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Sample records for dimensional fragment method

  1. Recent Advances in Fragment-Based QSAR and Multi-Dimensional QSAR Methods

    Directory of Open Access Journals (Sweden)

    Kyaw Zeyar Myint

    2010-10-01

    Full Text Available This paper provides an overview of recently developed two dimensional (2D fragment-based QSAR methods as well as other multi-dimensional approaches. In particular, we present recent fragment-based QSAR methods such as fragment-similarity-based QSAR (FS-QSAR, fragment-based QSAR (FB-QSAR, Hologram QSAR (HQSAR, and top priority fragment QSAR in addition to 3D- and nD-QSAR methods such as comparative molecular field analysis (CoMFA, comparative molecular similarity analysis (CoMSIA, Topomer CoMFA, self-organizing molecular field analysis (SOMFA, comparative molecular moment analysis (COMMA, autocorrelation of molecular surfaces properties (AMSP, weighted holistic invariant molecular (WHIM descriptor-based QSAR (WHIM, grid-independent descriptors (GRIND-based QSAR, 4D-QSAR, 5D-QSAR and 6D-QSAR methods.

  2. A Linear Scaling Three Dimensional Fragment Method for Large ScaleElectronic Structure Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lin-Wang; Zhao, Zhengji; Meza, Juan

    2007-07-26

    We present a novel linear scaling ab initio total energyelectronic structure calculation method, which is simple to implement,easily to parallelize, and produces essentially thesame results as thedirect ab initio method, while it could be thousands of times faster.Using this method, we have studied the dipole moments of CdSe quantumdots, and found both significant bulk and surface contributions. The bulkdipole contribution cannot simply be estimated from the bulk spontaneouspolarization value by a proportional volume factor. Instead it has ageometry dependent screening effect. The dipole moment also produces astrong internal electric field which induces a strong electron holeseparation.

  3. Efficient and accurate fragmentation methods.

    Science.gov (United States)

    Pruitt, Spencer R; Bertoni, Colleen; Brorsen, Kurt R; Gordon, Mark S

    2014-09-16

    Conspectus Three novel fragmentation methods that are available in the electronic structure program GAMESS (general atomic and molecular electronic structure system) are discussed in this Account. The fragment molecular orbital (FMO) method can be combined with any electronic structure method to perform accurate calculations on large molecular species with no reliance on capping atoms or empirical parameters. The FMO method is highly scalable and can take advantage of massively parallel computer systems. For example, the method has been shown to scale nearly linearly on up to 131 000 processor cores for calculations on large water clusters. There have been many applications of the FMO method to large molecular clusters, to biomolecules (e.g., proteins), and to materials that are used as heterogeneous catalysts. The effective fragment potential (EFP) method is a model potential approach that is fully derived from first principles and has no empirically fitted parameters. Consequently, an EFP can be generated for any molecule by a simple preparatory GAMESS calculation. The EFP method provides accurate descriptions of all types of intermolecular interactions, including Coulombic interactions, polarization/induction, exchange repulsion, dispersion, and charge transfer. The EFP method has been applied successfully to the study of liquid water, π-stacking in substituted benzenes and in DNA base pairs, solvent effects on positive and negative ions, electronic spectra and dynamics, non-adiabatic phenomena in electronic excited states, and nonlinear excited state properties. The effective fragment molecular orbital (EFMO) method is a merger of the FMO and EFP methods, in which interfragment interactions are described by the EFP potential, rather than the less accurate electrostatic potential. The use of EFP in this manner facilitates the use of a smaller value for the distance cut-off (Rcut). Rcut determines the distance at which EFP interactions replace fully quantum

  4. A divide-and-conquer linear scaling three dimensional fragment method for large scale electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lin-Wang; Zhao, Zhengji; Meza, Juan; Wang, Lin-Wang

    2008-07-11

    We present a new linear scaling ab initio total energy electronic structure calculation method based on the divide-and-conquer strategy. This method is simple to implement, easily to parallelize, and produces very accurate results when compared with the direct ab initio method. The method has been tested using up to 8,000 processors, and has been used to calculate nanosystems up to 15,000 atoms.

  5. Three-dimensional Statistical Jet Fragmentation

    CERN Document Server

    Urmossy, Karoly

    2016-01-01

    We reproduce the distribution of the longitudinal and transverse components of momenta of charged hadrons stemming from jets created in proton-proton collisions at $\\sqrt s$ = 7 TeV by a statistical fragmentation model. Our hadronisation model is based on microcanonical statistics and negative binomial multiplicity fluctuations. We describe the scale dependence of the fit parameters of the model with formulas obtained by approximating the exact solution of the DGLAP equation in the $\\phi^3$ theory with leading order splitting function and 1-loop coupling.

  6. Molecular energies from an incremental fragmentation method

    Science.gov (United States)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  7. Bootstrap embedding: An internally consistent fragment-based method

    Science.gov (United States)

    Welborn, Matthew; Tsuchimochi, Takashi; Van Voorhis, Troy

    2016-08-01

    Strong correlation poses a difficult problem for electronic structure theory, with computational cost scaling quickly with system size. Fragment embedding is an attractive approach to this problem. By dividing a large complicated system into smaller manageable fragments "embedded" in an approximate description of the rest of the system, we can hope to ameliorate the steep cost of correlated calculations. While appealing, these methods often converge slowly with fragment size because of small errors at the boundary between fragment and bath. We describe a new electronic embedding method, dubbed "Bootstrap Embedding," a self-consistent wavefunction-in-wavefunction embedding theory that uses overlapping fragments to improve the description of fragment edges. We apply this method to the one dimensional Hubbard model and a translationally asymmetric variant, and find that it performs very well for energies and populations. We find Bootstrap Embedding converges rapidly with embedded fragment size, overcoming the surface-area-to-volume-ratio error typical of many embedding methods. We anticipate that this method may lead to a low-scaling, high accuracy treatment of electron correlation in large molecular systems.

  8. Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    Science.gov (United States)

    van Agthoven, Maria A.; Barrow, Mark P.; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A.; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B.

    2015-12-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules.

  9. Material point method simulations of fragmenting cylinders

    CERN Document Server

    Banerjee, Biswajit

    2012-01-01

    Most research on the simulation of deformation and failure of metals has been and continues to be performed using the finite element method. However, the issues of mesh entanglement under large deformation, considerable complexity in handling contact, and difficulties encountered while solving large deformation fluid-structure interaction problems have led to the exploration of alternative approaches. The material point method uses Lagrangian solid particles embedded in an Eulerian grid. Particles interact via the grid with other particles in the same body, with other solid bodies, and with fluids. Thus, the three issues mentioned in the context of finite element analysis are circumvented. In this paper, we present simulations of cylinders which fragment due to explosively expanding gases generated by reactions in a high energy material contained inside. The material point method is the numerical method chosen for these simulations discussed in this paper. The plastic deformation of metals is simulated using ...

  10. Fragmentation and exfoliation of 2-dimensional materials: a statistical approach

    Science.gov (United States)

    Kouroupis-Agalou, Konstantinos; Liscio, Andrea; Treossi, Emanuele; Ortolani, Luca; Morandi, Vittorio; Pugno, Nicola Maria; Palermo, Vincenzo

    2014-05-01

    The main advantage for applications of graphene and related 2D materials is that they can be produced on large scales by liquid phase exfoliation. The exfoliation process shall be considered as a particular fragmentation process, where the 2D character of the exfoliated objects will influence significantly fragmentation dynamics as compared to standard materials. Here, we used automatized image processing of Atomic Force Microscopy (AFM) data to measure, one by one, the exact shape and size of thousands of nanosheets obtained by exfoliation of an important 2D-material, boron nitride, and used different statistical functions to model the asymmetric distribution of nanosheet sizes typically obtained. Being the resolution of AFM much larger than the average sheet size, analysis could be performed directly at the nanoscale and at the single sheet level. We find that the size distribution of the sheets at a given time follows a log-normal distribution, indicating that the exfoliation process has a ``typical'' scale length that changes with time and that exfoliation proceeds through the formation of a distribution of random cracks that follow Poisson statistics. The validity of this model implies that the size distribution does not depend on the different preparation methods used, but is a common feature in the exfoliation of this material and thus probably for other 2D materials.The main advantage for applications of graphene and related 2D materials is that they can be produced on large scales by liquid phase exfoliation. The exfoliation process shall be considered as a particular fragmentation process, where the 2D character of the exfoliated objects will influence significantly fragmentation dynamics as compared to standard materials. Here, we used automatized image processing of Atomic Force Microscopy (AFM) data to measure, one by one, the exact shape and size of thousands of nanosheets obtained by exfoliation of an important 2D-material, boron nitride, and used

  11. Research on the photoelectric measuring method of warhead fragment velocity

    Science.gov (United States)

    Liu, Ji; Yu, Lixia; Zhang, Bin; Liu, Xiaoyan

    2016-09-01

    The velocity of warhead fragment is the key criteria to determine its mutilation efficiency. But owing to the small size, larger quantity, irregular shape, high speed, arbitrary direction, large dispersion of warhead fragment and adverse environment, the test of fragment velocity parameter is very difficult. The paper designed an optoelectronic system to measure the average velocity of warhead fragments accurately. The apparatus included two parallel laser screens spaced apart at a known fixed distance for providing time measurement between start and stop signals. The large effective screen area was composed of laser source, retro-reflector and large area photo-diode. Whenever a moving fragment interrupted two optical screens, the system would generate a target signal. Due to partial obscuration of the incident energy and the poor test condition of the explosion, fragment target signal is easily disturbed. Therefore, fragments signal processing technology has become a key technology of the system. The noise of signal was reduced by employing wavelet decomposition and reconstruction. The time of fragment passing though the target was obtained by adopting peak detection algorithm. Based on the method of search peak in different width scale and waveform trend by using optima wavelet, the problem of rolling waveform was solved. Lots of fragments experiments of the different types of the warheads were conducted. Experimental results show that: warhead fragments capture rate of system is better than 98%, which can give velocity of each fragment in the density of less than 20 pieces per m2.

  12. Extension of moment projection method to the fragmentation process

    Science.gov (United States)

    Wu, Shaohua; Yapp, Edward K. Y.; Akroyd, Jethro; Mosbach, Sebastian; Xu, Rong; Yang, Wenming; Kraft, Markus

    2017-04-01

    The method of moments is a simple but efficient method of solving the population balance equation which describes particle dynamics. Recently, the moment projection method (MPM) was proposed and validated for particle inception, coagulation, growth and, more importantly, shrinkage; here the method is extended to include the fragmentation process. The performance of MPM is tested for 13 different test cases for different fragmentation kernels, fragment distribution functions and initial conditions. Comparisons are made with the quadrature method of moments (QMOM), hybrid method of moments (HMOM) and a high-precision stochastic solution calculated using the established direct simulation algorithm (DSA) and advantages of MPM are drawn.

  13. Extension of moment projection method to the fragmentation process

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Shaohua [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Yapp, Edward K.Y.; Akroyd, Jethro; Mosbach, Sebastian [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); Xu, Rong [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore); Yang, Wenming [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Kraft, Markus, E-mail: mk306@cam.ac.uk [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore)

    2017-04-15

    The method of moments is a simple but efficient method of solving the population balance equation which describes particle dynamics. Recently, the moment projection method (MPM) was proposed and validated for particle inception, coagulation, growth and, more importantly, shrinkage; here the method is extended to include the fragmentation process. The performance of MPM is tested for 13 different test cases for different fragmentation kernels, fragment distribution functions and initial conditions. Comparisons are made with the quadrature method of moments (QMOM), hybrid method of moments (HMOM) and a high-precision stochastic solution calculated using the established direct simulation algorithm (DSA) and advantages of MPM are drawn.

  14. Quantifying three dimensional reconnection in fragmented current layers

    Energy Technology Data Exchange (ETDEWEB)

    Wyper, P. F., E-mail: peter.f.wyper@nasa.gov; Hesse, M., E-mail: michael.hesse-1@nasa.gov [Goddard Space Flight Center, 8800 Greenbelt Rd, Greenbelt, Maryland 20771 (United States)

    2015-04-15

    There is growing evidence that when magnetic reconnection occurs in high Lundquist number plasmas such as in the Solar Corona or the Earth's Magnetosphere it does so within a fragmented, rather than a smooth current layer. Within the extent of these fragmented current regions, the associated magnetic flux transfer and energy release occur simultaneously in many different places. This investigation focusses on how best to quantify the rate at which reconnection occurs in such layers. An analytical theory is developed which describes the manner in which new connections form within fragmented current layers in the absence of magnetic nulls. It is shown that the collective rate at which new connections form can be characterized by two measures; a total rate which measures the true rate at which new connections are formed and a net rate which measures the net change of connection associated with the largest value of the integral of E{sub ||} through all of the non-ideal regions. Two simple analytical models are presented which demonstrate how each should be applied and what they quantify.

  15. Fragment Identification and Statistics Method of Hypervelocity Impact SPH Simulation

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiaotian; JIA Guanghui; HUANG Hai

    2011-01-01

    A comprehensive treatment to the fragment identification and statistics for the smoothed particle hydrodynamics (SPH) simulation of hypervelocity impact is presented.Based on SPH method, combined with finite element method (FEM), the computation is performed.The fragments are identified by a new pre- and post-processing algorithm and then converted into a binary graph.The number of fragments and the attached SPH particles are determined by counting the quantity of connected domains on the binary graph.The size, velocity vector and mass of each fragment are calculated by the particles' summation and weighted average.The dependence of this method on finite element edge length and simulation terminal time is discussed.An example of tungsten rods impacting steel plates is given for calibration.The computation results match experiments well and demonstrate the effectiveness of this method.

  16. Fragmented one dimensional man / El hombre unidimensional fragmentado

    Directory of Open Access Journals (Sweden)

    Juan Antonio Rodríguez del Pino

    2013-10-01

    Full Text Available Paraphrase the title of the famous essay by Herbert Marcuse, since the image has traditionally been generated of man, masculinity, has been one-dimensional. I mean, the man was characterized by traits and behaviors established and entrenched since ancient time, considering all other distinguishing signs as mere deviations from the normative improper. But observe that this undeniable reality, as analyzed various researchers through what has come to be called Men's studies, has proven to be a fallacy difficult to maintain throughout history and today turns into fallacious and ineffective against changes in our current existing corporate models.

  17. Applying EGO to large dimensional optimizations: a wideband fragmented patch example

    Science.gov (United States)

    O'Donnell, Teresa H.; Southall, Hugh; Santarelli, Scott; Steyskal, Hans

    2010-04-01

    Efficient Global Optimization (EGO) minimizes expensive cost function evaluations by correlating evaluated parameter sets and respective solutions to model the optimization space. For optimizations requiring destructive testing or lengthy simulations, this computational overhead represents a desirable tradeoff. However, the inspection of the predictor space to determine the next evaluation point can be a time-intensive operation. Although DACE predictor evaluation may be conducted for limited parameters by exhaustive sampling, this method is not extendable to large dimensions. We apply EGO here to the 11-dimensional optimization of a wide-band fragmented patch antenna and present an alternative genetic algorithm approach for selecting the next evaluation point. We compare results achieved with EGO on this optimization problem to previous results achieved with a genetic algorithm.

  18. Stochastic weighted particle methods for population balance equations with coagulation, fragmentation and spatial inhomogeneity

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kok Foong [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA (United Kingdom); Patterson, Robert I.A.; Wagner, Wolfgang [Weierstrass Institute for Applied Analysis and Stochastics, Mohrenstraße 39, 10117 Berlin (Germany); Kraft, Markus, E-mail: mk306@cam.ac.uk [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge CB2 3RA (United Kingdom); School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 (Singapore)

    2015-12-15

    Graphical abstract: -- Highlights: •Problems concerning multi-compartment population balance equations are studied. •A class of fragmentation weight transfer functions is presented. •Three stochastic weighted algorithms are compared against the direct simulation algorithm. •The numerical errors of the stochastic solutions are assessed as a function of fragmentation rate. •The algorithms are applied to a multi-dimensional granulation model. -- Abstract: This paper introduces stochastic weighted particle algorithms for the solution of multi-compartment population balance equations. In particular, it presents a class of fragmentation weight transfer functions which are constructed such that the number of computational particles stays constant during fragmentation events. The weight transfer functions are constructed based on systems of weighted computational particles and each of it leads to a stochastic particle algorithm for the numerical treatment of population balance equations. Besides fragmentation, the algorithms also consider physical processes such as coagulation and the exchange of mass with the surroundings. The numerical properties of the algorithms are compared to the direct simulation algorithm and an existing method for the fragmentation of weighted particles. It is found that the new algorithms show better numerical performance over the two existing methods especially for systems with significant amount of large particles and high fragmentation rates.

  19. Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry

    Science.gov (United States)

    Kuchibhotla, Bhanuramanand; Kola, Sankara Rao; Medicherla, Jagannadham V.; Cherukuvada, Swamy V.; Dhople, Vishnu M.; Nalam, Madhusudhana Rao

    2017-06-01

    Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. [Figure not available: see fulltext.

  20. The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

    Science.gov (United States)

    Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

    2012-01-01

    We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively. PMID:22844433

  1. Mapping enzymatic catalysis using the effective fragment molecular orbital method

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Fedorov, Dmitri G.; Jensen, Jan Halborg

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of ...

  2. Analysis methods for Kevlar shield response to rotor fragments

    Science.gov (United States)

    Gerstle, J. H.

    1977-01-01

    Several empirical and analytical approaches to rotor burst shield sizing are compared and principal differences in metal and fabric dynamic behavior are discussed. The application of transient structural response computer programs to predict Kevlar containment limits is described. For preliminary shield sizing, present analytical methods are useful if insufficient test data for empirical modeling are available. To provide other information useful for engineering design, analytical methods require further developments in material characterization, failure criteria, loads definition, and post-impact fragment trajectory prediction.

  3. Test method to measure resistance towards fragmentation by studded tires

    Science.gov (United States)

    Viman, L.

    1995-01-01

    In the Nordic countries most cars are equipped with studded tires during the winter. The studs increase the wear on the road surfaces and a special test method has been developed to measure the aggregates' resistance towards fragmentation by studded tires. The method has proven to correlate very well with the actual wear on the road surfaces. The Nordic countries Sweden, Norway and Finland have agreed to propose this method as a European Standard test method. One reason is to be able to set requirements on aggregates to be used in countries where studded tires are allowed. A cross-testing project regarding this Nordic abrasion test for studded tires was set up in order to determine the repeatability and the reproducibility of the methods to become European Standard.

  4. Mapping enzymatic catalysis using the effective fragment molecular orbital method

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Fedorov, Dmitri G.; Jensen, Jan Halborg

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path...... determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively....

  5. Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries.

    Science.gov (United States)

    Branscomb, E; Slezak, T; Pae, R; Galas, D; Carrano, A V; Waterman, M

    1990-10-01

    We present a statistical analysis of the problem of ordering large genomic cloned libraries through overlap detection based on restriction fingerprinting. Such ordering projects involve a large investment of effort involving many repetitious experiments. Our primary purpose here is to provide methods of maximizing the efficiency of such efforts. To this end, we adopt a statistical approach that uses the likelihood ratio as a statistic to detect overlap. The main advantages of this approach are that (1) it allows the relatively straightforward incorporation of the observed statistical properties of the data; (2) it permits the efficiency of a particular experimental method for detecting overlap to be quantitatively defined so that alternative experimental designs may be compared and optimized; and (3) it yields a direct estimate of the probability that any two library members overlap. This estimate is a critical tool for the accurate, automatic assembly of overlapping sets of fragments into islands called "contigs." These contigs must subsequently be connected by other methods to provide an ordered set of overlapping fragments covering the entire genome.

  6. Three-dimensional simulations of molecular cloud fragmentation regulated by magnetic fields and ambipolar diffusion

    CERN Document Server

    Kudoh, Takahiro; Ogata, Youichi; Yabe, Takashi

    2007-01-01

    We employ the first fully three-dimensional simulation to study the role of magnetic fields and ion-neutral friction in regulating gravitationally-driven fragmentation of molecular clouds. The cores in an initially subcritical cloud develop gradually over an ambipolar diffusion time while the cores in an initially supercritical cloud develop in a dynamical time. The infall speeds on to cores are subsonic in the case of an initially subcritical cloud, while an extended (\\ga 0.1 pc) region of supersonic infall exists in the case of an initially supercritical cloud. These results are consistent with previous two-dimensional simulations. We also found that a snapshot of the relation between density (rho) and the strength of the magnetic field (B) at different spatial points of the cloud coincides with the evolutionary track of an individual core. When the density becomes large, both relations tend to B \\propto \\rho^{0.5}.

  7. Post-Fragmentation Whole Genome Amplification-Based Method

    Science.gov (United States)

    Benardini, James; LaDuc, Myron T.; Langmore, John

    2011-01-01

    This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at

  8. Density functional theory based generalized effective fragment potential method

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Kiet A., E-mail: kiet.nguyen@wpafb.af.mil, E-mail: ruth.pachter@wpafb.af.mil [Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433 (United States); UES, Inc., Dayton, Ohio 45432 (United States); Pachter, Ruth, E-mail: kiet.nguyen@wpafb.af.mil, E-mail: ruth.pachter@wpafb.af.mil [Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433 (United States); Day, Paul N. [Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433 (United States); General Dynamics Information Technology, Inc., Dayton, Ohio 45431 (United States)

    2014-06-28

    We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.

  9. Investigation of Explosively Driven Fragmentation of Metals - Two Dimensional Fracture and Fragmentation of Metal Shells: Progress Report II

    Energy Technology Data Exchange (ETDEWEB)

    Grady, D

    2003-02-01

    High explosive enclosed by a metal case qualitatively describes an essential component of high energy systems of importance to the Department of Energy. Detonation of the high explosive causes intense transient pressure loading of the metal following arrival of normal or obliquely incident explosive detonation wave. Subsequent expansion and deformation of the metal case leads to eventual rupture and the opening of fractures and fissures. Details of the rupture process are critical to performance of the system. Consequently, it is essential that the material and kinematic issues governing the processes of dynamic loading and subsequent failure of an explosive-metal case component within a functioning system be adequately understood. Among the reasons are to quantify existing performance, characterize potential degradation of performance resulting from system aging, and optimizing or maintaining system performance through implementation of structural or material changes. The physical and engineering issues underlying this dynamic response and failure phenomena are not adequately understood. The purpose of the present program is to identify the key issues and develop theoretical, computational and experimental models needed to achieve a satisfactory theoretical and analysis framework for analysis of metal case failure in the explosive environment. Specific tasks within the present program include: (1) Models and theories currently being pursued based on physical principles of both the statistical fragmentation concepts of Mott and the energy-based concept of others show promise of providing the analytic and computational methodology capable of predicting explosion-induced fracture and fragmentation of metal components. Experimental studies initiated in the earlier effort offer promise to provide critical test data for validation. The present task shall involve the further refinement and development of the dynamic failure and fragmentation models and theories, and the

  10. Linearly Scaling 3D Fragment Method for Large-Scale Electronic Structure Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lin-Wang; Lee, Byounghak; Shan, Hongzhang; Zhao, Zhengji; Meza, Juan; Strohmaier, Erich; Bailey, David H.

    2008-07-01

    We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39percent of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFTcalculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N3) methods, and the potential for petascale computation using the LS3DF method.

  11. Linear scaling 3D fragment method for large-scale electronic structure calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Lin-Wang; Wang, Lin-Wang; Lee, Byounghak; Shan, HongZhang; Zhao, Zhengji; Meza, Juan; Strohmaier, Erich; Bailey, David

    2008-07-11

    We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39% of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFT calculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N{sup 3}) methods, and the potential for petascale computation using the LS3DF method.

  12. Synthesis of CCK-8 Tetrapeptide Fragment by Enzymatic Method

    Institute of Scientific and Technical Information of China (English)

    XIANG Guangya (项光亚); Heiner Eckstein

    2003-01-01

    The enzymatic synthesis of a tetrapeptide Phac-Met-Gly-Trp-Met-OEt, a fragment of thecholecystokinin C-terminal octapeptide CCK-8, was reported. This fragment was synthesized bycoupling Phac-Met-OEt with Gly-OMe, Trp-OMe and Met-OEt successively. These three stepswere catalyzed by α-chymotrpsin, Papain and α-chymotrpsin respectively. The results of FAB-MSshowed that all the products had the correct molecular mass.

  13. Iron meteorite fragment studied by atomic and nuclear analytical methods

    Science.gov (United States)

    Cesnek, Martin; Štefánik, Milan; Kmječ, Tomáš; Miglierini, Marcel

    2016-10-01

    Chemical and structural compositions of a fragment of Sikhote-Alin iron meteorite were investigated by X-ray fluorescence analysis (XRF), neutron activation analysis (NAA) and Mössbauer spectroscopy (MS). XRF and NAA revealed the presence of chemical elements which are characteristic for iron meteorites. XRF also showed a significant amount of Si and Al on the surface of the fragment. MS spectra revealed possible presence of α-Fe(Ni, Co) phase with different local Ni concentration. Furthermore, paramagnetic singlet was detected in Mössbauer spectra recorded at room temperature and at 4.2 K.

  14. An instrumented spacial linkage for monitoring relative three-dimensional motion between fracture fragments.

    Science.gov (United States)

    Gardner, T N; Evans, M; Kyberd, P J

    1996-11-01

    A mechanical linkage with electro-magnetic sensors (a displacement transducer) is described, which may be used to measure accurately the relative motion at a bony junction such as a fracture. The linkage may be fixed to bone screws of externally-fixated fractures during routine patient activity, to measure three-dimensional inter fragmentary displacements arising from dynamic loading. Movements of the linkage are monitored by six Hall Effect devices for the six degrees of freedom (three orthogonal translations and three rotations about the translating axes). Measurements are made within error bounds of +/- 0.025 mm and +/- 0.025 deg over a range of 5 mm for the two orthogonal transverse translations, 8 mm for axial translation and 8 deg for the three rotations. Movements at the linkage, remote from the fracture, are then translated mathematically to the fracture site, assuming rigid screw contact with the bone. Displacements of the distal fragment in relation to the proximal, at the fracture center, can then be expressed anatomically through anterior, medial, and distal translations, and rotations in the sagittal, coronal, or transverse planes.

  15. Fragmentation of DNA affects the accuracy of the DNA quantitation by the commonly used methods

    Directory of Open Access Journals (Sweden)

    Sedlackova Tatiana

    2013-02-01

    Full Text Available Abstract Background Specific applications and modern technologies, like non-invasive prenatal testing, non-invasive cancer diagnostic and next generation sequencing, are currently in the focus of researchers worldwide. These have common characteristics in use of highly fragmented DNA molecules for analysis. Hence, for the performance of molecular methods, DNA concentration is a crucial parameter; we compared the influence of different levels of DNA fragmentation on the accuracy of DNA concentration measurements. Results In our comparison, the performance of the currently most commonly used methods for DNA concentration measurement (spectrophotometric, fluorometric and qPCR based were tested on artificially fragmented DNA samples. In our comparison, unfragmented and three specifically fragmented DNA samples were used. According to our results, the level of fragmentation did not influence the accuracy of spectrophotometric measurements of DNA concentration, while other methods, fluorometric as well as qPCR-based, were significantly influenced and a decrease in measured concentration was observed with more intensive DNA fragmentation. Conclusions Our study has confirmed that the level of fragmentation of DNA has significant impact on accuracy of DNA concentration measurement with two of three mostly used methods (PicoGreen and qPCR. Only spectrophotometric measurement was not influenced by the level of fragmentation, but sensitivity of this method was lowest among the three tested. Therefore if it is possible the DNA quantification should be performed with use of equally fragmented control DNA.

  16. Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

    National Research Council Canada - National Science Library

    van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O’Connor, Peter B

    2015-01-01

    ...) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated...

  17. Multimodal Biometrics Recognition by Dimensionality Diminution Method

    Directory of Open Access Journals (Sweden)

    Suvarnsing Bhable

    2015-12-01

    Full Text Available Multimodal biometric system utilizes two or more character modalities, e.g., face, ear, and fingerprint, Signature, plamprint to improve the recognition accuracy of conventional unimodal methods. We propose a new dimensionality reduction method called Dimension Diminish Projection (DDP in this paper. DDP can not only preserve local information by capturing the intra-modal geometry, but also extract between-class relevant structures for classification effectively. Experimental results show that our proposed method performs better than other algorithms including PCA, LDA and MFA.

  18. Three-dimensional textural and compositional analysis of particle tracks and fragmentation history in aerogel

    Energy Technology Data Exchange (ETDEWEB)

    Ebel, Denton S.; Greenberg, Michael; Rivers, Mark L.; Newville, Matthew; (AMNH)

    2010-05-04

    We report analyses of aerogel tracks using (1) synchrotron X-ray computed microtomography (XRCMT), (2) laser confocal scanning microscopy (LCSM), and (3) synchrotron radiation X-ray fluorescence (SRXRF) of particles and their paths resulting from simulated hypervelocity impacts (1-2), and a single {approx}1 mm aerogel track from the Stardust cometary sample collector (1-3). Large aerogel pieces can be imaged sequentially, resulting in high spatial resolution images spanning many tomographic fields of view ('lambda-tomography'). We report calculations of energy deposited, and tests on aromatic hydrocarbons showing no alteration in tomography experiments. Imaging at resolutions from -17 to -1 micron/pixel edge (XRCMT) and to <100 nm/pixel edge (LCSM) illustrates track geometry and interaction of particles with aerogel, including rifling, particle fragmentation, and final particle location. We present a 3-D deconvolution method using an estimated point-spread function for aerogel, allowing basic corrections of LCSM data for axial distortion. LCSM allows rapid, comprehensive, non-destructive, high information return analysis of tracks in aerogel keystones, prior to destructive grain extraction. SRXRF with LCSM allows spatial correlation of grain size, chemical, and mineralogical data. If optical methods are precluded in future aerogel capture missions, XRCMT is a viable 3D imaging technique. Combinations of these methods allow for complete, nondestructive, quantitative 3-D analysis of captured materials at high spatial resolution. This data is fundamental to understanding the hypervelocity particle-aerogel interaction histories of Stardust grains.

  19. Three-dimensional patterning methods and related devices

    Energy Technology Data Exchange (ETDEWEB)

    Putnam, Morgan C.; Kelzenberg, Michael D.; Atwater, Harry A.; Boettcher, Shannon W.; Lewis, Nathan S.; Spurgeon, Joshua M.; Turner-Evans, Daniel B.; Warren, Emily L.

    2016-12-27

    Three-dimensional patterning methods of a three-dimensional microstructure, such as a semiconductor wire array, are described, in conjunction with etching and/or deposition steps to pattern the three-dimensional microstructure.

  20. Method for Measuring Velocity of Warhead Fragments Based on Photoelectric Detection

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    For measuring velocity and impacting position of single fragment of warhead, a non-contact measuring method is proposed, in which a six-light-screen array, a position indicator, a multi-channel chronograph and a computer are used.The principle of measurement is described. The key device of the system is a light screen array sensor which consists of six light screens allocated with certain geometrical parameters. When the fragment flies through the light screen array, the time of passing through each of the screens is recorded by the multi-channel chronograph. According to the time data and the geometrical parameters of the array, the velocity vector and the location of the fragment can be calculated immediately. The presented method can be used to locate the fragment and to measure the real velocity on its flying direction. It can also be used to measure the velocity of a fragment swarm after the system is engineered further.

  1. Thermodynamics from three-dimensional many-body fragmentation simulations on a cellular automaton model.

    Science.gov (United States)

    Lejeune, A; Perdang, J

    2004-10-01

    The thermal equilibrium of many-body systems subject to finite range interactions is investigated numerically, by means of a multipurpose 3D cellular automaton dynamic model developed by the authors. The numerical experiments, carried out at fixed number of bodies, volume and energy, demonstrate the formation of an equilibrium among 3D aggregates of bodies. The distribution of the aggregates against size obeys a power law of (negative) exponent tau approximately 2.2 (against 1.3 in 2D). Our experiments, indicating that the exponent is insensitive to the precise parameter values and the precise parametrization of the interactions, are consistent with the idea of the existence of a universality class corresponding to the thermal equilibrium. The numerical value for the exponent tau is in agreement with the theoretical thermal equilibrium analyses based on various other approaches, numerical and semianalytical, indicating that the cellular automaton approach provides an adequate methodology to investigate thermal equilibria. In this paper, as an illustration of this method, we refer to the problem of formation of clusters of nucleons in heavy ion collisions of nuclei leading on to fragmentation. The theoretical tau value, however, corresponding to the thermal equilibrium among the aggregation clusters, is 15 percent lower than the empirical value ( approximately 2.6 ) , as measured in laboratory nuclear fragmentation experiments induced by collision. There is then only a very approximate correspondence between the experimental and the thermal equilibrium value. On the basis of the results of this paper and of a previous paper of this series, we conjecture that the approximate agreement is due to a partial establishment of a thermodynamic equilibrium during the collision of the nuclei. The thermal equilibrium gives the main contribution to the observed tau value; the deviation from this possibly universal value is largely the consequence of the lack of full thermal

  2. THEORETICAL STUDY OF THREE-DIMENSIONAL NUMERICAL MANIFOLD METHOD

    Institute of Scientific and Technical Information of China (English)

    LUO Shao-ming; ZHANG Xiang-wei; L(U) Wen-ge; JIANG Dong-ru

    2005-01-01

    The three-dimensional numerical manifold method(NMM) is studied on the basis of two-dimensional numerical manifold method. The three-dimensional cover displacement function is studied. The mechanical analysis and Hammer integral method of three-dimensional numerical manifold method are put forward. The stiffness matrix of three-dimensional manifold element is derived and the dissection rules are given. The theoretical system and the numerical realizing method of three-dimensional numerical manifold method are systematically studied. As an example, the cantilever with load on the end is calculated, and the results show that the precision and efficiency are agreeable.

  3. Three-dimensional image signals: processing methods

    Science.gov (United States)

    Schiopu, Paul; Manea, Adrian; Craciun, Anca-Ileana; Craciun, Alexandru

    2010-11-01

    Over the years extensive studies have been carried out to apply coherent optics methods in real-time processing, communications and transmission image. This is especially true when a large amount of information needs to be processed, e.g., in high-resolution imaging. The recent progress in data-processing networks and communication systems has considerably increased the capacity of information exchange. We describe the results of literature investigation research of processing methods for the signals of the three-dimensional images. All commercially available 3D technologies today are based on stereoscopic viewing. 3D technology was once the exclusive domain of skilled computer-graphics developers with high-end machines and software. The images capture from the advanced 3D digital camera can be displayed onto screen of the 3D digital viewer with/ without special glasses. For this is needed considerable processing power and memory to create and render the complex mix of colors, textures, and virtual lighting and perspective necessary to make figures appear three-dimensional. Also, using a standard digital camera and a technique called phase-shift interferometry we can capture "digital holograms." These are holograms that can be stored on computer and transmitted over conventional networks. We present some research methods to process "digital holograms" for the Internet transmission and results.

  4. A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors

    DEFF Research Database (Denmark)

    Fidom, Kimberley; Isberg, Vignir; Hauser, Alexander Sebastian;

    2015-01-01

    We have developed a new method for the building of pharmacophores for G protein-coupled receptors, a major drug target family. The method is a combination of the ligand- and target-based pharmacophore methods and founded on the extraction of structural fragments, interacting ligand moiety...... for new targets. A validating retrospective virtual screening of histamine H1 and H3 receptor pharmacophores yielded area-under-the-curves of 0.88 and 0.82, respectively. The fragment-based method has the unique advantage that it can be applied to targets for which no (homologous) crystal structures...... or ligands are known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element pharmacophores. The fragment libraries can also be used to grow known ligands or for rotamer refinement of homology models. Researchers can download the complete fragment library or a subset...

  5. Improvement of the method of obtaining human IgA Fc-fragments

    Directory of Open Access Journals (Sweden)

    O. Y. Galkin

    2015-02-01

    Full Text Available To address a number of fundamental and applied problems in immunology, molecular and cellular biology and biotechnology it is necessary to obtain Fc-fragments of immunoglobulins. Fc-fragments may be used for studying of the effector functions of antibodies which are mediated by these areas. They are often used as an immunogen to produce anti-specie (based on so-called secondary antibody conjugate in the development of serological tests for diagnostics (predominantly such conjugate based on monoclonal antibodies. The work is aimed to develop improved methods of obtaining and allocation of Fc-fragments of human IgA. To achieve this objective, optimization of hydrolysis of IgA with subsequent purification of Fс-fragments have been carried out. Improved method of obtaining Fc-fragments of IgA provides: papain hydrolysis of immunoglobulin in the environment of nitrogen for 4 h, allowing to achieve maximum output of Fc-fragments without their further degradation: isolation and purification of Fc-fragments of human IgA by one-stage gel filtration on sephadex G-100; control of purity of the target product by electrophoresis in polyacrylamide gel with sodium dodecyl sulfate and Ouchterlony immunodiffusion. Enzymatic hydrolysis was carried out at the optimal temperature of papain (37 °C. As the oxygen in the air may have inhibitory effect on enzymatic hydrolysis reaction, the reaction mixture was incubated in the nitrogen atmosphere to prevent inactivation of papain. To reduce the incident degradation of immunoglobulin molecules, papain hydrolysis was carried out without using an enzyme activator (cysteine. Usage of the proposed scheme allows obtaining Fc-fragments of human IgA of high purity. Outcome of Fc-fragments after all stages of purification was about 18% of the initial amount of IgA in the preparation. Molecular weight from Fc-fragments of human IgA was equal to approximately 70 kDa.

  6. An efficient method for isolating antibody fragments against small peptides by antibody phage display

    DEFF Research Database (Denmark)

    Duan, Zhi; Siegumfeldt, Henrik

    2010-01-01

    We generated monoclonal scFv (single chain variable fragment) antibodies from an antibody phage display library towards three small synthetic peptides derived from the sequence of s1-casein. Key difficulties for selection of scFv-phages against small peptides were addressed. Small peptides do....... The scFvs were sequenced and characterized, and specificity was characterized by ELISA. The methods developed in this study are universally applicable for antibody phage display to efficiently produce antibody fragments against small peptides....

  7. Statistical methods for detecting periodic fragments in DNA sequence data

    Directory of Open Access Journals (Sweden)

    Ying Hua

    2011-04-01

    Full Text Available Abstract Background Period 10 dinucleotides are structurally and functionally validated factors that influence the ability of DNA to form nucleosomes, histone core octamers. Robust identification of periodic signals in DNA sequences is therefore required to understand nucleosome organisation in genomes. While various techniques for identifying periodic components in genomic sequences have been proposed or adopted, the requirements for such techniques have not been considered in detail and confirmatory testing for a priori specified periods has not been developed. Results We compared the estimation accuracy and suitability for confirmatory testing of autocorrelation, discrete Fourier transform (DFT, integer period discrete Fourier transform (IPDFT and a previously proposed Hybrid measure. A number of different statistical significance procedures were evaluated but a blockwise bootstrap proved superior. When applied to synthetic data whose period-10 signal had been eroded, or for which the signal was approximately period-10, the Hybrid technique exhibited superior properties during exploratory period estimation. In contrast, confirmatory testing using the blockwise bootstrap procedure identified IPDFT as having the greatest statistical power. These properties were validated on yeast sequences defined from a ChIP-chip study where the Hybrid metric confirmed the expected dominance of period-10 in nucleosome associated DNA but IPDFT identified more significant occurrences of period-10. Application to the whole genomes of yeast and mouse identified ~ 21% and ~ 19% respectively of these genomes as spanned by period-10 nucleosome positioning sequences (NPS. Conclusions For estimating the dominant period, we find the Hybrid period estimation method empirically to be the most effective for both eroded and approximate periodicity. The blockwise bootstrap was found to be effective as a significance measure, performing particularly well in the problem of

  8. Fragmentation properties of two-dimensional Proximity Graphs considering random failures and targeted attacks

    CERN Document Server

    Norrenbrock, Christoph; Hartmann, Alexander K

    2015-01-01

    The pivotal quality of proximity graphs is connectivity, i.e. all nodes in the graph are connected to one another either directly or via intermediate nodes. These types of graphs are robust, i.e., they are able to function well even if they are subject to limited removal of elementary building blocks, as it may occur for random failures or targeted attacks. Here, we study how the structure of these graphs is affected when nodes get removed successively until an extensive fraction is removed such that the graphs fragment. We study different types of proximity graphs for various node removal strategies. We use different types of observables to monitor the fragmentation process, simple ones like number and sizes of connected components, and more complex ones like the hop diameter and the backup capacity, which is needed to make a network N-1 resilient. The actual fragmentation turns out to be described by a second order phase transition. Using finite-size scaling analyses we numerically assess the threshold frac...

  9. Performance of heuristic methods driven by chaotic dynamics for ATSP and applications to DNA fragment assembly

    Science.gov (United States)

    Kato, Tomohiro; Hasegawa, Mikio

    Chaotic dynamics has been shown to be effective in improving the performance of combinatorial optimization algorithms. In this paper, the performance of chaotic dynamics in the asymmetric traveling salesman problem (ATSP) is investigated by introducing three types of heuristic solution update methods. Numerical simulation has been carried out to compare its performance with simulated annealing and tabu search; thus, the effectiveness of the approach using chaotic dynamics for driving heuristic methods has been shown. The chaotic method is also evaluated in the case of a combinatorial optimization problem in the real world, which can be solved by the same heuristic operation as that for the ATSP. We apply the chaotic method to the DNA fragment assembly problem, which involves building a DNA sequence from several hundred fragments obtained by the genome sequencer. Our simulation results show that the proposed algorithm using chaotic dynamics in a block shift operation exhibits the best performance for the DNA fragment assembly problem.

  10. Hot-stage microscopy for determination of API fragmentation: comparison with other methods.

    Science.gov (United States)

    Šimek, Michal; Grünwaldová, Veronika; Kratochvíl, Bohumil

    2016-08-01

    Although the fragmentation of the active pharmaceutical ingredient (API) is a phenomenon that is mentioned in many literature sources, no well-suited analytical tools for its investigation are currently known. We used the hot-stage microscopy method, already presented in our previous work, and studied the real fragmentation of the tadalafil particles in model tablets which were prepared under different compaction pressures. The morphology, spectral imaging and evaluation of plastic and elastic energies were also analyzed to support the hot-stage method. The prepared blend of tadalafil and excipients was compacted under a several forces from 5 to 35 kN to reveal the trend of fragmentation. The exact fragmentation of tadalafil with increased compaction pressure was revealed by the hot-stage microscopic method and it was in good agreement with plastic and elastic energies. Conversely, spectral imaging, which is being used for this analysis, was considered to be inaccurate methodology as mainly agglomerates, not individual particles, were measured. The availability of the hot-stage microscopic method equips pharmaceutical scientists with an in vitro assessment technique that will more reliably determine the fragmentation of the API in finished tablets and the behavior of the particles when compacted.

  11. A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method.

    Science.gov (United States)

    Kim, Diane Y; Countway, Peter D; Yamashita, Warren; Caron, David A

    2012-12-01

    Microbial eukaryotes in seawater samples collected from two depths (5 m and 500 m) at the USC Microbial Observatory off the coast of Southern California, USA, were characterized by cloning and sequencing of 18S rRNA genes, as well as DNA fragment analysis of these genes. The sequenced genes were assigned to operational taxonomic units (OTUs), and taxonomic information for the sequence-based OTUs was obtained by comparison to public sequence databases. The sequences were then subjected to in silico digestion to predict fragment sizes, and that information was compared to the results of the T-RFLP method applied to the same samples in order to provide taxonomic context for the environmental T-RFLP fragments. A total of 663 and 678 sequences were analyzed for the 5m and 500 m samples, respectively, which clustered into 157 OTUs and 183 OTUs. The sequences yielded substantially fewer taxonomic units as in silico fragment lengths (i.e., following in silico digestion), and the environmental T-RFLP resulted in the fewest unique OTUs (unique fragments). Bray-Curtis similarity analysis of protistan assemblages was greater using the T-RFLP dataset compared to the sequence-based OTU dataset, presumably due to the inability of the fragment method to differentiate some taxa and an inability to detect many rare taxa relative to the sequence-based approach. Nonetheless, fragments in our analysis generally represented the dominant sequence-based OTUs and putative identifications could be assigned to a majority of the fragments in the environmental T-RFLP results. Our empirical examination of the T-RFLP method identified limitations relative to sequence-based community analysis, but the relative ease and low cost of fragment analysis make this method a useful approach for characterizing the dominant taxa within complex assemblages of microbial eukaryotes in large datasets.

  12. A Quick, Cost-Free Method of Purification of DNA Fragments from Agarose Gel

    Directory of Open Access Journals (Sweden)

    Yuan Sun, Kannappan Sriramajayam, Dianzhong Luo, D. Joshua Liao

    2012-01-01

    Full Text Available In this short communication we report a quick, cost-free method of purification of DNA fragments from agarose gel. Unlike those procedures that involve commercial kits, this method uses glass wool or absorbent cotton to filter agarose gel during a quick spinning-down of DNA, thus significantly simplifying the routine practice of many molecular biologists and decreasing the cost.

