characteristic associations of fossil taxa. These boundaries need to be defined in a way that enables their worldwide recognition and correlation across different stratigraphic successions, using tools as different as bio-, magneto-, and chemo-stratigraphy, and astrochronology. Sedimentary sequences can be dated in numerical terms by applying high-precision chemical-abrasion, isotope-dilution, thermal-ionization mass spectrometry (CA-ID-TIMS) U-Pb age determination to zircon (ZrSiO4) in intercalated volcanic ashes. But, though volcanic activity is common in geological history, ashes are not necessarily close to the boundary we would like to date precisely and accurately. In addition, U-Pb zircon data sets may be very complex and difficult to interpret in terms of the age of ash deposition. To overcome these difficulties we use a multi-proxy approach we applied to the precise and accurate dating of the Permo-Triassic and Early-Middle Triassic boundaries in South China. a) Dense sampling of ashes across the critical time interval and a sufficiently large number of analysed zircons per ash sample can guarantee the recognition of all system complexities. Geochronological datasets from U-Pb dating of volcanic zircon may indeed combine effects of i) post-crystallization Pb loss from percolation of hydrothermal fluids (even using chemical abrasion), with ii) age dispersion from prolonged residence of earlier crystallized zircon in the magmatic system. As a result, U-Pb dates of individual zircons are both apparently younger and older than the depositional age

  2. Computational Approaches to Nucleic Acid Origami.

    PubMed

    Jabbari, Hosna; Aminpour, Maral; Montemagno, Carlo

    2015-10-12

    Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.

  3. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

    PubMed

    Hu, Jialu; Kehr, Birte; Reinert, Knut

    2014-02-15

    Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

  4. Fast and Accurate Approximation to Significance Tests in Genome-Wide Association Studies

    PubMed Central

    Zhang, Yu; Liu, Jun S.

    2011-01-01

    Genome-wide association studies commonly involve simultaneous tests of millions of single nucleotide polymorphisms (SNP) for disease association. The SNPs in nearby genomic regions, however, are often highly correlated due to linkage disequilibrium (LD, a genetic term for correlation). Simple Bonferonni correction for multiple comparisons is therefore too conservative. Permutation tests, which are often employed in practice, are both computationally expensive for genome-wide studies and limited in their scopes. We present an accurate and computationally efficient method, based on Poisson de-clumping heuristics, for approximating genome-wide significance of SNP associations. Compared with permutation tests and other multiple comparison adjustment approaches, our method computes the most accurate and robust p-value adjustments for millions of correlated comparisons within seconds. We demonstrate analytically that the accuracy and the efficiency of our method are nearly independent of the sample size, the number of SNPs, and the scale of p-values to be adjusted. In addition, our method can be easily adopted to estimate false discovery rate. When applied to genome-wide SNP datasets, we observed highly variable p-value adjustment results evaluated from different genomic regions. The variation in adjustments along the genome, however, are well conserved between the European and the African populations. The p-value adjustments are significantly correlated with LD among SNPs, recombination rates, and SNP densities. Given the large variability of sequence features in the genome, we further discuss a novel approach of using SNP-specific (local) thresholds to detect genome-wide significant associations. This article has supplementary material online. PMID:22140288

  5. Enabling fast, stable and accurate peridynamic computations using multi-time-step integration

    DOE PAGES

    Lindsay, P.; Parks, M. L.; Prakash, A.

    2016-04-13

    Peridynamics is a nonlocal extension of classical continuum mechanics that is well-suited for solving problems with discontinuities such as cracks. This paper extends the peridynamic formulation to decompose a problem domain into a number of smaller overlapping subdomains and to enable the use of different time steps in different subdomains. This approach allows regions of interest to be isolated and solved at a small time step for increased accuracy while the rest of the problem domain can be solved at a larger time step for greater computational efficiency. Lastly, performance of the proposed method in terms of stability, accuracy, andmore » computational cost is examined and several numerical examples are presented to corroborate the findings.« less

  6. Computational neuropharmacology: dynamical approaches in drug discovery.

    PubMed

    Aradi, Ildiko; Erdi, Péter

    2006-05-01

    Computational approaches that adopt dynamical models are widely accepted in basic and clinical neuroscience research as indispensable tools with which to understand normal and pathological neuronal mechanisms. Although computer-aided techniques have been used in pharmaceutical research (e.g. in structure- and ligand-based drug design), the power of dynamical models has not yet been exploited in drug discovery. We suggest that dynamical system theory and computational neuroscience--integrated with well-established, conventional molecular and electrophysiological methods--offer a broad perspective in drug discovery and in the search for novel targets and strategies for the treatment of neurological and psychiatric diseases.

  7. Developments toward more accurate molecular modeling of liquids

    NASA Astrophysics Data System (ADS)

    Evans, Tom J.

    2000-12-01

    The general goal of this research has been to improve upon existing combined quantum mechanics/molecular mechanics (QM/MM) methodologies. Error weighting functions have been introduced into the perturbative Monte Carlo (PMC) method for use with QM/MM. The PMC approach, introduced earlier, provides a means to reduce the number of full self-consistent field (SCF) calculations in simulations using the QM/MM potential by evoking perturbation theory to calculate energy changes due to displacements of a MM molecule. This will allow the ab initio QM/MM approach to be applied to systems that require more advanced, computationally demanding treatments of the QM and/or MM regions. Efforts have also been made to improve the accuracy of the representation of the solvent molecules usually represented by MM force fields. Results from an investigation of the applicability of the embedded density functional theory (EDFT) for studying physical properties of solutions will be presented. In this approach, the solute wavefunction is solved self- consistently in the field of individually frozen electron-density solvent molecules. To test its accuracy, the potential curves for interactions between Li+, Cl- and H2O with a single frozen-density H 2O molecule in different orientations have been calculated. With the development of the more sophisticated effective fragment potential (EFP) representation of solvent molecules, a QM/EFP technique was created. This hybrid QM/EFP approach was used to investigate the solvation of Li + by small clusters of water, as a test case for larger ionic dusters. The EFP appears to provide an accurate representation of the strong interactions that exist between Li+ and H2O. With the QM/EFP methodology comes an increased computational expense, resulting in an even greater need to rely on the PMC approach. However, while including the PMC into the hybrid QM/EFP technique, it was discovered that the previous implementation of the PMC was done incorrectly

  8. Computational Flow Modeling of Human Upper Airway Breathing

    NASA Astrophysics Data System (ADS)

    Mylavarapu, Goutham

    Computational modeling of biological systems have gained a lot of interest in biomedical research, in the recent past. This thesis focuses on the application of computational simulations to study airflow dynamics in human upper respiratory tract. With advancements in medical imaging, patient specific geometries of anatomically accurate respiratory tracts can now be reconstructed from Magnetic Resonance Images (MRI) or Computed Tomography (CT) scans, with better and accurate details than traditional cadaver cast models. Computational studies using these individualized geometrical models have advantages of non-invasiveness, ease, minimum patient interaction, improved accuracy over experimental and clinical studies. Numerical simulations can provide detailed flow fields including velocities, flow rates, airway wall pressure, shear stresses, turbulence in an airway. Interpretation of these physical quantities will enable to develop efficient treatment procedures, medical devices, targeted drug delivery etc. The hypothesis for this research is that computational modeling can predict the outcomes of a surgical intervention or a treatment plan prior to its application and will guide the physician in providing better treatment to the patients. In the current work, three different computational approaches Computational Fluid Dynamics (CFD), Flow-Structure Interaction (FSI) and Particle Flow simulations were used to investigate flow in airway geometries. CFD approach assumes airway wall as rigid, and relatively easy to simulate, compared to the more challenging FSI approach, where interactions of airway wall deformations with flow are also accounted. The CFD methodology using different turbulence models is validated against experimental measurements in an airway phantom. Two case-studies using CFD, to quantify a pre and post-operative airway and another, to perform virtual surgery to determine the best possible surgery in a constricted airway is demonstrated. The unsteady

  9. Feasibility of approaches combining sensor and source features in brain-computer interface.

    PubMed

    Ahn, Minkyu; Hong, Jun Hee; Jun, Sung Chan

    2012-02-15

    Brain-computer interface (BCI) provides a new channel for communication between brain and computers through brain signals. Cost-effective EEG provides good temporal resolution, but its spatial resolution is poor and sensor information is blurred by inherent noise. To overcome these issues, spatial filtering and feature extraction techniques have been developed. Source imaging, transformation of sensor signals into the source space through source localizer, has gained attention as a new approach for BCI. It has been reported that the source imaging yields some improvement of BCI performance. However, there exists no thorough investigation on how source imaging information overlaps with, and is complementary to, sensor information. Information (visible information) from the source space may overlap as well as be exclusive to information from the sensor space is hypothesized. Therefore, we can extract more information from the sensor and source spaces if our hypothesis is true, thereby contributing to more accurate BCI systems. In this work, features from each space (sensor or source), and two strategies combining sensor and source features are assessed. The information distribution among the sensor, source, and combined spaces is discussed through a Venn diagram for 18 motor imagery datasets. Additional 5 motor imagery datasets from the BCI Competition III site were examined. The results showed that the addition of source information yielded about 3.8% classification improvement for 18 motor imagery datasets and showed an average accuracy of 75.56% for BCI Competition data. Our proposed approach is promising, and improved performance may be possible with better head model. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Results of computer assisted mini-incision subvastus approach for total knee arthroplasty.

    PubMed

    Turajane, Thana; Larbpaiboonpong, Viroj; Kongtharvonskul, Jatupon; Maungsiri, Samart

    2009-12-01

    groups), and Knee society score preoperative and postoperative [64.6 (59.8-69.4) and 93.7 (90.8-96.65)]: 69 (63.6-74.39) 92.36 (88.22-96.5)]. The complications found in both groups were similar. No deep vein thrombosis, no fracture at both femur and tibia, no vascular injury, and no pin tract pain or infection was found in both groups. The computer assisted CMS-TKA) is one of the appropriate procedures for all varus deformity, no limitation with the associated bone loss, flexion contractor, BMI, except the fixed valgus deformity. To ensure the clinical outcomes, multiple key steps were considered as the appropriate techniques for this approach which included the accurate registration, precision bone cut and ligament balances, and the good cement techniques.

  11. An accurate and computationally efficient algorithm for ground peak identification in large footprint waveform LiDAR data

    NASA Astrophysics Data System (ADS)

    Zhuang, Wei; Mountrakis, Giorgos

    2014-09-01

    Large footprint waveform LiDAR sensors have been widely used for numerous airborne studies. Ground peak identification in a large footprint waveform is a significant bottleneck in exploring full usage of the waveform datasets. In the current study, an accurate and computationally efficient algorithm was developed for ground peak identification, called Filtering and Clustering Algorithm (FICA). The method was evaluated on Land, Vegetation, and Ice Sensor (LVIS) waveform datasets acquired over Central NY. FICA incorporates a set of multi-scale second derivative filters and a k-means clustering algorithm in order to avoid detecting false ground peaks. FICA was tested in five different land cover types (deciduous trees, coniferous trees, shrub, grass and developed area) and showed more accurate results when compared to existing algorithms. More specifically, compared with Gaussian decomposition, the RMSE ground peak identification by FICA was 2.82 m (5.29 m for GD) in deciduous plots, 3.25 m (4.57 m for GD) in coniferous plots, 2.63 m (2.83 m for GD) in shrub plots, 0.82 m (0.93 m for GD) in grass plots, and 0.70 m (0.51 m for GD) in plots of developed areas. FICA performance was also relatively consistent under various slope and canopy coverage (CC) conditions. In addition, FICA showed better computational efficiency compared to existing methods. FICA's major computational and accuracy advantage is a result of the adopted multi-scale signal processing procedures that concentrate on local portions of the signal as opposed to the Gaussian decomposition that uses a curve-fitting strategy applied in the entire signal. The FICA algorithm is a good candidate for large-scale implementation on future space-borne waveform LiDAR sensors.

  12. Critiquing: A Different Approach to Expert Computer Advice in Medicine

    PubMed Central

    Miller, Perry L.

    1984-01-01

    The traditional approach to computer-based advice in medicine has been to design systems which simulate a physician's decision process. This paper describes a different approach to computer advice in medicine: a critiquing approach. A critiquing system first asks how the physician is planning to manage his patient and then critiques that plan, discussing the advantages and disadvantages of the proposed approach, compared to other approaches which might be reasonable or preferred. Several critiquing systems are currently in different stages of implementation. The paper describes these systems and discusses the characteristics which make each domain suitable for critiquing. The critiquing approach may prove especially well-suited in domains where decisions involve a great deal of subjective judgement.

  13. Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

    PubMed Central

    2013-01-01

    Background A large-scale, highly accurate, machine-understandable drug-disease treatment relationship knowledge base is important for computational approaches to drug repurposing. The large body of published biomedical research articles and clinical case reports available on MEDLINE is a rich source of FDA-approved drug-disease indication as well as drug-repurposing knowledge that is crucial for applying FDA-approved drugs for new diseases. However, much of this information is buried in free text and not captured in any existing databases. The goal of this study is to extract a large number of accurate drug-disease treatment pairs from published literature. Results In this study, we developed a simple but highly accurate pattern-learning approach to extract treatment-specific drug-disease pairs from 20 million biomedical abstracts available on MEDLINE. We extracted a total of 34,305 unique drug-disease treatment pairs, the majority of which are not included in existing structured databases. Our algorithm achieved a precision of 0.904 and a recall of 0.131 in extracting all pairs, and a precision of 0.904 and a recall of 0.842 in extracting frequent pairs. In addition, we have shown that the extracted pairs strongly correlate with both drug target genes and therapeutic classes, therefore may have high potential in drug discovery. Conclusions We demonstrated that our simple pattern-learning relationship extraction algorithm is able to accurately extract many drug-disease pairs from the free text of biomedical literature that are not captured in structured databases. The large-scale, accurate, machine-understandable drug-disease treatment knowledge base that is resultant of our study, in combination with pairs from structured databases, will have high potential in computational drug repurposing tasks. PMID:23742147

  14. Accurate van der Waals coefficients from density functional theory

    PubMed Central

    Tao, Jianmin; Perdew, John P.; Ruzsinszky, Adrienn

    2012-01-01

    The van der Waals interaction is a weak, long-range correlation, arising from quantum electronic charge fluctuations. This interaction affects many properties of materials. A simple and yet accurate estimate of this effect will facilitate computer simulation of complex molecular materials and drug design. Here we develop a fast approach for accurate evaluation of dynamic multipole polarizabilities and van der Waals (vdW) coefficients of all orders from the electron density and static multipole polarizabilities of each atom or other spherical object, without empirical fitting. Our dynamic polarizabilities (dipole, quadrupole, octupole, etc.) are exact in the zero- and high-frequency limits, and exact at all frequencies for a metallic sphere of uniform density. Our theory predicts dynamic multipole polarizabilities in excellent agreement with more expensive many-body methods, and yields therefrom vdW coefficients C6, C8, C10 for atom pairs with a mean absolute relative error of only 3%. PMID:22205765

  15. Improving the Efficiency of Abdominal Aortic Aneurysm Wall Stress Computations

    PubMed Central

    Zelaya, Jaime E.; Goenezen, Sevan; Dargon, Phong T.; Azarbal, Amir-Farzin; Rugonyi, Sandra

    2014-01-01

    An abdominal aortic aneurysm is a pathological dilation of the abdominal aorta, which carries a high mortality rate if ruptured. The most commonly used surrogate marker of rupture risk is the maximal transverse diameter of the aneurysm. More recent studies suggest that wall stress from models of patient-specific aneurysm geometries extracted, for instance, from computed tomography images may be a more accurate predictor of rupture risk and an important factor in AAA size progression. However, quantification of wall stress is typically computationally intensive and time-consuming, mainly due to the nonlinear mechanical behavior of the abdominal aortic aneurysm walls. These difficulties have limited the potential of computational models in clinical practice. To facilitate computation of wall stresses, we propose to use a linear approach that ensures equilibrium of wall stresses in the aneurysms. This proposed linear model approach is easy to implement and eliminates the burden of nonlinear computations. To assess the accuracy of our proposed approach to compute wall stresses, results from idealized and patient-specific model simulations were compared to those obtained using conventional approaches and to those of a hypothetical, reference abdominal aortic aneurysm model. For the reference model, wall mechanical properties and the initial unloaded and unstressed configuration were assumed to be known, and the resulting wall stresses were used as reference for comparison. Our proposed linear approach accurately approximates wall stresses for varying model geometries and wall material properties. Our findings suggest that the proposed linear approach could be used as an effective, efficient, easy-to-use clinical tool to estimate patient-specific wall stresses. PMID:25007052

  16. Computer Mediated Social Network Approach to Software Support and Maintenance

    DTIC Science & Technology

    2010-06-01

    Page 1        Computer Mediated  Social   Network  Approach to  Software Support and Maintenance     LTC J. Carlos Vega  *Student Paper*    Point...DATES COVERED 00-00-2010 to 00-00-2010 4. TITLE AND SUBTITLE Computer Mediated Social Network Approach to Software Support and Maintenance...This research highlights the preliminary findings on the potential of computer mediated social networks . This research focused on social networks as

  17. Computation of elementary modes: a unifying framework and the new binary approach

    PubMed Central

    Gagneur, Julien; Klamt, Steffen

    2004-01-01

    Background Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous formalism to describe and assess pathways and has proven to be valuable for many applications. However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods. Results We show that computing the set of elementary modes is equivalent to computing the set of extreme rays of a convex cone. This standard mathematical representation provides a unified framework that encompasses the most prominent algorithmic methods that compute elementary modes and allows a clear comparison between them. Taking lessons from this benchmark, we here introduce a new method, the binary approach, which computes the elementary modes as binary patterns of participating reactions from which the respective stoichiometric coefficients can be computed in a post-processing step. We implemented the binary approach in FluxAnalyzer 5.1, a software that is free for academics. The binary approach decreases the memory demand up to 96% without loss of speed giving the most efficient method available for computing elementary modes to date. Conclusions The equivalence between elementary modes and extreme ray computations offers opportunities for employing tools from polyhedral computation for metabolic pathway analysis. The new binary approach introduced herein was derived from this general theoretical framework and facilitates the computation of elementary modes in considerably larger networks. PMID:15527509

  18. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    PubMed Central

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J.; Brewster, Aaron S.; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G.; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R.; Miahnahri, Alan; White, William E.; Schafer, Donald W.; Seibert, M. Marvin; Koglin, Jason E.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J.; Glatzel, Pieter; Zwart, Petrus H.; Grosse-Kunstleve, Ralf W.; Bogan, Michael J.; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K.; Adams, Paul D.; Sauter, Nicholas K.

    2014-01-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409

  19. A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chacón, Enrique, E-mail: echacon@icmm.csic.es; Tarazona, Pedro, E-mail: pedro.tarazona@uam.es; Bresme, Fernando, E-mail: f.bresme@imperial.ac.uk

    We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributionsmore » related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke’s law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.« less

  20. A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes.

    PubMed

    Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando

    2015-07-21

    We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke's law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.

  1. A computer simulation approach to quantify the true area and true area compressibility modulus of biological membranes

    NASA Astrophysics Data System (ADS)

    Chacón, Enrique; Tarazona, Pedro; Bresme, Fernando

    2015-07-01

    We present a new computational approach to quantify the area per lipid and the area compressibility modulus of biological membranes. Our method relies on the analysis of the membrane fluctuations using our recently introduced coupled undulatory (CU) mode [Tarazona et al., J. Chem. Phys. 139, 094902 (2013)], which provides excellent estimates of the bending modulus of model membranes. Unlike the projected area, widely used in computer simulations of membranes, the CU area is thermodynamically consistent. This new area definition makes it possible to accurately estimate the area of the undulating bilayer, and the area per lipid, by excluding any contributions related to the phospholipid protrusions. We find that the area per phospholipid and the area compressibility modulus features a negligible dependence with system size, making possible their computation using truly small bilayers, involving a few hundred lipids. The area compressibility modulus obtained from the analysis of the CU area fluctuations is fully consistent with the Hooke's law route. Unlike existing methods, our approach relies on a single simulation, and no a priori knowledge of the bending modulus is required. We illustrate our method by analyzing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers using the coarse grained MARTINI force-field. The area per lipid and area compressibility modulus obtained with our method and the MARTINI forcefield are consistent with previous studies of these bilayers.

  2. Fast and accurate reference-free alignment of subtomograms.

    PubMed

    Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

    2013-06-01

    In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. Ischemic stroke enhancement in computed tomography scans using a computational approach

    NASA Astrophysics Data System (ADS)

    Alves, Allan F. F.; Pavan, Ana L. M.; Jennane, Rachid; Miranda, José R. A.; Freitas, Carlos C. M.; Abdala, Nitamar; Pina, Diana R.

    2018-03-01

    In this work, a novel approach was proposed to enhance the visual perception of ischemic stroke in computed tomography scans. Through different image processing techniques, we enabled less experienced physicians, to reliably detect early signs of stroke. A set of 40 retrospective CT scans of patients were used, divided into two groups: 25 cases of acute ischemic stroke and 15 normal cases used as control group. All cases were obtained within 4 hours of symptoms onset. Our approach was based on the variational decomposition model and three different segmentation methods. A test determined observers' performance to correctly diagnose stroke cases. The Expectation Maximization method provided the best results among all observers. The overall sensitivity of the observer's analysis was 64% and increased to 79%. The overall specificity was 67% and increased to 78%. These results show the importance of a computational tool to assist neuroradiology decisions, especially in critical situations such as the diagnosis of ischemic stroke.

  4. A fast and accurate dihedral interpolation loop subdivision scheme

    NASA Astrophysics Data System (ADS)

    Shi, Zhuo; An, Yalei; Wang, Zhongshuai; Yu, Ke; Zhong, Si; Lan, Rushi; Luo, Xiaonan

    2018-04-01

    In this paper, we propose a fast and accurate dihedral interpolation Loop subdivision scheme for subdivision surfaces based on triangular meshes. In order to solve the problem of surface shrinkage, we keep the limit condition unchanged, which is important. Extraordinary vertices are handled using modified Butterfly rules. Subdivision schemes are computationally costly as the number of faces grows exponentially at higher levels of subdivision. To address this problem, our approach is to use local surface information to adaptively refine the model. This is achieved simply by changing the threshold value of the dihedral angle parameter, i.e., the angle between the normals of a triangular face and its adjacent faces. We then demonstrate the effectiveness of the proposed method for various 3D graphic triangular meshes, and extensive experimental results show that it can match or exceed the expected results at lower computational cost.

  5. A hybrid solution using computational prediction and measured data to accurately determine process corrections with reduced overlay sampling

    NASA Astrophysics Data System (ADS)

    Noyes, Ben F.; Mokaberi, Babak; Mandoy, Ram; Pate, Alex; Huijgen, Ralph; McBurney, Mike; Chen, Owen

    2017-03-01

    Reducing overlay error via an accurate APC feedback system is one of the main challenges in high volume production of the current and future nodes in the semiconductor industry. The overlay feedback system directly affects the number of dies meeting overlay specification and the number of layers requiring dedicated exposure tools through the fabrication flow. Increasing the former number and reducing the latter number is beneficial for the overall efficiency and yield of the fabrication process. An overlay feedback system requires accurate determination of the overlay error, or fingerprint, on exposed wafers in order to determine corrections to be automatically and dynamically applied to the exposure of future wafers. Since current and future nodes require correction per exposure (CPE), the resolution of the overlay fingerprint must be high enough to accommodate CPE in the overlay feedback system, or overlay control module (OCM). Determining a high resolution fingerprint from measured data requires extremely dense overlay sampling that takes a significant amount of measurement time. For static corrections this is acceptable, but in an automated dynamic correction system this method creates extreme bottlenecks for the throughput of said system as new lots have to wait until the previous lot is measured. One solution is using a less dense overlay sampling scheme and employing computationally up-sampled data to a dense fingerprint. That method uses a global fingerprint model over the entire wafer; measured localized overlay errors are therefore not always represented in its up-sampled output. This paper will discuss a hybrid system shown in Fig. 1 that combines a computationally up-sampled fingerprint with the measured data to more accurately capture the actual fingerprint, including local overlay errors. Such a hybrid system is shown to result in reduced modelled residuals while determining the fingerprint, and better on-product overlay performance.

  6. A multidisciplinary approach to solving computer related vision problems.

    PubMed

    Long, Jennifer; Helland, Magne

    2012-09-01

    This paper proposes a multidisciplinary approach to solving computer related vision issues by including optometry as a part of the problem-solving team. Computer workstation design is increasing in complexity. There are at least ten different professions who contribute to workstation design or who provide advice to improve worker comfort, safety and efficiency. Optometrists have a role identifying and solving computer-related vision issues and in prescribing appropriate optical devices. However, it is possible that advice given by optometrists to improve visual comfort may conflict with other requirements and demands within the workplace. A multidisciplinary approach has been advocated for solving computer related vision issues. There are opportunities for optometrists to collaborate with ergonomists, who coordinate information from physical, cognitive and organisational disciplines to enact holistic solutions to problems. This paper proposes a model of collaboration and examples of successful partnerships at a number of professional levels including individual relationships between optometrists and ergonomists when they have mutual clients/patients, in undergraduate and postgraduate education and in research. There is also scope for dialogue between optometry and ergonomics professional associations. A multidisciplinary approach offers the opportunity to solve vision related computer issues in a cohesive, rather than fragmented way. Further exploration is required to understand the barriers to these professional relationships. © 2012 The College of Optometrists.

  7. Application of CT-PSF-based computer-simulated lung nodules for evaluating the accuracy of computer-aided volumetry.

    PubMed

    Funaki, Ayumu; Ohkubo, Masaki; Wada, Shinichi; Murao, Kohei; Matsumoto, Toru; Niizuma, Shinji

    2012-07-01

    With the wide dissemination of computed tomography (CT) screening for lung cancer, measuring the nodule volume accurately with computer-aided volumetry software is increasingly important. Many studies for determining the accuracy of volumetry software have been performed using a phantom with artificial nodules. These phantom studies are limited, however, in their ability to reproduce the nodules both accurately and in the variety of sizes and densities required. Therefore, we propose a new approach of using computer-simulated nodules based on the point spread function measured in a CT system. The validity of the proposed method was confirmed by the excellent agreement obtained between computer-simulated nodules and phantom nodules regarding the volume measurements. A practical clinical evaluation of the accuracy of volumetry software was achieved by adding simulated nodules onto clinical lung images, including noise and artifacts. The tested volumetry software was revealed to be accurate within an error of 20 % for nodules >5 mm and with the difference between nodule density and background (lung) (CT value) being 400-600 HU. Such a detailed analysis can provide clinically useful information on the use of volumetry software in CT screening for lung cancer. We concluded that the proposed method is effective for evaluating the performance of computer-aided volumetry software.

  8. Introducing Computational Approaches in Intermediate Mechanics

    NASA Astrophysics Data System (ADS)

    Cook, David M.

    2006-12-01

    In the winter of 2003, we at Lawrence University moved Lagrangian mechanics and rigid body dynamics from a required sophomore course to an elective junior/senior course, freeing 40% of the time for computational approaches to ordinary differential equations (trajectory problems, the large amplitude pendulum, non-linear dynamics); evaluation of integrals (finding centers of mass and moment of inertia tensors, calculating gravitational potentials for various sources); and finding eigenvalues and eigenvectors of matrices (diagonalizing the moment of inertia tensor, finding principal axes), and to generating graphical displays of computed results. Further, students begin to use LaTeX to prepare some of their submitted problem solutions. Placed in the middle of the sophomore year, this course provides the background that permits faculty members as appropriate to assign computer-based exercises in subsequent courses. Further, students are encouraged to use our Computational Physics Laboratory on their own initiative whenever that use seems appropriate. (Curricular development supported in part by the W. M. Keck Foundation, the National Science Foundation, and Lawrence University.)

  9. Computational approach to compact Riemann surfaces

    NASA Astrophysics Data System (ADS)

    Frauendiener, Jörg; Klein, Christian

    2017-01-01

    A purely numerical approach to compact Riemann surfaces starting from plane algebraic curves is presented. The critical points of the algebraic curve are computed via a two-dimensional Newton iteration. The starting values for this iteration are obtained from the resultants with respect to both coordinates of the algebraic curve and a suitable pairing of their zeros. A set of generators of the fundamental group for the complement of these critical points in the complex plane is constructed from circles around these points and connecting lines obtained from a minimal spanning tree. The monodromies are computed by solving the defining equation of the algebraic curve on collocation points along these contours and by analytically continuing the roots. The collocation points are chosen to correspond to Chebychev collocation points for an ensuing Clenshaw-Curtis integration of the holomorphic differentials which gives the periods of the Riemann surface with spectral accuracy. At the singularities of the algebraic curve, Puiseux expansions computed by contour integration on the circles around the singularities are used to identify the holomorphic differentials. The Abel map is also computed with the Clenshaw-Curtis algorithm and contour integrals. As an application of the code, solutions to the Kadomtsev-Petviashvili equation are computed on non-hyperelliptic Riemann surfaces.

  10. FAMBE-pH: A Fast and Accurate Method to Compute the Total Solvation Free Energies of Proteins

    PubMed Central

    Vorobjev, Yury N.; Vila, Jorge A.

    2009-01-01

    A fast and accurate method to compute the total solvation free energies of proteins as a function of pH is presented. The method makes use of a combination of approaches, some of which have already appeared in the literature; (i) the Poisson equation is solved with an optimized fast adaptive multigrid boundary element (FAMBE) method; (ii) the electrostatic free energies of the ionizable sites are calculated for their neutral and charged states by using a detailed model of atomic charges; (iii) a set of optimal atomic radii is used to define a precise dielectric surface interface; (iv) a multilevel adaptive tessellation of this dielectric surface interface is achieved by using multisized boundary elements; and (v) 1:1 salt effects are included. The equilibrium proton binding/release is calculated with the Tanford–Schellman integral if the proteins contain more than ∼20–25 ionizable groups; for a smaller number of ionizable groups, the ionization partition function is calculated directly. The FAMBE method is tested as a function of pH (FAMBE-pH) with three proteins, namely, bovine pancreatic trypsin inhibitor (BPTI), hen egg white lysozyme (HEWL), and bovine pancreatic ribonuclease A (RNaseA). The results are (a) the FAMBE-pH method reproduces the observed pKa's of the ionizable groups of these proteins within an average absolute value of 0.4 pK units and a maximum error of 1.2 pK units and (b) comparison of the calculated total pH-dependent solvation free energy for BPTI, between the exact calculation of the ionization partition function and the Tanford–Schellman integral method, shows agreement within 1.2 kcal/mol. These results indicate that calculation of total solvation free energies with the FAMBE-pH method can provide an accurate prediction of protein conformational stability at a given fixed pH and, if coupled with molecular mechanics or molecular dynamics methods, can also be used for more realistic studies of protein folding, unfolding, and dynamics

  11. Mutations that Cause Human Disease: A Computational/Experimental Approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beernink, P; Barsky, D; Pesavento, B

    International genome sequencing projects have produced billions of nucleotides (letters) of DNA sequence data, including the complete genome sequences of 74 organisms. These genome sequences have created many new scientific opportunities, including the ability to identify sequence variations among individuals within a species. These genetic differences, which are known as single nucleotide polymorphisms (SNPs), are particularly important in understanding the genetic basis for disease susceptibility. Since the report of the complete human genome sequence, over two million human SNPs have been identified, including a large-scale comparison of an entire chromosome from twenty individuals. Of the protein coding SNPs (cSNPs), approximatelymore » half leads to a single amino acid change in the encoded protein (non-synonymous coding SNPs). Most of these changes are functionally silent, while the remainder negatively impact the protein and sometimes cause human disease. To date, over 550 SNPs have been found to cause single locus (monogenic) diseases and many others have been associated with polygenic diseases. SNPs have been linked to specific human diseases, including late-onset Parkinson disease, autism, rheumatoid arthritis and cancer. The ability to predict accurately the effects of these SNPs on protein function would represent a major advance toward understanding these diseases. To date several attempts have been made toward predicting the effects of such mutations. The most successful of these is a computational approach called ''Sorting Intolerant From Tolerant'' (SIFT). This method uses sequence conservation among many similar proteins to predict which residues in a protein are functionally important. However, this method suffers from several limitations. First, a query sequence must have a sufficient number of relatives to infer sequence conservation. Second, this method does not make use of or provide any information on protein structure, which can be used to

  12. Computational approaches to metabolic engineering utilizing systems biology and synthetic biology.

    PubMed

    Fong, Stephen S

    2014-08-01

    Metabolic engineering modifies cellular function to address various biochemical applications. Underlying metabolic engineering efforts are a host of tools and knowledge that are integrated to enable successful outcomes. Concurrent development of computational and experimental tools has enabled different approaches to metabolic engineering. One approach is to leverage knowledge and computational tools to prospectively predict designs to achieve the desired outcome. An alternative approach is to utilize combinatorial experimental tools to empirically explore the range of cellular function and to screen for desired traits. This mini-review focuses on computational systems biology and synthetic biology tools that can be used in combination for prospective in silico strain design.

  13. Combined inverse-forward artificial neural networks for fast and accurate estimation of the diffusion coefficients of cartilage based on multi-physics models.

    PubMed

    Arbabi, Vahid; Pouran, Behdad; Weinans, Harrie; Zadpoor, Amir A

    2016-09-06

    Analytical and numerical methods have been used to extract essential engineering parameters such as elastic modulus, Poisson׳s ratio, permeability and diffusion coefficient from experimental data in various types of biological tissues. The major limitation associated with analytical techniques is that they are often only applicable to problems with simplified assumptions. Numerical multi-physics methods, on the other hand, enable minimizing the simplified assumptions but require substantial computational expertise, which is not always available. In this paper, we propose a novel approach that combines inverse and forward artificial neural networks (ANNs) which enables fast and accurate estimation of the diffusion coefficient of cartilage without any need for computational modeling. In this approach, an inverse ANN is trained using our multi-zone biphasic-solute finite-bath computational model of diffusion in cartilage to estimate the diffusion coefficient of the various zones of cartilage given the concentration-time curves. Robust estimation of the diffusion coefficients, however, requires introducing certain levels of stochastic variations during the training process. Determining the required level of stochastic variation is performed by coupling the inverse ANN with a forward ANN that receives the diffusion coefficient as input and returns the concentration-time curve as output. Combined together, forward-inverse ANNs enable computationally inexperienced users to obtain accurate and fast estimation of the diffusion coefficients of cartilage zones. The diffusion coefficients estimated using the proposed approach are compared with those determined using direct scanning of the parameter space as the optimization approach. It has been shown that both approaches yield comparable results. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates

    NASA Astrophysics Data System (ADS)

    Carbogno, Christian; Scheffler, Matthias

    In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.

  15. Modeling weakly-ionized plasmas in magnetic field: A new computationally-efficient approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Parent, Bernard, E-mail: parent@pusan.ac.kr; Macheret, Sergey O.; Shneider, Mikhail N.

    2015-11-01

    Despite its success at simulating accurately both non-neutral and quasi-neutral weakly-ionized plasmas, the drift-diffusion model has been observed to be a particularly stiff set of equations. Recently, it was demonstrated that the stiffness of the system could be relieved by rewriting the equations such that the potential is obtained from Ohm's law rather than Gauss's law while adding some source terms to the ion transport equation to ensure that Gauss's law is satisfied in non-neutral regions. Although the latter was applicable to multicomponent and multidimensional plasmas, it could not be used for plasmas in which the magnetic field was significant.more » This paper hence proposes a new computationally-efficient set of electron and ion transport equations that can be used not only for a plasma with multiple types of positive and negative ions, but also for a plasma in magnetic field. Because the proposed set of equations is obtained from the same physical model as the conventional drift-diffusion equations without introducing new assumptions or simplifications, it results in the same exact solution when the grid is refined sufficiently while being more computationally efficient: not only is the proposed approach considerably less stiff and hence requires fewer iterations to reach convergence but it yields a converged solution that exhibits a significantly higher resolution. The combined faster convergence and higher resolution is shown to result in a hundredfold increase in computational efficiency for some typical steady and unsteady plasma problems including non-neutral cathode and anode sheaths as well as quasi-neutral regions.« less

  16. ACCURATE SPECTROSCOPIC CHARACTERIZATION OF PROTONATED OXIRANE: A POTENTIAL PREBIOTIC SPECIES IN TITAN'S ATMOSPHERE.

    PubMed

    Puzzarini, Cristina; Ali, Ashraf; Biczysko, Malgorzata; Barone, Vincenzo

    2014-09-10

    An accurate spectroscopic characterization of protonated oxirane has been carried out by means of state-of-the-art computational methods and approaches. The calculated spectroscopic parameters from our recent computational investigation of oxirane together with the corresponding experimental data available were used to assess the accuracy of our predicted rotational and IR spectra of protonated oxirane. We found an accuracy of about 10 cm -1 for vibrational transitions (fundamentals as well as overtones and combination bands) and, in relative terms, of 0.1% for rotational transitions. We are therefore confident that the spectroscopic data provided herein are a valuable support for the detection of protonated oxirane not only in Titan's atmosphere but also in the interstellar medium.

  17. Computational intelligence approaches for pattern discovery in biological systems.

    PubMed

    Fogel, Gary B

    2008-07-01

    Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as artificial neural networks, fuzzy systems and evolutionary computation are being used with increasing frequency to contend with this problem, in light of noise, non-linearity and temporal dynamics in the data. Such methods can be used to develop robust models of processes either on their own or in combination with standard statistical approaches. This is especially true for database mining, where modeling is a key component of scientific understanding. This review provides an introduction to current CI methods, their application to biological problems, and concludes with a commentary about the anticipated impact of these approaches in bioinformatics.

  18. Computational approaches for predicting biomedical research collaborations.

    PubMed

    Zhang, Qing; Yu, Hong

    2014-01-01

    Biomedical research is increasingly collaborative, and successful collaborations often produce high impact work. Computational approaches can be developed for automatically predicting biomedical research collaborations. Previous works of collaboration prediction mainly explored the topological structures of research collaboration networks, leaving out rich semantic information from the publications themselves. In this paper, we propose supervised machine learning approaches to predict research collaborations in the biomedical field. We explored both the semantic features extracted from author research interest profile and the author network topological features. We found that the most informative semantic features for author collaborations are related to research interest, including similarity of out-citing citations, similarity of abstracts. Of the four supervised machine learning models (naïve Bayes, naïve Bayes multinomial, SVMs, and logistic regression), the best performing model is logistic regression with an ROC ranging from 0.766 to 0.980 on different datasets. To our knowledge we are the first to study in depth how research interest and productivities can be used for collaboration prediction. Our approach is computationally efficient, scalable and yet simple to implement. The datasets of this study are available at https://github.com/qingzhanggithub/medline-collaboration-datasets.

  19. Sensing and perception: Connectionist approaches to subcognitive computing

    NASA Technical Reports Server (NTRS)

    Skrrypek, J.

    1987-01-01

    New approaches to machine sensing and perception are presented. The motivation for crossdisciplinary studies of perception in terms of AI and neurosciences is suggested. The question of computing architecture granularity as related to global/local computation underlying perceptual function is considered and examples of two environments are given. Finally, the examples of using one of the environments, UCLA PUNNS, to study neural architectures for visual function are presented.

  20. Computational approaches for drug discovery.

    PubMed

    Hung, Che-Lun; Chen, Chi-Chun

    2014-09-01

    Cellular proteins are the mediators of multiple organism functions being involved in physiological mechanisms and disease. By discovering lead compounds that affect the function of target proteins, the target diseases or physiological mechanisms can be modulated. Based on knowledge of the ligand-receptor interaction, the chemical structures of leads can be modified to improve efficacy, selectivity and reduce side effects. One rational drug design technology, which enables drug discovery based on knowledge of target structures, functional properties and mechanisms, is computer-aided drug design (CADD). The application of CADD can be cost-effective using experiments to compare predicted and actual drug activity, the results from which can used iteratively to improve compound properties. The two major CADD-based approaches are structure-based drug design, where protein structures are required, and ligand-based drug design, where ligand and ligand activities can be used to design compounds interacting with the protein structure. Approaches in structure-based drug design include docking, de novo design, fragment-based drug discovery and structure-based pharmacophore modeling. Approaches in ligand-based drug design include quantitative structure-affinity relationship and pharmacophore modeling based on ligand properties. Based on whether the structure of the receptor and its interaction with the ligand are known, different design strategies can be seed. After lead compounds are generated, the rule of five can be used to assess whether these have drug-like properties. Several quality validation methods, such as cost function analysis, Fisher's cross-validation analysis and goodness of hit test, can be used to estimate the metrics of different drug design strategies. To further improve CADD performance, multi-computers and graphics processing units may be applied to reduce costs. © 2014 Wiley Periodicals, Inc.

  1. A Supervised Statistical Learning Approach for Accurate Legionella pneumophila Source Attribution during Outbreaks

    PubMed Central

    Buultjens, Andrew H.; Chua, Kyra Y. L.; Baines, Sarah L.; Kwong, Jason; Gao, Wei; Cutcher, Zoe; Adcock, Stuart; Ballard, Susan; Schultz, Mark B.; Tomita, Takehiro; Subasinghe, Nela; Carter, Glen P.; Pidot, Sacha J.; Franklin, Lucinda; Seemann, Torsten; Gonçalves Da Silva, Anders

    2017-01-01

    ABSTRACT Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure, with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based on L. pneumophila core genome single nucleotide polymorphism (SNP) comparisons eliminates ambiguity for defining outbreak clusters and accurately predicts exposure sources for clinical cases. We illustrate the performance of our method by genome comparisons of 234 L. pneumophila isolates obtained from patients and cooling towers in Melbourne, Australia, between 1994 and 2014. This collection included one of the largest reported Legionnaires' disease outbreaks, which involved 125 cases at an aquarium. Using only sequence data from L. pneumophila cooling tower isolates and including all core genome variation, we built a multivariate model using discriminant analysis of principal components (DAPC) to find cooling tower-specific genomic signatures and then used it to predict the origin of clinical isolates. Model assignments were 93% congruent with epidemiological data, including the aquarium Legionnaires' disease outbreak and three other unrelated outbreak investigations. We applied the same approach to a recently described investigation of Legionnaires' disease within a UK hospital and observed a model predictive ability of 86%. We have developed a promising means to breach L. pneumophila genetic diversity extremes and provide objective source attribution data for outbreak investigations. IMPORTANCE Microbial outbreak investigations are moving to a paradigm where whole-genome sequencing and phylogenetic trees are used to support epidemiological

  2. A dynamical-systems approach for computing ice-affected streamflow

    USGS Publications Warehouse

    Holtschlag, David J.

    1996-01-01

    A dynamical-systems approach was developed and evaluated for computing ice-affected streamflow. The approach provides for dynamic simulation and parameter estimation of site-specific equations relating ice effects to routinely measured environmental variables. Comparison indicates that results from the dynamical-systems approach ranked higher than results from 11 analytical methods previously investigated on the basis of accuracy and feasibility criteria. Additional research will likely lead to further improvements in the approach.

  3. Accurate integration over atomic regions bounded by zero-flux surfaces.

    PubMed

    Polestshuk, Pavel M

    2013-01-30

    The approach for the integration over a region covered by zero-flux surface is described. This approach based on the surface triangulation technique is efficiently realized in a newly developed program TWOE. The elaborated method is tested on several atomic properties including the source function. TWOE results are compared with those produced by using well-known existing programs. Absolute errors in computed atomic properties are shown to range usually from 10(-6) to 10(-5) au. The demonstrative examples prove that present realization has perfect convergence of atomic properties with increasing size of angular grid and allows to obtain highly accurate data even in the most difficult cases. It is believed that the developed program can be bridgehead that allows to implement atomic partitioning of any desired molecular property with high accuracy. Copyright © 2012 Wiley Periodicals, Inc.

  4. An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function.

    PubMed

    Yu, Peng; Shaw, Chad A

    2014-06-01

    The Dirichlet-multinomial (DMN) distribution is a fundamental model for multicategory count data with overdispersion. This distribution has many uses in bioinformatics including applications to metagenomics data, transctriptomics and alternative splicing. The DMN distribution reduces to the multinomial distribution when the overdispersion parameter ψ is 0. Unfortunately, numerical computation of the DMN log-likelihood function by conventional methods results in instability in the neighborhood of [Formula: see text]. An alternative formulation circumvents this instability, but it leads to long runtimes that make it impractical for large count data common in bioinformatics. We have developed a new method for computation of the DMN log-likelihood to solve the instability problem without incurring long runtimes. The new approach is composed of a novel formula and an algorithm to extend its applicability. Our numerical experiments show that this new method both improves the accuracy of log-likelihood evaluation and the runtime by several orders of magnitude, especially in high-count data situations that are common in deep sequencing data. Using real metagenomic data, our method achieves manyfold runtime improvement. Our method increases the feasibility of using the DMN distribution to model many high-throughput problems in bioinformatics. We have included in our work an R package giving access to this method and a vingette applying this approach to metagenomic data. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. Analytical and Computational Properties of Distributed Approaches to MDO

    NASA Technical Reports Server (NTRS)

    Alexandrov, Natalia M.; Lewis, Robert Michael

    2000-01-01

    Historical evolution of engineering disciplines and the complexity of the MDO problem suggest that disciplinary autonomy is a desirable goal in formulating and solving MDO problems. We examine the notion of disciplinary autonomy and discuss the analytical properties of three approaches to formulating and solving MDO problems that achieve varying degrees of autonomy by distributing the problem along disciplinary lines. Two of the approaches-Optimization by Linear Decomposition and Collaborative Optimization-are based on bi-level optimization and reflect what we call a structural perspective. The third approach, Distributed Analysis Optimization, is a single-level approach that arises from what we call an algorithmic perspective. The main conclusion of the paper is that disciplinary autonomy may come at a price: in the bi-level approaches, the system-level constraints introduced to relax the interdisciplinary coupling and enable disciplinary autonomy can cause analytical and computational difficulties for optimization algorithms. The single-level alternative we discuss affords a more limited degree of autonomy than that of the bi-level approaches, but without the computational difficulties of the bi-level methods. Key Words: Autonomy, bi-level optimization, distributed optimization, multidisciplinary optimization, multilevel optimization, nonlinear programming, problem integration, system synthesis

  6. Computational Approaches to Simulation and Optimization of Global Aircraft Trajectories

    NASA Technical Reports Server (NTRS)

    Ng, Hok Kwan; Sridhar, Banavar

    2016-01-01

    This study examines three possible approaches to improving the speed in generating wind-optimal routes for air traffic at the national or global level. They are: (a) using the resources of a supercomputer, (b) running the computations on multiple commercially available computers and (c) implementing those same algorithms into NASAs Future ATM Concepts Evaluation Tool (FACET) and compares those to a standard implementation run on a single CPU. Wind-optimal aircraft trajectories are computed using global air traffic schedules. The run time and wait time on the supercomputer for trajectory optimization using various numbers of CPUs ranging from 80 to 10,240 units are compared with the total computational time for running the same computation on a single desktop computer and on multiple commercially available computers for potential computational enhancement through parallel processing on the computer clusters. This study also re-implements the trajectory optimization algorithm for further reduction of computational time through algorithm modifications and integrates that with FACET to facilitate the use of the new features which calculate time-optimal routes between worldwide airport pairs in a wind field for use with existing FACET applications. The implementations of trajectory optimization algorithms use MATLAB, Python, and Java programming languages. The performance evaluations are done by comparing their computational efficiencies and based on the potential application of optimized trajectories. The paper shows that in the absence of special privileges on a supercomputer, a cluster of commercially available computers provides a feasible approach for national and global air traffic system studies.