  13. Immobilization of Fab' fragments onto substrate surfaces: A survey of methods and applications.

    Science.gov (United States)

    Crivianu-Gaita, Victor; Thompson, Michael

    2015-08-15

    Antibody immobilization onto surfaces has widespread applications in many different fields. It is desirable to bind antibodies such that their fragment-antigen-binding (Fab) units are oriented away from the surface in order to maximize analyte binding. The immobilization of only Fab' fragments yields benefits over the more traditional whole antibody immobilization technique. Bound Fab' fragments display higher surface densities, yielding a higher binding capacity for the analyte. The nucleophilic sulfide of the Fab' fragments allows for specific orientations to be achieved. For biosensors, this indicates a higher sensitivity and lower detection limit for a target analyte. The last thirty years have shown tremendous progress in the immobilization of Fab' fragments onto gold, Si-based, polysaccharide-based, plastic-based, magnetic, and inorganic surfaces. This review will show the current scope of Fab' immobilization techniques available and illustrate methods employed to minimize non-specific adsorption of undesirables. Furthermore, a variety of examples will be given to show the versatility of immobilized Fab' fragments in different applications and future directions of the field will be addressed, especially regarding biosensors.

  14. Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide.

    Science.gov (United States)

    Suárez, Ernesto; Díaz, Natalia; Suárez, Dimas

    2009-06-09

    Herein, we first review different methodologies that have been proposed for computing the quantum mechanical (QM) energy and other molecular properties of large systems through a linear combination of subsystem (fragment) energies, which can be computed using conventional QM packages. Particularly, we emphasize the similarities among the different methods that can be considered as variants of the multibody expansion technique. Nevertheless, on the basis of thermochemical arguments, we propose yet another variant of the fragment energy methods, which could be useful for, and readily applicable to, biomolecules using either QM or hybrid quantum mechanical/molecular mechanics methods. The proposed computational scheme is applied to investigate the stability of a triple-helical collagen model peptide. To better address the actual applicability of the fragment QM method and to properly compare with experimental data, we compute average energies by carrying out single-point fragment QM calculations on structures generated by a classical molecular dynamics simulation. The QM calculations are done using a density functional level of theory combined with an implicit solvent model. Other free-energy terms such as attractive dispersion interactions or thermal contributions are included using molecular mechanics. The importance of correcting both the intermolecular and intramolecular basis set superposition error (BSSE) in the QM calculations is also discussed in detail. On the basis of the favorable comparison of our fragment-based energies with experimental data and former theoretical results, we conclude that the fragment QM energy strategy could be an interesting addition to the multimethod toolbox for biomolecular simulations in order to investigate those situations (e.g., interactions with metal clusters) that are beyond the range of applicability of common molecular mechanics methods.

  15. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates.

    Science.gov (United States)

    Wang, Bo; Yang, Ke R; Xu, Xuefei; Isegawa, Miho; Leverentz, Hannah R; Truhlar, Donald G

    2014-09-16

    Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine

  16. Numerical modeling of rock fracture and fragmentation under impact loading using discrete element method

    Directory of Open Access Journals (Sweden)

    Enan Chi

    2015-06-01

    Full Text Available The fracture and fragmentation of rock materials are basic and important problem in geomechanics and blasting engineering. An approach, which can simulate the process of fracture and fragmentation of rock materials, is introduced in this work. A beam–particle model is first introduced in the frame of the discrete element method. In the beam–particle model, the neighboring elements are connected by beams. Consequently, a beam network is formed in the particle system. The strength characteristics of rock materials are reflected by the beam network. The strength criterion was then built to verify whether a beam exists or not. The process of rock fracture and fragmentation is described by the gradual disappearance of beams. Finally, two cases were presented to indicate the validity of the method proposed in this work.

  17. Three-dimensional imaging of DNA fragments during electrophoresis using a confocal detector

    Science.gov (United States)

    Brewer, Laurence R.; Davidson, Courtney; Balch, Joseph W.; Carrano, Anthony

    1995-04-01

    We have measured the 3D distribution of DNA fragments within an electrophoretic band. The measurements were made using a confocal microscope and a photon counting photomultiplier detector. A DNA sequencing standard was loaded into glass microchannel plates containing polyacrylamide gel. The measurements were made by scanning the plates in three dimensions using a mechanical stage under computer control, while electrophoresis was taking place. We found that the distribution of DNA was the same for all the bands measured in the sequencing ladder with an approximate Gaussian distribution along all three axis. These measurements are important to understand what physical forces shape electrophoretic bands confined by a channel and also as an aid in the design of high throughput DNA sequencers.

  18. Optimisation and evaluation of restriction fragment length polimorfism method for apolipoprotein E

    Directory of Open Access Journals (Sweden)

    Drljević Nevena

    2014-01-01

    Full Text Available Introduction. Apolipoprotein E gene polymorphism is characterized by the presence of three common alleles, e2, e3 and e4, which encode three isoforms of apolipoprotein E in plasma E2, E3 and E4. Genetic polymorphisms of apolipoprotein E gene are predictive markers for the development of numerous disorders of lipid metabolism, already proven in a large number of clinical trials. This study was aimed at assessing the success rate of restriction fragment length polymorphism method for the detections of genes coding for isoenzymes E2, E3 and E4. Material and Methods. Deoxyribonucleic acid, used in this study, was extracted from blood by standard procedure using chloroform and phenol. The polymerase chain reaction method was used to amplify the coding sequence of fourth exon of the apolipoprotein E gene. Amplification products were digested with HhaI. The fragments obtained were separated by electrophoresis and visualized with ultraviolet light. Results. Our results showed that the restriction fragment length polymorphism method is optimal for detection of apolipoprotein E polymorphisms. The restriction enzyme HhaI achieved the cleavage of the gene on the specific loci, directly depend of presence or absence of mutations at positions 112 and 158, of different alleles. Conclusion. This method enables simple, rapid and efficient analysis of restriction fragment length polymorphisms, directly determining the patient’s genotype.

  19. Brownian shape motion on five-dimensional potential-energy surfaces:nuclear fission-fragment mass distributions.

    Science.gov (United States)

    Randrup, Jørgen; Möller, Peter

    2011-04-01

    Although nuclear fission can be understood qualitatively as an evolution of the nuclear shape, a quantitative description has proven to be very elusive. In particular, until now, there existed no model with demonstrated predictive power for the fission-fragment mass yields. Exploiting the expected strongly damped character of nuclear dynamics, we treat the nuclear shape evolution in analogy with Brownian motion and perform random walks on five-dimensional fission potential-energy surfaces which were calculated previously and are the most comprehensive available. Test applications give good reproduction of highly variable experimental mass yields. This novel general approach requires only a single new global parameter, namely, the critical neck size at which the mass split is frozen in, and the results are remarkably insensitive to its specific value.

  20. Brownian shape motion on five-dimensional potential-energy surfaces: Nuclear fission-fragment mass distributions

    CERN Document Server

    Randrup, Jorgen

    2011-01-01

    Although nuclear fission can be understood qualitatively as an evolution of the nuclear shape, a quantitative description has proven to be very elusive. In particular, until now, there exists no model with demonstrated predictive power for the fission fragment mass yields. Exploiting the expected strongly damped character of nuclear dynamics, we treat the nuclear shape evolution in analogy with Brownian motion and perform random walks on five-dimensional fission potential-energy surfaces which were calculated previously and are the most comprehensive available. Test applications give good reproduction of highly variable experimental mass yields. This novel general approach requires only a single new global parameter, namely the critical neck size at which the mass split is frozen in, and the results are remarkably insensitive to its specific value.

  1. Exact Three Dimensional Mathematical Model for Evaluation of Antipersonnel and Antimaterial Effectiveness of Fragmenting/ Preformed Conventional Warhead

    Directory of Open Access Journals (Sweden)

    Umesh Chandra Chandola

    1986-07-01

    Full Text Available The basic theory for the evalution of warhead-target interaction in three dimensional space on the concept of partitioning the target surface into sub-target surfaces having atleast two such mathematically defined boundaries which are projections of randomly fragmenting shapiro rings of the exploding shell with respect to the point of burst or preferably the centre of gravity of the shell lying on the shell-axis is presented. The equation for any given orientation of the shell-axis to the family of cones around the shell-axis has been derived for the cases: (i when both the warhead and the target are stationary, (ii when the warhead is moving and the target is stationary, and (iii when both the warhead and the target are moving. Expressions for the conditional probability of kill for at least one lethal hit, and for a finite number of lethal hits, p, among a group of r hits (r >- p on a tactical target by fragments/projectiles of an exploding warhead for use in the above three cases have been derived.

  2. Are fragment-based quantum chemistry methods applicable to medium-sized water clusters?

    Science.gov (United States)

    Yuan, Dandan; Shen, Xiaoling; Li, Wei; Li, Shuhua

    2016-06-28

    Fragment-based quantum chemistry methods are either based on the many-body expansion or the inclusion-exclusion principle. To compare the applicability of these two categories of methods, we have systematically evaluated the performance of the generalized energy based fragmentation (GEBF) method (J. Phys. Chem. A, 2007, 111, 2193) and the electrostatically embedded many-body (EE-MB) method (J. Chem. Theory Comput., 2007, 3, 46) for medium-sized water clusters (H2O)n (n = 10, 20, 30). Our calculations demonstrate that the GEBF method provides uniformly accurate ground-state energies for 10 low-energy isomers of three water clusters under study at a series of theory levels, while the EE-MB method (with one water molecule as a fragment and without using the cutoff distance) shows a poor convergence for (H2O)20 and (H2O)30 when the basis set contains diffuse functions. Our analysis shows that the neglect of the basis set superposition error for each subsystem has little effect on the accuracy of the GEBF method, but leads to much less accurate results for the EE-MB method. The accuracy of the EE-MB method can be dramatically improved by using an appropriate cutoff distance and using two water molecules as a fragment. For (H2O)30, the average deviation of the EE-MB method truncated up to the three-body level calculated using this strategy (relative to the conventional energies) is about 0.003 hartree at the M06-2X/6-311++G** level, while the deviation of the GEBF method with a similar computational cost is less than 0.001 hartree. The GEBF method is demonstrated to be applicable for electronic structure calculations of water clusters at any basis set.

  3. Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Svendsen, Casper Steinmann; Fedorov, Dmitri G

    2014-01-01

    The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory...... while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta...

  4. The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method.

    Science.gov (United States)

    Fedorov, Dmitri G; Kitaura, Kazuo

    2009-11-01

    We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree-Fock level with the 6-31G( *) and 6-311G( * *) basis sets.

  5. Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design.

    Science.gov (United States)

    Watanabe, Chiduru; Fukuzawa, Kaori; Okiyama, Yoshio; Tsukamoto, Takayuki; Kato, Akifumi; Tanaka, Shigenori; Mochizuki, Yuji; Nakano, Tatsuya

    2013-04-01

    We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design.

  6. Many-body expansion of the Fock matrix in the fragment molecular orbital method

    Science.gov (United States)

    Fedorov, Dmitri G.; Kitaura, Kazuo

    2017-09-01

    A many-body expansion of the Fock matrix in the fragment molecular orbital method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic orbital basis and compared to the expansion in the basis of fragment molecular orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon. The physical nature of metallicity is discussed, and it is shown what kinds of metallic systems can be treated by fragment-based methods. The density of states is calculated for a fully closed and a partially open nano-ring of boron nitride with a diameter of 105 nm.

  7. The successful merger of theoretical thermochemistry with fragment-based methods in quantum chemistry.

    Science.gov (United States)

    Ramabhadran, Raghunath O; Raghavachari, Krishnan

    2014-12-16

    CONSPECTUS: Quantum chemistry and electronic structure theory have proven to be essential tools to the experimental chemist, in terms of both a priori predictions that pave the way for designing new experiments and rationalizing experimental observations a posteriori. Translating the well-established success of electronic structure theory in obtaining the structures and energies of small chemical systems to increasingly larger molecules is an exciting and ongoing central theme of research in quantum chemistry. However, the prohibitive computational scaling of highly accurate ab initio electronic structure methods poses a fundamental challenge to this research endeavor. This scenario necessitates an indirect fragment-based approach wherein a large molecule is divided into small fragments and is subsequently reassembled to compute its energy accurately. In our quest to further reduce the computational expense associated with the fragment-based methods and overall enhance the applicability of electronic structure methods to large molecules, we realized that the broad ideas involved in a different area, theoretical thermochemistry, are transferable to the area of fragment-based methods. This Account focuses on the effective merger of these two disparate frontiers in quantum chemistry and how new concepts inspired by theoretical thermochemistry significantly reduce the total number of electronic structure calculations needed to be performed as part of a fragment-based method without any appreciable loss of accuracy. Throughout, the generalized connectivity based hierarchy (CBH), which we developed to solve a long-standing problem in theoretical thermochemistry, serves as the linchpin in this merger. The accuracy of our method is based on two strong foundations: (a) the apt utilization of systematic and sophisticated error-canceling schemes via CBH that result in an optimal cutting scheme at any given level of fragmentation and (b) the use of a less expensive second

  8. Robust three dimensional surface contouring method with digital holography

    Institute of Scientific and Technical Information of China (English)

    YUAN Cao-jin; ZHAI Hong-chen; WANG Xiao-lei; WU Lan

    2006-01-01

    In this paper,a digital holography system with short-coherence light source is used to record a series of holograms of a micro-object. The three dimensional reconstruction is completed by the least-square-polynomial-fitting with a series of two dimensional intensity images which are obtained through holographic reconstruction. This three dimensional reconstruction method can be used to carry out three-dimensional reconstruction of a micro-object with strong laser speckle noise,which can not be obtained from the conventional method.

  9. UPWIND DISCONTINUOUS GALERKIN METHODS FOR TWO DIMENSIONAL NEUTRON TRANSPORT EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    袁光伟; 沈智军; 闫伟

    2003-01-01

    In this paper the upwind discontinuous Galerkin methods with triangle meshes for two dimensional neutron transport equations will be studied.The stability for both of the semi-discrete and full-discrete method will be proved.

  10. Method of dimensionality reduction in contact mechanics and friction

    CERN Document Server

    Popov, Valentin L

    2015-01-01

    This book describes for the first time a simulation method for the fast calculation of contact properties and friction between rough surfaces in a complete form. In contrast to existing simulation methods, the method of dimensionality reduction (MDR) is based on the exact mapping of various types of three-dimensional contact problems onto contacts of one-dimensional foundations. Within the confines of MDR, not only are three dimensional systems reduced to one-dimensional, but also the resulting degrees of freedom are independent from another. Therefore, MDR results in an enormous reduction of the development time for the numerical implementation of contact problems as well as the direct computation time and can ultimately assume a similar role in tribology as FEM has in structure mechanics or CFD methods, in hydrodynamics. Furthermore, it substantially simplifies analytical calculation and presents a sort of “pocket book edition” of the entirety contact mechanics. Measurements of the rheology of bodies in...

  11. A general method to modify BACs to generate large recombinant DNA fragments.

    Science.gov (United States)

    Shen, Wei; Huang, Yue; Tang, Yi; Liu, De-Pei; Liang, Chih-Chuan

    2005-11-01

    Bacterial artificial chromosome (BAC) has the capacity to clone DNA fragments in excess of 300 kb. It also has the considerable advantages of stable propagation and ease of purification. These features make BAC suitable in genetic research, such as library construction, transgenic mice production, and gene targeting constructs. Homologous recombination in Escherichia coli, a process named recombineering, has made the modification of BACs easy and reliable. We report here a modified recombineering method that can efficiently mediate the fusion of large DNA fragments from two or more different BACs. With the introduction of kanamycin-resistant gene and proposed rare-cutting restriction endonuclease (RCRE) sites into two BACs, a 82.6-kb DNA fragment containing the inverted human alpha-globin genes (theta, alpha1, alpha2, and zeta) from BAC191K2 and the locus control region (LCR) of human beta-globin gene locus (from the BAC186D7) was reconstructed. This approach for combining different BAC DNA fragments should facilitate many kinds of genomic experiments.

  12. Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

    Science.gov (United States)

    Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

    2009-10-01

    We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.

  13. Extrudate Expansion Modelling through Dimensional Analysis Method

    DEFF Research Database (Denmark)

    A new model framework is proposed to correlate extrudate expansion and extrusion operation parameters for a food extrusion cooking process through dimensional analysis principle, i.e. Buckingham pi theorem. Three dimensionless groups, i.e. energy, water content and temperature, are suggested...... to describe the extrudates expansion. From the three dimensionless groups, an equation with three experimentally determined parameters is derived to express the extrudate expansion. The model is evaluated with whole wheat flour and aquatic feed extrusion experimental data. The average deviations...

  14. DIAGNOSTIC CHARACTERISTICS OF THE COMPUTER TESTS FORMED BY METHOD OF RESTORED FRAGMENTS

    Directory of Open Access Journals (Sweden)

    Oleksandr O. Petkov

    2013-03-01

    Full Text Available Definition of validity and reliability of tests which are formed by a method of restored fragments is considered in the article. The structure of the controlled theoretical material of limit field of knowledge, language expressions that describe the subject of control, and reliability of test, is analyzed. The technique of definition of the most important components of reliability of the considered tests is given: reliability of quantitative determination of coefficient of assimilation and technological reliability. Results of the lead pedagogical experiments have proved, that tests of the given class allow to make the control of mastering of a theoretical material over a level of reproduction in any field of knowledge with high reliability. It is shown, that validity tests with restored fragments basically caused by a degree of structurization and methodical study of a controllable material and can achieve beforehand set parameters, down to a level of absolute validity.

  15. Three-dimensional decomposition method of global atmospheric circulation

    Institute of Scientific and Technical Information of China (English)

    LIU HaiTao; HU ShuJuan; XU Ming; CHOU JiFan

    2008-01-01

    By adopting the idea of three-dimensional Walker, Hadley and Rossby stream functions, the global atmospheric circulation can be considered as the sum of three stream functions from a global perspective. Therefore, a mathematical model of three-dimensional decomposition of global atmospheric circulation is proposed and the existence and uniqueness of the model are proved. Besides, the model includes a numerical method leading to no truncation error in the discrete three-dimensional grid points. Results also show that the three-dimensional stream functions exist and are unique for a given velocity field. The mathematical model shows the generalized form of three-dimensional stream functions equal to the velocity field in representing the features of atmospheric motion. Besides, the vertical velocity calculated through the model can represent the main characteristics of the vertical motion. In sum, the three-dimensional decomposition of atmospheric circulation is convenient for the further investigation of the features of global atmospheric motions.

  16. Vasoinhibin, an N-terminal Prolactin Fragment, Directly Inhibits Cardiac Angiogenesis in Three-dimensional Heart Culture

    Science.gov (United States)

    Nakajima, Ryojun; Nakamura, Eri; Harigaya, Toshio

    2017-01-01

    Vasoinhibins (Vi) are fragments of the growth hormone/prolactin (PRL) family and have antiangiogenic functions in many species. It is considered that Vi derived from PRL are involved in the pathogenesis of peripartum cardiomyopathy (PPCM). However, the pathogenic mechanism of PPCM, as well as heart angiogenesis, is not yet clear. Therefore, the aim of the present study is to clarify whether Vi act directly on angiogenesis inhibition in heart blood vessels. Endothelial cell viability was decreased by Vi treatment in a culture experiment. Furthermore, expression of proangiogenic genes, such as vascular endothelial growth factor, endothelial nitric oxide synthase, and VE-cadherin, were decreased. On the other hand, apoptotic factor gene, caspase 3, and inflammatory factor genes, tumor necrosis factor α and interleukin 6, were increased by Vi treatment. In three-dimensional left ventricular wall angiogenesis assay in mice, Vi treatment also inhibited cell migration, neovessel sprouting, and growth toward collagen gel. These data demonstrate that Vi treatment directly suppresses angiogenesis of the heart and support the hypothesis that Vi induce PPCM. PMID:28163696

  17. Hypothesis-driven and field-validated method to prioritize fragmentation mitigation efforts in road projects.

    Science.gov (United States)

    Vanthomme, Hadrien; Kolowski, Joseph; Nzamba, Brave S; Alonso, Alfonso

    2015-10-01

    The active field of connectivity conservation has provided numerous methods to identify wildlife corridors with the aim of reducing the ecological effect of fragmentation. Nevertheless, these methods often rely on untested hypotheses of animal movements, usually fail to generate fine-scale predictions of road crossing sites, and do not allow managers to prioritize crossing sites for implementing road fragmentation mitigation measures. We propose a new method that addresses these limitations. We illustrate this method with data from southwestern Gabon (central Africa). We used stratified random transect surveys conducted in two seasons to model the distribution of African forest elephant (Loxodonta cyclotis), forest buffalo (Syncerus caffer nanus), and sitatunga (Tragelaphus spekii) in a mosaic landscape along a 38.5 km unpaved road scheduled for paving. Using a validation data set of recorded crossing locations, we evaluated the performance of three types of models (local suitability, local least-cost movement, and regional least-cost movement) in predicting actual road crossings for each species, and developed a unique and flexible scoring method for prioritizing road sections for the implementation of road fragmentation mitigation measures. With a data set collected in method was able to identify seasonal changes in animal movements for buffalo and sitatunga that shift from a local exploitation of the site in the wet season to movements through the study site in the dry season, whereas elephants use the entire study area in both seasons. These three species highlighted the need to use species- and season-specific modeling of movement. From these movement models, the method ranked road sections for their suitability for implementing fragmentation mitigation efforts, allowing managers to adjust priority thresholds based on budgets and management goals. The method relies on data that can be obtained in a period compatible with environmental impact assessment

  18. Analytic second derivatives of the energy in the fragment molecular orbital method.

    Science.gov (United States)

    Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro

    2013-04-28

    We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm(-1) in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.

  19. Direct Linear Transformation Method for Three-Dimensional Cinematography

    Science.gov (United States)

    Shapiro, Robert

    1978-01-01

    The ability of Direct Linear Transformation Method for three-dimensional cinematography to locate points in space was shown to meet the accuracy requirements associated with research on human movement. (JD)

  20. Uniform Deterministic Discrete Method for Three Dimensional Systems

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    For radiative direct exchange areas in three dimensional system,the Uniform Deterministic Discrete Method(UDDM) was adopted.The spherical surface dividing method for sending area element and the regular icosahedron for sending volume element can meet with the direct exchange area computation of any kind of zone pairs.The numerical examples of direct exchange area in three dimensional system with nonhomogeneous attenuation coefficients indicated that the UDDM can give very high numercal accuracy.

  1. Fragmentation, Cost and Environmental Effects of Plaster Stemming Method for Blasting at A Basalt Quarry

    Science.gov (United States)

    Cevizci, Halim

    2014-10-01

    In this study, the plaster stemming application for blasting at a basalt quarry is studied. Drill cuttings are generally used in open pits and quarries as the most common stemming material since these are most readily available at blast sites. However, dry drill cuttings eject very easily from blastholes without offering much resistance to blast energy. The plaster stemming method has been found to be better than the drill cuttings stemming method due to increased confinement inside the hole and better utilization of blast explosive energy in the rock. The main advantage of the new stemming method is the reduction in the cost of blasting. At a basalt quarry, blasting costs per unit volume of rock were reduced to 15% by increasing burden and spacing distances. In addition, better fragmentation was obtained by using the plaster stemming method. Blast trials showed that plaster stemming produced finer material. In the same blast tests, +30 cm size fragments were reduced to 47.3% of the total, compared to 32.6% in the conventional method of drill cuttings stemming. With this method of stemming, vibration and air shock values increased slightly due to more blast energy being available for rock breakage but generally these increased values were small and stayed under the permitted limit for blast damage criteria unless measuring distance is too close.

  2. Methods for two-dimensional cell confinement.

    Science.gov (United States)

    Le Berre, Maël; Zlotek-Zlotkiewicz, Ewa; Bonazzi, Daria; Lautenschlaeger, Franziska; Piel, Matthieu

    2014-01-01

    Protocols described in this chapter relate to a method to dynamically confine cells in two dimensions with various microenvironments. It can be used to impose on cells a given height, with an accuracy of less than 100 nm on large surfaces (cm(2)). The method is based on the gentle application of a modified glass coverslip onto a standard cell culture. Depending on the preparation, this confinement slide can impose on the cells a given geometry but also an environment of controlled stiffness, controlled adhesion, or a more complex environment. An advantage is that the method is compatible with most optical microscopy technologies and molecular biology protocols allowing advanced analysis of confined cells. In this chapter, we first explain the principle and issues of using these slides to confine cells in a controlled geometry and describe their fabrication. Finally, we discuss how the nature of the confinement slide can vary and provide an alternative method to confine cells with gels of controlled rigidity.

  3. Contingent dissociation between recognition and fragment completion: the method of triangulation.

    Science.gov (United States)

    Hayman, C A; Tulving, E

    1989-03-01

    Two experiments conforming to the logic of the method of triangulation were conducted. Following the study of a list of words, the first of two successive tests (recognition) was identical for two groups of subjects, but the second one, in which the same word-fragment cues were presented to both groups, differed with respect to retrieval instructions. Subjects in one group engaged in cued recall of study-list words, whereas those in the second group completed the fragments with the first word that came to mind. Both experiments yielded the same result: The dependency between the first and second tests, indexed by Yule's Q statistic, was greater for recognition and cued recall than it was for recognition and fragment completion. These results speak to the controversial issue of the usefulness of contingency analyses of data from successive memory tests. The results are interpreted in a theoretical framework consisting of an integration of the idea of a hypothetical quasi-memory system with the transfer-appropriate procedural approach.

  4. Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method

    Science.gov (United States)

    Roskop, Luke; Fedorov, Dmitri G.; Gordon, Mark S.

    2013-07-01

    The fragment molecular orbital (FMO) method is used to model truncated portions of mesoporous silica nanoparticle (MSN) pores. The application of the FMO/RHF (restricted Hartree-Fock) method to MCM-41 type MSNs is discussed and an error analysis is given. The FMO/RHF method is shown to reliably approximate the RHF energy (error ∼0.2 kcal/mol), dipole moment (error ∼0.2 debye) and energy gradient (root mean square [RMS] error ∼0.2 × 10-3 a.u./bohr). Several FMO fragmentation schemes are employed to provide guidance for future applications to MSN models. An MSN pore model is functionalised with (phenyl)propyl substituents and the diffusion barrier for benzene passing through the pore is computed by the FMO/RHF-D method with the Grimme dispersion correction (RHF-D). For the reaction coordinates examined here, the maximum FMO/RHF-D interaction energies range from -0.3 to -5.8 kcal/mol.

  5. [Analysis of Conformational Features of Watson-Crick Duplex Fragments by Molecular Mechanics and Quantum Mechanics Methods].

    Science.gov (United States)

    Poltev, V I; Anisimov, V M; Sanchez, C; Deriabina, A; Gonzalez, E; Garcia, D; Rivas, F; Polteva, N A

    2016-01-01

    It is generally accepted that the important characteristic features of the Watson-Crick duplex originate from the molecular structure of its subunits. However, it still remains to elucidate what properties of each subunit are responsible for the significant characteristic features of the DNA structure. The computations of desoxydinucleoside monophosphates complexes with Na-ions using density functional theory revealed a pivotal role of DNA conformational properties of single-chain minimal fragments in the development of unique features of the Watson-Crick duplex. We found that directionality of the sugar-phosphate backbone and the preferable ranges of its torsion angles, combined with the difference between purines and pyrimidines. in ring bases, define the dependence of three-dimensional structure of the Watson-Crick duplex on nucleotide base sequence. In this work, we extended these density functional theory computations to the minimal' fragments of DNA duplex, complementary desoxydinucleoside monophosphates complexes with Na-ions. Using several computational methods and various functionals, we performed a search for energy minima of BI-conformation for complementary desoxydinucleoside monophosphates complexes with different nucleoside sequences. Two sequences are optimized using ab initio method at the MP2/6-31++G** level of theory. The analysis of torsion angles, sugar ring puckering and mutual base positions of optimized structures demonstrates that the conformational characteristic features of complementary desoxydinucleoside monophosphates complexes with Na-ions remain within BI ranges and become closer to the corresponding characteristic features of the Watson-Crick duplex crystals. Qualitatively, the main characteristic features of each studied complementary desoxydinucleoside monophosphates complex remain invariant when different computational methods are used, although the quantitative values of some conformational parameters could vary lying within the

  6. Nonlinear Dimensionality Reduction Methods in Climate Data Analysis

    CERN Document Server

    Ross, Ian

    2008-01-01

    Linear dimensionality reduction techniques, notably principal component analysis, are widely used in climate data analysis as a means to aid in the interpretation of datasets of high dimensionality. These linear methods may not be appropriate for the analysis of data arising from nonlinear processes occurring in the climate system. Numerous techniques for nonlinear dimensionality reduction have been developed recently that may provide a potentially useful tool for the identification of low-dimensional manifolds in climate data sets arising from nonlinear dynamics. In this thesis I apply three such techniques to the study of El Nino/Southern Oscillation variability in tropical Pacific sea surface temperatures and thermocline depth, comparing observational data with simulations from coupled atmosphere-ocean general circulation models from the CMIP3 multi-model ensemble. The three methods used here are a nonlinear principal component analysis (NLPCA) approach based on neural networks, the Isomap isometric mappin...

  7. Charge-to-mass dispersion methods for abrasion-ablation fragmentation models

    Science.gov (United States)

    Townsend, L. W.; Norbury, J. W.

    1985-01-01

    Methods to describe the charge-to-mass dispersion distributions of projectile prefragments are presented and used to determine individual isotope cross-sections or various elements produced in the fragmentation of relativistic argon nuclei by carbon targets. Although slight improvements in predicted cross-sections are obtained for the quantum mechanical giant dipole resonance (GDR) distribution when compared qith the predictions of the geometric GDR model, the closest agreement between theory and experiment continues to be obtained with the simple hypergeometric distribution, which treats the nucleons in the nucleus as completely uncorrelated.

  8. TreePM Method for Two-Dimensional Cosmological Simulations

    Indian Academy of Sciences (India)

    Suryadeep Ray

    2004-09-01

    We describe the two-dimensional TreePM method in this paper. The 2d TreePM code is an accurate and efficient technique to carry out large two-dimensional N-body simulations in cosmology. This hybrid code combines the 2d Barnes and Hut Tree method and the 2d Particle–Mesh method. We describe the splitting of force between the PM and the Tree parts. We also estimate error in force for a realistic configuration. Finally, we discuss some tests of the code.

  9. A sparse grid based method for generative dimensionality reduction of high-dimensional data

    Science.gov (United States)

    Bohn, Bastian; Garcke, Jochen; Griebel, Michael

    2016-03-01

    Generative dimensionality reduction methods play an important role in machine learning applications because they construct an explicit mapping from a low-dimensional space to the high-dimensional data space. We discuss a general framework to describe generative dimensionality reduction methods, where the main focus lies on a regularized principal manifold learning variant. Since most generative dimensionality reduction algorithms exploit the representer theorem for reproducing kernel Hilbert spaces, their computational costs grow at least quadratically in the number n of data. Instead, we introduce a grid-based discretization approach which automatically scales just linearly in n. To circumvent the curse of dimensionality of full tensor product grids, we use the concept of sparse grids. Furthermore, in real-world applications, some embedding directions are usually more important than others and it is reasonable to refine the underlying discretization space only in these directions. To this end, we employ a dimension-adaptive algorithm which is based on the ANOVA (analysis of variance) decomposition of a function. In particular, the reconstruction error is used to measure the quality of an embedding. As an application, the study of large simulation data from an engineering application in the automotive industry (car crash simulation) is performed.

  10. Non perturbative methods in two dimensional quantum field theory

    CERN Document Server

    Abdalla, Elcio; Rothe, Klaus D

    1991-01-01

    This book is a survey of methods used in the study of two-dimensional models in quantum field theory as well as applications of these theories in physics. It covers the subject since the first model, studied in the fifties, up to modern developments in string theories, and includes exact solutions, non-perturbative methods of study, and nonlinear sigma models.

  11. A novel method to discover fluoroquinolone antibiotic resistance (qnr genes in fragmented nucleotide sequences

    Directory of Open Access Journals (Sweden)

    Boulund Fredrik

    2012-12-01

    Full Text Available Abstract Background Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail. Results In this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature. Conclusions The method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.

  12. Investigating of yeast species in wine fermentation using terminal restriction fragment length polymorphism method.

    Science.gov (United States)

    Sun, Yue; Liu, Yanlin

    2014-04-01

    The objective of this study was to examine the potential of terminal restriction fragment length polymorphism (T-RFLP) in monitoring yeast communities during wine fermentation and to reveal new information on yeast community of Chinese enology. Firstly, terminal restriction fragment (TRF) lengths database was constructed using 32 pure yeast species. Ten of these species were firstly documented. The species except for Candida vini, Issatchenkia orientalis/Candida krusei, Saccharomyces bayanus, Saccharomyces pastorianus, Saccharomyces cerevisiae, Saccharomyces kudriarzevii and Zygosaccharomyces bisporus could be distinguished by the T-RFLP targeting 5.8S-ITS rDNA. Moreover, the yeast communities in spontaneous fermentation of Chardonnay and Riesling were identified by T-RFLP and traditional methods, including colony morphology on Wallerstein Nutrient (WLN) medium and 5.8S-ITS-RFLP analysis. The result showed that T-RFLP profiles of the yeast community correlated well with that of the results identified by the traditional methods. The TRFs with the highest intensity and present in all the samples corresponded to Saccharomyces sp. Other species detected by both approaches were Hanseniaspora uvarum, Metschnikowia pulcherrima, Pichia minuta var. minuta, Saccharomycodes ludwigii/Torulaspora delbrueckii and Candida zemplinina. This study revealed that T-RFLP technique is a rapid and useful tool for monitoring the composition of yeast species during wine fermentation.

  13. Numerical methods for high-dimensional probability density function equations

    Science.gov (United States)

    Cho, H.; Venturi, D.; Karniadakis, G. E.

    2016-01-01

    In this paper we address the problem of computing the numerical solution to kinetic partial differential equations involving many phase variables. These types of equations arise naturally in many different areas of mathematical physics, e.g., in particle systems (Liouville and Boltzmann equations), stochastic dynamical systems (Fokker-Planck and Dostupov-Pugachev equations), random wave theory (Malakhov-Saichev equations) and coarse-grained stochastic systems (Mori-Zwanzig equations). We propose three different classes of new algorithms addressing high-dimensionality: The first one is based on separated series expansions resulting in a sequence of low-dimensional problems that can be solved recursively and in parallel by using alternating direction methods. The second class of algorithms relies on truncation of interaction in low-orders that resembles the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) framework of kinetic gas theory and it yields a hierarchy of coupled probability density function equations. The third class of algorithms is based on high-dimensional model representations, e.g., the ANOVA method and probabilistic collocation methods. A common feature of all these approaches is that they are reducible to the problem of computing the solution to high-dimensional equations via a sequence of low-dimensional problems. The effectiveness of the new algorithms is demonstrated in numerical examples involving nonlinear stochastic dynamical systems and partial differential equations, with up to 120 variables.

  14. Numerical methods for high-dimensional probability density function equations

    Energy Technology Data Exchange (ETDEWEB)

    Cho, H. [Department of Mathematics, University of Maryland College Park, College Park, MD 20742 (United States); Venturi, D. [Department of Applied Mathematics and Statistics, University of California Santa Cruz, Santa Cruz, CA 95064 (United States); Karniadakis, G.E., E-mail: gk@dam.brown.edu [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States)

    2016-01-15

    In this paper we address the problem of computing the numerical solution to kinetic partial differential equations involving many phase variables. These types of equations arise naturally in many different areas of mathematical physics, e.g., in particle systems (Liouville and Boltzmann equations), stochastic dynamical systems (Fokker–Planck and Dostupov–Pugachev equations), random wave theory (Malakhov–Saichev equations) and coarse-grained stochastic systems (Mori–Zwanzig equations). We propose three different classes of new algorithms addressing high-dimensionality: The first one is based on separated series expansions resulting in a sequence of low-dimensional problems that can be solved recursively and in parallel by using alternating direction methods. The second class of algorithms relies on truncation of interaction in low-orders that resembles the Bogoliubov–Born–Green–Kirkwood–Yvon (BBGKY) framework of kinetic gas theory and it yields a hierarchy of coupled probability density function equations. The third class of algorithms is based on high-dimensional model representations, e.g., the ANOVA method and probabilistic collocation methods. A common feature of all these approaches is that they are reducible to the problem of computing the solution to high-dimensional equations via a sequence of low-dimensional problems. The effectiveness of the new algorithms is demonstrated in numerical examples involving nonlinear stochastic dynamical systems and partial differential equations, with up to 120 variables.

  15. Errors in using two dimensional methods for ergonomic assessment of motion in three dimensional space

    Energy Technology Data Exchange (ETDEWEB)

    Hollerbach, K.; Van Vorhis, R.L. [Lawrence Livermore National Lab., CA (United States); Hollister, A. [Louisiana State Univ., Shreveport, LA (United States)

    1996-03-01

    Wrist posture and rapid wrist movements are risk factors for work related musculoskeletal disorders. Measurement studies frequently involve optoelectronic methods in which markers are placed on the subject`s hand and wrist and the trajectories of the markers are tracked in three dimensional space. A goal of wrist posture measurements is to quantitatively establish wrist posture orientation. Accuracy and fidelity of the measurement data with respect to kinematic mechanisms are essential in wrist motion studies. Fidelity with the physical kinematic mechanism can be limited by the choice of kinematic modeling techniques and the representation of motion. Frequently, ergonomic studies involving wrist kinematics make use of two dimensional measurement and analysis techniques. Two dimensional measurement of human joint motion involves the analysis of three dimensional displacements in an obersver selected measurement plane. Accurate marker placement and alignment of joint motion plane with the observer plane are difficult. In nature, joint axes can exist at any orientation and location relative to an arbitrarily chosen global reference frame. An arbitrary axis is any axis that is not coincident with a reference coordinate. We calculate the errors that result from measuring joint motion about an arbitrary axis using two dimensional methods.

  16. Three-dimensional decomposition method of global atmospheric circulation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    By adopting the idea of three-dimensional Walker, Hadley and Rossby stream functions, the global atmospheric circulation can be considered as the sum of three stream functions from a global per- spective. Therefore, a mathematical model of three-dimensional decomposition of global atmospheric circulation is proposed and the existence and uniqueness of the model are proved. Besides, the model includes a numerical method leading to no truncation error in the discrete three-dimensional grid points. Results also show that the three-dimensional stream functions exist and are unique for a given velocity field. The mathematical model shows the generalized form of three-dimensional stream func- tions equal to the velocity field in representing the features of atmospheric motion. Besides, the vertical velocity calculated through the model can represent the main characteristics of the vertical motion. In sum, the three-dimensional decomposition of atmospheric circulation is convenient for the further in- vestigation of the features of global atmospheric motions.

  17. MRFD Method for Scattering From Three Dimensional Dielectric Bodies

    Directory of Open Access Journals (Sweden)

    A. F. Yagli

    2011-09-01

    Full Text Available A three-dimensional multiresolution frequency domain (MRFD method is established to compute bistatic radar cross sections of arbitrarily shaped dielectric objects. The proposed formulation is successfully verified by computing the bistatic radar cross sections of a dielectric sphere and a dielectric cube. Comparing the results to those obtained from the finite difference frequency domain (FDFD method simulations and analytic calculations, we demonstrated the computational time and memory advantages of MRFD method.

  18. Low dimensional gyrokinetic PIC simulation by δf method

    Science.gov (United States)

    Chen, C. M.; Nishimura, Yasutaro; Cheng, C. Z.

    2015-11-01

    A step by step development of our low dimensional gyrokinetic Particle-in-Cell (PIC) simulation is reported. One dimensional PIC simulation of Langmuir wave dynamics is benchmarked. We then take temporal plasma echo as a test problem to incorporate the δf method. Electrostatic driftwave simulation in one dimensional slab geometry is resumed in the presence of finite density gradients. By carefully diagnosing contour plots of the δf values in the phase space, we discuss the saturation mechanism of the driftwave instabilities. A v∥ formulation is employed in our new electromagnetic gyrokinetic method by solving Helmholtz equation for time derivative of the vector potential. Electron and ion momentum balance equations are employed in the time derivative of the Ampere's law. This work is supported by Ministry of Science and Technology of Taiwan, MOST 103-2112-M-006-007 and MOST 104-2112-M-006-019.

  19. Computational methods for three-dimensional microscopy reconstruction

    CERN Document Server

    Frank, Joachim

    2014-01-01

    Approaches to the recovery of three-dimensional information on a biological object, which are often formulated or implemented initially in an intuitive way, are concisely described here based on physical models of the object and the image-formation process. Both three-dimensional electron microscopy and X-ray tomography can be captured in the same mathematical framework, leading to closely-related computational approaches, but the methodologies differ in detail and hence pose different challenges. The editors of this volume, Gabor T. Herman and Joachim Frank, are experts in the respective methodologies and present research at the forefront of biological imaging and structural biology.   Computational Methods for Three-Dimensional Microscopy Reconstruction will serve as a useful resource for scholars interested in the development of computational methods for structural biology and cell biology, particularly in the area of 3D imaging and modeling.

  20. Some methods for the determination and the evaluation of non-fragmented and minimal disturbed landscape areas

    Directory of Open Access Journals (Sweden)

    Olaf Kappler

    1998-12-01

    Full Text Available Summary The assessment of the effect and function of non-fragmented landscape areas with minimal disturbances for vertebrata with large spatial requirements can involve some methods. The research project of the German Ministry for Education and Research which is entitled "Effects and Functions of Non-Fragmented Spaces with Minimal Disturbances for Vertebrata and Populations with Large Spatial Requirements” and led by the Country Office for Environment and Nature of Mecklenburg-Vorpommern main...

  1. A method for clustering of miRNA sequences using fragmented programming

    Science.gov (United States)

    Ivashchenko, Anatoly; Pyrkova, Anna; Niyazova, Raigul

    2016-01-01

    Clustering of miRNA sequences is an important problem in molecular genetics associated cellular biology. Thousands of such sequences are known today through advancement in sophisticated molecular tools, sequencing techniques, computational resources and rule based mathematical models. Analysis of such large-scale miRNA sequences for inferring patterns towards deducing cellular function is a great challenge in modern molecular biology. Therefore, it is of interest to develop mathematical models specific for miRNA sequences. The process is to group (cluster) such miRNA sequences using well-defined known features. We describe a method for clustering of miRNA sequences using fragmented programming. Subsequently, we illustrated the utility of the model using a dendrogram (a tree diagram) for publically known A.thaliana miRNA nucleotide sequences towards the inference of observed conserved patterns PMID:27212839

  2. Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.

    Science.gov (United States)

    Steinmann, Casper; Fedorov, Dmitri G; Jensen, Jan H

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.

  3. An Alternative to Conventional Rock Fragmentation Methods Using SCDA: A Review

    Directory of Open Access Journals (Sweden)

    Radhika Vidanage De Silva

    2016-11-01

    Full Text Available Global energy and material consumption are expected to rise in exponential proportions during the next few decades, generating huge demands for deep earth energy (oil/gas recovery and mineral processing. Under such circumstances, the continuation of existing methods in rock fragmentation in such applications is questionable due to the proven adverse environmental impacts associated with them. In this regard; the possibility of using more environmentally friendly options as Soundless Chemical Demolition Agents (SCDAs play a vital role in replacing harmful conventional rock fragmentation techniques for gas; oil and mineral recovery. This study reviews up to date research on soundless cracking demolition agent (SCDA application on rock fracturing including its limitations and strengths, possible applications in the petroleum industry and the possibility of using existing rock fragmentation models for SCDA-based rock fragmentation; also known as fracking. Though the expansive properties of SCDAs are currently used in some demolition works, the poor usage guidelines available reflect the insufficient research carried out on its material’s behavior. SCDA is a cementitious powdery substance with quicklime (CaO as its primary ingredient that expands upon contact with water; which results in a huge expansive pressure if this CaO hydration reaction occurs in a confined condition. So, the mechanism can be used for rock fragmentation by injecting the SCDA into boreholes of a rock mass; where the resulting expansive pressure is sufficient to create an effective fracture network in the confined rock mass around the borehole. This expansive pressure development, however, dependent on many factors, where formation water content creates a negative influence on this due to required greater degree of hydration under greater water contents and temperature creates a positive influence by accelerating the reaction. Having a precise understanding of the fracture

  4. Two-Dimensional Change Detection Methods Remote Sensing Applications

    CERN Document Server

    Ilsever, Murat

    2012-01-01

    Change detection using remotely sensed images has many applications, such as urban monitoring, land-cover change analysis, and disaster management. This work investigates two-dimensional change detection methods. The existing methods in the literature are grouped into four categories: pixel-based, transformation-based, texture analysis-based, and structure-based. In addition to testing existing methods, four new change detection methods are introduced: fuzzy logic-based, shadow detection-based, local feature-based, and bipartite graph matching-based. The latter two methods form the basis for a

  5. Multi-dimensional blind separation method for STBC systems

    Institute of Scientific and Technical Information of China (English)

    Minggang Luo; Liping Li; Guobing Qian; Huaguo Zhang

    2013-01-01

    Intercepted signal blind separation is a research topic with high importance for both military and civilian communication systems. A blind separation method for space-time block code (STBC) systems is proposed by using the ordinary independent component analysis (ICA). This method cannot work when spe-cific complex modulations are employed since the assumption of mutual independence cannot be satisfied. The analysis shows that source signals, which are group-wise independent and use multi-dimensional ICA (MICA) instead of ordinary ICA, can be applied in this case. Utilizing the block-diagonal structure of the cumulant matrices, the JADE algorithm is generalized to the multi-dimensional case to separate the received data into mutual y in-dependent groups. Compared with ordinary ICA algorithms, the proposed method does not introduce additional ambiguities. Sim-ulations show that the proposed method overcomes the drawback and achieves a better performance without utilizing coding infor-mation than channel estimation based algorithms.

  6. Extension of modified power method to two-dimensional problems

    Science.gov (United States)

    Zhang, Peng; Lee, Hyunsuk; Lee, Deokjung

    2016-09-01

    In this study, the generalized modified power method was extended to two-dimensional problems. A direct application of the method to two-dimensional problems was shown to be unstable when the number of requested eigenmodes is larger than a certain problem dependent number. The root cause of this instability has been identified as the degeneracy of the transfer matrix. In order to resolve this instability, the number of sub-regions for the transfer matrix was increased to be larger than the number of requested eigenmodes; and a new transfer matrix was introduced accordingly which can be calculated by the least square method. The stability of the new method has been successfully demonstrated with a neutron diffusion eigenvalue problem and the 2D C5G7 benchmark problem.

  7. Lyapunov Computational Method for Two-Dimensional Boussinesq Equation

    CERN Document Server

    Mabrouk, Anouar Ben

    2010-01-01

    A numerical method is developed leading to Lyapunov operators to approximate the solution of two-dimensional Boussinesq equation. It consists of an order reduction method and a finite difference discretization. It is proved to be uniquely solvable and analyzed for local truncation error for consistency. The stability is checked by using Lyapunov criterion and the convergence is studied. Some numerical implementations are provided at the end of the paper to validate the theoretical results.

  8. Direct detection of red blood cell fragments: a new flow cytometric method to evaluate hemolysis in blood pumps.

    Science.gov (United States)

    Linneweber, J; Chow, T W; Takano, T; Maeda, T; Nonaka, K; Schulte-Eistrup, S; Kawahito, S; Elert, O; Moake, J L; Nosé, Y

    2001-01-01

    Pump induced hemolysis is presently evaluated by measuring plasma free hemoglobin (fHb). However, this method has disadvantages because quantification of fHb depends on hematocrit (HCT) and hemoglobin (Hb) levels. The aim of this work was to devise a hemoglobin independent method, capable of quantifying cell trauma directly by measuring the number of red blood cell (RBC) fragments. Whole blood flow cytometry was used to quantify circulating RBC fragments derived from a roller pump (Sarns, Inc. Model 2 M 6,002) and a centrifugal pump (Gyro C1E3, Kyocera Corp.). The pumps were tested in a mock circuit for 2 hr (5 L/min flow against 100 mm Hg pressure head). Red blood cell fragments were quantified by a phycoerythrin (PE) labeled glycophorin A antibody specific for erythrocytes. Red blood cell fragments were smaller than the intact RBC population and overlapped in size with the platelet population (based on forward- and side-light scattering measurements). For the roller pump, the values for RBC fragments increased from 1,090 +/- 260/microl at 0 min to 14,880 +/- 5,900/microl after 120 min. In contrast, using the centrifugal pump, there was little increase in RBC fragments (from 730 +/- 270/microl at 0 min to 1,400 +/- 840/microl after 120 min). Flow cytometry can be used for the rapid, sensitive, hemoglobin independent evaluation of pump induced RBC trauma.

  9. Two Dimensional Lattice Boltzmann Method for Cavity Flow Simulation

    Directory of Open Access Journals (Sweden)

    Panjit MUSIK

    2004-01-01

    Full Text Available This paper presents a simulation of incompressible viscous flow within a two-dimensional square cavity. The objective is to develop a method originated from Lattice Gas (cellular Automata (LGA, which utilises discrete lattice as well as discrete time and can be parallelised easily. Lattice Boltzmann Method (LBM, known as discrete Lattice kinetics which provide an alternative for solving the Navier–Stokes equations and are generally used for fluid simulation, is chosen for the study. A specific two-dimensional nine-velocity square Lattice model (D2Q9 Model is used in the simulation with the velocity at the top of the cavity kept fixed. LBM is an efficient method for reproducing the dynamics of cavity flow and the results which are comparable to those of previous work.

  10. A Liquid Chromatography/Mass Spectrometry Method for Screening Disulfide Tethering Fragments.

    Science.gov (United States)

    Hallenbeck, Kenneth K; Davies, Julia L; Merron, Connie; Ogden, Pierce; Sijbesma, Eline; Ottmann, Christian; Renslo, Adam R; Wilson, Christopher; Arkin, Michelle R

    2017-09-01

    We report the refinement of a high-throughput, liquid chromatography/mass spectrometry (LC/MS)-based screening method for the identification of covalent small-molecule binders to proteins. Using a custom library of 1600 disulfide-capped fragments targeting surface cysteine residues, we optimize sample preparation, chromatography, and ionization conditions to maximize the reliability and flexibility of the approach. Data collection at a rate of 84 s per sample balances speed with reliability for sustained screening over multiple, diverse projects run over a 24-month period. The method is applicable to protein targets of various classes and a range of molecular masses. Data are processed in a custom pipeline that calculates a percent bound value for each compound and identifies false positives by calculating significance of detected masses (signal significance). An example pipeline is available through Biovia's ScienceCloud Protocol Exchange. Data collection and analysis methods for the screening of covalent adducts of intact proteins are now fast enough to screen the largest covalent compound libraries in 1 to 2 days.

  11. The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water with the Fragment Molecular Orbital Method

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Spencer R.; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham D.; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, M

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.

  12. Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.

    Science.gov (United States)

    Yang, Jiaoyun; Wang, Haipeng; Ding, Huitong; An, Ning; Alterovitz, Gil

    2017-01-19

    Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately labeled data, etc. As crowdsourcing-based synthetic biology databases face similar data quality issues, we propose to visualize biobricks to tackle them. However, existing dimensionality reduction methods could not be directly applied on biobricks datasets. Hereby, we use normalized edit distance to enhance dimensionality reduction methods, including Isomap and Laplacian Eigenmaps. By extracting biobricks from synthetic biology database Registry of Standard Biological Parts, six combinations of various types of biobricks are tested. The visualization graphs illustrate discriminated biobricks and inappropriately labeled biobricks. Clustering algorithm K-means is adopted to quantify the reduction results. The average clustering accuracy for Isomap and Laplacian Eigenmaps are 0.857 and 0.844, respectively. Besides, Laplacian Eigenmaps is 5 times faster than Isomap, and its visualization graph is more concentrated to discriminate biobricks. By combining normalized edit distance with Isomap and Laplacian Eigenmaps, synthetic biology biobircks are successfully visualized in two dimensional space. Various types of biobricks could be discriminated and inappropriately labeled biobricks could be determined, which could help to assess crowdsourcing-based synthetic biology databases' quality, and make biobricks selection.

  13. Three-dimensional analysis of vesicle and crystal fragment textures in pumice using high-resolution X-ray CT: Textural evidence of eruptive processes

    Science.gov (United States)

    Ketcham, R. A.; Gardner, J. E.; Abbott, S.

    2011-12-01

    Three-dimensional analysis of high-resolution X-ray computed tomographic (CT) imagery of pumice from Popocatépetl Volcano in central Mexico yields fresh insights into processes of vesicle formation and coalescence and crystal fragmentation that occur during explosive volcanism. Six ~2 cm pumice fragments of varying bulk vesicularity were imaged at ~20 μm resolution. Three-dimensional blob and fabric analysis quantitatively document textural features, and visualization facilitated contextualization of measurements and overall interpretation. Vesicles range in size from mm-scale to below the resolution of the scan data. By comparing the whole-sample 3D vesicle size distributions derived from CT with more detailed distributions from sub-volumes obtained by standard petrographic analysis, we can discern two distinct, roughly log-normal populations in each sample. Vesicles in all samples have preferred orientations, and fabric analysis based on the star volume distribution and displayed as 3D rose diagrams documents a range of preferred shapes from elongate to flattened. Aspect ratios range from 1 to 6, and converge to values of ~2-3 with increasing size. Surface to volume ratios show increasing departure from sphericity with increasing size, which is probably attributable in large part to irregular shapes caused by coalescence. The vesicle fabric was strongest in the highest-vesicularity sample. Some pumices showed evidence of welding or poor mixing between two or more differently devolatilized portions of melt. Interfaces are in some cases apparently welded, with low-vesicularity glass contact zones, and in others are simply sub-planar intersections between distinct glasses. In one instance of the latter, correlated vesicle and phenocryst orientations across both melt portions and not parallel to their interface suggests that their juxtaposition took place before final eruption, while there was still time for fabric development. The pumices show abundant evidence of

  14. Addition to the method of dimensional analysis in hydraulic problems

    Directory of Open Access Journals (Sweden)

    A.M. Kalyakin

    2013-03-01

    Full Text Available The modern engineering design, structures, and especially machines running of new technologies set to engineers the problems that require immediate solution. Therefore, the importance of the method of dimensional analysis as a tool for ordinary engineer is increasing, allows developers to get quick and quite simple solution of even very complex tasks.The method of dimensional analysis is being applied to almost any field of physics and engineering, but it is especially effective at solving problems of mechanics and applied mechanics – hydraulics, fluid mechanics, structural mechanics, etc.Until now the main obstacle to the application of the method of dimensional analysis in its classic form was a multifactorial problem (with many arguments, the solution of which was rather difficult and sometimes impossible. In order to overcome these difficulties, the authors of this study proposed a simple method – application of the combined option avoiding these difficulties.The main result of the study is a simple algorithm which application will make it possible to solve a large class of previously unsolvable problems.

  15. A potential implicit particle method for high-dimensional systems

    Science.gov (United States)

    Weir, B.; Miller, R. N.; Spitz, Y. H.

    2013-11-01

    This paper presents a particle method designed for high-dimensional state estimation. Instead of weighing random forecasts by their distance to given observations, the method samples an ensemble of particles around an optimal solution based on the observations (i.e., it is implicit). It differs from other implicit methods because it includes the state at the previous assimilation time as part of the optimal solution (i.e., it is a lag-1 smoother). This is accomplished through the use of a mixture model for the background distribution of the previous state. In a high-dimensional, linear, Gaussian example, the mixture-based implicit particle smoother does not collapse. Furthermore, using only a small number of particles, the implicit approach is able to detect transitions in two nonlinear, multi-dimensional generalizations of a double-well. Adding a step that trains the sampled distribution to the target distribution prevents collapse during the transitions, which are strongly nonlinear events. To produce similar estimates, other approaches require many more particles.

  16. [ERIAD mass spectrometry (electrospray with controlled fragmentation) is the common method for metallomics and biochemistry of elementoorganic molecules].

    Science.gov (United States)

    Gall', N R; Fomina, N S; Bazhenov, A N; Masiukevich, S V; Kretinina, A V; Gall', L N

    2011-01-01

    The physical aspects of the ERIAD method (electrospray with controlled fragmentation) in terms of the problems of metallomics and biochemistry of elementoorganic compounds have been considered. It was shown that the method is well suited to study the objects of this class since it enables one to change from the molecular to the elemental analysis merely by changing the voltage between the nozzle and the skimmer. In the regime of molecular analysis, it is possible to determine the mass of the molecule as a whole and decipher its structure by controlled fragmentation, and in the regime of elemental analysis the number of atoms of heteroelements incorporated in the molecule can be quantified.

  17. Synthesis of the proteinase inhibitor LEKTI domain 6 by the fragment condensation method and regioselective disulfide bond formation.

    Science.gov (United States)

    Vasileiou, Zoe; Barlos, Kostas K; Gatos, Dimitrios; Adermann, Knut; Deraison, Celine; Barlos, Kleomenis

    2010-01-01

    Proteinase inhibitors are of high pharmaceutical interest and are drug candidates for a variety of indications. Specific kallikrein inhibitors are important for their antitumor activity and their potential application to the treatment of skin diseases. In this study we describe the synthesis of domain 6 of the kallikrein inhibitor Lympho-Epithilial Kazal-Type Inhibitor (LEKTI) by the fragment condensation method and site-directed cystine bridge formation. To obtain the linear LEKTI precursor, the condensation was best performed in solution, coupling the protected fragment 1-22 to 23-68. This method yielded LEKTI domain 6 of high purity and equipotent to the recombinantly produced peptide.

  18. Three-dimensional protein structure prediction: Methods and computational strategies.

    Science.gov (United States)

    Dorn, Márcio; E Silva, Mariel Barbachan; Buriol, Luciana S; Lamb, Luis C

    2014-10-12

    A long standing problem in structural bioinformatics is to determine the three-dimensional (3-D) structure of a protein when only a sequence of amino acid residues is given. Many computational methodologies and algorithms have been proposed as a solution to the 3-D Protein Structure Prediction (3-D-PSP) problem. These methods can be divided in four main classes: (a) first principle methods without database information; (b) first principle methods with database information; (c) fold recognition and threading methods; and (d) comparative modeling methods and sequence alignment strategies. Deterministic computational techniques, optimization techniques, data mining and machine learning approaches are typically used in the construction of computational solutions for the PSP problem. Our main goal with this work is to review the methods and computational strategies that are currently used in 3-D protein prediction.

  19. Developing an Experimental Simulation Method for Rock Avalanches: Fragmentation Behavior of Brittle Analogue Material

    Science.gov (United States)

    Thordén Haug, Øystein; Rosenau, Matthias; Leever, Karen; Oncken, Onno

    2013-04-01

    Gravitational mass movement on earth and other planets show a scale dependent behavior, of which the physics is not fully understood. In particular, the runout distance for small to medium sized landslides (volume granular material down a chute. Though such granular avalanche models provide important insights into avalanche dynamics, they imply that the material fully disintegrate instantaneously. Observations from nature, however, suggests that a transition from solid to "liquid" occurs over some finite distance downhill, critically controlling the mobility and energy budget of the avalanche. Few experimental studies simulated more realistically the material failing during sliding and those were realized in a labscale centrifuge, where the range of volumes/scales is limited. To develop a new modeling technique to study the scale dependent runout behavior of rock avalanches, we designed, tested and verified several brittle materials allowing fragmentation to occur under normal gravity conditions. According to the model similarity theory, the analogue material must behave dynamically similar to the rocks in natural rock avalanches. Ideally, the material should therefore deform in a brittle manner with limited elastic and ductile strains up to a certain critical stress, beyond which the material breaks and deforms irreversibly. According to scaling relations derived from dimensional analysis and for a model-to-prototype length ratio of 1/1000, the appropriate yield strength for an analogue material is in the order of 10 kPa, friction coefficient around 0.8 and stiffness in the order of MPa. We used different sand (garnet, quartz) in combination with different matrix materials (sugar, salt, starch, plaster) to cement it. The deformation behavior and strength of the samples was tested using triaxial compression tests at atmospheric confining pressures. Proper material properties were obtained using well-sorted, well-rounded, medium grained quartz sand with gypsum

  20. Two-Dimensional Impact Reconstruction Method for Rail Defect Inspection

    Directory of Open Access Journals (Sweden)

    Jie Zhao

    2014-01-01

    Full Text Available The safety of train operating is seriously menaced by the rail defects, so it is of great significance to inspect rail defects dynamically while the train is operating. This paper presents a two-dimensional impact reconstruction method to realize the on-line inspection of rail defects. The proposed method utilizes preprocessing technology to convert time domain vertical vibration signals acquired by wireless sensor network to space signals. The modern time-frequency analysis method is improved to reconstruct the obtained multisensor information. Then, the image fusion processing technology based on spectrum threshold processing and node color labeling is proposed to reduce the noise, and blank the periodic impact signal caused by rail joints and locomotive running gear. This method can convert the aperiodic impact signals caused by rail defects to partial periodic impact signals, and locate the rail defects. An application indicates that the two-dimensional impact reconstruction method could display the impact caused by rail defects obviously, and is an effective on-line rail defects inspection method.

  1. ALIS-FLP: Amplified ligation selected fragment-length polymorphism method for microbial genotyping

    DEFF Research Database (Denmark)

    Brillowska-Dabrowska, A.; Wianecka, M.; Dabrowski, Slawomir

    2008-01-01

    in that only one specific restriction enzyme (TspRI) is used. The cohesive ends of the DNA fragments are ligated with two types of oligonucleotide. A long oligonucleotide containing the primer site and the specific 9 nt 3 prime end, which is complementary to specific 9 nt, cohesive 3 prime end of the Tsp......RI genomic DNA fragment, and a short, degenerated, oligonucleotide covering the remaining TspRI cohesive ends. Other cohesive ends are covered by a short degenerated oligonucleotide lacking the primer site. The ligation mixture is used as a template for amplification using a single primer corresponding...... to the 5 prime end of the long, specific oligonucleotide. The selection of TspRI digested genomic DNA fragments for amplification is achieved by sequence selective ligation of the specific long oligonucleotide carrying the primer site to both ends of the specific target fragment. This technique allows...

  2. Benzene-pyridine interactions predicted by the effective fragment potential method.

    Science.gov (United States)

    Smith, Quentin A; Gordon, Mark S; Slipchenko, Lyudmila V

    2011-05-12

    The accurate representation of nitrogen-containing heterocycles is essential for modeling biological systems. In this study, the general effective fragment potential (EFP2) method is used to model dimers of benzene and pyridine, complexes for which high-level theoretical data -including large basis spin-component-scaled second-order perturbation theory (SCS-MP2), symmetry-adapted perturbation theory (SAPT), and coupled cluster with singles, doubles, and perturbative triples (CCSD(T))-are available. An extensive comparison of potential energy curves and components of the interaction energy is presented for sandwich, T-shaped, parallel displaced, and hydrogen-bonded structures of these dimers. EFP2 and CCSD(T) potential energy curves for the sandwich, T-shaped, and hydrogen-bonded dimers have an average root-mean-square deviation (RMSD) of 0.49 kcal/mol; EFP2 and SCS-MP2 curves for the parallel displaced dimers have an average RMSD of 0.52 kcal/mol. Additionally, results are presented from an EFP2 Monte Carlo/simulated annealing (MC/SA) computation to sample the potential energy surface of the benzene-pyridine and pyridine dimers.

  3. ABACUS, a direct method for protein NMR structure computation via assembly of fragments.

    Science.gov (United States)

    Grishaev, A; Steren, C A; Wu, B; Pineda-Lucena, A; Arrowsmith, C; Llinás, M

    2005-10-01

    The ABACUS algorithm obtains the protein NMR structure from unassigned NOESY distance restraints. ABACUS works as an integrated approach that uses the complete set of available NMR experimental information in parallel and yields spin system typing, NOE spin pair identities, sequence specific resonance assignments, and protein structure, all at once. The protocol starts from unassigned molecular fragments (including single amino acid spin systems) derived from triple-resonance (1)H/(13)C/(15)N NMR experiments. Identifications of connected spin systems and NOEs precede the full sequence specific resonance assignments. The latter are obtained iteratively via Monte Carlo-Metropolis and/or probabilistic sequence selections, molecular dynamics structure computation and BACUS filtering (A. Grishaev and M. Llinás, J Biomol NMR 2004;28:1-10). ABACUS starts from scratch, without the requirement of an initial approximate structure, and improves iteratively the NOE identities in a self-consistent fashion. The procedure was run as a blind test on data recorded on mth1743, a 70-amino acid genomic protein from M. thermoautotrophicum. It converges to a structure in ca. 15 cycles of computation on a 3-GHz processor PC. The calculated structures are very similar to the ones obtained via conventional methods (1.22 A backbone RMSD). The success of ABACUS on mth1743 further validates BACUS as a NOESY identification protocol.

  4. A Simple yet Accurate Method for Students to Determine Asteroid Rotation Periods from Fragmented Light Curve Data

    Science.gov (United States)

    Beare, R. A.

    2008-01-01

    Professional astronomers use specialized software not normally available to students to determine the rotation periods of asteroids from fragmented light curve data. This paper describes a simple yet accurate method based on Microsoft Excel[R] that enables students to find periods in asteroid light curve and other discontinuous time series data of…

  5. A Simple yet Accurate Method for Students to Determine Asteroid Rotation Periods from Fragmented Light Curve Data

    Science.gov (United States)

    Beare, R. A.

    2008-01-01

    Professional astronomers use specialized software not normally available to students to determine the rotation periods of asteroids from fragmented light curve data. This paper describes a simple yet accurate method based on Microsoft Excel[R] that enables students to find periods in asteroid light curve and other discontinuous time series data of…

  6. Quantifying habitat requirements of tree-living species in fragmented boreal forests with Bayesian methods.

    Science.gov (United States)

    Berglund, Håkan; O'Hara, Robert B; Jonsson, Bengt Gunnar

    2009-10-01

    Quantitative conservation objectives require detailed consideration of the habitat requirements of target species. Tree-living bryophytes, lichens, and fungi are a critical and declining biodiversity component of boreal forests. To understand their requirements, Bayesian methods were used to analyze the relationships between the occurrence of individual species and habitat factors at the tree and the stand scale in a naturally fragmented boreal forest landscape. The importance of unexplained between-stand variation in occurrence of species was estimated, and the ability of derived models to predict species' occurrence was tested. The occurrence of species was affected by quality of individual trees. Furthermore, the relationships between occurrence of species at the tree level and size and shape of stands indicated edge effects, implying that some species were restricted to interior habitats of large, regular stands. Yet for the habitat factors studied, requirements of many species appeared similar. Species occurrence also varied between stands; most of the seemingly suitable trees in some stands were unoccupied. The models captured most variation in species occurrence at tree level. They also successfully accounted for between-stand variation in species occurrence, thus providing realistic simulations of stand-level occupancy of species. Important unexplained between-stand variation in species occurrence warns against a simplified view that only local habitat factors influence species' occurrence. Apparently, similar stands will host populations of different sizes due to historical, spatial, and stochastic factors. Thus, habitat suitability cannot be assessed simply by population sizes, and stands lacking a species may still provide suitable habitat and merit protection.

  7. A novel human scFv fragment against TNF-alpha from de novo design method.

    Science.gov (United States)

    Chang, Hong; Qin, Weisong; Li, Yan; Zhang, Jiyan; Lin, Zhou; Lv, Ming; Sun, Yingxun; Feng, Jiannan; Shen, Beifen

    2007-07-01

    Anti-TNF antibody has been an effective therapeutic strategy for the diseases related to aberrant production of TNF-alpha, such as rheumatoid arthritis (RA) and Crohn's disease. The limitations of large molecule inhibitors in the therapy of these diseases prompted the search for other potent novel TNF-alpha antagonists. Antagonistic peptides, derived directly or designed rationally from complementarity-determining regions (CDRs) of neutralizing antibodies against TNF-alpha, have been demonstrated for their ability of inhibiting TNF-alpha. However, their activity is very low. In this study, to increase the affinity and bioactivity, human antibody variable region was used as scaffold to display antagonistic peptides, which were designed on the interaction between TNF-alpha and its neutralizing monoclonal antibody (mAb Z12). Based on the previously designed domain antibody (framework V(H)5), framework V(kappa)1 was used as light chain scaffold. On the basis of computer-guided molecular design method, a novel human scFv fragment (named as TSA1) was designed. Theoretical analysis showed that TSA1 could bind to TNF-alpha with more hydrogen bonds and lower binding free energy than the designed domain antibody. The biological experiments demonstrated that TSA1 could directly bind with TNF-alpha, competitively inhibit the binding of mAb Z12 to TNF-alpha and block the binding of TNF-alpha to TNFR I and TNFR II. TSA1 could also inhibit TNF-induced cytotoxicity on L929 cells and TNF-mediated NF-kappaB activation on HEK-293T cells. The bioactivity of TSA1 was significantly increased over the domain antibody. This study indicated that the framework of antibody variable region could serve as an ideal scaffold for displaying the peptides and provides a novel strategy to design TNF-alpha inhibitors with the ability to block the deleterious biological effects of TNF-alpha.

  8. Standard Test Method for Dimensional Stability of Sandwich Core Materials

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2002-01-01

    1.1 This test method covers the determination of the sandwich core dimensional stability in the two plan dimensions. 1.2 The values stated in SI units are to be regarded as the standard. The inch-pound units given may be approximate. This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

  9. Smoothed Particle Hydrodynamics Method for Two-dimensional Stefan Problem

    CERN Document Server

    Tarwidi, Dede

    2016-01-01

    Smoothed particle hydrodynamics (SPH) is developed for modelling of melting and solidification. Enthalpy method is used to solve heat conduction equations which involved moving interface between phases. At first, we study the melting of floating ice in the water for two-dimensional system. The ice objects are assumed as solid particles floating in fluid particles. The fluid and solid motion are governed by Navier-Stokes equation and basic rigid dynamics equation, respectively. We also propose a strategy to separate solid particles due to melting and solidification. Numerical results are obtained and plotted for several initial conditions.

  10. Numerical method of characteristics for one-dimensional blood flow

    CERN Document Server

    Acosta, Sebastian; Riviere, Beatrice; Penny, Daniel J; Rusin, Craig G

    2014-01-01

    Mathematical modeling at the level of the full cardiovascular system requires the numerical approximation of solutions to a one-dimensional nonlinear hyperbolic system describing flow in a single vessel. This model is often simulated by computationally intensive methods like finite elements and discontinuous Galerkin, while some recent applications require more efficient approaches (e.g. for real-time clinical decision support, phenomena occurring over multiple cardiac cycles, iterative solutions to optimization/inverse problems, and uncertainty quantification). Further, the high speed of pressure waves in blood vessels greatly restricts the time-step needed for stability in explicit schemes. We address both cost and stability by presenting an efficient and unconditionally stable method for approximating solutions to diagonal nonlinear hyperbolic systems. Theoretical analysis of the algorithm is given along with a comparison of our method to a discontinuous Galerkin implementation. Lastly, we demonstrate the ...

  11. Three-dimensional inverse method for turbomachine blades by the circulation method: The thickness problem

    Science.gov (United States)

    Jiang, Jun

    This dissertation summarizes a procedure to design blades with finite thickness in three dimensions. In this inverse method, the prescribed quantities are the blade pressure loading shape, the inlet and outlet spanwise distributions of swirl, and the blade thickness distributions, and the primary calculated quantity is the blade geometry. The method is formulated in the fully inverse mode for design of three-dimensional blades in rotational and compressible flows whereby the blade shape is determined iteratively using the flow tangency condition along the blade surfaces. This technique is demonstrated here in the first instance for the design of two-dimensional cascaded and three-dimensional blades with finite thickness in inviscid and incompressible flows. In addition, the incoming flow is assumed irrotational so that the only vorticity present in the flowfield is the blade bound and shed vorticities. Design calculations presented for two-dimensional cascaded blades include an inlet guide vane, an impulse turbine blade, and a compressor blade. Consistency check is carried out for these cascaded blade design calculations using a panel analysis method and the analytical solution for the Gostelow profile. Free-vortex design results are also shown for fully three-dimensional blades with finite thickness such as an inlet guide vane, a rotor of axial-flow pumps, and a high-flow-coefficient pump inducer with design parameters typically found in industrial applications. These three-dimensional inverse design results are verified using Adamczyk's inviscid code.

  12. New method of 2-dimensional metrology using mask contouring

    Science.gov (United States)

    Matsuoka, Ryoichi; Yamagata, Yoshikazu; Sugiyama, Akiyuki; Toyoda, Yasutaka

    2008-10-01

    We have developed a new method of accurately profiling and measuring of a mask shape by utilizing a Mask CD-SEM. The method is intended to realize high accuracy, stability and reproducibility of the Mask CD-SEM adopting an edge detection algorithm as the key technology used in CD-SEM for high accuracy CD measurement. In comparison with a conventional image processing method for contour profiling, this edge detection method is possible to create the profiles with much higher accuracy which is comparable with CD-SEM for semiconductor device CD measurement. This method realizes two-dimensional metrology for refined pattern that had been difficult to measure conventionally by utilizing high precision contour profile. In this report, we will introduce the algorithm in general, the experimental results and the application in practice. As shrinkage of design rule for semiconductor device has further advanced, an aggressive OPC (Optical Proximity Correction) is indispensable in RET (Resolution Enhancement Technology). From the view point of DFM (Design for Manufacturability), a dramatic increase of data processing cost for advanced MDP (Mask Data Preparation) for instance and surge of mask making cost have become a big concern to the device manufacturers. This is to say, demands for quality is becoming strenuous because of enormous quantity of data growth with increasing of refined pattern on photo mask manufacture. In the result, massive amount of simulated error occurs on mask inspection that causes lengthening of mask production and inspection period, cost increasing, and long delivery time. In a sense, it is a trade-off between the high accuracy RET and the mask production cost, while it gives a significant impact on the semiconductor market centered around the mask business. To cope with the problem, we propose the best method of a DFM solution using two-dimensional metrology for refined pattern.

  13. An explicit four-dimensional variational data assimilation method

    Institute of Scientific and Technical Information of China (English)

    QIU ChongJian; ZHANG Lei; SHAO AiMei

    2007-01-01

    A new data assimilation method called the explicit four-dimensional variational (4DVAR) method is proposed. In this method, the singular value decomposition (SVD) is used to construct the orthogonal basis vectors from a forecast ensemble in a 4D space. The basis vectors represent not only the spatial structure of the analysis variables but also the temporal evolution. After the analysis variables are expressed by a truncated expansion of the basis vectors in the 4D space, the control variables in the cost function appear explicitly, so that the adjoint model, which is used to derive the gradient of cost function with respect to the control variables, is no longer needed. The new technique significantly simplifies the data assimilation process. The advantage of the proposed method is demonstrated by several experiments using a shallow water numerical model and the results are compared with those of the conventional 4DVAR. It is shown that when the observation points are very dense, the conventional 4DVAR is better than the proposed method. However, when the observation points are sparse, the proposed method performs better. The sensitivity of the proposed method with respect to errors in the observations and the numerical model is lower than that of the conventional method.

  14. An explicit four-dimensional variational data assimilation method

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A new data assimilation method called the explicit four-dimensional variational (4DVAR) method is proposed. In this method, the singular value decomposition (SVD) is used to construct the orthogonal basis vectors from a forecast ensemble in a 4D space. The basis vectors represent not only the spatial structure of the analysis variables but also the temporal evolution. After the analysis variables are ex-pressed by a truncated expansion of the basis vectors in the 4D space, the control variables in the cost function appear explicitly, so that the adjoint model, which is used to derive the gradient of cost func-tion with respect to the control variables, is no longer needed. The new technique significantly simpli-fies the data assimilation process. The advantage of the proposed method is demonstrated by several experiments using a shallow water numerical model and the results are compared with those of the conventional 4DVAR. It is shown that when the observation points are very dense, the conventional 4DVAR is better than the proposed method. However, when the observation points are sparse, the proposed method performs better. The sensitivity of the proposed method with respect to errors in the observations and the numerical model is lower than that of the conventional method.

  15. Numerical Improvement of The Three-dimensional Boundary Element Method

    Science.gov (United States)

    Ortiz-Aleman, C.; Gil-Zepeda, A.; Sánchez-Sesma, F. J.; Luzon-Martinez, F.

    2001-12-01

    Boundary element methods have been applied to calculate the seismic response of various types of geological structures. Dimensionality reduction and a relatively easy fulfillment of radiation conditions at infinity are recognized advantages over domain approaches. Indirect Boundary Element Method (IBEM) formulations give rise to large systems of equations, and the considerable amount of operations required for solving them suggest the possibility of getting some benefit from exploitation of sparsity patterns. In this article, a brief study on the structure of the linear systems derived from the IBEM method is carried out. Applicability of a matrix static condensation algorithm to the inversion of the IBEM coefficient matrix is explored, in order to optimize the numerical burden of such method. Seismic response of a 3-D alluvial valley of irregular shape, as originally proposed by Sánchez-Sesma and Luzon (1995), was computed and comparisons on time consumption and memory allocation are established. An alternative way to deal with those linear systems is the use of threshold criteria for the truncation of the coefficient matrix, which implies the solution of sparse approximations instead of the original full IBEM systems (Ortiz-Aleman et al., 1998). Performance of this optimized approach is evaluated on its application to the case of a three-dimensional alluvial basin with irregular shape. Transfer functions were calculated for the frequency range from 0 to 1.25 Hz. Inversion of linear systems by using this algorithm lead to significant saving on computer time and memory allocation relative to the original IBEM formulation. Results represent an extension in the range of application of the IBEM method.

  16. The power to detect recent fragmentation events using genetic differentiation methods.

    Directory of Open Access Journals (Sweden)

    Michael W Lloyd

    Full Text Available Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright's F st, Hedrick' G'st , Sherwin's MI, and Jost's D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G'st , MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst , G'st , MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst , G'st , MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G'st , MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.

  17. Three-dimensional beam propagation method based on the variable transformed Galerkin's method

    Institute of Scientific and Technical Information of China (English)

    XIAO Jinbiao; SUN Xiaohan; ZHANG Mingde

    2004-01-01

    A novel three-dimensional beam propagation method (BPM) based on the variable transformed Galerkin's method is introduced for simulating optical field propagation in three-dimensional dielectric structures. The infinite Cartesian x-y plane is mapped into a unit square by a tangent-type function transformation. Consequently, the infinite region problem is converted into the finite region problem. Thus, the boundary truncation is eliminated and the calculation accuracy is promoted. The three-dimensional BPM basic equation is reduced to a set of first-order ordinary differential equations through sinusoidal basis function, which fits arbitrary cladding optical waveguide, then direct solution of the resulting equations by means of the Runge-Kutta method. In addition,the calculation is efficient due to the small matrix derived from the present technique.Both z-invariant and z-variant examples are considered to test both the accuracy and utility of this approach.

  18. Computational Methods for Multi-dimensional Neutron Diffusion Problems

    Energy Technology Data Exchange (ETDEWEB)

    Song Han

    2009-10-15

    Lead-cooled fast reactor (LFR) has potential for becoming one of the advanced reactor types in the future. Innovative computational tools for system design and safety analysis on such NPP systems are needed. One of the most popular trends is coupling multi-dimensional neutron kinetics (NK) with thermal-hydraulic (T-H) to enhance the capability of simulation of the NPP systems under abnormal conditions or during rare severe accidents. Therefore, various numerical methods applied in the NK module should be reevaluated to adapt the scheme of coupled code system. In the author's present work a neutronic module for the solution of two dimensional steady-state multigroup diffusion problems in nuclear reactor cores is developed. The module can produce both direct fluxes as well as adjoints, i.e. neutron importances. Different numerical schemes are employed. A standard finite-difference (FD) approach is firstly implemented, mainly to serve as a reference for less computationally challenging schemes, such as transverse-integrated nodal methods (TINM) and boundary element methods (BEM), which are considered in the second part of the work. The validation of the methods proposed is carried out by comparisons of the results for some reference structures. In particular a critical problem for a homogeneous reactor for which an analytical solution exists is considered as a benchmark. The computational module is then applied to a fast spectrum system, having physical characteristics similar to the proposed European Lead-cooled System (ELSY) project. The results show the effectiveness of the numerical techniques presented. The flexibility and the possibility to obtain neutron importances allow the use of the module for parametric studies, design assessments and integral parameter evaluations, as well as for future sensitivity and perturbation analyses and as a shape solver for time-dependent procedures

  19. Transplantation of storm-generated coral fragments to enhance Caribbean coral reefs: A successful method but not a solution

    Science.gov (United States)

    Garrison, V.H.; Ward, G.

    2012-01-01

    In response to dramatic losses of reef-building corals and ongoing lack of recovery, a small-scale coral transplant project was initiated in the Caribbean (U.S. Virgin Islands) in 1999 and was followed for 12 years. The primary objectives were to (1) identify a source of coral colonies for transplantation that would not result in damage to reefs, (2) test the feasibility of transplanting storm-generated coral fragments, and (3) develop a simple, inexpensive method for transplanting fragments that could be conducted by the local community. The ultimate goal was to enhance abundance of threatened reef-building species on local reefs. Storm-produced coral fragments of two threatened reef-building species [Acropora palmata and A. cervicornis (Acroporidae)] and another fast-growing species [Porites porites (Poritidae)] were collected from environments hostile to coral fragment survival and transplanted to degraded reefs. Inert nylon cable ties were used to attach transplanted coral fragments to dead coral substrate. Survival of 75 reference colonies and 60 transplants was assessed over 12 years. Only 9% of colonies were alive after 12 years: no A. cervicornis; 3% of A. palmata transplants and 18% of reference colonies; and 13% of P. porites transplants and 7% of reference colonies. Mortality rates for all species were high and were similar for transplant and reference colonies. Physical dislodgement resulted in the loss of 56% of colonies, whereas 35% died in place. Only A. palmata showed a difference between transplant and reference colony survival and that was in the first year only. Location was a factor in survival only for A. palmata reference colonies and after year 10. Even though the tested methods and concepts were proven effective in the field over the 12-year study, they do not present a solution. No coral conservation strategy will be effective until underlying intrinsic and/or extrinsic factors driving high mortality rates are understood and mitigated or

  20. Exact rebinning methods for three-dimensional PET.

    Science.gov (United States)

    Liu, X; Defrise, M; Michel, C; Sibomana, M; Comtat, C; Kinahan, P; Townsend, D

    1999-08-01

    The high computational cost of data processing in volume PET imaging is still hindering the routine application of this successful technique, especially in the case of dynamic studies. This paper describes two new algorithms based on an exact rebinning equation, which can be applied to accelerate the processing of three-dimensional (3-D) PET data. The first algorithm, FOREPROJ, is a fast-forward projection algorithm that allows calculation of the 3-D attenuation correction factors (ACF's) directly from a two-dimensional (2-D) transmission scan, without first reconstructing the attenuation map and then performing a 3-D forward projection. The use of FOREPROJ speeds up the estimation of the 3-D ACF's by more than a factor five. The second algorithm, FOREX, is a rebinning algorithm that is also more than five times faster, compared to the standard reprojection algorithm (3DRP) and does not suffer from the image distortions generated by the even faster approximate Fourier rebinning (FORE) method at large axial apertures. However, FOREX is probably not required by most existing scanners, as the axial apertures are not large enough to show improvements over FORE with clinical data. Both algorithms have been implemented and applied to data simulated for a scanner with a large axial aperture (30 degrees), and also to data acquired with the ECAT HR and the ECAT HR+ scanners. Results demonstrate the excellent accuracy achieved by these algorithms and the important speedup when the sinogram sizes are powers of two.

  1. Laplace method for the evolution of the fragmentation function of Bc mesons

    Science.gov (United States)

    Boroun, G. R.; Zarrin, S.; Dadfar, S.

    2016-09-01

    In high-energy processes, the predominant mechanism for b bar c bound states is the production of a high-energy b bar or c quark, which fragments into the b bar c state. An approximate approach for the evolution of the fragmentation functions for the production of the S-wave states of Bc and Bc* is presented using Laplace transform technique in the leading order (LO) and next-to-leading order (NLO) analyses. The cross sections, as a function of the transverse momentum for the direct hadro-production b bar (c) →Bc and b bar (c) →Bc* based on the nonrelativistic quantum chromodynamics (QCD) factorization, are determined and compared with the Large Hadron Collider (LHC) and Tevatron data at the 1S-wave state.

  2. Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods

    Science.gov (United States)

    DeGraan-Weber, Nick; Zhang, Jun; Reilly, James P.

    2016-12-01

    Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues.

  3. Brownian shape motion: Fission fragment mass distributions

    Directory of Open Access Journals (Sweden)

    Sierk Arnold J.

    2012-02-01

    Full Text Available It was recently shown that remarkably accurate fission-fragment mass distributions can be obtained by treating the nuclear shape evolution as a Brownian walk on previously calculated five-dimensional potential-energy surfaces; the current status of this novel method is described here.

  4. Flow cytometric method for measuring chromatin fragmentation in fixed sperm from yellow perch (Perca flavescens).

    Science.gov (United States)

    Jenkins, J A; Draugelis-Dale, R O; Pinkney, A E; Iwanowicz, L R; Blazer, V S

    2015-03-15

    Declining harvests of yellow perch, Perca flavescens, in urbanized watersheds of Chesapeake Bay have prompted investigations of their reproductive fitness. The purpose of this study was to establish a flow cytometric technique for DNA analysis of fixed samples sent from the field to provide reliable gamete quality measurements. Similar to the sperm chromatin structure assay, measures were made on the susceptibility of nuclear DNA to acid-induced denaturation, but used fixed rather than live or thawed cells. Nuclei were best exposed to the acid treatment for 1 minute at 37 °C followed by the addition of cold (4 °C) propidium iodide staining solution before flow cytometry. The rationale for protocol development is presented graphically through cytograms. Field results collected in 2008 and 2009 revealed DNA fragmentation up to 14.5%. In 2008, DNA fragmentation from the more urbanized watersheds was significantly greater than from reference sites (P = 0.026) and in 2009, higher percentages of haploid testicular cells were noted from the less urbanized watersheds (P = 0.032) indicating better reproductive condition at sites with less urbanization. For both years, total and progressive live sperm motilities by computer-assisted sperm motion analysis ranged from 19.1% to 76.5%, being significantly higher at the less urbanized sites (P fragmented DNA to be denatured under standard conditions, or 1 minute at 37 °C with 10% buffered formalin-fixed cells. The study of fixed sperm makes possible the restrospective investigation of germplasm fragmentation, spermatogenic ploidy patterns, and chromatin compaction levels from samples translocated over distance and time. The protocol provides an approach that can be modified for other species across taxa.

  5. Flow cytometric method for measuring chromatin fragmentation in fixed sperm from yellow perch (Perca flavescens)

    Science.gov (United States)

    Jenkins, Jill A.; Draugelis-Dale, Rassa O.; Pinkney, Alfred E.; Iwanowicz, Luke R.; Blazer, Vicki

    2015-01-01

    Declining harvests of yellow perch, Perca flavescens, in urbanized watersheds of Chesapeake Bay have prompted investigations of their reproductive fitness. The purpose of this study was to establish a flow cytometric technique for DNA analysis of fixed samples sent from the field to provide reliable gamete quality measurements. Similar to the sperm chromatin structure assay, measures were made on the susceptibility of nuclear DNA to acid-induced denaturation, but used fixed rather than live or thawed cells. Nuclei were best exposed to the acid treatment for 1 minute at 37 °C followed by the addition of cold (4 °C) propidium iodide staining solution before flow cytometry. The rationale for protocol development is presented graphically through cytograms. Field results collected in 2008 and 2009 revealed DNA fragmentation up to 14.5%. In 2008, DNA fragmentation from the more urbanized watersheds was significantly greater than from reference sites (P = 0.026) and in 2009, higher percentages of haploid testicular cells were noted from the less urbanized watersheds (P = 0.032) indicating better reproductive condition at sites with less urbanization. For both years, total and progressive live sperm motilities by computer-assisted sperm motion analysis ranged from 19.1% to 76.5%, being significantly higher at the less urbanized sites (P fragmented DNA to be denatured under standard conditions, or 1 minute at 37 °C with 10% buffered formalin–fixed cells. The study of fixed sperm makes possible the restrospective investigation of germplasm fragmentation, spermatogenic ploidy patterns, and chromatin compaction levels from samples translocated over distance and time. The protocol provides an approach that can be modified for other species across taxa.

  6. Fluorescent SSCP of overlapping fragments (FSSCP-OF): a highly sensitive method for the screening of mitochondrial DNA variation

    DEFF Research Database (Denmark)

    Salas, A; Rasmussen, Erik Michael; Lareu, M V

    2001-01-01

    of mtDNA sequencing implies a great lab effort when a high number of samples must be analyzed.The present work introduces a novel and reliable method for the screening of mtDNA variation in the first and second hypervariables (HV1 and HV2) regions which we have denominated fluorescent single strand...... conformation polymorphism (SSCP) of overlapping fragments (FSSCP-OF). FSSCP-OF is based on the basic theory of SSCP analysis and combines two complementary strategies: the use of PCR amplified overlapping fragments and fluorescent detection technology. The overlap region contains a high percentage (50......%) of the d-loop mtDNA variation and for this reason, the probability to detect a polymorphic position by SSCP analysis is clearly increased in comparison to conventional SSCP methods due to the fact that the same polymorphic position is usually placed in a different "relative" position in the two overlapped...

  7. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

    Directory of Open Access Journals (Sweden)

    Wasik Szymon

    2010-05-01

    Full Text Available Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA

  8. Combined effects of grain size, flow volume and channel width on geophysical flow mobility: three-dimensional discrete element modeling of dry and dense flows of angular rock fragments

    Science.gov (United States)

    Cagnoli, Bruno; Piersanti, Antonio

    2017-02-01

    We have carried out new three-dimensional numerical simulations by using a discrete element method (DEM) to study the mobility of dry granular flows of angular rock fragments. These simulations are relevant for geophysical flows such as rock avalanches and pyroclastic flows. The model is validated by previous laboratory experiments. We confirm that (1) the finer the grain size, the larger the mobility of the center of mass of granular flows; (2) the smaller the flow volume, the larger the mobility of the center of mass of granular flows and (3) the wider the channel, the larger the mobility of the center of mass of granular flows. The grain size effect is due to the fact that finer grain size flows dissipate intrinsically less energy. This volume effect is the opposite of that experienced by the flow fronts. The original contribution of this paper consists of providing a comparison of the mobility of granular flows in six channels with a different cross section each. This results in a new scaling parameter χ that has the product of grain size and the cubic root of flow volume as the numerator and the product of channel width and flow length as the denominator. The linear correlation between the reciprocal of mobility and parameter χ is statistically highly significant. Parameter χ confirms that the mobility of the center of mass of granular flows is an increasing function of the ratio of the number of fragments per unit of flow mass to the total number of fragments in the flow. These are two characteristic numbers of particles whose effect on mobility is scale invariant.