  7. Mapping Agricultural Fields in Sub-Saharan Africa with a Computer Vision Approach

    NASA Astrophysics Data System (ADS)

    Debats, S. R.; Luo, D.; Estes, L. D.; Fuchs, T.; Caylor, K. K.

    2014-12-01

    Sub-Saharan Africa is an important focus for food security research, because it is experiencing unprecedented population growth, agricultural activities are largely dominated by smallholder production, and the region is already home to 25% of the world's undernourished. One of the greatest challenges to monitoring and improving food security in this region is obtaining an accurate accounting of the spatial distribution of agriculture. Households are the primary units of agricultural production in smallholder communities and typically rely on small fields of less than 2 hectares. Field sizes are directly related to household crop productivity, management choices, and adoption of new technologies. As population and agriculture expand, it becomes increasingly important to understand both the distribution of field sizes as well as how agricultural communities are spatially embedded in the landscape. In addition, household surveys, a common tool for tracking agricultural productivity in Sub-Saharan Africa, would greatly benefit from spatially explicit accounting of fields. Current gridded land cover data sets do not provide information on individual agricultural fields or the distribution of field sizes. Therefore, we employ cutting edge approaches from the field of computer vision to map fields across Sub-Saharan Africa, including semantic segmentation, discriminative classifiers, and automatic feature selection. Our approach aims to not only improve the binary classification accuracy of cropland, but also to isolate distinct fields, thereby capturing crucial information on size and geometry. Our research focuses on the development of descriptive features across scales to increase the accuracy and geographic range of our computer vision algorithm. Relevant data sets include high-resolution remote sensing imagery and Landsat (30-m) multi-spectral imagery. Training data for field boundaries is derived from hand-digitized data sets as well as crowdsourcing.

  8. An approach to computing direction relations between separated object groups

    NASA Astrophysics Data System (ADS)

    Yan, H.; Wang, Z.; Li, J.

    2013-06-01

    Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on Gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups; and then it constructs the Voronoi Diagram between the two groups using the triangular network; after this, the normal of each Vornoi edge is calculated, and the quantitative expression of the direction relations is constructed; finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.

  9. An approach to computing direction relations between separated object groups

    NASA Astrophysics Data System (ADS)

    Yan, H.; Wang, Z.; Li, J.

    2013-09-01

    Direction relations between object groups play an important role in qualitative spatial reasoning, spatial computation and spatial recognition. However, none of existing models can be used to compute direction relations between object groups. To fill this gap, an approach to computing direction relations between separated object groups is proposed in this paper, which is theoretically based on gestalt principles and the idea of multi-directions. The approach firstly triangulates the two object groups, and then it constructs the Voronoi diagram between the two groups using the triangular network. After this, the normal of each Voronoi edge is calculated, and the quantitative expression of the direction relations is constructed. Finally, the quantitative direction relations are transformed into qualitative ones. The psychological experiments show that the proposed approach can obtain direction relations both between two single objects and between two object groups, and the results are correct from the point of view of spatial cognition.

  10. Accurate spectroscopic characterization of oxirane: A valuable route to its identification in Titan's atmosphere and the assignment of unidentified infrared bands

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Puzzarini, Cristina; Biczysko, Malgorzata; Bloino, Julien

    2014-04-20

    In an effort to provide an accurate spectroscopic characterization of oxirane, state-of-the-art computational methods and approaches have been employed to determine highly accurate fundamental vibrational frequencies and rotational parameters. Available experimental data were used to assess the reliability of our computations, and an accuracy on average of 10 cm{sup –1} for fundamental transitions as well as overtones and combination bands has been pointed out. Moving to rotational spectroscopy, relative discrepancies of 0.1%, 2%-3%, and 3%-4% were observed for rotational, quartic, and sextic centrifugal-distortion constants, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be usefulmore » for identification of oxirane in Titan's atmosphere and the assignment of unidentified infrared bands. Since oxirane was already observed in the interstellar medium and some astronomical objects are characterized by very high D/H ratios, we also considered the accurate determination of the spectroscopic parameters for the mono-deuterated species, oxirane-d1. For the latter, an empirical scaling procedure allowed us to improve our computed data and to provide predictions for rotational transitions with a relative accuracy of about 0.02% (i.e., an uncertainty of about 40 MHz for a transition lying at 200 GHz).« less

  11. The process group approach to reliable distributed computing

    NASA Technical Reports Server (NTRS)

    Birman, Kenneth P.

    1992-01-01

    The difficulty of developing reliable distribution software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems that are substantially easier to develop, exploit sophisticated forms of cooperative computation, and achieve high reliability. Six years of research on ISIS, describing the model, its implementation challenges, and the types of applications to which ISIS has been applied are reviewed.

  12. Digital test signal generation: An accurate SNR calibration approach for the DSN

    NASA Technical Reports Server (NTRS)

    Gutierrez-Luaces, Benito O.

    1993-01-01

    In support of the on-going automation of the Deep Space Network (DSN) a new method of generating analog test signals with accurate signal-to-noise ratio (SNR) is described. High accuracy is obtained by simultaneous generation of digital noise and signal spectra at the desired bandwidth (base-band or bandpass). The digital synthesis provides a test signal embedded in noise with the statistical properties of a stationary random process. Accuracy is dependent on test integration time and limited only by the system quantization noise (0.02 dB). The monitor and control as well as signal-processing programs reside in a personal computer (PC). Commands are transmitted to properly configure the specially designed high-speed digital hardware. The prototype can generate either two data channels modulated or not on a subcarrier, or one QPSK channel, or a residual carrier with one biphase data channel. The analog spectrum generated is on the DC to 10 MHz frequency range. These spectra may be up-converted to any desired frequency without loss on the characteristics of the SNR provided. Test results are presented.

  13. Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species.

    PubMed

    Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C

    2015-11-14

    In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations.

  14. A Hermite WENO reconstruction for fourth order temporal accurate schemes based on the GRP solver for hyperbolic conservation laws

    NASA Astrophysics Data System (ADS)

    Du, Zhifang; Li, Jiequan

    2018-02-01

    This paper develops a new fifth order accurate Hermite WENO (HWENO) reconstruction method for hyperbolic conservation schemes in the framework of the two-stage fourth order accurate temporal discretization in Li and Du (2016) [13]. Instead of computing the first moment of the solution additionally in the conventional HWENO or DG approach, we can directly take the interface values, which are already available in the numerical flux construction using the generalized Riemann problem (GRP) solver, to approximate the first moment. The resulting scheme is fourth order temporal accurate by only invoking the HWENO reconstruction twice so that it becomes more compact. Numerical experiments show that such compactness makes significant impact on the resolution of nonlinear waves.

  15. An accurate boundary element method for the exterior elastic scattering problem in two dimensions

    NASA Astrophysics Data System (ADS)

    Bao, Gang; Xu, Liwei; Yin, Tao

    2017-11-01

    This paper is concerned with a Galerkin boundary element method solving the two dimensional exterior elastic wave scattering problem. The original problem is first reduced to the so-called Burton-Miller [1] boundary integral formulation, and essential mathematical features of its variational form are discussed. In numerical implementations, a newly-derived and analytically accurate regularization formula [2] is employed for the numerical evaluation of hyper-singular boundary integral operator. A new computational approach is employed based on the series expansions of Hankel functions for the computation of weakly-singular boundary integral operators during the reduction of corresponding Galerkin equations into a discrete linear system. The effectiveness of proposed numerical methods is demonstrated using several numerical examples.

  16. Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach

    PubMed Central

    Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

    2015-01-01

    Abstract Objective Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Methods Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR–RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. Results PCR–RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR–RED. Conclusion NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR–RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic? Non-invasive prenatal diagnosis (NIPD) using PCR-based methods has been reported for the detection or exclusion of individual paternally inherited or de novo alleles in maternal plasma. What does this study add? NIPD using next generation sequencing provides an accurate, more sensitive approach which can be used to detect multiple mutations in a single assay and so is ideal when screening a gene with multiple potential pathogenic mutations. Next generation sequencing thus provides a flexible approach to non-invasive prenatal diagnosis ideal for use in a busy service laboratory. PMID:25728633

  17. Computational Approaches to Vestibular Research

    NASA Technical Reports Server (NTRS)

    Ross, Muriel D.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    The Biocomputation Center at NASA Ames Research Center is dedicated to a union between computational, experimental and theoretical approaches to the study of neuroscience and of life sciences in general. The current emphasis is on computer reconstruction and visualization of vestibular macular architecture in three-dimensions (3-D), and on mathematical modeling and computer simulation of neural activity in the functioning system. Our methods are being used to interpret the influence of spaceflight on mammalian vestibular maculas in a model system, that of the adult Sprague-Dawley rat. More than twenty 3-D reconstructions of type I and type II hair cells and their afferents have been completed by digitization of contours traced from serial sections photographed in a transmission electron microscope. This labor-intensive method has now been replace d by a semiautomated method developed in the Biocomputation Center in which conventional photography is eliminated. All viewing, storage and manipulation of original data is done using Silicon Graphics workstations. Recent improvements to the software include a new mesh generation method for connecting contours. This method will permit the investigator to describe any surface, regardless of complexity, including highly branched structures such as are routinely found in neurons. This same mesh can be used for 3-D, finite volume simulation of synapse activation and voltage spread on neuronal surfaces visualized via the reconstruction process. These simulations help the investigator interpret the relationship between neuroarchitecture and physiology, and are of assistance in determining which experiments will best test theoretical interpretations. Data are also used to develop abstract, 3-D models that dynamically display neuronal activity ongoing in the system. Finally, the same data can be used to visualize the neural tissue in a virtual environment. Our exhibit will depict capabilities of our computational approaches and

  18. Iterative feature refinement for accurate undersampled MR image reconstruction

    NASA Astrophysics Data System (ADS)

    Wang, Shanshan; Liu, Jianbo; Liu, Qiegen; Ying, Leslie; Liu, Xin; Zheng, Hairong; Liang, Dong

    2016-05-01

    Accelerating MR scan is of great significance for clinical, research and advanced applications, and one main effort to achieve this is the utilization of compressed sensing (CS) theory. Nevertheless, the existing CSMRI approaches still have limitations such as fine structure loss or high computational complexity. This paper proposes a novel iterative feature refinement (IFR) module for accurate MR image reconstruction from undersampled K-space data. Integrating IFR with CSMRI which is equipped with fixed transforms, we develop an IFR-CS method to restore meaningful structures and details that are originally discarded without introducing too much additional complexity. Specifically, the proposed IFR-CS is realized with three iterative steps, namely sparsity-promoting denoising, feature refinement and Tikhonov regularization. Experimental results on both simulated and in vivo MR datasets have shown that the proposed module has a strong capability to capture image details, and that IFR-CS is comparable and even superior to other state-of-the-art reconstruction approaches.

  19. Archiving Software Systems: Approaches to Preserve Computational Capabilities

    NASA Astrophysics Data System (ADS)

    King, T. A.

    2014-12-01

    A great deal of effort is made to preserve scientific data. Not only because data is knowledge, but it is often costly to acquire and is sometimes collected under unique circumstances. Another part of the science enterprise is the development of software to process and analyze the data. Developed software is also a large investment and worthy of preservation. However, the long term preservation of software presents some challenges. Software often requires a specific technology stack to operate. This can include software, operating systems and hardware dependencies. One past approach to preserve computational capabilities is to maintain ancient hardware long past its typical viability. On an archive horizon of 100 years, this is not feasible. Another approach to preserve computational capabilities is to archive source code. While this can preserve details of the implementation and algorithms, it may not be possible to reproduce the technology stack needed to compile and run the resulting applications. This future forward dilemma has a solution. Technology used to create clouds and process big data can also be used to archive and preserve computational capabilities. We explore how basic hardware, virtual machines, containers and appropriate metadata can be used to preserve computational capabilities and to archive functional software systems. In conjunction with data archives, this provides scientist with both the data and capability to reproduce the processing and analysis used to generate past scientific results.

  20. Computer-aided design/computer-aided manufacturing skull base drill.

    PubMed

    Couldwell, William T; MacDonald, Joel D; Thomas, Charles L; Hansen, Bradley C; Lapalikar, Aniruddha; Thakkar, Bharat; Balaji, Alagar K

    2017-05-01

    The authors have developed a simple device for computer-aided design/computer-aided manufacturing (CAD-CAM) that uses an image-guided system to define a cutting tool path that is shared with a surgical machining system for drilling bone. Information from 2D images (obtained via CT and MRI) is transmitted to a processor that produces a 3D image. The processor generates code defining an optimized cutting tool path, which is sent to a surgical machining system that can drill the desired portion of bone. This tool has applications for bone removal in both cranial and spine neurosurgical approaches. Such applications have the potential to reduce surgical time and associated complications such as infection or blood loss. The device enables rapid removal of bone within 1 mm of vital structures. The validity of such a machining tool is exemplified in the rapid (< 3 minutes machining time) and accurate removal of bone for transtemporal (for example, translabyrinthine) approaches.

  1. Reflections on John Monaghan's "Computer Algebra, Instrumentation, and the Anthropological Approach"

    ERIC Educational Resources Information Center

    Blume, Glen

    2007-01-01

    Reactions to John Monaghan's "Computer Algebra, Instrumentation and the Anthropological Approach" focus on a variety of issues related to the ergonomic approach (instrumentation) and anthropological approach to mathematical activity and practice. These include uses of the term technique; several possibilities for integration of the two approaches;…

  2. An Approach for Dynamic Grids

    NASA Technical Reports Server (NTRS)

    Slater, John W.; Liou, Meng-Sing; Hindman, Richard G.

    1994-01-01

    An approach is presented for the generation of two-dimensional, structured, dynamic grids. The grid motion may be due to the motion of the boundaries of the computational domain or to the adaptation of the grid to the transient, physical solution. A time-dependent grid is computed through the time integration of the grid speeds which are computed from a system of grid speed equations. The grid speed equations are derived from the time-differentiation of the grid equations so as to ensure that the dynamic grid maintains the desired qualities of the static grid. The grid equations are the Euler-Lagrange equations derived from a variational statement for the grid. The dynamic grid method is demonstrated for a model problem involving boundary motion, an inviscid flow in a converging-diverging nozzle during startup, and a viscous flow over a flat plate with an impinging shock wave. It is shown that the approach is more accurate for transient flows than an approach in which the grid speeds are computed using a finite difference with respect to time of the grid. However, the approach requires significantly more computational effort.

  3. A new computer approach to mixed feature classification for forestry application

    NASA Technical Reports Server (NTRS)

    Kan, E. P.

    1976-01-01

    A computer approach for mapping mixed forest features (i.e., types, classes) from computer classification maps is discussed. Mixed features such as mixed softwood/hardwood stands are treated as admixtures of softwood and hardwood areas. Large-area mixed features are identified and small-area features neglected when the nominal size of a mixed feature can be specified. The computer program merges small isolated areas into surrounding areas by the iterative manipulation of the postprocessing algorithm that eliminates small connected sets. For a forestry application, computer-classified LANDSAT multispectral scanner data of the Sam Houston National Forest were used to demonstrate the proposed approach. The technique was successful in cleaning the salt-and-pepper appearance of multiclass classification maps and in mapping admixtures of softwood areas and hardwood areas. However, the computer-mapped mixed areas matched very poorly with the ground truth because of inadequate resolution and inappropriate definition of mixed features.

  4. Computational methods for reactive transport modeling: A Gibbs energy minimization approach for multiphase equilibrium calculations

    NASA Astrophysics Data System (ADS)

    Leal, Allan M. M.; Kulik, Dmitrii A.; Kosakowski, Georg

    2016-02-01

    We present a numerical method for multiphase chemical equilibrium calculations based on a Gibbs energy minimization approach. The method can accurately and efficiently determine the stable phase assemblage at equilibrium independently of the type of phases and species that constitute the chemical system. We have successfully applied our chemical equilibrium algorithm in reactive transport simulations to demonstrate its effective use in computationally intensive applications. We used FEniCS to solve the governing partial differential equations of mass transport in porous media using finite element methods in unstructured meshes. Our equilibrium calculations were benchmarked with GEMS3K, the numerical kernel of the geochemical package GEMS. This allowed us to compare our results with a well-established Gibbs energy minimization algorithm, as well as their performance on every mesh node, at every time step of the transport simulation. The benchmark shows that our novel chemical equilibrium algorithm is accurate, robust, and efficient for reactive transport applications, and it is an improvement over the Gibbs energy minimization algorithm used in GEMS3K. The proposed chemical equilibrium method has been implemented in Reaktoro, a unified framework for modeling chemically reactive systems, which is now used as an alternative numerical kernel of GEMS.

  5. Accurate Valence Ionization Energies from Kohn-Sham Eigenvalues with the Help of Potential Adjustors.

    PubMed

    Thierbach, Adrian; Neiss, Christian; Gallandi, Lukas; Marom, Noa; Körzdörfer, Thomas; Görling, Andreas

    2017-10-10

    An accurate yet computationally very efficient and formally well justified approach to calculate molecular ionization potentials is presented and tested. The first as well as higher ionization potentials are obtained as the negatives of the Kohn-Sham eigenvalues of the neutral molecule after adjusting the eigenvalues by a recently [ Görling Phys. Rev. B 2015 , 91 , 245120 ] introduced potential adjustor for exchange-correlation potentials. Technically the method is very simple. Besides a Kohn-Sham calculation of the neutral molecule, only a second Kohn-Sham calculation of the cation is required. The eigenvalue spectrum of the neutral molecule is shifted such that the negative of the eigenvalue of the highest occupied molecular orbital equals the energy difference of the total electronic energies of the cation minus the neutral molecule. For the first ionization potential this simply amounts to a ΔSCF calculation. Then, the higher ionization potentials are obtained as the negatives of the correspondingly shifted Kohn-Sham eigenvalues. Importantly, this shift of the Kohn-Sham eigenvalue spectrum is not just ad hoc. In fact, it is formally necessary for the physically correct energetic adjustment of the eigenvalue spectrum as it results from ensemble density-functional theory. An analogous approach for electron affinities is equally well obtained and justified. To illustrate the practical benefits of the approach, we calculate the valence ionization energies of test sets of small- and medium-sized molecules and photoelectron spectra of medium-sized electron acceptor molecules using a typical semilocal (PBE) and two typical global hybrid functionals (B3LYP and PBE0). The potential adjusted B3LYP and PBE0 eigenvalues yield valence ionization potentials that are in very good agreement with experimental values, reaching an accuracy that is as good as the best G 0 W 0 methods, however, at much lower computational costs. The potential adjusted PBE eigenvalues result in

  6. A More Accurate and Efficient Technique Developed for Using Computational Methods to Obtain Helical Traveling-Wave Tube Interaction Impedance

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.

    1999-01-01

    The phenomenal growth of commercial communications has created a great demand for traveling-wave tube (TWT) amplifiers. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. For the first time, an accurate three-dimensional helical model was developed that allows accurate prediction of TWT cold-test characteristics including operating frequency, interaction impedance, and attenuation. This computational model, which was developed at the NASA Lewis Research Center, allows TWT designers to obtain a more accurate value of interaction impedance than is possible using experimental methods. Obtaining helical slow-wave circuit interaction impedance is an important part of the design process for a TWT because it is related to the gain and efficiency of the tube. This impedance cannot be measured directly; thus, conventional methods involve perturbing a helical circuit with a cylindrical dielectric rod placed on the central axis of the circuit and obtaining the difference in resonant frequency between the perturbed and unperturbed circuits. A mathematical relationship has been derived between this frequency difference and the interaction impedance (ref. 1). However, because of the complex configuration of the helical circuit, deriving this relationship involves several approximations. In addition, this experimental procedure is time-consuming and expensive, but until recently it was widely accepted as the most accurate means of determining interaction impedance. The advent of an accurate three-dimensional helical circuit model (ref. 2) made it possible for Lewis researchers to fully investigate standard approximations made in deriving the relationship between measured perturbation data and interaction impedance. The most prominent approximations made

  7. On numerically accurate finite element

    NASA Technical Reports Server (NTRS)

    Nagtegaal, J. C.; Parks, D. M.; Rice, J. R.

    1974-01-01

    A general criterion for testing a mesh with topologically similar repeat units is given, and the analysis shows that only a few conventional element types and arrangements are, or can be made suitable for computations in the fully plastic range. Further, a new variational principle, which can easily and simply be incorporated into an existing finite element program, is presented. This allows accurate computations to be made even for element designs that would not normally be suitable. Numerical results are given for three plane strain problems, namely pure bending of a beam, a thick-walled tube under pressure, and a deep double edge cracked tensile specimen. The effects of various element designs and of the new variational procedure are illustrated. Elastic-plastic computation at finite strain are discussed.

  8. Accurate ω-ψ Spectral Solution of the Singular Driven Cavity Problem

    NASA Astrophysics Data System (ADS)

    Auteri, F.; Quartapelle, L.; Vigevano, L.

    2002-08-01

    This article provides accurate spectral solutions of the driven cavity problem, calculated in the vorticity-stream function representation without smoothing the corner singularities—a prima facie impossible task. As in a recent benchmark spectral calculation by primitive variables of Botella and Peyret, closed-form contributions of the singular solution for both zero and finite Reynolds numbers are subtracted from the unknown of the problem tackled here numerically in biharmonic form. The method employed is based on a split approach to the vorticity and stream function equations, a Galerkin-Legendre approximation of the problem for the perturbation, and an evaluation of the nonlinear terms by Gauss-Legendre numerical integration. Results computed for Re=0, 100, and 1000 compare well with the benchmark steady solutions provided by the aforementioned collocation-Chebyshev projection method. The validity of the proposed singularity subtraction scheme for computing time-dependent solutions is also established.

  9. Computation of records of streamflow at control structures

    USGS Publications Warehouse

    Collins, Dannie L.

    1977-01-01

    Traditional methods of computing streamflow records on large, low-gradient streams require a continuous record of water-surface slope over a natural channel reach. This slope must be of sufficient magnitude to be accuratly measured with available stage measuring devices. On highly regulated streams, this slope approaches zero during periods of low flow and accurate measurement is difficult. Methods are described to calibrate multipurpose regulating control structures to more accurately compute streamflow records on highly-regulated streams. Hydraulic theory, assuming steady, uniform flow during a computational interval, is described for five different types of flow control. The controls are: Tainter gates, hydraulic turbines, fixed spillways, navigation locks, and crest gates. Detailed calibration procedures are described for the five different controls as well as for several flow regimes for some of the controls. The instrumentation package and computer programs necessary to collect and process the field data are discussed. Two typical calibration procedures and measurement data are presented to illustrate the accuracy of the methods. (Woodard-USGS)

  10. An accurate and efficient reliability-based design optimization using the second order reliability method and improved stability transformation method

    NASA Astrophysics Data System (ADS)

    Meng, Zeng; Yang, Dixiong; Zhou, Huanlin; Yu, Bo

    2018-05-01

    The first order reliability method has been extensively adopted for reliability-based design optimization (RBDO), but it shows inaccuracy in calculating the failure probability with highly nonlinear performance functions. Thus, the second order reliability method is required to evaluate the reliability accurately. However, its application for RBDO is quite challenge owing to the expensive computational cost incurred by the repeated reliability evaluation and Hessian calculation of probabilistic constraints. In this article, a new improved stability transformation method is proposed to search the most probable point efficiently, and the Hessian matrix is calculated by the symmetric rank-one update. The computational capability of the proposed method is illustrated and compared to the existing RBDO approaches through three mathematical and two engineering examples. The comparison results indicate that the proposed method is very efficient and accurate, providing an alternative tool for RBDO of engineering structures.

  11. Accurate atomistic potentials and training sets for boron-nitride nanostructures

    NASA Astrophysics Data System (ADS)

    Tamblyn, Isaac

    Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

  12. A comparison of basic deinterlacing approaches for a computer assisted diagnosis approach of videoscope images

    NASA Astrophysics Data System (ADS)

    Kage, Andreas; Canto, Marcia; Gorospe, Emmanuel; Almario, Antonio; Münzenmayer, Christian

    2010-03-01

    In the near future, Computer Assisted Diagnosis (CAD) which is well known in the area of mammography might be used to support clinical experts in the diagnosis of images derived from imaging modalities such as endoscopy. In the recent past, a few first approaches for computer assisted endoscopy have been presented already. These systems use a video signal as an input that is provided by the endoscopes video processor. Despite the advent of high-definition systems most standard endoscopy systems today still provide only analog video signals. These signals consist of interlaced images that can not be used in a CAD approach without deinterlacing. Of course, there are many different deinterlacing approaches known today. But most of them are specializations of some basic approaches. In this paper we present four basic deinterlacing approaches. We have used a database of non-interlaced images which have been degraded by artificial interlacing and afterwards processed by these approaches. The database contains regions of interest (ROI) of clinical relevance for the diagnosis of abnormalities in the esophagus. We compared the classification rates on these ROIs on the original images and after the deinterlacing. The results show that the deinterlacing has an impact on the classification rates. The Bobbing approach and the Motion Compensation approach achieved the best classification results in most cases.

  13. Fast and accurate mock catalogue generation for low-mass galaxies

    NASA Astrophysics Data System (ADS)

    Koda, Jun; Blake, Chris; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2016-06-01

    We present an accurate and fast framework for generating mock catalogues including low-mass haloes, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realizations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate-mass galaxies in 1012 M⊙ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k ≤ 0.15 h Mpc-1, and with only 3-per cent error for k ≤ 0.2 h Mpc-1. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at github.com/junkoda/cola_halo.

  14. Computational approaches to schizophrenia: A perspective on negative symptoms.

    PubMed

    Deserno, Lorenz; Heinz, Andreas; Schlagenhauf, Florian

    2017-08-01

    Schizophrenia is a heterogeneous spectrum disorder often associated with detrimental negative symptoms. In recent years, computational approaches to psychiatry have attracted growing attention. Negative symptoms have shown some overlap with general cognitive impairments and were also linked to impaired motivational processing in brain circuits implementing reward prediction. In this review, we outline how computational approaches may help to provide a better understanding of negative symptoms in terms of the potentially underlying behavioural and biological mechanisms. First, we describe the idea that negative symptoms could arise from a failure to represent reward expectations to enable flexible behavioural adaptation. It has been proposed that these impairments arise from a failure to use prediction errors to update expectations. Important previous studies focused on processing of so-called model-free prediction errors where learning is determined by past rewards only. However, learning and decision-making arise from multiple cognitive mechanisms functioning simultaneously, and dissecting them via well-designed tasks in conjunction with computational modelling is a promising avenue. Second, we move on to a proof-of-concept example on how generative models of functional imaging data from a cognitive task enable the identification of subgroups of patients mapping on different levels of negative symptoms. Combining the latter approach with behavioural studies regarding learning and decision-making may allow the identification of key behavioural and biological parameters distinctive for different dimensions of negative symptoms versus a general cognitive impairment. We conclude with an outlook on how this computational framework could, at some point, enrich future clinical studies. Copyright © 2016. Published by Elsevier B.V.

  15. Perturbation approach for nuclear magnetic resonance solid-state quantum computation

    DOE PAGES

    Berman, G. P.; Kamenev, D. I.; Tsifrinovich, V. I.

    2003-01-01

    A dynmore » amics of a nuclear-spin quantum computer with a large number ( L = 1000 ) of qubits is considered using a perturbation approach. Small parameters are introduced and used to compute the error in an implementation of an entanglement between remote qubits, using a sequence of radio-frequency pulses. The error is computed up to the different orders of the perturbation theory and tested using exact numerical solution.« less

  16. ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS

    PubMed Central

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-01-01

    The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multi-finite buffers for reducing the state space by O(n!), exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes, and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be pre-computed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multi-scale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks. PMID:27761104

  17. Hybrid computational and experimental approach for the study and optimization of mechanical components

    NASA Astrophysics Data System (ADS)

    Furlong, Cosme; Pryputniewicz, Ryszard J.

    1998-05-01

    Increased demands on the performance and efficiency of mechanical components impose challenges on their engineering design and optimization, especially when new and more demanding applications must be developed in relatively short periods of time while satisfying design objectives, as well as cost and manufacturability. In addition, reliability and durability must be taken into consideration. As a consequence, effective quantitative methodologies, computational and experimental, should be applied in the study and optimization of mechanical components. Computational investigations enable parametric studies and the determination of critical engineering design conditions, while experimental investigations, especially those using optical techniques, provide qualitative and quantitative information on the actual response of the structure of interest to the applied load and boundary conditions. We discuss a hybrid experimental and computational approach for investigation and optimization of mechanical components. The approach is based on analytical, computational, and experimental resolutions methodologies in the form of computational, noninvasive optical techniques, and fringe prediction analysis tools. Practical application of the hybrid approach is illustrated with representative examples that demonstrate the viability of the approach as an effective engineering tool for analysis and optimization.

  18. Computing Interactions Of Free-Space Radiation With Matter

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Cucinotta, F. A.; Shinn, J. L.; Townsend, L. W.; Badavi, F. F.; Tripathi, R. K.; Silberberg, R.; Tsao, C. H.; Badwar, G. D.

    1995-01-01

    High Charge and Energy Transport (HZETRN) computer program computationally efficient, user-friendly package of software adressing problem of transport of, and shielding against, radiation in free space. Designed as "black box" for design engineers not concerned with physics of underlying atomic and nuclear radiation processes in free-space environment, but rather primarily interested in obtaining fast and accurate dosimetric information for design and construction of modules and devices for use in free space. Computational efficiency achieved by unique algorithm based on deterministic approach to solution of Boltzmann equation rather than computationally intensive statistical Monte Carlo method. Written in FORTRAN.

  19. Computational Design of DNA-Binding Proteins.

    PubMed

    Thyme, Summer; Song, Yifan

    2016-01-01

    Predicting the outcome of engineered and naturally occurring sequence perturbations to protein-DNA interfaces requires accurate computational modeling technologies. It has been well established that computational design to accommodate small numbers of DNA target site substitutions is possible. This chapter details the basic method of design used in the Rosetta macromolecular modeling program that has been successfully used to modulate the specificity of DNA-binding proteins. More recently, combining computational design and directed evolution has become a common approach for increasing the success rate of protein engineering projects. The power of such high-throughput screening depends on computational methods producing multiple potential solutions. Therefore, this chapter describes several protocols for increasing the diversity of designed output. Lastly, we describe an approach for building comparative models of protein-DNA complexes in order to utilize information from homologous sequences. These models can be used to explore how nature modulates specificity of protein-DNA interfaces and potentially can even be used as starting templates for further engineering.

  20. Cloud Computing - A Unified Approach for Surveillance Issues

    NASA Astrophysics Data System (ADS)

    Rachana, C. R.; Banu, Reshma, Dr.; Ahammed, G. F. Ali, Dr.; Parameshachari, B. D., Dr.

    2017-08-01

    Cloud computing describes highly scalable resources provided as an external service via the Internet on a basis of pay-per-use. From the economic point of view, the main attractiveness of cloud computing is that users only use what they need, and only pay for what they actually use. Resources are available for access from the cloud at any time, and from any location through networks. Cloud computing is gradually replacing the traditional Information Technology Infrastructure. Securing data is one of the leading concerns and biggest issue for cloud computing. Privacy of information is always a crucial pointespecially when an individual’s personalinformation or sensitive information is beingstored in the organization. It is indeed true that today; cloud authorization systems are notrobust enough. This paper presents a unified approach for analyzing the various security issues and techniques to overcome the challenges in the cloud environment.

  1. Memory conformity affects inaccurate memories more than accurate memories.

    PubMed

    Wright, Daniel B; Villalba, Daniella K

    2012-01-01

    After controlling for initial confidence, inaccurate memories were shown to be more easily distorted than accurate memories. In two experiments groups of participants viewed 50 stimuli and were then presented with these stimuli plus 50 fillers. During this test phase participants reported their confidence that each stimulus was originally shown. This was followed by computer-generated responses from a bogus participant. After being exposed to this response participants again rated the confidence of their memory. The computer-generated responses systematically distorted participants' responses. Memory distortion depended on initial memory confidence, with uncertain memories being more malleable than confident memories. This effect was moderated by whether the participant's memory was initially accurate or inaccurate. Inaccurate memories were more malleable than accurate memories. The data were consistent with a model describing two types of memory (i.e., recollective and non-recollective memories), which differ in how susceptible these memories are to memory distortion.

  2. The preliminary exploration of 64-slice volume computed tomography in the accurate measurement of pleural effusion.

    PubMed

    Guo, Zhi-Jun; Lin, Qiang; Liu, Hai-Tao; Lu, Jun-Ying; Zeng, Yan-Hong; Meng, Fan-Jie; Cao, Bin; Zi, Xue-Rong; Han, Shu-Ming; Zhang, Yu-Huan

    2013-09-01

    Using computed tomography (CT) to rapidly and accurately quantify pleural effusion volume benefits medical and scientific research. However, the precise volume of pleural effusions still involves many challenges and currently does not have a recognized accurate measuring. To explore the feasibility of using 64-slice CT volume-rendering technology to accurately measure pleural fluid volume and to then analyze the correlation between the volume of the free pleural effusion and the different diameters of the pleural effusion. The 64-slice CT volume-rendering technique was used to measure and analyze three parts. First, the fluid volume of a self-made thoracic model was measured and compared with the actual injected volume. Second, the pleural effusion volume was measured before and after pleural fluid drainage in 25 patients, and the volume reduction was compared with the actual volume of the liquid extract. Finally, the free pleural effusion volume was measured in 26 patients to analyze the correlation between it and the diameter of the effusion, which was then used to calculate the regression equation. After using the 64-slice CT volume-rendering technique to measure the fluid volume of the self-made thoracic model, the results were compared with the actual injection volume. No significant differences were found, P = 0.836. For the 25 patients with drained pleural effusions, the comparison of the reduction volume with the actual volume of the liquid extract revealed no significant differences, P = 0.989. The following linear regression equation was used to compare the pleural effusion volume (V) (measured by the CT volume-rendering technique) with the pleural effusion greatest depth (d): V = 158.16 × d - 116.01 (r = 0.91, P = 0.000). The following linear regression was used to compare the volume with the product of the pleural effusion diameters (l × h × d): V = 0.56 × (l × h × d) + 39.44 (r = 0.92, P = 0.000). The 64-slice CT volume-rendering technique can

  3. An efficient and accurate 3D displacements tracking strategy for digital volume correlation

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo; Wu, Dafang; Lubineau, Gilles

    2014-07-01

    Owing to its inherent computational complexity, practical implementation of digital volume correlation (DVC) for internal displacement and strain mapping faces important challenges in improving its computational efficiency. In this work, an efficient and accurate 3D displacement tracking strategy is proposed for fast DVC calculation. The efficiency advantage is achieved by using three improvements. First, to eliminate the need of updating Hessian matrix in each iteration, an efficient 3D inverse compositional Gauss-Newton (3D IC-GN) algorithm is introduced to replace existing forward additive algorithms for accurate sub-voxel displacement registration. Second, to ensure the 3D IC-GN algorithm that converges accurately and rapidly and avoid time-consuming integer-voxel displacement searching, a generalized reliability-guided displacement tracking strategy is designed to transfer accurate and complete initial guess of deformation for each calculation point from its computed neighbors. Third, to avoid the repeated computation of sub-voxel intensity interpolation coefficients, an interpolation coefficient lookup table is established for tricubic interpolation. The computational complexity of the proposed fast DVC and the existing typical DVC algorithms are first analyzed quantitatively according to necessary arithmetic operations. Then, numerical tests are performed to verify the performance of the fast DVC algorithm in terms of measurement accuracy and computational efficiency. The experimental results indicate that, compared with the existing DVC algorithm, the presented fast DVC algorithm produces similar precision and slightly higher accuracy at a substantially reduced computational cost.

  4. Computer-aided diagnostic approach of dermoscopy images acquiring relevant features

    NASA Astrophysics Data System (ADS)

    Castillejos-Fernández, H.; Franco-Arcega, A.; López-Ortega, O.

    2016-09-01

    In skin cancer detection, automated analysis of borders, colors, and structures of a lesion relies upon an accurate segmentation process and it is an important first step in any Computer-Aided Diagnosis (CAD) system. However, irregular and disperse lesion borders, low contrast, artifacts in images and variety of colors within the interest region make the problem difficult. In this paper, we propose an efficient approach of automatic classification which considers specific lesion features. First, for the selection of lesion skin we employ the segmentation algorithm W-FCM.1 Then, in the feature extraction stage we consider several aspects: the area of the lesion, which is calculated by correlating axes and we calculate the specific the value of asymmetry in both axes. For color analysis we employ an ensemble of clusterers including K-Means, Fuzzy K-Means and Kohonep maps, all of which estimate the presence of one or more colors defined in ABCD rule and the values for each of the segmented colors. Another aspect to consider is the type of structures that appear in the lesion Those are defined by using the ell-known GLCM method. During the classification stage we compare several methods in order to define if the lesion is benign or malignant. An important contribution of the current approach in segmentation-classification problem resides in the use of information from all color channels together, as well as the measure of each color in the lesion and the axes correlation. The segmentation and classification measures have been performed using sensibility, specificity, accuracy and AUC metric over a set of dermoscopy images from ISDIS data set

  5. Accurate Simulation of Parametrically Excited Micromirrors via Direct Computation of the Electrostatic Stiffness

    PubMed Central

    Frangi, Attilio; Guerrieri, Andrea; Boni, Nicoló

    2017-01-01

    Electrostatically actuated torsional micromirrors are key elements in Micro-Opto-Electro- Mechanical-Systems. When forced by means of in-plane comb-fingers, the dynamics of the main torsional response is known to be strongly non-linear and governed by parametric resonance. Here, in order to also trace unstable branches of the mirror response, we implement a simplified continuation method with arc-length control and propose an innovative technique based on Finite Elements and the concepts of material derivative in order to compute the electrostatic stiffness; i.e., the derivative of the torque with respect to the torsional angle, as required by the continuation approach. PMID:28383483

  6. Accurate Simulation of Parametrically Excited Micromirrors via Direct Computation of the Electrostatic Stiffness.

    PubMed

    Frangi, Attilio; Guerrieri, Andrea; Boni, Nicoló

    2017-04-06

    Electrostatically actuated torsional micromirrors are key elements in Micro-Opto-Electro- Mechanical-Systems. When forced by means of in-plane comb-fingers, the dynamics of the main torsional response is known to be strongly non-linear and governed by parametric resonance. Here, in order to also trace unstable branches of the mirror response, we implement a simplified continuation method with arc-length control and propose an innovative technique based on Finite Elements and the concepts of material derivative in order to compute the electrostatic stiffness; i.e., the derivative of the torque with respect to the torsional angle, as required by the continuation approach.

  7. Efficient and accurate approach to modeling the microstructure and defect properties of LaCoO3

    NASA Astrophysics Data System (ADS)

    Buckeridge, J.; Taylor, F. H.; Catlow, C. R. A.

    2016-04-01

    Complex perovskite oxides are promising materials for cathode layers in solid oxide fuel cells. Such materials have intricate electronic, magnetic, and crystalline structures that prove challenging to model accurately. We analyze a wide range of standard density functional theory approaches to modeling a highly promising system, the perovskite LaCoO3, focusing on optimizing the Hubbard U parameter to treat the self-interaction of the B-site cation's d states, in order to determine the most appropriate method to study defect formation and the effect of spin on local structure. By calculating structural and electronic properties for different magnetic states we determine that U =4 eV for Co in LaCoO3 agrees best with available experiments. We demonstrate that the generalized gradient approximation (PBEsol +U ) is most appropriate for studying structure versus spin state, while the local density approximation (LDA +U ) is most appropriate for determining accurate energetics for defect properties.

  8. Digging deeper on "deep" learning: A computational ecology approach.

    PubMed

    Buscema, Massimo; Sacco, Pier Luigi

    2017-01-01

    We propose an alternative approach to "deep" learning that is based on computational ecologies of structurally diverse artificial neural networks, and on dynamic associative memory responses to stimuli. Rather than focusing on massive computation of many different examples of a single situation, we opt for model-based learning and adaptive flexibility. Cross-fertilization of learning processes across multiple domains is the fundamental feature of human intelligence that must inform "new" artificial intelligence.

  9. Understanding Plant Nitrogen Metabolism through Metabolomics and Computational Approaches

    PubMed Central

    Beatty, Perrin H.; Klein, Matthias S.; Fischer, Jeffrey J.; Lewis, Ian A.; Muench, Douglas G.; Good, Allen G.

    2016-01-01

    A comprehensive understanding of plant metabolism could provide a direct mechanism for improving nitrogen use efficiency (NUE) in crops. One of the major barriers to achieving this outcome is our poor understanding of the complex metabolic networks, physiological factors, and signaling mechanisms that affect NUE in agricultural settings. However, an exciting collection of computational and experimental approaches has begun to elucidate whole-plant nitrogen usage and provides an avenue for connecting nitrogen-related phenotypes to genes. Herein, we describe how metabolomics, computational models of metabolism, and flux balance analysis have been harnessed to advance our understanding of plant nitrogen metabolism. We introduce a model describing the complex flow of nitrogen through crops in a real-world agricultural setting and describe how experimental metabolomics data, such as isotope labeling rates and analyses of nutrient uptake, can be used to refine these models. In summary, the metabolomics/computational approach offers an exciting mechanism for understanding NUE that may ultimately lead to more effective crop management and engineered plants with higher yields. PMID:27735856

  10. A computer vision-based approach for structural displacement measurement

    NASA Astrophysics Data System (ADS)

    Ji, Yunfeng

    2010-04-01

    Along with the incessant advancement in optics, electronics and computer technologies during the last three decades, commercial digital video cameras have experienced a remarkable evolution, and can now be employed to measure complex motions of objects with sufficient accuracy, which render great assistance to structural displacement measurement in civil engineering. This paper proposes a computer vision-based approach for dynamic measurement of structures. One digital camera is used to capture image sequences of planar targets mounted on vibrating structures. The mathematical relationship between image plane and real space is established based on computer vision theory. Then, the structural dynamic displacement at the target locations can be quantified using point reconstruction rules. Compared with other tradition displacement measurement methods using sensors, such as accelerometers, linear-variable-differential-transducers (LVDTs) and global position system (GPS), the proposed approach gives the main advantages of great flexibility, a non-contact working mode and ease of increasing measurement points. To validate, four tests of sinusoidal motion of a point, free vibration of a cantilever beam, wind tunnel test of a cross-section bridge model, and field test of bridge displacement measurement, are performed. Results show that the proposed approach can attain excellent accuracy compared with the analytical ones or the measurements using conventional transducers, and proves to deliver an innovative and low cost solution to structural displacement measurement.

  11. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  12. Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks.

    PubMed

    He, Jieyue; Li, Chaojun; Ye, Baoliu; Zhong, Wei

    2012-06-25

    Most computational algorithms mainly focus on detecting highly connected subgraphs in PPI networks as protein complexes but ignore their inherent organization. Furthermore, many of these algorithms are computationally expensive. However, recent analysis indicates that experimentally detected protein complexes generally contain Core/attachment structures. In this paper, a Greedy Search Method based on Core-Attachment structure (GSM-CA) is proposed. The GSM-CA method detects densely connected regions in large protein-protein interaction networks based on the edge weight and two criteria for determining core nodes and attachment nodes. The GSM-CA method improves the prediction accuracy compared to other similar module detection approaches, however it is computationally expensive. Many module detection approaches are based on the traditional hierarchical methods, which is also computationally inefficient because the hierarchical tree structure produced by these approaches cannot provide adequate information to identify whether a network belongs to a module structure or not. In order to speed up the computational process, the Greedy Search Method based on Fast Clustering (GSM-FC) is proposed in this work. The edge weight based GSM-FC method uses a greedy procedure to traverse all edges just once to separate the network into the suitable set of modules. The proposed methods are applied to the protein interaction network of S. cerevisiae. Experimental results indicate that many significant functional modules are detected, most of which match the known complexes. Results also demonstrate that the GSM-FC algorithm is faster and more accurate as compared to other competing algorithms. Based on the new edge weight definition, the proposed algorithm takes advantages of the greedy search procedure to separate the network into the suitable set of modules. Experimental analysis shows that the identified modules are statistically significant. The algorithm can reduce the

  13. The accurate particle tracer code

    NASA Astrophysics Data System (ADS)

    Wang, Yulei; Liu, Jian; Qin, Hong; Yu, Zhi; Yao, Yicun

    2017-11-01

    The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runaway electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world's fastest computer, the Sunway TaihuLight supercomputer, by supporting master-slave architecture of Sunway many-core processors. Based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.

  14. The accurate particle tracer code

    DOE PAGES

    Wang, Yulei; Liu, Jian; Qin, Hong; ...