  9. Rapid Identification Method of Omphalotus japonicus by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP).

    Science.gov (United States)

    Sugano, Yohei; Sakata, Kozue; Nakamura, Kosuke; Noguchi, Akio; Fukuda, Nozomi; Suzuki, Tomohiro; Kondo, Kazunari

    2017-01-01

    Omphalotus japonicus is a poisonous mushroom that grows in Japan. It can be mistaken for edible mushrooms (Shiitake, Hiratake and Mukitake), and if ingested, it causes food poisoning within 30 min to 1 hr. We established a rapid detection method using PCR-RFLP to identify O. japonicus by restriction digestion of the amplified ITS region. By using Sau96I, Bpu10I, SfcI or DrdI/HincII as a restriction enzyme, it was possible to rapidly identify and discriminate O. japonicus based on the fragment length. This study also provided a short PCR-RFLP system comprising amplification and digestion of a short 200-bp DNA fragment within the ITS region. The system could identify and discriminate O. japonicus after in vitro gastric digestion of native and heated mushroom samples as a model of food poisoning. In addition, a confirmatory assay using real-time PCR was developed to achieve more sensitive detection of O. japonicus.

  10. Modern methods of analysis for three-dimensional orientational data

    Science.gov (United States)

    Davis, Joshua R.; Titus, Sarah J.

    2017-03-01

    Structural geology studies commonly include data about orientations of objects in space. By ;orientation; we mean not just a single direction, such as a foliation pole or the long axis of an ellipsoid, but a complete three-dimensional orientation of a body such as a foliation-lineation pair, a fold, an ellipsoid, etc. Over the past four decades, researchers in various fields have developed theory and algorithms for dealing with such data. In this paper, we explain how to apply orientation statistics to common geologic data types. We review plotting systems, measures of location and dispersion, inference (confidence/credible regions and hypothesis tests) for population means, and regression. We pay special attention to methods that work for small sample sizes and widely dispersed data. Our original contributions include a concept of Kamb contouring for orientations, a technique for handling anisotropy in confidence/credible regions, and large-scale numerical experiments on the performance of various inference methods. We conclude with a detailed study of foliation-lineations from the western Idaho shear zone, using statistical results to argue that the data are not consistent with a published model for them.

  11. A three-dimensional measurement method for medical electric endoscope

    Science.gov (United States)

    Zhou, Tingting; Tao, Pei; Yuan, Bo; Wang, Liqiang

    2017-01-01

    One method for three-dimensional (3D) measurement based on structured light is proposed for the medical electric endoscope in the present study. The structured light of black and white strips is generated by that the point sources illuminate the grating mask plate. Four point sources are aligned linearly by a certain space and they are lighted sequentially. Then four images of modulated fringes by the height of object with different phase shifts can be obtained. The algorithm proposed by Wang Z is employed to extract the accurate phase shift from the fringe images since the phase shift cannot be exactly set as π/2 by hardware. An experimental prototype endoscope was built according to the proposed method. One high-definition CMOS camera module developed by ourselves was used to acquire the endoscopic images and the structured light was generated by four fiber LEDs and a transmission grating with a pitch of 0.1 mm. one C# program was designed to light up LEDs in turn, acquire the phase shifted images and calculate the 3D information. The experimental results indicate that its precise of depth measurement at the working distance of 40 mm is better than 0.5 mm and its consuming time of 3D depth calculation is less than 0.5 s.

  12. Generalized non-separable two-dimensional Dammann encoding method

    Science.gov (United States)

    Yu, Junjie; Zhou, Changhe; Zhu, Linwei; Lu, Yancong; Wu, Jun; Jia, Wei

    2017-01-01

    We generalize for the first time, to the best of our knowledge, the Dammann encoding method into non-separable two-dimensional (2D) structures for designing various pure-phase Dammann encoding gratings (DEGs). For examples, three types of non-separable 2D DEGs, including non-separable binary Dammann vortex gratings, non-separable binary distorted Dammann gratings, and non-separable continuous-phase cubic gratings, are designed theoretically and demonstrated experimentally. Correspondingly, it is shown that 2D square arrays of optical vortices with topological charges proportional to the diffraction orders, focus spots shifting along both transversal and axial directions with equal spacings, and Airy-like beams with controllable orientation for each beam, are generated in symmetry or asymmetry by these three DEGs, respectively. Also, it is shown that a more complex-shaped array of modulated beams could be achieved by this non-separable 2D Dammann encoding method, which will be a big challenge for those conventional separable 2D Dammann encoding gratings. Furthermore, the diffractive efficiency of the gratings can be improved around ∼10% when the non-separable structure is applied, compared with their conventional separable counterparts. Such improvement in the efficiency should be of high significance for some specific applications.

  13. Efficient computation method for two-dimensional nonlinear waves

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The theory and simulation of fully-nonlinear waves in a truncated two-dimensional wave tank in time domain are presented. A piston-type wave-maker is used to generate gravity waves into the tank field in finite water depth. A damping zone is added in front of the wave-maker which makes it become one kind of absorbing wave-maker and ensures the prescribed Neumann condition. The efficiency of nmerical tank is further enhanced by installation of a sponge layer beach (SLB) in front of downtank to absorb longer weak waves that leak through the entire wave train front. Assume potential flow, the space- periodic irrotational surface waves can be represented by mixed Euler- Lagrange particles. Solving the integral equation at each time step for new normal velocities, the instantaneous free surface is integrated following time history by use of fourth-order Runge- Kutta method. The double node technique is used to deal with geometric discontinuity at the wave- body intersections. Several precise smoothing methods have been introduced to treat surface point with high curvature. No saw-tooth like instability is observed during the total simulation.The advantage of proposed wave tank has been verified by comparing with linear theoretical solution and other nonlinear results, excellent agreement in the whole range of frequencies of interest has been obtained.

  14. A Three Dimensional Simulation Method of the Gantry Crane

    Directory of Open Access Journals (Sweden)

    Jingsong LI

    2013-04-01

    Full Text Available Until now, many companies have developed lots of the port machinery remote monitoring systems. However, these monitoring systems usual display the operating status of the port machinery by the schematic diagram, Legend and data. The presentation of information is unable to describe the status of the large number of port machinery. In order to solve the problem, a three-dimensional simulation method of the gantry crane based on the WPF is proposed. This paper studies WPF technology and 3D modeling techniques, on this basis, proposes a kind of the gantry crane 3D simulation method based on WPF, establishes a new generation monitoring system based on 3D, immersive and interactive real-time simulation environment. This system could simulate the real-time 3D virtual scene of the gantry crane, and real-time 3D analog display port machinery running posture and operating environment. Experiments show that CPU and memory usage rate is low enough when the system is running.

  15. Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library.

    Science.gov (United States)

    Kaliman, Ilya A; Slipchenko, Lyudmila V

    2015-01-15

    A new hybrid MPI/OpenMP parallelization scheme is introduced for the Effective Fragment Potential (EFP) method implemented in the libefp software library. The new implementation employs dynamic load balancing algorithm that uses a master/slave model. The software shows excellent parallel scaling up to several hundreds of CPU-cores across multiple nodes. The code uses functions only from the well-established MPI-1 standard that simplifies portability of the library. This new parallel EFP implementation greatly expands the applicability of the EFP and QM/EFP methods by extending attainable time- and length-scales.

  16. Synthetic Spectrum Methods for Three-Dimensional Supernova Models

    CERN Document Server

    Thomas, R C

    2003-01-01

    Current observations stimulate the production of fully three-dimensional explosion models, which in turn motivates three-dimensional spectrum synthesis for supernova atmospheres. We briefly discuss techniques adapted to address the latter problem, and consider some fundamentals of line formation in supernovae without recourse to spherical symmetry. Direct and detailed extensions of the technique are discussed, and future work is outlined.

  17. Experimental research of methods for clustering and selecting image fragments using spatial invariant equivalent models

    Science.gov (United States)

    Krasilenko, Vladimir G.; Lazarev, Alexander A.; Nikitovich, Diana V.

    2014-08-01

    In the paper, we show that the nonlinear spatial non-linear equivalency functions on the basis of continuous logic equivalence (nonequivalence) operations have better discriminatory properties for comparing images. Further, using the equivalent model of multiport neural networks and associative memory, (including matrix-matrix and matrix-tensor with adaptive-weighted correlation, multi-port neural-net auto-associative and hetero-associative memory (MP NN AAM and HAM ) and the proposed architecture based on them, we show how we can modify these models and architectures for space-invariant associative recognition and clustering (high performance parallel clustering processing) images. We consider possible implementations of 2D image classifiers, devices for partitioning image fragments into clusters and their architectures. The main base unit of such architectures is a matrix-matrix or matrix-tensor equivalentor, which can be implemented on the basis of two traditional correlators. We show that the classifiers based on the equivalency paradigm and optoelectronic architectures with space-time integration and parallel-serial 2D images processing have advantages such as increased memory capacity (more than ten times of the number of neurons!), High performance in different modes . We present the results of associative significant dimension (128x128, 610x340) image recognition - renewal modeling. It will be shown that these models are capable to recognize images with a significant percentage (20- 30%) damaged pixels. The experimental results show that such models can be successfully used for auto-and heteroassociative pattern recognition. We show simulation results of using these modifications for clustering and learning models and algorithms for cluster analysis of specific images and divide them into categories of the array. Show example of a cluster division of image fragments, letters and graphics for clusters with simultaneous formation of the outputweighted spatial

  18. A novel method for in Situ detection of hydrolyzable casein fragments in a cheese matrix by antibody phage display technique and CLSM

    DEFF Research Database (Denmark)

    Duan, Zhi; Brüggemann, Dagmar Adeline; Siegumfeldt, Henrik

    2009-01-01

    A novel method to monitor in situ hydrolyzable casein fragments during cheese ripening by using immunofluorescent labeling and confocal laser scanning microscopy (CLSM) was developed. Monoclonal single chain variable fragments of antibody (scFvs) were generated by antibody phage display toward th...

  19. Discovery of Potent Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods and Structure-Based Design

    Energy Technology Data Exchange (ETDEWEB)

    Friberg, Anders [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Vigil, Dominico [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Zhao, Bin [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Daniels, R. Nathan [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Burke, Jason P. [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Garcia-Barrantes, Pedro M. [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Camper, DeMarco [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Chauder, Brian A. [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Lee, Taekyu [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Olejniczak, Edward T. [Vanderbilt Univ. School of Medicine, Nashville, TN (United States); Fesik, Stephen W. [Vanderbilt Univ. School of Medicine, Nashville, TN (United States)

    2012-12-17

    Myeloid cell leukemia 1 (Mcl-1), a member of the Bcl-2 family of proteins, is overexpressed and amplified in various cancers and promotes the aberrant survival of tumor cells that otherwise would undergo apoptosis. Here we describe the discovery of potent and selective Mcl-1 inhibitors using fragment-based methods and structure-based design. NMR-based screening of a large fragment library identified two chemically distinct hit series that bind to different sites on Mcl-1. Members of the two fragment classes were merged together to produce lead compounds that bind to Mcl-1 with a dissociation constant of <100 nM with selectivity for Mcl-1 over Bcl-xL and Bcl-2. Structures of merged compounds when complexed to Mcl-1 were obtained by X-ray crystallography and provide detailed information about the molecular recognition of small-molecule ligands binding Mcl-1. The compounds represent starting points for the discovery of clinically useful Mcl-1 inhibitors for the treatment of a wide variety of cancers.

  20. An Isoratio Method to Study Free Energy and Temperature Effects in Intermediate Mass Fragments Produced in Heavy-Ion Collisions

    Science.gov (United States)

    Ma, Chun-Wang; Qiao, Chun-Yuan; Ding, Tian-Tian; Niu, Fei; Song, Yi-Dan; Niu, Yi-Fei

    2016-07-01

    An isoratio method, i.e., the isotopic (isotonic) ratio among three isotopes (isotones), is proposed to study the free energy and temperature effects in the intermediate mass fragments produced in heavy-ion collisions. The parameterizations for the free energy of nucleus at low temperature, which have been proposed in the framework of the density functional theory using the SKM skymre interaction, are adopted to calculate the temperature-dependent free energy of fragment. By analyzing the measured yields of fragments in the 140A MeV 58,64Ni + 9Be reactions, it is verified that the free energy in the isoratio is almost the same for different reactions. A temperature-dependent pairing-energy is introduced into the parameterizations for free energy, which reveals that the weakened pairing energy at the low temperature accounts for the weakened or disappearing odd-even staggering in isoratio. Supported by the Program for Science and Technology Innovation Talents in Universities of Henan Province under Grant No. 13HASTIT046, the Creative Experimental Project of National Undergraduate Students (CEPNU201510476017)

  1. A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

    Science.gov (United States)

    Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

    2016-03-14

    The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

  2. Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking.

    Directory of Open Access Journals (Sweden)

    Jiabing Ji

    Full Text Available BACKGROUND: Insertion mutant isolation and characterization are extremely valuable for linking genes to physiological function. Once an insertion mutant phenotype is identified, the challenge is to isolate the responsible gene. Multiple strategies have been employed to isolate unknown genomic DNA that flanks mutagenic insertions, however, all these methods suffer from limitations due to inefficient ligation steps, inclusion of restriction sites within the target DNA, and non-specific product generation. These limitations become close to insurmountable when the goal is to identify insertion sites in a high throughput manner. METHODOLOGY/PRINCIPAL FINDINGS: We designed a novel strategy called Restriction Site Extension PCR (RSE-PCR to efficiently conduct large-scale isolation of unknown genomic DNA fragments linked to DNA insertions. The strategy is a modified adaptor-mediated PCR without ligation. An adapter, with complementarity to the 3' overhang of the endonuclease (KpnI, NsiI, PstI, or SacI restricted DNA fragments, extends the 3' end of the DNA fragments in the first cycle of the primary RSE-PCR. During subsequent PCR cycles and a second semi-nested PCR (secondary RSE-PCR, touchdown and two-step PCR are combined to increase the amplification specificity of target fragments. The efficiency and specificity was demonstrated in our characterization of 37 tex mutants of Arabidopsis. All the steps of RSE-PCR can be executed in a 96 well PCR plate. Finally, RSE-PCR serves as a successful alternative to Genome Walker as demonstrated by gene isolation from maize, a plant with a more complex genome than Arabidopsis. CONCLUSIONS/SIGNIFICANCE: RSE-PCR has high potential application in identifying tagged (T-DNA or transposon sequence or walking from known DNA toward unknown regions in large-genome plants, with likely application in other organisms as well.

  3. Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method.

    Directory of Open Access Journals (Sweden)

    Ryunosuke Yoshino

    Full Text Available Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH by fragment molecular orbital (FMO calculation for orotate, oxonate, and 43 orotate derivatives.Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN, whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue.FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.

  4. Method and system for determining a volume of an object from two-dimensional images

    Science.gov (United States)

    Abercrombie, Robert K [Knoxville, TN; Schlicher, Bob G [Portsmouth, NH

    2010-08-10

    The invention provides a method and a computer program stored in a tangible medium for automatically determining a volume of three-dimensional objects represented in two-dimensional images, by acquiring at two least two-dimensional digitized images, by analyzing the two-dimensional images to identify reference points and geometric patterns, by determining distances between the reference points and the component objects utilizing reference data provided for the three-dimensional object, and by calculating a volume for the three-dimensional object.

  5. Theories to support method development in comprehensive two-dimensional liquid chromatography - A review

    NARCIS (Netherlands)

    Bedani, F.; Schoenmakers, P.J.; Janssen, H.-G.

    2012-01-01

    On-line comprehensive two-dimensional liquid chromatography techniques promise to resolve samples that current one-dimensional liquid chromatography methods cannot adequately deal with. To make full use of the potential of two-dimensional liquid chromatography, optimization is required. Optimization

  6. Multiple and sequential data acquisition method: an improved method for fragmentation and detection of cross-linked peptides on a hybrid linear trap quadrupole Orbitrap Velos mass spectrometer.

    Science.gov (United States)

    Rudashevskaya, Elena L; Breitwieser, Florian P; Huber, Marie L; Colinge, Jacques; Müller, André C; Bennett, Keiryn L

    2013-02-05

    The identification and validation of cross-linked peptides by mass spectrometry remains a daunting challenge for protein-protein cross-linking approaches when investigating protein interactions. This includes the fragmentation of cross-linked peptides in the mass spectrometer per se and following database searching, the matching of the molecular masses of the fragment ions to the correct cross-linked peptides. The hybrid linear trap quadrupole (LTQ) Orbitrap Velos combines the speed of the tandem mass spectrometry (MS/MS) duty circle with high mass accuracy, and these features were utilized in the current study to substantially improve the confidence in the identification of cross-linked peptides. An MS/MS method termed multiple and sequential data acquisition method (MSDAM) was developed. Preliminary optimization of the MS/MS settings was performed with a synthetic peptide (TP1) cross-linked with bis[sulfosuccinimidyl] suberate (BS(3)). On the basis of these results, MSDAM was created and assessed on the BS(3)-cross-linked bovine serum albumin (BSA) homodimer. MSDAM applies a series of multiple sequential fragmentation events with a range of different normalized collision energies (NCE) to the same precursor ion. The combination of a series of NCE enabled a considerable improvement in the quality of the fragmentation spectra for cross-linked peptides, and ultimately aided in the identification of the sequences of the cross-linked peptides. Concurrently, MSDAM provides confirmatory evidence from the formation of reporter ions fragments, which reduces the false positive rate of incorrectly assigned cross-linked peptides.

  7. Methods, apparatuses, and computer-readable media for projectional morphological analysis of N-dimensional signals

    Science.gov (United States)

    Glazoff, Michael V.; Gering, Kevin L.; Garnier, John E.; Rashkeev, Sergey N.; Pyt'ev, Yuri Petrovich

    2016-05-17

    Embodiments discussed herein in the form of methods, systems, and computer-readable media deal with the application of advanced "projectional" morphological algorithms for solving a broad range of problems. In a method of performing projectional morphological analysis, an N-dimensional input signal is supplied. At least one N-dimensional form indicative of at least one feature in the N-dimensional input signal is identified. The N-dimensional input signal is filtered relative to the at least one N-dimensional form and an N-dimensional output signal is generated indicating results of the filtering at least as differences in the N-dimensional input signal relative to the at least one N-dimensional form.

  8. Large-scale purification of the synthetic peptide fragment 163-171 of human interleukin-beta by multi-dimensional displacement chromatography.

    Science.gov (United States)

    Viscomi, G C; Cardinali, C; Longobardi, M G; Verdini, A S

    1991-07-19

    Multi-dimensional chromatography has been used successfully in the displacement mode for the purification of the synthetic peptide H-Val-Gln-Gly-Glu-Glu-Ser-Asn-Asp-Lys-OH, the fragment 163-171 of human interleukin-beta. This peptide can mimic several of the in vivo and in vitro immunostimulatory activities of the entire protein, except for the inflammatory effect. A large-scale procedure has been developed to purify the synthetic peptide by reversed-phase (RP) and ion-exchange (IE) displacement chromatography (DC) in a single run without any pretreatment. Masses from 100 mg to about 35 g of the unpurified compounds synthesized by a solid-phase technique on a Merrifield-type resin and obtained by acidolytic cleavage from the solid support, can be purified in this way. In the RP-DC mode the carrier and the displacer were aqueous solutions of 0.1% trifluoroacetic acid and 50 mM benzyltributylammonium chloride, respectively, whereas in the IE-DC mode the carrier was water and the displacer 50 mM ammonium citrate solution. RP-DC and IE-DC were also performed in series by directing the effluent of the RP column onto the IE column. Peptide purities and recoveries greater than 96 and 90%, respectively, were obtained.

  9. Novel extraction method of genomic DNA suitable for long-fragment amplification from small amounts of milk.

    Science.gov (United States)

    Liu, Y F; Gao, J L; Yang, Y F; Ku, T; Zan, L S

    2014-11-01

    Isolation of genomic DNA is a prerequisite for assessment of milk quality. As a source of genomic DNA, milk somatic cells from milking ruminants are practical, animal friendly, and cost-effective sources. Extracting DNA from milk can avoid the stress response caused by blood and tissue sampling of cows. In this study, we optimized a novel DNA extraction method for amplifying long (>1,000 bp) DNA fragments and used it to evaluate the isolation of DNA from small amounts of milk. The techniques used for the separation of milk somatic cell were explored and combined with a sodium dodecyl sulfate (SDS)-phenol method for optimizing DNA extraction from milk. Spectrophotometry was used to determine the concentration and purity of the extracted DNA. Gel electrophoresis and DNA amplification technologies were used for to determine DNA size and quality. The DNA of 112 cows was obtained from milk (samples of 13 ± 1 mL) and the corresponding optical density ratios at 260:280 nm were between 1.65 and 1.75. Concentrations were between 12 and 45 μg/μL and DNA size and quality were acceptable. The specific PCR amplification of 1,019- and 729-bp bovine DNA fragments was successfully carried out. This novel method can be used as a practical, fast, and economical mean for long genomic DNA extraction from a small amount of milk. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  10. Structural models of antibody variable fragments: A method for investigating binding mechanisms

    Science.gov (United States)

    Petit, Samuel; Brard, Frédéric; Coquerel, Gérard; Perez, Guy; Tron, François

    1998-03-01

    The value of comparative molecular modeling for elucidating structure-function relationships was demonstrated by analyzing six anti-nucleosome autoantibody variable fragments. Structural models were built using the automated procedure developed in the COMPOSER software, subsequently minimized with the AMBER force field, and validated according to several standard geometric and chemical criteria. Canonical class assignment from Chothia and Lesk's [Chottin and Lesk, J. Mol. Biol., 196 (1987) 901; Chothia et al., Nature, 342 (1989) 877] work was used as a supplementary validation tool for five of the six hypervariable loops. The analysis, based on the hypothesis that antigen binding could occur through electrostatic interactions, reveals a diversity of possible binding mechanisms of anti-nucleosome or anti-histone antibodies to their cognate antigen. These results lead us to postulate that anti-nucleosome autoantibodies could have different origins. Since both anti-DNA and anti-nculeosome autoantibodies are produced during the course of systemic lupus erythematosus, a non-organ specific autoimmune disease, a comparative structural and electrostatic analysis of the two populations of autoantibodies may constitute a way to elucidate their origin and the role of the antigen in tolerance breakdown. The present study illustrates some interests, advantages and limits of a methodology based on the use of comparative modeling and analysis of molecular surface properties.

  11. Lattice Methods for Pricing American Strangles with Two-Dimensional Stochastic Volatility Models

    Directory of Open Access Journals (Sweden)

    Xuemei Gao

    2014-01-01

    Full Text Available The aim of this paper is to extend the lattice method proposed by Ritchken and Trevor (1999 for pricing American options with one-dimensional stochastic volatility models to the two-dimensional cases with strangle payoff. This proposed method is compared with the least square Monte-Carlo method via numerical examples.

  12. Three-dimensional nanoelectronic device simulation using spectral element methods

    Science.gov (United States)

    Cheng, Candong

    The purpose of this thesis is to develop an efficient 3-Dimensional (3-D) nanoelectronic device simulator. Specifically, the self-consistent Schrodinger-Poisson model was implemented in this simulator to simulate band structures and quantum transport properties. Also, an efficient fast algorithm, spectral element method (SEM), was used in this simulator to achieve spectral accuracy where the error decreases exponentially with the increase of sampling densities and the basis order of the polynomial functions, thus significantly reducing the CPU time and memory usage. Moreover, within this simulator, a perfectly matched layer (PML) boundary condition method was used for the Schrodinger solver, which significantly simplifies the problem and reduces the computational time. Furthermore, the effective mass in semiconductor devices was treated as a full anisotropic mass tensor, which provides an excellent tool to study the anisotropy characteristics along arbitrary orientation of the device. Nanoelectronic devices usually involve the simulations of energy band and quantum transport properties. One of the models to perform these simulations is by solving a self-consistent Schrodinger-Poisson system. Two efficient fast algorithms, spectral grid method (SGM) and SEM, are investigated and implemented in this thesis. The spectral accuracy is achieved in both algorithms, whose errors decrease exponentially with the increase of the sampling density and basis orders. The spectral grid method is a pseudospectral method to achieve a high-accuracy result by choosing special nonuniform grid set and high-order Lagrange interpolants for a partial differential equation. Spectral element method is a high-order finite element method which uses the Gauss-Lobatto-Legendre (GLL) polynomials to represent the field variables in the Schrodinger-Poisson system and, therefore, to achieve spectral accuracy. We have implemented the SGM in the Schrodinger equation to solve the energy band structures

  13. Propagation of the threatened staghorn coral Acropora cervicornis: methods to minimize the impacts of fragment collection and maximize production

    Science.gov (United States)

    Lirman, D.; Thyberg, T.; Herlan, J.; Hill, C.; Young-Lahiff, C.; Schopmeyer, S.; Huntington, B.; Santos, R.; Drury, C.

    2010-09-01

    Coral reef restoration methods such as coral gardening are becoming increasingly considered as viable options to mitigate reef degradation and enhance recovery of depleted coral populations. In this study, we describe several aspects of the coral gardening approach that demonstrate this methodology is an effective way of propagating the threatened Caribbean staghorn coral Acropora cervicornis: (1) the growth of colonies within the nursery exceeded the growth rates of wild staghorn colonies in the same region; (2) the collection of branch tips did not result in any further mortality to the donor colonies beyond the coral removed for transplantation; (3) decreases in linear extension of the donor branches were only temporary and donor branches grew faster than control branches after an initial recovery period of approximately 3-6 weeks; (4) fragmentation did not affect the growth rates of non-donor branches within the same colony; (5) small branch tips experienced initial mortality due to handling and transportation but surviving tips grew well over time; and (6) when the growth of the branch tips is added to the regrowth of the fragmented donor branches, the new coral produced was 1.4-1.8 times more than new growth in undisturbed colonies. Based on these results, the collection of small (2.5-3.5 cm) branch tips was an effective propagation method for this branching coral species resulting in increased biomass accumulation and limited damage to parental stocks.

  14. Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083 (Japan); Fedorov, Dmitri G., E-mail: d.g.fedorov@aist.go.jp [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Zahariev, Federico; Schmidt, Michael W.; Gordon, Mark S. [Department of Chemistry and Ames Laboratory, US-DOE, Iowa State University, Ames, Iowa 50011 (United States); Kitaura, Kazuo [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Nakamura, Shinichiro [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2015-03-28

    Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in S{sub N}2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.

  15. Nudged elastic band method and density functional theory calculation for finding a local minimum energy pathway of p-benzoquinone and phenol fragmentation in mass spectrometry.

    Science.gov (United States)

    Sugimura, Natsuhiko; Igarashi, Yoko; Aoyama, Reiko; Shibue, Toshimichi

    2017-02-01

    Analysis of the fragmentation pathways of molecules in mass spectrometry gives a fundamental insight into gas-phase ion chemistry. However, the conventional intrinsic reaction coordinates method requires knowledge of the transition states of ion structures in the fragmentation pathways. Herein, we use the nudged elastic band method, using only the initial and final state ion structures in the fragmentation pathways, and report the advantages and limitations of the method. We found a minimum energy path of p-benzoquinone ion fragmentation with two saddle points and one intermediate structure. The primary energy barrier, which corresponded to the cleavage of the C-C bond adjacent to the CO group, was calculated to be 1.50 eV. An additional energy barrier, which corresponded to the cleavage of the CO group, was calculated to be 0.68 eV. We also found an energy barrier of 3.00 eV, which was the rate determining step of the keto-enol tautomerization in CO elimination from the molecular ion of phenol. The nudged elastic band method allowed the determination of a minimum energy path using only the initial and final state ion structures in the fragmentation pathways, and it provided faster than the conventional intrinsic reaction coordinates method. In addition, this method was found to be effective in the analysis of the charge structures of the molecules during the fragmentation in mass spectrometry.

  16. Chemosensitivity assay in mice prostate tumor: Preliminary report of flow cytometry, DNA fragmentation, ion ratiometric methods of anti-neoplastic drug monitoring

    Directory of Open Access Journals (Sweden)

    Kline Richard

    2004-03-01

    Full Text Available Abstract Flow cytometry, DNA fragmentation, ion ratiomateric analysis and NMR peaks characterized drug chemosensitivity of antineoplastic drugs. Hypotheses were: 1. The chemosensitive effect of different cancer cell lines is characteristic; 2. DNA fragmentation, ion ratiometric analysis suggest apoptosis status of tumor cells. Methods PC-3 cell lines were compared with DU-145, LNCaP cell lines in culture for the [Na]i and [Ca]i ion sensing dyes, cell death, NMR peaks and apoptosis staining for chemotherapeutic action of different drugs. Results DNA fragmentation, ratiometric ions and fluorescence endlabelling plots were characteristic for cell lines and drug response. 31P-23Na NMR spectra showed characteristic high phospho-choline and sodium peaks. Conclusion Flow cytometry, DNA fragmentation, ion ratiometric methods and NMR peaks indicated apoptosis and offered in vivo drug monitoring method.

  17. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    Science.gov (United States)

    Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

  18. Comparison of SEC and CE-SDS methods for monitoring hinge fragmentation in IgG1 monoclonal antibodies.

    Science.gov (United States)

    Dada, Oluwatosin O; Rao, Romesh; Jones, Natalie; Jaya, Nomalie; Salas-Solano, Oscar

    2017-10-25

    Fragmentation of monoclonal antibodies is a critical quality attribute routinely monitored to assess the purity and integrity of the product from development to commercialization. Cleavage in the upper hinge region of IgG1 monoclonal antibodies is a common fragmentation pattern widely studied by size exclusion chromatography (SEC). Capillary electrophoresis with sodium dodecylsulfate (CE-SDS) is a well-established technique commonly used for monitoring antibody fragments as well, but its comparability to SEC in monitoring hinge fragments has not been established until now. We report a characterization strategy that establishes the correlation between hinge region fragments analyzed by SEC and CE-SDS. Monoclonal antibodies with elevated hinge fragments were generated under low pH stress conditions and analyzed by SEC and CE-SDS. The masses of the fragments generated were determined by LC-MS. Electrophoretic migration of the hinge fragmentation products in CE-SDS were determined based on their mass values. Comparative assessment of fragments by SEC, and CE-SDS showed similar correlation with incubation time. This study demonstrates that CE-SDS can be employed as a surrogate technique to SEC for monitoring hinge region fragments. Most importantly, combination of these techniques can be used to obtain comprehensive understanding of fragment related characteristics of therapeutic protein products. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Unrestricted density functional theory based on the fragment molecular orbital method for the ground and excited state calculations of large systems

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Fedorov, Dmitri G. [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Yokojima, Satoshi [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachioji-shi, Tokyo 192-0392 (Japan); Kitaura, Kazuo [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Sakurai, Minoru [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); Nakamura, Shinichiro [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2014-04-14

    We extended the fragment molecular orbital (FMO) method interfaced with density functional theory (DFT) into spin unrestricted formalism (UDFT) and developed energy gradients for the ground state and single point excited state energies based on time-dependent DFT. The accuracy of FMO is evaluated in comparison to the full calculations without fragmentation. Electronic excitations in solvated organic radicals and in the blue copper protein, plastocyanin (PDB code: 1BXV), are reported. The contributions of solvent molecules to the electronic excitations are analyzed in terms of the fragment polarization and quantum effects such as interfragment charge transfer.

  20. Simple and rapid human papillomavirus genotyping method by restriction fragment length polymorphism analysis with two restriction enzymes.

    Science.gov (United States)

    Chen, Linghan; Watanabe, Ken; Haruyama, Takahiro; Kobayashi, Nobuyuki

    2013-07-01

    Cervical cancer, the third most common cancer that affects women worldwide, is caused by the human papillomavirus (HPV) and is treatable when detected at an early stage. To date, more than 100 different HPV types have been described, and the development of simple, low-cost, and accurate methods to distinguish HPV genotypes is highly warranted. In this study, an HPV genotyping assay based on polymerase chain reaction (PCR) was evaluated. This method involved the use of MY09/11 primers followed by restriction fragment length polymorphism (RFLP) analysis with the restriction enzymes HpyCH4V and NlaIII. Cervical specimens preserved using CytoRich Blue fluid were collected from 1,134 female volunteers for HPV detection, and 1,111 valid samples were amplified using PCR. The PCR method was sensitive enough to detect 25 copies of HPV18, and three copies of HPV16. Out of 202 PCR-positive samples, HPV genotypes were determined in 189 samples (93.6%) by this RFLP method. Results were then evaluated further by capillary sequencing method. Concordant results between the two tests were as high as 96.0%. Thirteen samples, which tested negative with RFLP, were verified as non-specific amplifications with PCR. In conclusion, this PCR-RFLP method using restriction enzymes HpyCH4V and NlaIII is simple, non-labor intensive, and is applicable for the inexpensive determination of HPV genotypes in clinical samples.

  1. The development of a ballistic method for simulating fragments from buried explosive devices

    NARCIS (Netherlands)

    Jagt-Deutekom, M.J. van der

    2016-01-01

    No standard scientific methodology currently exists to assess the performance of personal protection equipment (PPE) against secondary debris, such as soil, grit and stones, ejected when a buried improvised explosive device (IED) detonates. Different test methods are used for this evaluation. The PP

  2. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize phytochemicals in plant extracts

    Science.gov (United States)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. New methods a...

  3. Chemosensitivity assay in mice prostate tumor: Preliminary report of flow cytometry, DNA fragmentation, ion ratiometric methods of anti-neoplastic drug monitoring

    OpenAIRE

    2004-01-01

    Abstract Flow cytometry, DNA fragmentation, ion ratiomateric analysis and NMR peaks characterized drug chemosensitivity of antineoplastic drugs. Hypotheses were: 1. The chemosensitive effect of different cancer cell lines is characteristic; 2. DNA fragmentation, ion ratiometric analysis suggest apoptosis status of tumor cells. Methods PC-3 cell lines were compared with DU-145, LNCaP cell lines in culture for the [Na]i and [Ca]i ion sensing dyes, cell death, NMR peaks and apoptosis staining fo...

  4. Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods.

    Science.gov (United States)

    Taverniers, Isabel; Van Bockstaele, Erik; De Loose, Marc

    2004-03-01

    Analytical real-time PCR technology is a powerful tool for implementation of the GMO labeling regulations enforced in the EU. The quality of analytical measurement data obtained by quantitative real-time PCR depends on the correct use of calibrator and reference materials (RMs). For GMO methods of analysis, the choice of appropriate RMs is currently under debate. So far, genomic DNA solutions from certified reference materials (CRMs) are most often used as calibrators for GMO quantification by means of real-time PCR. However, due to some intrinsic features of these CRMs, errors may be expected in the estimations of DNA sequence quantities. In this paper, two new real-time PCR methods are presented for Roundup Ready soybean, in which two types of plasmid DNA fragments are used as calibrators. Single-target plasmids (STPs) diluted in a background of genomic DNA were used in the first method. Multiple-target plasmids (MTPs) containing both sequences in one molecule were used as calibrators for the second method. Both methods simultaneously detect a promoter 35S sequence as GMO-specific target and a lectin gene sequence as endogenous reference target in a duplex PCR. For the estimation of relative GMO percentages both "delta C(T)" and "standard curve" approaches are tested. Delta C(T) methods are based on direct comparison of measured C(T) values of both the GMO-specific target and the endogenous target. Standard curve methods measure absolute amounts of target copies or haploid genome equivalents. A duplex delta C(T) method with STP calibrators performed at least as well as a similar method with genomic DNA calibrators from commercial CRMs. Besides this, high quality results were obtained with a standard curve method using MTP calibrators. This paper demonstrates that plasmid DNA molecules containing either one or multiple target sequences form perfect alternative calibrators for GMO quantification and are especially suitable for duplex PCR reactions.

  5. Solution of two-dimensional Fredholm integral equation via RBF-triangular method

    Directory of Open Access Journals (Sweden)

    Amir Fallahzadeh

    2012-04-01

    Full Text Available In this paper, a new method is introduced to solve a two-dimensional Fredholm integral equation. The method is based on the approximation by Gaussian radial basis functions and triangular nodes and weights. Also, a new quadrature is introduced to approximate the two dimensional integrals which is called the triangular method. The results of the example illustrate the accuracy of the proposed method increases.

  6. Six-dimensional Methods for Four-dimensional Conformal Field Theories II: Irreducible Fields

    CERN Document Server

    Weinberg, Steven

    2012-01-01

    This note supplements an earlier paper on conformal field theories. There it was shown how to construct tensor, spinor, and spinor-tensor primary fields in four dimensions from their counterparts in six dimensions, where conformal transformations act simply as SO(4,2) Lorentz transformations. Here we show how to constrain fields in six dimensions so that the corresponding primary fields in four dimensions transform according to irreducible representations of the four-dimensional Lorentz group, even when the irreducibility conditions on these representations involve the four-component Levi-Civita tensor $\\epsilon_{\\mu\

  7. Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

    Institute of Scientific and Technical Information of China (English)

    YAN XiuFen; JIANG Nan; MA Jing

    2009-01-01

    A series of theoretical approaches,including conventional FF03 and FF03-based polarization model,as well as the generalized energy-based fragmentation (GEBF) quantum chemistry method,have been applied to investigate the interactions between acetate ion (CH_3COO~-) and the α-subunit of human adult hemoglobin (designated as Hb-α) at four binding sites (Lys16,Lys90,Arg92,and Lys127),respectively.The FF03-based polarizable force fields show that the interaction energies between the CH_3COO~-group and Hb-α follow the trend of Arg92>Lys127>Lys90>Lys16.The complexation of CH_3COO~-with Hb-α is governed by the long-range electrostatic interactions and steric effect.

  8. Theoretical study of interactions between human adult hemoglobin and acetate ion by polarizable force field and fragmentation quantum chemistry methods

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A series of theoretical approaches,including conventional FF03 and FF03-based polarization model,as well as the generalized energy-based fragmentation(GEBF) quantum chemistry method,have been applied to investigate the interactions between acetate ion(CH3COO-) and the α-subunit of human adult hemoglobin(designated as Hb-α) at four binding sites(Lys16,Lys90,Arg92,and Lys127),respectively.The FF03-based polarizable force fields show that the interaction energies between the CH3COO-group and Hb-α follow the trend of Arg92>Lys127>Lys90>Lys16.The complexation of CH3COO-with Hb-α is governed by the long-range electrostatic interactions and steric effect.

  9. Novel Online Dimensionality Reduction Method with Improved Topology Representing and Radial Basis Function Networks.

    Science.gov (United States)

    Ni, Shengqiao; Lv, Jiancheng; Cheng, Zhehao; Li, Mao

    2015-01-01

    This paper presents improvements to the conventional Topology Representing Network to build more appropriate topology relationships. Based on this improved Topology Representing Network, we propose a novel method for online dimensionality reduction that integrates the improved Topology Representing Network and Radial Basis Function Network. This method can find meaningful low-dimensional feature structures embedded in high-dimensional original data space, process nonlinear embedded manifolds, and map the new data online. Furthermore, this method can deal with large datasets for the benefit of improved Topology Representing Network. Experiments illustrate the effectiveness of the proposed method.

  10. Novel Online Dimensionality Reduction Method with Improved Topology Representing and Radial Basis Function Networks.

    Directory of Open Access Journals (Sweden)

    Shengqiao Ni

    Full Text Available This paper presents improvements to the conventional Topology Representing Network to build more appropriate topology relationships. Based on this improved Topology Representing Network, we propose a novel method for online dimensionality reduction that integrates the improved Topology Representing Network and Radial Basis Function Network. This method can find meaningful low-dimensional feature structures embedded in high-dimensional original data space, process nonlinear embedded manifolds, and map the new data online. Furthermore, this method can deal with large datasets for the benefit of improved Topology Representing Network. Experiments illustrate the effectiveness of the proposed method.

  11. Parallax scanning methods for stereoscopic three-dimensional imaging

    Science.gov (United States)

    Mayhew, Christopher A.; Mayhew, Craig M.

    2012-03-01

    Under certain circumstances, conventional stereoscopic imagery is subject to being misinterpreted. Stereo perception created from two static horizontally separated views can create a "cut out" 2D appearance for objects at various planes of depth. The subject volume looks three-dimensional, but the objects themselves appear flat. This is especially true if the images are captured using small disparities. One potential explanation for this effect is that, although three-dimensional perception comes primarily from binocular vision, a human's gaze (the direction and orientation of a person's eyes with respect to their environment) and head motion also contribute additional sub-process information. The absence of this information may be the reason that certain stereoscopic imagery appears "odd" and unrealistic. Another contributing factor may be the absence of vertical disparity information in a traditional stereoscopy display. Recently, Parallax Scanning technologies have been introduced, which provide (1) a scanning methodology, (2) incorporate vertical disparity, and (3) produce stereo images with substantially smaller disparities than the human interocular distances.1 To test whether these three features would improve the realism and reduce the cardboard cutout effect of stereo images, we have applied Parallax Scanning (PS) technologies to commercial stereoscopic digital cinema productions and have tested the results with a panel of stereo experts. These informal experiments show that the addition of PS information into the left and right image capture improves the overall perception of three-dimensionality for most viewers. Parallax scanning significantly increases the set of tools available for 3D storytelling while at the same time presenting imagery that is easy and pleasant to view.

  12. Three dimensional stress vector sensor array and method therefor

    Science.gov (United States)

    Pfeifer, Kent Bryant; Rudnick, Thomas Jeffery

    2005-07-05

    A sensor array is configured based upon capacitive sensor techniques to measure stresses at various positions in a sheet simultaneously and allow a stress map to be obtained in near real-time. The device consists of single capacitive elements applied in a one or two dimensional array to measure the distribution of stresses across a mat surface in real-time as a function of position for manufacturing and test applications. In-plane and normal stresses in rolling bodies such as tires may thus be monitored.

  13. Methods for preparation of three-dimensional bodies

    Energy Technology Data Exchange (ETDEWEB)

    Mulligan, Anthony C [Tucson, AZ; Rigali, Mark J [Carlsbad, NM; Sutaria, Manish P [Malden, MA; Artz, Gregory J [Tucson, AZ; Gafner, Felix H [Tucson, AZ; Vaidyanathan, K Ranji [Tucson, AZ

    2008-06-17

    Processes for mechanically fabricating two and three-dimensional fibrous monolith composites include preparing a fibrous monolith filament from a core composition of a first powder material and a boundary material of a second powder material. The filament includes a first portion of the core composition surrounded by a second portion of the boundary composition. One or more filaments are extruded through a mechanically-controlled deposition nozzle onto a working surface to create a fibrous monolith composite object. The objects may be formed directly from computer models and have complex geometries.

  14. An improved PCR-restriction fragment length polymorphism (RFLP) method for the identification of cry1-type genes.

    Science.gov (United States)

    Shu, Changlong; Liu, Dongming; Zhou, Zishan; Cai, Jilin; Peng, Qi; Gao, Jiguo; Song, Fuping; Zhang, Jie

    2013-11-01

    The cry1-type genes of Bacillus thuringiensis represent the largest cry gene family, which contains 50 distinct holotypes. It is becoming more and more difficult to identify cry1-type genes using current methods because of the increasing number of cry1-type genes. In the present study, an improved PCR-restriction fragment length polymorphism (PCR-RFLP) method which can distinguish 41 holotypes of cry1-type genes was developed. This improved method was used to identify cry1-type genes in 20 B. thuringiensis strains that are toxic to lepidoptera. The results showed that the improved method can efficiently identify single and clustered cry1-type genes and can be used to evaluate cry1-type genes in novel strain collections of B. thuringiensis. Among the detected cry1-type genes, we identified four novel genes, cry1Ai, cry1Bb, cry1Ja, and cry1La. The bioassay results from the expressed products of the four novel cry genes showed that Cry1Ai2, Cry1Bb2, and Cry1Ja2 were highly toxic against Plutella xylostella, whereas Cry1La2 exhibited no activity. Moreover, Cry1Ai2 had good lethal activity against Ostrinia furnacalis, Hyphantria cunea, Chilo suppressalis, and Bombyx mori larvae and considerable weight loss activity against Helicoverpa armigera.

  15. A simple two-step, 'hit and fix' method to generate subtle mutations in BACs using short denatured PCR fragments.

    Science.gov (United States)

    Yang, Yongping; Sharan, Shyam K

    2003-08-01

    The bacteriophage lambda recombination system has proven to be a valuable tool for engineering bacterial artificial chromosomes (BAC). Due to its high efficiency, subtle alterations in the BACs can be generated using oligonucleotides as targeting vectors. Since no selection marker is used, recombinant clones are identified utilizing a selective PCR screening method. However, occasionally the selective PCR screening is not feasible. We describe here a two-step 'hit and fix' method that can be reliably used for generating any subtle alteration in BACs using short denatured PCR fragments as targeting vectors. In the first step of this method, 6-20 nucleotides are changed around the base where the mutation has to be generated. In the second step, these altered nucleotides are reverted to the original sequence and simultaneously a subtle alteration is introduced. Since in each step several nucleotides are changed, PCR primers specific for such alterations can be designed. This two-step method provides a simple and efficient tool for generating subtle alterations in BACs that can be very valuable for functional analysis of genes.