    2017-07-20

    The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runawaymore » electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world’s fastest computer, the Sunway TaihuLight supercomputer, by supporting master–slave architecture of Sunway many-core processors. Here, based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.« less

  15. The accurate particle tracer code

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Yulei; Liu, Jian; Qin, Hong

    The Accurate Particle Tracer (APT) code is designed for systematic large-scale applications of geometric algorithms for particle dynamical simulations. Based on a large variety of advanced geometric algorithms, APT possesses long-term numerical accuracy and stability, which are critical for solving multi-scale and nonlinear problems. To provide a flexible and convenient I/O interface, the libraries of Lua and Hdf5 are used. Following a three-step procedure, users can efficiently extend the libraries of electromagnetic configurations, external non-electromagnetic forces, particle pushers, and initialization approaches by use of the extendible module. APT has been used in simulations of key physical problems, such as runawaymore » electrons in tokamaks and energetic particles in Van Allen belt. As an important realization, the APT-SW version has been successfully distributed on the world’s fastest computer, the Sunway TaihuLight supercomputer, by supporting master–slave architecture of Sunway many-core processors. Here, based on large-scale simulations of a runaway beam under parameters of the ITER tokamak, it is revealed that the magnetic ripple field can disperse the pitch-angle distribution significantly and improve the confinement of energetic runaway beam on the same time.« less

  16. Accurate Solution of Multi-Region Continuum Biomolecule Electrostatic Problems Using the Linearized Poisson-Boltzmann Equation with Curved Boundary Elements

    PubMed Central

    Altman, Michael D.; Bardhan, Jaydeep P.; White, Jacob K.; Tidor, Bruce

    2009-01-01

    We present a boundary-element method (BEM) implementation for accurately solving problems in biomolecular electrostatics using the linearized Poisson–Boltzmann equation. Motivating this implementation is the desire to create a solver capable of precisely describing the geometries and topologies prevalent in continuum models of biological molecules. This implementation is enabled by the synthesis of four technologies developed or implemented specifically for this work. First, molecular and accessible surfaces used to describe dielectric and ion-exclusion boundaries were discretized with curved boundary elements that faithfully reproduce molecular geometries. Second, we avoided explicitly forming the dense BEM matrices and instead solved the linear systems with a preconditioned iterative method (GMRES), using a matrix compression algorithm (FFTSVD) to accelerate matrix-vector multiplication. Third, robust numerical integration methods were employed to accurately evaluate singular and near-singular integrals over the curved boundary elements. Finally, we present a general boundary-integral approach capable of modeling an arbitrary number of embedded homogeneous dielectric regions with differing dielectric constants, possible salt treatment, and point charges. A comparison of the presented BEM implementation and standard finite-difference techniques demonstrates that for certain classes of electrostatic calculations, such as determining absolute electrostatic solvation and rigid-binding free energies, the improved convergence properties of the BEM approach can have a significant impact on computed energetics. We also demonstrate that the improved accuracy offered by the curved-element BEM is important when more sophisticated techniques, such as non-rigid-binding models, are used to compute the relative electrostatic effects of molecular modifications. In addition, we show that electrostatic calculations requiring multiple solves using the same molecular geometry

  17. A new computational approach to simulate pattern formation in Paenibacillus dendritiformis bacterial colonies

    NASA Astrophysics Data System (ADS)

    Tucker, Laura Jane

    Under the harsh conditions of limited nutrient and hard growth surface, Paenibacillus dendritiformis in agar plates form two classes of patterns (morphotypes). The first class, called the dendritic morphotype, has radially directed branches. The second class, called the chiral morphotype, exhibits uniform handedness. The dendritic morphotype has been modeled successfully using a continuum model on a regular lattice; however, a suitable computational approach was not known to solve a continuum chiral model. This work details a new computational approach to solving the chiral continuum model of pattern formation in P. dendritiformis. The approach utilizes a random computational lattice and new methods for calculating certain derivative terms found in the model.

  18. Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach.

    PubMed

    Liu, Yang; Fan, Xiaoli; Jin, Yingdi; Hu, Xiangqian; Hu, Hao

    2013-09-10

    Accurate computation of the pKa value of a compound in solution is important but challenging. Here, a new mixing quantum mechanical/molecular mechanical (QM/MM) Hamiltonian method is developed to simulate the free-energy change associated with the protonation/deprotonation processes in solution. The mixing Hamiltonian method is designed for efficient quantum mechanical free-energy simulations by alchemically varying the nuclear potential, i.e., the nuclear charge of the transforming nucleus. In pKa calculation, the charge on the proton is varied in fraction between 0 and 1, corresponding to the fully deprotonated and protonated states, respectively. Inspired by the mixing potential QM/MM free energy simulation method developed previously [H. Hu and W. T. Yang, J. Chem. Phys. 2005, 123, 041102], this method succeeds many advantages of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theory and technique details of this method, along with the calculation results of the pKa of methanol and methanethiol molecules in aqueous solution, are reported. The results show satisfactory agreement with the experimental data.

  19. Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.

    PubMed

    Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

    2015-07-01

    Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR-RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. PCR-RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR-RED. NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR-RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 John Wiley & Sons, Ltd.

  20. In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.

    PubMed

    Gray, Alan; Harlen, Oliver G; Harris, Sarah A; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J; Pearson, Arwen R; Read, Daniel J; Richardson, Robin A

    2015-01-01

    Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.

  1. A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments.

    PubMed

    Heskes, Tom; Eisinga, Rob; Breitling, Rainer

    2014-11-21

    The rank product method is a powerful statistical technique for identifying differentially expressed molecules in replicated experiments. A critical issue in molecule selection is accurate calculation of the p-value of the rank product statistic to adequately address multiple testing. Both exact calculation and permutation and gamma approximations have been proposed to determine molecule-level significance. These current approaches have serious drawbacks as they are either computationally burdensome or provide inaccurate estimates in the tail of the p-value distribution. We derive strict lower and upper bounds to the exact p-value along with an accurate approximation that can be used to assess the significance of the rank product statistic in a computationally fast manner. The bounds and the proposed approximation are shown to provide far better accuracy over existing approximate methods in determining tail probabilities, with the slightly conservative upper bound protecting against false positives. We illustrate the proposed method in the context of a recently published analysis on transcriptomic profiling performed in blood. We provide a method to determine upper bounds and accurate approximate p-values of the rank product statistic. The proposed algorithm provides an order of magnitude increase in throughput as compared with current approaches and offers the opportunity to explore new application domains with even larger multiple testing issue. The R code is published in one of the Additional files and is available at http://www.ru.nl/publish/pages/726696/rankprodbounds.zip .

  2. Computation-aware algorithm selection approach for interlaced-to-progressive conversion

    NASA Astrophysics Data System (ADS)

    Park, Sang-Jun; Jeon, Gwanggil; Jeong, Jechang

    2010-05-01

    We discuss deinterlacing results in a computationally constrained and varied environment. The proposed computation-aware algorithm selection approach (CASA) for fast interlaced to progressive conversion algorithm consists of three methods: the line-averaging (LA) method for plain regions, the modified edge-based line-averaging (MELA) method for medium regions, and the proposed covariance-based adaptive deinterlacing (CAD) method for complex regions. The proposed CASA uses two criteria, mean-squared error (MSE) and CPU time, for assigning the method. We proposed a CAD method. The principle idea of CAD is based on the correspondence between the high and low-resolution covariances. We estimated the local covariance coefficients from an interlaced image using Wiener filtering theory and then used these optimal minimum MSE interpolation coefficients to obtain a deinterlaced image. The CAD method, though more robust than most known methods, was not found to be very fast compared to the others. To alleviate this issue, we proposed an adaptive selection approach using a fast deinterlacing algorithm rather than using only one CAD algorithm. The proposed hybrid approach of switching between the conventional schemes (LA and MELA) and our CAD was proposed to reduce the overall computational load. A reliable condition to be used for switching the schemes was presented after a wide set of initial training processes. The results of computer simulations showed that the proposed methods outperformed a number of methods presented in the literature.

  3. Conformational dynamics of proanthocyanidins: physical and computational approaches

    Treesearch

    Fred L. Tobiason; Richard W. Hemingway; T. Hatano

    1998-01-01

    The interaction of plant polyphenols with proteins accounts for a good part of their commercial (e.g., leather manufacture) and biological (e.g., antimicrobial activity) significance. The interplay between observations of physical data such as crystal structure, NMR analyses, and time-resolved fluorescence with results of computational chemistry approaches has been...

  4. Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

    PubMed

    Patel, Trushar R; Chojnowski, Grzegorz; Astha; Koul, Amit; McKenna, Sean A; Bujnicki, Janusz M

    2017-04-15

    The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  5. Accurate chemical master equation solution using multi-finite buffers

    DOE PAGES

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-06-29

    Here, the discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multiscale nature of many networks where reaction rates have a large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multifinite buffers for reducing the state spacemore » by $O(n!)$, exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be precomputed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multiscale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks.« less

  6. Accurate chemical master equation solution using multi-finite buffers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cao, Youfang; Terebus, Anna; Liang, Jie

    Here, the discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multiscale nature of many networks where reaction rates have a large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multifinite buffers for reducing the state spacemore » by $O(n!)$, exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be precomputed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multiscale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks.« less

  7. A spline-based approach for computing spatial impulse responses.

    PubMed

    Ellis, Michael A; Guenther, Drake; Walker, William F

    2007-05-01

    Computer simulations are an essential tool for the design of phased-array ultrasonic imaging systems. FIELD II, which determines the two-way temporal response of a transducer at a point in space, is the current de facto standard for ultrasound simulation tools. However, the need often arises to obtain two-way spatial responses at a single point in time, a set of dimensions for which FIELD II is not well optimized. This paper describes an analytical approach for computing the two-way, far-field, spatial impulse response from rectangular transducer elements under arbitrary excitation. The described approach determines the response as the sum of polynomial functions, making computational implementation quite straightforward. The proposed algorithm, named DELFI, was implemented as a C routine under Matlab and results were compared to those obtained under similar conditions from the well-established FIELD II program. Under the specific conditions tested here, the proposed algorithm was approximately 142 times faster than FIELD II for computing spatial sensitivity functions with similar amounts of error. For temporal sensitivity functions with similar amounts of error, the proposed algorithm was about 1.7 times slower than FIELD II using rectangular elements and 19.2 times faster than FIELD II using triangular elements. DELFI is shown to be an attractive complement to FIELD II, especially when spatial responses are needed at a specific point in time.

  8. Toward accurate tooth segmentation from computed tomography images using a hybrid level set model

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gan, Yangzhou; Zhao, Qunfei; Xia, Zeyang, E-mail: zy.xia@siat.ac.cn, E-mail: jing.xiong@siat.ac.cn

    Purpose: A three-dimensional (3D) model of the teeth provides important information for orthodontic diagnosis and treatment planning. Tooth segmentation is an essential step in generating the 3D digital model from computed tomography (CT) images. The aim of this study is to develop an accurate and efficient tooth segmentation method from CT images. Methods: The 3D dental CT volumetric images are segmented slice by slice in a two-dimensional (2D) transverse plane. The 2D segmentation is composed of a manual initialization step and an automatic slice by slice segmentation step. In the manual initialization step, the user manually picks a starting slicemore » and selects a seed point for each tooth in this slice. In the automatic slice segmentation step, a developed hybrid level set model is applied to segment tooth contours from each slice. Tooth contour propagation strategy is employed to initialize the level set function automatically. Cone beam CT (CBCT) images of two subjects were used to tune the parameters. Images of 16 additional subjects were used to validate the performance of the method. Volume overlap metrics and surface distance metrics were adopted to assess the segmentation accuracy quantitatively. The volume overlap metrics were volume difference (VD, mm{sup 3}) and Dice similarity coefficient (DSC, %). The surface distance metrics were average symmetric surface distance (ASSD, mm), RMS (root mean square) symmetric surface distance (RMSSSD, mm), and maximum symmetric surface distance (MSSD, mm). Computation time was recorded to assess the efficiency. The performance of the proposed method has been compared with two state-of-the-art methods. Results: For the tested CBCT images, the VD, DSC, ASSD, RMSSSD, and MSSD for the incisor were 38.16 ± 12.94 mm{sup 3}, 88.82 ± 2.14%, 0.29 ± 0.03 mm, 0.32 ± 0.08 mm, and 1.25 ± 0.58 mm, respectively; the VD, DSC, ASSD, RMSSSD, and MSSD for the canine were 49.12 ± 9.33 mm{sup 3}, 91.57 ± 0.82%, 0.27 ± 0

  9. A Computational Approach for Modeling Neutron Scattering Data from Lipid Bilayers

    DOE PAGES

    Carrillo, Jan-Michael Y.; Katsaras, John; Sumpter, Bobby G.; ...

    2017-01-12

    Biological cell membranes are responsible for a range of structural and dynamical phenomena crucial to a cell's well-being and its associated functions. Due to the complexity of cell membranes, lipid bilayer systems are often used as biomimetic models. These systems have led to signficant insights into vital membrane phenomena such as domain formation, passive permeation and protein insertion. Experimental observations of membrane structure and dynamics are, however, limited in resolution, both spatially and temporally. Importantly, computer simulations are starting to play a more prominent role in interpreting experimental results, enabling a molecular under- standing of lipid membranes. Particularly, the synergymore » between scattering experiments and simulations offers opportunities for new discoveries in membrane physics, as the length and time scales probed by molecular dynamics (MD) simulations parallel those of experiments. We also describe a coarse-grained MD simulation approach that mimics neutron scattering data from large unilamellar lipid vesicles over a range of bilayer rigidity. Specfically, we simulate vesicle form factors and membrane thickness fluctuations determined from small angle neutron scattering (SANS) and neutron spin echo (NSE) experiments, respectively. Our simulations accurately reproduce trends from experiments and lay the groundwork for investigations of more complex membrane systems.« less

  10. Computational Approaches for Designing Protein/Inhibitor Complexes and Membrane Protein Variants

    NASA Astrophysics Data System (ADS)

    Vijayendran, Krishna Gajan

    Drug discovery of small-molecule protein inhibitors is a vast enterprise that involves several scientific disciplines (i.e. genomics, cell biology, x-ray crystallography, chemistry, computer science, statistics), with each discipline focusing on a particular aspect of the process. In this thesis, I use computational and experimental approaches to explore the most fundamental aspect of drug discovery: the molecular interactions of small-molecules inhibitors with proteins. In Part I (Chapters I and II), I describe how computational docking approaches can be used to identify structurally diverse molecules that can inhibit multiple protein targets in the brain. I illustrate this approach using the examples of microtubule-stabilizing agents and inhibitors of cyclooxygenase(COX)-I and 5-lipoxygenase (5-LOX). In Part II (Chapters III and IV), I focus on membrane proteins, which are notoriously difficult to work with due to their low natural abundances, low yields for heterologous over expression, and propensities toward aggregation. I describe a general approach for designing water-soluble variants of membrane proteins, for the purpose of developing cell-free, label-free, detergent-free, solution-phase studies of protein structure and small-molecule binding. I illustrate this approach through the design of a water-soluble variant of the membrane protein Smoothened, wsSMO. This wsSMO stands to serve as a first-step towards developing membrane protein analogs of this important signaling protein and drug target.

  11. A Cognitive Computing Approach for Classification of Complaints in the Insurance Industry

    NASA Astrophysics Data System (ADS)

    Forster, J.; Entrup, B.

    2017-10-01

    In this paper we present and evaluate a cognitive computing approach for classification of dissatisfaction and four complaint specific complaint classes in correspondence documents between insurance clients and an insurance company. A cognitive computing approach includes the combination classical natural language processing methods, machine learning algorithms and the evaluation of hypothesis. The approach combines a MaxEnt machine learning algorithm with language modelling, tf-idf and sentiment analytics to create a multi-label text classification model. The result is trained and tested with a set of 2500 original insurance communication documents written in German, which have been manually annotated by the partnering insurance company. With a F1-Score of 0.9, a reliable text classification component has been implemented and evaluated. A final outlook towards a cognitive computing insurance assistant is given in the end.

  12. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nakhleh, Luay

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbialmore » genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.« less

  13. Computer Synthesis Approaches of Hyperboloid Gear Drives with Linear Contact

    NASA Astrophysics Data System (ADS)

    Abadjiev, Valentin; Kawasaki, Haruhisa

    2014-09-01

    The computer design has improved forming different type software for scientific researches in the field of gearing theory as well as performing an adequate scientific support of the gear drives manufacture. Here are attached computer programs that are based on mathematical models as a result of scientific researches. The modern gear transmissions require the construction of new mathematical approaches to their geometric, technological and strength analysis. The process of optimization, synthesis and design is based on adequate iteration procedures to find out an optimal solution by varying definite parameters. The study is dedicated to accepted methodology in the creation of soft- ware for the synthesis of a class high reduction hyperboloid gears - Spiroid and Helicon ones (Spiroid and Helicon are trademarks registered by the Illinois Tool Works, Chicago, Ill). The developed basic computer products belong to software, based on original mathematical models. They are based on the two mathematical models for the synthesis: "upon a pitch contact point" and "upon a mesh region". Computer programs are worked out on the basis of the described mathematical models, and the relations between them are shown. The application of the shown approaches to the synthesis of commented gear drives is illustrated.

  14. Design synthesis and optimization of permanent magnet synchronous machines based on computationally-efficient finite element analysis

    NASA Astrophysics Data System (ADS)

    Sizov, Gennadi Y.

    In this dissertation, a model-based multi-objective optimal design of permanent magnet ac machines, supplied by sine-wave current regulated drives, is developed and implemented. The design procedure uses an efficient electromagnetic finite element-based solver to accurately model nonlinear material properties and complex geometric shapes associated with magnetic circuit design. Application of an electromagnetic finite element-based solver allows for accurate computation of intricate performance parameters and characteristics. The first contribution of this dissertation is the development of a rapid computational method that allows accurate and efficient exploration of large multi-dimensional design spaces in search of optimum design(s). The computationally efficient finite element-based approach developed in this work provides a framework of tools that allow rapid analysis of synchronous electric machines operating under steady-state conditions. In the developed modeling approach, major steady-state performance parameters such as, winding flux linkages and voltages, average, cogging and ripple torques, stator core flux densities, core losses, efficiencies and saturated machine winding inductances, are calculated with minimum computational effort. In addition, the method includes means for rapid estimation of distributed stator forces and three-dimensional effects of stator and/or rotor skew on the performance of the machine. The second contribution of this dissertation is the development of the design synthesis and optimization method based on a differential evolution algorithm. The approach relies on the developed finite element-based modeling method for electromagnetic analysis and is able to tackle large-scale multi-objective design problems using modest computational resources. Overall, computational time savings of up to two orders of magnitude are achievable, when compared to current and prevalent state-of-the-art methods. These computational savings allow

  15. THE FUTURE OF COMPUTER-BASED TOXICITY PREDICTION: MECHANISM-BASED MODELS VS. INFORMATION MINING APPROACHES

    EPA Science Inventory


    The Future of Computer-Based Toxicity Prediction:
    Mechanism-Based Models vs. Information Mining Approaches

    When we speak of computer-based toxicity prediction, we are generally referring to a broad array of approaches which rely primarily upon chemical structure ...

  16. A Computational Approach to Quantifiers as an Explanation for Some Language Impairments in Schizophrenia

    ERIC Educational Resources Information Center

    Zajenkowski, Marcin; Styla, Rafal; Szymanik, Jakub

    2011-01-01

    We compared the processing of natural language quantifiers in a group of patients with schizophrenia and a healthy control group. In both groups, the difficulty of the quantifiers was consistent with computational predictions, and patients with schizophrenia took more time to solve the problems. However, they were significantly less accurate only…

  17. Using an Adjoint Approach to Eliminate Mesh Sensitivities in Computational Design

    NASA Technical Reports Server (NTRS)

    Nielsen, Eric J.; Park, Michael A.

    2006-01-01

    An algorithm for efficiently incorporating the effects of mesh sensitivities in a computational design framework is introduced. The method is based on an adjoint approach and eliminates the need for explicit linearizations of the mesh movement scheme with respect to the geometric parameterization variables, an expense that has hindered practical large-scale design optimization using discrete adjoint methods. The effects of the mesh sensitivities can be accounted for through the solution of an adjoint problem equivalent in cost to a single mesh movement computation, followed by an explicit matrix-vector product scaling with the number of design variables and the resolution of the parameterized surface grid. The accuracy of the implementation is established and dramatic computational savings obtained using the new approach are demonstrated using several test cases. Sample design optimizations are also shown.

  18. Using an Adjoint Approach to Eliminate Mesh Sensitivities in Computational Design

    NASA Technical Reports Server (NTRS)

    Nielsen, Eric J.; Park, Michael A.

    2005-01-01

    An algorithm for efficiently incorporating the effects of mesh sensitivities in a computational design framework is introduced. The method is based on an adjoint approach and eliminates the need for explicit linearizations of the mesh movement scheme with respect to the geometric parameterization variables, an expense that has hindered practical large-scale design optimization using discrete adjoint methods. The effects of the mesh sensitivities can be accounted for through the solution of an adjoint problem equivalent in cost to a single mesh movement computation, followed by an explicit matrix-vector product scaling with the number of design variables and the resolution of the parameterized surface grid. The accuracy of the implementation is established and dramatic computational savings obtained using the new approach are demonstrated using several test cases. Sample design optimizations are also shown.

  19. A full-spectral Bayesian reconstruction approach based on the material decomposition model applied in dual-energy computed tomography.

    PubMed

    Cai, C; Rodet, T; Legoupil, S; Mohammad-Djafari, A

    2013-11-01

    Dual-energy computed tomography (DECT) makes it possible to get two fractions of basis materials without segmentation. One is the soft-tissue equivalent water fraction and the other is the hard-matter equivalent bone fraction. Practical DECT measurements are usually obtained with polychromatic x-ray beams. Existing reconstruction approaches based on linear forward models without counting the beam polychromaticity fail to estimate the correct decomposition fractions and result in beam-hardening artifacts (BHA). The existing BHA correction approaches either need to refer to calibration measurements or suffer from the noise amplification caused by the negative-log preprocessing and the ill-conditioned water and bone separation problem. To overcome these problems, statistical DECT reconstruction approaches based on nonlinear forward models counting the beam polychromaticity show great potential for giving accurate fraction images. This work proposes a full-spectral Bayesian reconstruction approach which allows the reconstruction of high quality fraction images from ordinary polychromatic measurements. This approach is based on a Gaussian noise model with unknown variance assigned directly to the projections without taking negative-log. Referring to Bayesian inferences, the decomposition fractions and observation variance are estimated by using the joint maximum a posteriori (MAP) estimation method. Subject to an adaptive prior model assigned to the variance, the joint estimation problem is then simplified into a single estimation problem. It transforms the joint MAP estimation problem into a minimization problem with a nonquadratic cost function. To solve it, the use of a monotone conjugate gradient algorithm with suboptimal descent steps is proposed. The performance of the proposed approach is analyzed with both simulated and experimental data. The results show that the proposed Bayesian approach is robust to noise and materials. It is also necessary to have the

  20. Computational oncology.

    PubMed

    Lefor, Alan T

    2011-08-01

    Oncology research has traditionally been conducted using techniques from the biological sciences. The new field of computational oncology has forged a new relationship between the physical sciences and oncology to further advance research. By applying physics and mathematics to oncologic problems, new insights will emerge into the pathogenesis and treatment of malignancies. One major area of investigation in computational oncology centers around the acquisition and analysis of data, using improved computing hardware and software. Large databases of cellular pathways are being analyzed to understand the interrelationship among complex biological processes. Computer-aided detection is being applied to the analysis of routine imaging data including mammography and chest imaging to improve the accuracy and detection rate for population screening. The second major area of investigation uses computers to construct sophisticated mathematical models of individual cancer cells as well as larger systems using partial differential equations. These models are further refined with clinically available information to more accurately reflect living systems. One of the major obstacles in the partnership between physical scientists and the oncology community is communications. Standard ways to convey information must be developed. Future progress in computational oncology will depend on close collaboration between clinicians and investigators to further the understanding of cancer using these new approaches.

  1. RIO: a new computational framework for accurate initial data of binary black holes

    NASA Astrophysics Data System (ADS)

    Barreto, W.; Clemente, P. C. M.; de Oliveira, H. P.; Rodriguez-Mueller, B.

    2018-06-01

    We present a computational framework ( Rio) in the ADM 3+1 approach for numerical relativity. This work enables us to carry out high resolution calculations for initial data of two arbitrary black holes. We use the transverse conformal treatment, the Bowen-York and the puncture methods. For the numerical solution of the Hamiltonian constraint we use the domain decomposition and the spectral decomposition of Galerkin-Collocation. The nonlinear numerical code solves the set of equations for the spectral modes using the standard Newton-Raphson method, LU decomposition and Gaussian quadratures. We show the convergence of the Rio code. This code allows for easy deployment of large calculations. We show how the spin of one of the black holes is manifest in the conformal factor.

  2. The soft computing-based approach to investigate allergic diseases: a systematic review.

    PubMed

    Tartarisco, Gennaro; Tonacci, Alessandro; Minciullo, Paola Lucia; Billeci, Lucia; Pioggia, Giovanni; Incorvaia, Cristoforo; Gangemi, Sebastiano

    2017-01-01

    Early recognition of inflammatory markers and their relation to asthma, adverse drug reactions, allergic rhinitis, atopic dermatitis and other allergic diseases is an important goal in allergy. The vast majority of studies in the literature are based on classic statistical methods; however, developments in computational techniques such as soft computing-based approaches hold new promise in this field. The aim of this manuscript is to systematically review the main soft computing-based techniques such as artificial neural networks, support vector machines, bayesian networks and fuzzy logic to investigate their performances in the field of allergic diseases. The review was conducted following PRISMA guidelines and the protocol was registered within PROSPERO database (CRD42016038894). The research was performed on PubMed and ScienceDirect, covering the period starting from September 1, 1990 through April 19, 2016. The review included 27 studies related to allergic diseases and soft computing performances. We observed promising results with an overall accuracy of 86.5%, mainly focused on asthmatic disease. The review reveals that soft computing-based approaches are suitable for big data analysis and can be very powerful, especially when dealing with uncertainty and poorly characterized parameters. Furthermore, they can provide valuable support in case of lack of data and entangled cause-effect relationships, which make it difficult to assess the evolution of disease. Although most works deal with asthma, we believe the soft computing approach could be a real breakthrough and foster new insights into other allergic diseases as well.

  3. Accurate interlaminar stress recovery from finite element analysis

    NASA Technical Reports Server (NTRS)

    Tessler, Alexander; Riggs, H. Ronald

    1994-01-01

    The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

  4. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  5. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory

    DOE PAGES

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; ...

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can bemore » rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.« less

  6. Accurate X-Ray Spectral Predictions: An Advanced Self-Consistent-Field Approach Inspired by Many-Body Perturbation Theory.

    PubMed

    Liang, Yufeng; Vinson, John; Pemmaraju, Sri; Drisdell, Walter S; Shirley, Eric L; Prendergast, David

    2017-03-03

    Constrained-occupancy delta-self-consistent-field (ΔSCF) methods and many-body perturbation theories (MBPT) are two strategies for obtaining electronic excitations from first principles. Using the two distinct approaches, we study the O 1s core excitations that have become increasingly important for characterizing transition-metal oxides and understanding strong electronic correlation. The ΔSCF approach, in its current single-particle form, systematically underestimates the pre-edge intensity for chosen oxides, despite its success in weakly correlated systems. By contrast, the Bethe-Salpeter equation within MBPT predicts much better line shapes. This motivates one to reexamine the many-electron dynamics of x-ray excitations. We find that the single-particle ΔSCF approach can be rectified by explicitly calculating many-electron transition amplitudes, producing x-ray spectra in excellent agreement with experiments. This study paves the way to accurately predict x-ray near-edge spectral fingerprints for physics and materials science beyond the Bethe-Salpether equation.

  7. Computer Forensics Education - the Open Source Approach

    NASA Astrophysics Data System (ADS)

    Huebner, Ewa; Bem, Derek; Cheung, Hon

    In this chapter we discuss the application of the open source software tools in computer forensics education at tertiary level. We argue that open source tools are more suitable than commercial tools, as they provide the opportunity for students to gain in-depth understanding and appreciation of the computer forensic process as opposed to familiarity with one software product, however complex and multi-functional. With the access to all source programs the students become more than just the consumers of the tools as future forensic investigators. They can also examine the code, understand the relationship between the binary images and relevant data structures, and in the process gain necessary background to become the future creators of new and improved forensic software tools. As a case study we present an advanced subject, Computer Forensics Workshop, which we designed for the Bachelor's degree in computer science at the University of Western Sydney. We based all laboratory work and the main take-home project in this subject on open source software tools. We found that without exception more than one suitable tool can be found to cover each topic in the curriculum adequately. We argue that this approach prepares students better for forensic field work, as they gain confidence to use a variety of tools, not just a single product they are familiar with.

  8. A distributed computing approach to mission operations support. [for spacecraft

    NASA Technical Reports Server (NTRS)

    Larsen, R. L.

    1975-01-01

    Computing mission operation support includes orbit determination, attitude processing, maneuver computation, resource scheduling, etc. The large-scale third-generation distributed computer network discussed is capable of fulfilling these dynamic requirements. It is shown that distribution of resources and control leads to increased reliability, and exhibits potential for incremental growth. Through functional specialization, a distributed system may be tuned to very specific operational requirements. Fundamental to the approach is the notion of process-to-process communication, which is effected through a high-bandwidth communications network. Both resource-sharing and load-sharing may be realized in the system.

  9. A Randomized Rounding Approach for Optimization of Test Sheet Composing and Exposure Rate Control in Computer-Assisted Testing

    ERIC Educational Resources Information Center

    Wang, Chu-Fu; Lin, Chih-Lung; Deng, Jien-Han

    2012-01-01

    Testing is an important stage of teaching as it can assist teachers in auditing students' learning results. A good test is able to accurately reflect the capability of a learner. Nowadays, Computer-Assisted Testing (CAT) is greatly improving traditional testing, since computers can automatically and quickly compose a proper test sheet to meet user…

  10. A computational approach to animal breeding.

    PubMed

    Berger-Wolf, Tanya Y; Moore, Cristopher; Saia, Jared

    2007-02-07

    We propose a computational model of mating strategies for controlled animal breeding programs. A mating strategy in a controlled breeding program is a heuristic with some optimization criteria as a goal. Thus, it is appropriate to use the computational tools available for analysis of optimization heuristics. In this paper, we propose the first discrete model of the controlled animal breeding problem and analyse heuristics for two possible objectives: (1) breeding for maximum diversity and (2) breeding a target individual. These two goals are representative of conservation biology and agricultural livestock management, respectively. We evaluate several mating strategies and provide upper and lower bounds for the expected number of matings. While the population parameters may vary and can change the actual number of matings for a particular strategy, the order of magnitude of the number of expected matings and the relative competitiveness of the mating heuristics remains the same. Thus, our simple discrete model of the animal breeding problem provides a novel viable and robust approach to designing and comparing breeding strategies in captive populations.

  11. Probabilistic Damage Characterization Using the Computationally-Efficient Bayesian Approach

    NASA Technical Reports Server (NTRS)

    Warner, James E.; Hochhalter, Jacob D.

    2016-01-01

    This work presents a computationally-ecient approach for damage determination that quanti es uncertainty in the provided diagnosis. Given strain sensor data that are polluted with measurement errors, Bayesian inference is used to estimate the location, size, and orientation of damage. This approach uses Bayes' Theorem to combine any prior knowledge an analyst may have about the nature of the damage with information provided implicitly by the strain sensor data to form a posterior probability distribution over possible damage states. The unknown damage parameters are then estimated based on samples drawn numerically from this distribution using a Markov Chain Monte Carlo (MCMC) sampling algorithm. Several modi cations are made to the traditional Bayesian inference approach to provide signi cant computational speedup. First, an ecient surrogate model is constructed using sparse grid interpolation to replace a costly nite element model that must otherwise be evaluated for each sample drawn with MCMC. Next, the standard Bayesian posterior distribution is modi ed using a weighted likelihood formulation, which is shown to improve the convergence of the sampling process. Finally, a robust MCMC algorithm, Delayed Rejection Adaptive Metropolis (DRAM), is adopted to sample the probability distribution more eciently. Numerical examples demonstrate that the proposed framework e ectively provides damage estimates with uncertainty quanti cation and can yield orders of magnitude speedup over standard Bayesian approaches.

  12. A time accurate prediction of the viscous flow in a turbine stage including a rotor in motion

    NASA Astrophysics Data System (ADS)

    Shavalikul, Akamol

    In this current study, the flow field in the Pennsylvania State University Axial Flow Turbine Research Facility (AFTRF) was simulated. This study examined four sets of simulations. The first two sets are for an individual NGV and for an individual rotor. The last two sets use a multiple reference frames approach for a complete turbine stage with two different interface models: a steady circumferential average approach called a mixing plane model, and a time accurate flow simulation approach called a sliding mesh model. The NGV passage flow field was simulated using a three-dimensional Reynolds Averaged Navier-Stokes finite volume solver (RANS) with a standard kappa -- epsilon turbulence model. The mean flow distributions on the NGV surfaces and endwall surfaces were computed. The numerical solutions indicate that two passage vortices begin to be observed approximately at the mid axial chord of the NGV suction surface. The first vortex is a casing passage vortex which occurs at the corner formed by the NGV suction surface and the casing. This vortex is created by the interaction of the passage flow and the radially inward flow, while the second vortex, the hub passage vortex, is observed near the hub. These two vortices become stronger towards the NGV trailing edge. By comparing the results from the X/Cx = 1.025 plane and the X/Cx = 1.09 plane, it can be concluded that the NGV wake decays rapidly within a short axial distance downstream of the NGV. For the rotor, a set of simulations was carried out to examine the flow fields associated with different pressure side tip extension configurations, which are designed to reduce the tip leakage flow. The simulation results show that significant reductions in tip leakage mass flow rate and aerodynamic loss reduction are possible by using suitable tip platform extensions located near the pressure side corner of the blade tip. The computations used realistic turbine rotor inlet flow conditions in a linear cascade arrangement

  13. An optimization approach for fitting canonical tensor decompositions.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dunlavy, Daniel M.; Acar, Evrim; Kolda, Tamara Gibson

    Tensor decompositions are higher-order analogues of matrix decompositions and have proven to be powerful tools for data analysis. In particular, we are interested in the canonical tensor decomposition, otherwise known as the CANDECOMP/PARAFAC decomposition (CPD), which expresses a tensor as the sum of component rank-one tensors and is used in a multitude of applications such as chemometrics, signal processing, neuroscience, and web analysis. The task of computing the CPD, however, can be difficult. The typical approach is based on alternating least squares (ALS) optimization, which can be remarkably fast but is not very accurate. Previously, nonlinear least squares (NLS) methodsmore » have also been recommended; existing NLS methods are accurate but slow. In this paper, we propose the use of gradient-based optimization methods. We discuss the mathematical calculation of the derivatives and further show that they can be computed efficiently, at the same cost as one iteration of ALS. Computational experiments demonstrate that the gradient-based optimization methods are much more accurate than ALS and orders of magnitude faster than NLS.« less

  14. Cost-Effectiveness of Alternative Approaches to Computer-Assisted Instruction.

    ERIC Educational Resources Information Center

    Levin, Henry M.; And Others

    Operating on the premise that different approaches to computer-assisted instruction (CAI) may use different configurations of hardware and software, different curricula, and different organizational and personnel arrangements, this study explored the feasibility of collecting evaluations of CAI to evaluate the comparative cost-effectiveness of…

  15. Computational Approach for Securing Radiology-Diagnostic Data in Connected Health Network using High-Performance GPU-Accelerated AES.

    PubMed

    Adeshina, A M; Hashim, R

    2017-03-01

    Diagnostic radiology is a core and integral part of modern medicine, paving ways for the primary care physicians in the disease diagnoses, treatments and therapy managements. Obviously, all recent standard healthcare procedures have immensely benefitted from the contemporary information technology revolutions, apparently revolutionizing those approaches to acquiring, storing and sharing of diagnostic data for efficient and timely diagnosis of diseases. Connected health network was introduced as an alternative to the ageing traditional concept in healthcare system, improving hospital-physician connectivity and clinical collaborations. Undoubtedly, the modern medicinal approach has drastically improved healthcare but at the expense of high computational cost and possible breach of diagnosis privacy. Consequently, a number of cryptographical techniques are recently being applied to clinical applications, but the challenges of not being able to successfully encrypt both the image and the textual data persist. Furthermore, processing time of encryption-decryption of medical datasets, within a considerable lower computational cost without jeopardizing the required security strength of the encryption algorithm, still remains as an outstanding issue. This study proposes a secured radiology-diagnostic data framework for connected health network using high-performance GPU-accelerated Advanced Encryption Standard. The study was evaluated with radiology image datasets consisting of brain MR and CT datasets obtained from the department of Surgery, University of North Carolina, USA, and the Swedish National Infrastructure for Computing. Sample patients' notes from the University of North Carolina, School of medicine at Chapel Hill were also used to evaluate the framework for its strength in encrypting-decrypting textual data in the form of medical report. Significantly, the framework is not only able to accurately encrypt and decrypt medical image datasets, but it also

  16. An efficient and accurate framework for calculating lattice thermal conductivity of solids: AFLOW—AAPL Automatic Anharmonic Phonon Library

    NASA Astrophysics Data System (ADS)

    Plata, Jose J.; Nath, Pinku; Usanmaz, Demet; Carrete, Jesús; Toher, Cormac; de Jong, Maarten; Asta, Mark; Fornari, Marco; Nardelli, Marco Buongiorno; Curtarolo, Stefano

    2017-10-01

    One of the most accurate approaches for calculating lattice thermal conductivity, , is solving the Boltzmann transport equation starting from third-order anharmonic force constants. In addition to the underlying approximations of ab-initio parameterization, two main challenges are associated with this path: high computational costs and lack of automation in the frameworks using this methodology, which affect the discovery rate of novel materials with ad-hoc properties. Here, the Automatic Anharmonic Phonon Library (AAPL) is presented. It efficiently computes interatomic force constants by making effective use of crystal symmetry analysis, it solves the Boltzmann transport equation to obtain , and allows a fully integrated operation with minimum user intervention, a rational addition to the current high-throughput accelerated materials development framework AFLOW. An "experiment vs. theory" study of the approach is shown, comparing accuracy and speed with respect to other available packages, and for materials characterized by strong electron localization and correlation. Combining AAPL with the pseudo-hybrid functional ACBN0 is possible to improve accuracy without increasing computational requirements.

  17. WPS mediation: An approach to process geospatial data on different computing backends

    NASA Astrophysics Data System (ADS)

    Giuliani, Gregory; Nativi, Stefano; Lehmann, Anthony; Ray, Nicolas

    2012-10-01

    The OGC Web Processing Service (WPS) specification allows generating information by processing distributed geospatial data made available through Spatial Data Infrastructures (SDIs). However, current SDIs have limited analytical capacities and various problems emerge when trying to use them in data and computing-intensive domains such as environmental sciences. These problems are usually not or only partially solvable using single computing resources. Therefore, the Geographic Information (GI) community is trying to benefit from the superior storage and computing capabilities offered by distributed computing (e.g., Grids, Clouds) related methods and technologies. Currently, there is no commonly agreed approach to grid-enable WPS. No implementation allows one to seamlessly execute a geoprocessing calculation following user requirements on different computing backends, ranging from a stand-alone GIS server up to computer clusters and large Grid infrastructures. Considering this issue, this paper presents a proof of concept by mediating different geospatial and Grid software packages, and by proposing an extension of WPS specification through two optional parameters. The applicability of this approach will be demonstrated using a Normalized Difference Vegetation Index (NDVI) mediated WPS process, highlighting benefits, and issues that need to be further investigated to improve performances.

  18. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  19. Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations

    NASA Astrophysics Data System (ADS)

    Heidari, M.; Cortes-Huerto, R.; Donadio, D.; Potestio, R.

    2016-10-01

    In adaptive resolution simulations the same system is concurrently modeled with different resolution in different subdomains of the simulation box, thereby enabling an accurate description in a small but relevant region, while the rest is treated with a computationally parsimonious model. In this framework, electrostatic interaction, whose accurate treatment is a crucial aspect in the realistic modeling of soft matter and biological systems, represents a particularly acute problem due to the intrinsic long-range nature of Coulomb potential. In the present work we propose and validate the usage of a short-range modification of Coulomb potential, the Damped shifted force (DSF) model, in the context of the Hamiltonian adaptive resolution simulation (H-AdResS) scheme. This approach, which is here validated on bulk water, ensures a reliable reproduction of the structural and dynamical properties of the liquid, and enables a seamless embedding in the H-AdResS framework. The resulting dual-resolution setup is implemented in the LAMMPS simulation package, and its customized version employed in the present work is made publicly available.

  20. A computer-aided approach to nonlinear control systhesis

    NASA Technical Reports Server (NTRS)

    Wie, Bong; Anthony, Tobin

    1988-01-01

    The major objective of this project is to develop a computer-aided approach to nonlinear stability analysis and nonlinear control system design. This goal is to be obtained by refining the describing function method as a synthesis tool for nonlinear control design. The interim report outlines the approach by this study to meet these goals including an introduction to the INteractive Controls Analysis (INCA) program which was instrumental in meeting these study objectives. A single-input describing function (SIDF) design methodology was developed in this study; coupled with the software constructed in this study, the results of this project provide a comprehensive tool for design and integration of nonlinear control systems.

  1. A new approach for reducing beam hardening artifacts in polychromatic X-ray computed tomography using more accurate prior image.

    PubMed

    Wang, Hui; Xu, Yanan; Shi, Hongli

    2018-03-15

    Metal artifacts severely degrade CT image quality in clinical diagnosis, which are difficult to removed, especially for the beam hardening artifacts. The metal artifact reduction (MAR) based on prior images are the most frequently-used methods. However, there exists a lot misclassification in most prior images caused by absence of prior information such as spectrum distribution of X-ray beam source, especially when multiple or big metal are included. This work aims is to identify a more accurate prior image to improve image quality. The proposed method includes four steps. First, the metal image is segmented by thresholding an initial image, where the metal traces are identified in the initial projection data using the forward projection of the metal image. Second, the accurate absorbent model of certain metal image is calculated according to the spectrum distribution of certain X-ray beam source and energy-dependent attenuation coefficients of metal. Third, a new metal image is reconstructed by the general analytical reconstruction algorithm such as filtered back projection (FPB). The prior image is obtained by segmenting the difference image between the initial image and the new metal image into air, tissue and bone. Fourth, the initial projection data are normalized by dividing the projection data of prior image pixel to pixel. The final corrected image is obtained by interpolation, denormalization and reconstruction. Several clinical images with dental fillings and knee prostheses were used to evaluate the proposed algorithm and normalized metal artifact reduction (NMAR) and linear interpolation (LI) method. The results demonstrate the artifacts were reduced efficiently by the proposed method. The proposed method could obtain an exact prior image using the prior information about X-ray beam source and energy-dependent attenuation coefficients of metal. As a result, better performance of reducing beam hardening artifacts can be achieved. Moreover, the process of

  2. Multistate approaches in computational protein design

    PubMed Central

    Davey, James A; Chica, Roberto A

    2012-01-01

    Computational protein design (CPD) is a useful tool for protein engineers. It has been successfully applied towards the creation of proteins with increased thermostability, improved binding affinity, novel enzymatic activity, and altered ligand specificity. Traditionally, CPD calculations search and rank sequences using a single fixed protein backbone template in an approach referred to as single-state design (SSD). While SSD has enjoyed considerable success, certain design objectives require the explicit consideration of multiple conformational and/or chemical states. Cases where a “multistate” approach may be advantageous over the SSD approach include designing conformational changes into proteins, using native ensembles to mimic backbone flexibility, and designing ligand or oligomeric association specificities. These design objectives can be efficiently tackled using multistate design (MSD), an emerging methodology in CPD that considers any number of protein conformational or chemical states as inputs instead of a single protein backbone template, as in SSD. In this review article, recent examples of the successful design of a desired property into proteins using MSD are described. These studies employing MSD are divided into two categories—those that utilized multiple conformational states, and those that utilized multiple chemical states. In addition, the scoring of competing states during negative design is discussed as a current challenge for MSD. PMID:22811394

  3. Acute Perforated Diverticulitis: Assessment With Multidetector Computed Tomography.

    PubMed

    Sessa, Barbara; Galluzzo, Michele; Ianniello, Stefania; Pinto, Antonio; Trinci, Margherita; Miele, Vittorio

    2016-02-01

    Colonic diverticulitis is a common condition in the western population. Complicated diverticulitis is defined as the presence of extraluminal air or abscess, peritonitis, colon occlusion, or fistulas. Multidetector row computed tomography (MDCT) is the modality of choice for the diagnosis and the staging of diverticulitis and its complications, which enables performing an accurate differential diagnosis and addressing the patients to a correct management. MDCT is accurate in diagnosing the site of perforation in approximately 85% of cases, by the detection of direct signs (focal bowel wall discontinuity, extraluminal gas, and extraluminal enteric contrast) and indirect signs, which are represented by segmental bowel wall thickening, abnormal bowel wall enhancement, perivisceral fat stranding of fluid, and abscess. MDCT is accurate in the differentiation from complicated colon diverticulitis and colon cancer, often with a similar imaging. The computed tomography-guided classification is recommended to discriminate patients with mild diverticulitis, generally treated with antibiotics, from those with severe diverticulitis with a large abscess, which may be drained with a percutaneous approach. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. A Bayesian approach for parameter estimation and prediction using a computationally intensive model

    DOE PAGES

    Higdon, Dave; McDonnell, Jordan D.; Schunck, Nicolas; ...

    2015-02-05

    Bayesian methods have been successful in quantifying uncertainty in physics-based problems in parameter estimation and prediction. In these cases, physical measurements y are modeled as the best fit of a physics-based modelmore » $$\\eta (\\theta )$$, where θ denotes the uncertain, best input setting. Hence the statistical model is of the form $$y=\\eta (\\theta )+\\epsilon ,$$ where $$\\epsilon $$ accounts for measurement, and possibly other, error sources. When nonlinearity is present in $$\\eta (\\cdot )$$, the resulting posterior distribution for the unknown parameters in the Bayesian formulation is typically complex and nonstandard, requiring computationally demanding computational approaches such as Markov chain Monte Carlo (MCMC) to produce multivariate draws from the posterior. Although generally applicable, MCMC requires thousands (or even millions) of evaluations of the physics model $$\\eta (\\cdot )$$. This requirement is problematic if the model takes hours or days to evaluate. To overcome this computational bottleneck, we present an approach adapted from Bayesian model calibration. This approach combines output from an ensemble of computational model runs with physical measurements, within a statistical formulation, to carry out inference. A key component of this approach is a statistical response surface, or emulator, estimated from the ensemble of model runs. We demonstrate this approach with a case study in estimating parameters for a density functional theory model, using experimental mass/binding energy measurements from a collection of atomic nuclei. Lastly, we also demonstrate how this approach produces uncertainties in predictions for recent mass measurements obtained at Argonne National Laboratory.« less

  5. A modeling approach to predict acoustic nonlinear field generated by a transmitter with an aluminum lens.

    PubMed

    Fan, Tingbo; Liu, Zhenbo; Chen, Tao; Li, Faqi; Zhang, Dong

    2011-09-01

    In this work, the authors propose a modeling approach to compute the nonlinear acoustic field generated by a flat piston transmitter with an attached aluminum lens. In this approach, the geometrical parameters (radius and focal length) of a virtual source are initially determined by Snell's refraction law and then adjusted based on the Rayleigh integral result in the linear case. Then, this virtual source is used with the nonlinear spheroidal beam equation (SBE) model to predict the nonlinear acoustic field in the focal region. To examine the validity of this approach, the calculated nonlinear result is compared with those from the Westervelt and (Khokhlov-Zabolotskaya-Kuznetsov) KZK equations for a focal intensity of 7 kW/cm(2). Results indicate that this approach could accurately describe the nonlinear acoustic field in the focal region with less computation time. The proposed modeling approach is shown to accurately describe the nonlinear acoustic field in the focal region. Compared with the Westervelt equation, the computation time of this approach is significantly reduced. It might also be applicable for the widely used concave focused transmitter with a large aperture angle.

  6. Cloud computing approaches to accelerate drug discovery value chain.

    PubMed

    Garg, Vibhav; Arora, Suchir; Gupta, Chitra

    2011-12-01

    Continued advancements in the area of technology have helped high throughput screening (HTS) evolve from a linear to parallel approach by performing system level screening. Advanced experimental methods used for HTS at various steps of drug discovery (i.e. target identification, target validation, lead identification and lead validation) can generate data of the order of terabytes. As a consequence, there is pressing need to store, manage, mine and analyze this data to identify informational tags. This need is again posing challenges to computer scientists to offer the matching hardware and software infrastructure, while managing the varying degree of desired computational power. Therefore, the potential of "On-Demand Hardware" and "Software as a Service (SAAS)" delivery mechanisms cannot be denied. This on-demand computing, largely referred to as Cloud Computing, is now transforming the drug discovery research. Also, integration of Cloud computing with parallel computing is certainly expanding its footprint in the life sciences community. The speed, efficiency and cost effectiveness have made cloud computing a 'good to have tool' for researchers, providing them significant flexibility, allowing them to focus on the 'what' of science and not the 'how'. Once reached to its maturity, Discovery-Cloud would fit best to manage drug discovery and clinical development data, generated using advanced HTS techniques, hence supporting the vision of personalized medicine.

  7. FILMPAR: A parallel algorithm designed for the efficient and accurate computation of thin film flow on functional surfaces containing micro-structure

    NASA Astrophysics Data System (ADS)

    Lee, Y. C.; Thompson, H. M.; Gaskell, P. H.

    2009-12-01

    FILMPAR is a highly efficient and portable parallel multigrid algorithm for solving a discretised form of the lubrication approximation to three-dimensional, gravity-driven, continuous thin film free-surface flow over substrates containing micro-scale topography. While generally applicable to problems involving heterogeneous and distributed features, for illustrative purposes the algorithm is benchmarked on a distributed memory IBM BlueGene/P computing platform for the case of flow over a single trench topography, enabling direct comparison with complementary experimental data and existing serial multigrid solutions. Parallel performance is assessed as a function of the number of processors employed and shown to lead to super-linear behaviour for the production of mesh-independent solutions. In addition, the approach is used to solve for the case of flow over a complex inter-connected topographical feature and a description provided of how FILMPAR could be adapted relatively simply to solve for a wider class of related thin film flow problems. Program summaryProgram title: FILMPAR Catalogue identifier: AEEL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 530 421 No. of bytes in distributed program, including test data, etc.: 1 960 313 Distribution format: tar.gz Programming language: C++ and MPI Computer: Desktop, server Operating system: Unix/Linux Mac OS X Has the code been vectorised or parallelised?: Yes. Tested with up to 128 processors RAM: 512 MBytes Classification: 12 External routines: GNU C/C++, MPI Nature of problem: Thin film flows over functional substrates containing well-defined single and complex topographical features are of enormous significance, having a wide variety of engineering

  8. A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach.

    PubMed

    Estrada, T; Zhang, B; Cicotti, P; Armen, R S; Taufer, M

    2012-07-01

    We present a scalable and accurate method for classifying protein-ligand binding geometries in molecular docking. Our method is a three-step process: the first step encodes the geometry of a three-dimensional (3D) ligand conformation into a single 3D point in the space; the second step builds an octree by assigning an octant identifier to every single point in the space under consideration; and the third step performs an octree-based clustering on the reduced conformation space and identifies the most dense octant. We adapt our method for MapReduce and implement it in Hadoop. The load-balancing, fault-tolerance, and scalability in MapReduce allow screening of very large conformation spaces not approachable with traditional clustering methods. We analyze results for docking trials for 23 protein-ligand complexes for HIV protease, 21 protein-ligand complexes for Trypsin, and 12 protein-ligand complexes for P38alpha kinase. We also analyze cross docking trials for 24 ligands, each docking into 24 protein conformations of the HIV protease, and receptor ensemble docking trials for 24 ligands, each docking in a pool of HIV protease receptors. Our method demonstrates significant improvement over energy-only scoring for the accurate identification of native ligand geometries in all these docking assessments. The advantages of our clustering approach make it attractive for complex applications in real-world drug design efforts. We demonstrate that our method is particularly useful for clustering docking results using a minimal ensemble of representative protein conformational states (receptor ensemble docking), which is now a common strategy to address protein flexibility in molecular docking. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

    PubMed

    Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

    2015-01-01

    The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

  10. Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

    PubMed Central

    Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A.; Lundström, Patrik

    2015-01-01

    The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628

  11. Extracting Time-Accurate Acceleration Vectors From Nontrivial Accelerometer Arrangements.

    PubMed

    Franck, Jennifer A; Blume, Janet; Crisco, Joseph J; Franck, Christian

    2015-09-01

    Sports-related concussions are of significant concern in many impact sports, and their detection relies on accurate measurements of the head kinematics during impact. Among the most prevalent recording technologies are videography, and more recently, the use of single-axis accelerometers mounted in a helmet, such as the HIT system. Successful extraction of the linear and angular impact accelerations depends on an accurate analysis methodology governed by the equations of motion. Current algorithms are able to estimate the magnitude of acceleration and hit location, but make assumptions about the hit orientation and are often limited in the position and/or orientation of the accelerometers. The newly formulated algorithm presented in this manuscript accurately extracts the full linear and rotational acceleration vectors from a broad arrangement of six single-axis accelerometers directly from the governing set of kinematic equations. The new formulation linearizes the nonlinear centripetal acceleration term with a finite-difference approximation and provides a fast and accurate solution for all six components of acceleration over long time periods (>250 ms). The approximation of the nonlinear centripetal acceleration term provides an accurate computation of the rotational velocity as a function of time and allows for reconstruction of a multiple-impact signal. Furthermore, the algorithm determines the impact location and orientation and can distinguish between glancing, high rotational velocity impacts, or direct impacts through the center of mass. Results are shown for ten simulated impact locations on a headform geometry computed with three different accelerometer configurations in varying degrees of signal noise. Since the algorithm does not require simplifications of the actual impacted geometry, the impact vector, or a specific arrangement of accelerometer orientations, it can be easily applied to many impact investigations in which accurate kinematics need

  12. Computational approaches to vision

    NASA Technical Reports Server (NTRS)

    Barrow, H. G.; Tenenbaum, J. M.

    1986-01-01

    Vision is examined in terms of a computational process, and the competence, structure, and control of computer vision systems are analyzed. Theoretical and experimental data on the formation of a computer vision system are discussed. Consideration is given to early vision, the recovery of intrinsic surface characteristics, higher levels of interpretation, and system integration and control. A computational visual processing model is proposed and its architecture and operation are described. Examples of state-of-the-art vision systems, which include some of the levels of representation and processing mechanisms, are presented.

  13. Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding.

    PubMed

    Montalvo-Acosta, Joel José; Cecchini, Marco

    2016-12-01

    The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. A Computationally-Efficient Inverse Approach to Probabilistic Strain-Based Damage Diagnosis

    NASA Technical Reports Server (NTRS)

    Warner, James E.; Hochhalter, Jacob D.; Leser, William P.; Leser, Patrick E.; Newman, John A

    2016-01-01

    This work presents a computationally-efficient inverse approach to probabilistic damage diagnosis. Given strain data at a limited number of measurement locations, Bayesian inference and Markov Chain Monte Carlo (MCMC) sampling are used to estimate probability distributions of the unknown location, size, and orientation of damage. Substantial computational speedup is obtained by replacing a three-dimensional finite element (FE) model with an efficient surrogate model. The approach is experimentally validated on cracked test specimens where full field strains are determined using digital image correlation (DIC). Access to full field DIC data allows for testing of different hypothetical sensor arrangements, facilitating the study of strain-based diagnosis effectiveness as the distance between damage and measurement locations increases. The ability of the framework to effectively perform both probabilistic damage localization and characterization in cracked plates is demonstrated and the impact of measurement location on uncertainty in the predictions is shown. Furthermore, the analysis time to produce these predictions is orders of magnitude less than a baseline Bayesian approach with the FE method by utilizing surrogate modeling and effective numerical sampling approaches.

  15. Approach to Computer Implementation of Mathematical Model of 3-Phase Induction Motor

    NASA Astrophysics Data System (ADS)

    Pustovetov, M. Yu

    2018-03-01

    This article discusses the development of the computer model of an induction motor based on the mathematical model in a three-phase stator reference frame. It uses an approach that allows combining during preparation of the computer model dual methods: means of visual programming circuitry (in the form of electrical schematics) and logical one (in the form of block diagrams). The approach enables easy integration of the model of an induction motor as part of more complex models of electrical complexes and systems. The developed computer model gives the user access to the beginning and the end of a winding of each of the three phases of the stator and rotor. This property is particularly important when considering the asymmetric modes of operation or when powered by the special circuitry of semiconductor converters.

  16. Vibronic Coupling Investigation to Compute Phosphorescence Spectra of Pt(II) Complexes.

    PubMed

    Vazart, Fanny; Latouche, Camille; Bloino, Julien; Barone, Vincenzo

    2015-06-01

    The present paper reports a comprehensive quantum mechanical investigation on the luminescence properties of several mono- and dinuclear platinum(II) complexes. The electronic structures and geometric parameters are briefly analyzed together with the absorption bands of all complexes. In all cases agreement with experiment is remarkable. Next, emission (phosphorescence) spectra from the first triplet states have been investigated by comparing different computational approaches and taking into account also vibronic effects. Once again, agreement with experiment is good, especially using unrestricted electronic computations coupled to vibronic contributions. Together with the intrinsic interest of the results, the robustness and generality of the approach open the opportunity for computationally oriented chemists to provide accurate results for the screening of large targets which could be of interest in molecular materials design.

  17. Integrating structure-based and ligand-based approaches for computational drug design.

    PubMed

    Wilson, Gregory L; Lill, Markus A

    2011-04-01

    Methods utilized in computer-aided drug design can be classified into two major categories: structure based and ligand based, using information on the structure of the protein or on the biological and physicochemical properties of bound ligands, respectively. In recent years there has been a trend towards integrating these two methods in order to enhance the reliability and efficiency of computer-aided drug-design approaches by combining information from both the ligand and the protein. This trend resulted in a variety of methods that include: pseudoreceptor methods, pharmacophore methods, fingerprint methods and approaches integrating docking with similarity-based methods. In this article, we will describe the concepts behind each method and selected applications.

  18. Time-Accurate Local Time Stepping and High-Order Time CESE Methods for Multi-Dimensional Flows Using Unstructured Meshes

    NASA Technical Reports Server (NTRS)

    Chang, Chau-Lyan; Venkatachari, Balaji Shankar; Cheng, Gary

    2013-01-01

    With the wide availability of affordable multiple-core parallel supercomputers, next generation numerical simulations of flow physics are being focused on unsteady computations for problems involving multiple time scales and multiple physics. These simulations require higher solution accuracy than most algorithms and computational fluid dynamics codes currently available. This paper focuses on the developmental effort for high-fidelity multi-dimensional, unstructured-mesh flow solvers using the space-time conservation element, solution element (CESE) framework. Two approaches have been investigated in this research in order to provide high-accuracy, cross-cutting numerical simulations for a variety of flow regimes: 1) time-accurate local time stepping and 2) highorder CESE method. The first approach utilizes consistent numerical formulations in the space-time flux integration to preserve temporal conservation across the cells with different marching time steps. Such approach relieves the stringent time step constraint associated with the smallest time step in the computational domain while preserving temporal accuracy for all the cells. For flows involving multiple scales, both numerical accuracy and efficiency can be significantly enhanced. The second approach extends the current CESE solver to higher-order accuracy. Unlike other existing explicit high-order methods for unstructured meshes, the CESE framework maintains a CFL condition of one for arbitrarily high-order formulations while retaining the same compact stencil as its second-order counterpart. For large-scale unsteady computations, this feature substantially enhances numerical efficiency. Numerical formulations and validations using benchmark problems are discussed in this paper along with realistic examples.

  19. Sentinel nodes identified by computed tomography-lymphography accurately stage the axilla in patients with breast cancer

    PubMed Central

    2013-01-01

    Background Sentinel node biopsy often results in the identification and removal of multiple nodes as sentinel nodes, although most of these nodes could be non-sentinel nodes. This study investigated whether computed tomography-lymphography (CT-LG) can distinguish sentinel nodes from non-sentinel nodes and whether sentinel nodes identified by CT-LG can accurately stage the axilla in patients with breast cancer. Methods This study included 184 patients with breast cancer and clinically negative nodes. Contrast agent was injected interstitially. The location of sentinel nodes was marked on the skin surface using a CT laser light navigator system. Lymph nodes located just under the marks were first removed as sentinel nodes. Then, all dyed nodes or all hot nodes were removed. Results The mean number of sentinel nodes identified by CT-LG was significantly lower than that of dyed and/or hot nodes removed (1.1 vs 1.8, p <0.0001). Twenty-three (12.5%) patients had ≥2 sentinel nodes identified by CT-LG removed, whereas 94 (51.1%) of patients had ≥2 dyed and/or hot nodes removed (p <0.0001). Pathological evaluation demonstrated that 47 (25.5%) of 184 patients had metastasis to at least one node. All 47 patients demonstrated metastases to at least one of the sentinel nodes identified by CT-LG. Conclusions CT-LG can distinguish sentinel nodes from non-sentinel nodes, and sentinel nodes identified by CT-LG can accurately stage the axilla in patients with breast cancer. Successful identification of sentinel nodes using CT-LG may facilitate image-based diagnosis of metastasis, possibly leading to the omission of sentinel node biopsy. PMID:24321242

  20. Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

    NASA Astrophysics Data System (ADS)

    Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

    2018-04-01

    One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community

  1. Computational approaches to motor learning by imitation.

    PubMed Central

    Schaal, Stefan; Ijspeert, Auke; Billard, Aude

    2003-01-01

    Movement imitation requires a complex set of mechanisms that map an observed movement of a teacher onto one's own movement apparatus. Relevant problems include movement recognition, pose estimation, pose tracking, body correspondence, coordinate transformation from external to egocentric space, matching of observed against previously learned movement, resolution of redundant degrees-of-freedom that are unconstrained by the observation, suitable movement representations for imitation, modularization of motor control, etc. All of these topics by themselves are active research problems in computational and neurobiological sciences, such that their combination into a complete imitation system remains a daunting undertaking-indeed, one could argue that we need to understand the complete perception-action loop. As a strategy to untangle the complexity of imitation, this paper will examine imitation purely from a computational point of view, i.e. we will review statistical and mathematical approaches that have been suggested for tackling parts of the imitation problem, and discuss their merits, disadvantages and underlying principles. Given the focus on action recognition of other contributions in this special issue, this paper will primarily emphasize the motor side of imitation, assuming that a perceptual system has already identified important features of a demonstrated movement and created their corresponding spatial information. Based on the formalization of motor control in terms of control policies and their associated performance criteria, useful taxonomies of imitation learning can be generated that clarify different approaches and future research directions. PMID:12689379

  2. Time-Accurate Computations of Isolated Circular Synthetic Jets in Crossflow

    NASA Technical Reports Server (NTRS)

    Rumsey, C. L.; Schaeffler, N. W.; Milanovic, I. M.; Zaman, K. B. M. Q.

    2007-01-01

    Results from unsteady Reynolds-averaged Navier-Stokes computations are described for two different synthetic jet flows issuing into a turbulent boundary layer crossflow through a circular orifice. In one case the jet effect is mostly contained within the boundary layer, while in the other case the jet effect extends beyond the boundary layer edge. Both cases have momentum flux ratios less than 2. Several numerical parameters are investigated, and some lessons learned regarding the CFD methods for computing these types of flow fields are summarized. Results in both cases are compared to experiment.

  3. Accurate position estimation methods based on electrical impedance tomography measurements

    NASA Astrophysics Data System (ADS)

    Vergara, Samuel; Sbarbaro, Daniel; Johansen, T. A.

    2017-08-01

    than 0.05% of the tomograph radius value. These results demonstrate that the proposed approaches can estimate an object’s position accurately based on EIT measurements if enough process information is available for training or modelling. Since they do not require complex calculations it is possible to use them in real-time applications without requiring high-performance computers.

  4. High accurate time system of the Low Latitude Meridian Circle.

    NASA Astrophysics Data System (ADS)

    Yang, Jing; Wang, Feng; Li, Zhiming

    In order to obtain the high accurate time signal for the Low Latitude Meridian Circle (LLMC), a new GPS accurate time system is developed which include GPS, 1 MC frequency source and self-made clock system. The second signal of GPS is synchronously used in the clock system and information can be collected by a computer automatically. The difficulty of the cancellation of the time keeper can be overcomed by using this system.

  5. ceRNAs in plants: computational approaches and associated challenges for target mimic research.

    PubMed

    Paschoal, Alexandre Rossi; Lozada-Chávez, Irma; Domingues, Douglas Silva; Stadler, Peter F

    2017-05-30

    The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions. We divided this article in three main contributions. First, a general overview of research on TMs in plants is presented with practical descriptions of the available literature, tools, data, databases and computational reports. Second, we describe a common protocol for the computational and experimental analyses of TM. Third, we provide a bioinformatics approach for the prediction of TM motifs potentially cross-targeting both members within the same or from different miRNA families, based on the identification of consensus miRNA-binding sites from known TMs across sequenced genomes, transcriptomes and known miRNAs. This computational approach is promising because, in contrast to animals, miRNA families in plants are large with identical or similar members, several of which are also highly conserved. From the three consensus TM motifs found with our approach: MIM166, MIM171 and MIM159/319, the last one has found strong support on the recent experimental work by Reichel and Millar [Specificity of plant microRNA TMs: cross-targeting of mir159 and mir319. J Plant Physiol 2015;180:45-8]. Finally, we stress the discussion on the major computational and associated experimental challenges that have to be faced in future ceRNA studies. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. Targeted intervention: Computational approaches to elucidate and predict relapse in alcoholism.

    PubMed

    Heinz, Andreas; Deserno, Lorenz; Zimmermann, Ulrich S; Smolka, Michael N; Beck, Anne; Schlagenhauf, Florian

    2017-05-01

    Alcohol use disorder (AUD) and addiction in general is characterized by failures of choice resulting in repeated drug intake despite severe negative consequences. Behavioral change is hard to accomplish and relapse after detoxification is common and can be promoted by consumption of small amounts of alcohol as well as exposure to alcohol-associated cues or stress. While those environmental factors contributing to relapse have long been identified, the underlying psychological and neurobiological mechanism on which those factors act are to date incompletely understood. Based on the reinforcing effects of drugs of abuse, animal experiments showed that drug, cue and stress exposure affect Pavlovian and instrumental learning processes, which can increase salience of drug cues and promote habitual drug intake. In humans, computational approaches can help to quantify changes in key learning mechanisms during the development and maintenance of alcohol dependence, e.g. by using sequential decision making in combination with computational modeling to elucidate individual differences in model-free versus more complex, model-based learning strategies and their neurobiological correlates such as prediction error signaling in fronto-striatal circuits. Computational models can also help to explain how alcohol-associated cues trigger relapse: mechanisms such as Pavlovian-to-Instrumental Transfer can quantify to which degree Pavlovian conditioned stimuli can facilitate approach behavior including alcohol seeking and intake. By using generative models of behavioral and neural data, computational approaches can help to quantify individual differences in psychophysiological mechanisms that underlie the development and maintenance of AUD and thus promote targeted intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Computational neuroscience approach to biomarkers and treatments for mental disorders.

    PubMed

    Yahata, Noriaki; Kasai, Kiyoto; Kawato, Mitsuo

    2017-04-01

    Psychiatry research has long experienced a stagnation stemming from a lack of understanding of the neurobiological underpinnings of phenomenologically defined mental disorders. Recently, the application of computational neuroscience to psychiatry research has shown great promise in establishing a link between phenomenological and pathophysiological aspects of mental disorders, thereby recasting current nosology in more biologically meaningful dimensions. In this review, we highlight recent investigations into computational neuroscience that have undertaken either theory- or data-driven approaches to quantitatively delineate the mechanisms of mental disorders. The theory-driven approach, including reinforcement learning models, plays an integrative role in this process by enabling correspondence between behavior and disorder-specific alterations at multiple levels of brain organization, ranging from molecules to cells to circuits. Previous studies have explicated a plethora of defining symptoms of mental disorders, including anhedonia, inattention, and poor executive function. The data-driven approach, on the other hand, is an emerging field in computational neuroscience seeking to identify disorder-specific features among high-dimensional big data. Remarkably, various machine-learning techniques have been applied to neuroimaging data, and the extracted disorder-specific features have been used for automatic case-control classification. For many disorders, the reported accuracies have reached 90% or more. However, we note that rigorous tests on independent cohorts are critically required to translate this research into clinical applications. Finally, we discuss the utility of the disorder-specific features found by the data-driven approach to psychiatric therapies, including neurofeedback. Such developments will allow simultaneous diagnosis and treatment of mental disorders using neuroimaging, thereby establishing 'theranostics' for the first time in clinical

  8. Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma

    PubMed Central

    Sharma, Vivek; Salwan, Richa; Sharma, P. N.; Gulati, Arvind

    2017-01-01

    Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process. In biocontrol agents (BCAs), the molecular response at translational level may represents noise-like response of absolute transcript level and an adaptive response to physiological and pathological situations representing subset of mRNAs population actively translated in a cell. The molecular responses of biocontrol are complex and involve multistage regulation of number of genes. The use of high-throughput techniques has led to rapid increase in volume of transcriptomics data of Trichoderma. In general, almost half of the variations of transcriptome and protein level are due to translational control. Thus, studies are required to integrate raw information from different “omics” approaches for accurate depiction of translational response of BCAs in interaction with plants and plant pathogens. The studies on translational status of only active mRNAs bridging with proteome data will help in accurate characterization of only a subset of mRNAs actively engaged in translation. This review highlights the associated bottlenecks and use of state-of-the-art procedures in addressing the gap to accelerate future accomplishment of biocontrol mechanisms. PMID:28900417

  9. Precollege Computer Literacy: A Personal Computing Approach. Second Edition.

    ERIC Educational Resources Information Center

    Moursund, David

    Intended for elementary and secondary teachers and curriculum specialists, this booklet discusses and defines computer literacy as a functional knowledge of computers and their effects on students and the rest of society. It analyzes personal computing and the aspects of computers that have direct impact on students. Outlining computer-assisted…

  10. Dataflow computing approach in high-speed digital simulation

    NASA Technical Reports Server (NTRS)

    Ercegovac, M. D.; Karplus, W. J.

    1984-01-01

    New computational tools and methodologies for the digital simulation of continuous systems were explored. Programmability, and cost effective performance in multiprocessor organizations for real time simulation was investigated. Approach is based on functional style languages and data flow computing principles, which allow for the natural representation of parallelism in algorithms and provides a suitable basis for the design of cost effective high performance distributed systems. The objectives of this research are to: (1) perform comparative evaluation of several existing data flow languages and develop an experimental data flow language suitable for real time simulation using multiprocessor systems; (2) investigate the main issues that arise in the architecture and organization of data flow multiprocessors for real time simulation; and (3) develop and apply performance evaluation models in typical applications.

  11. Computational approaches to understand cardiac electrophysiology and arrhythmias

    PubMed Central

    Roberts, Byron N.; Yang, Pei-Chi; Behrens, Steven B.; Moreno, Jonathan D.

    2012-01-01

    Cardiac rhythms arise from electrical activity generated by precisely timed opening and closing of ion channels in individual cardiac myocytes. These impulses spread throughout the cardiac muscle to manifest as electrical waves in the whole heart. Regularity of electrical waves is critically important since they signal the heart muscle to contract, driving the primary function of the heart to act as a pump and deliver blood to the brain and vital organs. When electrical activity goes awry during a cardiac arrhythmia, the pump does not function, the brain does not receive oxygenated blood, and death ensues. For more than 50 years, mathematically based models of cardiac electrical activity have been used to improve understanding of basic mechanisms of normal and abnormal cardiac electrical function. Computer-based modeling approaches to understand cardiac activity are uniquely helpful because they allow for distillation of complex emergent behaviors into the key contributing components underlying them. Here we review the latest advances and novel concepts in the field as they relate to understanding the complex interplay between electrical, mechanical, structural, and genetic mechanisms during arrhythmia development at the level of ion channels, cells, and tissues. We also discuss the latest computational approaches to guiding arrhythmia therapy. PMID:22886409

  12. Computing camera heading: A study

    NASA Astrophysics Data System (ADS)

    Zhang, John Jiaxiang

    2000-08-01

    An accurate estimate of the motion of a camera is a crucial first step for the 3D reconstruction of sites, objects, and buildings from video. Solutions to the camera heading problem can be readily applied to many areas, such as robotic navigation, surgical operation, video special effects, multimedia, and lately even in internet commerce. From image sequences of a real world scene, the problem is to calculate the directions of the camera translations. The presence of rotations makes this problem very hard. This is because rotations and translations can have similar effects on the images, and are thus hard to tell apart. However, the visual angles between the projection rays of point pairs are unaffected by rotations, and their changes over time contain sufficient information to determine the direction of camera translation. We developed a new formulation of the visual angle disparity approach, first introduced by Tomasi, to the camera heading problem. Our new derivation makes theoretical analysis possible. Most notably, a theorem is obtained that locates all possible singularities of the residual function for the underlying optimization problem. This allows identifying all computation trouble spots beforehand, and to design reliable and accurate computational optimization methods. A bootstrap-jackknife resampling method simultaneously reduces complexity and tolerates outliers well. Experiments with image sequences show accurate results when compared with the true camera motion as measured with mechanical devices.

  13. Discovery and Development of ATP-Competitive mTOR Inhibitors Using Computational Approaches.

    PubMed

    Luo, Yao; Wang, Ling

    2017-11-16

    The mammalian target of rapamycin (mTOR) is a central controller of cell growth, proliferation, metabolism, and angiogenesis. This protein is an attractive target for new anticancer drug development. Significant progress has been made in hit discovery, lead optimization, drug candidate development and determination of the three-dimensional (3D) structure of mTOR. Computational methods have been applied to accelerate the discovery and development of mTOR inhibitors helping to model the structure of mTOR, screen compound databases, uncover structure-activity relationship (SAR) and optimize the hits, mine the privileged fragments and design focused libraries. Besides, computational approaches were also applied to study protein-ligand interactions mechanisms and in natural product-driven drug discovery. Herein, we survey the most recent progress on the application of computational approaches to advance the discovery and development of compounds targeting mTOR. Future directions in the discovery of new mTOR inhibitors using computational methods are also discussed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  14. An integrated computational tool for precipitation simulation

    NASA Astrophysics Data System (ADS)

    Cao, W.; Zhang, F.; Chen, S.-L.; Zhang, C.; Chang, Y. A.

    2011-07-01

    Computer aided materials design is of increasing interest because the conventional approach solely relying on experimentation is no longer viable within the constraint of available resources. Modeling of microstructure and mechanical properties during precipitation plays a critical role in understanding the behavior of materials and thus accelerating the development of materials. Nevertheless, an integrated computational tool coupling reliable thermodynamic calculation, kinetic simulation, and property prediction of multi-component systems for industrial applications is rarely available. In this regard, we are developing a software package, PanPrecipitation, under the framework of integrated computational materials engineering to simulate precipitation kinetics. It is seamlessly integrated with the thermodynamic calculation engine, PanEngine, to obtain accurate thermodynamic properties and atomic mobility data necessary for precipitation simulation.

  15. An alternative approach for computing seismic response with accidental eccentricity

    NASA Astrophysics Data System (ADS)

    Fan, Xuanhua; Yin, Jiacong; Sun, Shuli; Chen, Pu

    2014-09-01

    Accidental eccentricity is a non-standard assumption for seismic design of tall buildings. Taking it into consideration requires reanalysis of seismic resistance, which requires either time consuming computation of natural vibration of eccentric structures or finding a static displacement solution by applying an approximated equivalent torsional moment for each eccentric case. This study proposes an alternative modal response spectrum analysis (MRSA) approach to calculate seismic responses with accidental eccentricity. The proposed approach, called the Rayleigh Ritz Projection-MRSA (RRP-MRSA), is developed based on MRSA and two strategies: (a) a RRP method to obtain a fast calculation of approximate modes of eccentric structures; and (b) an approach to assemble mass matrices of eccentric structures. The efficiency of RRP-MRSA is tested via engineering examples and compared with the standard MRSA (ST-MRSA) and one approximate method, i.e., the equivalent torsional moment hybrid MRSA (ETM-MRSA). Numerical results show that RRP-MRSA not only achieves almost the same precision as ST-MRSA, and is much better than ETM-MRSA, but is also more economical. Thus, RRP-MRSA can be in place of current accidental eccentricity computations in seismic design.

  16. Spin density and orbital optimization in open shell systems: A rational and computationally efficient proposal

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Giner, Emmanuel, E-mail: gnrmnl@unife.it; Angeli, Celestino, E-mail: anc@unife.it

    2016-03-14

    The present work describes a new method to compute accurate spin densities for open shell systems. The proposed approach follows two steps: first, it provides molecular orbitals which correctly take into account the spin delocalization; second, a proper CI treatment allows to account for the spin polarization effect while keeping a restricted formalism and avoiding spin contamination. The main idea of the optimization procedure is based on the orbital relaxation of the various charge transfer determinants responsible for the spin delocalization. The algorithm is tested and compared to other existing methods on a series of organic and inorganic open shellmore » systems. The results reported here show that the new approach (almost black-box) provides accurate spin densities at a reasonable computational cost making it suitable for a systematic study of open shell systems.« less

  17. MRPack: Multi-Algorithm Execution Using Compute-Intensive Approach in MapReduce

    PubMed Central

    2015-01-01

    Large quantities of data have been generated from multiple sources at exponential rates in the last few years. These data are generated at high velocity as real time and streaming data in variety of formats. These characteristics give rise to challenges in its modeling, computation, and processing. Hadoop MapReduce (MR) is a well known data-intensive distributed processing framework using the distributed file system (DFS) for Big Data. Current implementations of MR only support execution of a single algorithm in the entire Hadoop cluster. In this paper, we propose MapReducePack (MRPack), a variation of MR that supports execution of a set of related algorithms in a single MR job. We exploit the computational capability of a cluster by increasing the compute-intensiveness of MapReduce while maintaining its data-intensive approach. It uses the available computing resources by dynamically managing the task assignment and intermediate data. Intermediate data from multiple algorithms are managed using multi-key and skew mitigation strategies. The performance study of the proposed system shows that it is time, I/O, and memory efficient compared to the default MapReduce. The proposed approach reduces the execution time by 200% with an approximate 50% decrease in I/O cost. Complexity and qualitative results analysis shows significant performance improvement. PMID:26305223

  18. MRPack: Multi-Algorithm Execution Using Compute-Intensive Approach in MapReduce.

    PubMed

    Idris, Muhammad; Hussain, Shujaat; Siddiqi, Muhammad Hameed; Hassan, Waseem; Syed Muhammad Bilal, Hafiz; Lee, Sungyoung

    2015-01-01

    Large quantities of data have been generated from multiple sources at exponential rates in the last few years. These data are generated at high velocity as real time and streaming data in variety of formats. These characteristics give rise to challenges in its modeling, computation, and processing. Hadoop MapReduce (MR) is a well known data-intensive distributed processing framework using the distributed file system (DFS) for Big Data. Current implementations of MR only support execution of a single algorithm in the entire Hadoop cluster. In this paper, we propose MapReducePack (MRPack), a variation of MR that supports execution of a set of related algorithms in a single MR job. We exploit the computational capability of a cluster by increasing the compute-intensiveness of MapReduce while maintaining its data-intensive approach. It uses the available computing resources by dynamically managing the task assignment and intermediate data. Intermediate data from multiple algorithms are managed using multi-key and skew mitigation strategies. The performance study of the proposed system shows that it is time, I/O, and memory efficient compared to the default MapReduce. The proposed approach reduces the execution time by 200% with an approximate 50% decrease in I/O cost. Complexity and qualitative results analysis shows significant performance improvement.

  19. Model Reduction of Computational Aerothermodynamics for Multi-Discipline Analysis in High Speed Flows

    NASA Astrophysics Data System (ADS)

    Crowell, Andrew Rippetoe

    This dissertation describes model reduction techniques for the computation of aerodynamic heat flux and pressure loads for multi-disciplinary analysis of hypersonic vehicles. NASA and the Department of Defense have expressed renewed interest in the development of responsive, reusable hypersonic cruise vehicles capable of sustained high-speed flight and access to space. However, an extensive set of technical challenges have obstructed the development of such vehicles. These technical challenges are partially due to both the inability to accurately test scaled vehicles in wind tunnels and to the time intensive nature of high-fidelity computational modeling, particularly for the fluid using Computational Fluid Dynamics (CFD). The aim of this dissertation is to develop efficient and accurate models for the aerodynamic heat flux and pressure loads to replace the need for computationally expensive, high-fidelity CFD during coupled analysis. Furthermore, aerodynamic heating and pressure loads are systematically evaluated for a number of different operating conditions, including: simple two-dimensional flow over flat surfaces up to three-dimensional flows over deformed surfaces with shock-shock interaction and shock-boundary layer interaction. An additional focus of this dissertation is on the implementation and computation of results using the developed aerodynamic heating and pressure models in complex fluid-thermal-structural simulations. Model reduction is achieved using a two-pronged approach. One prong focuses on developing analytical corrections to isothermal, steady-state CFD flow solutions in order to capture flow effects associated with transient spatially-varying surface temperatures and surface pressures (e.g., surface deformation, surface vibration, shock impingements, etc.). The second prong is focused on minimizing the computational expense of computing the steady-state CFD solutions by developing an efficient surrogate CFD model. The developed two

  20. One approach for evaluating the Distributed Computing Design System (DCDS)

    NASA Technical Reports Server (NTRS)

    Ellis, J. T.

    1985-01-01

    The Distributed Computer Design System (DCDS) provides an integrated environment to support the life cycle of developing real-time distributed computing systems. The primary focus of DCDS is to significantly increase system reliability and software development productivity, and to minimize schedule and cost risk. DCDS consists of integrated methodologies, languages, and tools to support the life cycle of developing distributed software and systems. Smooth and well-defined transistions from phase to phase, language to language, and tool to tool provide a unique and unified environment. An approach to evaluating DCDS highlights its benefits.

  1. X-ray solution scattering combined with computation characterizing protein folds and multiple conformational states : computation and application.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, S.; Park, S.; Makowski, L.

    Small angle X-ray scattering (SAXS) is an increasingly powerful technique to characterize the structure of biomolecules in solution. We present a computational method for accurately and efficiently computing the solution scattering curve from a protein with dynamical fluctuations. The method is built upon a coarse-grained (CG) representation of the protein. This CG approach takes advantage of the low-resolution character of solution scattering. It allows rapid determination of the scattering pattern from conformations extracted from CG simulations to obtain scattering characterization of the protein conformational landscapes. Important elements incorporated in the method include an effective residue-based structure factor for each aminomore » acid, an explicit treatment of the hydration layer at the surface of the protein, and an ensemble average of scattering from all accessible conformations to account for macromolecular flexibility. The CG model is calibrated and illustrated to accurately reproduce the experimental scattering curve of Hen egg white lysozyme. We then illustrate the computational method by calculating the solution scattering pattern of several representative protein folds and multiple conformational states. The results suggest that solution scattering data, when combined with a reliable computational method, have great potential for a better structural description of multi-domain complexes in different functional states, and for recognizing structural folds when sequence similarity to a protein of known structure is low. Possible applications of the method are discussed.« less

  2. A Research Roadmap for Computation-Based Human Reliability Analysis

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Boring, Ronald; Mandelli, Diego; Joe, Jeffrey

    2015-08-01

    The United States (U.S.) Department of Energy (DOE) is sponsoring research through the Light Water Reactor Sustainability (LWRS) program to extend the life of the currently operating fleet of commercial nuclear power plants. The Risk Informed Safety Margin Characterization (RISMC) research pathway within LWRS looks at ways to maintain and improve the safety margins of these plants. The RISMC pathway includes significant developments in the area of thermalhydraulics code modeling and the development of tools to facilitate dynamic probabilistic risk assessment (PRA). PRA is primarily concerned with the risk of hardware systems at the plant; yet, hardware reliability is oftenmore » secondary in overall risk significance to human errors that can trigger or compound undesirable events at the plant. This report highlights ongoing efforts to develop a computation-based approach to human reliability analysis (HRA). This computation-based approach differs from existing static and dynamic HRA approaches in that it: (i) interfaces with a dynamic computation engine that includes a full scope plant model, and (ii) interfaces with a PRA software toolset. The computation-based HRA approach presented in this report is called the Human Unimodels for Nuclear Technology to Enhance Reliability (HUNTER) and incorporates in a hybrid fashion elements of existing HRA methods to interface with new computational tools developed under the RISMC pathway. The goal of this research effort is to model human performance more accurately than existing approaches, thereby minimizing modeling uncertainty found in current plant risk models.« less

  3. Rayleigh Scattering in Planetary Atmospheres: Corrected Tables Through Accurate Computation of X and Y Functions

    NASA Astrophysics Data System (ADS)

    Natraj, Vijay; Li, King-Fai; Yung, Yuk L.

    2009-02-01

    Tables that have been used as a reference for nearly 50 years for the intensity and polarization of reflected and transmitted light in Rayleigh scattering atmospheres have been found to be inaccurate, even to four decimal places. We convert the integral equations describing the X and Y functions into a pair of coupled integro-differential equations that can be efficiently solved numerically. Special care has been taken in evaluating Cauchy principal value integrals and their derivatives that appear in the solution of the Rayleigh scattering problem. The new approach gives results accurate to eight decimal places for the entire range of tabulation (optical thicknesses 0.02-1.0, surface reflectances 0-0.8, solar and viewing zenith angles 0°-88.85°, and relative azimuth angles 0°-180°), including the most difficult case of direct transmission in the direction of the sun. Revised tables have been created and stored electronically for easy reference by the planetary science and astrophysics community.

  4. A Computational Approach to Estimate Interorgan Metabolic Transport in a Mammal

    PubMed Central

    Cui, Xiao; Geffers, Lars; Eichele, Gregor; Yan, Jun

    2014-01-01

    In multicellular organisms metabolism is distributed across different organs, each of which has specific requirements to perform its own specialized task. But different organs also have to support the metabolic homeostasis of the organism as a whole by interorgan metabolite transport. Recent studies have successfully reconstructed global metabolic networks in tissues and cell types and attempts have been made to connect organs with interorgan metabolite transport. Instead of these complicated approaches to reconstruct global metabolic networks, we proposed in this study a novel approach to study interorgan metabolite transport focusing on transport processes mediated by solute carrier (Slc) transporters and their couplings to cognate enzymatic reactions. We developed a computational approach to identify and score potential interorgan metabolite transports based on the integration of metabolism and transports in different organs in the adult mouse from quantitative gene expression data. This allowed us to computationally estimate the connectivity between 17 mouse organs via metabolite transport. Finally, by applying our method to circadian metabolism, we showed that our approach can shed new light on the current understanding of interorgan metabolite transport at a whole-body level in mammals. PMID:24971892

  5. Sonographically guided posteromedial approach for intra-articular knee injections: a safe, accurate, and efficient method.

    PubMed

    Tresley, Jonathan; Jose, Jean

    2015-04-01

    Osteoarthritis of the knee can be a debilitating and extremely painful condition. In patients who desire to postpone knee arthroplasty or in those who are not surgical candidates, percutaneous knee injection therapies have the potential to reduce pain and swelling, maintain joint mobility, and minimize disability. Published studies cite poor accuracy of intra-articular knee joint injections without imaging guidance. We present a sonographically guided posteromedial approach to intra-articular knee joint injections with 100% accuracy and no complications in a consecutive series of 67 patients undergoing subsequent computed tomographic or magnetic resonance arthrography. Although many other standard approaches are available, a posteromedial intra-articular technique is particularly useful in patients with a large body habitus and theoretically allows for simultaneous aspiration of Baker cysts with a single sterile preparation and without changing the patient's position. The posteromedial technique described in this paper is not compared or deemed superior to other standard approaches but, rather, is presented as a potentially safe and efficient alternative. © 2015 by the American Institute of Ultrasound in Medicine.

  6. Whole-genome CNV analysis: advances in computational approaches.

    PubMed

    Pirooznia, Mehdi; Goes, Fernando S; Zandi, Peter P

    2015-01-01

    Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a significant contribution to human diversity and also play an important role in disease susceptibility. Recent advances in genome sequencing technologies have enabled the characterization of a variety of genomic features, including CNVs. This has led to the development of several bioinformatics approaches to detect CNVs from next-generation sequencing data. Here, we review recent advances in CNV detection from whole genome sequencing. We discuss the informatics approaches and current computational tools that have been developed as well as their strengths and limitations. This review will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development.

  7. Variational mode decomposition based approach for accurate classification of color fundus images with hemorrhages

    NASA Astrophysics Data System (ADS)

    Lahmiri, Salim; Shmuel, Amir

    2017-11-01

    Diabetic retinopathy is a disease that can cause a loss of vision. An early and accurate diagnosis helps to improve treatment of the disease and prognosis. One of the earliest characteristics of diabetic retinopathy is the appearance of retinal hemorrhages. The purpose of this study is to design a fully automated system for the detection of hemorrhages in a retinal image. In the first stage of our proposed system, a retinal image is processed with variational mode decomposition (VMD) to obtain the first variational mode, which captures the high frequency components of the original image. In the second stage, four texture descriptors are extracted from the first variational mode. Finally, a classifier trained with all computed texture descriptors is used to distinguish between images of healthy and unhealthy retinas with hemorrhages. Experimental results showed evidence of the effectiveness of the proposed system for detection of hemorrhages in the retina, since a perfect detection rate was achieved. Our proposed system for detecting diabetic retinopathy is simple and easy to implement. It requires only short processing time, and it yields higher accuracy in comparison with previously proposed methods for detecting diabetic retinopathy.

  8. Second-order accurate nonoscillatory schemes for scalar conservation laws

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1989-01-01

    Explicit finite difference schemes for the computation of weak solutions of nonlinear scalar conservation laws is presented and analyzed. These schemes are uniformly second-order accurate and nonoscillatory in the sense that the number of extrema of the discrete solution is not increasing in time.

  9. Computational Approach to Musical Consonance and Dissonance

    PubMed Central

    Trulla, Lluis L.; Di Stefano, Nicola; Giuliani, Alessandro

    2018-01-01

    In sixth century BC, Pythagoras discovered the mathematical foundation of musical consonance and dissonance. When auditory frequencies in small-integer ratios are combined, the result is a harmonious perception. In contrast, most frequency combinations result in audible, off-centered by-products labeled “beating” or “roughness;” these are reported by most listeners to sound dissonant. In this paper, we consider second-order beats, a kind of beating recognized as a product of neural processing, and demonstrate that the data-driven approach of Recurrence Quantification Analysis (RQA) allows for the reconstruction of the order in which interval ratios are ranked in music theory and harmony. We take advantage of computer-generated sounds containing all intervals over the span of an octave. To visualize second-order beats, we use a glissando from the unison to the octave. This procedure produces a profile of recurrence values that correspond to subsequent epochs along the original signal. We find that the higher recurrence peaks exactly match the epochs corresponding to just intonation frequency ratios. This result indicates a link between consonance and the dynamical features of the signal. Our findings integrate a new element into the existing theoretical models of consonance, thus providing a computational account of consonance in terms of dynamical systems theory. Finally, as it considers general features of acoustic signals, the present approach demonstrates a universal aspect of consonance and dissonance perception and provides a simple mathematical tool that could serve as a common framework for further neuro-psychological and music theory research. PMID:29670552

  10. Nuclear-relaxed elastic and piezoelectric constants of materials: Computational aspects of two quantum-mechanical approaches.

    PubMed

    Erba, Alessandro; Caglioti, Dominique; Zicovich-Wilson, Claudio Marcelo; Dovesi, Roberto

    2017-02-15

    Two alternative approaches for the quantum-mechanical calculation of the nuclear-relaxation term of elastic and piezoelectric tensors of crystalline materials are illustrated and their computational aspects discussed: (i) a numerical approach based on the geometry optimization of atomic positions at strained lattice configurations and (ii) a quasi-analytical approach based on the evaluation of the force- and displacement-response internal-strain tensors as combined with the interatomic force-constant matrix. The two schemes are compared both as regards their computational accuracy and performance. The latter approach, not being affected by the many numerical parameters and procedures of a typical quasi-Newton geometry optimizer, constitutes a more reliable and robust mean to the evaluation of such properties, at a reduced computational cost for most crystalline systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  11. A computational approach to negative priming

    NASA Astrophysics Data System (ADS)

    Schrobsdorff, H.; Ihrke, M.; Kabisch, B.; Behrendt, J.; Hasselhorn, M.; Herrmann, J. Michael

    2007-09-01

    Priming is characterized by a sensitivity of reaction times to the sequence of stimuli in psychophysical experiments. The reduction of the reaction time observed in positive priming is well-known and experimentally understood (Scarborough et al., J. Exp. Psycholol: Hum. Percept. Perform., 3, pp. 1-17, 1977). Negative priming—the opposite effect—is experimentally less tangible (Fox, Psychonom. Bull. Rev., 2, pp. 145-173, 1995). The dependence on subtle parameter changes (such as response-stimulus interval) usually varies. The sensitivity of the negative priming effect bears great potential for applications in research in fields such as memory, selective attention, and ageing effects. We develop and analyse a computational realization, CISAM, of a recent psychological model for action decision making, the ISAM (Kabisch, PhD thesis, Friedrich-Schiller-Universitat, 2003), which is sensitive to priming conditions. With the dynamical systems approach of the CISAM, we show that a single adaptive threshold mechanism is sufficient to explain both positive and negative priming effects. This is achieved by comparing results obtained by the computational modelling with experimental data from our laboratory. The implementation provides a rich base from which testable predictions can be derived, e.g. with respect to hitherto untested stimulus combinations (e.g. single-object trials).