  16. Quantum fragmentation

    CERN Document Server

    Peschanski, R

    1993-01-01

    Phenomenological and theoretical aspects of fragmentation for elementary particles (resp. nuclei) are discussed. It is shown that some concepts of classical fragmentation remain relevant in a microscopic framework, exhibiting non-trivial properties of quantum relativistic field theory (resp. lattice percolation). Email contact: pesch@amoco.saclay.cea.fr

  17. Antiepidermal growth factor variant III scFv fragment: effect of radioiodination method on tumor targeting and normal tissue clearance

    Energy Technology Data Exchange (ETDEWEB)

    Shankar, Sriram [Department of Radiology, Duke University Medical Center, Durham, NC 27710 (United States); Vaidyanathan, Ganesan [Department of Radiology, Duke University Medical Center, Durham, NC 27710 (United States); Kuan, C.-T. [Department of Pathology, Duke University Medical Center, Durham, NC 27710 (United States); Bigner, Darell D. [Department of Pathology, Duke University Medical Center, Durham, NC 27710 (United States); Zalutsky, Michael R. [Department of Radiology, Duke University Medical Center, Durham, NC 27710 (United States) and Department of Pathology, Duke University Medical Center, Durham, NC 27710 (United States) and Department of Biomedical Engineering, Duke University, Durham, NC 27708 (United States)]. E-mail: zalut001@duke.edu

    2006-01-15

    Introduction: MR1-1 is a single-chain Fv (scFv) fragment that binds with high affinity to epidermal growth factor receptor variant III, which is overexpressed on gliomas and other tumors but is not present on normal tissues. The objective of this study was to evaluate four different methods for labeling MR1-1 scFv that had been previously investigated for the radioiodinating of an intact anti-epidermal growth factor receptor variant III (anti-EGFRvIII) monoclonal antibody (mAb) L8A4. Methods: The MR1-1 scFv was labeled with {sup 125}I/{sup 131}I using the Iodogen method, and was also radiohalogenated with acylation agents bearing substituents that were positively charged-N-succinimidyl-3-[*I]iodo-5-pyridine carboxylate and N-succinimidyl-4-guanidinomethyl-3-[*I]iodobenzoate ([*I]SGMIB)-and negatively charged-N-succinimidyl-3-[*I]iodo-4-phosphonomethylbenzoate ([*I]SIPMB). In vitro internalization assays were performed with the U87MG{delta}EGFR cell line, and the tissue distribution of the radioiodinated scFv fragments was evaluated in athymic mice bearing subcutaneous U87MG{delta}EGFR xenografts. Results and Conclusion: As seen previously with the anti-EGFRvIII IgG mAb, retention of radioiodine activity in U87MG{delta}EGFR cells in the internalization assay was labeling method dependent, with SGMIB and SIPMB yielding the most prolonged retention. However, unlike the case with the intact mAb, the results of the internalization assays were not predictive of in vivo tumor localization capacity of the labeled scFv. Renal activity was dependent on the nature of the labeling method. With MR1-1 labeled using SIPMB, kidney uptake was highest and most prolonged; catabolism studies indicated that this uptake primarily was in the form of {epsilon}-N-3-[*I]iodo-4-phosphonomethylbenzoyl lysine.

  18. Restoration of Scanning Tunneling Microscope Images by means of Two-Dimensional Maximum Entropy Method

    Science.gov (United States)

    Matsumoto, Hisanori; Tokiwano, Kazuo; Hosoi, Hirotaka; Sueoka, Kazuhisa; Mukasa, Koichi

    2002-05-01

    We present a new technique for the restoration of scanning tunneling microscopy (STM) images, which is a two-dimensional extension of a recently developed statistical approach based on the one-dimensional least-squares method (LSM). An STM image is regarded as a realization of a stochastic process and assumed to be a composition of an underlying image and noise. We express the underlying image in terms of a two-dimensional generalized trigonometric polynomial suitable for representing the atomic protrusions in STM images. The optimization of the polynomial is performed by the two-dimensional LSM combined with the power spectral density function estimated by means of the maximum entropy method (MEM) iterative algorithm for two-dimensional signals. The restored images are obtained as the optimum least-squares fitting polynomial which is a continuous surface. We apply this technique to modeled and actual STM data. Results show that the present method yields a reasonable restoration of STM images.

  19. 基于Tanimoto系数的JPEG碎片数据识别方法%A JPEG DATA FRAGMENT IDENTIFICATION METHOD BASED ON TANIMOTO COEFFICIENT

    Institute of Scientific and Technical Information of China (English)

    汤燕彬; 许榕生

    2011-01-01

    当前市面上存在多种功能强大的电子取证工具,但这些取证工具缺乏对特定碎片数据类型的识别.提出满足当前实际需求的一种碎片数据类型识别方法.该方法以数据的字节频率分布为基础,首次将Tanimoto系数应用于JPEG碎片数据类型识别,利用文件类型特有的结构特征以及相邻碎片数据的关联性作为优化参数,提高识别率.实验结果表明,该方法能较好地识别出JPEG碎片数据类型.%Several powerful digital forensics tools have been employed in the progress of obtaining judicial evidences. However, there is lack of identification of specific data fragments. In this article, a method that meets actual demands is proposed, which, based on the byte frequency distribution of data fragments, applies tanimoto coefficient to the identification of JPEG data fragments for the first time and promotes the chances to identifying those fragments by using special structural features and relationship between adjacent fragments as optimization parameters. Experimental results show that this method is able to efficiently identify the JPEG data fragments.

  20. Method and system for manipulating a digital representation of a three-dimensional object

    DEFF Research Database (Denmark)

    2010-01-01

    A method of manipulating a three-dimensional virtual building block model by means of two-dimensional cursor movements, the virtual building block model including a plurality of virtual building blocks each including a number of connection elements for connecting the virtual building block...

  1. Method and system for manipulating a digital representation of a three-dimensional object

    DEFF Research Database (Denmark)

    2010-01-01

    A method of manipulating a three-dimensional virtual building block model by means of two-dimensional cursor movements, the virtual building block model including a plurality of virtual building blocks each including a number of connection elements for connecting the virtual building block with a...

  2. Efficient Evaluation of Casimir Force in Arbitrary Three-dimensional Geometries by Integral Equation Methods

    CERN Document Server

    Xiong, Jie L; Atkins, Phillip; Chew, Weng Cho

    2010-01-01

    In this paper, we generalized the surface integral equation method for the evaluation of Casimir force in arbitrary three-dimensional geometries. Similar to the two-dimensional case, the evaluation of the mean Maxwell stress tensor is cast into solving a series of three-dimensional scattering problems. The formulation and solution of the three-dimensional scattering problem is well-studied in classical computational electromagnetics. This paper demonstrates that this quantum electrodynamic phenomena can be studied using the knowledge and techniques of classical electrodynamics.

  3. Natural position of the head: review of two-dimensional and three-dimensional methods of recording.

    Science.gov (United States)

    Cassi, D; De Biase, C; Tonni, I; Gandolfini, M; Di Blasio, A; Piancino, M G

    2016-04-01

    Both the correct position of the patient's head and a standard system for the acquisition of images are essential for objective evaluation of the facial profile and the skull, and for longitudinal superimposition. The natural position of the head was introduced into orthodontics in the late 1950s, and is used as a postural basis for craniocervical and craniofacial morphological analysis. It can also have a role in the planning of the surgical correction of craniomaxillofacial deformities. The relatively recent transition in orthodontics from 2-dimensional to 3-dimensional imaging, and from analogue to digital technology, has renewed attention in finding a versatile method for the establishment of an accurate and reliable head position during the acquisition of serial records. In this review we discuss definition, clinical applications, and procedures to establish the natural head position and their reproducibility. We also consider methods to reproduce and record the position in two and three planes.

  4. Polymerase chain reaction-restriction fragment length polymorphism method for differentiation of uropathogenic specific protein gene types.

    Science.gov (United States)

    Lai, Yun Mei; Zaw, Myo Thura; Shamsudin, Shamsul Bahari; Lin, Zaw

    2016-08-01

    The putative pathogenicity island (PAI) containing the uropathogenic specific protein (usp) gene and three small open reading frames (orfU1, orfU2, and orfU3) encoding 98, 97, and 96 amino acid proteins is widely distributed among uropathogenic Escherichia coli (UPEC) strains. This PAI was designated as PAIusp. Sequencing analysis of PAIusp has revealed that the usp gene can be divided into two types - uspI and uspII - based on sequence variation at the 3' terminal region and the number and position of orfUs differ from strain to strain. Based on usp gene types and orfU sequential patterns, PAIusp can be divided into four subtypes. Subtyping of PAIusp is a useful method to characterize UPEC strains. In this study, we developed a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to differentiate usp gene types. This method could correctly identify the usp gene type in usp-positive UPEC strains in our laboratory.

  5. Reduced basis ANOVA methods for partial differential equations with high-dimensional random inputs

    Energy Technology Data Exchange (ETDEWEB)

    Liao, Qifeng, E-mail: liaoqf@shanghaitech.edu.cn [School of Information Science and Technology, ShanghaiTech University, Shanghai 200031 (China); Lin, Guang, E-mail: guanglin@purdue.edu [Department of Mathematics & School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907 (United States)

    2016-07-15

    In this paper we present a reduced basis ANOVA approach for partial deferential equations (PDEs) with random inputs. The ANOVA method combined with stochastic collocation methods provides model reduction in high-dimensional parameter space through decomposing high-dimensional inputs into unions of low-dimensional inputs. In this work, to further reduce the computational cost, we investigate spatial low-rank structures in the ANOVA-collocation method, and develop efficient spatial model reduction techniques using hierarchically generated reduced bases. We present a general mathematical framework of the methodology, validate its accuracy and demonstrate its efficiency with numerical experiments.

  6. Reduced basis ANOVA methods for partial differential equations with high-dimensional random inputs

    Science.gov (United States)

    Liao, Qifeng; Lin, Guang

    2016-07-01

    In this paper we present a reduced basis ANOVA approach for partial deferential equations (PDEs) with random inputs. The ANOVA method combined with stochastic collocation methods provides model reduction in high-dimensional parameter space through decomposing high-dimensional inputs into unions of low-dimensional inputs. In this work, to further reduce the computational cost, we investigate spatial low-rank structures in the ANOVA-collocation method, and develop efficient spatial model reduction techniques using hierarchically generated reduced bases. We present a general mathematical framework of the methodology, validate its accuracy and demonstrate its efficiency with numerical experiments.

  7. Fragmented Authoritarianism or Integrated Fragmentation

    DEFF Research Database (Denmark)

    Brødsgaard, Kjeld Erik

    of these business leaders prompts the question of whether we are seeing the development of distinct interest groups that could challenge Party and state authority and create a fragmented polity. However, through the nomenklatura system the Party has an important instrument of control to wield over business groups...... and the Party-state, I suggest the notion of integrated fragmentation....

  8. Electronic coupling calculation and pathway analysis of electron transfer reaction using ab initio fragment-based method. I. FMO-LCMO approach.

    Science.gov (United States)

    Nishioka, Hirotaka; Ando, Koji

    2011-05-28

    By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling T(DA) of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate T(DA). Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable T(DA) for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.

  9. Parametric study on single shot peening by dimensional analysis method incorporated with finite element method

    Institute of Scientific and Technical Information of China (English)

    Xian-Qian Wu; Xi Wang; Yan-Peng Wei; Hong-Wei Song; Chen-Guang Huang

    2012-01-01

    Shot peening is a widely used surface treatment method by generating compressive residual stress near the surface of metallic materials to increase fatigue life and resistance to corrosion fatigue,cracking,etc.Compressive residual stress and dent profile are important factors to evaluate the effectiveness of shot peening process.In this paper,the influence of dimensionless parameters on maximum compressive residual stress and maximum depth of the dent were investigated.Firstly,dimensionless relations of processing parameters that affect the maximum compressive residual stress and the maximum depth of the dent were deduced by dimensional analysis method.Secondly,the influence of each dimensionless parameter on dimensionless variables was investigated by the finite element method.Furthermore,related empirical formulas were given for each dimensionless parameter based on the simulation results.Finally,comparison was made and good agreement was found between the simulation results and the empirical formula,which shows that a useful approach is provided in this paper for analyzing the influence of each individual parameter.

  10. A three dimensional implicit immersed boundary method with application

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Most algorithms of the immersed boundary method originated by Peskin are explicit when it comes to the computation of the elastic forces exerted by the immersed boundary to the fluid. A drawback of such an explicit approach is a severe restriction on the time step size for maintaining numerical stability. An implicit immersed boundary method in two dimensions using the lattice Boltzmann approach has been proposed. This paper reports an extension of the method to three dimensions and its application to simul...

  11. Fragmentation trees reloaded.

    Science.gov (United States)

    Böcker, Sebastian; Dührkop, Kai

    2016-01-01

    Untargeted metabolomics commonly uses liquid chromatography mass spectrometry to measure abundances of metabolites; subsequent tandem mass spectrometry is used to derive information about individual compounds. One of the bottlenecks in this experimental setup is the interpretation of fragmentation spectra to accurately and efficiently identify compounds. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are determined from the data using combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. Fragmentation tree computation does not require spectral or structural databases. To obtain biochemically meaningful trees, one needs an elaborate optimization function (scoring). We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a Maximum A Posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our method SIRIUS 3, performs significantly better than the previous version of our method, as well as other methods for this task. SIRIUS 3 can be a part of an untargeted metabolomics workflow, allowing researchers to investigate unknowns using automated computational methods.Graphical abstractWe present a new scoring for computing fragmentation trees from tandem mass spectrometry data based on Bayesian statistics. The best scoring fragmentation tree most likely explains the molecular formula of the measured parent ion.

  12. Research on a Rotating Machinery Fault Prognosis Method Using Three-Dimensional Spatial Representations

    Directory of Open Access Journals (Sweden)

    Xiaoni Dong

    2016-01-01

    Full Text Available Process models and parameters are two critical steps for fault prognosis in the operation of rotating machinery. Due to the requirement for a short and rapid response, it is important to study robust sensor data representation schemes. However, the conventional holospectrum defined by one-dimensional or two-dimensional methods does not sufficiently present this information in both the frequency and time domains. To supply a complete holospectrum model, a new three-dimensional spatial representation method is proposed. This method integrates improved three-dimensional (3D holospectra and 3D filtered orbits, leading to the integration of radial and axial vibration features in one bearing section. The results from simulation and experimental analysis on a complex compressor show that the proposed method can present the real operational status and clearly reveal early faults, thus demonstrating great potential for condition-based maintenance prediction in industrial machinery.

  13. NONLINEAR GALERKIN METHODS FOR SOLVING TWO DIMENSIONAL NEWTON-BOUSSINESQ EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    GUOBOLING

    1995-01-01

    The nonlinear Galerkin methods for solving two-dimensional Newton-Boussinesq equations are proposed. The existence and uniqueness of global generalized solution of these equations,and the convergence of approximate solutions are also obtained.

  14. Three-dimensional velocity obstacle method for UAV deconflicting maneuvers

    NARCIS (Netherlands)

    Jenie, Y.I.; Van Kampen, E.J.; De Visser, C.C.; Ellerbroek, J.; Hoekstra, J.M.

    2015-01-01

    Autonomous systems are required in order to enable UAVs to conduct self-separation and collision avoidance, especially for flights within the civil airspace system. A method called the Velocity Obstacle Method can provide the necessary situational awareness for UAVs in a dynamic environment, and can

  15. Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays

    Directory of Open Access Journals (Sweden)

    Malloff Chad A

    2004-01-01

    Full Text Available Abstract Background The recent development of array based comparative genomic hybridization (CGH technology provides improved resolution for detection of genomic DNA copy number alterations. In array CGH, generating spotting solution is a multi-step process where bacterial artificial chromosome (BAC clones are converted to replenishable PCR amplified fragments pools (AFP for use as spotting solution in a microarray format on glass substrate. With completion of the human and mouse genome sequencing, large BAC clone sets providing complete genome coverage are available for construction of whole genome BAC arrays. Currently, Southern hybridization, fluorescent in-situ hybridization (FISH, and BAC end sequencing methods are commonly used to identify the initial BAC clone but not the end product used for spotting arrays. The AFP sequencing technique described in this study is a novel method designed to verify the identity of array spotting solution in a high throughput manner. Results We show here that Southern hybridization, FISH, and AFP sequencing can be used to verify the identity of final spotting solutions using less than 10% of the AFP product. Single pass AFP sequencing identified over half of the 960 AFPs analyzed. Moreover, using two vector primers approximately 90% of the AFP spotting solutions can be identified. Conclusions In this feasibility study we demonstrate that current methods for identifying initial BAC clones can be adapted to verify the identity of AFP spotting solutions used in printing arrays. Of these methods, AFP sequencing proves to be the most efficient for large scale identification of spotting solution in a high throughput manner.

  16. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

    Directory of Open Access Journals (Sweden)

    Skolnick Jeffrey

    2008-12-01

    Full Text Available Abstract Background Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TM-align, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9% and coverage (~7% in comparison to those generated by TM-align. Fr-TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr-TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.

  17. Methods and devices for fabricating three-dimensional nanoscale structures

    Science.gov (United States)

    Rogers, John A.; Jeon, Seokwoo; Park, Jangung

    2010-04-27

    The present invention provides methods and devices for fabricating 3D structures and patterns of 3D structures on substrate surfaces, including symmetrical and asymmetrical patterns of 3D structures. Methods of the present invention provide a means of fabricating 3D structures having accurately selected physical dimensions, including lateral and vertical dimensions ranging from 10s of nanometers to 1000s of nanometers. In one aspect, methods are provided using a mask element comprising a conformable, elastomeric phase mask capable of establishing conformal contact with a radiation sensitive material undergoing photoprocessing. In another aspect, the temporal and/or spatial coherence of electromagnetic radiation using for photoprocessing is selected to fabricate complex structures having nanoscale features that do not extend entirely through the thickness of the structure fabricated.

  18. Two-Dimensional Rectangular Stock Cutting Problem and Solution Methods

    Institute of Scientific and Technical Information of China (English)

    Zhao Hui; Yu Liang; Ning Tao; Xi Ping

    2001-01-01

    Optimal layout of rectangular stock cutting is still in great demand from industry for diversified applications. This paper introduces four basic solution methods to the problem: linear programming, dynamic programming, tree search and heuristic approach. A prototype of application software is developed to verify the pros and cons of various approaches.

  19. Discontinuous Galerkin Method for Total Variation Minimization on one-dimensional Inpainting Problem

    CERN Document Server

    Wang, Xijian

    2011-01-01

    This paper is concerned with the numerical minimization of energy functionals in $BV(\\Omega)$ (the space of bounded variation functions) involving total variation for gray-scale 1-dimensional inpainting problem. Applications are shown by finite element method and discontinuous Galerkin method for total variation minimization. We include the numerical examples which show the different recovery image by these two methods.

  20. A Method of Three-Dimensional Recording of Mandibular Movement Based on Two-Dimensional Image Feature Extraction.

    Directory of Open Access Journals (Sweden)

    Fusong Yuan

    Full Text Available To develop a real-time recording system based on computer binocular vision and two-dimensional image feature extraction to accurately record mandibular movement in three dimensions.A computer-based binocular vision device with two digital cameras was used in conjunction with a fixed head retention bracket to track occlusal movement. Software was developed for extracting target spatial coordinates in real time based on two-dimensional image feature recognition. A plaster model of a subject's upper and lower dentition were made using conventional methods. A mandibular occlusal splint was made on the plaster model, and then the occlusal surface was removed. Temporal denture base resin was used to make a 3-cm handle extending outside the mouth connecting the anterior labial surface of the occlusal splint with a detection target with intersecting lines designed for spatial coordinate extraction. The subject's head was firmly fixed in place, and the occlusal splint was fully seated on the mandibular dentition. The subject was then asked to make various mouth movements while the mandibular movement target locus point set was recorded. Comparisons between the coordinate values and the actual values of the 30 intersections on the detection target were then analyzed using paired t-tests.The three-dimensional trajectory curve shapes of the mandibular movements were consistent with the respective subject movements. Mean XYZ coordinate values and paired t-test results were as follows: X axis: -0.0037 ± 0.02953, P = 0.502; Y axis: 0.0037 ± 0.05242, P = 0.704; and Z axis: 0.0007 ± 0.06040, P = 0.952. The t-test result showed that the coordinate values of the 30 cross points were considered statistically no significant. (P<0.05.Use of a real-time recording system of three-dimensional mandibular movement based on computer binocular vision and two-dimensional image feature recognition technology produced a recording accuracy of approximately ± 0.1 mm, and is

  1. Magma Fragmentation

    Science.gov (United States)

    Gonnermann, Helge M.

    2015-05-01

    Magma fragmentation is the breakup of a continuous volume of molten rock into discrete pieces, called pyroclasts. Because magma contains bubbles of compressible magmatic volatiles, decompression of low-viscosity magma leads to rapid expansion. The magma is torn into fragments, as it is stretched into hydrodynamically unstable sheets and filaments. If the magma is highly viscous, resistance to bubble growth will instead lead to excess gas pressure and the magma will deform viscoelastically by fracturing like a glassy solid, resulting in the formation of a violently expanding gas-pyroclast mixture. In either case, fragmentation represents the conversion of potential energy into the surface energy of the newly created fragments and the kinetic energy of the expanding gas-pyroclast mixture. If magma comes into contact with external water, the conversion of thermal energy will vaporize water and quench magma at the melt-water interface, thus creating dynamic stresses that cause fragmentation and the release of kinetic energy. Lastly, shear deformation of highly viscous magma may cause brittle fractures and release seismic energy.

  2. VARIATION METHOD FOR ACOUSTIC WAVE IMAGING OF TWO DIMENSIONAL TARGETS

    Institute of Scientific and Technical Information of China (English)

    冯文杰; 邹振祝

    2003-01-01

    A new way of acoustic wave imaging was investigated. By using the Green function theory a system of integral equations, which linked wave number perturbation function with wave field, was firstly deduced. By taking variation on these integral equations an inversion equation, which reflected the relation between the little variation of wave number perturbation function and that of scattering field, was further obtained. Finally, the perturbation functions of some identical targets were reconstructed, and some properties of the novel method including converging speed, inversion accuracy and the abilities to resist random noise and identify complex targets were discussed. Results of numerical simulation show that the method based on the variation principle has great theoretical and applicable value to quantitative nondestructive evaluation.

  3. Application of Symmetry Methods to Low-Dimensional Heisenberg Magnets

    Directory of Open Access Journals (Sweden)

    Irene G. Bostrem

    2010-04-01

    Full Text Available An account of symmetry is very fruitful in studies of quantum spin systems. In the present paper we demonstrate how to use the spin SU(2 and the point symmetries in optimization of the theoretical condensed matter tools: the exact diagonalization, the renormalization group approach, the cluster perturbation theory. We apply the methods for study of Bose-Einstein condensation in dimerized antiferromagnets, for investigations of magnetization processes and magnetocaloric effect in quantum ferrimagnetic chain.

  4. Solution of (3+1-Dimensional Nonlinear Cubic Schrodinger Equation by Differential Transform Method

    Directory of Open Access Journals (Sweden)

    Hassan A. Zedan

    2012-01-01

    Full Text Available Four-dimensional differential transform method has been introduced and fundamental theorems have been defined for the first time. Moreover, as an application of four-dimensional differential transform, exact solutions of nonlinear system of partial differential equations have been investigated. The results of the present method are compared very well with analytical solution of the system. Differential transform method can easily be applied to linear or nonlinear problems and reduces the size of computational work. With this method, exact solutions may be obtained without any need of cumbersome work, and it is a useful tool for analytical and numerical solutions.

  5. PERTURBATION TRANSFER MATRIX METHOD FOR EIGENDATA OF ONE-DIMENSIONAL STRUCTURAL SYSTEM WITH PARAMETER UNCERTAINTIES

    Institute of Scientific and Technical Information of China (English)

    刘保国; 殷学纲; 蹇开林; 吴永

    2003-01-01

    A general method based on Riccati transfer matrix is presented to calculate the2 nd order perturbations of eigendatas for one-dimensional structural system with parameteruncertainties. The method is applicable to both real and complex eigendatas of any one-dimensional structural system. The formulas for calculating the sensitivity derivatives ofeigendatas based on this method are also presented. The method is applied to theperturbation analysis for the eigendatas of a rotor with gyroscopic moment, and thedifferences between the perturbation results and the accurate calculating results are small.

  6. DD-HDS: A method for visualization and exploration of high-dimensional data.

    Science.gov (United States)

    Lespinats, Sylvain; Verleysen, Michel; Giron, Alain; Fertil, Bernard

    2007-09-01

    Mapping high-dimensional data in a low-dimensional space, for example, for visualization, is a problem of increasingly major concern in data analysis. This paper presents data-driven high-dimensional scaling (DD-HDS), a nonlinear mapping method that follows the line of multidimensional scaling (MDS) approach, based on the preservation of distances between pairs of data. It improves the performance of existing competitors with respect to the representation of high-dimensional data, in two ways. It introduces (1) a specific weighting of distances between data taking into account the concentration of measure phenomenon and (2) a symmetric handling of short distances in the original and output spaces, avoiding false neighbor representations while still allowing some necessary tears in the original distribution. More precisely, the weighting is set according to the effective distribution of distances in the data set, with the exception of a single user-defined parameter setting the tradeoff between local neighborhood preservation and global mapping. The optimization of the stress criterion designed for the mapping is realized by "force-directed placement" (FDP). The mappings of low- and high-dimensional data sets are presented as illustrations of the features and advantages of the proposed algorithm. The weighting function specific to high-dimensional data and the symmetric handling of short distances can be easily incorporated in most distance preservation-based nonlinear dimensionality reduction methods.

  7. Framing Fragmentation

    DEFF Research Database (Denmark)

    Bundgaard, Charlotte

    2009-01-01

    , contain distinctive architectural traits, not only based on rational repetition, but also supporting composition and montage as dynamic concepts. Prefab architecture is an architecture of fragmentation, individualization and changeability, and this sets up new challenges for the architect. This paper...... into separate parts or systems: skeleton, skin, services, internal cladding, etc. Each building part/system is being conceived, produced, delivered and maintained by different construction companies. Basically the building is being fragmented into separate parts living their separate lives. The architect has...... to create architectural meaning and give character to an architecture of fragmentation. Layers are both seen as conceptual as well as material frames which define certain strong properties or meanings in the architectural work. Defining layers is a way of separating and organizing; it both defines...

  8. A new three-dimensional topology optimization method based on moving morphable components (MMCs)

    Science.gov (United States)

    Zhang, Weisheng; Li, Dong; Yuan, Jie; Song, Junfu; Guo, Xu

    2017-04-01

    In the present paper, a new method for solving three-dimensional topology optimization problem is proposed. This method is constructed under the so-called moving morphable components based solution framework. The novel aspect of the proposed method is that a set of structural components is introduced to describe the topology of a three-dimensional structure and the optimal structural topology is found by optimizing the layout of the components explicitly. The standard finite element method with ersatz material is adopted for structural response analysis and the shape sensitivity analysis only need to be carried out along the structural boundary. Compared to the existing methods, the description of structural topology is totally independent of the finite element/finite difference resolution in the proposed solution framework and therefore the number of design variables can be reduced substantially. Some widely investigated benchmark examples, in the three-dimensional topology optimization designs, are presented to demonstrate the effectiveness of the proposed approach.

  9. Dimensional analysis and self-similarity methods for engineers and scientists

    CERN Document Server

    Zohuri, Bahman

    2015-01-01

    This ground-breaking reference provides an overview of key concepts in dimensional analysis, and then pushes well beyond traditional applications in fluid mechanics to demonstrate how powerful this tool can be in solving complex problems across many diverse fields. Of particular interest is the book's coverage of  dimensional analysis and self-similarity methods in nuclear and energy engineering. Numerous practical examples of dimensional problems are presented throughout, allowing readers to link the book's theoretical explanations and step-by-step mathematical solutions to practical impleme

  10. Generalized Kudryashov method for solving some (3+1-dimensional nonlinear evolution equations

    Directory of Open Access Journals (Sweden)

    Md. Shafiqul Islam

    2015-06-01

    Full Text Available In this work, we have applied the generalized Kudryashov methods to obtain the exact travelling wave solutions for the (3+1-dimensional Jimbo-Miwa (JM equation, the (3+1-dimensional Kadomtsev-Petviashvili (KP equation and the (3+1-dimensional Zakharov-Kuznetsov (ZK. The attained solutions show distinct physical configurations. The constraints that will guarantee the existence of specific solutions will be investigated. These solutions may be useful and desirable for enlightening specific nonlinear physical phenomena in genuinely nonlinear dynamical systems.

  11. Computational method for the quantum Hamilton-Jacobi equation: one-dimensional scattering problems.

    Science.gov (United States)

    Chou, Chia-Chun; Wyatt, Robert E

    2006-12-01

    One-dimensional scattering problems are investigated in the framework of the quantum Hamilton-Jacobi formalism. First, the pole structure of the quantum momentum function for scattering wave functions is analyzed. The significant differences of the pole structure of this function between scattering wave functions and bound state wave functions are pointed out. An accurate computational method for the quantum Hamilton-Jacobi equation for general one-dimensional scattering problems is presented to obtain the scattering wave function and the reflection and transmission coefficients. The computational approach is demonstrated by analysis of scattering from a one-dimensional potential barrier. We not only present an alternative approach to the numerical solution of the wave function and the reflection and transmission coefficients but also provide a computational aspect within the quantum Hamilton-Jacobi formalism. The method proposed here should be useful for general one-dimensional scattering problems.

  12. FORMULATIONS OF THE THREE-DIMENSIONAL DISCONTINUOUS DEFORMATION ANALYSIS METHOD

    Institute of Scientific and Technical Information of China (English)

    LIU Jun; KONG Xianjing; LIN Gao

    2004-01-01

    This paper extends the original 2D discontinuous deformation analysis (DDA) method proposed by Shi to 3D cases, and presents the formulations of the 3D DDA. The formulations maintain the characteristics of the original 2D DDA approach. Contacts between the blocks are detected by using Common-Plane (C-P) approach and the non-smooth contact, such as of vertex-to-vertex, vertex-to-edge and edge-to-edge types, can be handled easily based on the C-P method. The matrices of equilibrium equations have been given in detail for programming purposes. The C program codes for the 3D DDA are developed. The ability and accuracy of the formulations and the program are verified by the analytical solutions of several dynamic examples. The robustness and versatility of the algorithms presented in this paper are demonstrated with the aid of an example of scattering of densely packed cubes. Finally, implications and future extensions are discussed.

  13. Two-Dimensional Correlation Method for Polymer Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Herman, Matthew Joseph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-06-08

    Since its introduction by Noda in 1986 two-dimension correlation spectroscopy has been offering polymer scientists an opportunity to look more deeply into collected spectroscopic data. When the spectra are recorded in response to an external perturbation, it is possible to correlate the spectra and expand the information over a separate spectra axis allow for enhancement of spectral resolution, the ability to determine synchronous change, and a unique way to organize observed changes in the spectra into sequential order following a set of three simple rules. By organizing the 2D spectra into synchronous change plots and asynchronous change plots it is possible to correlate change between spectral regions and develop their temporal relationships to one another. With the introduction of moving-window correlation-spectroscopy by Thomas and Richardson in 2000, a method of binning and processing data, it became possible to directly correlate relationships generated in the spectra from the change in the perturbation variable. This method takes advantage of the added resolution of two-dimension spectroscopy and has been applied to study very week transitions found in polymer materials. Appling both of these techniques we are beginning to develop an understanding of how polymers decay under radiolytic aging, to develop a stronger understanding of changes in mechanical properties and the service capabilities of materials.

  14. Multi-Symplectic Splitting Method for Two-Dimensional Nonlinear Schriidinger Equation

    Institute of Scientific and Technical Information of China (English)

    陈亚铭; 朱华君; 宋松和

    2011-01-01

    Using the idea of splitting numerical methods and the multi-symplectic methods, we propose a multisymplectic splitting (MSS) method to solve the two-dimensional nonlinear Schrodinger equation (2D-NLSE) in this paper. It is further shown that the method constructed in this way preserve the global symplectieity exactly. Numerical experiments for the plane wave solution and singular solution of the 2D-NLSE show the accuracy and effectiveness of the proposed method.

  15. Vacuum solutions of five dimensional Einstein equations generated by inverse scattering method

    CERN Document Server

    Tomizawa, S; Yasui, Y; Morisawa, Yoshiyuki; Tomizawa, Shinya; Yasui, Yukinori

    2006-01-01

    We study stationary and axially symmetric two solitonic solutions of five dimensional vacuum Einstein equations by using the inverse scattering method developed by Belinski and Zakharov. In this generation of the solutions, we use five dimensional Minkowski spacetime as a seed. It is shown that if we restrict ourselves to the case of one angular momentum component, the generated solution coincides with a black ring solution with a rotating two sphere which was found by Mishima and Iguchi recently.

  16. Investigation of Three-Dimensional Flow Structure in a Transonic Diffuser by the LIF Method

    OpenAIRE

    小野, 大輔; 半田, 太郎; 青木, 俊之; 益田, 光治

    2007-01-01

    The three-dimensional flow structure induced by normal shock-wave/boundary-layer interaction in a transonic diffuser is investigated by a laser-induced fluorescence (LIF) method. This diagnostic system uses an argon-ion laser as a light source, and target gas is dry nitrogen with iodine seeded as a fluorescence material. The Mach-number distributions in the diffuser are obtained from the measured fluorescence intensity, and the three-dimensional shape of the boundary layers is obtained immedi...

  17. Spectral (Finite) Volume Method for One Dimensional Euler Equations

    Science.gov (United States)

    Wang, Z. J.; Liu, Yen; Kwak, Dochan (Technical Monitor)

    2002-01-01

    Consider a mesh of unstructured triangular cells. Each cell is called a Spectral Volume (SV), denoted by Si, which is further partitioned into subcells named Control Volumes (CVs), indicated by C(sub i,j). To represent the solution as a polynomial of degree m in two dimensions (2D) we need N = (m+1)(m+2)/2 pieces of independent information, or degrees of freedom (DOFs). The DOFs in a SV method are the volume-averaged mean variables at the N CVs. For example, to build a quadratic reconstruction in 2D, we need at least (2+1)(3+1)/2 = 6 DOFs. There are numerous ways of partitioning a SV, and not every partition is admissible in the sense that the partition may not be capable of producing a degree m polynomial. Once N mean solutions in the CVs of a SV are given, a unique polynomial reconstruction can be obtained.

  18. Method and apparatus for two-dimensional spectroscopy

    Science.gov (United States)

    DeCamp, Matthew F.; Tokmakoff, Andrei

    2010-10-12

    Preferred embodiments of the invention provide for methods and systems of 2D spectroscopy using ultrafast, first light and second light beams and a CCD array detector. A cylindrically-focused second light beam interrogates a target that is optically interactive with a frequency-dispersed excitation (first light) pulse, whereupon the second light beam is frequency-dispersed at right angle orientation to its line of focus, so that the horizontal dimension encodes the spatial location of the second light pulse and the first light frequency, while the vertical dimension encodes the second light frequency. Differential spectra of the first and second light pulses result in a 2D frequency-frequency surface equivalent to double-resonance spectroscopy. Because the first light frequency is spatially encoded in the sample, an entire surface can be acquired in a single interaction of the first and second light pulses.

  19. On High Dimensional Searching Spaces and Learning Methods

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Choros, Kazimierz

    2017-01-01

    In data science, there are important parameters that affect the accuracy of the algorithms used. Some of these parameters are: the type of data objects, the membership assignments, and distance or similarity functions. In this chapter we describe different data types , membership functions...... , and similarity functions and discuss the pros and cons of using each of them. Conventional similarity functions evaluate objects in the vector space. Contrarily, Weighted Feature Distance (WFD) functions compare data objects in both feature and vector spaces, preventing the system from being affected by some...... dominant features. Traditional membership functions assign membership values to data objects but impose some restrictions. Bounded Fuzzy Possibilistic Method (BFPM) makes possible for data objects to participate fully or partially in several clusters or even in all clusters. BFPM introduces intervals...

  20. Three dimensional wavefield modeling using the pseudospectral method; Pseudospectral ho ni yoru sanjigen hadoba modeling

    Energy Technology Data Exchange (ETDEWEB)

    Sato, T.; Matsuoka, T. [Japan Petroleum Exploration Corp., Tokyo (Japan); Saeki, T. [Japan National Oil Corp., Tokyo (Japan). Technology Research Center

    1997-05-27

    Discussed in this report is a wavefield simulation in the 3-dimensional seismic survey. With the level of the object of exploration growing deeper and the object more complicated in structure, the survey method is now turning 3-dimensional. There are several modelling methods for numerical calculation of 3-dimensional wavefields, such as the difference method, pseudospectral method, and the like, all of which demand an exorbitantly large memory and long calculation time, and are costly. Such methods have of late become feasible, however, thanks to the advent of the parallel computer. As compared with the difference method, the pseudospectral method requires a smaller computer memory and shorter computation time, and is more flexible in accepting models. It outputs the result in fullwave just like the difference method, and does not cause wavefield numerical variance. As the computation platform, the parallel computer nCUBE-2S is used. The object domain is divided into the number of the processors, and each of the processors takes care only of its share so that parallel computation as a whole may realize a very high-speed computation. By the use of the pseudospectral method, a 3-dimensional simulation is completed within a tolerable computation time length. 7 refs., 3 figs., 1 tab.

  1. High-dimensional Sparse Inverse Covariance Estimation using Greedy Methods

    CERN Document Server

    Johnson, Christopher C; Ravikumar, Pradeep

    2011-01-01

    In this paper we consider the task of estimating the non-zero pattern of the sparse inverse covariance matrix of a zero-mean Gaussian random vector from a set of iid samples. Note that this is also equivalent to recovering the underlying graph structure of a sparse Gaussian Markov Random Field (GMRF). We present two novel greedy approaches to solving this problem. The first estimates the non-zero covariates of the overall inverse covariance matrix using a series of global forward and backward greedy steps. The second estimates the neighborhood of each node in the graph separately, again using greedy forward and backward steps, and combines the intermediate neighborhoods to form an overall estimate. The principal contribution of this paper is a rigorous analysis of the sparsistency, or consistency in recovering the sparsity pattern of the inverse covariance matrix. Surprisingly, we show that both the local and global greedy methods learn the full structure of the model with high probability given just $O(d\\log...

  2. The complex variable meshless local Petrov-Galerkin method of solving two-dimensional potential problems

    Institute of Scientific and Technical Information of China (English)

    Yang Xiu-Li; Dai Bao-Dong; Zhang Wei-Wei

    2012-01-01

    Based on the complex variable moving least-square (CVMLS) approximation and a local symmetric weak form,the complex variable meshless local Petrov-Galerkin (CVMLPG) method of solving two-dimensional potential problems is presented in this paper.In the present formulation,the trial function of a two-dimensional problem is formed with a one-dimensional basis function.The number of unknown coefficients in the trial function of the CVMLS approximation is less than that in the trial function of the moving least-square (MLS) approximation.The essential boundary conditions are imposed by the penalty method.The main advantage of this approach over the conventional meshless local PetrovGalerkin (MLPG) method is its computational efficiency.Several numerical examples are presented to illustrate the implementation and performance of the present CVMLPG method.

  3. The cohomological reduction method for computing n-dimensional cocyclic matrices

    CERN Document Server

    Álvarez, Víctor; Frau, María-Dolores; Real, Pedro

    2012-01-01

    Provided that a cohomological model for G is known, we describe a method for constructing a basis for n-cocycles over G, from which the whole set of n-dimensional cocyclic matrices over G may be straightforwardly calculated. Focusing in the case n=2 (which is of special interest, e.g. for looking for cocyclic Hadamard matrices), our method provides a basis for 2-cocycles in such a way that representative 2-cocycles are calculated all at once, so that there is no need to distinguish between inflation and transgression 2-cocycles (as it has traditionally been the case until now). When n>2, this method provide an uniform way of looking for higher dimensional cocyclic Hadamard matrices for the first time. We illustrate the method with some examples, for n=2,3. In particular, we give some examples of improper 3-dimensional cocyclic Hadamard matrices.

  4. Repositioning the substrate activity screening (SAS) approach as a fragment-based method for identification of weak binders.

    Science.gov (United States)

    Gladysz, Rafaela; Cleenewerck, Matthias; Joossens, Jurgen; Lambeir, Anne-Marie; Augustyns, Koen; Van der Veken, Pieter

    2014-10-13

    Fragment-based drug discovery (FBDD) has evolved into an established approach for "hit" identification. Typically, most applications of FBDD depend on specialised cost- and time-intensive biophysical techniques. The substrate activity screening (SAS) approach has been proposed as a relatively cheap and straightforward alternative for identification of fragments for enzyme inhibitors. We have investigated SAS for the discovery of inhibitors of oncology target urokinase (uPA). Although our results support the key hypotheses of SAS, we also encountered a number of unreported limitations. In response, we propose an efficient modified methodology: "MSAS" (modified substrate activity screening). MSAS circumvents the limitations of SAS and broadens its scope by providing additional fragments and more coherent SAR data. As well as presenting and validating MSAS, this study expands existing SAR knowledge for the S1 pocket of uPA and reports new reversible and irreversible uPA inhibitor scaffolds.

  5. A finite-dimensional reduction method for slightly supercritical elliptic problems

    Directory of Open Access Journals (Sweden)

    Riccardo Molle

    2004-01-01

    Full Text Available We describe a finite-dimensional reduction method to find solutions for a class of slightly supercritical elliptic problems. A suitable truncation argument allows us to work in the usual Sobolev space even in the presence of supercritical nonlinearities: we modify the supercritical term in such a way to have subcritical approximating problems; for these problems, the finite-dimensional reduction can be obtained applying the methods already developed in the subcritical case; finally, we show that, if the truncation is realized at a sufficiently large level, then the solutions of the approximating problems, given by these methods, also solve the supercritical problems when the parameter is small enough.

  6. Development of a three dimensional circulation model based on fractional step method

    Science.gov (United States)

    Abualtayef, Mazen; Kuroiwa, Masamitsu; Seif, Ahmed Khaled; Matsubara, Yuhei; Aly, Ahmed M.; Sayed, Ahmed A.; Sambe, Alioune Nar

    2010-03-01

    A numerical model was developed for simulating a three-dimensional multilayer hydrodynamic and thermodynamic model in domains with irregular bottom topography. The model was designed for examining the interactions between flow and topography. The model was based on the three-dimensional Navier-Stokes equations and was solved using the fractional step method, which combines the finite difference method in the horizontal plane and the finite element method in the vertical plane. The numerical techniques were described and the model test and application were presented. For the model application to the northern part of Ariake Sea, the hydrodynamic.

  7. A numerical method for three-dimensional vortical structure of spiral vortex in wind turbine with two-dimensional velocity data at plural azimuthal angles

    Science.gov (United States)

    Nakayama, Katsuyuki; Mizushima, Lucas Dias; Murata, Junsuke; Maeda, Takao

    2016-06-01

    A numerical method is presented to extract three-dimensional vortical structure of a spiral vortex (wing tip vortex) in a wind turbine, from two-dimensional velocity data at several azimuthal angles. This numerical method contributes to analyze a vortex observed in experiment where three-dimensional velocity field is difficult to be measured. This analysis needs two-dimensional velocity data in parallel planes at different azimuthal angles of a rotating blade, which facilitates the experiment since the angle of the plane does not change. The vortical structure is specified in terms of the invariant flow topology derived from eigenvalues and eigenvectors of three-dimensional velocity gradient tensor and corresponding physical properties. In addition, this analysis enables to investigate not only vortical flow topology but also important vortical features such as pressure minimum and vortex stretching that are derived from the three-dimensional velocity gradient tensor.

  8. Cryopreservation method affects DNA fragmentation in trophectoderm and the speed of re-expansion in bovine blastocysts.

    Science.gov (United States)

    Inaba, Yasushi; Miyashita, Satoshi; Somfai, Tamás; Geshi, Masaya; Matoba, Satoko; Dochi, Osamu; Nagai, Takashi

    2016-04-01

    This study investigated re-expansion dynamics during culture of bovine blastocysts cryopreserved either by slow-freezing or vitrification. Also, the extent and localization of membrane damage and DNA fragmentation in re-expanded embryos were studied. Frozen-thawed embryos showed a significantly lower re-expansion rate during 24 h of post-thawing culture compared to vitrified embryos. Vitrified embryos reached the maximum level of re-expansion rate by 12 h of culture whereas frozen embryos showed a gradual increase in re-expansion rate by 24 h of culture. When assayed by Hoechst/propidium iodide staining there was no difference in the numbers and ratio of membrane damaged cells between re-expanded frozen and vitrified embryos; however, the extent of membrane damage in blastomeres was significantly higher in both groups compared with non-cryopreserved embryos (control). TUNEL assay combined with differential ICM and TE staining revealed a significantly higher number and ratio of TE cells showing DNA-fragmentation in frozen-thawed re-expanded blastocysts compared to vitrified ones; however, vitrification also resulted in an increased extent of DNA fragmentation in TE cells compared with control blastocysts. In frozen-thawed blastocysts increased extent of DNA fragmentation was associated with reduced numbers and proportion of TE cells compared with vitrified and control embryos. The number and ratio of ICM cells and the extent of DNA fragmentation in ICM did not differ among control, frozen and vitrified groups. In conclusion, compared with vitrified embryos, blastocysts preserved by slow-freezing showed a delayed timing of re-expansion which was associated with an increased frequency of DNA fragmentation in TE cells. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. A new method to the(2+1)-dimensional modified KP equation

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    By means of the auxiliary ordinary differential equation method,we have obtained many solitary wave solutions,periodic wave solutions and variable separation solutions for the (2+1)-dimensional KP equation.Using a mixed method,many exact solutions have been obtained.