  12. An Improved Treatment of External Boundary for Three-Dimensional Flow Computations

    NASA Technical Reports Server (NTRS)

    Tsynkov, Semyon V.; Vatsa, Veer N.

    1997-01-01

    We present an innovative numerical approach for setting highly accurate nonlocal boundary conditions at the external computational boundaries when calculating three-dimensional compressible viscous flows over finite bodies. The approach is based on application of the difference potentials method by V. S. Ryaben'kii and extends our previous technique developed for the two-dimensional case. The new boundary conditions methodology has been successfully combined with the NASA-developed code TLNS3D and used for the analysis of wing-shaped configurations in subsonic and transonic flow regimes. As demonstrated by the computational experiments, the improved external boundary conditions allow one to greatly reduce the size of the computational domain while still maintaining high accuracy of the numerical solution. Moreover, they may provide for a noticeable speedup of convergence of the multigrid iterations.

  13. Accurate computational design of multipass transmembrane proteins.

    PubMed

    Lu, Peilong; Min, Duyoung; DiMaio, Frank; Wei, Kathy Y; Vahey, Michael D; Boyken, Scott E; Chen, Zibo; Fallas, Jorge A; Ueda, George; Sheffler, William; Mulligan, Vikram Khipple; Xu, Wenqing; Bowie, James U; Baker, David

    2018-03-02

    The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer-a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices-are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  14. Development and Validation of a Multidisciplinary Tool for Accurate and Efficient Rotorcraft Noise Prediction (MUTE)

    NASA Technical Reports Server (NTRS)

    Liu, Yi; Anusonti-Inthra, Phuriwat; Diskin, Boris

    2011-01-01

    A physics-based, systematically coupled, multidisciplinary prediction tool (MUTE) for rotorcraft noise was developed and validated with a wide range of flight configurations and conditions. MUTE is an aggregation of multidisciplinary computational tools that accurately and efficiently model the physics of the source of rotorcraft noise, and predict the noise at far-field observer locations. It uses systematic coupling approaches among multiple disciplines including Computational Fluid Dynamics (CFD), Computational Structural Dynamics (CSD), and high fidelity acoustics. Within MUTE, advanced high-order CFD tools are used around the rotor blade to predict the transonic flow (shock wave) effects, which generate the high-speed impulsive noise. Predictions of the blade-vortex interaction noise in low speed flight are also improved by using the Particle Vortex Transport Method (PVTM), which preserves the wake flow details required for blade/wake and fuselage/wake interactions. The accuracy of the source noise prediction is further improved by utilizing a coupling approach between CFD and CSD, so that the effects of key structural dynamics, elastic blade deformations, and trim solutions are correctly represented in the analysis. The blade loading information and/or the flow field parameters around the rotor blade predicted by the CFD/CSD coupling approach are used to predict the acoustic signatures at far-field observer locations with a high-fidelity noise propagation code (WOPWOP3). The predicted results from the MUTE tool for rotor blade aerodynamic loading and far-field acoustic signatures are compared and validated with a variation of experimental data sets, such as UH60-A data, DNW test data and HART II test data.

  15. Uncertainty Aware Structural Topology Optimization Via a Stochastic Reduced Order Model Approach

    NASA Technical Reports Server (NTRS)

    Aguilo, Miguel A.; Warner, James E.

    2017-01-01

    This work presents a stochastic reduced order modeling strategy for the quantification and propagation of uncertainties in topology optimization. Uncertainty aware optimization problems can be computationally complex due to the substantial number of model evaluations that are necessary to accurately quantify and propagate uncertainties. This computational complexity is greatly magnified if a high-fidelity, physics-based numerical model is used for the topology optimization calculations. Stochastic reduced order model (SROM) methods are applied here to effectively 1) alleviate the prohibitive computational cost associated with an uncertainty aware topology optimization problem; and 2) quantify and propagate the inherent uncertainties due to design imperfections. A generic SROM framework that transforms the uncertainty aware, stochastic topology optimization problem into a deterministic optimization problem that relies only on independent calls to a deterministic numerical model is presented. This approach facilitates the use of existing optimization and modeling tools to accurately solve the uncertainty aware topology optimization problems in a fraction of the computational demand required by Monte Carlo methods. Finally, an example in structural topology optimization is presented to demonstrate the effectiveness of the proposed uncertainty aware structural topology optimization approach.

  16. Superpixel-based graph cuts for accurate stereo matching

    NASA Astrophysics Data System (ADS)

    Feng, Liting; Qin, Kaihuai

    2017-06-01

    Estimating the surface normal vector and disparity of a pixel simultaneously, also known as three-dimensional label method, has been widely used in recent continuous stereo matching problem to achieve sub-pixel accuracy. However, due to the infinite label space, it’s extremely hard to assign each pixel an appropriate label. In this paper, we present an accurate and efficient algorithm, integrating patchmatch with graph cuts, to approach this critical computational problem. Besides, to get robust and precise matching cost, we use a convolutional neural network to learn a similarity measure on small image patches. Compared with other MRF related methods, our method has several advantages: its sub-modular property ensures a sub-problem optimality which is easy to perform in parallel; graph cuts can simultaneously update multiple pixels, avoiding local minima caused by sequential optimizers like belief propagation; it uses segmentation results for better local expansion move; local propagation and randomization can easily generate the initial solution without using external methods. Middlebury experiments show that our method can get higher accuracy than other MRF-based algorithms.

  17. Computational modeling of human oral bioavailability: what will be next?

    PubMed

    Cabrera-Pérez, Miguel Ángel; Pham-The, Hai

    2018-06-01

    The oral route is the most convenient way of administrating drugs. Therefore, accurate determination of oral bioavailability is paramount during drug discovery and development. Quantitative structure-property relationship (QSPR), rule-of-thumb (RoT) and physiologically based-pharmacokinetic (PBPK) approaches are promising alternatives to the early oral bioavailability prediction. Areas covered: The authors give insight into the factors affecting bioavailability, the fundamental theoretical framework and the practical aspects of computational methods for predicting this property. They also give their perspectives on future computational models for estimating oral bioavailability. Expert opinion: Oral bioavailability is a multi-factorial pharmacokinetic property with its accurate prediction challenging. For RoT and QSPR modeling, the reliability of datasets, the significance of molecular descriptor families and the diversity of chemometric tools used are important factors that define model predictability and interpretability. Likewise, for PBPK modeling the integrity of the pharmacokinetic data, the number of input parameters, the complexity of statistical analysis and the software packages used are relevant factors in bioavailability prediction. Although these approaches have been utilized independently, the tendency to use hybrid QSPR-PBPK approaches together with the exploration of ensemble and deep-learning systems for QSPR modeling of oral bioavailability has opened new avenues for development promising tools for oral bioavailability prediction.

  18. Comparison of Computational Approaches for Rapid Aerodynamic Assessment of Small UAVs

    NASA Technical Reports Server (NTRS)

    Shafer, Theresa C.; Lynch, C. Eric; Viken, Sally A.; Favaregh, Noah; Zeune, Cale; Williams, Nathan; Dansie, Jonathan

    2014-01-01

    Computational Fluid Dynamic (CFD) methods were used to determine the basic aerodynamic, performance, and stability and control characteristics of the unmanned air vehicle (UAV), Kahu. Accurate and timely prediction of the aerodynamic characteristics of small UAVs is an essential part of military system acquisition and air-worthiness evaluations. The forces and moments of the UAV were predicted using a variety of analytical methods for a range of configurations and conditions. The methods included Navier Stokes (N-S) flow solvers (USM3D, Kestrel and Cobalt) that take days to set up and hours to converge on a single solution; potential flow methods (PMARC, LSAERO, and XFLR5) that take hours to set up and minutes to compute; empirical methods (Datcom) that involve table lookups and produce a solution quickly; and handbook calculations. A preliminary aerodynamic database can be developed very efficiently by using a combination of computational tools. The database can be generated with low-order and empirical methods in linear regions, then replacing or adjusting the data as predictions from higher order methods are obtained. A comparison of results from all the data sources as well as experimental data obtained from a wind-tunnel test will be shown and the methods will be evaluated on their utility during each portion of the flight envelope.

  19. Generic approach to access barriers in dehydrogenation reactions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

    The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

  20. Generic approach to access barriers in dehydrogenation reactions

    DOE PAGES

    Yu, Liang; Vilella, Laia; Abild-Pedersen, Frank

    2018-03-08

    The introduction of linear energy correlations, which explicitly relate adsorption energies of reaction intermediates and activation energies in heterogeneous catalysis, has proven to be a key component in the computational search for new and promising catalysts. A simple linear approach to estimate activation energies still requires a significant computational effort. To simplify this process and at the same time incorporate the need for enhanced complexity of reaction intermediates, we generalize a recently proposed approach that evaluates transition state energies based entirely on bond-order conservation arguments. Here, we show that similar variation of the local electronic structure along the reaction coordinatemore » introduces a set of general functions that accurately defines the transition state energy and are transferable to other reactions with similar bonding nature. With such an approach, more complex reaction intermediates can be targeted with an insignificant increase in computational effort and without loss of accuracy.« less

  1. Novel density functional methodology for the computation of accurate electronic and thermodynamic properties of molecular systems and improved long-range behavior

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kafafi, S.A.

    1998-12-10

    A novel general purpose density functional methodology for the computation of accurate electronic and thermodynamic properties of molecules and improved long-range behavior is reported. Assuming the separability of the exchange (E{sub x}) and correlation (E{sub c}) contributions to the total exchange-correlation energy functional (E{sub xc}), the E{sub x} term consists of a hybrid mixture of 37.5% Hartree-Fock exchange and the appropriate local spin density exchange using the adiabatic connection formula. He demonstrated that E{sub x} and its corresponding potential V{sub x} [=dE{sub x}/d{rho}(r)] have the proper asymptotic limits at r = 0 and r {r_arrow} {infinity}, E{sub c} consists ofmore » the Vosko, Wilk, and Nusair formula for the free-electron gas correlation energy and a generalized gradient approximation term with one adjustable parameter. V{sub c} [=dE{sub c}/d{rho}(r)] was shown to obey the r {r_arrow} {infinity} limit of the corresponding potential derived from exact atomic exchange-correlation computations; namely, V{sub c} is proportional to r{sup {minus}4}. Most importantly, he demonstrated that, at r values where dispersion forces are operating, V{sub c} is proportional to 1/r{sup n} (n = 4, 6, 8, {hor_ellipsis}). The reported method was denoted by K2-BVWN because it used two adjustable parameters in its formulation. The K2-BVWN scheme scales as N{sup 3}, where N is the number of basis functions, compared to {approximately}N{sup 7} for Gaussian-2 (G2) ab initio theory and related methods, {approximately}N{sup 5} for Barone`s mPW1,3PW, and {approximately}N{sup 4} for Becke`s three-parameter density functional approaches. The G2 data set complemented by the reported molecular systems investigated in this work was recommended as a critical test for evaluating novel ab initio and density functional methodologies. The K2-BVWN method has been implemented in the Gaussian series of programs.« less

  2. Cartesian Off-Body Grid Adaption for Viscous Time- Accurate Flow Simulation

    NASA Technical Reports Server (NTRS)

    Buning, Pieter G.; Pulliam, Thomas H.

    2011-01-01

    An improved solution adaption capability has been implemented in the OVERFLOW overset grid CFD code. Building on the Cartesian off-body approach inherent in OVERFLOW and the original adaptive refinement method developed by Meakin, the new scheme provides for automated creation of multiple levels of finer Cartesian grids. Refinement can be based on the undivided second-difference of the flow solution variables, or on a specific flow quantity such as vorticity. Coupled with load-balancing and an inmemory solution interpolation procedure, the adaption process provides very good performance for time-accurate simulations on parallel compute platforms. A method of using refined, thin body-fitted grids combined with adaption in the off-body grids is presented, which maximizes the part of the domain subject to adaption. Two- and three-dimensional examples are used to illustrate the effectiveness and performance of the adaption scheme.

  3. Interactions of spatial strategies producing generalization gradient and blocking: A computational approach

    PubMed Central

    Dollé, Laurent; Chavarriaga, Ricardo

    2018-01-01

    We present a computational model of spatial navigation comprising different learning mechanisms in mammals, i.e., associative, cognitive mapping and parallel systems. This model is able to reproduce a large number of experimental results in different variants of the Morris water maze task, including standard associative phenomena (spatial generalization gradient and blocking), as well as navigation based on cognitive mapping. Furthermore, we show that competitive and cooperative patterns between different navigation strategies in the model allow to explain previous apparently contradictory results supporting either associative or cognitive mechanisms for spatial learning. The key computational mechanism to reconcile experimental results showing different influences of distal and proximal cues on the behavior, different learning times, and different abilities of individuals to alternatively perform spatial and response strategies, relies in the dynamic coordination of navigation strategies, whose performance is evaluated online with a common currency through a modular approach. We provide a set of concrete experimental predictions to further test the computational model. Overall, this computational work sheds new light on inter-individual differences in navigation learning, and provides a formal and mechanistic approach to test various theories of spatial cognition in mammals. PMID:29630600

  4. Fast and accurate quantum molecular dynamics of dense plasmas across temperature regimes

    DOE PAGES

    Sjostrom, Travis; Daligault, Jerome

    2014-10-10

    Here, we develop and implement a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation of density functional theory. The results for hydrogen and aluminum are in very good agreement with Kohn-Sham (orbital-based) density functional theory and path integral Monte Carlo calculations for microscopic features such as the electron density as well as the equation of state. The present approach does not scale with temperature and hence extends to higher temperatures than is accessible in the Kohn-Sham method and lowermore » temperatures than is accessible by path integral Monte Carlo calculations, while being significantly less computationally expensive than either of those two methods.« less

  5. Ab initio approaches for the determination of heavy element energetics: Ionization energies of trivalent lanthanides (Ln = La-Eu)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peterson, Charles; Penchoff, Deborah A.; Wilson, Angela K., E-mail: wilson@chemistry.msu.edu

    2015-11-21

    An effective approach for the determination of lanthanide energetics, as demonstrated by application to the third ionization energy (in the gas phase) for the first half of the lanthanide series, has been developed. This approach uses a combination of highly correlated and fully relativistic ab initio methods to accurately describe the electronic structure of heavy elements. Both scalar and fully relativistic methods are used to achieve an approach that is both computationally feasible and accurate. The impact of basis set choice and the number of electrons included in the correlation space has also been examined.

  6. A fourth order accurate finite difference scheme for the computation of elastic waves

    NASA Technical Reports Server (NTRS)

    Bayliss, A.; Jordan, K. E.; Lemesurier, B. J.; Turkel, E.

    1986-01-01

    A finite difference for elastic waves is introduced. The model is based on the first order system of equations for the velocities and stresses. The differencing is fourth order accurate on the spatial derivatives and second order accurate in time. The model is tested on a series of examples including the Lamb problem, scattering from plane interf aces and scattering from a fluid-elastic interface. The scheme is shown to be effective for these problems. The accuracy and stability is insensitive to the Poisson ratio. For the class of problems considered here it is found that the fourth order scheme requires for two-thirds to one-half the resolution of a typical second order scheme to give comparable accuracy.

  7. Flexible Approximation Model Approach for Bi-Level Integrated System Synthesis

    NASA Technical Reports Server (NTRS)

    Sobieszczanski-Sobieski, Jaroslaw; Kim, Hongman; Ragon, Scott; Soremekun, Grant; Malone, Brett

    2004-01-01

    Bi-Level Integrated System Synthesis (BLISS) is an approach that allows design problems to be naturally decomposed into a set of subsystem optimizations and a single system optimization. In the BLISS approach, approximate mathematical models are used to transfer information from the subsystem optimizations to the system optimization. Accurate approximation models are therefore critical to the success of the BLISS procedure. In this paper, new capabilities that are being developed to generate accurate approximation models for BLISS procedure will be described. The benefits of using flexible approximation models such as Kriging will be demonstrated in terms of convergence characteristics and computational cost. An approach of dealing with cases where subsystem optimization cannot find a feasible design will be investigated by using the new flexible approximation models for the violated local constraints.

  8. Time-Accurate Solutions of Incompressible Navier-Stokes Equations for Potential Turbopump Applications

    NASA Technical Reports Server (NTRS)

    Kiris, Cetin; Kwak, Dochan

    2001-01-01

    Two numerical procedures, one based on artificial compressibility method and the other pressure projection method, are outlined for obtaining time-accurate solutions of the incompressible Navier-Stokes equations. The performance of the two method are compared by obtaining unsteady solutions for the evolution of twin vortices behind a at plate. Calculated results are compared with experimental and other numerical results. For an un- steady ow which requires small physical time step, pressure projection method was found to be computationally efficient since it does not require any subiterations procedure. It was observed that the artificial compressibility method requires a fast convergence scheme at each physical time step in order to satisfy incompressibility condition. This was obtained by using a GMRES-ILU(0) solver in our computations. When a line-relaxation scheme was used, the time accuracy was degraded and time-accurate computations became very expensive.

  9. An optimization-based approach for high-order accurate discretization of conservation laws with discontinuous solutions

    NASA Astrophysics Data System (ADS)

    Zahr, M. J.; Persson, P.-O.

    2018-07-01

    This work introduces a novel discontinuity-tracking framework for resolving discontinuous solutions of conservation laws with high-order numerical discretizations that support inter-element solution discontinuities, such as discontinuous Galerkin or finite volume methods. The proposed method aims to align inter-element boundaries with discontinuities in the solution by deforming the computational mesh. A discontinuity-aligned mesh ensures the discontinuity is represented through inter-element jumps while smooth basis functions interior to elements are only used to approximate smooth regions of the solution, thereby avoiding Gibbs' phenomena that create well-known stability issues. Therefore, very coarse high-order discretizations accurately resolve the piecewise smooth solution throughout the domain, provided the discontinuity is tracked. Central to the proposed discontinuity-tracking framework is a discrete PDE-constrained optimization formulation that simultaneously aligns the computational mesh with discontinuities in the solution and solves the discretized conservation law on this mesh. The optimization objective is taken as a combination of the deviation of the finite-dimensional solution from its element-wise average and a mesh distortion metric to simultaneously penalize Gibbs' phenomena and distorted meshes. It will be shown that our objective function satisfies two critical properties that are required for this discontinuity-tracking framework to be practical: (1) possesses a local minima at a discontinuity-aligned mesh and (2) decreases monotonically to this minimum in a neighborhood of radius approximately h / 2, whereas other popular discontinuity indicators fail to satisfy the latter. Another important contribution of this work is the observation that traditional reduced space PDE-constrained optimization solvers that repeatedly solve the conservation law at various mesh configurations are not viable in this context since severe overshoot and

  10. New Approaches to the Computer Simulation of Amorphous Alloys: A Review.

    PubMed

    Valladares, Ariel A; Díaz-Celaya, Juan A; Galván-Colín, Jonathan; Mejía-Mendoza, Luis M; Reyes-Retana, José A; Valladares, Renela M; Valladares, Alexander; Alvarez-Ramirez, Fernando; Qu, Dongdong; Shen, Jun

    2011-04-13

    In this work we review our new methods to computer generate amorphous atomic topologies of several binary alloys: SiH, SiN, CN; binary systems based on group IV elements like SiC; the GeSe 2 chalcogenide; aluminum-based systems: AlN and AlSi, and the CuZr amorphous alloy. We use an ab initio approach based on density functionals and computationally thermally-randomized periodically-continued cells with at least 108 atoms. The computational thermal process to generate the amorphous alloys is the undermelt-quench approach, or one of its variants, that consists in linearly heating the samples to just below their melting (or liquidus) temperatures, and then linearly cooling them afterwards. These processes are carried out from initial crystalline conditions using short and long time steps. We find that a step four-times the default time step is adequate for most of the simulations. Radial distribution functions (partial and total) are calculated and compared whenever possible with experimental results, and the agreement is very good. For some materials we report studies of the effect of the topological disorder on their electronic and vibrational densities of states and on their optical properties.

  11. New Approaches to the Computer Simulation of Amorphous Alloys: A Review

    PubMed Central

    Valladares, Ariel A.; Díaz-Celaya, Juan A.; Galván-Colín, Jonathan; Mejía-Mendoza, Luis M.; Reyes-Retana, José A.; Valladares, Renela M.; Valladares, Alexander; Alvarez-Ramirez, Fernando; Qu, Dongdong; Shen, Jun

    2011-01-01

    In this work we review our new methods to computer generate amorphous atomic topologies of several binary alloys: SiH, SiN, CN; binary systems based on group IV elements like SiC; the GeSe2 chalcogenide; aluminum-based systems: AlN and AlSi, and the CuZr amorphous alloy. We use an ab initio approach based on density functionals and computationally thermally-randomized periodically-continued cells with at least 108 atoms. The computational thermal process to generate the amorphous alloys is the undermelt-quench approach, or one of its variants, that consists in linearly heating the samples to just below their melting (or liquidus) temperatures, and then linearly cooling them afterwards. These processes are carried out from initial crystalline conditions using short and long time steps. We find that a step four-times the default time step is adequate for most of the simulations. Radial distribution functions (partial and total) are calculated and compared whenever possible with experimental results, and the agreement is very good. For some materials we report studies of the effect of the topological disorder on their electronic and vibrational densities of states and on their optical properties. PMID:28879948

  12. Non-conforming finite-element formulation for cardiac electrophysiology: an effective approach to reduce the computation time of heart simulations without compromising accuracy

    NASA Astrophysics Data System (ADS)

    Hurtado, Daniel E.; Rojas, Guillermo

    2018-04-01

    Computer simulations constitute a powerful tool for studying the electrical activity of the human heart, but computational effort remains prohibitively high. In order to recover accurate conduction velocities and wavefront shapes, the mesh size in linear element (Q1) formulations cannot exceed 0.1 mm. Here we propose a novel non-conforming finite-element formulation for the non-linear cardiac electrophysiology problem that results in accurate wavefront shapes and lower mesh-dependance in the conduction velocity, while retaining the same number of global degrees of freedom as Q1 formulations. As a result, coarser discretizations of cardiac domains can be employed in simulations without significant loss of accuracy, thus reducing the overall computational effort. We demonstrate the applicability of our formulation in biventricular simulations using a coarse mesh size of ˜ 1 mm, and show that the activation wave pattern closely follows that obtained in fine-mesh simulations at a fraction of the computation time, thus improving the accuracy-efficiency trade-off of cardiac simulations.

  13. A Hybrid MPI/OpenMP Approach for Parallel Groundwater Model Calibration on Multicore Computers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tang, Guoping; D'Azevedo, Ed F; Zhang, Fan

    2010-01-01

    Groundwater model calibration is becoming increasingly computationally time intensive. We describe a hybrid MPI/OpenMP approach to exploit two levels of parallelism in software and hardware to reduce calibration time on multicore computers with minimal parallelization effort. At first, HydroGeoChem 5.0 (HGC5) is parallelized using OpenMP for a uranium transport model with over a hundred species involving nearly a hundred reactions, and a field scale coupled flow and transport model. In the first application, a single parallelizable loop is identified to consume over 97% of the total computational time. With a few lines of OpenMP compiler directives inserted into the code,more » the computational time reduces about ten times on a compute node with 16 cores. The performance is further improved by selectively parallelizing a few more loops. For the field scale application, parallelizable loops in 15 of the 174 subroutines in HGC5 are identified to take more than 99% of the execution time. By adding the preconditioned conjugate gradient solver and BICGSTAB, and using a coloring scheme to separate the elements, nodes, and boundary sides, the subroutines for finite element assembly, soil property update, and boundary condition application are parallelized, resulting in a speedup of about 10 on a 16-core compute node. The Levenberg-Marquardt (LM) algorithm is added into HGC5 with the Jacobian calculation and lambda search parallelized using MPI. With this hybrid approach, compute nodes at the number of adjustable parameters (when the forward difference is used for Jacobian approximation), or twice that number (if the center difference is used), are used to reduce the calibration time from days and weeks to a few hours for the two applications. This approach can be extended to global optimization scheme and Monte Carol analysis where thousands of compute nodes can be efficiently utilized.« less

  14. The Assessment of Taiwanese College Students' Conceptions of and Approaches to Learning Computer Science and Their Relationships

    ERIC Educational Resources Information Center

    Liang, Jyh-Chong; Su, Yi-Ching; Tsai, Chin-Chung

    2015-01-01

    The aim of this study was to explore Taiwanese college students' conceptions of and approaches to learning computer science and then explore the relationships between the two. Two surveys, Conceptions of Learning Computer Science (COLCS) and Approaches to Learning Computer Science (ALCS), were administered to 421 college students majoring in…

  15. A very efficient approach to compute the first-passage probability density function in a time-changed Brownian model: Applications in finance

    NASA Astrophysics Data System (ADS)

    Ballestra, Luca Vincenzo; Pacelli, Graziella; Radi, Davide

    2016-12-01

    We propose a numerical method to compute the first-passage probability density function in a time-changed Brownian model. In particular, we derive an integral representation of such a density function in which the integrand functions must be obtained solving a system of Volterra equations of the first kind. In addition, we develop an ad-hoc numerical procedure to regularize and solve this system of integral equations. The proposed method is tested on three application problems of interest in mathematical finance, namely the calculation of the survival probability of an indebted firm, the pricing of a single-knock-out put option and the pricing of a double-knock-out put option. The results obtained reveal that the novel approach is extremely accurate and fast, and performs significantly better than the finite difference method.

  16. [Computational chemistry in structure-based drug design].

    PubMed

    Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

    2013-07-01

    Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

  17. An accurate evaluation of the performance of asynchronous DS-CDMA systems with zero-correlation-zone coding in Rayleigh fading

    NASA Astrophysics Data System (ADS)

    Walker, Ernest; Chen, Xinjia; Cooper, Reginald L.

    2010-04-01

    An arbitrarily accurate approach is used to determine the bit-error rate (BER) performance for generalized asynchronous DS-CDMA systems, in Gaussian noise with Raleigh fading. In this paper, and the sequel, new theoretical work has been contributed which substantially enhances existing performance analysis formulations. Major contributions include: substantial computational complexity reduction, including a priori BER accuracy bounding; an analytical approach that facilitates performance evaluation for systems with arbitrary spectral spreading distributions, with non-uniform transmission delay distributions. Using prior results, augmented by these enhancements, a generalized DS-CDMA system model is constructed and used to evaluated the BER performance, in a variety of scenarios. In this paper, the generalized system modeling was used to evaluate the performance of both Walsh- Hadamard (WH) and Walsh-Hadamard-seeded zero-correlation-zone (WH-ZCZ) coding. The selection of these codes was informed by the observation that WH codes contain N spectral spreading values (0 to N - 1), one for each code sequence; while WH-ZCZ codes contain only two spectral spreading values (N/2 - 1,N/2); where N is the sequence length in chips. Since these codes span the spectral spreading range for DS-CDMA coding, by invoking an induction argument, the generalization of the system model is sufficiently supported. The results in this paper, and the sequel, support the claim that an arbitrary accurate performance analysis for DS-CDMA systems can be evaluated over the full range of binary coding, with minimal computational complexity.

  18. Accurate and cost-effective MTF measurement system for lens modules of digital cameras

    NASA Astrophysics Data System (ADS)

    Chang, Gao-Wei; Liao, Chia-Cheng; Yeh, Zong-Mu

    2007-01-01

    For many years, the widening use of digital imaging products, e.g., digital cameras, has given rise to much attention in the market of consumer electronics. However, it is important to measure and enhance the imaging performance of the digital ones, compared to that of conventional cameras (with photographic films). For example, the effect of diffraction arising from the miniaturization of the optical modules tends to decrease the image resolution. As a figure of merit, modulation transfer function (MTF) has been broadly employed to estimate the image quality. Therefore, the objective of this paper is to design and implement an accurate and cost-effective MTF measurement system for the digital camera. Once the MTF of the sensor array is provided, that of the optical module can be then obtained. In this approach, a spatial light modulator (SLM) is employed to modulate the spatial frequency of light emitted from the light-source. The modulated light going through the camera under test is consecutively detected by the sensors. The corresponding images formed from the camera are acquired by a computer and then, they are processed by an algorithm for computing the MTF. Finally, through the investigation on the measurement accuracy from various methods, such as from bar-target and spread-function methods, it appears that our approach gives quite satisfactory results.

  19. A comparative approach to computer aided design model of a dog femur.

    PubMed

    Turamanlar, O; Verim, O; Karabulut, A

    2016-01-01

    Computer assisted technologies offer new opportunities in medical imaging and rapid prototyping in biomechanical engineering. Three dimensional (3D) modelling of soft tissues and bones are becoming more important. The accuracy of the analysis in modelling processes depends on the outline of the tissues derived from medical images. The aim of this study is the evaluation of the accuracy of 3D models of a dog femur derived from computed tomography data by using point cloud method and boundary line method on several modelling software. Solidworks, Rapidform and 3DSMax software were used to create 3D models and outcomes were evaluated statistically. The most accurate 3D prototype of the dog femur was created with stereolithography method using rapid prototype device. Furthermore, the linearity of the volumes of models was investigated between software and the constructed models. The difference between the software and real models manifests the sensitivity of the software and the devices used in this manner.

  20. A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE).

    PubMed

    Stacey, R Greg; Skinnider, Michael A; Scott, Nichollas E; Foster, Leonard J

    2017-10-23

    An organism's protein interactome, or complete network of protein-protein interactions, defines the protein complexes that drive cellular processes. Techniques for studying protein complexes have traditionally applied targeted strategies such as yeast two-hybrid or affinity purification-mass spectrometry to assess protein interactions. However, given the vast number of protein complexes, more scalable methods are necessary to accelerate interaction discovery and to construct whole interactomes. We recently developed a complementary technique based on the use of protein correlation profiling (PCP) and stable isotope labeling in amino acids in cell culture (SILAC) to assess chromatographic co-elution as evidence of interacting proteins. Importantly, PCP-SILAC is also capable of measuring protein interactions simultaneously under multiple biological conditions, allowing the detection of treatment-specific changes to an interactome. Given the uniqueness and high dimensionality of co-elution data, new tools are needed to compare protein elution profiles, control false discovery rates, and construct an accurate interactome. Here we describe a freely available bioinformatics pipeline, PrInCE, for the analysis of co-elution data. PrInCE is a modular, open-source library that is computationally inexpensive, able to use label and label-free data, and capable of detecting tens of thousands of protein-protein interactions. Using a machine learning approach, PrInCE offers greatly reduced run time, more predicted interactions at the same stringency, prediction of protein complexes, and greater ease of use over previous bioinformatics tools for co-elution data. PrInCE is implemented in Matlab (version R2017a). Source code and standalone executable programs for Windows and Mac OSX are available at https://github.com/fosterlab/PrInCE , where usage instructions can be found. An example dataset and output are also provided for testing purposes. PrInCE is the first fast and easy

  1. A brief overview of computational structures technology related activities at NASA Lewis Research Center

    NASA Technical Reports Server (NTRS)

    Hopkins, Dale A.

    1992-01-01

    The presentation gives a partial overview of research and development underway in the Structures Division of LeRC, which collectively is referred to as the Computational Structures Technology Program. The activities in the program are diverse and encompass four major categories: (1) composite materials and structures; (2) probabilistic analysis and reliability; (3) design optimization and expert systems; and (4) computational methods and simulation. The approach of the program is comprehensive and entails exploration of fundamental theories of structural mechanics to accurately represent the complex physics governing engine structural performance, formulation, and implementation of computational techniques and integrated simulation strategies to provide accurate and efficient solutions of the governing theoretical models by exploiting the emerging advances in computer technology, and validation and verification through numerical and experimental tests to establish confidence and define the qualities and limitations of the resulting theoretical models and computational solutions. The program comprises both in-house and sponsored research activities. The remainder of the presentation provides a sample of activities to illustrate the breadth and depth of the program and to demonstrate the accomplishments and benefits that have resulted.

  2. COMPUTATIONAL TOXICOLOGY - OBJECTIVE 2: DEVELOPING APPROACHES FOR PRIORITIZING CHEMICALS FOR SUBSEQUENT SCREENING AND TESTING

    EPA Science Inventory

    One of the strategic objectives of the Computational Toxicology Program is to develop approaches for prioritizing chemicals for subsequent screening and testing. Approaches currently available for this process require extensive resources. Therefore, less costly and time-extensi...

  3. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    PubMed

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

  4. An automated method for accurate vessel segmentation.

    PubMed

    Yang, Xin; Liu, Chaoyue; Le Minh, Hung; Wang, Zhiwei; Chien, Aichi; Cheng, Kwang-Ting Tim

    2017-05-07

    Vessel segmentation is a critical task for various medical applications, such as diagnosis assistance of diabetic retinopathy, quantification of cerebral aneurysm's growth, and guiding surgery in neurosurgical procedures. Despite technology advances in image segmentation, existing methods still suffer from low accuracy for vessel segmentation in the two challenging while common scenarios in clinical usage: (1) regions with a low signal-to-noise-ratio (SNR), and (2) at vessel boundaries disturbed by adjacent non-vessel pixels. In this paper, we present an automated system which can achieve highly accurate vessel segmentation for both 2D and 3D images even under these challenging scenarios. Three key contributions achieved by our system are: (1) a progressive contrast enhancement method to adaptively enhance contrast of challenging pixels that were otherwise indistinguishable, (2) a boundary refinement method to effectively improve segmentation accuracy at vessel borders based on Canny edge detection, and (3) a content-aware region-of-interests (ROI) adjustment method to automatically determine the locations and sizes of ROIs which contain ambiguous pixels and demand further verification. Extensive evaluation of our method is conducted on both 2D and 3D datasets. On a public 2D retinal dataset (named DRIVE (Staal 2004 IEEE Trans. Med. Imaging 23 501-9)) and our 2D clinical cerebral dataset, our approach achieves superior performance to the state-of-the-art methods including a vesselness based method (Frangi 1998 Int. Conf. on Medical Image Computing and Computer-Assisted Intervention) and an optimally oriented flux (OOF) based method (Law and Chung 2008 European Conf. on Computer Vision). An evaluation on 11 clinical 3D CTA cerebral datasets shows that our method can achieve 94% average accuracy with respect to the manual segmentation reference, which is 23% to 33% better than the five baseline methods (Yushkevich 2006 Neuroimage 31 1116-28; Law and Chung 2008

  5. Time-Accurate Unsteady Pressure Loads Simulated for the Space Launch System at Wind Tunnel Conditions

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.; Brauckmann, Gregory J.; Kleb, William L.; Glass, Christopher E.; Streett, Craig L.; Schuster, David M.

    2015-01-01

    A transonic flow field about a Space Launch System (SLS) configuration was simulated with the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics (CFD) code at wind tunnel conditions. Unsteady, time-accurate computations were performed using second-order Delayed Detached Eddy Simulation (DDES) for up to 1.5 physical seconds. The surface pressure time history was collected at 619 locations, 169 of which matched locations on a 2.5 percent wind tunnel model that was tested in the 11 ft. x 11 ft. test section of the NASA Ames Research Center's Unitary Plan Wind Tunnel. Comparisons between computation and experiment showed that the peak surface pressure RMS level occurs behind the forward attach hardware, and good agreement for frequency and power was obtained in this region. Computational domain, grid resolution, and time step sensitivity studies were performed. These included an investigation of pseudo-time sub-iteration convergence. Using these sensitivity studies and experimental data comparisons, a set of best practices to date have been established for FUN3D simulations for SLS launch vehicle analysis. To the author's knowledge, this is the first time DDES has been used in a systematic approach and establish simulation time needed, to analyze unsteady pressure loads on a space launch vehicle such as the NASA SLS.

  6. The process group approach to reliable distributed computing

    NASA Technical Reports Server (NTRS)

    Birman, Kenneth P.

    1991-01-01

    The difficulty of developing reliable distributed software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems which are substantially easier to develop, fault-tolerance, and self-managing. Six years of research on ISIS are reviewed, describing the model, the types of applications to which ISIS was applied, and some of the reasoning that underlies a recent effort to redesign and reimplement ISIS as a much smaller, lightweight system.

  7. Cerebral perfusion computed tomography deconvolution via structure tensor total variation regularization

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zeng, Dong; Zhang, Xinyu; Bian, Zhaoying, E-mail: zybian@smu.edu.cn, E-mail: jhma@smu.edu.cn

    Purpose: Cerebral perfusion computed tomography (PCT) imaging as an accurate and fast acute ischemic stroke examination has been widely used in clinic. Meanwhile, a major drawback of PCT imaging is the high radiation dose due to its dynamic scan protocol. The purpose of this work is to develop a robust perfusion deconvolution approach via structure tensor total variation (STV) regularization (PD-STV) for estimating an accurate residue function in PCT imaging with the low-milliampere-seconds (low-mAs) data acquisition. Methods: Besides modeling the spatio-temporal structure information of PCT data, the STV regularization of the present PD-STV approach can utilize the higher order derivativesmore » of the residue function to enhance denoising performance. To minimize the objective function, the authors propose an effective iterative algorithm with a shrinkage/thresholding scheme. A simulation study on a digital brain perfusion phantom and a clinical study on an old infarction patient were conducted to validate and evaluate the performance of the present PD-STV approach. Results: In the digital phantom study, visual inspection and quantitative metrics (i.e., the normalized mean square error, the peak signal-to-noise ratio, and the universal quality index) assessments demonstrated that the PD-STV approach outperformed other existing approaches in terms of the performance of noise-induced artifacts reduction and accurate perfusion hemodynamic maps (PHM) estimation. In the patient data study, the present PD-STV approach could yield accurate PHM estimation with several noticeable gains over other existing approaches in terms of visual inspection and correlation analysis. Conclusions: This study demonstrated the feasibility and efficacy of the present PD-STV approach in utilizing STV regularization to improve the accuracy of residue function estimation of cerebral PCT imaging in the case of low-mAs.« less

  8. A unified momentum equation approach for computing thermal residual stresses during melting and solidification

    NASA Astrophysics Data System (ADS)

    Yeo, Haram; Ki, Hyungson

    2018-03-01

    In this article, we present a novel numerical method for computing thermal residual stresses from a viewpoint of fluid-structure interaction (FSI). In a thermal processing of a material, residual stresses are developed as the material undergoes melting and solidification, and liquid, solid, and a mixture of liquid and solid (or mushy state) coexist and interact with each other during the process. In order to accurately account for the stress development during phase changes, we derived a unified momentum equation from the momentum equations of incompressible fluids and elastoplastic solids. In this approach, the whole fluid-structure system is treated as a single continuum, and the interaction between fluid and solid phases across the mushy zone is naturally taken into account in a monolithic way. For thermal analysis, an enthalpy-based method was employed. As a numerical example, a two-dimensional laser heating problem was considered, where a carbon steel sheet was heated by a Gaussian laser beam. Momentum and energy equations were discretized on a uniform Cartesian grid in a finite volume framework, and temperature-dependent material properties were used. The austenite-martensite phase transformation of carbon steel was also considered. In this study, the effects of solid strains, fluid flow, mushy zone size, and laser heating time on residual stress formation were investigated.

  9. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.

    PubMed

    Tangprasertchai, Narin S; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S; Qin, Peter Z

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. © 2015 Elsevier Inc. All rights reserved.

  10. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids

    PubMed Central

    Tangprasertchai, Narin S.; Zhang, Xiaojun; Ding, Yuan; Tham, Kenneth; Rohs, Remo; Haworth, Ian S.; Qin, Peter Z.

    2015-01-01

    The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve “correct” all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements. PMID:26477260

  11. Computation of entropy and Lyapunov exponent by a shift transform.

    PubMed

    Matsuoka, Chihiro; Hiraide, Koichi

    2015-10-01

    We present a novel computational method to estimate the topological entropy and Lyapunov exponent of nonlinear maps using a shift transform. Unlike the computation of periodic orbits or the symbolic dynamical approach by the Markov partition, the method presented here does not require any special techniques in computational and mathematical fields to calculate these quantities. In spite of its simplicity, our method can accurately capture not only the chaotic region but also the non-chaotic region (window region) such that it is important physically but the (Lebesgue) measure zero and usually hard to calculate or observe. Furthermore, it is shown that the Kolmogorov-Sinai entropy of the Sinai-Ruelle-Bowen measure (the physical measure) coincides with the topological entropy.

  12. Highly accurate symplectic element based on two variational principles

    NASA Astrophysics Data System (ADS)

    Qing, Guanghui; Tian, Jia

    2018-02-01

    For the stability requirement of numerical resultants, the mathematical theory of classical mixed methods are relatively complex. However, generalized mixed methods are automatically stable, and their building process is simple and straightforward. In this paper, based on the seminal idea of the generalized mixed methods, a simple, stable, and highly accurate 8-node noncompatible symplectic element (NCSE8) was developed by the combination of the modified Hellinger-Reissner mixed variational principle and the minimum energy principle. To ensure the accuracy of in-plane stress results, a simultaneous equation approach was also suggested. Numerical experimentation shows that the accuracy of stress results of NCSE8 are nearly the same as that of displacement methods, and they are in good agreement with the exact solutions when the mesh is relatively fine. NCSE8 has advantages of the clearing concept, easy calculation by a finite element computer program, higher accuracy and wide applicability for various linear elasticity compressible and nearly incompressible material problems. It is possible that NCSE8 becomes even more advantageous for the fracture problems due to its better accuracy of stresses.

  13. Creation of an idealized nasopharynx geometry for accurate computational fluid dynamics simulations of nasal airflow in patient-specific models lacking the nasopharynx anatomy

    PubMed Central

    Borojeni, Azadeh A.T.; Frank-Ito, Dennis O.; Kimbell, Julia S.; Rhee, John S.; Garcia, Guilherme J. M.

    2016-01-01

    Virtual surgery planning based on computational fluid dynamics (CFD) simulations has the potential to improve surgical outcomes for nasal airway obstruction (NAO) patients, but the benefits of virtual surgery planning must outweigh the risks of radiation exposure. Cone beam computed tomography (CBCT) scans represent an attractive imaging modality for virtual surgery planning due to lower costs and lower radiation exposures compared with conventional CT scans. However, to minimize the radiation exposure, the CBCT sinusitis protocol sometimes images only the nasal cavity, excluding the nasopharynx. The goal of this study was to develop an idealized nasopharynx geometry for accurate representation of outlet boundary conditions when the nasopharynx geometry is unavailable. Anatomically-accurate models of the nasopharynx created from thirty CT scans were intersected with planes rotated at different angles to obtain an average geometry. Cross sections of the idealized nasopharynx were approximated as ellipses with cross-sectional areas and aspect ratios equal to the average in the actual patient-specific models. CFD simulations were performed to investigate whether nasal airflow patterns were affected when the CT-based nasopharynx was replaced by the idealized nasopharynx in 10 NAO patients. Despite the simple form of the idealized geometry, all biophysical variables (nasal resistance, airflow rate, and heat fluxes) were very similar in the idealized vs. patient-specific models. The results confirmed the expectation that the nasopharynx geometry has a minimal effect in the nasal airflow patterns during inspiration. The idealized nasopharynx geometry will be useful in future CFD studies of nasal airflow based on medical images that exclude the nasopharynx. PMID:27525807

  14. A systematic approach for the accurate non-invasive estimation of blood glucose utilizing a novel light-tissue interaction adaptive modelling scheme

    NASA Astrophysics Data System (ADS)

    Rybynok, V. O.; Kyriacou, P. A.

    2007-10-01

    Diabetes is one of the biggest health challenges of the 21st century. The obesity epidemic, sedentary lifestyles and an ageing population mean prevalence of the condition is currently doubling every generation. Diabetes is associated with serious chronic ill health, disability and premature mortality. Long-term complications including heart disease, stroke, blindness, kidney disease and amputations, make the greatest contribution to the costs of diabetes care. Many of these long-term effects could be avoided with earlier, more effective monitoring and treatment. Currently, blood glucose can only be monitored through the use of invasive techniques. To date there is no widely accepted and readily available non-invasive monitoring technique to measure blood glucose despite the many attempts. This paper challenges one of the most difficult non-invasive monitoring techniques, that of blood glucose, and proposes a new novel approach that will enable the accurate, and calibration free estimation of glucose concentration in blood. This approach is based on spectroscopic techniques and a new adaptive modelling scheme. The theoretical implementation and the effectiveness of the adaptive modelling scheme for this application has been described and a detailed mathematical evaluation has been employed to prove that such a scheme has the capability of extracting accurately the concentration of glucose from a complex biological media.

  15. A computational workflow for designing silicon donor qubits

    DOE PAGES

    Humble, Travis S.; Ericson, M. Nance; Jakowski, Jacek; ...

    2016-09-19

    Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to performmore » detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. In conclusion, the resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.« less

  16. An efficient two-stage approach for image-based FSI analysis of atherosclerotic arteries

    PubMed Central

    Rayz, Vitaliy L.; Mofrad, Mohammad R. K.; Saloner, David

    2010-01-01

    Patient-specific biomechanical modeling of atherosclerotic arteries has the potential to aid clinicians in characterizing lesions and determining optimal treatment plans. To attain high levels of accuracy, recent models use medical imaging data to determine plaque component boundaries in three dimensions, and fluid–structure interaction is used to capture mechanical loading of the diseased vessel. As the plaque components and vessel wall are often highly complex in shape, constructing a suitable structured computational mesh is very challenging and can require a great deal of time. Models based on unstructured computational meshes require relatively less time to construct and are capable of accurately representing plaque components in three dimensions. These models unfortunately require additional computational resources and computing time for accurate and meaningful results. A two-stage modeling strategy based on unstructured computational meshes is proposed to achieve a reasonable balance between meshing difficulty and computational resource and time demand. In this method, a coarsegrained simulation of the full arterial domain is used to guide and constrain a fine-scale simulation of a smaller region of interest within the full domain. Results for a patient-specific carotid bifurcation model demonstrate that the two-stage approach can afford a large savings in both time for mesh generation and time and resources needed for computation. The effects of solid and fluid domain truncation were explored, and were shown to minimally affect accuracy of the stress fields predicted with the two-stage approach. PMID:19756798

  17. GlycoDeNovo - an Efficient Algorithm for Accurate de novo Glycan Topology Reconstruction from Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Hong, Pengyu; Sun, Hui; Sha, Long; Pu, Yi; Khatri, Kshitij; Yu, Xiang; Tang, Yang; Lin, Cheng

    2017-08-01

    A major challenge in glycomics is the characterization of complex glycan structures that are essential for understanding their diverse roles in many biological processes. We present a novel efficient computational approach, named GlycoDeNovo, for accurate elucidation of the glycan topologies from their tandem mass spectra. Given a spectrum, GlycoDeNovo first builds an interpretation-graph specifying how to interpret each peak using preceding interpreted peaks. It then reconstructs the topologies of peaks that contribute to interpreting the precursor ion. We theoretically prove that GlycoDeNovo is highly efficient. A major innovative feature added to GlycoDeNovo is a data-driven IonClassifier which can be used to effectively rank candidate topologies. IonClassifier is automatically learned from experimental spectra of known glycans to distinguish B- and C-type ions from all other ion types. Our results showed that GlycoDeNovo is robust and accurate for topology reconstruction of glycans from their tandem mass spectra. [Figure not available: see fulltext.

  18. Automated Approach to Very High-Order Aeroacoustic Computations. Revision

    NASA Technical Reports Server (NTRS)

    Dyson, Rodger W.; Goodrich, John W.

    2001-01-01

    Computational aeroacoustics requires efficient, high-resolution simulation tools. For smooth problems, this is best accomplished with very high-order in space and time methods on small stencils. However, the complexity of highly accurate numerical methods can inhibit their practical application, especially in irregular geometries. This complexity is reduced by using a special form of Hermite divided-difference spatial interpolation on Cartesian grids, and a Cauchy-Kowalewski recursion procedure for time advancement. In addition, a stencil constraint tree reduces the complexity of interpolating grid points that am located near wall boundaries. These procedures are used to develop automatically and to implement very high-order methods (> 15) for solving the linearized Euler equations that can achieve less than one grid point per wavelength resolution away from boundaries by including spatial derivatives of the primitive variables at each grid point. The accuracy of stable surface treatments is currently limited to 11th order for grid aligned boundaries and to 2nd order for irregular boundaries.

  19. DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins.

    PubMed

    Meher, Prabina Kumar; Sahu, Tanmaya Kumar; Banchariya, Anjali; Rao, Atmakuri Ramakrishna

    2017-03-24

    Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the proteins encoded from certain class of genes of the insects. To distinguish the insecticide resistant proteins from non-resistant proteins, no computational tool is available till date. Thus, development of such a computational tool will be helpful in predicting the insecticide resistant proteins, which can be targeted for developing appropriate insecticides. Five different sets of feature viz., amino acid composition (AAC), di-peptide composition (DPC), pseudo amino acid composition (PAAC), composition-transition-distribution (CTD) and auto-correlation function (ACF) were used to map the protein sequences into numeric feature vectors. The encoded numeric vectors were then used as input in support vector machine (SVM) for classification of insecticide resistant and non-resistant proteins. Higher accuracies were obtained under RBF kernel than that of other kernels. Further, accuracies were observed to be higher for DPC feature set as compared to others. The proposed approach achieved an overall accuracy of >90% in discriminating resistant from non-resistant proteins. Further, the two classes of resistant proteins i.e., detoxification-based and target-based were discriminated from non-resistant proteins with >95% accuracy. Besides, >95% accuracy was also observed for discrimination of proteins involved in detoxification- and target-based resistance mechanisms. The proposed approach not only outperformed Blastp, PSI-Blast and Delta-Blast algorithms, but also achieved >92% accuracy while assessed using an independent dataset of 75 insecticide resistant proteins. This paper presents the first computational approach for discriminating the insecticide resistant proteins from non-resistant proteins. Based on the proposed approach, an online prediction server DIRProt has

  20. Teaching of real numbers by using the Archimedes-Cantor approach and computer algebra systems

    NASA Astrophysics Data System (ADS)

    Vorob'ev, Evgenii M.

    2015-11-01

    Computer technologies and especially computer algebra systems (CAS) allow students to overcome some of the difficulties they encounter in the study of real numbers. The teaching of calculus can be considerably more effective with the use of CAS provided the didactics of the discipline makes it possible to reveal the full computational potential of CAS. In the case of real numbers, the Archimedes-Cantor approach satisfies this requirement. The name of Archimedes brings back the exhaustion method. Cantor's name reminds us of the use of Cauchy rational sequences to represent real numbers. The usage of CAS with the Archimedes-Cantor approach enables the discussion of various representations of real numbers such as graphical, decimal, approximate decimal with precision estimates, and representation as points on a straight line. Exercises with numbers such as e, π, the golden ratio ϕ, and algebraic irrational numbers can help students better understand the real numbers. The Archimedes-Cantor approach also reveals a deep and close relationship between real numbers and continuity, in particular the continuity of functions.

  1. Multiscale Methods, Parallel Computation, and Neural Networks for Real-Time Computer Vision.

    NASA Astrophysics Data System (ADS)

    Battiti, Roberto

    1990-01-01

    This thesis presents new algorithms for low and intermediate level computer vision. The guiding ideas in the presented approach are those of hierarchical and adaptive processing, concurrent computation, and supervised learning. Processing of the visual data at different resolutions is used not only to reduce the amount of computation necessary to reach the fixed point, but also to produce a more accurate estimation of the desired parameters. The presented adaptive multiple scale technique is applied to the problem of motion field estimation. Different parts of the image are analyzed at a resolution that is chosen in order to minimize the error in the coefficients of the differential equations to be solved. Tests with video-acquired images show that velocity estimation is more accurate over a wide range of motion with respect to the homogeneous scheme. In some cases introduction of explicit discontinuities coupled to the continuous variables can be used to avoid propagation of visual information from areas corresponding to objects with different physical and/or kinematic properties. The human visual system uses concurrent computation in order to process the vast amount of visual data in "real -time." Although with different technological constraints, parallel computation can be used efficiently for computer vision. All the presented algorithms have been implemented on medium grain distributed memory multicomputers with a speed-up approximately proportional to the number of processors used. A simple two-dimensional domain decomposition assigns regions of the multiresolution pyramid to the different processors. The inter-processor communication needed during the solution process is proportional to the linear dimension of the assigned domain, so that efficiency is close to 100% if a large region is assigned to each processor. Finally, learning algorithms are shown to be a viable technique to engineer computer vision systems for different applications starting from

  2. Adaptive zooming in X-ray computed tomography.

    PubMed

    Dabravolski, Andrei; Batenburg, Kees Joost; Sijbers, Jan

    2014-01-01

    In computed tomography (CT), the source-detector system commonly rotates around the object in a circular trajectory. Such a trajectory does not allow to exploit a detector fully when scanning elongated objects. Increase the spatial resolution of the reconstructed image by optimal zooming during scanning. A new approach is proposed, in which the full width of the detector is exploited for every projection angle. This approach is based on the use of prior information about the object's convex hull to move the source as close as possible to the object, while avoiding truncation of the projections. Experiments show that the proposed approach can significantly improve reconstruction quality, producing reconstructions with smaller errors and revealing more details in the object. The proposed approach can lead to more accurate reconstructions and increased spatial resolution in the object compared to the conventional circular trajectory.

  3. Optimal simulations of ultrasonic fields produced by large thermal therapy arrays using the angular spectrum approach

    PubMed Central

    Zeng, Xiaozheng; McGough, Robert J.

    2009-01-01

    The angular spectrum approach is evaluated for the simulation of focused ultrasound fields produced by large thermal therapy arrays. For an input pressure or normal particle velocity distribution in a plane, the angular spectrum approach rapidly computes the output pressure field in a three dimensional volume. To determine the optimal combination of simulation parameters for angular spectrum calculations, the effect of the size, location, and the numerical accuracy of the input plane on the computed output pressure is evaluated. Simulation results demonstrate that angular spectrum calculations performed with an input pressure plane are more accurate than calculations with an input velocity plane. Results also indicate that when the input pressure plane is slightly larger than the array aperture and is located approximately one wavelength from the array, angular spectrum simulations have very small numerical errors for two dimensional planar arrays. Furthermore, the root mean squared error from angular spectrum simulations asymptotically approaches a nonzero lower limit as the error in the input plane decreases. Overall, the angular spectrum approach is an accurate and robust method for thermal therapy simulations of large ultrasound phased arrays when the input pressure plane is computed with the fast nearfield method and an optimal combination of input parameters. PMID:19425640

  4. A machine-learning approach for computation of fractional flow reserve from coronary computed tomography.

    PubMed

    Itu, Lucian; Rapaka, Saikiran; Passerini, Tiziano; Georgescu, Bogdan; Schwemmer, Chris; Schoebinger, Max; Flohr, Thomas; Sharma, Puneet; Comaniciu, Dorin

    2016-07-01

    Fractional flow reserve (FFR) is a functional index quantifying the severity of coronary artery lesions and is clinically obtained using an invasive, catheter-based measurement. Recently, physics-based models have shown great promise in being able to noninvasively estimate FFR from patient-specific anatomical information, e.g., obtained from computed tomography scans of the heart and the coronary arteries. However, these models have high computational demand, limiting their clinical adoption. In this paper, we present a machine-learning-based model for predicting FFR as an alternative to physics-based approaches. The model is trained on a large database of synthetically generated coronary anatomies, where the target values are computed using the physics-based model. The trained model predicts FFR at each point along the centerline of the coronary tree, and its performance was assessed by comparing the predictions against physics-based computations and against invasively measured FFR for 87 patients and 125 lesions in total. Correlation between machine-learning and physics-based predictions was excellent (0.9994, P < 0.001), and no systematic bias was found in Bland-Altman analysis: mean difference was -0.00081 ± 0.0039. Invasive FFR ≤ 0.80 was found in 38 lesions out of 125 and was predicted by the machine-learning algorithm with a sensitivity of 81.6%, a specificity of 83.9%, and an accuracy of 83.2%. The correlation was 0.729 (P < 0.001). Compared with the physics-based computation, average execution time was reduced by more than 80 times, leading to near real-time assessment of FFR. Average execution time went down from 196.3 ± 78.5 s for the CFD model to ∼2.4 ± 0.44 s for the machine-learning model on a workstation with 3.4-GHz Intel i7 8-core processor. Copyright © 2016 the American Physiological Society.

  5. Computation of transonic separated wing flows using an Euler/Navier-Stokes zonal approach

    NASA Technical Reports Server (NTRS)

    Kaynak, Uenver; Holst, Terry L.; Cantwell, Brian J.

    1986-01-01

    A computer program called Transonic Navier Stokes (TNS) has been developed which solves the Euler/Navier-Stokes equations around wings using a zonal grid approach. In the present zonal scheme, the physical domain of interest is divided into several subdomains called zones and the governing equations are solved interactively. The advantages of the Zonal Grid approach are as follows: (1) the grid for any subdomain can be generated easily; (2) grids can be, in a sense, adapted to the solution; (3) different equation sets can be used in different zones; and, (4) this approach allows for a convenient data base organization scheme. Using this code, separated flows on a NACA 0012 section wing and on the NASA Ames WING C have been computed. First, the effects of turbulence and artificial dissipation models incorporated into the code are assessed by comparing the TNS results with other CFD codes and experiments. Then a series of flow cases is described where data are available. The computed results, including cases with shock-induced separation, are in good agreement with experimental data. Finally, some futuristic cases are presented to demonstrate the abilities of the code for massively separated cases which do not have experimental data.

  6. Convergent Close-Coupling Approach to Electron-Atom Collisions

    NASA Technical Reports Server (NTRS)

    Bray, Igor; Stelbovics, Andris

    2007-01-01

    It was with great pleasure and honour to accept the invitation to make a presentation at the symposium celebrating the life-long work of Aaron Temkin and Richard Drachman. The work of Aaron Temkin was particularly influential on our own during the development of the CCC method for electron-atom collisions. There are a number of key problems that need to be dealt with when developing a general computational approach to such collisions. Traditionally, the electron energy range was subdivided into the low, intermediate, and high energies. At the low energies only a finite number of channels are open and variational or close-coupling techniques could be used to obtain accurate results. At high energies an infinite number of discrete channels and the target continuum are open, but perturbative techniques are able to yield accurate results. However, at the intermediate energies perturbative techniques fail and computational approaches need to be found for treating the infinite number of open channels. In addition, there are also problems associated with the identical nature of electrons and the difficulty of implementing the boundary conditions for ionization processes. The beauty of the Temkin-Poet model of electron-hydrogen scattering is that it simplifies the full computational problem by neglecting any non-zero orbital angular momenta in the partial-wave expansion, without loosing the complexity associated with the above-mentioned problems. The unique nature of the problem allowed for accurate solution leading to benchmark results which could then be used to test the much more general approaches to electron-atom collision problems. The immense value of the Temkin-Poet model is readily summarised by the fact that the initial papers of Temkin and Poet have been collectively cited around 250 times to date and are still being cited in present times. Many of the citations came from our own work during the course of the development of the CCC method, which we now describe.

  7. An approach for the accurate measurement of social morality levels.

    PubMed

    Liu, Haiyan; Chen, Xia; Zhang, Bo

    2013-01-01

    In the social sciences, computer-based modeling has become an increasingly important tool receiving widespread attention. However, the derivation of the quantitative relationships linking individual moral behavior and social morality levels, so as to provide a useful basis for social policy-making, remains a challenge in the scholarly literature today. A quantitative measurement of morality from the perspective of complexity science constitutes an innovative attempt. Based on the NetLogo platform, this article examines the effect of various factors on social morality levels, using agents modeling moral behavior, immoral behavior, and a range of environmental social resources. Threshold values for the various parameters are obtained through sensitivity analysis; and practical solutions are proposed for reversing declines in social morality levels. The results show that: (1) Population size may accelerate or impede the speed with which immoral behavior comes to determine the overall level of social morality, but it has no effect on the level of social morality itself; (2) The impact of rewards and punishment on social morality levels follows the "5∶1 rewards-to-punishment rule," which is to say that 5 units of rewards have the same effect as 1 unit of punishment; (3) The abundance of public resources is inversely related to the level of social morality; (4) When the cost of population mobility reaches 10% of the total energy level, immoral behavior begins to be suppressed (i.e. the 1/10 moral cost rule). The research approach and methods presented in this paper successfully address the difficulties involved in measuring social morality levels, and promise extensive application potentials.

  8. A convenient and accurate parallel Input/Output USB device for E-Prime.

    PubMed

    Canto, Rosario; Bufalari, Ilaria; D'Ausilio, Alessandro

    2011-03-01

    Psychological and neurophysiological experiments require the accurate control of timing and synchrony for Input/Output signals. For instance, a typical Event-Related Potential (ERP) study requires an extremely accurate synchronization of stimulus delivery with recordings. This is typically done via computer software such as E-Prime, and fast communications are typically assured by the Parallel Port (PP). However, the PP is an old and disappearing technology that, for example, is no longer available on portable computers. Here we propose a convenient USB device enabling parallel I/O capabilities. We tested this device against the PP on both a desktop and a laptop machine in different stress tests. Our data demonstrate the accuracy of our system, which suggests that it may be a good substitute for the PP with E-Prime.

  9. 4D laser camera for accurate patient positioning, collision avoidance, image fusion and adaptive approaches during diagnostic and therapeutic procedures.

    PubMed

    Brahme, Anders; Nyman, Peter; Skatt, Björn

    2008-05-01

    A four-dimensional (4D) laser camera (LC) has been developed for accurate patient imaging in diagnostic and therapeutic radiology. A complementary metal-oxide semiconductor camera images the intersection of a scanned fan shaped laser beam with the surface of the patient and allows real time recording of movements in a three-dimensional (3D) or four-dimensional (4D) format (3D +time). The LC system was first designed as an accurate patient setup tool during diagnostic and therapeutic applications but was found to be of much wider applicability as a general 4D photon "tag" for the surface of the patient in different clinical procedures. It is presently used as a 3D or 4D optical benchmark or tag for accurate delineation of the patient surface as demonstrated for patient auto setup, breathing and heart motion detection. Furthermore, its future potential applications in gating, adaptive therapy, 3D or 4D image fusion between most imaging modalities and image processing are discussed. It is shown that the LC system has a geometrical resolution of about 0, 1 mm and that the rigid body repositioning accuracy is about 0, 5 mm below 20 mm displacements, 1 mm below 40 mm and better than 2 mm at 70 mm. This indicates a slight need for repeated repositioning when the initial error is larger than about 50 mm. The positioning accuracy with standard patient setup procedures for prostate cancer at Karolinska was found to be about 5-6 mm when independently measured using the LC system. The system was found valuable for positron emission tomography-computed tomography (PET-CT) in vivo tumor and dose delivery imaging where it potentially may allow effective correction for breathing artifacts in 4D PET-CT and image fusion with lymph node atlases for accurate target volume definition in oncology. With a LC system in all imaging and radiation therapy rooms, auto setup during repeated diagnostic and therapeutic procedures may save around 5 min per session, increase accuracy and allow

  10. Load Forecasting Based Distribution System Network Reconfiguration -- A Distributed Data-Driven Approach

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jiang, Huaiguang; Zhang, Yingchen; Muljadi, Eduard

    In this paper, a short-term load forecasting approach based network reconfiguration is proposed in a parallel manner. Specifically, a support vector regression (SVR) based short-term load forecasting approach is designed to provide an accurate load prediction and benefit the network reconfiguration. Because of the nonconvexity of the three-phase balanced optimal power flow, a second-order cone program (SOCP) based approach is used to relax the optimal power flow problem. Then, the alternating direction method of multipliers (ADMM) is used to compute the optimal power flow in distributed manner. Considering the limited number of the switches and the increasing computation capability, themore » proposed network reconfiguration is solved in a parallel way. The numerical results demonstrate the feasible and effectiveness of the proposed approach.« less

  11. A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

    NASA Technical Reports Server (NTRS)

    Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

    2015-01-01

    Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

  12. Flowing Hot or Cold: User-Friendly Computational Models of Terrestrial and Planetary Lava Channels and Lakes

    NASA Astrophysics Data System (ADS)

    Sakimoto, S. E. H.

    2016-12-01

    Planetary volcanism has redefined what is considered volcanism. "Magma" now may be considered to be anything from the molten rock familiar at terrestrial volcanoes to cryovolcanic ammonia-water mixes erupted on an outer solar system moon. However, even with unfamiliar compositions and source mechanisms, we find familiar landforms such as volcanic channels, lakes, flows, and domes and thus a multitude of possibilities for modeling. As on Earth, these landforms lend themselves to analysis for estimating storage, eruption and/or flow rates. This has potential pitfalls, as extension of the simplified analytic models we often use for terrestrial features into unfamiliar parameter space might yield misleading results. Our most commonly used tools for estimating flow and cooling have tended to lag significantly behind state-of-the-art; the easiest methods to use are neither realistic or accurate, but the more realistic and accurate computational methods are not simple to use. Since the latter computational tools tend to be both expensive and require a significant learning curve, there is a need for a user-friendly approach that still takes advantage of their accuracy. One method is use of the computational package for generation of a server-based tool that allows less computationally inclined users to get accurate results over their range of input parameters for a given problem geometry. A second method is to use the computational package for the generation of a polynomial empirical solution for each class of flow geometry that can be fairly easily solved by anyone with a spreadsheet. In this study, we demonstrate both approaches for several channel flow and lava lake geometries with terrestrial and extraterrestrial examples and compare their results. Specifically, we model cooling rectangular channel flow with a yield strength material, with applications to Mauna Loa, Kilauea, Venus, and Mars. This approach also shows promise with model applications to lava lakes, magma

  13. Crowd Computing as a Cooperation Problem: An Evolutionary Approach

    NASA Astrophysics Data System (ADS)

    Christoforou, Evgenia; Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Sánchez, Angel

    2013-05-01

    Cooperation is one of the socio-economic issues that has received more attention from the physics community. The problem has been mostly considered by studying games such as the Prisoner's Dilemma or the Public Goods Game. Here, we take a step forward by studying cooperation in the context of crowd computing. We introduce a model loosely based on Principal-agent theory in which people (workers) contribute to the solution of a distributed problem by computing answers and reporting to the problem proposer (master). To go beyond classical approaches involving the concept of Nash equilibrium, we work on an evolutionary framework in which both the master and the workers update their behavior through reinforcement learning. Using a Markov chain approach, we show theoretically that under certain----not very restrictive—conditions, the master can ensure the reliability of the answer resulting of the process. Then, we study the model by numerical simulations, finding that convergence, meaning that the system reaches a point in which it always produces reliable answers, may in general be much faster than the upper bounds given by the theoretical calculation. We also discuss the effects of the master's level of tolerance to defectors, about which the theory does not provide information. The discussion shows that the system works even with very large tolerances. We conclude with a discussion of our results and possible directions to carry this research further.

  14. 76 FR 52353 - Assumption Buster Workshop: “Current Implementations of Cloud Computing Indicate a New Approach...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-22

    ... explored in this series is cloud computing. The workshop on this topic will be held in Gaithersburg, MD on October 21, 2011. Assertion: ``Current implementations of cloud computing indicate a new approach to security'' Implementations of cloud computing have provided new ways of thinking about how to secure data...

  15. A Context-Aware Ubiquitous Learning Approach for Providing Instant Learning Support in Personal Computer Assembly Activities

    ERIC Educational Resources Information Center

    Hsu, Ching-Kun; Hwang, Gwo-Jen

    2014-01-01

    Personal computer assembly courses have been recognized as being essential in helping students understand computer structure as well as the functionality of each computer component. In this study, a context-aware ubiquitous learning approach is proposed for providing instant assistance to individual students in the learning activity of a…

  16. Third-order accurate conservative method on unstructured meshes for gasdynamic simulations

    NASA Astrophysics Data System (ADS)

    Shirobokov, D. A.

    2017-04-01

    A third-order accurate finite-volume method on unstructured meshes is proposed for solving viscous gasdynamic problems. The method is described as applied to the advection equation. The accuracy of the method is verified by computing the evolution of a vortex on meshes of various degrees of detail with variously shaped cells. Additionally, unsteady flows around a cylinder and a symmetric airfoil are computed. The numerical results are presented in the form of plots and tables.

  17. Linear stability analysis of detonations via numerical computation and dynamic mode decomposition

    NASA Astrophysics Data System (ADS)

    Kabanov, Dmitry I.; Kasimov, Aslan R.

    2018-03-01

    We introduce a new method to investigate linear stability of gaseous detonations that is based on an accurate shock-fitting numerical integration of the linearized reactive Euler equations with a subsequent analysis of the computed solution via the dynamic mode decomposition. The method is applied to the detonation models based on both the standard one-step Arrhenius kinetics and two-step exothermic-endothermic reaction kinetics. Stability spectra for all cases are computed and analyzed. The new approach is shown to be a viable alternative to the traditional normal-mode analysis used in detonation theory.

  18. Linking Individual Learning Styles to Approach-Avoidance Motivational Traits and Computational Aspects of Reinforcement Learning

    PubMed Central

    Carl Aberg, Kristoffer; Doell, Kimberly C.; Schwartz, Sophie

    2016-01-01

    Learning how to gain rewards (approach learning) and avoid punishments (avoidance learning) is fundamental for everyday life. While individual differences in approach and avoidance learning styles have been related to genetics and aging, the contribution of personality factors, such as traits, remains undetermined. Moreover, little is known about the computational mechanisms mediating differences in learning styles. Here, we used a probabilistic selection task with positive and negative feedbacks, in combination with computational modelling, to show that individuals displaying better approach (vs. avoidance) learning scored higher on measures of approach (vs. avoidance) trait motivation, but, paradoxically, also displayed reduced learning speed following positive (vs. negative) outcomes. These data suggest that learning different types of information depend on associated reward values and internal motivational drives, possibly determined by personality traits. PMID:27851807

  19. Current Trend Towards Using Soft Computing Approaches to Phase Synchronization in Communication Systems

    NASA Technical Reports Server (NTRS)

    Drake, Jeffrey T.; Prasad, Nadipuram R.

    1999-01-01

    This paper surveys recent advances in communications that utilize soft computing approaches to phase synchronization. Soft computing, as opposed to hard computing, is a collection of complementary methodologies that act in producing the most desirable control, decision, or estimation strategies. Recently, the communications area has explored the use of the principal constituents of soft computing, namely, fuzzy logic, neural networks, and genetic algorithms, for modeling, control, and most recently for the estimation of phase in phase-coherent communications. If the receiver in a digital communications system is phase-coherent, as is often the case, phase synchronization is required. Synchronization thus requires estimation and/or control at the receiver of an unknown or random phase offset.

  20. Tensor scale: An analytic approach with efficient computation and applications☆

    PubMed Central

    Xu, Ziyue; Saha, Punam K.; Dasgupta, Soura

    2015-01-01

    Scale is a widely used notion in computer vision and image understanding that evolved in the form of scale-space theory where the key idea is to represent and analyze an image at various resolutions. Recently, we introduced a notion of local morphometric scale referred to as “tensor scale” using an ellipsoidal model that yields a unified representation of structure size, orientation and anisotropy. In the previous work, tensor scale was described using a 2-D algorithmic approach and a precise analytic definition was missing. Also, the application of tensor scale in 3-D using the previous framework is not practical due to high computational complexity. In this paper, an analytic definition of tensor scale is formulated for n-dimensional (n-D) images that captures local structure size, orientation and anisotropy. Also, an efficient computational solution in 2- and 3-D using several novel differential geometric approaches is presented and the accuracy of results is experimentally examined. Also, a matrix representation of tensor scale is derived facilitating several operations including tensor field smoothing to capture larger contextual knowledge. Finally, the applications of tensor scale in image filtering and n-linear interpolation are presented and the performance of their results is examined in comparison with respective state-of-art methods. Specifically, the performance of tensor scale based image filtering is compared with gradient and Weickert’s structure tensor based diffusive filtering algorithms. Also, the performance of tensor scale based n-linear interpolation is evaluated in comparison with standard n-linear and windowed-sinc interpolation methods. PMID:26236148

  1. A multiresolution approach to iterative reconstruction algorithms in X-ray computed tomography.

    PubMed

    De Witte, Yoni; Vlassenbroeck, Jelle; Van Hoorebeke, Luc

    2010-09-01

    In computed tomography, the application of iterative reconstruction methods in practical situations is impeded by their high computational demands. Especially in high resolution X-ray computed tomography, where reconstruction volumes contain a high number of volume elements (several giga voxels), this computational burden prevents their actual breakthrough. Besides the large amount of calculations, iterative algorithms require the entire volume to be kept in memory during reconstruction, which quickly becomes cumbersome for large data sets. To overcome this obstacle, we present a novel multiresolution reconstruction, which greatly reduces the required amount of memory without significantly affecting the reconstructed image quality. It is shown that, combined with an efficient implementation on a graphical processing unit, the multiresolution approach enables the application of iterative algorithms in the reconstruction of large volumes at an acceptable speed using only limited resources.

  2. Methodological study of computational approaches to address the problem of strong correlations

    NASA Astrophysics Data System (ADS)

    Lee, Juho

    The main focus of this thesis is the detailed investigation of computational methods to tackle strongly correlated materials in which a rich variety of exotic phenomena are found. A many-body problem with sizable electronic correlations can no longer be explained by independent-particle approximations such as density functional theory (DFT) or tight-binding approaches. The influence of an electron to the others is too strong for each electron to be treated as an independent quasiparticle and consequently those standard band-structure methods fail even at a qualitative level. One of the most powerful approaches for strong correlations is the dynamical mean-field theory (DMFT), which has enlightened the understanding of the Mott transition based on the Hubbard model. For realistic applications, the dynamical mean-field theory is combined with various independent-particles approaches. The most widely used one is the DMFT combined with the DFT in the local density approximation (LDA), so-called LDA+DMFT. In this approach, the electrons in the weakly correlated orbitals are calculated by LDA while others in the strongly correlated orbitals are treated by DMFT. Recently, the method combining DMFT with Hedin's GW approximation was also developed, in which the momentum-dependent self-energy is also added. In this thesis, we discuss the application of those methodologies based on DMFT. First, we apply the dynamical mean-field theory to solve the 3-dimensional Hubbard model in Chap. 3. In this application, we model the interface between the thermodynamically coexisting metal and Mott insulator. We show how to model the required slab geometry and extract the electronic spectra. We construct an effective Landau free energy and compute the variation of its parameters across the phase diagram. Finally, using a linear mixture of the density and double-occupancy, we identify a natural Ising order parameter which unifies the treatment of the bandwidth and filling controlled Mott

  3. Computational mechanics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Raboin, P J

    1998-01-01

    The Computational Mechanics thrust area is a vital and growing facet of the Mechanical Engineering Department at Lawrence Livermore National Laboratory (LLNL). This work supports the development of computational analysis tools in the areas of structural mechanics and heat transfer. Over 75 analysts depend on thrust area-supported software running on a variety of computing platforms to meet the demands of LLNL programs. Interactions with the Department of Defense (DOD) High Performance Computing and Modernization Program and the Defense Special Weapons Agency are of special importance as they support our ParaDyn project in its development of new parallel capabilities for DYNA3D.more » Working with DOD customers has been invaluable to driving this technology in directions mutually beneficial to the Department of Energy. Other projects associated with the Computational Mechanics thrust area include work with the Partnership for a New Generation Vehicle (PNGV) for ''Springback Predictability'' and with the Federal Aviation Administration (FAA) for the ''Development of Methodologies for Evaluating Containment and Mitigation of Uncontained Engine Debris.'' In this report for FY-97, there are five articles detailing three code development activities and two projects that synthesized new code capabilities with new analytic research in damage/failure and biomechanics. The article this year are: (1) Energy- and Momentum-Conserving Rigid-Body Contact for NIKE3D and DYNA3D; (2) Computational Modeling of Prosthetics: A New Approach to Implant Design; (3) Characterization of Laser-Induced Mechanical Failure Damage of Optical Components; (4) Parallel Algorithm Research for Solid Mechanics Applications Using Finite Element Analysis; and (5) An Accurate One-Step Elasto-Plasticity Algorithm for Shell Elements in DYNA3D.« less

  4. An accurate binding interaction model in de novo computational protein design of interactions: if you build it, they will bind.

    PubMed

    London, Nir; Ambroggio, Xavier

    2014-02-01

    Computational protein design efforts aim to create novel proteins and functions in an automated manner and, in the process, these efforts shed light on the factors shaping natural proteins. The focus of these efforts has progressed from the interior of proteins to their surface and the design of functions, such as binding or catalysis. Here we examine progress in the development of robust methods for the computational design of non-natural interactions between proteins and molecular targets such as other proteins or small molecules. This problem is referred to as the de novo computational design of interactions. Recent successful efforts in de novo enzyme design and the de novo design of protein-protein interactions open a path towards solving this problem. We examine the common themes in these efforts, and review recent studies aimed at understanding the nature of successes and failures in the de novo computational design of interactions. While several approaches culminated in success, the use of a well-defined structural model for a specific binding interaction in particular has emerged as a key strategy for a successful design, and is therefore reviewed with special consideration. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. An Approach to Experimental Design for the Computer Analysis of Complex Phenomenon

    NASA Technical Reports Server (NTRS)

    Rutherford, Brian

    2000-01-01

    The ability to make credible system assessments, predictions and design decisions related to engineered systems and other complex phenomenon is key to a successful program for many large-scale investigations in government and industry. Recently, many of these large-scale analyses have turned to computational simulation to provide much of the required information. Addressing specific goals in the computer analysis of these complex phenomenon is often accomplished through the use of performance measures that are based on system response models. The response models are constructed using computer-generated responses together with physical test results where possible. They are often based on probabilistically defined inputs and generally require estimation of a set of response modeling parameters. As a consequence, the performance measures are themselves distributed quantities reflecting these variabilities and uncertainties. Uncertainty in the values of the performance measures leads to uncertainties in predicted performance and can cloud the decisions required of the analysis. A specific goal of this research has been to develop methodology that will reduce this uncertainty in an analysis environment where limited resources and system complexity together restrict the number of simulations that can be performed. An approach has been developed that is based on evaluation of the potential information provided for each "intelligently selected" candidate set of computer runs. Each candidate is evaluated by partitioning the performance measure uncertainty into two components - one component that could be explained through the additional computational simulation runs and a second that would remain uncertain. The portion explained is estimated using a probabilistic evaluation of likely results for the additional computational analyses based on what is currently known about the system. The set of runs indicating the largest potential reduction in uncertainty is then selected

  6. Fan Flutter Computations Using the Harmonic Balance Method

    NASA Technical Reports Server (NTRS)

    Bakhle, Milind A.; Thomas, Jeffrey P.; Reddy, T.S.R.

    2009-01-01

    An experimental forward-swept fan encountered flutter at part-speed conditions during wind tunnel testing. A new propulsion aeroelasticity code, based on a computational fluid dynamics (CFD) approach, was used to model the aeroelastic behavior of this fan. This threedimensional code models the unsteady flowfield due to blade vibrations using a harmonic balance method to solve the Navier-Stokes equations. This paper describes the flutter calculations and compares the results to experimental measurements and previous results from a time-accurate propulsion aeroelasticity code.

  7. A Computational Intelligence (CI) Approach to the Precision Mars Lander Problem

    NASA Technical Reports Server (NTRS)

    Birge, Brian; Walberg, Gerald

    2002-01-01

    A Mars precision landing requires a landed footprint of no more than 100 meters. Obstacles to reducing the landed footprint include trajectory dispersions due to initial atmospheric entry conditions such as entry angle, parachute deployment height, environment parameters such as wind, atmospheric density, parachute deployment dynamics, unavoidable injection error or propagated error from launch, etc. Computational Intelligence (CI) techniques such as Artificial Neural Nets and Particle Swarm Optimization have been shown to have great success with other control problems. The research period extended previous work on investigating applicability of the computational intelligent approaches. The focus of this investigation was on Particle Swarm Optimization and basic Neural Net architectures. The research investigating these issues was performed for the grant cycle from 5/15/01 to 5/15/02. Matlab 5.1 and 6.0 along with NASA's POST were the primary computational tools.

  8. Time-Accurate, Unstructured-Mesh Navier-Stokes Computations with the Space-Time CESE Method

    NASA Technical Reports Server (NTRS)

    Chang, Chau-Lyan

    2006-01-01

    Application of the newly emerged space-time conservation element solution element (CESE) method to compressible Navier-Stokes equations is studied. In contrast to Euler equations solvers, several issues such as boundary conditions, numerical dissipation, and grid stiffness warrant systematic investigations and validations. Non-reflecting boundary conditions applied at the truncated boundary are also investigated from the stand point of acoustic wave propagation. Validations of the numerical solutions are performed by comparing with exact solutions for steady-state as well as time-accurate viscous flow problems. The test cases cover a broad speed regime for problems ranging from acoustic wave propagation to 3D hypersonic configurations. Model problems pertinent to hypersonic configurations demonstrate the effectiveness of the CESE method in treating flows with shocks, unsteady waves, and separations. Good agreement with exact solutions suggests that the space-time CESE method provides a viable alternative for time-accurate Navier-Stokes calculations of a broad range of problems.

  9. Fractional labelmaps for computing accurate dose volume histograms

    NASA Astrophysics Data System (ADS)

    Sunderland, Kyle; Pinter, Csaba; Lasso, Andras; Fichtinger, Gabor

    2017-03-01

    PURPOSE: In radiation therapy treatment planning systems, structures are represented as parallel 2D contours. For treatment planning algorithms, structures must be converted into labelmap (i.e. 3D image denoting structure inside/outside) representations. This is often done by triangulated a surface from contours, which is converted into a binary labelmap. This surface to binary labelmap conversion can cause large errors in small structures. Binary labelmaps are often represented using one byte per voxel, meaning a large amount of memory is unused. Our goal is to develop a fractional labelmap representation containing non-binary values, allowing more information to be stored in the same amount of memory. METHODS: We implemented an algorithm in 3D Slicer, which converts surfaces to fractional labelmaps by creating 216 binary labelmaps, changing the labelmap origin on each iteration. The binary labelmap values are summed to create the fractional labelmap. In addition, an algorithm is implemented in the SlicerRT toolkit that calculates dose volume histograms (DVH) using fractional labelmaps. RESULTS: We found that with manually segmented RANDO head and neck structures, fractional labelmaps represented structure volume up to 19.07% (average 6.81%) more accurately than binary labelmaps, while occupying the same amount of memory. When compared to baseline DVH from treatment planning software, DVH from fractional labelmaps had agreement acceptance percent (1% ΔD, 1% ΔV) up to 57.46% higher (average 4.33%) than DVH from binary labelmaps. CONCLUSION: Fractional labelmaps promise to be an effective method for structure representation, allowing considerably more information to be stored in the same amount of memory.

  10. Contextual Computing: A Bluetooth based approach for tracking healthcare providers in the emergency room.

    PubMed

    Frisby, Joshua; Smith, Vernon; Traub, Stephen; Patel, Vimla L

    2017-01-01

    Hospital Emergency Departments (EDs) frequently experience crowding. One of the factors that contributes to this crowding is the "door to doctor time", which is the time from a patient's registration to when the patient is first seen by a physician. This is also one of the Meaningful Use (MU) performance measures that emergency departments report to the Center for Medicare and Medicaid Services (CMS). Current documentation methods for this measure are inaccurate due to the imprecision in manual data collection. We describe a method for automatically (in real time) and more accurately documenting the door to physician time. Using sensor-based technology, the distance between the physician and the computer is calculated by using the single board computers installed in patient rooms that log each time a Bluetooth signal is seen from a device that the physicians carry. This distance is compared automatically with the accepted room radius to determine if the physicians are present in the room at the time logged to provide greater precision. The logged times, accurate to the second, were compared with physicians' handwritten times, showing automatic recordings to be more precise. This real time automatic method will free the physician from extra cognitive load of manually recording data. This method for evaluation of performance is generic and can be used in any other setting outside the ED, and for purposes other than measuring physician time. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Characterization of potential driver mutations involved in human breast cancer by computational approaches

    PubMed Central

    Rajendran, Barani Kumar; Deng, Chu-Xia

    2017-01-01

    Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis. PMID:28477017

  12. Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

    PubMed

    Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

    2015-05-12

    Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.

  13. Computation of entropy and Lyapunov exponent by a shift transform

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Matsuoka, Chihiro, E-mail: matsuoka.chihiro.mm@ehime-u.ac.jp; Hiraide, Koichi

    2015-10-15

    We present a novel computational method to estimate the topological entropy and Lyapunov exponent of nonlinear maps using a shift transform. Unlike the computation of periodic orbits or the symbolic dynamical approach by the Markov partition, the method presented here does not require any special techniques in computational and mathematical fields to calculate these quantities. In spite of its simplicity, our method can accurately capture not only the chaotic region but also the non-chaotic region (window region) such that it is important physically but the (Lebesgue) measure zero and usually hard to calculate or observe. Furthermore, it is shown thatmore » the Kolmogorov-Sinai entropy of the Sinai-Ruelle-Bowen measure (the physical measure) coincides with the topological entropy.« less

  14. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    PubMed

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

    PubMed

    Davenport, Colin F; Neugebauer, Jens; Beckmann, Nils; Friedrich, Benedikt; Kameri, Burim; Kokott, Svea; Paetow, Malte; Siekmann, Björn; Wieding-Drewes, Matthias; Wienhöfer, Markus; Wolf, Stefan; Tümmler, Burkhard; Ahlers, Volker; Sprengel, Frauke

    2012-01-01

    Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer. The Genometa program, a step by step tutorial and Java source code are freely available from http://genomics1.mh-hannover.de/genometa/ and on http://code.google.com/p/genometa/. This program has been tested on Ubuntu Linux and Windows XP/7.

  16. Effects of a Peer Assessment System Based on a Grid-Based Knowledge Classification Approach on Computer Skills Training

    ERIC Educational Resources Information Center

    Hsu, Ting-Chia

    2016-01-01

    In this study, a peer assessment system using the grid-based knowledge classification approach was developed to improve students' performance during computer skills training. To evaluate the effectiveness of the proposed approach, an experiment was conducted in a computer skills certification course. The participants were divided into three…

  17. Soft computing approach to 3D lung nodule segmentation in CT.

    PubMed

    Badura, P; Pietka, E

    2014-10-01

    This paper presents a novel, multilevel approach to the segmentation of various types of pulmonary nodules in computed tomography studies. It is based on two branches of computational intelligence: the fuzzy connectedness (FC) and the evolutionary computation. First, the image and auxiliary data are prepared for the 3D FC analysis during the first stage of an algorithm - the masks generation. Its main goal is to process some specific types of nodules connected to the pleura or vessels. It consists of some basic image processing operations as well as dedicated routines for the specific cases of nodules. The evolutionary computation is performed on the image and seed points in order to shorten the FC analysis and improve its accuracy. After the FC application, the remaining vessels are removed during the postprocessing stage. The method has been validated using the first dataset of studies acquired and described by the Lung Image Database Consortium (LIDC) and by its latest release - the LIDC-IDRI (Image Database Resource Initiative) database. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Rapid and Accurate Multiple Testing Correction and Power Estimation for Millions of Correlated Markers

    PubMed Central

    Han, Buhm; Kang, Hyun Min; Eskin, Eleazar

    2009-01-01

    With the development of high-throughput sequencing and genotyping technologies, the number of markers collected in genetic association studies is growing rapidly, increasing the importance of methods for correcting for multiple hypothesis testing. The permutation test is widely considered the gold standard for accurate multiple testing correction, but it is often computationally impractical for these large datasets. Recently, several studies proposed efficient alternative approaches to the permutation test based on the multivariate normal distribution (MVN). However, they cannot accurately correct for multiple testing in genome-wide association studies for two reasons. First, these methods require partitioning of the genome into many disjoint blocks and ignore all correlations between markers from different blocks. Second, the true null distribution of the test statistic often fails to follow the asymptotic distribution at the tails of the distribution. We propose an accurate and efficient method for multiple testing correction in genome-wide association studies—SLIDE. Our method accounts for all correlation within a sliding window and corrects for the departure of the true null distribution of the statistic from the asymptotic distribution. In simulations using the Wellcome Trust Case Control Consortium data, the error rate of SLIDE's corrected p-values is more than 20 times smaller than the error rate of the previous MVN-based methods' corrected p-values, while SLIDE is orders of magnitude faster than the permutation test and other competing methods. We also extend the MVN framework to the problem of estimating the statistical power of an association study with correlated markers and propose an efficient and accurate power estimation method SLIP. SLIP and SLIDE are available at http://slide.cs.ucla.edu. PMID:19381255

  19. Computational approaches in the design of synthetic receptors - A review.

    PubMed

    Cowen, Todd; Karim, Kal; Piletsky, Sergey

    2016-09-14

    The rational design of molecularly imprinted polymers (MIPs) has been a major contributor to their reputation as "plastic antibodies" - high affinity robust synthetic receptors which can be optimally designed, and produced for a much reduced cost than their biological equivalents. Computational design has become a routine procedure in the production of MIPs, and has led to major advances in functional monomer screening, selection of cross-linker and solvent, optimisation of monomer(s)-template ratio and selectivity analysis. In this review the various computational methods will be discussed with reference to all the published relevant literature since the end of 2013, with each article described by the target molecule, the computational approach applied (whether molecular mechanics/molecular dynamics, semi-empirical quantum mechanics, ab initio quantum mechanics (Hartree-Fock, Møller-Plesset, etc.) or DFT) and the purpose for which they were used. Detailed analysis is given to novel techniques including analysis of polymer binding sites, the use of novel screening programs and simulations of MIP polymerisation reaction. The further advances in molecular modelling and computational design of synthetic receptors in particular will have serious impact on the future of nanotechnology and biotechnology, permitting the further translation of MIPs into the realms of analytics and medical technology. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Possible Computer Vision Systems and Automated or Computer-Aided Edging and Trimming

    Treesearch

    Philip A. Araman

    1990-01-01

    This paper discusses research which is underway to help our industry reduce costs, increase product volume and value recovery, and market more accurately graded and described products. The research is part of a team effort to help the hardwood sawmill industry automate with computer vision systems, and computer-aided or computer controlled processing. This paper...

  1. A Computer-Aided Approach for Designing Edge-Slot Waveguide Arrays

    NASA Technical Reports Server (NTRS)

    Gosselin, Renee Brian

    2003-01-01

    Traditional techniques for designing resonant edge-slot waveguide arrays have required an iterative trial-and-error process of measuring slot data from several prototypes. Since very little meaningful data has been published, this technology remains relatively immature and prohibitive for many smaller programs that could benefit from some advantages this antenna has to offer. A new Computer-Aided Design technique for designing resonant edge-slot waveguide arrays was used to successfuliy design such an X-band radiometer antenna for the NASA Light Rainfall Radiometer (LRR) instrument. Having the ability to rapidly create such an extremely accurate and efficient antenna design without the need to manufacture prototypes has also enabled inexpensive research that promises to improve the system-level performance of microwave radiometers for upcoming space-flight missions. This paper will present details of the LRR antenna design and describe some other current edge-slot array accomplishments at Goddard Space Flight Center.

  2. A fast method to compute Three-Dimensional Infrared Radiative Transfer in non scattering medium

    NASA Astrophysics Data System (ADS)

    Makke, Laurent; Musson-Genon, Luc; Carissimo, Bertrand

    2014-05-01

    The Atmospheric Radiation field has seen the development of more accurate and faster methods to take into account absoprtion in participating media. Radiative fog appears with clear sky condition due to a significant cooling during the night, so scattering is left out. Fog formation modelling requires accurate enough method to compute cooling rates. Thanks to High Performance Computing, multi-spectral approach of Radiative Transfer Equation resolution is most often used. Nevertheless, the coupling of three-dimensionnal radiative transfer with fluid dynamics is very detrimental to the computational cost. To reduce the time spent in radiation calculations, the following method uses analytical absorption functions fitted by Sasamori (1968) on Yamamoto's charts (Yamamoto,1956) to compute a local linear absorption coefficient. By averaging radiative properties, this method eliminates the spectral integration. For an isothermal atmosphere, analytical calculations lead to an explicit formula between emissivities functions and linear absorption coefficient. In the case of cooling to space approximation, this analytical expression gives very accurate results compared to correlated k-distribution. For non homogeneous paths, we propose a two steps algorithm. One-dimensional radiative quantities and linear absorption coefficient are computed by a two-flux method. Then, three-dimensional RTE under the grey medium assumption is solved with the DOM. Comparisons with measurements of radiative quantities during ParisFOG field (2006) shows the cability of this method to handle strong vertical variations of pressure/temperature and gases concentrations.