  10. A superelement-based method for computing unsteady three-dimensional potential flows in hydraulic turbomachines

    NARCIS (Netherlands)

    Kruyt, N.P.; Esch, van B.P.M.; Jonker, J.B.

    1999-01-01

    A numerical method is presented for the computation of unsteady, three-dimensional potential flows in hydraulic pumps and turbines. The superelement method has been extended in order to eliminate slave degrees of freedom not only from the governing Laplace equation, but also from the Kutta condition

  11. A Generalized F-expansion Method and Its Application in High-Dimensional Nonlinear Evolution Equation

    Institute of Scientific and Technical Information of China (English)

    CHEN Jiang; HE Hong-Sheng; YANG Kong-Qing

    2005-01-01

    A generalized F-expansion method is introduced and applied to (3+ 1)-dimensional Kadomstev-Petviashvili(KP) equation. As a result, some new Jacobi elliptic function solutions of the equation are found, from which the trigonometric function solutions and the solitary wave solutions can be obtained. The method can also be extended to other types of nonlinear evolution equations in mathematical physics.

  12. New Generalized Transformation Method and Its Application in Higher-Dimensional Soliton Equation

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A new generalized transformation method is presented to find more exact solutions of nonlinear partial differential equation. As an application of the method, we choose the (3+1)-dimensional breaking soliton equation to illustrate the method. As a result many types of explicit and exact traveling wave solutions, which contain solitary wave solutions, trigonometric function solutions, Jacobian elliptic function solutions, and rational solutions, are obtained. The new method can be extended to other nonlinear partial differential equations in mathematical physics.

  13. Numerical Solution of One-dimensional Telegraph Equation using Cubic B-spline Collocation Method

    Directory of Open Access Journals (Sweden)

    J. Rashidinia

    2014-02-01

    Full Text Available In this paper, a collocation approach is employed for the solution of the one-dimensional telegraph equation based on cubic B-spline. The derived method leads to a tri-diagonal linear system. Computational efficiency of the method is confirmed through numerical examples whose results are in good agreement with theory. The obtained numerical results have been compared with the results obtained by some existing methods to verify the accurate nature of our method.

  14. Extended Complex tanh-Function Method and Exact Solutions to (2+1)-Dimensional Hirota Equation

    Institute of Scientific and Technical Information of China (English)

    ZHAO Hong

    2007-01-01

    In this paper,a new extended complex tanh-function method is presented for constructing traveling wave,non-traveling wave,and coefficient functions' soliton-like solutions of nonlinear equations.This method is nore powerful than the complex tanh-function method [Chaos,Solitons and Fractals 20 (2004) 1037].Abundant new solutions of (2+1)-dimensional Hirota equation are obtained by using this method and symbolic computation system Maple.

  15. The first integral method to study the (2+1)-dimensional Jaulent–Miodek equations

    Indian Academy of Sciences (India)

    M Matinfar; M Eslami; S Roshandel

    2015-10-01

    In this paper, we have presented the applicability of the first integral method for constructing exact solutions of (2+1)-dimensional Jaulent–Miodek equations. The first integral method is a powerful and effective method for solving nonlinear partial differential equations which can be applied to nonintegrable as well as integrable equations. The present paper confirms the significant features of the method employed and exact kink and soliton solutions are constructed through the established first integrals.

  16. Fragmentation of monoclonal antibodies

    Science.gov (United States)

    Vlasak, Josef

    2011-01-01

    Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5–6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule. PMID:21487244

  17. Triggered fragmentation in gravitationally unstable discs: forming fragments at small radii

    Directory of Open Access Journals (Sweden)

    Meru Farzana

    2013-04-01

    Full Text Available We carry out three dimensional radiation hydrodynamical simulations of gravitationally unstable discs using to explore the movement of mass in a disc following its fragmentation. Compared to a more quiescent state before it fragments, the radial velocity of the gas increases by up to a factor of ≈ 2 – 3 after fragmentation. While the mass movement occurs both inwards and outwards, the inwards motion can cause the inner spirals to be suciently dense that they may become unstable and potentially fragment. Consequently, the dynamical behaviour of fragmented discs may cause subsequent fragmentation at smaller radii after an initial fragment has formed in the outer disc.

  18. Two-Dimensional DOA Estimation for Uniform Rectangular Array Using Reduced-Dimension Propagator Method

    Directory of Open Access Journals (Sweden)

    Ming Zhou

    2015-01-01

    Full Text Available A novel algorithm is proposed for two-dimensional direction of arrival (2D-DOA estimation with uniform rectangular array using reduced-dimension propagator method (RD-PM. The proposed algorithm requires no eigenvalue decomposition of the covariance matrix of the receive data and simplifies two-dimensional global searching in two-dimensional PM (2D-PM to one-dimensional local searching. The complexity of the proposed algorithm is much lower than that of 2D-PM. The angle estimation performance of the proposed algorithm is better than that of estimation of signal parameters via rotational invariance techniques (ESPRIT algorithm and conventional PM algorithms, also very close to 2D-PM. The angle estimation error and Cramér-Rao bound (CRB are derived in this paper. Furthermore, the proposed algorithm can achieve automatically paired 2D-DOA estimation. The simulation results verify the effectiveness of the algorithm.

  19. Hydrogeophysical exploration of three-dimensional salinity anomalies with the time-domain electromagnetic method (TDEM)

    Science.gov (United States)

    Bauer-Gottwein, Peter; Gondwe, Bibi N.; Christiansen, Lars; Herckenrath, Daan; Kgotlhang, Lesego; Zimmermann, Stephanie

    2010-01-01

    SummaryThe time-domain electromagnetic method (TDEM) is widely used in groundwater exploration and geological mapping applications. TDEM measures subsurface electrical conductivity, which is strongly correlated with groundwater salinity. TDEM offers a cheap and non-invasive option for mapping saltwater intrusion and groundwater salinization. Traditionally, TDEM data is interpreted using one-dimensional layered-earth models of the subsurface. However, most saltwater intrusion and groundwater salinization phenomena are characterized by three-dimensional anomalies. To fully exploit the information content of TDEM data in this context, three-dimensional modeling of the TDEM response is required. We present a finite-element solution for three-dimensional forward modeling of TDEM responses from arbitrary subsurface electrical conductivity distributions. The solution is benchmarked against standard layered-earth models and previously published three-dimensional forward TDEM modeling results. Concentration outputs from a groundwater flow and salinity transport model are converted to subsurface electrical conductivity using standard petrophysical relationships. TDEM responses over the resulting subsurface electrical conductivity distribution are generated using the three-dimensional TDEM forward model. The parameters of the hydrodynamic model are constrained by matching observed and simulated TDEM responses. As an application example, a field dataset of ground-based TDEM data from an island in the Okavango Delta is presented. Evaporative salt enrichment causes a strong salinity anomaly under the island. We show that the TDEM field data cannot be interpreted in terms of standard one-dimensional layered-earth TDEM models, because of the strongly three-dimensional nature of the salinity anomaly. Three-dimensional interpretation of the field data allows for detailed and consistent mapping of this anomaly and makes better use of the information contained in the TDEM field

  20. A Multifunctional Interface Method for Coupling Finite Element and Finite Difference Methods: Two-Dimensional Scalar-Field Problems

    Science.gov (United States)

    Ransom, Jonathan B.

    2002-01-01

    A multifunctional interface method with capabilities for variable-fidelity modeling and multiple method analysis is presented. The methodology provides an effective capability by which domains with diverse idealizations can be modeled independently to exploit the advantages of one approach over another. The multifunctional method is used to couple independently discretized subdomains, and it is used to couple the finite element and the finite difference methods. The method is based on a weighted residual variational method and is presented for two-dimensional scalar-field problems. A verification test problem and a benchmark application are presented, and the computational implications are discussed.

  1. A new Lagrangian method for three-dimensional steady supersonic flows

    Science.gov (United States)

    Loh, Ching-Yuen; Liou, Meng-Sing

    1993-01-01

    In this report, the new Lagrangian method introduced by Loh and Hui is extended for three-dimensional, steady supersonic flow computation. The derivation of the conservation form and the solution of the local Riemann solver using the Godunov and the high-resolution TVD (total variation diminished) scheme is presented. This new approach is accurate and robust, capable of handling complicated geometry and interactions between discontinuous waves. Test problems show that the extended Lagrangian method retains all the advantages of the two-dimensional method (e.g., crisp resolution of a slip-surface (contact discontinuity) and automatic grid generation). In this report, we also suggest a novel three dimensional Riemann problem in which interesting and intricate flow features are present.

  2. Anisotropic interpolation method of silicon carbide oxidation growth rates for three-dimensional simulation

    Science.gov (United States)

    Šimonka, Vito; Nawratil, Georg; Hössinger, Andreas; Weinbub, Josef; Selberherr, Siegfried

    2017-02-01

    We investigate anisotropical and geometrical aspects of hexagonal structures of Silicon Carbide and propose a direction dependent interpolation method for oxidation growth rates. We compute three-dimensional oxidation rates and perform one-, two-, and three-dimensional simulations for 4H- and 6H-Silicon Carbide thermal oxidation. The rates of oxidation are computed according to the four known growth rate values for the Si- (0 0 0 1) , a- (1 1 2 bar 0) , m- (1 1 bar 0 0) , and C-face (0 0 0 1 bar) . The simulations are based on the proposed interpolation method together with available thermal oxidation models. We additionally analyze the temperature dependence of Silicon Carbide oxidation rates for different crystal faces using Arrhenius plots. The proposed interpolation method is an essential step towards highly accurate three-dimensional oxide growth simulations which help to better understand the anisotropic nature and oxidation mechanism of Silicon Carbide.

  3. A GPU-based calculation using the three-dimensional FDTD method for electromagnetic field analysis.

    Science.gov (United States)

    Nagaoka, Tomoaki; Watanabe, Soichi

    2010-01-01

    Numerical simulations with the numerical human model using the finite-difference time domain (FDTD) method have recently been performed frequently in a number of fields in biomedical engineering. However, the FDTD calculation runs too slowly. We focus, therefore, on general purpose programming on the graphics processing unit (GPGPU). The three-dimensional FDTD method was implemented on the GPU using Compute Unified Device Architecture (CUDA). In this study, we used the NVIDIA Tesla C1060 as a GPGPU board. The performance of the GPU is evaluated in comparison with the performance of a conventional CPU and a vector supercomputer. The results indicate that three-dimensional FDTD calculations using a GPU can significantly reduce run time in comparison with that using a conventional CPU, even a native GPU implementation of the three-dimensional FDTD method, while the GPU/CPU speed ratio varies with the calculation domain and thread block size.

  4. A new complex variable element-free Galerkin method for two-dimensional potential problems

    Institute of Scientific and Technical Information of China (English)

    Cheng Yu-Min; Wang Jian-Fei; Bai Fu-Nong

    2012-01-01

    In this paper,based on the element-free Galerkin (EFG) method and the improved complex variable moving least-square (ICVMLS) approximation,a new meshless method,which is the improved complex variable element-free Galerkin (ICVEFG) method for two-dimensional potential problems,is presented. In the method,the integral weak form of control equations is employed,and the Lagrange multiplier is used to apply the essential boundary conditions.Then the corresponding formulas of the ICVEFG method for two-dimensional potential problems are obtained.Compared with the complex variable moving least-square (CVMLS) approximation proposed by Cheng,the functional in the ICVMLS approximation has an explicit physical meaning.Furthermore,the ICVEFG method has greater computational precision and efficiency.Three numerical examples are given to show the validity of the proposed method.

  5. A new method for three-dimensional laparoscopic ultrasound model reconstruction

    DEFF Research Database (Denmark)

    Fristrup, C W; Pless, T; Durup, J;

    2004-01-01

    was to perform a volumetric test and a clinical feasibility test of a new 3D method using standard laparoscopic ultrasound equipment. METHODS: Three-dimensional models were reconstructed from a series of two-dimensional ultrasound images using either electromagnetic tracking or a new 3D method. The volumetric...... accuracy of the new method was tested ex vivo, and the clinical feasibility was tested on a small series of patients. RESULTS: Both electromagnetic tracked reconstructions and the new 3D method gave good volumetric information with no significant difference. Clinical use of the new 3D method showed...... accurate models comparable to findings at surgery and pathology. CONCLUSIONS: The use of the new 3D method is technically feasible, and its volumetrically, accurate compared to 3D with electromagnetic tracking....

  6. Evaluation of left ventricular rotation by two-dimensional speckle tracking method and real-time three-dimensional echocardiography: comparison with MRI tagging method.

    Science.gov (United States)

    Hayashi, Hidetaka; Izumi, Chisato; Takahashi, Shuichi; Uchikoshi, Masato; Yamazaki, Ryou; Asanuma, Toshihiko; Ishikura, Fuminobu; Beppu, Shintaro; Nakatani, Satoshi

    2011-09-01

    Recently, it has become possible to evaluate left ventricular (LV) torsion by two-dimensional (2D) speckle tracking images. However, LV torsion is a three-dimensional (3D) performance, which per se cannot be assessed by the 2D speckle tracking method. The present study investigated the accuracy of the 2D speckle tracking method and real-time 3D echocardiography in measuring LV rotation, comparing with the MRI tagging method. We assessed LV apical rotation using the 2D speckle tracking method, real-time 3D echocardiography, and MRI tagging method in 26 normal subjects, and compared the results of these three methods. LV apical rotation was measured just before the level in which the posterior papillary muscle was absorbed into the free wall. The degree of LV apical rotation evaluated by the 2D speckle tracking method (Δθ 2D) was significantly smaller than that evaluated by 3D echocardiography (Δθ 3D) and the MRI tagging method (Δθ MRI) (Δθ 2D 7.3 ± 2.8°; Δθ 3D 8.8 ± 3.4°; Δθ MRI 9.0 ± 3.4°; Δθ 2D vs. Δθ 3D, p = 0.0001; Δθ 2D vs. Δθ MRI, p speckle tracking method compared with the MRI tagging method, whereas it could be precisely measured by 3D echocardiography.

  7. AFLP fragment isolation technique as a method to produce random sequences for single nucleotide polymorphism discovery in the green turtle, Chelonia mydas.

    Science.gov (United States)

    Roden, Suzanne E; Dutton, Peter H; Morin, Phillip A

    2009-01-01

    The green sea turtle, Chelonia mydas, was used as a case study for single nucleotide polymorphism (SNP) discovery in a species that has little genetic sequence information available. As green turtles have a complex population structure, additional nuclear markers other than microsatellites could add to our understanding of their complex life history. Amplified fragment length polymorphism technique was used to generate sets of random fragments of genomic DNA, which were then electrophoretically separated with precast gels, stained with SYBR green, excised, and directly sequenced. It was possible to perform this method without the use of polyacrylamide gels, radioactive or fluorescent labeled primers, or hybridization methods, reducing the time, expense, and safety hazards of SNP discovery. Within 13 loci, 2547 base pairs were screened, resulting in the discovery of 35 SNPs. Using this method, it was possible to yield a sufficient number of loci to screen for SNP markers without the availability of prior sequence information.

  8. Quadrature Rules and Iterative Method for Numerical Solution of Two-Dimensional Fuzzy Integral Equations

    Directory of Open Access Journals (Sweden)

    S. M. Sadatrasoul

    2014-01-01

    Full Text Available We introduce some generalized quadrature rules to approximate two-dimensional, Henstock integral of fuzzy-number-valued functions. We also give error bounds for mappings of bounded variation in terms of uniform modulus of continuity. Moreover, we propose an iterative procedure based on quadrature formula to solve two-dimensional linear fuzzy Fredholm integral equations of the second kind (2DFFLIE2, and we present the error estimation of the proposed method. Finally, some numerical experiments confirm the theoretical results and illustrate the accuracy of the method.

  9. Semiclassical "Divide-and-Conquer" Method for Spectroscopic Calculations of High Dimensional Molecular Systems

    Science.gov (United States)

    Ceotto, Michele; Di Liberto, Giovanni; Conte, Riccardo

    2017-07-01

    A new semiclassical "divide-and-conquer" method is presented with the aim of demonstrating that quantum dynamics simulations of high dimensional molecular systems are doable. The method is first tested by calculating the quantum vibrational power spectra of water, methane, and benzene—three molecules of increasing dimensionality for which benchmark quantum results are available—and then applied to C60 , a system characterized by 174 vibrational degrees of freedom. Results show that the approach can accurately account for quantum anharmonicities, purely quantum features like overtones, and the removal of degeneracy when the molecular symmetry is broken.

  10. A discontinuous Galerkin method for two-dimensional PDE models of Asian options

    Science.gov (United States)

    Hozman, J.; Tichý, T.; Cvejnová, D.

    2016-06-01

    In our previous research we have focused on the problem of plain vanilla option valuation using discontinuous Galerkin method for numerical PDE solution. Here we extend a simple one-dimensional problem into two-dimensional one and design a scheme for valuation of Asian options, i.e. options with payoff depending on the average of prices collected over prespecified horizon. The algorithm is based on the approach combining the advantages of the finite element methods together with the piecewise polynomial generally discontinuous approximations. Finally, an illustrative example using DAX option market data is provided.

  11. Multi-dimensional and complicated electromagnetic interference hardware-in-the-loop simulation method

    Institute of Scientific and Technical Information of China (English)

    Shuxia Guo; Yafeng Wang; Ruibing Liu; Ying Gao

    2015-01-01

    A typical electronic communication system, such as GPS receiver, unmanned aerial vehicle’s (UAV’s) data link, and radar, faces multi-dimensional and complicated electromagnetic interference in operating environment. To measure the anti-interference performance of the electronic communication system in the complicated electromagnetic interference environment, a method of multi-dimensional and complicated electromagnetic in-terference hardware-in-the-loop simulation in an anechoic room is proposed. It takes into account the characteristics of interference signals and the positional relationship among interference, the re-ceiver and the transmitter of the electronic communication system. It uses the grey relational method and the angular domain map-ping error correction method to control the relevant parameters, the microwave switch and so on, thus achieving the approximately actual mapping of the outdoor multi-dimensional and complicated electromagnetic interference in the anechoic room. To verify the ef-fectiveness of this method, the multi-dimensional and complicated electromagnetic interference of the UAV’s data link is simulated as an example. The results show that the degree of correlation between the calculated signal to interference ratio of the data link receiver in the actual scene and the measured signal to interfer-ence ratio of the data link receiver simulated with this method in the anechoic room is 0.968 1, proving that the method is effective for simulating the complicated electromagnetic interference.

  12. Computational hydrodynamics of animal swimming: boundary element method and three-dimensional vortex wake structure.

    Science.gov (United States)

    Cheng, J Y; Chahine, G L

    2001-12-01

    The slender body theory, lifting surface theories, and more recently panel methods and Navier-Stokes solvers have been used to study the hydrodynamics of fish swimming. This paper presents progress on swimming hydrodynamics using a boundary integral equation method (or boundary element method) based on potential flow model. The unsteady three-dimensional BEM code 3DynaFS that we developed and used is able to model realistic body geometries, arbitrary movements, and resulting wake evolution. Pressure distribution over the body surface, vorticity in the wake, and the velocity field around the body can be computed. The structure and dynamic behavior of the vortex wakes generated by the swimming body are responsible for the underlying fluid dynamic mechanisms to realize the high-efficiency propulsion and high-agility maneuvering. Three-dimensional vortex wake structures are not well known, although two-dimensional structures termed 'reverse Karman Vortex Street' have been observed and studied. In this paper, simulations about a swimming saithe (Pollachius virens) using our BEM code have demonstrated that undulatory swimming reduces three-dimensional effects due to substantially weakened tail tip vortex, resulting in a reverse Karman Vortex Street as the major flow pattern in the three-dimensional wake of an undulating swimming fish.

  13. Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data.

    Science.gov (United States)

    Weber, Lukas M; Robinson, Mark D

    2016-12-01

    Recent technological developments in high-dimensional flow cytometry and mass cytometry (CyTOF) have made it possible to detect expression levels of dozens of protein markers in thousands of cells per second, allowing cell populations to be characterized in unprecedented detail. Traditional data analysis by "manual gating" can be inefficient and unreliable in these high-dimensional settings, which has led to the development of a large number of automated analysis methods. Methods designed for unsupervised analysis use specialized clustering algorithms to detect and define cell populations for further downstream analysis. Here, we have performed an up-to-date, extensible performance comparison of clustering methods for high-dimensional flow and mass cytometry data. We evaluated methods using several publicly available data sets from experiments in immunology, containing both major and rare cell populations, with cell population identities from expert manual gating as the reference standard. Several methods performed well, including FlowSOM, X-shift, PhenoGraph, Rclusterpp, and flowMeans. Among these, FlowSOM had extremely fast runtimes, making this method well-suited for interactive, exploratory analysis of large, high-dimensional data sets on a standard laptop or desktop computer. These results extend previously published comparisons by focusing on high-dimensional data and including new methods developed for CyTOF data. R scripts to reproduce all analyses are available from GitHub (https://github.com/lmweber/cytometry-clustering-comparison), and pre-processed data files are available from FlowRepository (FR-FCM-ZZPH), allowing our comparisons to be extended to include new clustering methods and reference data sets. © 2016 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of ISAC.

  14. A novel computing three-dimensional differential transform method for solving fuzzy partial differential equations

    OpenAIRE

    Farshid Mirzaee; Mohammad Komak Yari

    2016-01-01

    In this paper, we introduce three-dimensional fuzzy differential transform method and we utilize it to solve fuzzy partial differential equations. This technique is a successful method because of reducing such problems to solve a system of algebraic equations; so, the problem can be solved directly. A considerable advantage of this method is to obtain the analytical solutions if the equation has an exact solution that is a polynomial function. Numerical examples are included to demonstrate th...

  15. The CABARET method for a weakly compressible fluid flows in one- and two-dimensional implementations

    Science.gov (United States)

    Kulikov, Yu M.; Son, E. E.

    2016-11-01

    The CABARET method implementation for a weakly compressible fluid flow is in the focus of present paper. Testing both one-dimensional pressure balancing problem and a classical plane Poiseuille flow, we analyze this method in terms of discontinuity resolution, dispersion and dissipation. The method is proved to have an adequate convergence to an analytical solution for a velocity profile. We also show that a flow formation process represents a set of self-similar solutions under varying pressure differential and sound speed.

  16. Three-dimensional adaptive coordinate transformations for the Fourier modal method.

    Science.gov (United States)

    Küchenmeister, Jens

    2014-01-27

    The concepts of adaptive coordinates and adaptive spatial resolution have proved to be a valuable tool to improve the convergence characteristics of the Fourier Modal Method (FMM), especially for metallo-dielectric systems. Yet, only two-dimensional adaptive coordinates were used so far. This paper presents the first systematic construction of three-dimensional adaptive coordinate and adaptive spatial resolution transformations in the context of the FMM. For that, the construction of a three-dimensional mesh for a periodic system consisting of two layers of mutually rotated, metallic crosses is discussed. The main impact of this method is that it can be used with any classic FMM code that is able to solve the large FMM eigenproblem. Since the transformation starts and ends in a Cartesian mesh, only the transformed material tensors need to be computed and entered into an existing FMM code.

  17. DUAL RECIPROCITY HYBRID BOUNDARY NODE METHOD FOR THREE-DIMENSIONAL ELASTICITY WITH BODY FORCE

    Institute of Scientific and Technical Information of China (English)

    Fei Yan; Yuanhan Wang; Yu Miao; Fei Tan

    2008-01-01

    Combining Dual Reciprocity Method (DRM) with Hybrid Bòundary Node Method(HBNM),the Dual Reciprocity Hybrid Boundary Node Method (DRHBNM) is developed for three-dimensional linear elasticity problems with body force.This method can be used to solve the elasticity problems with body force without domain integral,which is inevitable by HBNM.To demonstrate the versatility and the fast convergence of this method,some numerical examples of 3-D elasticity problems with body forces are examined.The computational results show that the present method is effective and can be widely applied in solving practical engineering problems.

  18. Unsupervised nonlinear dimensionality reduction machine learning methods applied to multiparametric MRI in cerebral ischemia: preliminary results

    Science.gov (United States)

    Parekh, Vishwa S.; Jacobs, Jeremy R.; Jacobs, Michael A.

    2014-03-01

    The evaluation and treatment of acute cerebral ischemia requires a technique that can determine the total area of tissue at risk for infarction using diagnostic magnetic resonance imaging (MRI) sequences. Typical MRI data sets consist of T1- and T2-weighted imaging (T1WI, T2WI) along with advanced MRI parameters of diffusion-weighted imaging (DWI) and perfusion weighted imaging (PWI) methods. Each of these parameters has distinct radiological-pathological meaning. For example, DWI interrogates the movement of water in the tissue and PWI gives an estimate of the blood flow, both are critical measures during the evolution of stroke. In order to integrate these data and give an estimate of the tissue at risk or damaged; we have developed advanced machine learning methods based on unsupervised non-linear dimensionality reduction (NLDR) techniques. NLDR methods are a class of algorithms that uses mathematically defined manifolds for statistical sampling of multidimensional classes to generate a discrimination rule of guaranteed statistical accuracy and they can generate a two- or three-dimensional map, which represents the prominent structures of the data and provides an embedded image of meaningful low-dimensional structures hidden in their high-dimensional observations. In this manuscript, we develop NLDR methods on high dimensional MRI data sets of preclinical animals and clinical patients with stroke. On analyzing the performance of these methods, we observed that there was a high of similarity between multiparametric embedded images from NLDR methods and the ADC map and perfusion map. It was also observed that embedded scattergram of abnormal (infarcted or at risk) tissue can be visualized and provides a mechanism for automatic methods to delineate potential stroke volumes and early tissue at risk.

  19. Quantitative analysis of scaling error compensation methods in dimensional X-ray computed tomography

    DEFF Research Database (Denmark)

    Müller, P.; Hiller, Jochen; Dai, Y.;

    2015-01-01

    and repeatability of dimensional and geometrical measurements. The aim of this paper is to discuss different methods for the correction of scaling errors and to quantify their influence on dimensional measurements. Scaling errors occur first and foremost in CT systems with no built-in compensation of positioning...... errors of the manipulator system (magnification axis). This article also introduces a new compensation method for scaling errors using a database of reference scaling factors and discusses its advantages and disadvantages. In total, three methods for the correction of scaling errors – using the CT ball...... geometry and is made of brass, which makes its measurements with CT challenging. It is shown that each scaling error correction method results in different deviations between CT measurements and reference measurements from a CMM. Measurement uncertainties were estimated for each method, taking...

  20. Nested chromosomal fragmentation in yeast using the meganuclease I-Sce I: a new method for physical mapping of eukaryotic genomes.

    Science.gov (United States)

    Thierry, A; Dujon, B

    1992-11-11

    We have developed a new method for the physical mapping of genomes and the rapid sorting of genomic libraries which is based on chromosome fragmentation by the meganuclease I-Sce I, the first available member of a new class of endonucleases with very long recognition sequences. I-Sce I allows complete cleavage at a single artificially inserted site in an entire genome. Sites can be inserted by homologous recombination using specific cassettes containing selectable markers or, at random, using transposons. This method has been applied to the physical mapping of chromosome XI (620 kb) of Saccharomyces cerevisi and to the sorting of a cosmid library. Our strategy has potential applications to various genome mapping projects. A set of transgenic yeast strains carrying the I-Sce I sites at various locations along a chromosome defines physical intervals against which new genes, DNA fragments or clones can be mapped directly by simple hybridizations.

  1. Anti-HIV activity of HEPT, TIBO, and cyclic urea derivatives: structure-property studies, focused combinatorial library generation, and hits selection using substructural molecular fragments method.

    Science.gov (United States)

    Solov'ev, V P; Varnek, A

    2003-01-01

    Substructural molecular fragments (SMF) method [Solov'ev, V. P.; Varnek, A.; Wipff, G. J. Chem. Inf. Comput. Sci. 2000, 40, 847-858] was applied to assess anti-HIV activity for large data sets for three families of compounds: 1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives, tetrahydroimidazobenzodiazepinone (TIBO) derivatives, and cyclic urea (CU) derivatives. The SMF method uses 49 types of topological descriptors (atom/bond sequences and "augmented atoms") which, being coupled with 3 linear and nonlinear fitting equations, allows the user to generate up to 147 structure-property models. For each family of compounds, the modeling was performed on several training sets followed by the validation calculations where three best fit models were applied. Calculated activities well reproduce available experimental data. On the basis of the "optimal" molecular fragments, the focused combinatorial library containing 252 virtual HEPT derivatives has been generated. Its filtering led to several hits potentially possessing anti-HIV activity.

  2. Distinguishing between the bone fragments of medium-sized mammals and children. A histological identification method for archaeology.

    Science.gov (United States)

    Cuijpers, Saddha A G F M

    2009-06-01

    In archaeology, it is not always possible to identify bone fragments. A novel approach was chosen to assess the potential of histology as an identification tool. Instead of studying a few bones of different categories from many species, this study concentrated on the diaphyses of long bones in four species of comparable size which are relevant to archaeology; young humans, pigs, sheep and goats, to broaden the insight into variations in diaphyseal bone structure within and between these species. A general difference in the primary bone structure was found between children older than one year and the three medium-sized mammals, namely lamellar vs. fibro-lamellar primary bone. Although, the diaphyseal bone structure of children below the age of one year also showed (developing) fibro-lamellar bone, its composition was distinctive from the medium-sized mammals. A difference in the secondary bone structure was also observed. Connecting (Volkmann's) canals, giving the secondary bone a reticular aspect, were seen in the medium-sized mammals but not in the young human long bones. To confirm the validity and applicability of these observed histological differences, a blind test was conducted on 14 diaphyseal fragments of identified long bones from archaeological sites. The results were very promising. All the bone fragments were correctly attributed using the difference in primary bone structure, even when the bone was severely degraded.

  3. A New Ensemble Method with Feature Space Partitioning for High-Dimensional Data Classification

    Directory of Open Access Journals (Sweden)

    Yongjun Piao

    2015-01-01

    Full Text Available Ensemble data mining methods, also known as classifier combination, are often used to improve the performance of classification. Various classifier combination methods such as bagging, boosting, and random forest have been devised and have received considerable attention in the past. However, data dimensionality increases rapidly day by day. Such a trend poses various challenges as these methods are not suitable to directly apply to high-dimensional datasets. In this paper, we propose an ensemble method for classification of high-dimensional data, with each classifier constructed from a different set of features determined by partitioning of redundant features. In our method, the redundancy of features is considered to divide the original feature space. Then, each generated feature subset is trained by a support vector machine, and the results of each classifier are combined by majority voting. The efficiency and effectiveness of our method are demonstrated through comparisons with other ensemble techniques, and the results show that our method outperforms other methods.

  4. Mechanistic aspects of the oxidative and reductive fragmentation of n-nitrosoamines: a new method for generating nitrenium cations, amide anions, and aminyl radicals

    OpenAIRE

    Piech, Krzysztof; Bally, Thomas; Sikora, Adam; Marcinek, Andrzej

    2008-01-01

    A new method for investigating the mechanisms of nitric oxide release from NO donors under oxidative and reductive conditions is presented. Based on the fragmentation of N-nitrosoamines, it allows generation and spectroscopic characterization of nitrenium cations, amide anions, and aminyl radicals. X-irradiation of N-nitroso-N,N-diphenylamine 1 in Ar matrices at 10 K is found to yield the corresponding radical ions, which apparently undergo spontaneous loss of NO° under the conditions of this...

  5. Calculating Two-Dimensional Spectra with the Mixed Quantum-Classical Ehrenfest Method

    NARCIS (Netherlands)

    van der Vegte, C. P.; Dijkstra, A. G.; Knoester, J.; Jansen, T. L. C.

    2013-01-01

    We present a mixed quantum-classical simulation approach to calculate two-dimensional spectra of coupled two-level electronic model systems. We include the change in potential energy of the classical system due to transitions in the quantum system using the Ehrenfest method. We study how this

  6. Geotechnical applications of a two-dimensional elastodynamic displacement discontinuity method

    CSIR Research Space (South Africa)

    Siebrits, E

    1993-12-01

    Full Text Available A general two-dimensional elastodynamic displacement discontinuity method is used to model a variety of application problems. The plane strain problems are: the elastodynamic motions induced on a cavity by shear slip on a nearby crack; the dynamic...

  7. Methods of numerical analysis of 1-dimensional 2-body problem in Wheeler-Feynman electrodynamics

    Science.gov (United States)

    Klimenko, S. V.; Nikitin, I. N.; Urazmetov, W. F.

    2000-04-01

    Numerical methods for solution of differential equations with deviating arguments describing 1-dimensional ultra-relativistic scattering of 2 identical charged particles in classical electrodynamics with half-retarded/halfadvanced interaction (Wheeler and Feynman, 1949) are developed. A bifurcation of solutions and violation of their reflectional symmetries in the region of velocities v>0.937c are found in numerical analysis.

  8. Assessment of Volumetric Changes With a Best-Fit Method in Three-Dimensional Stereophotograms

    NARCIS (Netherlands)

    Ongkosuwito, E. M.; Goos, J. A. C.; Wattel, E.; van der Wal, K. G. H.; van Adrichem, L. N. A.; van Neck, J. W.

    2012-01-01

    Objective: Different three-dimensional stereophotogrammetry systems and analyzing methods exist that often use landmarks for comparison. Measurement errors in landmark or surface comparison are mostly within 1 mm, which seems clinically acceptable. The aim of this study was to validate a three-dimen

  9. Assessment of volumetric changes with a best-fit method in three-dimensional stereophotograms

    NARCIS (Netherlands)

    E.M. Ongkosuwito (Edwin); J.A.C. Goos (Jacqueline); E. Wattel; K.G.H. van der Wal (Karel); L.N.A. van Adrichem (Léon); J.W. van Neck (Han)

    2012-01-01

    textabstractObjective: Different three-dimensional stereophotogrammetry systems and analyzing methods exist that often use landmarks for comparison. Measurement errors in landmark or surface comparison are mostly within 1 mm, which seems clinically acceptable. The aim of this study was to validate a

  10. Multisymplectic Structure-Preserving in Simple Finite Element Method in High Dimensional Case

    Institute of Scientific and Technical Information of China (English)

    BAI Yong-Qiang; LIU Zhen; PEI Ming; ZHENG Zhu-Jun

    2003-01-01

    In this paper, we study a finite element scheme of some semi-linear elliptic boundary value problems inhigh-dimensional space. With uniform mesh, we find that, the numerical scheme derived from finite element method cankeep a preserved multisymplectic structure.

  11. A greedy method for reconstructing polycrystals from three-dimensional X-ray diffraction data

    DEFF Research Database (Denmark)

    Kulshreshth, Arun Kumar; Alpers, Andreas; Herman, Gabor T.

    2009-01-01

    An iterative search method is proposed for obtaining orientation maps inside polycrystals from three-dimensional X-ray diffraction (3DXRD) data. In each step, detector pixel intensities are calculated by a forward model based on the current estimate of the orientation map. The pixel at which the ...

  12. Calculating Two-Dimensional Spectra with the Mixed Quantum-Classical Ehrenfest Method

    NARCIS (Netherlands)

    van der Vegte, C. P.; Dijkstra, A. G.; Knoester, J.; Jansen, T. L. C.

    2013-01-01

    We present a mixed quantum-classical simulation approach to calculate two-dimensional spectra of coupled two-level electronic model systems. We include the change in potential energy of the classical system due to transitions in the quantum system using the Ehrenfest method. We study how this feedba

  13. 3-Dimensional and Interactive Istanbul University Virtual Laboratory Based on Active Learning Methods

    Science.gov (United States)

    Ince, Elif; Kirbaslar, Fatma Gulay; Yolcu, Ergun; Aslan, Ayse Esra; Kayacan, Zeynep Cigdem; Alkan Olsson, Johanna; Akbasli, Ayse Ceylan; Aytekin, Mesut; Bauer, Thomas; Charalambis, Dimitris; Gunes, Zeliha Ozsoy; Kandemir, Ceyhan; Sari, Umit; Turkoglu, Suleyman; Yaman, Yavuz; Yolcu, Ozgu

    2014-01-01

    The purpose of this study is to develop a 3-dimensional interactive multi-user and multi-admin IUVIRLAB featuring active learning methods and techniques for university students and to introduce the Virtual Laboratory of Istanbul University and to show effects of IUVIRLAB on students' attitudes on communication skills and IUVIRLAB. Although…

  14. Solution to the one-dimensional Rayleigh-Plesset equation by the Differential Transform method

    CERN Document Server

    Narendranath, Aneet Dharmavaram

    2016-01-01

    The differential transform method (DTM) is a relatively new technique that may be used to find a series solution to differential equations (both linear and nonlinear) through an iterative process. This brief manuscript is an initial effort in applying the DTM to provide a series solution to the one-dimensional Rayleigh-Plesset equation (RPE).

  15. Bespoke Fragments

    DEFF Research Database (Denmark)

    Kruse Aagaard, Anders

    2016-01-01

    The Ph.D. -project Bespoke Fragments seeks to explore and utilise the space emerging between the potentials of digital drawing and fabrication and the field of materials and their properties and capacities. Within this span, the project is situated in a shuttling between the virtual and the actual......, the emergence of virtual space is no longer limited to the computer's digital world, but extends into the materials' world. Creation and uncertainty are allowed as virtual parameters in both the digital and reality. Based on this notion the project suggests utilising that exact potential to develop...

  16. Identification of Anthropogenic Compounds in Urban Environments and Evaluation of Automated Methods for Reading Fragmentation-A Case of River Water.

    Science.gov (United States)

    Yamamoto, Atsushi; Matsumoto, Naoko; Kawasaki, Hideya; Arakawa, Ryuichi

    2016-01-01

    A workflow based on liquid chromatography/high-resolution mass spectrometry (LC/HR-MS) was applied for the identification of compounds in urban environments. Substances extracted by solid-phase extraction from river water were wholly analyzed by LC/HR-MS without any purification. Fragmentation in collision-induced dissociation was manually studied for the 20 most intense ions in positive- and negative-ion electrospray ionization with accurate mass determination at a resolution of 100,000. Sixteen anthropogenic compounds in the extract were identified and confirmed using standard reference reagents. These compounds consisted of pharmaceuticals, surfactants, flame retardants, and industrial intermediates. The majority of the compounds are common in our daily life. In the identification process, two automated methods, MAGMa and MetFrag/MetFusion, for reading fragmentation were evaluated for the sixteen compounds. Although automated methods could be used to retrieve the correct molecular structures in most cases, they could not always be promoted to the top rank. Automated methods have yet to be a complete solution for identifying chemical compounds, but will considerably reduce the burden for humans in reading fragmentation.

  17. A new Riccati equation rational expansion method and its application to (2 + 1)-dimensional Burgers equation

    Energy Technology Data Exchange (ETDEWEB)

    Wang Qi [Department of Applied Mathematics, Dalian University of Technology, Dalian 116024 (China); Department of Physics, Shanghai Jiao Tong University, Shanghai 200030 (China); Chen Yong [M.M. Key Lab, Chinese Academy of Sciences, Beijing 100080 (China); Nonlinear Science Center and Department of Mathematics, Ningbo University, Ningbo 315211 (China); Department of Physics, Shanghai Jiao Tong University, Shanghai 200030 (China); E-mail: chenyong@dlut.edu.cn; Zhang Hongqing [Department of Applied Mathematics, Dalian University of Technology, Dalian 116024 (China); Department of Physics, Shanghai Jiao Tong University, Shanghai 200030 (China)

    2005-09-01

    In this paper, we present a new Riccati equation rational expansion method to uniformly construct a series of exact solutions for nonlinear evolution equations. Compared with most existing tanh methods and other sophisticated methods, the proposed method not only recover some known solutions, but also find some new and general solutions. The solutions obtained in this paper include rational triangular periodic wave solutions, rational solitary wave solutions and rational wave solutions. The efficiency of the method can be demonstrated on (2 + 1)-dimensional Burgers equation.

  18. Variational Homotopy Perturbation Method for Solving Higher Dimensional Initial Boundary Value Problems

    Directory of Open Access Journals (Sweden)

    Muhammad Aslam Noor

    2008-01-01

    Full Text Available We suggest and analyze a technique by combining the variational iteration method and the homotopy perturbation method. This method is called the variational homotopy perturbation method (VHPM. We use this method for solving higher dimensional initial boundary value problems with variable coefficients. The developed algorithm is quite efficient and is practically well suited for use in these problems. The proposed scheme finds the solution without any discritization, transformation, or restrictive assumptions and avoids the round-off errors. Several examples are given to check the reliability and efficiency of the proposed technique.

  19. Solution of D dimensional Dirac equation for coulombic potential using NU method and its thermodynamics properties

    Energy Technology Data Exchange (ETDEWEB)

    Cari, C., E-mail: cari@staff.uns.ac.id; Suparmi, A., E-mail: soeparmi@staff.uns.ac.id; Yunianto, M., E-mail: muhtaryunianto@staff.uns.ac.id; Husein, A. S. [Physics Department, Faculty of Mathematics and Science, SebelasMaret University, Jl. Ir. Sutami 36A Kentingan Surakarta 57126 (Indonesia)

    2016-02-08

    The analytical solution of Ddimensional Dirac equation for Coulombic potential is investigated using Nikiforov-Uvarov method. The D dimensional relativistic energy spectra are obtained from relativistic energy eigenvalue equation by using Mat Lab software.The corresponding D dimensional radial wave functions are formulated in the form of generalized Jacobi and Laguerre Polynomials. In the non-relativistic limit, the relativistic energy equation reduces to the non-relativistic energy which will be applied to determine some thermodynamical properties of the system. The thermodynamical properties of the system are expressed in terms of error function and imaginary error function.

  20. Complete denture base assessments using holograms: dimensional alterations after different activation methods

    Science.gov (United States)

    Dughir, Ciprian; Popovschi, Ana Maria; Cojocariu, Andreea Codruta; Topala, Florin Ionel; Negrutiu, Meda Lavinia; Sinescu, Cosmin; de Sabata, Aldo; Duma, Virgil-Florin

    2016-03-01

    Holography is a well-developed method with a large range of applications, including dentistry. This study uses holographic methods for the study of total dental prosthesis. The issue is that the transformation of wax denture base in polymethylacrylate causes dimensional alterations and retractions in the final dental constructs. These could cause the failure of the stability of the complete denture in the oral cavity. Thus, the aim of this study is to determine and to compare using holography, total prosthesis obtained using three different manufacturing methods: pressing, injection, and polymerization. Each of the three types of dentures thus produced were recorded over the previously wax complete base holographic plates. The dimensional alterations that appear after using the different activation methods were thus determined. The most significant modification was remarked in the custom press technology, while the smallest variations were detected in the injection alternative.

  1. Cubic B-Spline Collocation Method for One-Dimensional Heat and Advection-Diffusion Equations

    OpenAIRE

    Joan Goh; Ahmad Abd. Majid; Ahmad Izani Md. Ismail

    2012-01-01

    Numerical solutions of one-dimensional heat and advection-diffusion equations are obtained by collocation method based on cubic B-spline. Usual finite difference scheme is used for time and space integrations. Cubic B-spline is applied as interpolation function. The stability analysis of the scheme is examined by the Von Neumann approach. The efficiency of the method is illustrated by some test problems. The numerical results are found to be in good agreement with the exact solution.

  2. Moving Least Squares Method for a One-Dimensional Parabolic Inverse Problem

    Directory of Open Access Journals (Sweden)

    Baiyu Wang

    2014-01-01

    Full Text Available This paper investigates the numerical solution of a class of one-dimensional inverse parabolic problems using the moving least squares approximation; the inverse problem is the determination of an unknown source term depending on time. The collocation method is used for solving the equation; some numerical experiments are presented and discussed to illustrate the stability and high efficiency of the method.

  3. Quadrature-free spline method for two-dimensional Navier-Stokes equation

    Institute of Scientific and Technical Information of China (English)

    HU Xian-liang; HAN Dan-fu

    2008-01-01

    In this paper,a quadrature-free scheme of spline method for two-dimensional Navier-Stokes equation is derived,which can dramatically improve the efficiency of spline method for fluid problems proposed by Lai and Wenston(2004). Additionally,the explicit formulation for boundary condition with up to second order derivatives is presented. The numerical simulations on several benchmark problems show that the scheme is very efficient.

  4. Microstructure modeling and virtual test of asphalt mixture based on three-dimensional discrete element method

    Institute of Scientific and Technical Information of China (English)

    马涛; 张德育; 张垚; 赵永利; 黄晓明

    2016-01-01

    The objective of this work is to model the microstructure of asphalt mixture and build virtual test for asphalt mixture by using Particle Flow Code in three dimensions (PFC3D) based on three-dimensional discrete element method. A randomly generating algorithm was proposed to capture the three-dimensional irregular shape of coarse aggregate. And then, modeling algorithm and method for graded aggregates were built. Based on the combination of modeling of coarse aggregates, asphalt mastic and air voids, three-dimensional virtual sample of asphalt mixture was modeled by using PFC3D. Virtual tests for penetration test of aggregate and uniaxial creep test of asphalt mixture were built and conducted by using PFC3D. By comparison of the testing results between virtual tests and actual laboratory tests, the validity of the microstructure modeling and virtual test built in this study was verified. Additionally, compared with laboratory test, the virtual test is easier to conduct and has less variability. It is proved that microstructure modeling and virtual test based on three-dimensional discrete element method is a promising way to conduct research of asphalt mixture.

  5. Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data.