  3. A Knowledge Engineering Approach to Developing Educational Computer Games for Improving Students' Differentiating Knowledge

    ERIC Educational Resources Information Center

    Hwang, Gwo-Jen; Sung, Han-Yu; Hung, Chun-Ming; Yang, Li-Hsueh; Huang, Iwen

    2013-01-01

    Educational computer games have been recognized as being a promising approach for motivating students to learn. Nevertheless, previous studies have shown that without proper learning strategies or supportive models, the learning achievement of students might not be as good as expected. In this study, a knowledge engineering approach is proposed…

  4. On the accurate estimation of gap fraction during daytime with digital cover photography

    NASA Astrophysics Data System (ADS)

    Hwang, Y. R.; Ryu, Y.; Kimm, H.; Macfarlane, C.; Lang, M.; Sonnentag, O.

    2015-12-01

    Digital cover photography (DCP) has emerged as an indirect method to obtain gap fraction accurately. Thus far, however, the intervention of subjectivity, such as determining the camera relative exposure value (REV) and threshold in the histogram, hindered computing accurate gap fraction. Here we propose a novel method that enables us to measure gap fraction accurately during daytime under various sky conditions by DCP. The novel method computes gap fraction using a single DCP unsaturated raw image which is corrected for scattering effects by canopies and a reconstructed sky image from the raw format image. To test the sensitivity of the novel method derived gap fraction to diverse REVs, solar zenith angles and canopy structures, we took photos in one hour interval between sunrise to midday under dense and sparse canopies with REV 0 to -5. The novel method showed little variation of gap fraction across different REVs in both dense and spares canopies across diverse range of solar zenith angles. The perforated panel experiment, which was used to test the accuracy of the estimated gap fraction, confirmed that the novel method resulted in the accurate and consistent gap fractions across different hole sizes, gap fractions and solar zenith angles. These findings highlight that the novel method opens new opportunities to estimate gap fraction accurately during daytime from sparse to dense canopies, which will be useful in monitoring LAI precisely and validating satellite remote sensing LAI products efficiently.

  5. An Approach for the Accurate Measurement of Social Morality Levels

    PubMed Central

    Liu, Haiyan; Chen, Xia; Zhang, Bo

    2013-01-01

    In the social sciences, computer-based modeling has become an increasingly important tool receiving widespread attention. However, the derivation of the quantitative relationships linking individual moral behavior and social morality levels, so as to provide a useful basis for social policy-making, remains a challenge in the scholarly literature today. A quantitative measurement of morality from the perspective of complexity science constitutes an innovative attempt. Based on the NetLogo platform, this article examines the effect of various factors on social morality levels, using agents modeling moral behavior, immoral behavior, and a range of environmental social resources. Threshold values for the various parameters are obtained through sensitivity analysis; and practical solutions are proposed for reversing declines in social morality levels. The results show that: (1) Population size may accelerate or impede the speed with which immoral behavior comes to determine the overall level of social morality, but it has no effect on the level of social morality itself; (2) The impact of rewards and punishment on social morality levels follows the “5∶1 rewards-to-punishment rule,” which is to say that 5 units of rewards have the same effect as 1 unit of punishment; (3) The abundance of public resources is inversely related to the level of social morality; (4) When the cost of population mobility reaches 10% of the total energy level, immoral behavior begins to be suppressed (i.e. the 1/10 moral cost rule). The research approach and methods presented in this paper successfully address the difficulties involved in measuring social morality levels, and promise extensive application potentials. PMID:24312189

  6. A Computer Vision Approach to Identify Einstein Rings and Arcs

    NASA Astrophysics Data System (ADS)

    Lee, Chien-Hsiu

    2017-03-01

    Einstein rings are rare gems of strong lensing phenomena; the ring images can be used to probe the underlying lens gravitational potential at every position angles, tightly constraining the lens mass profile. In addition, the magnified images also enable us to probe high-z galaxies with enhanced resolution and signal-to-noise ratios. However, only a handful of Einstein rings have been reported, either from serendipitous discoveries or or visual inspections of hundred thousands of massive galaxies or galaxy clusters. In the era of large sky surveys, an automated approach to identify ring pattern in the big data to come is in high demand. Here, we present an Einstein ring recognition approach based on computer vision techniques. The workhorse is the circle Hough transform that recognise circular patterns or arcs in the images. We propose a two-tier approach by first pre-selecting massive galaxies associated with multiple blue objects as possible lens, than use Hough transform to identify circular pattern. As a proof-of-concept, we apply our approach to SDSS, with a high completeness, albeit with low purity. We also apply our approach to other lenses in DES, HSC-SSP, and UltraVISTA survey, illustrating the versatility of our approach.

  7. A New Domain Decomposition Approach for the Gust Response Problem

    NASA Technical Reports Server (NTRS)

    Scott, James R.; Atassi, Hafiz M.; Susan-Resiga, Romeo F.

    2002-01-01

    A domain decomposition method is developed for solving the aerodynamic/aeroacoustic problem of an airfoil in a vortical gust. The computational domain is divided into inner and outer regions wherein the governing equations are cast in different forms suitable for accurate computations in each region. Boundary conditions which ensure continuity of pressure and velocity are imposed along the interface separating the two regions. A numerical study is presented for reduced frequencies ranging from 0.1 to 3.0. It is seen that the domain decomposition approach in providing robust and grid independent solutions.

  8. Computational models for the nonlinear analysis of reinforced concrete plates

    NASA Technical Reports Server (NTRS)

    Hinton, E.; Rahman, H. H. A.; Huq, M. M.

    1980-01-01

    A finite element computational model for the nonlinear analysis of reinforced concrete solid, stiffened and cellular plates is briefly outlined. Typically, Mindlin elements are used to model the plates whereas eccentric Timoshenko elements are adopted to represent the beams. The layering technique, common in the analysis of reinforced concrete flexural systems, is incorporated in the model. The proposed model provides an inexpensive and reasonably accurate approach which can be extended for use with voided plates.

  9. Computational modeling of an endovascular approach to deep brain stimulation

    NASA Astrophysics Data System (ADS)

    Teplitzky, Benjamin A.; Connolly, Allison T.; Bajwa, Jawad A.; Johnson, Matthew D.

    2014-04-01

    Objective. Deep brain stimulation (DBS) therapy currently relies on a transcranial neurosurgical technique to implant one or more electrode leads into the brain parenchyma. In this study, we used computational modeling to investigate the feasibility of using an endovascular approach to target DBS therapy. Approach. Image-based anatomical reconstructions of the human brain and vasculature were used to identify 17 established and hypothesized anatomical targets of DBS, of which five were found adjacent to a vein or artery with intraluminal diameter ≥1 mm. Two of these targets, the fornix and subgenual cingulate white matter (SgCwm) tracts, were further investigated using a computational modeling framework that combined segmented volumes of the vascularized brain, finite element models of the tissue voltage during DBS, and multi-compartment axon models to predict the direct electrophysiological effects of endovascular DBS. Main results. The models showed that: (1) a ring-electrode conforming to the vessel wall was more efficient at neural activation than a guidewire design, (2) increasing the length of a ring-electrode had minimal effect on neural activation thresholds, (3) large variability in neural activation occurred with suboptimal placement of a ring-electrode along the targeted vessel, and (4) activation thresholds for the fornix and SgCwm tracts were comparable for endovascular and stereotactic DBS, though endovascular DBS was able to produce significantly larger contralateral activation for a unilateral implantation. Significance. Together, these results suggest that endovascular DBS can serve as a complementary approach to stereotactic DBS in select cases.

  10. Utilizing Adjoint-Based Error Estimates for Surrogate Models to Accurately Predict Probabilities of Events

    DOE PAGES

    Butler, Troy; Wildey, Timothy

    2018-01-01

    In thist study, we develop a procedure to utilize error estimates for samples of a surrogate model to compute robust upper and lower bounds on estimates of probabilities of events. We show that these error estimates can also be used in an adaptive algorithm to simultaneously reduce the computational cost and increase the accuracy in estimating probabilities of events using computationally expensive high-fidelity models. Specifically, we introduce the notion of reliability of a sample of a surrogate model, and we prove that utilizing the surrogate model for the reliable samples and the high-fidelity model for the unreliable samples gives preciselymore » the same estimate of the probability of the output event as would be obtained by evaluation of the original model for each sample. The adaptive algorithm uses the additional evaluations of the high-fidelity model for the unreliable samples to locally improve the surrogate model near the limit state, which significantly reduces the number of high-fidelity model evaluations as the limit state is resolved. Numerical results based on a recently developed adjoint-based approach for estimating the error in samples of a surrogate are provided to demonstrate (1) the robustness of the bounds on the probability of an event, and (2) that the adaptive enhancement algorithm provides a more accurate estimate of the probability of the QoI event than standard response surface approximation methods at a lower computational cost.« less

  11. Utilizing Adjoint-Based Error Estimates for Surrogate Models to Accurately Predict Probabilities of Events

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Butler, Troy; Wildey, Timothy

    In thist study, we develop a procedure to utilize error estimates for samples of a surrogate model to compute robust upper and lower bounds on estimates of probabilities of events. We show that these error estimates can also be used in an adaptive algorithm to simultaneously reduce the computational cost and increase the accuracy in estimating probabilities of events using computationally expensive high-fidelity models. Specifically, we introduce the notion of reliability of a sample of a surrogate model, and we prove that utilizing the surrogate model for the reliable samples and the high-fidelity model for the unreliable samples gives preciselymore » the same estimate of the probability of the output event as would be obtained by evaluation of the original model for each sample. The adaptive algorithm uses the additional evaluations of the high-fidelity model for the unreliable samples to locally improve the surrogate model near the limit state, which significantly reduces the number of high-fidelity model evaluations as the limit state is resolved. Numerical results based on a recently developed adjoint-based approach for estimating the error in samples of a surrogate are provided to demonstrate (1) the robustness of the bounds on the probability of an event, and (2) that the adaptive enhancement algorithm provides a more accurate estimate of the probability of the QoI event than standard response surface approximation methods at a lower computational cost.« less

  12. Reliability of computer-assisted periacetabular osteotomy using a minimally invasive approach.

    PubMed

    De Raedt, Sepp; Mechlenburg, Inger; Stilling, Maiken; Rømer, Lone; Murphy, Ryan J; Armand, Mehran; Lepistö, Jyri; de Bruijne, Marleen; Søballe, Kjeld

    2018-06-06

    Periacetabular osteotomy (PAO) is the treatment of choice for younger patients with developmental hip dysplasia. The procedure aims to normalize the joint configuration, reduce the peak-pressure, and delay the development of osteoarthritis. The procedure is technically demanding and no previous study has validated the use of computer navigation with a minimally invasive transsartorial approach. Computer-assisted PAO was performed on ten patients. Patients underwent pre- and postoperative computed tomography (CT) scanning with a standardized protocol. Preoperative preparation consisted of outlining the lunate surface and segmenting the pelvis and femur from CT data. The Biomechanical Guidance System was used intra-operatively to automatically calculate diagnostic angles and peak-pressure measurements. Manual diagnostic angle measurements were performed based on pre- and postoperative CT. Differences in angle measurements were investigated with summary statistics, intraclass correlation coefficient, and Bland-Altman plots. The percentage postoperative change in peak-pressure was calculated. Intra-operative reported angle measurements show a good agreement with manual angle measurements with intraclass correlation coefficient between 0.94 and 0.98. Computer navigation reported angle measurements were significantly higher for the posterior sector angle ([Formula: see text], [Formula: see text]) and the acetabular anteversion angle ([Formula: see text], [Formula: see text]). No significant difference was found for the center-edge ([Formula: see text]), acetabular index ([Formula: see text]), and anterior sector angle ([Formula: see text]). Peak-pressure after PAO decreased by a mean of 13% and was significantly different ([Formula: see text]). We found that computer navigation can reliably be used with a minimally invasive transsartorial approach PAO. Angle measurements generally agree with manual measurements and peak-pressure was shown to decrease postoperatively

  13. An automated method for accurate vessel segmentation

    NASA Astrophysics Data System (ADS)

    Yang, Xin; Liu, Chaoyue; Le Minh, Hung; Wang, Zhiwei; Chien, Aichi; (Tim Cheng, Kwang-Ting

    2017-05-01

    Vessel segmentation is a critical task for various medical applications, such as diagnosis assistance of diabetic retinopathy, quantification of cerebral aneurysm’s growth, and guiding surgery in neurosurgical procedures. Despite technology advances in image segmentation, existing methods still suffer from low accuracy for vessel segmentation in the two challenging while common scenarios in clinical usage: (1) regions with a low signal-to-noise-ratio (SNR), and (2) at vessel boundaries disturbed by adjacent non-vessel pixels. In this paper, we present an automated system which can achieve highly accurate vessel segmentation for both 2D and 3D images even under these challenging scenarios. Three key contributions achieved by our system are: (1) a progressive contrast enhancement method to adaptively enhance contrast of challenging pixels that were otherwise indistinguishable, (2) a boundary refinement method to effectively improve segmentation accuracy at vessel borders based on Canny edge detection, and (3) a content-aware region-of-interests (ROI) adjustment method to automatically determine the locations and sizes of ROIs which contain ambiguous pixels and demand further verification. Extensive evaluation of our method is conducted on both 2D and 3D datasets. On a public 2D retinal dataset (named DRIVE (Staal 2004 IEEE Trans. Med. Imaging 23 501-9)) and our 2D clinical cerebral dataset, our approach achieves superior performance to the state-of-the-art methods including a vesselness based method (Frangi 1998 Int. Conf. on Medical Image Computing and Computer-Assisted Intervention) and an optimally oriented flux (OOF) based method (Law and Chung 2008 European Conf. on Computer Vision). An evaluation on 11 clinical 3D CTA cerebral datasets shows that our method can achieve 94% average accuracy with respect to the manual segmentation reference, which is 23% to 33% better than the five baseline methods (Yushkevich 2006 Neuroimage 31 1116-28; Law and Chung 2008

  14. ACCURATE SOLUTION AND GRADIENT COMPUTATION FOR ELLIPTIC INTERFACE PROBLEMS WITH VARIABLE COEFFICIENTS

    PubMed Central

    LI, ZHILIN; JI, HAIFENG; CHEN, XIAOHONG

    2016-01-01

    A new augmented method is proposed for elliptic interface problems with a piecewise variable coefficient that has a finite jump across a smooth interface. The main motivation is not only to get a second order accurate solution but also a second order accurate gradient from each side of the interface. The key of the new method is to introduce the jump in the normal derivative of the solution as an augmented variable and re-write the interface problem as a new PDE that consists of a leading Laplacian operator plus lower order derivative terms near the interface. In this way, the leading second order derivatives jump relations are independent of the jump in the coefficient that appears only in the lower order terms after the scaling. An upwind type discretization is used for the finite difference discretization at the irregular grid points near or on the interface so that the resulting coefficient matrix is an M-matrix. A multi-grid solver is used to solve the linear system of equations and the GMRES iterative method is used to solve the augmented variable. Second order convergence for the solution and the gradient from each side of the interface has also been proved in this paper. Numerical examples for general elliptic interface problems have confirmed the theoretical analysis and efficiency of the new method. PMID:28983130

  15. A deep learning approach to estimate stress distribution: a fast and accurate surrogate of finite-element analysis.

    PubMed

    Liang, Liang; Liu, Minliang; Martin, Caitlin; Sun, Wei

    2018-01-01

    Structural finite-element analysis (FEA) has been widely used to study the biomechanics of human tissues and organs, as well as tissue-medical device interactions, and treatment strategies. However, patient-specific FEA models usually require complex procedures to set up and long computing times to obtain final simulation results, preventing prompt feedback to clinicians in time-sensitive clinical applications. In this study, by using machine learning techniques, we developed a deep learning (DL) model to directly estimate the stress distributions of the aorta. The DL model was designed and trained to take the input of FEA and directly output the aortic wall stress distributions, bypassing the FEA calculation process. The trained DL model is capable of predicting the stress distributions with average errors of 0.492% and 0.891% in the Von Mises stress distribution and peak Von Mises stress, respectively. This study marks, to our knowledge, the first study that demonstrates the feasibility and great potential of using the DL technique as a fast and accurate surrogate of FEA for stress analysis. © 2018 The Author(s).

  16. A high-throughput screening approach for the optoelectronic properties of conjugated polymers.

    PubMed

    Wilbraham, Liam; Berardo, Enrico; Turcani, Lukas; Jelfs, Kim E; Zwijnenburg, Martijn A

    2018-06-25

    We propose a general high-throughput virtual screening approach for the optical and electronic properties of conjugated polymers. This approach makes use of the recently developed xTB family of low-computational-cost density functional tight-binding methods from Grimme and co-workers, calibrated here to (TD-)DFT data computed for a representative diverse set of (co-)polymers. Parameters drawn from the resulting calibration using a linear model can then be applied to the xTB derived results for new polymers, thus generating near DFT-quality data with orders of magnitude reduction in computational cost. As a result, after an initial computational investment for calibration, this approach can be used to quickly and accurately screen on the order of thousands of polymers for target applications. We also demonstrate that the (opto)electronic properties of the conjugated polymers show only a very minor variation when considering different conformers and that the results of high-throughput screening are therefore expected to be relatively insensitive with respect to the conformer search methodology applied.

  17. Computational approaches to protein inference in shotgun proteomics

    PubMed Central

    2012-01-01

    Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput manner by coupling liquid chromatography with tandem mass spectrometry. As a consequence of its high throughput nature, shotgun proteomics faces challenges with respect to the analysis and interpretation of experimental data. Among such challenges, the identification of proteins present in a sample has been recognized as an important computational task. This task generally consists of (1) assigning experimental tandem mass spectra to peptides derived from a protein database, and (2) mapping assigned peptides to proteins and quantifying the confidence of identified proteins. Protein identification is fundamentally a statistical inference problem with a number of methods proposed to address its challenges. In this review we categorize current approaches into rule-based, combinatorial optimization and probabilistic inference techniques, and present them using integer programing and Bayesian inference frameworks. We also discuss the main challenges of protein identification and propose potential solutions with the goal of spurring innovative research in this area. PMID:23176300

  18. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin

    DOE PAGES

    Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; ...

    2016-07-08

    In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co III, Co II, and Co I species, respectively, and the second model features saturation of each vacant axial coordination site on Co II and Co I species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pK as and 2.3 log units for two log K on/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in

  19. An efficient and accurate technique to compute the absorption, emission, and transmission of radiation by the Martian atmosphere

    NASA Technical Reports Server (NTRS)

    Lindner, Bernhard Lee; Ackerman, Thomas P.; Pollack, James B.

    1990-01-01

    CO2 comprises 95 pct. of the composition of the Martian atmosphere. However, the Martian atmosphere also has a high aerosol content. Dust particles vary from less than 0.2 to greater than 3.0. CO2 is an active absorber and emitter in near IR and IR wavelengths; the near IR absorption bands of CO2 provide significant heating of the atmosphere, and the 15 micron band provides rapid cooling. Including both CO2 and aerosol radiative transfer simultaneously in a model is difficult. Aerosol radiative transfer requires a multiple scattering code, while CO2 radiative transfer must deal with complex wavelength structure. As an alternative to the pure atmosphere treatment in most models which causes inaccuracies, a treatment was developed called the exponential sum or k distribution approximation. The chief advantage of the exponential sum approach is that the integration over k space of f(k) can be computed more quickly than the integration of k sub upsilon over frequency. The exponential sum approach is superior to the photon path distribution and emissivity techniques for dusty conditions. This study was the first application of the exponential sum approach to Martian conditions.

  20. Computation of Transonic Nozzle Sound Transmission and Rotor Problems by the Dispersion-Relation-Preserving Scheme

    NASA Technical Reports Server (NTRS)

    Tam, Christopher K. W.; Aganin, Alexei

    2000-01-01

    The transonic nozzle transmission problem and the open rotor noise radiation problem are solved computationally. Both are multiple length scales problems. For efficient and accurate numerical simulation, the multiple-size-mesh multiple-time-step Dispersion-Relation-Preserving scheme is used to calculate the time periodic solution. To ensure an accurate solution, high quality numerical boundary conditions are also needed. For the nozzle problem, a set of nonhomogeneous, outflow boundary conditions are required. The nonhomogeneous boundary conditions not only generate the incoming sound waves but also, at the same time, allow the reflected acoustic waves and entropy waves, if present, to exit the computation domain without reflection. For the open rotor problem, there is an apparent singularity at the axis of rotation. An analytic extension approach is developed to provide a high quality axis boundary treatment.

  1. The Effective-One-Body Approach to the General Relativistic Two Body Problem

    NASA Astrophysics Data System (ADS)

    Damour, Thibault; Nagar, Alessandro

    The two-body problem in General Relativity has been the subject of many analytical investigations. After reviewing some of the methods used to tackle this problem (and, more generally, the N-body problem), we focus on a new, recently introduced approach to the motion and radiation of (comparable mass) binary systems: the Effective One Body (EOB) formalism. We review the basic elements of this formalism, and discuss some of its recent developments. Several recent comparisons between EOB predictions and Numerical Relativity (NR) simulations have shown the aptitude of the EOB formalism to provide accurate descriptions of the dynamics and radiation of various binary systems (comprising black holes or neutron stars) in regimes that are inaccessible to other analytical approaches (such as the last orbits and the merger of comparable mass black holes). In synergy with NR simulations, post-Newtonian (PN) theory and Gravitational Self-Force (GSF) computations, the EOB formalism is likely to provide an efficient way of computing the very many accurate template waveforms that are needed for Gravitational Wave (GW) data analysis purposes.

  2. Oligomerization of G protein-coupled receptors: computational methods.

    PubMed

    Selent, J; Kaczor, A A

    2011-01-01

    Recent research has unveiled the complexity of mechanisms involved in G protein-coupled receptor (GPCR) functioning in which receptor dimerization/oligomerization may play an important role. Although the first high-resolution X-ray structure for a likely functional chemokine receptor dimer has been deposited in the Protein Data Bank, the interactions and mechanisms of dimer formation are not yet fully understood. In this respect, computational methods play a key role for predicting accurate GPCR complexes. This review outlines computational approaches focusing on sequence- and structure-based methodologies as well as discusses their advantages and limitations. Sequence-based approaches that search for possible protein-protein interfaces in GPCR complexes have been applied with success in several studies, but did not yield always consistent results. Structure-based methodologies are a potent complement to sequence-based approaches. For instance, protein-protein docking is a valuable method especially when guided by experimental constraints. Some disadvantages like limited receptor flexibility and non-consideration of the membrane environment have to be taken into account. Molecular dynamics simulation can overcome these drawbacks giving a detailed description of conformational changes in a native-like membrane. Successful prediction of GPCR complexes using computational approaches combined with experimental efforts may help to understand the role of dimeric/oligomeric GPCR complexes for fine-tuning receptor signaling. Moreover, since such GPCR complexes have attracted interest as potential drug target for diverse diseases, unveiling molecular determinants of dimerization/oligomerization can provide important implications for drug discovery.

  3. Computational approach to integrate 3D X-ray microtomography and NMR data.

    PubMed

    Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G; Trevizan, Willian A; Fortulan, Carlos A; Bonagamba, Tito J

    2018-05-04

    Nowadays, most of the efforts in NMR applied to porous media are dedicated to studying the molecular fluid dynamics within and among the pores. These analyses have a higher complexity due to morphology and chemical composition of rocks, besides dynamic effects as restricted diffusion, diffusional coupling, and exchange processes. Since the translational nuclear spin diffusion in a confined geometry (e.g. pores and fractures) requires specific boundary conditions, the theoretical solutions are restricted to some special problems and, in many cases, computational methods are required. The Random Walk Method is a classic way to simulate self-diffusion along a Digital Porous Medium. Bergman model considers the magnetic relaxation process of the fluid molecules by including a probability rate of magnetization survival under surface interactions. Here we propose a statistical approach to correlate surface magnetic relaxivity with the computational method applied to the NMR relaxation in order to elucidate the relationship between simulated relaxation time and pore size of the Digital Porous Medium. The proposed computational method simulates one- and two-dimensional NMR techniques reproducing, for example, longitudinal and transverse relaxation times (T 1 and T 2 , respectively), diffusion coefficients (D), as well as their correlations. For a good approximation between the numerical and experimental results, it is necessary to preserve the complexity of translational diffusion through the microstructures in the digital rocks. Therefore, we use Digital Porous Media obtained by 3D X-ray microtomography. To validate the method, relaxation times of ideal spherical pores were obtained and compared with the previous determinations by the Brownstein-Tarr model, as well as the computational approach proposed by Bergman. Furthermore, simulated and experimental results of synthetic porous media are compared. These results make evident the potential of computational physics in the

  4. Computational approach to integrate 3D X-ray microtomography and NMR data

    NASA Astrophysics Data System (ADS)

    Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G.; Trevizan, Willian A.; Fortulan, Carlos A.; Bonagamba, Tito J.

    2018-07-01

    Nowadays, most of the efforts in NMR applied to porous media are dedicated to studying the molecular fluid dynamics within and among the pores. These analyses have a higher complexity due to morphology and chemical composition of rocks, besides dynamic effects as restricted diffusion, diffusional coupling, and exchange processes. Since the translational nuclear spin diffusion in a confined geometry (e.g. pores and fractures) requires specific boundary conditions, the theoretical solutions are restricted to some special problems and, in many cases, computational methods are required. The Random Walk Method is a classic way to simulate self-diffusion along a Digital Porous Medium. Bergman model considers the magnetic relaxation process of the fluid molecules by including a probability rate of magnetization survival under surface interactions. Here we propose a statistical approach to correlate surface magnetic relaxivity with the computational method applied to the NMR relaxation in order to elucidate the relationship between simulated relaxation time and pore size of the Digital Porous Medium. The proposed computational method simulates one- and two-dimensional NMR techniques reproducing, for example, longitudinal and transverse relaxation times (T1 and T2, respectively), diffusion coefficients (D), as well as their correlations. For a good approximation between the numerical and experimental results, it is necessary to preserve the complexity of translational diffusion through the microstructures in the digital rocks. Therefore, we use Digital Porous Media obtained by 3D X-ray microtomography. To validate the method, relaxation times of ideal spherical pores were obtained and compared with the previous determinations by the Brownstein-Tarr model, as well as the computational approach proposed by Bergman. Furthermore, simulated and experimental results of synthetic porous media are compared. These results make evident the potential of computational physics in the

  5. Multi-Objective Approach for Energy-Aware Workflow Scheduling in Cloud Computing Environments

    PubMed Central

    Kadima, Hubert; Granado, Bertrand

    2013-01-01

    We address the problem of scheduling workflow applications on heterogeneous computing systems like cloud computing infrastructures. In general, the cloud workflow scheduling is a complex optimization problem which requires considering different criteria so as to meet a large number of QoS (Quality of Service) requirements. Traditional research in workflow scheduling mainly focuses on the optimization constrained by time or cost without paying attention to energy consumption. The main contribution of this study is to propose a new approach for multi-objective workflow scheduling in clouds, and present the hybrid PSO algorithm to optimize the scheduling performance. Our method is based on the Dynamic Voltage and Frequency Scaling (DVFS) technique to minimize energy consumption. This technique allows processors to operate in different voltage supply levels by sacrificing clock frequencies. This multiple voltage involves a compromise between the quality of schedules and energy. Simulation results on synthetic and real-world scientific applications highlight the robust performance of the proposed approach. PMID:24319361

  6. Multi-objective approach for energy-aware workflow scheduling in cloud computing environments.

    PubMed

    Yassa, Sonia; Chelouah, Rachid; Kadima, Hubert; Granado, Bertrand

    2013-01-01

    We address the problem of scheduling workflow applications on heterogeneous computing systems like cloud computing infrastructures. In general, the cloud workflow scheduling is a complex optimization problem which requires considering different criteria so as to meet a large number of QoS (Quality of Service) requirements. Traditional research in workflow scheduling mainly focuses on the optimization constrained by time or cost without paying attention to energy consumption. The main contribution of this study is to propose a new approach for multi-objective workflow scheduling in clouds, and present the hybrid PSO algorithm to optimize the scheduling performance. Our method is based on the Dynamic Voltage and Frequency Scaling (DVFS) technique to minimize energy consumption. This technique allows processors to operate in different voltage supply levels by sacrificing clock frequencies. This multiple voltage involves a compromise between the quality of schedules and energy. Simulation results on synthetic and real-world scientific applications highlight the robust performance of the proposed approach.

  7. Computational Chemical Imaging for Cardiovascular Pathology: Chemical Microscopic Imaging Accurately Determines Cardiac Transplant Rejection

    PubMed Central

    Tiwari, Saumya; Reddy, Vijaya B.; Bhargava, Rohit; Raman, Jaishankar

    2015-01-01

    Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR) spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients’ biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures. PMID:25932912

  8. Meso-scale framework for modeling granular material using computed tomography

    DOE PAGES

    Turner, Anne K.; Kim, Felix H.; Penumadu, Dayakar; ...

    2016-03-17

    Numerical modeling of unconsolidated granular materials is comprised of multiple nonlinear phenomena. Accurately capturing these phenomena, including grain deformation and intergranular forces depends on resolving contact regions several orders of magnitude smaller than the grain size. Here, we investigate a method for capturing the morphology of the individual particles using computed X-ray and neutron tomography, which allows for accurate characterization of the interaction between grains. The ability of these numerical approaches to determine stress concentrations at grain contacts is important in order to capture catastrophic splitting of individual grains, which has been shown to play a key role in themore » plastic behavior of the granular material on the continuum level. Discretization approaches, including mesh refinement and finite element type selection are presented to capture high stress concentrations at contact points between grains. The effect of a grain’s coordination number on the stress concentrations is also investigated.« less

  9. Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

    USGS Publications Warehouse

    Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

    2004-01-01

    A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

  10. Accurate HLA type inference using a weighted similarity graph.

    PubMed

    Xie, Minzhu; Li, Jing; Jiang, Tao

    2010-12-14

    The human leukocyte antigen system (HLA) contains many highly variable genes. HLA genes play an important role in the human immune system, and HLA gene matching is crucial for the success of human organ transplantations. Numerous studies have demonstrated that variation in HLA genes is associated with many autoimmune, inflammatory and infectious diseases. However, typing HLA genes by serology or PCR is time consuming and expensive, which limits large-scale studies involving HLA genes. Since it is much easier and cheaper to obtain single nucleotide polymorphism (SNP) genotype data, accurate computational algorithms to infer HLA gene types from SNP genotype data are in need. To infer HLA types from SNP genotypes, the first step is to infer SNP haplotypes from genotypes. However, for the same SNP genotype data set, the haplotype configurations inferred by different methods are usually inconsistent, and it is often difficult to decide which one is true. In this paper, we design an accurate HLA gene type inference algorithm by utilizing SNP genotype data from pedigrees, known HLA gene types of some individuals and the relationship between inferred SNP haplotypes and HLA gene types. Given a set of haplotypes inferred from the genotypes of a population consisting of many pedigrees, the algorithm first constructs a weighted similarity graph based on a new haplotype similarity measure and derives constraint edges from known HLA gene types. Based on the principle that different HLA gene alleles should have different background haplotypes, the algorithm searches for an optimal labeling of all the haplotypes with unknown HLA gene types such that the total weight among the same HLA gene types is maximized. To deal with ambiguous haplotype solutions, we use a genetic algorithm to select haplotype configurations that tend to maximize the same optimization criterion. Our experiments on a previously typed subset of the HapMap data show that the algorithm is highly accurate

  11. Cross-Talk in Superconducting Transmon Quantum Computing Architecture

    NASA Astrophysics Data System (ADS)

    Abraham, David; Chow, Jerry; Corcoles, Antonio; Rothwell, Mary; Keefe, George; Gambetta, Jay; Steffen, Matthias; IBM Quantum Computing Team

    2013-03-01

    Superconducting transmon quantum computing test structures often exhibit significant undesired cross-talk. For experiments with only a handful of qubits this cross-talk can be quantified and understood, and therefore corrected. As quantum computing circuits become more complex, and thereby contain increasing numbers of qubits and resonators, it becomes more vital that the inadvertent coupling between these elements is minimized. The task of accurately controlling each single qubit to the level of precision required throughout the realization of a quantum algorithm is difficult by itself, but coupled with the need of nulling out leakage signals from neighboring qubits or resonators would quickly become impossible. We discuss an approach to solve this critical problem. We acknowledge support from IARPA under contract W911NF-10-1-0324.

  12. Computer-aided detection and quantification of endolymphatic hydrops within the mouse cochlea in vivo using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Liu, George S.; Kim, Jinkyung; Applegate, Brian E.; Oghalai, John S.

    2017-07-01

    Diseases that cause hearing loss and/or vertigo in humans such as Meniere's disease are often studied using animal models. The volume of endolymph within the inner ear varies with these diseases. Here, we used a mouse model of increased endolymph volume, endolymphatic hydrops, to develop a computer-aided objective approach to measure endolymph volume from images collected in vivo using optical coherence tomography. The displacement of Reissner's membrane from its normal position was measured in cochlear cross sections. We validated our computer-aided measurements with manual measurements and with trained observer labels. This approach allows for computer-aided detection of endolymphatic hydrops in mice, with test performance showing sensitivity of 91% and specificity of 87% using a running average of five measurements. These findings indicate that this approach is accurate and reliable for classifying endolymphatic hydrops and quantifying endolymph volume.

  13. On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems

    NASA Astrophysics Data System (ADS)

    Junge, Oliver; Kevrekidis, Ioannis G.

    2017-06-01

    We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

  14. On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems.

    PubMed

    Junge, Oliver; Kevrekidis, Ioannis G

    2017-06-01

    We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.

  15. Computing Accurate Grammatical Feedback in a Virtual Writing Conference for German-Speaking Elementary-School Children: An Approach Based on Natural Language Generation

    ERIC Educational Resources Information Center

    Harbusch, Karin; Itsova, Gergana; Koch, Ulrich; Kuhner, Christine

    2009-01-01

    We built a natural language processing (NLP) system implementing a "virtual writing conference" for elementary-school children, with German as the target language. Currently, state-of-the-art computer support for writing tasks is restricted to multiple-choice questions or quizzes because automatic parsing of the often ambiguous and fragmentary…

  16. A Very High Order, Adaptable MESA Implementation for Aeroacoustic Computations

    NASA Technical Reports Server (NTRS)

    Dydson, Roger W.; Goodrich, John W.

    2000-01-01

    Since computational efficiency and wave resolution scale with accuracy, the ideal would be infinitely high accuracy for problems with widely varying wavelength scales. Currently, many of the computational aeroacoustics methods are limited to 4th order accurate Runge-Kutta methods in time which limits their resolution and efficiency. However, a new procedure for implementing the Modified Expansion Solution Approximation (MESA) schemes, based upon Hermitian divided differences, is presented which extends the effective accuracy of the MESA schemes to 57th order in space and time when using 128 bit floating point precision. This new approach has the advantages of reducing round-off error, being easy to program. and is more computationally efficient when compared to previous approaches. Its accuracy is limited only by the floating point hardware. The advantages of this new approach are demonstrated by solving the linearized Euler equations in an open bi-periodic domain. A 500th order MESA scheme can now be created in seconds, making these schemes ideally suited for the next generation of high performance 256-bit (double quadruple) or higher precision computers. This ease of creation makes it possible to adapt the algorithm to the mesh in time instead of its converse: this is ideal for resolving varying wavelength scales which occur in noise generation simulations. And finally, the sources of round-off error which effect the very high order methods are examined and remedies provided that effectively increase the accuracy of the MESA schemes while using current computer technology.

  17. Exploiting Self-organization in Bioengineered Systems: A Computational Approach.

    PubMed

    Davis, Delin; Doloman, Anna; Podgorski, Gregory J; Vargis, Elizabeth; Flann, Nicholas S

    2017-01-01

    The productivity of bioengineered cell factories is limited by inefficiencies in nutrient delivery and waste and product removal. Current solution approaches explore changes in the physical configurations of the bioreactors. This work investigates the possibilities of exploiting self-organizing vascular networks to support producer cells within the factory. A computational model simulates de novo vascular development of endothelial-like cells and the resultant network functioning to deliver nutrients and extract product and waste from the cell culture. Microbial factories with vascular networks are evaluated for their scalability, robustness, and productivity compared to the cell factories without a vascular network. Initial studies demonstrate that at least an order of magnitude increase in production is possible, the system can be scaled up, and the self-organization of an efficient vascular network is robust. The work suggests that bioengineered multicellularity may offer efficiency improvements difficult to achieve with physical engineering approaches.

  18. Computational approaches to define a human milk metaglycome

    PubMed Central

    Agravat, Sanjay B.; Song, Xuezheng; Rojsajjakul, Teerapat; Cummings, Richard D.; Smith, David F.

    2016-01-01

    Motivation: The goal of deciphering the human glycome has been hindered by the lack of high-throughput sequencing methods for glycans. Although mass spectrometry (MS) is a key technology in glycan sequencing, MS alone provides limited information about the identification of monosaccharide constituents, their anomericity and their linkages. These features of individual, purified glycans can be partly identified using well-defined glycan-binding proteins, such as lectins and antibodies that recognize specific determinants within glycan structures. Results: We present a novel computational approach to automate the sequencing of glycans using metadata-assisted glycan sequencing, which combines MS analyses with glycan structural information from glycan microarray technology. Success in this approach was aided by the generation of a ‘virtual glycome’ to represent all potential glycan structures that might exist within a metaglycomes based on a set of biosynthetic assumptions using known structural information. We exploited this approach to deduce the structures of soluble glycans within the human milk glycome by matching predicted structures based on experimental data against the virtual glycome. This represents the first meta-glycome to be defined using this method and we provide a publically available web-based application to aid in sequencing milk glycans. Availability and implementation: http://glycomeseq.emory.edu Contact: sagravat@bidmc.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26803164

  19. Time Accurate Unsteady Pressure Loads Simulated for the Space Launch System at a Wind Tunnel Condition

    NASA Technical Reports Server (NTRS)

    Alter, Stephen J.; Brauckmann, Gregory J.; Kleb, Bil; Streett, Craig L; Glass, Christopher E.; Schuster, David M.

    2015-01-01

    Using the Fully Unstructured Three-Dimensional (FUN3D) computational fluid dynamics code, an unsteady, time-accurate flow field about a Space Launch System configuration was simulated at a transonic wind tunnel condition (Mach = 0.9). Delayed detached eddy simulation combined with Reynolds Averaged Naiver-Stokes and a Spallart-Almaras turbulence model were employed for the simulation. Second order accurate time evolution scheme was used to simulate the flow field, with a minimum of 0.2 seconds of simulated time to as much as 1.4 seconds. Data was collected at 480 pressure taps at locations, 139 of which matched a 3% wind tunnel model, tested in the Transonic Dynamic Tunnel (TDT) facility at NASA Langley Research Center. Comparisons between computation and experiment showed agreement within 5% in terms of location for peak RMS levels, and 20% for frequency and magnitude of power spectral densities. Grid resolution and time step sensitivity studies were performed to identify methods for improved accuracy comparisons to wind tunnel data. With limited computational resources, accurate trends for reduced vibratory loads on the vehicle were observed. Exploratory methods such as determining minimized computed errors based on CFL number and sub-iterations, as well as evaluating frequency content of the unsteady pressures and evaluation of oscillatory shock structures were used in this study to enhance computational efficiency and solution accuracy. These techniques enabled development of a set of best practices, for the evaluation of future flight vehicle designs in terms of vibratory loads.

  20. Deciphering Epithelial–Mesenchymal Transition Regulatory Networks in Cancer through Computational Approaches

    PubMed Central

    Burger, Gerhard A.; Danen, Erik H. J.; Beltman, Joost B.

    2017-01-01

    Epithelial–mesenchymal transition (EMT), the process by which epithelial cells can convert into motile mesenchymal cells, plays an important role in development and wound healing but is also involved in cancer progression. It is increasingly recognized that EMT is a dynamic process involving multiple intermediate or “hybrid” phenotypes rather than an “all-or-none” process. However, the role of EMT in various cancer hallmarks, including metastasis, is debated. Given the complexity of EMT regulation, computational modeling has proven to be an invaluable tool for cancer research, i.e., to resolve apparent conflicts in experimental data and to guide experiments by generating testable hypotheses. In this review, we provide an overview of computational modeling efforts that have been applied to regulation of EMT in the context of cancer progression and its associated tumor characteristics. Moreover, we identify possibilities to bridge different modeling approaches and point out outstanding questions in which computational modeling can contribute to advance our understanding of pathological EMT. PMID:28824874

  1. An Integrated Approach to Teaching Students the Use of Computers in Science.

    ERIC Educational Resources Information Center

    Hood, B. James

    1991-01-01

    Reported is an approach to teaching the use of Macintosh computers to sixth, seventh, and eighth grade students within the context of a simplified model of scientific research including proposal, data collection and analyses, and presentation of findings. Word processing, graphing, statistical, painting, and poster software were sequentially…

  2. Computer-assisted neurosurgical navigational system for transsphenoidal surgery--technical note.

    PubMed

    Onizuka, M; Tokunaga, Y; Shibayama, A; Miyazaki, H

    2001-11-01

    Transsphenoidal surgery carries the risk of carotid artery injury even for very experienced neurosurgeons. The computer-assisted neurosurgical (CANS) navigational system was used to obtain more precise guidance, based on the axial and coronal images during the transsphenoidal approach for nine pituitary adenomas. The CANS navigator consists of a three-dimensional digitizer, a computer, and a graphic unit, which utilizes electromagnetic coupling technology to detect the spatial position of a suction tube attached to a magnetic sensor. Preoperatively, the magnetic resonance images are transferred and stored in the computer and the tip of the suction tube is shown on a real-time basis superimposed on the preoperative images. The CANS navigation system correctly displayed the surgical orientation and provided localization in all nine patients. No intraoperative complications were associated with the use of this system. However, outflow of cerebrospinal fluid during tumor removal may affect the accuracy, so the position of the probe when the tumor is removed must be accurately determined. The CANS navigator enables precise localization of the suction tube during the transsphenoidal approach and allows safer and less-invasive surgery.

  3. A computer-aided approach to detect the fetal behavioral states using multi-sensor Magnetocardiographic recordings.

    PubMed

    Vairavan, S; Ulusar, U D; Eswaran, H; Preissl, H; Wilson, J D; Mckelvey, S S; Lowery, C L; Govindan, R B

    2016-02-01

    We propose a novel computational approach to automatically identify the fetal heart rate patterns (fHRPs), which are reflective of sleep/awake states. By combining these patterns with presence or absence of movements, a fetal behavioral state (fBS) was determined. The expert scores were used as the gold standard and objective thresholds for the detection procedure were obtained using Receiver Operating Characteristics (ROC) analysis. To assess the performance, intraclass correlation was computed between the proposed approach and the mutually agreed expert scores. The detected fHRPs were then associated to their corresponding fBS based on the fetal movement obtained from fetal magnetocardiogaphic (fMCG) signals. This approach may aid clinicians in objectively assessing the fBS and monitoring fetal wellbeing. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Matrix-vector multiplication using digital partitioning for more accurate optical computing

    NASA Technical Reports Server (NTRS)

    Gary, C. K.

    1992-01-01

    Digital partitioning offers a flexible means of increasing the accuracy of an optical matrix-vector processor. This algorithm can be implemented with the same architecture required for a purely analog processor, which gives optical matrix-vector processors the ability to perform high-accuracy calculations at speeds comparable with or greater than electronic computers as well as the ability to perform analog operations at a much greater speed. Digital partitioning is compared with digital multiplication by analog convolution, residue number systems, and redundant number representation in terms of the size and the speed required for an equivalent throughput as well as in terms of the hardware requirements. Digital partitioning and digital multiplication by analog convolution are found to be the most efficient alogrithms if coding time and hardware are considered, and the architecture for digital partitioning permits the use of analog computations to provide the greatest throughput for a single processor.

  5. Applications of computer-aided approaches in the development of hepatitis C antiviral agents.

    PubMed

    Ganesan, Aravindhan; Barakat, Khaled

    2017-04-01

    Hepatitis C virus (HCV) is a global health problem that causes several chronic life-threatening liver diseases. The numbers of people affected by HCV are rising annually. Since 2011, the FDA has approved several anti-HCV drugs; while many other promising HCV drugs are currently in late clinical trials. Areas covered: This review discusses the applications of different computational approaches in HCV drug design. Expert opinion: Molecular docking and virtual screening approaches have emerged as a low-cost tool to screen large databases and identify potential small-molecule hits against HCV targets. Ligand-based approaches are useful for filtering-out compounds with rich physicochemical properties to inhibit HCV targets. Molecular dynamics (MD) remains a useful tool in optimizing the ligand-protein complexes and understand the ligand binding modes and drug resistance mechanisms in HCV. Despite their varied roles, the application of in-silico approaches in HCV drug design is still in its infancy. A more mature application should aim at modelling the whole HCV replicon in its active form and help to identify new effective druggable sites within the replicon system. With more technological advancements, the roles of computer-aided methods are only going to increase several folds in the development of next-generation HCV drugs.

  6. Approaches to Classroom-Based Computational Science.

    ERIC Educational Resources Information Center

    Guzdial, Mark

    Computational science includes the use of computer-based modeling and simulation to define and test theories about scientific phenomena. The challenge for educators is to develop techniques for implementing computational science in the classroom. This paper reviews some previous work on the use of simulation alone (without modeling), modeling…

  7. A Computational Approach for Probabilistic Analysis of Water Impact Simulations

    NASA Technical Reports Server (NTRS)

    Horta, Lucas G.; Mason, Brian H.; Lyle, Karen H.

    2009-01-01

    NASA's development of new concepts for the Crew Exploration Vehicle Orion presents many similar challenges to those worked in the sixties during the Apollo program. However, with improved modeling capabilities, new challenges arise. For example, the use of the commercial code LS-DYNA, although widely used and accepted in the technical community, often involves high-dimensional, time consuming, and computationally intensive simulations. The challenge is to capture what is learned from a limited number of LS-DYNA simulations to develop models that allow users to conduct interpolation of solutions at a fraction of the computational time. This paper presents a description of the LS-DYNA model, a brief summary of the response surface techniques, the analysis of variance approach used in the sensitivity studies, equations used to estimate impact parameters, results showing conditions that might cause injuries, and concluding remarks.

  8. Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: Application to H2O, N2H+, NO2+, and C2H2

    NASA Astrophysics Data System (ADS)

    Huang, Xinchuan; Valeev, Edward F.; Lee, Timothy J.

    2010-12-01

    One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H2O, N2H+, NO2+, and C2H2 molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N2H+ where it is concluded that basis set extrapolation is still preferred. The differences for H2O and NO2+ are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C2H2, however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)R12, incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N2H+ and NO2+ were computed, including basis set extrapolation, core-correlation, scalar relativity, and higher

  9. Templet Web: the use of volunteer computing approach in PaaS-style cloud

    NASA Astrophysics Data System (ADS)

    Vostokin, Sergei; Artamonov, Yuriy; Tsarev, Daniil

    2018-03-01

    This article presents the Templet Web cloud service. The service is designed for high-performance scientific computing automation. The use of high-performance technology is specifically required by new fields of computational science such as data mining, artificial intelligence, machine learning, and others. Cloud technologies provide a significant cost reduction for high-performance scientific applications. The main objectives to achieve this cost reduction in the Templet Web service design are: (a) the implementation of "on-demand" access; (b) source code deployment management; (c) high-performance computing programs development automation. The distinctive feature of the service is the approach mainly used in the field of volunteer computing, when a person who has access to a computer system delegates his access rights to the requesting user. We developed an access procedure, algorithms, and software for utilization of free computational resources of the academic cluster system in line with the methods of volunteer computing. The Templet Web service has been in operation for five years. It has been successfully used for conducting laboratory workshops and solving research problems, some of which are considered in this article. The article also provides an overview of research directions related to service development.

  10. Moment-Preserving Computational Approach for High Energy Charged Particle Transport

    DTIC Science & Technology

    2016-05-16

    Kirtland AFB, NM 87117-5776 AFRL /RVBXR 11. SPONSOR/MONITOR’S REPORT NUMBER(S) AFRL -RV-PS-TR-2016-0102 12. DISTRIBUTION / AVAILABILITY...VA 22060-6218 1 cy AFRL /RVIL Kirtland AFB, NM 87117-5776 2 cys Official Record Copy AFRL /RVBXR/Adrian Wheelock 1 cy Approved for public release; distribution is unlimited. 78 ... AFRL -RV-PS- AFRL -RV-PS- TR-2016-0102 TR-2016-0102 MOMENT-PRESERVING COMPUTATIONAL APPROACH FOR HIGH ENERGY CHARGED PARTICLE TRANSPORT Anil

  11. Information and psychomotor skills knowledge acquisition: A student-customer-centered and computer-supported approach.

    PubMed

    Nicholson, Anita; Tobin, Mary

    2006-01-01

    This presentation will discuss coupling commercial and customized computer-supported teaching aids to provide BSN nursing students with a friendly customer-centered self-study approach to psychomotor skill acquisition.

  12. Combined Experimental and Computational Approach to Predict the Glass-Water Reaction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pierce, Eric M.; Bacon, Diana H.

    2011-10-01

    The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic timescales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models be validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test B, and pressurized unsaturated flow (PUF)], thereby reducingmore » the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year-long PUF experiment was conducted with the Subsurface Transport Over Reactive Multiphases (STORM) code. Results show that parameterization of the computer model by combining direct bench scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year-long test duration, the rate decreased from 0.2 to 0.01 g/(m2 day) based on B release for low-activity waste glass LAWA44. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by four orders of magnitude) and suggests that the gel-layer properties are less protective under these dynamic

  13. Combined Experimental and Computational Approach to Predict the Glass-Water Reaction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pierce, Eric M; Bacon, Diana

    2011-01-01

    The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic time-scales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models are validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test-B, and pressurized unsaturated flow (PUF)], thereby reducing themore » duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year long PUF experiment was conducted with the subsurface transport over reactive multi-phases code. Results show that parameterization of the computer model by combining direct bench-scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year long test duration, the rate decreased from 0.2 to 0.01 g/(m2 d) base on B release. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by 4 orders of magnitude) and suggest the gel-layer properties are less protective under these dynamic conditions.« less

  14. Computing the multifractal spectrum from time series: an algorithmic approach.

    PubMed

    Harikrishnan, K P; Misra, R; Ambika, G; Amritkar, R E

    2009-12-01

    We show that the existing methods for computing the f(alpha) spectrum from a time series can be improved by using a new algorithmic scheme. The scheme relies on the basic idea that the smooth convex profile of a typical f(alpha) spectrum can be fitted with an analytic function involving a set of four independent parameters. While the standard existing schemes [P. Grassberger et al., J. Stat. Phys. 51, 135 (1988); A. Chhabra and R. V. Jensen, Phys. Rev. Lett. 62, 1327 (1989)] generally compute only an incomplete f(alpha) spectrum (usually the top portion), we show that this can be overcome by an algorithmic approach, which is automated to compute the D(q) and f(alpha) spectra from a time series for any embedding dimension. The scheme is first tested with the logistic attractor with known f(alpha) curve and subsequently applied to higher-dimensional cases. We also show that the scheme can be effectively adapted for analyzing practical time series involving noise, with examples from two widely different real world systems. Moreover, some preliminary results indicating that the set of four independent parameters may be used as diagnostic measures are also included.

  15. Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.

    PubMed

    Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S

    2015-01-01

    G-protein-coupled receptors (GPCRs) are a versatile family of membrane-bound signaling proteins. Despite the recent successes in obtaining crystal structures of GPCRs, much needs to be learned about the conformational changes associated with their activation. Furthermore, the mechanism by which ligands modulate the activation of GPCRs has remained elusive. Molecular simulations provide a way of obtaining detailed an atomistic description of GPCR activation dynamics. However, simulating GPCR activation is challenging due to the long timescales involved and the associated challenge of gaining insights from the "Big" simulation datasets. Here, we demonstrate how cloud-computing approaches have been used to tackle these challenges and obtain insights into the activation mechanism of GPCRs. In particular, we review the use of Markov state model (MSM)-based sampling algorithms for sampling milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2-AR. MSMs of agonist and inverse agonist-bound β2-AR reveal multiple activation pathways and how ligands function via modulation of the ensemble of activation pathways. We target this ensemble of conformations with computer-aided drug design approaches, with the goal of designing drugs that interact more closely with diverse receptor states, for overall increased efficacy and specificity. We conclude by discussing how cloud-based approaches present a powerful and broadly available tool for studying the complex biological systems routinely. © 2015 Elsevier Inc. All rights reserved.

  16. A computational efficient modelling of laminar separation bubbles

    NASA Technical Reports Server (NTRS)

    Dini, Paolo; Maughmer, Mark D.

    1990-01-01

    In predicting the aerodynamic characteristics of airfoils operating at low Reynolds numbers, it is often important to account for the effects of laminar (transitional) separation bubbles. Previous approaches to the modelling of this viscous phenomenon range from fast but sometimes unreliable empirical correlations for the length of the bubble and the associated increase in momentum thickness, to more accurate but significantly slower displacement-thickness iteration methods employing inverse boundary-layer formulations in the separated regions. Since the penalty in computational time associated with the more general methods is unacceptable for airfoil design applications, use of an accurate yet computationally efficient model is highly desirable. To this end, a semi-empirical bubble model was developed and incorporated into the Eppler and Somers airfoil design and analysis program. The generality and the efficiency was achieved by successfully approximating the local viscous/inviscid interaction, the transition location, and the turbulent reattachment process within the framework of an integral boundary-layer method. Comparisons of the predicted aerodynamic characteristics with experimental measurements for several airfoils show excellent and consistent agreement for Reynolds numbers from 2,000,000 down to 100,000.

  17. Computational Methods for MOF/Polymer Membranes.

    PubMed

    Erucar, Ilknur; Keskin, Seda

    2016-04-01

    Metal-organic framework (MOF)/polymer mixed matrix membranes (MMMs) have received significant interest in the last decade. MOFs are incorporated into polymers to make MMMs that exhibit improved gas permeability and selectivity compared with pure polymer membranes. The fundamental challenge in this area is to choose the appropriate MOF/polymer combinations for a gas separation of interest. Even if a single polymer is considered, there are thousands of MOFs that could potentially be used as fillers in MMMs. As a result, there has been a large demand for computational studies that can accurately predict the gas separation performance of MOF/polymer MMMs prior to experiments. We have developed computational approaches to assess gas separation potentials of MOF/polymer MMMs and used them to identify the most promising MOF/polymer pairs. In this Personal Account, we aim to provide a critical overview of current computational methods for modeling MOF/polymer MMMs. We give our perspective on the background, successes, and failures that led to developments in this area and discuss the opportunities and challenges of using computational methods for MOF/polymer MMMs. © 2016 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Fast Eigensolver for Computing 3D Earth's Normal Modes

    NASA Astrophysics Data System (ADS)

    Shi, J.; De Hoop, M. V.; Li, R.; Xi, Y.; Saad, Y.

    2017-12-01

    We present a novel parallel computational approach to compute Earth's normal modes. We discretize Earth via an unstructured tetrahedral mesh and apply the continuous Galerkin finite element method to the elasto-gravitational system. To resolve the eigenvalue pollution issue, following the analysis separating the seismic point spectrum, we utilize explicitly a representation of the displacement for describing the oscillations of the non-seismic modes in the fluid outer core. Effectively, we separate out the essential spectrum which is naturally related to the Brunt-Väisälä frequency. We introduce two Lanczos approaches with polynomial and rational filtering for solving this generalized eigenvalue problem in prescribed intervals. The polynomial filtering technique only accesses the matrix pair through matrix-vector products and is an ideal candidate for solving three-dimensional large-scale eigenvalue problems. The matrix-free scheme allows us to deal with fluid separation and self-gravitation in an efficient way, while the standard shift-and-invert method typically needs an explicit shifted matrix and its factorization. The rational filtering method converges much faster than the standard shift-and-invert procedure when computing all the eigenvalues inside an interval. Both two Lanczos approaches solve for the internal eigenvalues extremely accurately, comparing with the standard eigensolver. In our computational experiments, we compare our results with the radial earth model benchmark, and visualize the normal modes using vector plots to illustrate the properties of the displacements in different modes.

  19. Accurate Vehicle Location System Using RFID, an Internet of Things Approach.

    PubMed

    Prinsloo, Jaco; Malekian, Reza

    2016-06-04

    Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved.

  20. Accurate Vehicle Location System Using RFID, an Internet of Things Approach

    PubMed Central

    Prinsloo, Jaco; Malekian, Reza

    2016-01-01

    Modern infrastructure, such as dense urban areas and underground tunnels, can effectively block all GPS signals, which implies that effective position triangulation will not be achieved. The main problem that is addressed in this project is the design and implementation of an accurate vehicle location system using radio-frequency identification (RFID) technology in combination with GPS and the Global system for Mobile communication (GSM) technology, in order to provide a solution to the limitation discussed above. In essence, autonomous vehicle tracking will be facilitated with the use of RFID technology where GPS signals are non-existent. The design of the system and the results are reflected in this paper. An extensive literature study was done on the field known as the Internet of Things, as well as various topics that covered the integration of independent technology in order to address a specific challenge. The proposed system is then designed and implemented. An RFID transponder was successfully designed and a read range of approximately 31 cm was obtained in the low frequency communication range (125 kHz to 134 kHz). The proposed system was designed, implemented, and field tested and it was found that a vehicle could be accurately located and tracked. It is also found that the antenna size of both the RFID reader unit and RFID transponder plays a critical role in the maximum communication range that can be achieved. PMID:27271638

  1. Randomized Approaches for Nearest Neighbor Search in Metric Space When Computing the Pairwise Distance Is Extremely Expensive

    NASA Astrophysics Data System (ADS)

    Wang, Lusheng; Yang, Yong; Lin, Guohui

    Finding the closest object for a query in a database is a classical problem in computer science. For some modern biological applications, computing the similarity between two objects might be very time consuming. For example, it takes a long time to compute the edit distance between two whole chromosomes and the alignment cost of two 3D protein structures. In this paper, we study the nearest neighbor search problem in metric space, where the pair-wise distance between two objects in the database is known and we want to minimize the number of distances computed on-line between the query and objects in the database in order to find the closest object. We have designed two randomized approaches for indexing metric space databases, where objects are purely described by their distances with each other. Analysis and experiments show that our approaches only need to compute O(logn) objects in order to find the closest object, where n is the total number of objects in the database.

  2. Identification of Protein–Excipient Interaction Hotspots Using Computational Approaches

    PubMed Central

    Barata, Teresa S.; Zhang, Cheng; Dalby, Paul A.; Brocchini, Steve; Zloh, Mire

    2016-01-01

    Protein formulation development relies on the selection of excipients that inhibit protein–protein interactions preventing aggregation. Empirical strategies involve screening many excipient and buffer combinations using force degradation studies. Such methods do not readily provide information on intermolecular interactions responsible for the protective effects of excipients. This study describes a molecular docking approach to screen and rank interactions allowing for the identification of protein–excipient hotspots to aid in the selection of excipients to be experimentally screened. Previously published work with Drosophila Su(dx) was used to develop and validate the computational methodology, which was then used to determine the formulation hotspots for Fab A33. Commonly used excipients were examined and compared to the regions in Fab A33 prone to protein–protein interactions that could lead to aggregation. This approach could provide information on a molecular level about the protective interactions of excipients in protein formulations to aid the more rational development of future formulations. PMID:27258262

  3. Symbolic Computational Approach to the Marangoni Convection Problem With Soret Diffusion

    NASA Technical Reports Server (NTRS)

    Skarda, J. Raymond

    1998-01-01

    A recently reported solution for stationary stability of a thermosolutal system with Soret diffusion is re-derived and examined using a symbolic computational package. Symbolic computational languages are well suited for such an analysis and facilitate a pragmatic approach that is adaptable to similar problems. Linearization of the equations, normal mode analysis, and extraction of the final solution are performed in a Mathematica notebook format. An exact solution is obtained for stationary stability in the limit of zero gravity. A closed form expression is also obtained for the location of asymptotes in relevant parameter, (Sm(sub c), Mac(sub c)), space. The stationary stability behavior is conveniently examined within the symbolic language environment. An abbreviated version of the Mathematica notebook is given in the Appendix.

  4. Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model.

    PubMed

    Kroonblawd, Matthew P; Pietrucci, Fabio; Saitta, Antonino Marco; Goldman, Nir

    2018-04-10

    We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol -1 .

  5. Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

    DOE PAGES

    Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco; ...

    2018-03-15

    Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

  6. Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kroonblawd, Matthew P.; Pietrucci, Fabio; Saitta, Antonino Marco

    Here, we demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTBmore » model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol –1.« less

  7. Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

    NASA Technical Reports Server (NTRS)

    Kory, Carol L.; Dayton, James A., Jr.

    1997-01-01

    Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

  8. Computational model of precision grip in Parkinson's disease: a utility based approach

    PubMed Central

    Gupta, Ankur; Balasubramani, Pragathi P.; Chakravarthy, V. Srinivasa

    2013-01-01

    We propose a computational model of Precision Grip (PG) performance in normal subjects and Parkinson's Disease (PD) patients. Prior studies on grip force generation in PD patients show an increase in grip force during ON medication and an increase in the variability of the grip force during OFF medication (Ingvarsson et al., 1997; Fellows et al., 1998). Changes in grip force generation in dopamine-deficient PD conditions strongly suggest contribution of the Basal Ganglia, a deep brain system having a crucial role in translating dopamine signals to decision making. The present approach is to treat the problem of modeling grip force generation as a problem of action selection, which is one of the key functions of the Basal Ganglia. The model consists of two components: (1) the sensory-motor loop component, and (2) the Basal Ganglia component. The sensory-motor loop component converts a reference position and a reference grip force, into lift force and grip force profiles, respectively. These two forces cooperate in grip-lifting a load. The sensory-motor loop component also includes a plant model that represents the interaction between two fingers involved in PG, and the object to be lifted. The Basal Ganglia component is modeled using Reinforcement Learning with the significant difference that the action selection is performed using utility distribution instead of using purely Value-based distribution, thereby incorporating risk-based decision making. The proposed model is able to account for the PG results from normal and PD patients accurately (Ingvarsson et al., 1997; Fellows et al., 1998). To our knowledge the model is the first model of PG in PD conditions. PMID:24348373

  9. Efficient Parallel Kernel Solvers for Computational Fluid Dynamics Applications

    NASA Technical Reports Server (NTRS)

    Sun, Xian-He

    1997-01-01

    Distributed-memory parallel computers dominate today's parallel computing arena. These machines, such as Intel Paragon, IBM SP2, and Cray Origin2OO, have successfully delivered high performance computing power for solving some of the so-called "grand-challenge" problems. Despite initial success, parallel machines have not been widely accepted in production engineering environments due to the complexity of parallel programming. On a parallel computing system, a task has to be partitioned and distributed appropriately among processors to reduce communication cost and to attain load balance. More importantly, even with careful partitioning and mapping, the performance of an algorithm may still be unsatisfactory, since conventional sequential algorithms may be serial in nature and may not be implemented efficiently on parallel machines. In many cases, new algorithms have to be introduced to increase parallel performance. In order to achieve optimal performance, in addition to partitioning and mapping, a careful performance study should be conducted for a given application to find a good algorithm-machine combination. This process, however, is usually painful and elusive. The goal of this project is to design and develop efficient parallel algorithms for highly accurate Computational Fluid Dynamics (CFD) simulations and other engineering applications. The work plan is 1) developing highly accurate parallel numerical algorithms, 2) conduct preliminary testing to verify the effectiveness and potential of these algorithms, 3) incorporate newly developed algorithms into actual simulation packages. The work plan has well achieved. Two highly accurate, efficient Poisson solvers have been developed and tested based on two different approaches: (1) Adopting a mathematical geometry which has a better capacity to describe the fluid, (2) Using compact scheme to gain high order accuracy in numerical discretization. The previously developed Parallel Diagonal Dominant (PDD) algorithm

  10. Computer-aided detection of renal calculi from noncontrast CT images using TV-flow and MSER features.

    PubMed

    Liu, Jianfei; Wang, Shijun; Turkbey, Evrim B; Linguraru, Marius George; Yao, Jianhua; Summers, Ronald M

    2015-01-01

    Renal calculi are common extracolonic incidental findings on computed tomographic colonography (CTC). This work aims to develop a fully automated computer-aided diagnosis system to accurately detect renal calculi on CTC images. The authors developed a total variation (TV) flow method to reduce image noise within the kidneys while maintaining the characteristic appearance of renal calculi. Maximally stable extremal region (MSER) features were then calculated to robustly identify calculi candidates. Finally, the authors computed texture and shape features that were imported to support vector machines for calculus classification. The method was validated on a dataset of 192 patients and compared to a baseline approach that detects calculi by thresholding. The authors also compared their method with the detection approaches using anisotropic diffusion and nonsmoothing. At a false positive rate of 8 per patient, the sensitivities of the new method and the baseline thresholding approach were 69% and 35% (p < 1e - 3) on all calculi from 1 to 433 mm(3) in the testing dataset. The sensitivities of the detection methods using anisotropic diffusion and nonsmoothing were 36% and 0%, respectively. The sensitivity of the new method increased to 90% if only larger and more clinically relevant calculi were considered. Experimental results demonstrated that TV-flow and MSER features are efficient means to robustly and accurately detect renal calculi on low-dose, high noise CTC images. Thus, the proposed method can potentially improve diagnosis.

  11. Computer-aided detection of renal calculi from noncontrast CT images using TV-flow and MSER features

    PubMed Central

    Liu, Jianfei; Wang, Shijun; Turkbey, Evrim B.; Linguraru, Marius George; Yao, Jianhua; Summers, Ronald M.

    2015-01-01

    Purpose: Renal calculi are common extracolonic incidental findings on computed tomographic colonography (CTC). This work aims to develop a fully automated computer-aided diagnosis system to accurately detect renal calculi on CTC images. Methods: The authors developed a total variation (TV) flow method to reduce image noise within the kidneys while maintaining the characteristic appearance of renal calculi. Maximally stable extremal region (MSER) features were then calculated to robustly identify calculi candidates. Finally, the authors computed texture and shape features that were imported to support vector machines for calculus classification. The method was validated on a dataset of 192 patients and compared to a baseline approach that detects calculi by thresholding. The authors also compared their method with the detection approaches using anisotropic diffusion and nonsmoothing. Results: At a false positive rate of 8 per patient, the sensitivities of the new method and the baseline thresholding approach were 69% and 35% (p < 1e − 3) on all calculi from 1 to 433 mm3 in the testing dataset. The sensitivities of the detection methods using anisotropic diffusion and nonsmoothing were 36% and 0%, respectively. The sensitivity of the new method increased to 90% if only larger and more clinically relevant calculi were considered. Conclusions: Experimental results demonstrated that TV-flow and MSER features are efficient means to robustly and accurately detect renal calculi on low-dose, high noise CTC images. Thus, the proposed method can potentially improve diagnosis. PMID:25563255

  12. LCC-Demons: a robust and accurate symmetric diffeomorphic registration algorithm.

    PubMed

    Lorenzi, M; Ayache, N; Frisoni, G B; Pennec, X

    2013-11-01

    Non-linear registration is a key instrument for computational anatomy to study the morphology of organs and tissues. However, in order to be an effective instrument for the clinical practice, registration algorithms must be computationally efficient, accurate and most importantly robust to the multiple biases affecting medical images. In this work we propose a fast and robust registration framework based on the log-Demons diffeomorphic registration algorithm. The transformation is parameterized by stationary velocity fields (SVFs), and the similarity metric implements a symmetric local correlation coefficient (LCC). Moreover, we show how the SVF setting provides a stable and consistent numerical scheme for the computation of the Jacobian determinant and the flux of the deformation across the boundaries of a given region. Thus, it provides a robust evaluation of spatial changes. We tested the LCC-Demons in the inter-subject registration setting, by comparing with state-of-the-art registration algorithms on public available datasets, and in the intra-subject longitudinal registration problem, for the statistically powered measurements of the longitudinal atrophy in Alzheimer's disease. Experimental results show that LCC-Demons is a generic, flexible, efficient and robust algorithm for the accurate non-linear registration of images, which can find several applications in the field of medical imaging. Without any additional optimization, it solves equally well intra & inter-subject registration problems, and compares favorably to state-of-the-art methods. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Accurately measuring the height of (real) forest trees

    Treesearch

    Don C. Bragg

    2014-01-01

    Quick and accurate tree height measurement has always been a goal of foresters. The techniques and technology to measure height were developed long ago—even the earliest textbooks on mensuration showcased hypsometers (e.g., Schlich 1895, Mlodziansky 1898, Schenck 1905, Graves 1906), and approaches to refine these sometimes remarkable tools appeared in the first issues...

  14. Computational approaches to substrate-based cell motility

    DOE PAGES

    Ziebert, Falko; Aranson, Igor S.

    2016-07-15

    Substrate-based crawling motility of eukaryotic cells is essential for many biological functions, both in developing and mature organisms. Motility dysfunctions are involved in several life-threatening pathologies such as cancer and metastasis. Motile cells are also a natural realization of active, self-propelled ‘particles’, a popular research topic in nonequilibrium physics. Finally, from the materials perspective, assemblies of motile cells and evolving tissues constitute a class of adaptive self-healing materials that respond to the topography, elasticity, and surface chemistry of the environment and react to external stimuli. Although a comprehensive understanding of substrate-based cell motility remains elusive, progress has been achieved recentlymore » in its modeling on the whole cell level. Furthermore we survey the most recent advances in computational approaches to cell movement and demonstrate how these models improve our understanding of complex self-organized systems such as living cells.« less

  15. Highly accurate potential energy surface for the He-H2 dimer

    NASA Astrophysics Data System (ADS)

    Bakr, Brandon W.; Smith, Daniel G. A.; Patkowski, Konrad

    2013-10-01

    A new highly accurate interaction potential is constructed for the He-H2 van der Waals complex. This potential is fitted to 1900 ab initio energies computed at the very large-basis coupled-cluster level and augmented by corrections for higher-order excitations (up to full configuration interaction level) and the diagonal Born-Oppenheimer correction. At the vibrationally averaged H-H bond length of 1.448736 bohrs, the well depth of our potential, 15.870 ± 0.065 K, is nearly 1 K larger than the most accurate previous studies have indicated. In addition to constructing our own three-dimensional potential in the van der Waals region, we present a reparameterization of the Boothroyd-Martin-Peterson potential surface [A. I. Boothroyd, P. G. Martin, and M. R. Peterson, J. Chem. Phys. 119, 3187 (2003)] that is suitable for all configurations of the triatomic system. Finally, we use the newly developed potentials to compute the properties of the lone bound states of 4He-H2 and 3He-H2 and the interaction second virial coefficient of the hydrogen-helium mixture.

  16. Accurate First-Principles Spectra Predictions for Planetological and Astrophysical Applications at Various T-Conditions

    NASA Astrophysics Data System (ADS)

    Rey, M.; Nikitin, A. V.; Tyuterev, V.

    2014-06-01

    Knowledge of near infrared intensities of rovibrational transitions of polyatomic molecules is essential for the modeling of various planetary atmospheres, brown dwarfs and for other astrophysical applications 1,2,3. For example, to analyze exoplanets, atmospheric models have been developed, thus making the need to provide accurate spectroscopic data. Consequently, the spectral characterization of such planetary objects relies on the necessity of having adequate and reliable molecular data in extreme conditions (temperature, optical path length, pressure). On the other hand, in the modeling of astrophysical opacities, millions of lines are generally involved and the line-by-line extraction is clearly not feasible in laboratory measurements. It is thus suggested that this large amount of data could be interpreted only by reliable theoretical predictions. There exists essentially two theoretical approaches for the computation and prediction of spectra. The first one is based on empirically-fitted effective spectroscopic models. Another way for computing energies, line positions and intensities is based on global variational calculations using ab initio surfaces. They do not yet reach the spectroscopic accuracy stricto sensu but implicitly account for all intramolecular interactions including resonance couplings in a wide spectral range. The final aim of this work is to provide reliable predictions which could be quantitatively accurate with respect to the precision of available observations and as complete as possible. All this thus requires extensive first-principles quantum mechanical calculations essentially based on three necessary ingredients which are (i) accurate intramolecular potential energy surface and dipole moment surface components well-defined in a large range of vibrational displacements and (ii) efficient computational methods combined with suitable choices of coordinates to account for molecular symmetry properties and to achieve a good numerical

  17. The feasibility of an efficient drug design method with high-performance computers.

    PubMed

    Yamashita, Takefumi; Ueda, Akihiko; Mitsui, Takashi; Tomonaga, Atsushi; Matsumoto, Shunji; Kodama, Tatsuhiko; Fujitani, Hideaki

    2015-01-01

    In this study, we propose a supercomputer-assisted drug design approach involving all-atom molecular dynamics (MD)-based binding free energy prediction after the traditional design/selection step. Because this prediction is more accurate than the empirical binding affinity scoring of the traditional approach, the compounds selected by the MD-based prediction should be better drug candidates. In this study, we discuss the applicability of the new approach using two examples. Although the MD-based binding free energy prediction has a huge computational cost, it is feasible with the latest 10 petaflop-scale computer. The supercomputer-assisted drug design approach also involves two important feedback procedures: The first feedback is generated from the MD-based binding free energy prediction step to the drug design step. While the experimental feedback usually provides binding affinities of tens of compounds at one time, the supercomputer allows us to simultaneously obtain the binding free energies of hundreds of compounds. Because the number of calculated binding free energies is sufficiently large, the compounds can be classified into different categories whose properties will aid in the design of the next generation of drug candidates. The second feedback, which occurs from the experiments to the MD simulations, is important to validate the simulation parameters. To demonstrate this, we compare the binding free energies calculated with various force fields to the experimental ones. The results indicate that the prediction will not be very successful, if we use an inaccurate force field. By improving/validating such simulation parameters, the next prediction can be made more accurate.

  18. Nasal computed tomography.

    PubMed

    Kuehn, Ned F

    2006-05-01

    Chronic nasal disease is often a challenge to diagnose. Computed tomography greatly enhances the ability to diagnose chronic nasal disease in dogs and cats. Nasal computed tomography provides detailed information regarding the extent of disease, accurate discrimination of neoplastic versus nonneoplastic diseases, and identification of areas of the nose to examine rhinoscopically and suspicious regions to target for biopsy.

  19. Algorithms for Stellar Perturbation Computations on Oort Cloud Comets

    NASA Astrophysics Data System (ADS)

    Rickman, Hans; Fouchard, Marc; Valsecchi, Giovanni B.; Froeschlé, Christiane

    2005-12-01

    We investigate different approximate methods of computing the perturbations on the orbits of Oort cloud comets caused by passing stars, by checking them against an accurate numerical integration using Everhart’s RA15 code. The scenario under study is the one relevant for long-term simulations of the cloud’s response to a predefined set of stellar passages. Our sample of stellar encounters simulates those experienced by the Solar System currently, but extrapolated over a time of 1010 years. We measure the errors of perihelion distance perturbations for high-eccentricity orbits introduced by several estimators including the classical impulse approximation and Dybczyński’s (1994, Celest. Mech. Dynam. Astron. 58, 1330 1338) method and we study how they depend on the encounter parameters (approach distance and relative velocity). We introduce a sequential variant of Dybczyński’s approach, cutting the encounter into several steps whereby the heliocentric motion of the comet is taken into account. For the scenario at hand this is found to offer an efficient means to obtain accurate results for practically any domain of the parameter space.

  20. Debugging embedded computer programs. [tactical missile computers

    NASA Technical Reports Server (NTRS)

    Kemp, G. H.

    1980-01-01

    Every embedded computer program must complete its debugging cycle using some system that will allow real time debugging. Many of the common items addressed during debugging are listed. Seven approaches to debugging are analyzed to evaluate how well they treat those items. Cost evaluations are also included in the comparison. The results indicate that the best collection of capabilities to cover the common items present in the debugging task occurs in the approach where a minicomputer handles the environment simulation with an emulation of some kind representing the embedded computer. This approach can be taken at a reasonable cost. The case study chosen is an embedded computer in a tactical missile. Several choices of computer for the environment simulation are discussed as well as different approaches to the embedded emulator.

  1. COMPUTER-AIDED DRUG DISCOVERY AND DEVELOPMENT (CADDD): in silico-chemico-biological approach

    PubMed Central

    Kapetanovic, I.M.

    2008-01-01

    It is generally recognized that drug discovery and development are very time and resources consuming processes. There is an ever growing effort to apply computational power to the combined chemical and biological space in order to streamline drug discovery, design, development and optimization. In biomedical arena, computer-aided or in silico design is being utilized to expedite and facilitate hit identification, hit-to-lead selection, optimize the absorption, distribution, metabolism, excretion and toxicity profile and avoid safety issues. Commonly used computational approaches include ligand-based drug design (pharmacophore, a 3-D spatial arrangement of chemical features essential for biological activity), structure-based drug design (drug-target docking), and quantitative structure-activity and quantitative structure-property relationships. Regulatory agencies as well as pharmaceutical industry are actively involved in development of computational tools that will improve effectiveness and efficiency of drug discovery and development process, decrease use of animals, and increase predictability. It is expected that the power of CADDD will grow as the technology continues to evolve. PMID:17229415

  2. Prediction of electronic structure of organic radicaloid anions using efficient, economical multireference gradient approach.

    PubMed

    Chattopadhyay, Sudip; Chaudhuri, Rajat K; Freed, Karl F

    2011-04-28

    The improved virtual orbital-complete active space configuration interaction (IVO-CASCI) method enables an economical and reasonably accurate treatment of static correlation in systems with significant multireference character, even when using a moderate basis set. This IVO-CASCI method supplants the computationally more demanding complete active space self-consistent field (CASSCF) method by producing comparable accuracy with diminished computational effort because the IVO-CASCI approach does not require additional iterations beyond an initial SCF calculation, nor does it encounter convergence difficulties or multiple solutions that may be found in CASSCF calculations. Our IVO-CASCI analytical gradient approach is applied to compute the equilibrium geometry for the ground and lowest excited state(s) of the theoretically very challenging 2,6-pyridyne, 1,2,3-tridehydrobenzene and 1,3,5-tridehydrobenzene anionic systems for which experiments are lacking, accurate quantum calculations are almost completely absent, and commonly used calculations based on single reference configurations fail to provide reasonable results. Hence, the computational complexity provides an excellent test for the efficacy of multireference methods. The present work clearly illustrates that the IVO-CASCI analytical gradient method provides a good description of the complicated electronic quasi-degeneracies during the geometry optimization process for the radicaloid anions. The IVO-CASCI treatment produces almost identical geometries as the CASSCF calculations (performed for this study) at a fraction of the computational labor. Adiabatic energy gaps to low lying excited states likewise emerge from the IVO-CASCI and CASSCF methods as very similar. We also provide harmonic vibrational frequencies to demonstrate the stability of the computed geometries.

  3. A Computer-Assisted Multiliteracies Programme as an Alternative Approach to EFL Instruction

    ERIC Educational Resources Information Center

    Lee, Kyungmee; Ardeshiri, Minoo; Cummins, Jim

    2016-01-01

    The aim of this article is to introduce a computer-assisted multiliteracies programme (CaMP) as an alternative approach to English as a Foreign Language (EFL) instruction in order to overcome the educational limitations that are inherent in most EFL settings. In a number of monolingual societies with a dominant language other than English,…

  4. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  5. Integrative computational approach for genome-based study of microbial lipid-degrading enzymes.

    PubMed

    Vorapreeda, Tayvich; Thammarongtham, Chinae; Laoteng, Kobkul

    2016-07-01

    Lipid-degrading or lipolytic enzymes have gained enormous attention in academic and industrial sectors. Several efforts are underway to discover new lipase enzymes from a variety of microorganisms with particular catalytic properties to be used for extensive applications. In addition, various tools and strategies have been implemented to unravel the functional relevance of the versatile lipid-degrading enzymes for special purposes. This review highlights the study of microbial lipid-degrading enzymes through an integrative computational approach. The identification of putative lipase genes from microbial genomes and metagenomic libraries using homology-based mining is discussed, with an emphasis on sequence analysis of conserved motifs and enzyme topology. Molecular modelling of three-dimensional structure on the basis of sequence similarity is shown to be a potential approach for exploring the structural and functional relationships of candidate lipase enzymes. The perspectives on a discriminative framework of cutting-edge tools and technologies, including bioinformatics, computational biology, functional genomics and functional proteomics, intended to facilitate rapid progress in understanding lipolysis mechanism and to discover novel lipid-degrading enzymes of microorganisms are discussed.

  6. Covariance approximation for fast and accurate computation of channelized Hotelling observer statistics

    NASA Astrophysics Data System (ADS)

    Bonetto, P.; Qi, Jinyi; Leahy, R. M.

    2000-08-01

    Describes a method for computing linear observer statistics for maximum a posteriori (MAP) reconstructions of PET images. The method is based on a theoretical approximation for the mean and covariance of MAP reconstructions. In particular, the authors derive here a closed form for the channelized Hotelling observer (CHO) statistic applied to 2D MAP images. The theoretical analysis models both the Poission statistics of PET data and the inhomogeneity of tracer uptake. The authors show reasonably good correspondence between these theoretical results and Monte Carlo studies. The accuracy and low computational cost of the approximation allow the authors to analyze the observer performance over a wide range of operating conditions and parameter settings for the MAP reconstruction algorithm.

  7. Prediction of Scour below Flip Bucket using Soft Computing Techniques

    NASA Astrophysics Data System (ADS)

    Azamathulla, H. Md.; Ab Ghani, Aminuddin; Azazi Zakaria, Nor

    2010-05-01

    The accurate prediction of the depth of scour around hydraulic structure (trajectory spillways) has been based on the experimental studies and the equations developed are mainly empirical in nature. This paper evaluates the performance of the soft computing (intelligence) techiques, Adaptive Neuro-Fuzzy System (ANFIS) and Genetic expression Programming (GEP) approach, in prediction of scour below a flip bucket spillway. The results are very promising, which support the use of these intelligent techniques in prediction of highly non-linear scour parameters.

  8. Approach for computing 1D fracture density: application to fracture corridor characterization

    NASA Astrophysics Data System (ADS)

    Viseur, Sophie; Chatelée, Sebastien; Akriche, Clement; Lamarche, Juliette

    2016-04-01

    Fracture density is an important parameter for characterizing fractured reservoirs. Many stochastic simulation algorithms that generate fracture networks indeed rely on the determination of a fracture density on volumes (P30) to populate the reservoir zones with individual fracture surfaces. However, only 1D fracture density (P10) are available from subsurface data and it is then important to be able to accurately estimate this entity. In this paper, a novel approach is proposed to estimate fracture density from scan-line or well data. This method relies on regression, hypothesis testing and clustering techniques. The objective of the proposed approach is to highlight zones where fracture density are statistically very different or similar. This technique has been applied on both synthetic and real case studies. These studies concern fracture corridors, which are particular tectonic features that are generally difficult to characterize from subsurface data. These tectonic features are still not well known and studies must be conducted to better understand their internal spatial organization and variability. The presented synthetic cases aim at showing the ability of the approach to extract known features. The real case study illustrates how this approach allows the internal spatial organization of fracture corridors to be characterized.

  9. Is the Bethe–Salpeter Formalism Accurate for Excitation Energies? Comparisons with TD-DFT, CASPT2, and EOM-CCSD

    PubMed Central

    2017-01-01

    Developing ab initio approaches able to provide accurate excited-state energies at a reasonable computational cost is one of the biggest challenges in theoretical chemistry. In that framework, the Bethe–Salpeter equation approach, combined with the GW exchange-correlation self-energy, which maintains the same scaling with system size as TD-DFT, has recently been the focus of a rapidly increasing number of applications in molecular chemistry. Using a recently proposed set encompassing excitation energies of many kinds [J. Phys. Chem. Lett.2016, 7, 586–591], we investigate here the performances of BSE/GW. We compare these results to CASPT2, EOM-CCSD, and TD-DFT data and show that BSE/GW provides an accuracy comparable to the two wave function methods. It is particularly remarkable that the BSE/GW is equally efficient for valence, Rydberg, and charge-transfer excitations. In contrast, it provides a poor description of triplet excited states, for which EOM-CCSD and CASPT2 clearly outperform BSE/GW. This contribution therefore supports the use of the Bethe–Salpeter approach for spin-conserving transitions. PMID:28301726

  10. Unfitted Two-Phase Flow Simulations in Pore-Geometries with Accurate

    NASA Astrophysics Data System (ADS)

    Heimann, Felix; Engwer, Christian; Ippisch, Olaf; Bastian, Peter

    2013-04-01

    The development of better macro scale models for multi-phase flow in porous media is still impeded by the lack of suitable methods for the simulation of such flow regimes on the pore scale. The highly complicated geometry of natural porous media imposes requirements with regard to stability and computational efficiency which current numerical methods fail to meet. Therefore, current simulation environments are still unable to provide a thorough understanding of porous media in multi-phase regimes and still fail to reproduce well known effects like hysteresis or the more peculiar dynamics of the capillary fringe with satisfying accuracy. Although flow simulations in pore geometries were initially the domain of Lattice-Boltzmann and other particle methods, the development of Galerkin methods for such applications is important as they complement the range of feasible flow and parameter regimes. In the recent past, it has been shown that unfitted Galerkin methods can be applied efficiently to topologically demanding geometries. However, in the context of two-phase flows, the interface of the two immiscible fluids effectively separates the domain in two sub-domains. The exact representation of such setups with multiple independent and time depending geometries exceeds the functionality of common unfitted methods. We present a new approach to pore scale simulations with an unfitted discontinuous Galerkin (UDG) method. Utilizing a recursive sub-triangulation algorithm, we extent the UDG method to setups with multiple independent geometries. This approach allows an accurate representation of the moving contact line and the interface conditions, i.e. the pressure jump across the interface. Example simulations in two and three dimensions illustrate and verify the stability and accuracy of this approach.

  11. Method for accurate sizing of pulmonary vessels from 3D medical images

    NASA Astrophysics Data System (ADS)

    O'Dell, Walter G.

    2015-03-01

    Detailed characterization of vascular anatomy, in particular the quantification of changes in the distribution of vessel sizes and of vascular pruning, is essential for the diagnosis and management of a variety of pulmonary vascular diseases and for the care of cancer survivors who have received radiation to the thorax. Clinical estimates of vessel radii are typically based on setting a pixel intensity threshold and counting how many "On" pixels are present across the vessel cross-section. A more objective approach introduced recently involves fitting the image with a library of spherical Gaussian filters and utilizing the size of the best matching filter as the estimate of vessel diameter. However, both these approaches have significant accuracy limitations including mis-match between a Gaussian intensity distribution and that of real vessels. Here we introduce and demonstrate a novel approach for accurate vessel sizing using 3D appearance models of a tubular structure along a curvilinear trajectory in 3D space. The vessel branch trajectories are represented with cubic Hermite splines and the tubular branch surfaces represented as a finite element surface mesh. An iterative parameter adjustment scheme is employed to optimally match the appearance models to a patient's chest X-ray computed tomography (CT) scan to generate estimates for branch radii and trajectories with subpixel resolution. The method is demonstrated on pulmonary vasculature in an adult human CT scan, and on 2D simulated test cases.

  12. COSP - A computer model of cyclic oxidation

    NASA Technical Reports Server (NTRS)

    Lowell, Carl E.; Barrett, Charles A.; Palmer, Raymond W.; Auping, Judith V.; Probst, Hubert B.

    1991-01-01

    A computer model useful in predicting the cyclic oxidation behavior of alloys is presented. The model considers the oxygen uptake due to scale formation during the heating cycle and the loss of oxide due to spalling during the cooling cycle. The balance between scale formation and scale loss is modeled and used to predict weight change and metal loss kinetics. A simple uniform spalling model is compared to a more complex random spall site model. In nearly all cases, the simpler uniform spall model gave predictions as accurate as the more complex model. The model has been applied to several nickel-base alloys which, depending upon composition, form Al2O3 or Cr2O3 during oxidation. The model has been validated by several experimental approaches. Versions of the model that run on a personal computer are available.

  13. Methodical Approaches to Teaching of Computer Modeling in Computer Science Course

    ERIC Educational Resources Information Center

    Rakhimzhanova, B. Lyazzat; Issabayeva, N. Darazha; Khakimova, Tiyshtik; Bolyskhanova, J. Madina

    2015-01-01

    The purpose of this study was to justify of the formation technique of representation of modeling methodology at computer science lessons. The necessity of studying computer modeling is that the current trends of strengthening of general education and worldview functions of computer science define the necessity of additional research of the…

  14. A Computer-Based Approach for Deriving and Measuring Individual and Team Knowledge Structure from Essay Questions

    ERIC Educational Resources Information Center

    Clariana, Roy B.; Wallace, Patricia

    2007-01-01

    This proof-of-concept investigation describes a computer-based approach for deriving the knowledge structure of individuals and of groups from their written essays, and considers the convergent criterion-related validity of the computer-based scores relative to human rater essay scores and multiple-choice test scores. After completing a…

  15. Computational Discovery of Materials Using the Firefly Algorithm

    NASA Astrophysics Data System (ADS)

    Avendaño-Franco, Guillermo; Romero, Aldo

    Our current ability to model physical phenomena accurately, the increase computational power and better algorithms are the driving forces behind the computational discovery and design of novel materials, allowing for virtual characterization before their realization in the laboratory. We present the implementation of a novel firefly algorithm, a population-based algorithm for global optimization for searching the structure/composition space. This novel computation-intensive approach naturally take advantage of concurrency, targeted exploration and still keeping enough diversity. We apply the new method in both periodic and non-periodic structures and we present the implementation challenges and solutions to improve efficiency. The implementation makes use of computational materials databases and network analysis to optimize the search and get insights about the geometric structure of local minima on the energy landscape. The method has been implemented in our software PyChemia, an open-source package for materials discovery. We acknowledge the support of DMREF-NSF 1434897 and the Donors of the American Chemical Society Petroleum Research Fund for partial support of this research under Contract 54075-ND10.

  16. Accurate and fast multiple-testing correction in eQTL studies.

    PubMed

    Sul, Jae Hoon; Raj, Towfique; de Jong, Simone; de Bakker, Paul I W; Raychaudhuri, Soumya; Ophoff, Roel A; Stranger, Barbara E; Eskin, Eleazar; Han, Buhm

    2015-06-04

    In studies of expression quantitative trait loci (eQTLs), it is of increasing interest to identify eGenes, the genes whose expression levels are associated with variation at a particular genetic variant. Detecting eGenes is important for follow-up analyses and prioritization because genes are the main entities in biological processes. To detect eGenes, one typically focuses on the genetic variant with the minimum p value among all variants in cis with a gene and corrects for multiple testing to obtain a gene-level p value. For performing multiple-testing correction, a permutation test is widely used. Because of growing sample sizes of eQTL studies, however, the permutation test has become a computational bottleneck in eQTL studies. In this paper, we propose an efficient approach for correcting for multiple testing and assess eGene p values by utilizing a multivariate normal distribution. Our approach properly takes into account the linkage-disequilibrium structure among variants, and its time complexity is independent of sample size. By applying our small-sample correction techniques, our method achieves high accuracy in both small and large studies. We have shown that our method consistently produces extremely accurate p values (accuracy > 98%) for three human eQTL datasets with different sample sizes and SNP densities: the Genotype-Tissue Expression pilot dataset, the multi-region brain dataset, and the HapMap 3 dataset. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  17. Discovering and understanding oncogenic gene fusions through data intensive computational approaches

    PubMed Central

    Latysheva, Natasha S.; Babu, M. Madan

    2016-01-01

    Abstract Although gene fusions have been recognized as important drivers of cancer for decades, our understanding of the prevalence and function of gene fusions has been revolutionized by the rise of next-generation sequencing, advances in bioinformatics theory and an increasing capacity for large-scale computational biology. The computational work on gene fusions has been vastly diverse, and the present state of the literature is fragmented. It will be fruitful to merge three camps of gene fusion bioinformatics that appear to rarely cross over: (i) data-intensive computational work characterizing the molecular biology of gene fusions; (ii) development research on fusion detection tools, candidate fusion prioritization algorithms and dedicated fusion databases and (iii) clinical research that seeks to either therapeutically target fusion transcripts and proteins or leverages advances in detection tools to perform large-scale surveys of gene fusion landscapes in specific cancer types. In this review, we unify these different—yet highly complementary and symbiotic—approaches with the view that increased synergy will catalyze advancements in gene fusion identification, characterization and significance evaluation. PMID:27105842

  18. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

    2016-06-13

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less

  19. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

    PubMed

    Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  20. An Approach to Integrate a Space-Time GIS Data Model with High Performance Computers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Dali; Zhao, Ziliang; Shaw, Shih-Lung

    2011-01-01

    In this paper, we describe an approach to integrate a Space-Time GIS data model on a high performance computing platform. The Space-Time GIS data model has been developed on a desktop computing environment. We use the Space-Time GIS data model to generate GIS module, which organizes a series of remote sensing data. We are in the process of porting the GIS module into an HPC environment, in which the GIS modules handle large dataset directly via parallel file system. Although it is an ongoing project, authors hope this effort can inspire further discussions on the integration of GIS on highmore » performance computing platforms.« less