    Science.gov (United States)

    Carazo, J M; Sorzano, C O S; Otón, J; Marabini, R; Vargas, J

    2015-09-01

    The Transmission Electron Microscope provides two-dimensional (2D) images of the specimens under study. However, the architecture of these specimens is defined in a three-dimensional (3D) coordinate space, in volumetric terms, making the direct microscope output somehow "short" in terms of dimensionality. This situation has prompted the development of methods to quantitatively estimate 3D volumes from sets of 2D images, which are usually referred to as "three-dimensional reconstruction methods". These 3D reconstruction methods build on four considerations: (1) The relationship between the 2D images and the 3D volume must be of a particularly simple type, (2) many 2D images are needed to gain 3D volumetric information, (3) the 2D images and the 3D volume have to be in the same coordinate reference frame and (4), in practical terms, the reconstructed 3D volume will only be an approximation to the original 3D volume which gave raise to the 2D projections. In this work we will adopt a quite general view, trying to address a large community of interested readers, although some sections will be particularly devoted to the 3D analysis of isolated macromolecular complexes in the application area normally referred to as Single Particle Analysis (SPA).

  6. Systems and methods that generate height map models for efficient three dimensional reconstruction from depth information

    Energy Technology Data Exchange (ETDEWEB)

    Frahm, Jan-Michael; Pollefeys, Marc Andre Leon; Gallup, David Robert

    2015-12-08

    Methods of generating a three dimensional representation of an object in a reference plane from a depth map including distances from a reference point to pixels in an image of the object taken from a reference point. Weights are assigned to respective voxels in a three dimensional grid along rays extending from the reference point through the pixels in the image based on the distances in the depth map from the reference point to the respective pixels, and a height map including an array of height values in the reference plane is formed based on the assigned weights. An n-layer height map may be constructed by generating a probabilistic occupancy grid for the voxels and forming an n-dimensional height map comprising an array of layer height values in the reference plane based on the probabilistic occupancy grid.

  7. Band Gap Optimization of Two-Dimensional Photonic Crystals Using Semidefinite Programming and Subspace Methods

    CERN Document Server

    Men, Han; Freund, Robert M; Parrilo, Pablo A; Peraire, Jaume

    2009-01-01

    In this paper, we consider the optimal design of photonic crystal band structures for two-dimensional square lattices. The mathematical formulation of the band gap optimization problem leads to an infinite-dimensional Hermitian eigenvalue optimization problem parametrized by the dielectric material and the wave vector. To make the problem tractable, the original eigenvalue problem is discretized using the finite element method into a series of finite-dimensional eigenvalue problems for multiple values of the wave vector parameter. The resulting optimization problem is large-scale and non-convex, with low regularity and non-differentiable objective. By restricting to appropriate eigenspaces, we reduce the large-scale non-convex optimization problem via reparametrization to a sequence of small-scale convex semidefinite programs (SDPs) for which modern SDP solvers can be efficiently applied. Numerical results are presented for both transverse magnetic (TM) and transverse electric (TE) polarizations at several fr...

  8. Semi-implicit integration factor methods on sparse grids for high-dimensional systems

    Science.gov (United States)

    Wang, Dongyong; Chen, Weitao; Nie, Qing

    2015-07-01

    Numerical methods for partial differential equations in high-dimensional spaces are often limited by the curse of dimensionality. Though the sparse grid technique, based on a one-dimensional hierarchical basis through tensor products, is popular for handling challenges such as those associated with spatial discretization, the stability conditions on time step size due to temporal discretization, such as those associated with high-order derivatives in space and stiff reactions, remain. Here, we incorporate the sparse grids with the implicit integration factor method (IIF) that is advantageous in terms of stability conditions for systems containing stiff reactions and diffusions. We combine IIF, in which the reaction is treated implicitly and the diffusion is treated explicitly and exactly, with various sparse grid techniques based on the finite element and finite difference methods and a multi-level combination approach. The overall method is found to be efficient in terms of both storage and computational time for solving a wide range of PDEs in high dimensions. In particular, the IIF with the sparse grid combination technique is flexible and effective in solving systems that may include cross-derivatives and non-constant diffusion coefficients. Extensive numerical simulations in both linear and nonlinear systems in high dimensions, along with applications of diffusive logistic equations and Fokker-Planck equations, demonstrate the accuracy, efficiency, and robustness of the new methods, indicating potential broad applications of the sparse grid-based integration factor method.

  9. Multigrid finite element method in stress analysis of three-dimensional elastic bodies of heterogeneous structure

    Science.gov (United States)

    Matveev, A. D.

    2016-11-01

    To calculate the three-dimensional elastic body of heterogeneous structure under static loading, a method of multigrid finite element is provided, when implemented on the basis of algorithms of finite element method (FEM), using homogeneous and composite threedimensional multigrid finite elements (MFE). Peculiarities and differences of MFE from the currently available finite elements (FE) are to develop composite MFE (without increasing their dimensions), arbitrarily small basic partition of composite solids consisting of single-grid homogeneous FE of the first order can be used, i.e. in fact, to use micro approach in finite element form. These small partitions allow one to take into account in MFE, i.e. in the basic discrete models of composite solids, complex heterogeneous and microscopically inhomogeneous structure, shape, the complex nature of the loading and fixation and describe arbitrarily closely the stress and stain state by the equations of three-dimensional elastic theory without any additional simplifying hypotheses. When building the m grid FE, m of nested grids is used. The fine grid is generated by a basic partition of MFE, the other m —1 large grids are applied to reduce MFE dimensionality, when m is increased, MFE dimensionality becomes smaller. The procedures of developing MFE of rectangular parallelepiped, irregular shape, plate and beam types are given. MFE generate the small dimensional discrete models and numerical solutions with a high accuracy. An example of calculating the laminated plate, using three-dimensional 3-grid FE and the reference discrete model is given, with that having 2.2 milliards of FEM nodal unknowns.

  10. Multi-fragment site-directed mutagenic overlap extension polymerase chain reaction as a competitive alternative to the enzymatic assembly method.

    Science.gov (United States)

    Wäneskog, Marcus; Bjerling, Pernilla

    2014-01-01

    Methods for introducing multiple site-directed mutations are important experimental tools in molecular biology. Research areas that use these methods include the investigation of various protein modifications in cellular processes, modifying proteins for efficient recombinant expression, and the stabilization of mRNAs to allow for increased protein expression. Introducing multiple site-directed mutations is also an important tool in the field of synthetic biology. There are two main methods used in the assembling of fragments generated by mutagenic primers: enzymatic assembly and overlap extension polymerase chain reaction (OE-PCR). In this article, we present an improved OE-PCR method that can be used for the generation of large DNA fragments (up to 7.4 kb) where at least 13 changes can be introduced using a genomic template. The improved method is faster (due to fewer reaction steps) and more accurate (due to fewer PCR cycles), meaning that it can effectively compete with the enzymatic assembly method. Data presented here show that the site-directed mutations can be introduced anywhere between 50 and 1800 bp from each other. The method is highly reliable and predicted to be applicable to most DNA engineering when the introduction of multiple changes in a DNA sequence is required.

  11. A novel computing three-dimensional differential transform method for solving fuzzy partial differential equations

    Directory of Open Access Journals (Sweden)

    Farshid Mirzaee

    2016-06-01

    Full Text Available In this paper, we introduce three-dimensional fuzzy differential transform method and we utilize it to solve fuzzy partial differential equations. This technique is a successful method because of reducing such problems to solve a system of algebraic equations; so, the problem can be solved directly. A considerable advantage of this method is to obtain the analytical solutions if the equation has an exact solution that is a polynomial function. Numerical examples are included to demonstrate the validity and applicability of the method.

  12. Incremental Unknowns Method for Solving Three-Dimensional Convection-Diffusion Equations

    Institute of Scientific and Technical Information of China (English)

    Lunji Song; Yujiang Wu

    2007-01-01

    We use the incremental unknowns method in conjunction with the iterative methods to approximate the solution of the nonsymmetric and positive-definite linear systems generated from a multilevel discretization of three-dimensional convection-diffusion equations. The condition numbers of incremental unknowns matrices associated with the convection-diffusion equations and the number of iterations needed to attain an acceptable accuracy are estimated. Numerical results are presented with two-level approximations,which demonstrate that the incremental unknowns method when combined with some iterative methods is very efficient.

  13. A Convergent Method of Auxiliary Sources for Two-Dimensional Impedance Scatterers With Edges

    DEFF Research Database (Denmark)

    Karamehmedovic, Mirza; Breinbjerg, Olav

    2001-01-01

    A modification to the Method of Auxiliary Sources (MAS) is introduced which renders the method operational for two-dimensional impedance scatterers with edges. The modification consists in letting the auxiliary surface converge to the scatterer physical surface for increasing number of auxiliary...... sources, whereby MAS approaches a surface integral equation (IE) method. Hereby, a systematic procedure for selecting the number and locations of the auxiliary sources is provided, and convergence of numerical results is obtained. The new method resulting from this modification thus combines the desirable...

  14. A multi-dimensional method for evaluating a product's conceptual schemes

    Directory of Open Access Journals (Sweden)

    Jing Zhou

    2015-11-01

    Full Text Available The use of conceptual scheme evaluation is a key step in the development of new products. In this paper, a multi-dimensional evaluation method that involves subjective evaluation, eye-tracking, and product image evaluation is established. In this study, subjective evaluation is used to test customers’ initial reactions to conceptual schemes, and eye- tracking is used to highlight the features of conceptual schemes that are most attractive to customers. With the help of Kansei engineering, the most attractive features of a particular product are described and clarified from the product image evaluation. This multi- dimensional method can be applied not only in screening conceptual schemes, but also in exploring the reasons and suggestions for product improvement. The method was assessed in this study through a case study evaluation of conceptual design schemes for a mobile phone.

  15. Quantitative interferometric microscopy with two dimensional Hilbert transform based phase retrieval method

    Science.gov (United States)

    Wang, Shouyu; Yan, Keding; Xue, Liang

    2017-01-01

    In order to obtain high contrast images and detailed descriptions of label free samples, quantitative interferometric microscopy combining with phase retrieval is designed to obtain sample phase distributions from fringes. As accuracy and efficiency of recovered phases are affected by phase retrieval methods, thus approaches owning higher precision and faster processing speed are still in demand. Here, two dimensional Hilbert transform based phase retrieval method is adopted in cellular phase imaging, it not only reserves more sample specifics compared to classical fast Fourier transform based method, but also overcomes disadvantages of traditional algorithm according to Hilbert transform which is a one dimensional processing causing phase ambiguities. Both simulations and experiments are provided, proving the proposed phase retrieval approach can acquire quantitative sample phases with high accuracy and fast speed.

  16. Multi-GPU accelerated three-dimensional FDTD method for electromagnetic simulation.

    Science.gov (United States)

    Nagaoka, Tomoaki; Watanabe, Soichi

    2011-01-01

    Numerical simulation with a numerical human model using the finite-difference time domain (FDTD) method has recently been performed in a number of fields in biomedical engineering. To improve the method's calculation speed and realize large-scale computing with the numerical human model, we adapt three-dimensional FDTD code to a multi-GPU environment using Compute Unified Device Architecture (CUDA). In this study, we used NVIDIA Tesla C2070 as GPGPU boards. The performance of multi-GPU is evaluated in comparison with that of a single GPU and vector supercomputer. The calculation speed with four GPUs was approximately 3.5 times faster than with a single GPU, and was slightly (approx. 1.3 times) slower than with the supercomputer. Calculation speed of the three-dimensional FDTD method using GPUs can significantly improve with an expanding number of GPUs.

  17. Development of a three dimensional circulation model based on fractional step method

    Directory of Open Access Journals (Sweden)

    Mazen Abualtayef

    2010-03-01

    Full Text Available A numerical model was developed for simulating a three-dimensional multilayer hydrodynamic and thermodynamic model in domains with irregular bottom topography. The model was designed for examining the interactions between flow and topography. The model was based on the three-dimensional Navier-Stokes equations and was solved using the fractional step method, which combines the finite difference method in the horizontal plane and the finite element method in the vertical plane. The numerical techniques were described and the model test and application were presented. For the model application to the northern part of Ariake Sea, the hydrodynamic and thermodynamic results were predicted. The numerically predicted amplitudes and phase angles were well consistent with the field observations.

  18. Solution of two-dimensional scattering problem in piezoelectric/piezomagnetic media using a polarization method

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Using a polarization method, the scattering problem for a two-dimensional inclusion embedded in infinite piezoelectric/piezomagnetic matrices is investigated. To achieve the purpose, the polarization method for a two-dimensional piezoelectric/piezo-magnetic "comparison body" is formulated. For simple harmonic motion, kernel of the polarization method reduces to a 2-D time-harmonic Green's function, which is ob-tained using the Radon transform. The expression is further simplified under condi-tions of low frequency of the incident wave and small diameter of the inclusion. Some analytical expressions are obtained. The analytical solutions for generalized piezoelec-tric/piezomagnetic anisotropic composites are given followed by simplified results for piezoelectric composites. Based on the latter results, two numerical results are provided for an elliptical cylindrical inclusion in a PZT-5H-matrix, showing the effect of different factors including size, shape, material properties, and piezoelectricity on the scattering cross-section.

  19. A hyper-spherical adaptive sparse-grid method for high-dimensional discontinuity detection

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guannan [ORNL; Webster, Clayton G [ORNL; Gunzburger, Max D [ORNL; Burkardt, John V [ORNL

    2014-03-01

    This work proposes and analyzes a hyper-spherical adaptive hi- erarchical sparse-grid method for detecting jump discontinuities of functions in high-dimensional spaces is proposed. The method is motivated by the the- oretical and computational inefficiencies of well-known adaptive sparse-grid methods for discontinuity detection. Our novel approach constructs a func- tion representation of the discontinuity hyper-surface of an N-dimensional dis- continuous quantity of interest, by virtue of a hyper-spherical transformation. Then, a sparse-grid approximation of the transformed function is built in the hyper-spherical coordinate system, whose value at each point is estimated by solving a one-dimensional discontinuity detection problem. Due to the smooth- ness of the hyper-surface, the new technique can identify jump discontinuities with significantly reduced computational cost, compared to existing methods. Moreover, hierarchical acceleration techniques are also incorporated to further reduce the overall complexity. Rigorous error estimates and complexity anal- yses of the new method are provided as are several numerical examples that illustrate the effectiveness of the approach.

  20. Far-field method for the characterisation of three-dimensional fields: vectorial polarimetry

    Directory of Open Access Journals (Sweden)

    Dainty C.

    2010-06-01

    Full Text Available The first attempt to completely characterise a three-dimensional field was done by Ellis and Dogariu with excellent results reported [1] . However, their method is based on near-field techniques, which limits its range of applications. In this work, we present an alternative far-field method for the characterisation of the three-dimensional field that results from the interaction of a tightly focused three-dimensional field [2] with a sub-resolution specimen. Our method is based on the analysis of the scattering-angle-resolved polarisation state distribution across the exit pupil of a high numerical aperture (NA collector lens using standard polarimetry techniques. Details of the method, the experimental setup built to verify its capabilities, and numerical and first experimental evidence demonstrating that the method allows for high sensitivit y on sub-resolution displacements of a sub-resolution specimen shall be presented [3]. This work is funded by Science Foundation Ireland grant No. 07/IN.1/I906 and Shimadzu Corporation, Japan. Oscar Rodríguez is grateful to the National Council for Science and Technology (CONACYT, Mexico for the Ph D scholarship 177627.

  1. Far-field method for the characterisation of three-dimensional fields: vectorial polarimetry

    Science.gov (United States)

    Rodríguez, O.; Lara, D.; Dainty, C.

    2010-06-01

    The first attempt to completely characterise a three-dimensional field was done by Ellis and Dogariu with excellent results reported [1] . However, their method is based on near-field techniques, which limits its range of applications. In this work, we present an alternative far-field method for the characterisation of the three-dimensional field that results from the interaction of a tightly focused three-dimensional field [2] with a sub-resolution specimen. Our method is based on the analysis of the scattering-angle-resolved polarisation state distribution across the exit pupil of a high numerical aperture (NA) collector lens using standard polarimetry techniques. Details of the method, the experimental setup built to verify its capabilities, and numerical and first experimental evidence demonstrating that the method allows for high sensitivit y on sub-resolution displacements of a sub-resolution specimen shall be presented [3]. This work is funded by Science Foundation Ireland grant No. 07/IN.1/I906 and Shimadzu Corporation, Japan. Oscar Rodríguez is grateful to the National Council for Science and Technology (CONACYT, Mexico) for the Ph D scholarship 177627.

  2. Wavelet-based method for computing elastic band gaps of one-dimensional phononic crystals

    Institute of Scientific and Technical Information of China (English)

    YAN; ZhiZhong; WANG; YueSheng

    2007-01-01

    A wavelet-based method was developed to compute elastic band gaps of one-dimensional phononic crystals. The wave field was expanded in the wavelet basis and an equivalent eigenvalue problem was derived in a matrix form involving the adaptive computation of integrals of the wavelets. The method was then applied to a binary system. For comparison, the elastic band gaps of the same one-di- mensional phononic crystals computed with the wavelet method and the well- known plane wave expansion (PWE) method are both presented in this paper. The numerical results of the two methods are in good agreement while the computation costs of the wavelet method are much lower than that of PWE method. In addition, the adaptability of wavelets makes the method possible for efficient band gap computation of more complex phononic structures.

  3. Conjugation of R-Phycoerythrin to a Polyclonal Antibody and F (ab')2 Fragment of a Polyclonal Antibody by Two Different Methods.

    Science.gov (United States)

    Mahmoudian, Jafar; Jeddi-Tehrani, Mahmood; Rabbani, Hodjattallah; Mahmoudi, Ahmad Reza; Akhondi, Mohammad Mehdi; Zarnani, Amir Hassan; Goli, Leila Balaei; Babaei, Mahdokht; Ghods, Roya

    2010-04-01

    R-Phycoerythrin (R-PE), a fluorescent protein from phycobiliprotein family, is isolated from red algae. Conjugation of antibodies to R-PE facilitates multiple fluorescent staining methods. In the present study polyclonal antibodies and polyclonal F(ab')2 fragment antibodies were conjugated to R-PE by two different methods. The efficiency of the methods was evaluated using Immunocytochemistry (ICC) and Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE). In the first conjugation method, PE was attached to SMCC linker followed by conjugation of antibody to PE-SMCC. In the second method, SH groups were added onto R-PE molecule, while the antibody was attached to SPDP linker. Then, the antibody-SPDP molecule was conjugated to R-PE. Our results showed that the two conjugation methods did not have any abrogative effects on the antibody binding activity.

  4. A Comparison of Machine Learning Methods in a High-Dimensional Classification Problem

    Directory of Open Access Journals (Sweden)

    Zekić-Sušac Marijana

    2014-09-01

    Full Text Available Background: Large-dimensional data modelling often relies on variable reduction methods in the pre-processing and in the post-processing stage. However, such a reduction usually provides less information and yields a lower accuracy of the model. Objectives: The aim of this paper is to assess the high-dimensional classification problem of recognizing entrepreneurial intentions of students by machine learning methods. Methods/Approach: Four methods were tested: artificial neural networks, CART classification trees, support vector machines, and k-nearest neighbour on the same dataset in order to compare their efficiency in the sense of classification accuracy. The performance of each method was compared on ten subsamples in a 10-fold cross-validation procedure in order to assess computing sensitivity and specificity of each model. Results: The artificial neural network model based on multilayer perceptron yielded a higher classification rate than the models produced by other methods. The pairwise t-test showed a statistical significance between the artificial neural network and the k-nearest neighbour model, while the difference among other methods was not statistically significant. Conclusions: Tested machine learning methods are able to learn fast and achieve high classification accuracy. However, further advancement can be assured by testing a few additional methodological refinements in machine learning methods.

  5. The equivalence of information-theoretic and likelihood-based methods for neural dimensionality reduction.

    Directory of Open Access Journals (Sweden)

    Ross S Williamson

    2015-04-01

    Full Text Available Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron's probability of spiking. One popular method, known as maximally informative dimensions (MID, uses an information-theoretic quantity known as "single-spike information" to identify this space. Here we examine MID from a model-based perspective. We show that MID is a maximum-likelihood estimator for the parameters of a linear-nonlinear-Poisson (LNP model, and that the empirical single-spike information corresponds to the normalized log-likelihood under a Poisson model. This equivalence implies that MID does not necessarily find maximally informative stimulus dimensions when spiking is not well described as Poisson. We provide several examples to illustrate this shortcoming, and derive a lower bound on the information lost when spiking is Bernoulli in discrete time bins. To overcome this limitation, we introduce model-based dimensionality reduction methods for neurons with non-Poisson firing statistics, and show that they can be framed equivalently in likelihood-based or information-theoretic terms. Finally, we show how to overcome practical limitations on the number of stimulus dimensions that MID can estimate by constraining the form of the non-parametric nonlinearity in an LNP model. We illustrate these methods with simulations and data from primate visual cortex.

  6. The equivalence of information-theoretic and likelihood-based methods for neural dimensionality reduction.

    Science.gov (United States)

    Williamson, Ross S; Sahani, Maneesh; Pillow, Jonathan W

    2015-04-01

    Stimulus dimensionality-reduction methods in neuroscience seek to identify a low-dimensional space of stimulus features that affect a neuron's probability of spiking. One popular method, known as maximally informative dimensions (MID), uses an information-theoretic quantity known as "single-spike information" to identify this space. Here we examine MID from a model-based perspective. We show that MID is a maximum-likelihood estimator for the parameters of a linear-nonlinear-Poisson (LNP) model, and that the empirical single-spike information corresponds to the normalized log-likelihood under a Poisson model. This equivalence implies that MID does not necessarily find maximally informative stimulus dimensions when spiking is not well described as Poisson. We provide several examples to illustrate this shortcoming, and derive a lower bound on the information lost when spiking is Bernoulli in discrete time bins. To overcome this limitation, we introduce model-based dimensionality reduction methods for neurons with non-Poisson firing statistics, and show that they can be framed equivalently in likelihood-based or information-theoretic terms. Finally, we show how to overcome practical limitations on the number of stimulus dimensions that MID can estimate by constraining the form of the non-parametric nonlinearity in an LNP model. We illustrate these methods with simulations and data from primate visual cortex.

  7. Advanced numerical methods for three dimensional two-phase flow calculations

    Energy Technology Data Exchange (ETDEWEB)

    Toumi, I. [Laboratoire d`Etudes Thermiques des Reacteurs, Gif sur Yvette (France); Caruge, D. [Institut de Protection et de Surete Nucleaire, Fontenay aux Roses (France)

    1997-07-01

    This paper is devoted to new numerical methods developed for both one and three dimensional two-phase flow calculations. These methods are finite volume numerical methods and are based on the use of Approximate Riemann Solvers concepts to define convective fluxes versus mean cell quantities. The first part of the paper presents the numerical method for a one dimensional hyperbolic two-fluid model including differential terms as added mass and interface pressure. This numerical solution scheme makes use of the Riemann problem solution to define backward and forward differencing to approximate spatial derivatives. The construction of this approximate Riemann solver uses an extension of Roe`s method that has been successfully used to solve gas dynamic equations. As far as the two-fluid model is hyperbolic, this numerical method seems very efficient for the numerical solution of two-phase flow problems. The scheme was applied both to shock tube problems and to standard tests for two-fluid computer codes. The second part describes the numerical method in the three dimensional case. The authors discuss also some improvements performed to obtain a fully implicit solution method that provides fast running steady state calculations. Such a scheme is not implemented in a thermal-hydraulic computer code devoted to 3-D steady-state and transient computations. Some results obtained for Pressurised Water Reactors concerning upper plenum calculations and a steady state flow in the core with rod bow effect evaluation are presented. In practice these new numerical methods have proved to be stable on non staggered grids and capable of generating accurate non oscillating solutions for two-phase flow calculations.

  8. Development of a polymerase chain reaction-restriction fragment length polymorphism method for identification of the Fusarium genus using the transcription elongation factor-1α gene.

    Science.gov (United States)

    Zarrin, Majid; Ganj, Farzaneh; Faramarzi, Sama

    2016-12-01

    Fusarium species are well-known plant pathogens and food contaminants that have also appeared as one of the most important groups of medically significant fungi. The sequences of the translation elongation factor (TEF)-1α gene have been broadly employed for species detection. A total of 50 strains of Fusarium spp., including environmental, clinical and reference isolates were used for the current study. The primer sets, Fu3f and Fu3r, were used to amplify an ~420-bp DNA fragment of the TEF-1α gene. Double digestion with two restriction enzymes, XhoI and SduI was used for discrimination of the Fusarium species in the TEF-1α gene fragment. Double digestion of the TEF-1α gene fragment from five clinically important Fusarium species were clearly differentiated from each other: The F. solani species complex, F. oxysporum species complex, F. verticillioides, F. proliferatum and F. fujikuroi. This method facilitates detection and enables verification of the Fusarium genus; therefore, it may be applied for disease control.

  9. Design of Aspirated Compressor Blades Using Three-dimensional Inverse Method

    Science.gov (United States)

    Dang, T. Q.; Rooij, M. Van; Larosiliere, L. M.

    2003-01-01

    A three-dimensional viscous inverse method is extended to allow blading design with full interaction between the prescribed pressure-loading distribution and a specified transpiration scheme. Transpiration on blade surfaces and endwalls is implemented as inflow/outflow boundary conditions, and the basic modifications to the method are outlined. This paper focuses on a discussion concerning an application of the method to the design and analysis of a supersonic rotor with aspiration. Results show that an optimum combination of pressure-loading tailoring with surface aspiration can lead to a minimization of the amount of sucked flow required for a net performance improvement at design and off-design operations.

  10. APPLICATION OF EXP-FUNCTION METHOD TO THE (2+1-DIMENSIONAL CALOGERO BOGOYAVLANSKII SCHIFF EQUATION

    Directory of Open Access Journals (Sweden)

    Z. AYATI

    2009-07-01

    Full Text Available In this paper, the Exp-function method, with the aid of a symbolic computation system such as Maple, is applied to the (2+1 -dimensional Calogero Bogoyavlanskii Schiff equation. Exact and explicit generalized solitary solutions are obtained in more general forms. The free parameters can be determined by initial or boundary conditions. The method is straightforward and concise, and its applications are promising. It is shown that the Exp-function method, with the help of symbolic computation, provides a very effective and powerful mathematical tool for solving Calogero Bogoyavlanskii Schiff equation.

  11. A method for phase reconstruction in optical three-dimensional shape measurement

    Institute of Scientific and Technical Information of China (English)

    Qiao Nao-Sheng; He Zhi

    2012-01-01

    In optical three-dimensional shape measurement,a method of improving the measurement precision for phase reconstruction without phase unwrapping is analyzed in detail.Intensities of any five consecutive pixels that lie in the x-axis direction of the phase domain are given.Partial derivatives of the phase function in the x- and y-axis directions are obtained with a phase-shifting mechanism,the origin of which is analysed.Furthermore,to avoid phase unwrapping in the phase reconstruction,we derive the gradient of the phase function and perform a two-dimensional integral along the x- and y-axis directions.The reconstructed phase can be obtained directly by performing numerical integration,and thus it is of great convenience for phase reconstruction.Finally,the results of numerical simulations and practical experiments verify the correctness of the proposed method.

  12. A fast three-dimensional reconstruction method applied for the fabric defect detection

    Science.gov (United States)

    Song, Limei; Zhang, Chunbo; Xiong, Hui; Wei, Yiying; Chen, Huawei

    2010-11-01

    The fabric quality defect detection is very useful for improving the qualities of the products. It is also very important to increase the reputation and the economic benefits of a company. However, there are some shortcomings in the traditional manual detection methods, such as the low detection efficiency, the fatigue problem of the operator, and the detection inaccuracy, etc. The existing 2D image processing methods are difficult to solve the interference which is caused by non-defect case, just like the cloth folds, the flying thick silk floss, the noise from the background light and ambient light, etc. In order to solve those problem, the BCCSL (Binocular Camera Color Structure Light) method and SFMS (Shape from Multi Shading) method is proposed in this paper. The three-dimensional color coordinates of the fabric can be quickly and highly-precision obtained, thus to judge the defects shape and location. The BCCSL method and SFMS method can quickly obtain the three-dimensional coordinates' information of the fabric defects. The BCCSL method collects the 3D skeleton's information of a fabric image through the binocular video capture device and the color structured light projection device in real-time. And the details 3D coordinates of fabric outside strip structural are obtained through the proposed method SFMS. The interference information, such as the cloth fold, the flying thick silk floss, and the noise from the background light and ambient light can be excluded by using the three-dimensional defect identification. What is more, according to the characteristics of 3D structure of the defect, the fabric can be identified and classified. Further more, the possible problems from the production line can be summarized.

  13. Precision of meshfree methods and application to forward modeling of two-dimensional electromagnetic sources

    Science.gov (United States)

    Li, Jun-Jie; Yan, Jia-Bin; Huang, Xiang-Yu

    2015-12-01

    Meshfree method offers high accuracy and computational capability and constructs the shape function without relying on predefined elements. We comparatively analyze the global weak form meshfree methods, such as element-free Galerkin method (EFGM), the point interpolation method (PIM), and the radial point interpolation method (RPIM). Taking two dimensional Poisson equation as an example, we discuss the support-domain dimensionless size, the field nodes, and background element settings with respect to their effect on calculation accuracy of the meshfree method. RPIM and EFGM are applied to controlled-source two-dimensional electromagnetic modeling with fixed shape parameters. The accuracy of boundary conditions imposed directly and by a penalty function are discussed in the case of forward modeling of two-dimensional magnetotellurics in a homogeneous medium model. The coupling algorithm of EFG-PIM and EFG-RPIM are generated by integrating the PIM or RPIM and EFGM. The results of the numerical modeling suggest the following. First, the proposed meshfree method and corresponding coupled methods are well-suited for electromagnetic numerical modeling. The accuracy of the algorithm is the highest when the support-domain dimensionless size is 1.0 and the distribution of field nodes is consistent with the nodes of background elements. Second, the accuracy of PIM and RPIM are lower than that of EFGM for the Poisson equation but higher than EFGM for the homogeneous medium MT response. Third, RPIM overcomes the matrix inversion problem of PIM and has a wider selection of support-domain dimensionless sizes as compared to RPIM.

  14. Moment-based method for computing the two-dimensional discrete Hartley transform

    Science.gov (United States)

    Dong, Zhifang; Wu, Jiasong; Shu, Huazhong

    2009-10-01

    In this paper, we present a fast algorithm for computing the two-dimensional (2-D) discrete Hartley transform (DHT). By using kernel transform and Taylor expansion, the 2-D DHT is approximated by a linear sum of 2-D geometric moments. This enables us to use the fast algorithms developed for computing the 2-D moments to efficiently calculate the 2-D DHT. The proposed method achieves a simple computational structure and is suitable to deal with any sequence lengths.

  15. On the asymptotic behaviour of a one-dimensional monocharged plasma and a rescaling method

    OpenAIRE

    Batt, Jürgen; Kunze, Markus; Rein, Gerhard

    1998-01-01

    We consider a one-dimensional, monocharged plasma as described by the Vlasov--Poisson system and investigate the behaviour of the solutions for large times. Using a rescaling method we are able to determine an explicit solution of the system which corresponds to a globally attractive steady state for the rescaled system. We investigate in which sense and at which rate the solutions of the rescaled system converge to this global attractor and interpret the results for the origin...

  16. CONVERGENCE OF AN EXPLICIT UPWIND FINITE ELEMENT METHOD TO MULTI-DIMENSIONAL CONSERVATION LAWS

    Institute of Scientific and Technical Information of China (English)

    Jin-chao Xu; Lung-an Ying

    2001-01-01

    An explicit upwind finite element method is given for the numerical computation to multi-dimensional scalar conservation laws. It is proved that this scheme is consistent to the equation and monotone, and the approximate solution satisfies discrete entropy inequality.To guarantee the limit of approximate solutions to be a measure valued solution, we prove an energy estimate. Then the Lp strong convergence of this scheme is proved.

  17. An immersed interface method for two-dimensional modelling of stratified flow in pipes

    OpenAIRE

    Berthelsen, Petter Andreas

    2004-01-01

    This thesis deals with the construction of a numerical method for solving two-dimensional elliptic interface problems, such as fully developed stratified flow in pipes. Interface problems are characterized by its non-smooth and often discontinuous behaviour along a sharp boundary separating the fluids or other materials. Classical numerical schemes are not suitable for these problems due to the irregular geometry of the interface. Standard finite difference discretization across the interface...

  18. Finite volume evolution Galerkin (FVEG) methods for three-dimensional wave equation system

    OpenAIRE

    Lukácová-Medvid'ová, Maria; Warnecke, Gerald; Zahaykah, Yousef

    2004-01-01

    The subject of the paper is the derivation of finite volume evolution Galerkin schemes for three-dimensional wave equation system. The aim is to construct methods which take into account all of the infinitely many directions of propagation of bicharacteristics. The idea is to evolve the initial function using the characteristic cone and then to project onto a finite element space. Numerical experiments are presented to demonstrate the accuracy and the multidimensional behaviour of the solutio...

  19. Soliton solutions of the two-dimensional KdV-Burgers equation by homotopy perturbation method

    Energy Technology Data Exchange (ETDEWEB)

    Molabahrami, A. [Department of Mathematics, Ilam University, PO Box 69315516, Ilam (Iran, Islamic Republic of)], E-mail: a_m_bahrami@yahoo.com; Khani, F. [Department of Mathematics, Ilam University, PO Box 69315516, Ilam (Iran, Islamic Republic of); Bakhtar Institute of Higher Education, PO Box 696, Ilam (Iran, Islamic Republic of)], E-mail: farzad_khani59@yahoo.com; Hamedi-Nezhad, S. [Bakhtar Institute of Higher Education, PO Box 696, Ilam (Iran, Islamic Republic of)

    2007-10-29

    In this Letter, the He's homotopy perturbation method (HPM) to finding the soliton solutions of the two-dimensional Korteweg-de Vries Burgers' equation (tdKdVB) for the initial conditions was applied. Numerical solutions of the equation were obtained. The obtained solutions, in comparison with the exact solutions admit a remarkable accuracy. The results reveal that the HPM is very effective and simple.

  20. Prandtl's Boundary Layer Equation for Two-Dimensional Flow: Exact Solutions via the Simplest Equation Method

    Directory of Open Access Journals (Sweden)

    Taha Aziz

    2013-01-01

    Full Text Available The simplest equation method is employed to construct some new exact closed-form solutions of the general Prandtl's boundary layer equation for two-dimensional flow with vanishing or uniform mainstream velocity. We obtain solutions for the case when the simplest equation is the Bernoulli equation or the Riccati equation. Prandtl's boundary layer equation arises in the study of various physical models of fluid dynamics. Thus finding the exact solutions of this equation is of great importance and interest.

  1. [Study on the methods for establishing virtual three-dimensional models of cerebral arteries with the three-dimensional moulding software].

    Science.gov (United States)

    Wei, Xin; Xie, Xiaodong; Wang, Chaohua

    2007-12-01

    This study was conducted to establish the methods of virtual three-dimensional cerebral arteries models by use of three-dimensional moulding software. The virtual models of the cerebral arteries were established using the three-dimensional moulding software of 3D Studio MAX R3 with 46 cases of normal cerebral DSA image as the original. The results showed there was similarity in appearance between the virtual cerebral arteries and DSA image. This is of benefit to understanding the vascular three-dimensional spatial relation in visual sense. Several models of different variant anatomy could be easily established on the copy files of the virtual cerebral arteries model. The virtual model could help learners to create and increase the three-dimensional space concept of arteries and aneurysms in clinical teaching. The results indicated that the virtual three-dimensional cerebral arteries models could display the three-dimensional spatial relation of the cerebral arterial system distinctly, and could serve as a morphologic foundation in the researches on vascular disease.

  2. Deriving Shape-Based Features for C. elegans Locomotion Using Dimensionality Reduction Methods

    Science.gov (United States)

    Gyenes, Bertalan; Brown, André E. X.

    2016-01-01

    High-throughput analysis of animal behavior is increasingly common following the advances of recording technology, leading to large high-dimensional data sets. This dimensionality can sometimes be reduced while still retaining relevant information. In the case of the nematode worm Caenorhabditis elegans, more than 90% of the shape variance can be captured using just four principal components. However, it remains unclear if other methods can achieve a more compact representation or contribute further biological insight to worm locomotion. Here we take a data-driven approach to worm shape analysis using independent component analysis (ICA), non-negative matrix factorization (NMF), a cosine series, and jPCA (a dynamic variant of principal component analysis [PCA]) and confirm that the dimensionality of worm shape space is close to four. Projecting worm shapes onto the bases derived using each method gives interpretable features ranging from head movements to tail oscillation. We use these as a comparison method to find differences between the wild type N2 worms and various mutants. For example, we find that the neuropeptide mutant nlp-1(ok1469) has an exaggerated head movement suggesting a mode of action for the previously described increased turning rate. The different bases provide complementary views of worm behavior and we expect that closer examination of the time series of projected amplitudes will lead to new results in the future. PMID:27582697

  3. Suppression method of low-frequency noise for two-dimensional integrated magnetic sensor

    Science.gov (United States)

    Kimura, Takayuki; Sakairi, Yusuke; Mori, Akihiro; Masuzawa, Toru

    2017-04-01

    A new correlated double sampling method for two-dimensional magnetic sensors was proposed. In this method, output from a magnetic sensor is controlled by adjusting the drain bias of a MOSFET used as a Hall element. The two-dimensional integrated magnetic sensor used for the demonstration of correlated double sampling was composed of a 64 × 64 array of Hall sensors and fabricated by a 0.18 µm CMOS standard process. The size of a Hall element was 2.7 × 2.7 µm2. The dimensions of one pixel in which a Hall element was embedded were 7 × 7 µm2. The magnitude of residual noise after correlated double sampling with drain bias control was 0.81 mVp–p. This value is 16% of the original low-frequency noise. From the experimental results, the proposed correlated double sampling method is found to be suitable for low-frequency noise suppression in the two-dimensional magnetic sensors.

  4. A Method of Three-Dimensional Micro-Rotational Flow Generation for Biological Applications

    Directory of Open Access Journals (Sweden)

    Yaxiaer Yalikun

    2016-08-01

    Full Text Available We report a convenient method to create a three-dimensional micro-rotational fluidic platform for biological applications in the direction of a vertical plane (out-of-plane without contact in an open space. Unlike our previous complex fluidic manipulation system, this method uses a micro-rotational flow generated near a single orifice when the solution is pushed from the orifice by using a single pump. The three-dimensional fluidic platform shows good potential for fluidic biological applications such as culturing, stimulating, sorting, and manipulating cells. The pattern and velocity of the micro-rotational flow can be controlled by tuning the parameters such as the flow rate and the liquid-air interface height. We found that bio-objects captured by the micro-rotational flow showed self-rotational motion and orbital motion. Furthermore, the path length and position, velocity, and pattern of the orbital motion of the bio-object could be controlled. To demonstrate our method, we used embryoid body cells. As a result, the orbital motion had a maximum length of 2.4 mm, a maximum acceleration of 0.63 m/s2, a frequency of approximately 0.45 Hz, a maximum velocity of 15.4 mm/s, and a maximum rotation speed of 600 rpm. The capability to have bio-objects rotate or move orbitally in three dimensions without contact opens up new research opportunities in three-dimensional microfluidic technology.

  5. Two-dimensional nonlinear geophysical data filtering using the multidimensional EEMD method

    Science.gov (United States)

    Chen, Chih-Sung; Jeng, Yih

    2014-12-01

    A variety of two-dimensional (2D) empirical mode decomposition (EMD) methods have been proposed in the last decade. Furthermore, the multidimensional EMD algorithm and its parallel class, multivariate EMD (MEMD), are available in recent years. From those achievements, it is possible to design an efficient 2D nonlinear filter for geophysical data processing. We introduce a robust 2D nonlinear filter which can be applied to enhance the signal of 2D geophysical data or to highlight the feature component on an image. We did this by replacing the conventionally used smooth interpolation in the ensemble empirical mode decomposition (EEMD) algorithm with a piecewise interpolation method. The one-dimensional (1D) EEMD procedures were consecutively performed in all directions, and then the comparable minimal scale combination technique was applied to the decomposed components. The theoretical derivation, model simulation, and real data applications are demonstrated in this paper. The proposed filtering method is effective in improving the image resolution by suppressing the random noise added in the simulation example and strong low frequency track corrugation noise bands with background noise in the field example. Furthermore, the algorithm can be easily extended to higher dimensions by repeating the same procedure in the succeeding dimension. To evaluate the proposed method, one data set is processed separately by using the enhanced analytic signal method and the multivariate EMD (MEMD) algorithm, and the results from these two methods are compared with that of the proposed method. A general equation for generating three-dimensional (3D) EEMD components based on the comparable minimal scale combination principle is derived for further applications.

  6. Simulation of Thermal Stratification in BWR Suppression Pools with One Dimensional Modeling Method

    Energy Technology Data Exchange (ETDEWEB)

    Haihua Zhao; Ling Zou; Hongbin Zhang

    2014-01-01

    The suppression pool in a boiling water reactor (BWR) plant not only is the major heat sink within the containment system, but also provides the major emergency cooling water for the reactor core. In several accident scenarios, such as a loss-of-coolant accident and extended station blackout, thermal stratification tends to form in the pool after the initial rapid venting stage. Accurately predicting the pool stratification phenomenon is important because it affects the peak containment pressure; the pool temperature distribution also affects the NPSHa (available net positive suction head) and therefore the performance of the Emergency Core Cooling System and Reactor Core Isolation Cooling System pumps that draw cooling water back to the core. Current safety analysis codes use zero dimensional (0-D) lumped parameter models to calculate the energy and mass balance in the pool; therefore, they have large uncertainties in the prediction of scenarios in which stratification and mixing are important. While three-dimensional (3-D) computational fluid dynamics (CFD) methods can be used to analyze realistic 3-D configurations, these methods normally require very fine grid resolution to resolve thin substructures such as jets and wall boundaries, resulting in a long simulation time. For mixing in stably stratified large enclosures, the BMIX++ code (Berkeley mechanistic MIXing code in C++) has been developed to implement a highly efficient analysis method for stratification where the ambient fluid volume is represented by one-dimensional (1-D) transient partial differential equations and substructures (such as free or wall jets) are modeled with 1-D integral models. This allows very large reductions in computational effort compared to multi-dimensional CFD modeling. One heat-up experiment performed at the Finland POOLEX facility, which was designed to study phenomena relevant to Nordic design BWR suppression pool including thermal stratification and mixing, is used for

  7. Mycobacterium avium restriction fragment lenght polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains

    Directory of Open Access Journals (Sweden)

    Patrícia Carvalho de Sequeira

    2005-11-01

    Full Text Available Simple double repetitive element polymerase chain reaction (MaDRE-PCR and Pvu II-IS1245 restriction fragment length polymorphism (RFLP typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 Aids inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.

  8. A fast method to compute Three-Dimensional Infrared Radiative Transfer in non scattering medium

    Science.gov (United States)

    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.

  9. Kernel based methods for accelerated failure time model with ultra-high dimensional data

    Directory of Open Access Journals (Sweden)

    Jiang Feng

    2010-12-01

    Full Text Available Abstract Background Most genomic data have ultra-high dimensions with more than 10,000 genes (probes. Regularization methods with L1 and Lp penalty have been extensively studied in survival analysis with high-dimensional genomic data. However, when the sample size n ≪ m (the number of genes, directly identifying a small subset of genes from ultra-high (m > 10, 000 dimensional data is time-consuming and not computationally efficient. In current microarray analysis, what people really do is select a couple of thousands (or hundreds of genes using univariate analysis or statistical tests, and then apply the LASSO-type penalty to further reduce the number of disease associated genes. This two-step procedure may introduce bias and inaccuracy and lead us to miss biologically important genes. Results The accelerated failure time (AFT model is a linear regression model and a useful alternative to the Cox model for survival analysis. In this paper, we propose a nonlinear kernel based AFT model and an efficient variable selection method with adaptive kernel ridge regression. Our proposed variable selection method is based on the kernel matrix and dual problem with a much smaller n × n matrix. It is very efficient when the number of unknown variables (genes is much larger than the number of samples. Moreover, the primal variables are explicitly updated and the sparsity in the solution is exploited. Conclusions Our proposed methods can simultaneously identify survival associated prognostic factors and predict survival outcomes with ultra-high dimensional genomic data. We have demonstrated the performance of our methods with both simulation and real data. The proposed method performs superbly with limited computational studies.

  10. Cubic B-Spline Collocation Method for One-Dimensional Heat and Advection-Diffusion Equations

    Directory of Open Access Journals (Sweden)

    Joan Goh

    2012-01-01

    Full Text Available Numerical solutions of one-dimensional heat and advection-diffusion equations are obtained by collocation method based on cubic B-spline. Usual finite difference scheme is used for time and space integrations. Cubic B-spline is applied as interpolation function. The stability analysis of the scheme is examined by the Von Neumann approach. The efficiency of the method is illustrated by some test problems. The numerical results are found to be in good agreement with the exact solution.

  11. Towards a d-bar reconstruction method for three-dimensional EIT

    DEFF Research Database (Denmark)

    Cornean, Horia Decebal; Knudsen, Kim

    Three-dimensional electrical impedance tomography (EIT) is considered. Both uniqueness proofs and theoretical reconstruction algorithms available for this problem rely on the use of exponentially growing solutions to the governing conductivity equation. The study of those solutions is continued...... here. It is shown that exponentially growing solutions exist for low complex frequencies without imposing any regularity assumption on the conductivity. Further, a reconstruction method for conductivities close to a constant is given. In this method the complex frequency is taken to zero instead...

  12. Finite Differences and Collocation Methods for the Solution of the Two Dimensional Heat Equation

    Science.gov (United States)

    Kouatchou, Jules

    1999-01-01

    In this paper we combine finite difference approximations (for spatial derivatives) and collocation techniques (for the time component) to numerically solve the two dimensional heat equation. We employ respectively a second-order and a fourth-order schemes for the spatial derivatives and the discretization method gives rise to a linear system of equations. We show that the matrix of the system is non-singular. Numerical experiments carried out on serial computers, show the unconditional stability of the proposed method and the high accuracy achieved by the fourth-order scheme.

  13. A mixed finite difference/Galerkin method for three-dimensional Rayleigh-Benard convection

    Science.gov (United States)

    Buell, Jeffrey C.

    1988-01-01

    A fast and accurate numerical method, for nonlinear conservation equation systems whose solutions are periodic in two of the three spatial dimensions, is presently implemented for the case of Rayleigh-Benard convection between two rigid parallel plates in the parameter region where steady, three-dimensional convection is known to be stable. High-order streamfunctions secure the reduction of the system of five partial differential equations to a system of only three. Numerical experiments are presented which verify both the expected convergence rates and the absolute accuracy of the method.

  14. Contact position controlling for two-dimensional motion bodies by the boundary element method

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    An algorithm is presented for controlling two-dimensional motion contact bodies with conforming discretization. Since a kind of special boundary element is utilized in the algorithm, the displacement compatibility and traction equilibrium conditions at nodes can be satisfied simultaneously in arbitrary locations of the contact interface. In addition, a method is also proposed in which the contact boundary location can be moved flexibly on the possible contact boundary. This method is effective to deal with moving and rolling contact problems on a possible larger moving or rolling contact region. Numerical examples show effectiveness of the presented scheme.

  15. Alternating Direction Finite Volume Element Methods for Three-Dimensional Parabolic Equations

    Institute of Scientific and Technical Information of China (English)

    Tongke

    2010-01-01

    This paper presents alternating direction finite volume element methods for three-dimensional parabolic partial differential equations and gives four computational schemes, one is analogous to Douglas finite difference scheme with second-order splitting error, the other two schemes have third-order splitting error, and the last one is an extended LOD scheme. The L2 norm and H1 semi-norm error estimates are obtained for the first scheme and second one, respectively. Finally, two numerical examples are provided to illustrate the efficiency and accuracy of the methods.

  16. THE ELLIPSOID ARTIFICIAL BOUNDARY METHOD FOR THREE-DIMENSIONAL UNBOUNDED DOMAINS

    Institute of Scientific and Technical Information of China (English)

    Hongying Huang; Dehao Yu

    2009-01-01

    The artificial boundary method is applied to solve three-dimensional exterior problems.Two kind of rotating ellipsoids are chosen as the artificial boundaries and the exact artificial boundary conditions are derived explicitly in terms of an infinite series. Then the well-posedness of the coupled variational problem is obtained. It is found that error estimates derived depend on the mesh size, truncation term and the location of the artificial boundary. Three numerical examples are presented to demonstrate the effectiveness and accuracy of the proposed method.

  17. Numerical method for solving the three-dimensional time-dependent neutron diffusion equation

    Energy Technology Data Exchange (ETDEWEB)

    Khaled, S.M. [Institute of Nuclear Techniques, Budapest University of Technology and Economics, Budapest (Hungary)]. E-mail: K_S_MAHMOUD@hotmail.com; Szatmary, Z. [Institute of Nuclear Techniques, Budapest University of Technology and Economics, Budapest (Hungary)]. E-mail: szatmary@reak.bme.hu

    2005-07-01

    A numerical time-implicit method has been developed for solving the coupled three-dimensional time-dependent multi-group neutron diffusion and delayed neutron precursor equations. The numerical stability of the implicit computation scheme and the convergence of the iterative associated processes have been evaluated. The computational scheme requires the solution of large linear systems at each time step. For this purpose, the point over-relaxation Gauss-Seidel method was chosen. A new scheme was introduced instead of the usual source iteration scheme. (author)

  18. The PLSI Method of Stabilizing Two-Dimensional Nonsymmetric Half-Plane Recursive Digital Filters

    OpenAIRE

    Gangatharan N; Reddy PS

    2003-01-01

    Two-dimensional (2D) recursive digital filters find applications in image processing as in medical X-ray processing. Nonsymmetric half-plane (NSHP) filters have definitely positive magnitude characteristics as opposed to quarter-plane (QP) filters. In this paper, we provide methods for stabilizing the given 2D NSHP polynomial by the planar least squares inverse (PLSI) method. We have proved in this paper that if the given 2D unstable NSHP polynomial and its PLSI are of the same degree, the P...

  19. Research on image matching method of big data image of three-dimensional reconstruction

    Science.gov (United States)

    Zhang, Chunsen; Qiu, Zhenguo; Zhu, Shihuan; Wang, Xiqi; Xu, Xiaolei; Zhong, Sidong

    2015-12-01

    Image matching is the main flow of a three-dimensional reconstruction. With the development of computer processing technology, seeking the image to be matched from the large date image sets which acquired from different image formats, different scales and different locations has put forward a new request for image matching. To establish the three dimensional reconstruction based on image matching from big data images, this paper put forward a new effective matching method based on visual bag of words model. The main technologies include building the bag of words model and image matching. First, extracting the SIFT feature points from images in the database, and clustering the feature points to generate the bag of words model. We established the inverted files based on the bag of words. The inverted files can represent all images corresponding to each visual word. We performed images matching depending on the images under the same word to improve the efficiency of images matching. Finally, we took the three-dimensional model with those images. Experimental results indicate that this method is able to improve the matching efficiency, and is suitable for the requirements of large data reconstruction.

  20. Bacterial beta-lactamase fragmentation complementation strategy can be used as a method for identifying interacting protein pairs.

    Science.gov (United States)

    Park, Jong-Hwa; Back, Jung Ho; Hahm, Soo Hyun; Shim, Hye-Young; Park, Min Ju; Ko, Sung Il; Han, Ye Sun

    2007-10-01

    We investigated the applicability of the TEM-1 beta- lactamase fragment complementation (BFC) system to develop a strategy for the screening of protein-protein interactions in bacteria. A BFC system containing a human Fas-associated death domain (hFADD) and human Fas death domain (hFasDD) was generated. The hFADD-hFasDD interaction was verified by cell survivability in ampicillin-containing medium and the colorimetric change of nitrocefin. It was also confirmed by His pull-down assay using cell lysates obtained in selection steps. A coiled-coil helix coiled-coil domain-containing protein 5 (CHCH5) was identified as an interacting protein of human uracil DNA glycosylase (hUNG) from the bacterial BFC cDNA library strategy. The interaction between hUNG and CHCH5 was further confirmed with immunoprecipitation using a mammalian expression system. CHCH5 enhanced the DNA glycosylase activity of hUNG to remove uracil from DNA duplexes containing a U/G mismatch pair. These results suggest that the bacterial BFC cDNA library strategy can be effectively used to identify interacting protein pairs.

  1. Numerical methods for one-dimensional reaction-diffusion equations arising in combustion theory

    Science.gov (United States)

    Ramos, J. I.

    1987-01-01

    A review of numerical methods for one-dimensional reaction-diffusion equations arising in combustion theory is presented. The methods reviewed include explicit, implicit, quasi-linearization, time linearization, operator-splitting, random walk and finite-element techniques and methods of lines. Adaptive and nonadaptive procedures are also reviewed. These techniques are applied first to solve two model problems which have exact traveling wave solutions with which the numerical results can be compared. This comparison is performed in terms of both the wave profile and computed wave speed. It is shown that the computed wave speed is not a good indicator of the accuracy of a particular method. A fourth-order time-linearized, Hermitian compact operator technique is found to be the most accurate method for a variety of time and space sizes.

  2. AN IMPROVED HYBRID BOUNDARY NODE METHOD IN TWO-DIMENSIONAL SOLIDS

    Institute of Scientific and Technical Information of China (English)

    Miao Yu; Wang Yuanhan; Jiang Heyang

    2005-01-01

    The hybrid boundary node method (HBNM) is a promising method for solving boundary value problems with the hybrid displacement variational formulation and shape functions from the moving least squares(MLS) approximation. The main idea is to reduce the dimensionality of the former and keep the meshless advantage of the latter. Following its application in solving potential problems, it is further developed and numerically implemented for 2D solids in this paper. The rigid movement method is employed to solve the hyper-singular integrations. Numerical examples for some 2D solids have been given to show the characteristics. The computation results obtained by the present method are in excellent agreement with the analytical solution.The parameters that influence the performance of this method are studied through numerical examples.

  3. An improved complex variable element-free Galerkin method for two-dimensional elasticity problems

    Institute of Scientific and Technical Information of China (English)

    Bai Fu-Nong; Li Dong-Ming; Wang Jian-Fei; Cheng Yu-Min

    2012-01-01

    In this paper,the improved complex variable moving least-squares (ICVMLS) approximation is presented.The ICVMLS approximation has an explicit physics meaning.Compared with the complex variable moving least-squares (CVMLS) approximations presented by Cheng and Ren,the ICVMLS approximation has a great computational precision and efficiency. Based on the element-free Galerkin (EFG) method and the ICVMLS approximation,the improved complex variable element-free Galerkin (ICVEFG) method is presented for two-dimensional elasticity problems,and the corresponding formulae are obtained.Compared with the conventional EFG method,the ICVEFG method has a great computational accuracy and efficiency.For the purpose of demonstration,three selected numerical examples are solved using the ICVEFG method.

  4. A new method to calculate Berry phase in one-dimensional quantum anomalous Hall insulator

    Science.gov (United States)

    Liao, Yi

    2016-08-01

    Based on the residue theorem and degenerate perturbation theory, we derive a new, simple and general formula for Berry phase calculation in a two-level system for which the Hamiltonian is a real symmetric matrix. The special torus topology possessed by the first Brillouin zone (1 BZ) of this kind of systems ensures the existence of a nonzero Berry phase. We verify the correctness of our formula on the Su-Schrieffer-Heeger (SSH) model. Then the Berry phase of one-dimensional quantum anomalous Hall insulator (1DQAHI) is calculated analytically by applying our method, the result being -π/2 -π/4 sgn (B) [ sgn (Δ - 4 B) + sgn (Δ) ]. Finally, illuminated by this idea, we investigate the Chern number in the two-dimensional case, and find a very simple way to determine the parameter range of the non-trivial Chern number in the phase diagram.

  5. Short-pulsed laser transport in two-dimensional scattering media by natural element method.

    Science.gov (United States)

    Zhang, Yong; Yi, Hong-Liang; Xie, Ming; Tan, He-Ping

    2014-04-01

    The natural element method (NEM) is extended to solve transient radiative transfer (TRT) in two-dimensional semitransparent media subjected to a collimated short laser irradiation. The least-squares (LS) weighted residuals approach is employed to spatially discretize the transient radiative heat transfer equation. First, for the case of the refractive index matched boundary, LSNEM solutions to TRT are validated by comparison with results reported in the literature. Effects of the incident angle on time-resolved signals of transmittance and reflectance are investigated. Afterward, the accuracy of this algorithm for the case of the refractive index mismatched boundary is studied. Finally, the LSNEM is extended to study the TRT in a two-dimensional semitransparent medium with refractive index discontinuity irradiated by the short pulse laser. The effects of scattering albedo, optical thickness, scattering phase function, and refractive index on transmittance and reflectance signals are investigated. Several interesting trends on the time-resolved signals are observed and analyzed.

  6. A three-dimensional sound ray tracing method by deploying regular tetrahedrons

    Institute of Scientific and Technical Information of China (English)

    JIANG Wei; LI Taibao

    2005-01-01

    A sound ray tracing algorithm is presented, which helps to rapidly find the sound ray trajectories in three-dimensional (3-D) space. At each step of ray tracing, a small regular tetrahedron is made in front of a ray, so that the sound speed field inside may be approximately regarded as linear. Since a ray trajectory in the linear sound speed field is always on a plane, it may be obtained by the two-dimensional (2-D) sound ray tracing method by deploying triangles.The theoretical derivation is given and a numerical model is discussed. It shows that the algorithm is fast and precise. It is also more concise and reliable than the traditional 3-D algorithms, and may be used to avoid the damage to the precision by the acoustic refraction in the 3-D ultrasound computerized tomography.

  7. New Clustering Method in High-Dimensional Space Based on Hypergraph-Models

    Institute of Scientific and Technical Information of China (English)

    CHEN Jian-bin; WANG Shu-jing; SONG Han-tao

    2006-01-01

    To overcome the limitation of the traditional clustering algorithms which fail to produce meanirigful clusters in high-dimensional, sparseness and binary value data sets, a new method based on hypergraph model is proposed. The hypergraph model maps the relationship present in the original data in high dimensional space into a hypergraph. A hyperedge represents the similarity of attribute-value distribution between two points. A hypergraph partitioning algorithm is used to find a partitioning of the vertices such that the corresponding data items in each partition are highly related and the weight of the hyperedges cut by the partitioning is minimized. The quality of the clustering result can be evaluated by applying the intra-cluster singularity value.Analysis and experimental results have demonstrated that this approach is applicable and effective in wide ranging scheme.

  8. Three-Dimensional Computed Tomography as a Method for Finding Die Attach Voids in Diodes

    Science.gov (United States)

    Brahm, E. N.; Rolin, T. D.

    2010-01-01

    NASA analyzes electrical, electronic, and electromechanical (EEE) parts used in space vehicles to understand failure modes of these components. The diode is an EEE part critical to NASA missions that can fail due to excessive voiding in the die attach. Metallography, one established method for studying the die attach, is a time-intensive, destructive, and equivocal process whereby mechanical grinding of the diodes is performed to reveal voiding in the die attach. Problems such as die attach pull-out tend to complicate results and can lead to erroneous conclusions. The objective of this study is to determine if three-dimensional computed tomography (3DCT), a nondestructive technique, is a viable alternative to metallography for detecting die attach voiding. The die attach voiding in two- dimensional planes created from 3DCT scans was compared to several physical cross sections of the same diode to determine if the 3DCT scan accurately recreates die attach volumetric variability

  9. PARALLEL ALGORITHM FOR THREE-DIMENSIONAL STOKES FLOW SIMULATION USING BOUNDARY ELEMENT METHOD

    Directory of Open Access Journals (Sweden)

    D. G. Pribytok

    2016-01-01

    Full Text Available Parallel computing technique for modeling three-dimensional viscous flow (Stokes flow using direct boundary element method is presented. The problem is solved in three phases: sampling and construction of system of linear algebraic equations (SLAE, its decision and finding the velocity of liquid at predetermined points. For construction of the system and finding the velocity, the parallel algorithms using graphics CUDA cards programming technology have been developed and implemented. To solve the system of linear algebraic equations the implemented software libraries are used. A comparison of time consumption for three main algorithms on the example of calculation of viscous fluid motion in three-dimensional cavity is performed.

  10. Two-dimensional wood drying stress simulation using control-volume mixed finite element methods (CVFEM

    Directory of Open Access Journals (Sweden)

    Carlos Salinas

    2011-05-01

    Full Text Available  The work was aimed at simulating two-dimensional wood drying stress using the control-volume finite element method (CVFEM. Stress/strain was modeled by moisture content gradients regarding shrinkage and mechanical sorption in a cross-section of wood. CVFEM was implemented with triangular finite elements and lineal interpolation of the independent variable which were programmed in Fortran 90 language. The model was validated by contrasting results with similar ones available in the specialised literature. The present model’s results came from isothermal (20ºC drying of quaking aspen (Populus tremuloides: two-dimensional distribution of stress/strain and water content, 40, 80, 130, 190 and 260 hour drying time and evolution of normal stress (2.5 <σ͓ ͓ < 1.2, MPa, from the interior to the exterior of wood. 

  11. Fast global convergence of gradient methods for high-dimensional statistical recovery

    CERN Document Server

    Agarwal, Alekh; Wainwright, Martin J

    2011-01-01

    Many statistical M-estimators are based on convex optimization problems formed by the combination of a data-dependent loss function with a norm-based regularizer. We analyze the convergence rates of projected gradient methods for solving such problems, working within a high-dimensional framework that allows the data dimension d to grow with (and possibly exceed) the sample size n. This high-dimensional structure precludes the usual global assumptions---namely, strong convexity and smoothness conditions---that underlie much of classical optimization analysis. We define appropriately restricted versions of these conditions, and show that they are satisfied with high probability for various statistical models. Under these conditions, our theory guarantees that projected gradient descent has a globally geometric rate of convergence up to the \\emph{statistical precision} of the model, meaning the typical distance between the true unknown parameter $\\theta^*$ and an optimal solution $\\hat{\\theta}$. This result is s...

  12. Multiconfigurational time-dependent Hartree method for bosons with internal degrees of freedom: Theory and composite fragmentation of multicomponent Bose-Einstein condensates

    Science.gov (United States)

    Lode, Axel U. J.

    2016-06-01

    In this paper, the multiconfigurational time-dependent Hartree for bosons (MCTDHB) method is derived for the case of N identical bosons with internal degrees of freedom. The theory for bosons with internal degrees of freedom constitutes a generalization of the MCTDHB method that substantially enriches the many-body physics that can be described. We demonstrate that the numerically exact solution of the time-dependent many-body Schrödinger equation for interacting bosonic particles with internal degrees of freedom is now feasible. We report on the MCTDHB equations of motion for bosons with internal degrees of freedom and their implementation for a general many-body Hamiltonian with one-body and two-body terms, both of which may depend on the internal states of the considered particles and time. To demonstrate the capabilities of the theory and its software implementation integrated in the mctdh-x software, we apply MCTDHB to the emergence of fragmentation of parabolically trapped bosons with two internal states: we study the ground state of N =100 bosons as a function of the separation between the state-dependent minima of the two parabolic potentials. To quantify the coherence of the system, we compute its normalized first-order correlation function. We find that the coherence within each internal state of the atoms is maintained, while it is lost between the different internal states. This is a hallmark of a kind of fragmentation absent in bosons without internal structure. We term the emergent phenomenon "composite fragmentation."

  13. A Novel Method for High Efficiency Amplification of Short DNA Fragments%一种高效扩增小片段DNA方法的建立

    Institute of Scientific and Technical Information of China (English)

    李岩; 李珊珊; 张玉祥

    2011-01-01

    目的 建立一种高效扩增小片段DNA的方法.方法 本方法利用单链DNA连接酶(single strand DNA ligase,ssDNA ligase)可以连接单链DNA的性质将小片段DNA自连成环,随后利用phi29 DNA聚合酶进行恒温的滚环复制,将扩增产物进行酶切,得到了扩增后的小片段DNA.结果 单链DNA连接酶可以有效的将30 bp的小片段DNA自连成环,phi29 DNA聚合酶可以扩增出大于10 kb的DNA片段,扩增产物经酶切后又可进行第二轮扩增,并且证明了其成环方式为自成环.结论 通过单链成环后滚环复制的这种方法可以有效的将小片段 DNA进行扩增,解决了PCR无法扩增小片段DNA的问题,并有着广阔的应用前景.%Objective To establish a method for highly efficient amplification of small fragment DNA. Methods Single-strand DNA intramolecular ligation was made by using single-stranded DNA ligase( ssDNA ligase), which can link small DNA fragments into a ring, and then isothermal rolling circle replication was carried out by using phi29 DNA polymerase. The amplified products were cut by incision enzyme. In this way, the small fragment DNA can be amplified at high efficiency. Results SsDNA ligase can make 30 bp oligonucleotide DNA cyclization, and phi29 DNA polymerase can make amplification products more than 10 kb in length. Amplification products can be amplified second times after being cut by incision enzyme. It was also proved that the way of single strand DNA cyclization was intramolecular. Conclusion This method can effectively amplify the small DNA fragments, and has broad prospects of application.

  14. Traveling wave solutions of the (2 + 1-dimensional Zoomeron equation and the Burgers equations via the MSE method and the Exp-function method

    Directory of Open Access Journals (Sweden)

    Kamruzzaman Khan

    2014-03-01

    Full Text Available The modified simple equation (MSE method is promising for finding exact traveling wave solutions of nonlinear evolution equations (NLEEs in mathematical physics. In this letter, we investigate solutions of the (2 + 1-dimensional Zoomeron equation and the (2 + 1-dimensional Burgers equation by using the MSE method and the Exp-function method. The competence of the methods for constructing exact solutions has been established.

  15. Molecular Fingerprinting of Mycobacterium tuberculosis Isolates Obtained in Havana, Cuba, by IS6110 Restriction Fragment Length Polymorphism Analysis and by the Double-Repetitive-Element PCR Method

    Science.gov (United States)

    Montoro, Ernesto; Valdivia, José; Leão, Sylvia Cardoso

    1998-01-01

    Mycobacterium tuberculosis sputum isolates from 38 patients, obtained in the first 6 months of 1997 in Havana, Cuba, were characterized by IS6110 restriction fragment length polymorphism (RFLP) analysis and the double-repetitive-element PCR (DRE-PCR) method. Among 41 strains from 38 patients, 24 and 25 unique patterns, and 5 and 4 cluster patterns, were found by the RFLP and DRE-PCR methods, respectively. Patients within two of these clusters were found to be epidemiologically related, while no relation was observed in patients in the other clusters. The DRE-PCR method is rapid, and it was as discriminating as IS6110 RFLP analysis in identifying an epidemiological association. Its simplicity makes the technique accessible for subtyping of M. tuberculosis strains in laboratories not equipped to perform RFLP analysis. PMID:9738082

  16. Simple and efficient method for isolating cDNA fragments of lea3 genes with potential for wide application in the grasses (Poaceae).

    Science.gov (United States)

    Yu, L; Wu, X; Tang, X; Yan, B

    2010-07-06

    cDNA fragments of lea3 genes with a high GC content (from 68 to 77%) were found in several Poaceae, including Sorghum vulgare, Saccharum officinarum, Oryza officinalis, Oryza meyeriana, Ampelocalamus calcareus, Cynodon dactylon, and Zizania latifoli. They were successfully isolated by means of optimal experimental parameters, which included dimethyl sulfoxide as additive and degenerate primers "AGETKAS" and "AGKDKTG", and their sequences were analyzed. Compared to the method of isolating genes by screening of a cDNA library using abscisic acid- and other stress-responsive cDNA clones, which is time-consuming and costly, this method is relatively easy and inexpensive. Using this new method, many new homologue lea3 genes were rapidly determined.

  17. Restriction fragment length polymorphism of the 5S-rRNA-NTS region: a rapid and precise method for plant identification.

    Science.gov (United States)

    Bertea, Cinzia Margherita; Gnavi, Giorgio

    2012-01-01

    Molecular genetic methods have several advantages over classical morphological and chemical analyses. The genetic method requires genotype instead than phenotype, therefore PCR-based techniques have been widely used for a rapid identification of plant species, varieties and chemotypes. Recently, the molecular discrimination of some higher plant species has been evaluated using sequences of a 5S-rRNA gene spacer region. The variation in the nontranscribed sequence (NTS) region has been used in a number of plant species for studying intraspecific variation, genome evolution, and phylogenetic reconstruction. Here, we describe a rapid method based on the use of the 5S-rRNA-NTS region as a tool for plant DNA fingerprinting, which combines PCR, sequencing and restriction fragment length polymorphism analyses.

  18. A method for measuring post-extraction alveolar dimensional changes with volumetric computed tomography.

    Science.gov (United States)

    Bontá, Hernán; Galli, Federico G; Caride, Facundo; Carranza, Nelson

    2012-01-01

    The aim of this study is to present a predictable method for evaluating dimensional changes in the alveolar ridge through cone beam computed tomography (CT). Twenty subjects with single-rooted tooth extraction indication were selected for this preliminary report, which is part of a larger ongoing investigation. After extraction, two CT scans were performed; the first within 24 hours post-extraction (TC1) and the second 6 months (TC2) later. A radiographic guide with a radiopaque element placed along the tooth axis was developed to locate the same plane of reference in two different CT scans. For each patient, backtrack analysis was performed in order to establish the reproducibility error of a predetermined point in space between two CT scans. Briefly, an anatomical landmark was selected and its coordinates to the radiopaque marker were recorded. One week later, the coordinates were followed backwards in the same CT scan to obtain the position where the reference point should be located. A similar process was carried out between two different CT scans taken 6 months apart. The distance between the anatomical reference and the obtained point of position was calculated to establish the accuracy of the method. Additionally, a novel method for evaluating dimensional changes of the alveolus after tooth extraction is presented. The backtrack analysis determined an average within-examiner discrepancy between both measurements from the same CT scan of 0.19 mm. SD +/- 0.05. With the method presented herein, a reference point in a CT scan can be accurately backtracked and located in a second CT scan taken six months later. Taken together they open the possibility of calculating dimensional changes that occur in the alveolar ridge over time, such as post-extraction alveolar resorption, or the bone volume gained after different augmentation procedures.

  19. T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids.

    Science.gov (United States)

    Nai, Yu-Shin; Chen, Tzu-Han; Huang, Yu-Feng; Midha, Mohit K; Shiau, Hsin-Chieh; Shen, Chen-Yang; Chen, Chien-Jen; Yu, Alice L; Chiu, Kuo Ping

    2017-01-17

    Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous "half adaptor" (HA), generated by annealing P oligo (carrying a phosphate group at the 5' end) and T oligo (carrying a T-tail at the 3' end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification.

  20. T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids

    Science.gov (United States)

    Nai, Yu-Shin; Chen, Tzu-Han; Huang, Yu-Feng; Midha, Mohit K.; Shiau, Hsin-Chieh; Shen, Chen-Yang; Chen, Chien-Jen; Yu, Alice L.; Chiu, Kuo Ping

    2017-01-01

    Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous “half adaptor” (HA), generated by annealing P oligo (carrying a phosphate group at the 5′ end) and T oligo (carrying a T-tail at the 3′ end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification. PMID:28094343

  1. Parallel processing method for two-dimensional Sn transport code DOT3.5

    Energy Technology Data Exchange (ETDEWEB)

    Uematsu, Mikio [Toshiba Corp., Kawasaki, Kanagawa (Japan)

    1998-03-01

    A parallel processing method for the two-dimensional Sn transport code DOT3.5 has been developed to achieve drastic reduction of computation time. In the proposed method, parallelization is made with angular domain decomposition and/or space domain decomposition. Calculational speedup for parallel processing by angular domain decomposition is achieved by minimizing frequency of communications between processing elements. As for parallel processing by space domain decomposition, two-step rescaling method consisting of segmentwise rescaling and the ordinary pointwise rescaling have been developed to accelerate convergence, which will otherwise be degraded because of discontinuity at the segment boundaries. The developed method was examined with a Sun workstation using the PVM message-passing library, and sufficient speedup was observed. (author)

  2. A FINITE DIFFERENCE METHOD FOR THE ONE-DIMENSIONAL VARIATIONAL BOUSSINESQ EQUATIONS

    Directory of Open Access Journals (Sweden)

    A. Suryanto

    2012-06-01

    Full Text Available The variational Boussinesq equations derived by Klopman et. al. (2005 con-verse mass, momentum and positive-definite energy. Moreover, they were shown to have significantly improved frequency dispersion characteristics, making it suitable for wave simulation from relatively deep to shallow water. In this paper we develop a numerica lcode for the variational Boussinesq equations. This code uses a fourth-order predictor-corrector method for time derivatives and fourth-order finite difference method for the first-order spatial derivatives. The numerical method is validated against experimen-tal data for one-dimensional nonlinear wave transformation problems. Furthermore, the method is used to illustrate the dispersive effects on tsunami-type of wave propagation.

  3. Lattice Boltzmann method for three-dimensional moving particles in a Newtonian fluid

    Institute of Scientific and Technical Information of China (English)

    Fang Hai-Ping; Chen Shi-Yi

    2004-01-01

    @@ A lattice Boltzmann method is developed to simulate three-dimensional solid particle motions in fluids. In the present model, a uniform grid is used and the exact spatial location of the physical boundary of the suspended particles is determined using an interpolation scheme. The numerical accuracy and efficiency of the proposed lattice Boltzmann method is demonstrated by simulating the sedimentation of a single sphere in a square cylinder. Highly accurate simulation results can be achieved with few meshes, compared with the previous lattice Boltzmann methods. The present method is expected to find applications on the flow systems with moving boundaries, such as the blood flow in distensible vessels, the particle-flow interaction and the solidification of alloys.

  4. Trefftz method for the solution of three-dimensional forward and inverse problems of geoelectrics

    Science.gov (United States)

    Yegorov, I. V.

    2011-02-01

    The Trefftz method is applied to the numerical solution of the three-dimensional (3D) forward problem for an electromagnetic field harmonically oscillating with time in a 3D environment, which ensures the possibility to solve a 3D inverse problem. Here, the known idea of simultaneous joint interpretation of the tangential components of electric and magnetic fields measured on the Earth's surface, which was suggested by A.N. Tikhonov for the development of the electromagnetic sounding method, is employed in the context of the numerical-analytical representation of the forward problem solution in accordance with the Trefftz method. Application of this method allows enables one to generalize the basic plane-stratified vertically 1D model of the medium by allowing for lateral variations in electric conductivity.

  5. The solution of the two-dimensional sine-Gordon equation using the method of lines

    Science.gov (United States)

    Bratsos, A. G.

    2007-09-01

    The method of lines is used to transform the initial/boundary-value problem associated with the two-dimensional sine-Gordon equation in two space variables into a second-order initial-value problem. The finite-difference methods are developed by replacing the matrix-exponential term in a recurrence relation with rational approximants. The resulting finite-difference methods are analyzed for local truncation error, stability and convergence. To avoid solving the nonlinear system a predictor-corrector scheme using the explicit method as predictor and the implicit as corrector is applied. Numerical solutions for cases involving the most known from the bibliography line and ring solitons are given.

  6. A characteristic mapping method for two-dimensional incompressible Euler flows

    Science.gov (United States)

    Yadav, Badal; Mercier, Olivier; Nave, Jean-Christophe; Schneider, Kai

    2016-11-01

    We propose an efficient semi-Lagrangian method for solving the two-dimensional incompressible Euler equations with high precision on a coarse grid. The new approach evolves the flow map using the gradient-augmented level set method (GALSM). Since the flow map can be decomposed into submaps (each over a finite time interval), the error can be controlled by choosing the remapping times appropriately. This leads to a numerical scheme that has exponential resolution in linear time. The computational efficiency and the high precision of the method are illustrated for a vortex merger and a four mode flow. Comparisons with a Cauchy-Lagrangian method are also presented. KS thankfully acknowledges financial support from the French Research Federation for Fusion Studies within the framework of the European Fusion Development Agreement (EFDA).

  7. Wave Number Method for Three-Dimensional Steady-State Acoustic Problems

    Institute of Scientific and Technical Information of China (English)

    HUANG Fei; HE Zeng; WEI Jun-hong; PENG Wei-cai

    2007-01-01

    Based on the indirect Trefftz approach, a wave number method (WNM) is proposed to deal with three-dimensional steady-state acoustic problems. In the WNM, the dynamic pressure response variable is approximated by a set of wave functions, which exactly satisfy the Helmholtz equation. The set of wave functions comprise the exact solutions of the homogeneous part of the governing equations and some particular solution functions. The unknown coefficients of the wave functions can be obtained by enforcing the pressure approximation to satisfy the boundary conditions. Compared with the boundary element method (BEM), the WNM have a smaller system matrix, and is applicable to the radiation problems since the wave functions are independent of the domain size. A 3D acoustic cavity is exemplified to show the properties of the method. The results show that the wave number method is more efficient than the BEM, and it is fairly accurate.

  8. Fragmentation and Hadronization

    OpenAIRE

    Webber, B. R.

    1999-01-01

    Experimental data, theoretical ideas and models concerning jet fragmentation and the hadronization process are reviewed, concentrating on the following topics: factorization and small-x resummation of fragmentation functions, hadronization models, single-particle yields and spectra in Z decay, comparisons between quark and gluon jets, current and target fragmentation in deep inelastic scattering, heavy quark fragmentation, Bose-Einstein correlations and WW fragmentation.

  9. Band structure of one-dimensional plasma photonic crystals using the Fresnel coefficients method

    Science.gov (United States)

    Jafari, A.; Rahmat, A.

    2016-11-01

    The current study has examined the band structures of two types of photonic crystals (PCs). The first is a one-dimensional metamaterial photonic crystal (1DMMPC) composed of double-layered units for which both layers of each unit are dielectric. The second type is a very similar one-dimensional plasma photonic crystal (1DPPC) also composed of double-layered units in which the first layer is a dielectric material but the second is a plasma layer. This study compares the band structures of the 1DMMPC with specific optical characteristics of the 1DPPC using the Fresnel coefficients method and also compares the results of this method with the results of the transfer matrix method. It is concluded that the dependency of the electric permittivity of the plasma layer on the incident field frequency causes differences in the band structures in 1DMMPC and 1DPPC for both TE and TM polarizations and their gaps reside in different frequencies. The band structures of the 1DMMPC and 1DPPC are confirmed by the results of the transfer matrix method.

  10. Three-Dimensional Transient Electromagnetic Modeling Based on Fictitious Wave Domain Methods

    Science.gov (United States)

    Ji, Yanju; Hu, Yanpu; Imamura, Naoto

    2017-05-01

    Finite-difference time domain (FDTD) methods, which have been widely employed in three-dimensional transient electromagnetic (TEM) modeling, require very small time steps to simulate the electromagnetic fields and this will be time consuming. We present an efficient numerical method for three-dimensional TEM forward modeling. Its key features are based on a correspondence principle between the diffusive and fictitious wave fields. The diffusive Maxwell's equations are transformed and solved in a so-called fictitious wave domain. This scheme allows larger time steps than conventional FDTD methods, allows including air layers, and allows simulating topography. The need for initial field calculations is avoided by including an electric current source in the governing equations. This also avoids a traditional assumption of a flat earth surface in TEM modeling. We test the accuracy of the electromagnetic fields' responses using our method with the spectral differential difference (SLDM) solutions. The results show good agreement even under the existence of air layers and topography in the model.

  11. Kernel Local Linear Discriminate Method for Dimensionality Reduction and Its Application in Machinery Fault Diagnosis

    Directory of Open Access Journals (Sweden)

    Kunju Shi

    2014-01-01

    Full Text Available Dimensionality reduction is a crucial task in machinery fault diagnosis. Recently, as a popular dimensional reduction technology, manifold learning has been successfully used in many fields. However, most of these technologies are not suitable for the task, because they are unsupervised in nature and fail to discover the discriminate structure in the data. To overcome these weaknesses, kernel local linear discriminate (KLLD algorithm is proposed. KLLD algorithm is a novel algorithm which combines the advantage of neighborhood preserving projections (NPP, Floyd, maximum margin criterion (MMC, and kernel trick. KLLD has four advantages. First of all, KLLD is a supervised dimension reduction method that can overcome the out-of-sample problems. Secondly, short-circuit problem can be avoided. Thirdly, KLLD algorithm can use between-class scatter matrix and inner-class scatter matrix more efficiently. Lastly, kernel trick is included in KLLD algorithm to find more precise solution. The main feature of the proposed method is that it attempts to both preserve the intrinsic neighborhood geometry of the increased data and exact the discriminate information. Experiments have been performed to evaluate the new method. The results show that KLLD has more benefits than traditional methods.

  12. A Kernel—based Nonlinear Subspace Projection Method for Dimensionality Reduction of Hyperspectral Image Data

    Institute of Scientific and Technical Information of China (English)

    GUYanfeng; ZHANGYe; QUANTaifan

    2003-01-01

    A challenging problem in using hyper-spectral data is to eliminate redundancy and preserve useful spectral information for applications. In this pa-per, a kernel-based nonlinear subspace projection (KNSP)method is proposed for feature extraction and dimension-ality reduction in hyperspectral images. The proposed method includes three key steps: subspace partition of hyperspectral data, feature extraction using kernel-based principal component analysis (KPCA) and feature selec-tion based on class separability in the subspaces. Accord-ing to the strong correlation between neighboring bands,the whole data space is partitioned to requested subspaces.In each subspace, the KPCA method is used to effectively extract spectral feature and eliminate redundancies. A criterion function based on class discrimination and sepa-rability is used for the transformed feature selection. For the purpose of testifying its effectiveness, the proposed new method is compared with the classical principal component analysis (PCA) and segmented principal component trans-formation (SPCT). A hyperspectral image classification is performed on AVIRIS data. which have 224 svectral bands.Experimental results show that KNSP is very effective for feature extraction and dimensionality reduction of hyper-spectral data and provides significant improvement over classical PCA and current SPCT technique.

  13. Numerical simulation of two-dimensional spouted bed with draft plates by discrete element method

    Institute of Scientific and Technical Information of China (English)

    Yongzhi ZHAO; Yi CHENG; Maoqiang JIANG; Yong JIN

    2008-01-01

    A discrete element method (DEM)-computa-tional fluid dynamics (CFD) two-way coupling method was employed to simulate the hydrodynamics in a two-dimensional spouted bed with draft plates. The motion of particles was modeled by the DEM and the gas flow was modeled by the Navier-Stokes equation. The interactions between gas and particles were considered using a two-way coupling method. The motion of particles in the spouted bed with complex geometry was solved by com-bining DEM and boundary element method (BEM). The minimal spouted velocity was obtained by the BEM-DEM-CFD simulation and the variation of the flow pat-tern in the bed with different superficial gas velocity was studied. The relationship between the pressure drop of the spouted bed and the superficial gas velocity was achieved from the simulations. The radial profile of the averaged vertical velocities of particles and the profile of the aver-aged void fraction in the spout and the annulus were stat-istically analyzed. The flow characteristics of the gas-solid system in the two-dimensional spouted bed were clearly described by the simulation results.

  14. New Traveling Wave Solutions of the Higher Dimensional Nonlinear Partial Differential Equation by the Exp-Function Method

    Directory of Open Access Journals (Sweden)

    Hasibun Naher

    2012-01-01

    Full Text Available We construct new analytical solutions of the (3+1-dimensional modified KdV-Zakharov-Kuznetsev equation by the Exp-function method. Plentiful exact traveling wave solutions with arbitrary parameters are effectively obtained by the method. The obtained results show that the Exp-function method is effective and straightforward mathematical tool for searching analytical solutions with arbitrary parameters of higher-dimensional nonlinear partial differential equation.

  15. Bibliography of papers, reports, and presentations related to point-sample dimensional measurement methods for machined part evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Baldwin, J.M. [Sandia National Labs., Livermore, CA (United States). Integrated Manufacturing Systems

    1996-04-01

    The Dimensional Inspection Techniques Specification (DITS) Project is an ongoing effort to produce tools and guidelines for optimum sampling and data analysis of machined parts, when measured using point-sample methods of dimensional metrology. This report is a compilation of results of a literature survey, conducted in support of the DITS. Over 160 citations are included, with author abstracts where available.

  16. A two-dimensional adaptive spectral element method for the direct simulation of incompressible flow

    Science.gov (United States)

    Hsu, Li-Chieh

    The spectral element method is a high order discretization scheme for the solution of nonlinear partial differential equations. The method draws its strengths from the finite element method for geometrical flexibility and spectral methods for high accuracy. Although the method is, in theory, very powerful for complex phenomena such as transitional flows, its practical implementation is limited by the arbitrary choice of domain discretization. For instance, it is hard to estimate the appropriate number of elements for a specific case. Selection of regions to be refined or coarsened is difficult especially as the flow becomes more complex and memory limits of the computer are stressed. We present an adaptive spectral element method in which the grid is automatically refined or coarsened in order to capture underresolved regions of the domain and to follow regions requiring high resolution as they develop in time. The objective is to provide the best and most efficient solution to a time-dependent nonlinear problem by continually optimizing resource allocation. The adaptivity is based on an error estimator which determines which regions need more resolution. The solution strategy is as follows: compute an initial solution with a suitable initial mesh, estimate errors in the solution locally in each element, modify the mesh according to the error estimators, interpolate old mesh solutions onto the new elements, and resume the numerical solution process. A two-dimensional adaptive spectral element method for the direct simulation of incompressible flows has been developed. The adaptive algorithm effectively diagnoses and refines regions of the flow where complexity of the solution requires increased resolution. The method has been demonstrated on two-dimensional examples in heat conduction, Stokes and Navier-Stokes flows.

  17. A three-dimensional measurement method based on mesh candidates assisted with structured light

    Science.gov (United States)

    Xu, Gang; Zhang, Wenming; Li, Haibin; Liu, Bin

    2009-07-01

    Rendering three-dimensional information of a scene from optical measurement is very important for a wide variety of applications such as robot navigation, rapid prototyping, medical imaging, industrial inspection, etc. In this paper, a new 3D measurement method based on mesh candidate with structured light illuminating is proposed. The vision sensor consists of two CCD cameras and a DLP projector. The measurement system combines the technology of binocular stereo vision and structured light, so as to simplify the process of acquiring depth information using mesh candidates. The measurement method is based on mesh candidates which represent the potential depth in the three dimensional scene. First the mesh grid was created along the direction of axes in world coordinate system, and the nodes were considered as depth candidates on the surface of object. Then each group of the mesh nodes varying along z axis were mapped to the captured image planes of both cameras. At last, according to the similarity measure of the corresponding pixel pairs, the depth of the object surface can be obtained. The matching process is between the pixels in both camera planes corresponding to the spatial mesh candidates. Aided by the structured light pattern, the accuracy of measurement system improved. Appending the periodic sawtooth pattern on the scene by structured light made measurement easier, while the computational cost did not increased since the projector had no need to be calibrated. The 3DS MAX and Matlab software were used to simulate measurement system and reconstruct the surface of the object. After the positioned cameras have been calibrated using Matlab calibration toolbox, the projector is used to project structured light pattern on the scene. Indicated by experimental results, the mesh-candidate-based method is obviously superior in computation and accuracy. Compared with traditional methods based on image matching, our method has several advantages: (1) the complex

  18. The correction of the distortion of human face based on three-dimensional modeling methods

    Science.gov (United States)

    Ye, Qingmin; Chen, Kuo; Feng, Huajun; Xu, Zhihai; Li, Qi

    2015-08-01

    When the human face is on the edge of field of the camera which has a large view, serious deformation will be captured. To correct the distortion of the human face, we present an approach based on setting up a 3D model. Firstly, we construct 3D target face modeling by using the data and depth information of the standard human face, which is set up by the three-dimensional model with three-dimensional Gaussian function with sectional type. According to the size of the face in the image and the parameters of the camera, we can obtain the information of relative position and depth of the human face. Then by translating the virtual camera axis to the center of the face, we can achieve the goal to correct the distortion of the face based on the theory of three-dimensional imaging. Finally, we have made a lot of experiments, and we study the influence of parameters of the 3D model of human face. The result indicates that the method presented by this paper can play an effective role in correcting the distortion of the face in the edge of the view, and we can get better results if the model appreciates the real human face.

  19. Advanced three-dimensional scan methods in the nanopositioning and nanomeasuring machine

    Science.gov (United States)

    Hausotte, T.; Percle, B.; Jäger, G.

    2009-08-01

    The nanopositioning and nanomeasuring machine developed at the Ilmenau University of Technology was originally designed for surface measurements within a measuring volume of 25 mm × 25 mm × 5 mm. The interferometric length measuring and drive systems make it possible to move the stage with a resolution of 0.1 nm and a positioning uncertainty of less than 10 nm in all three axes. Various measuring tasks are possible depending on the installed probe system. Most of the sensors utilized are one-dimensional surface probes; however, some tasks require measuring sidewalls and other three-dimensional features. A new control system, based on the I++ DME specification, was implemented in the device. The I++ DME scan functions were improved and special scan functions added to allow advanced three-dimensional scan methods, further fulfilling the demands of scanning force microscopy and micro-coordinate measurements. This work gives an overview of these new functions and the application of them for several different measurements.

  20. Enhanced spectral resolution by high-dimensional NMR using the filter diagonalization method and "hidden" dimensions.

    Science.gov (United States)

    Meng, Xi; Nguyen, Bao D; Ridge, Clark; Shaka, A J

    2009-01-01

    High-dimensional (HD) NMR spectra have poorer digital resolution than low-dimensional (LD) spectra, for a fixed amount of experiment time. This has led to "reduced-dimensionality" strategies, in which several LD projections of the HD NMR spectrum are acquired, each with higher digital resolution; an approximate HD spectrum is then inferred by some means. We propose a strategy that moves in the opposite direction, by adding more time dimensions to increase the information content of the data set, even if only a very sparse time grid is used in each dimension. The full HD time-domain data can be analyzed by the filter diagonalization method (FDM), yielding very narrow resonances along all of the frequency axes, even those with sparse sampling. Integrating over the added dimensions of HD FDM NMR spectra reconstitutes LD spectra with enhanced resolution, often more quickly than direct acquisition of the LD spectrum with a larger number of grid points in each of the fewer dimensions. If the extra-dimensions do not appear in the final spectrum, and are used solely to boost information content, we propose the moniker hidden-dimension NMR. This work shows that HD peaks have unmistakable frequency signatures that can be detected as single HD objects by an appropriate algorithm, even though their patterns would be tricky for a human operator to visualize or recognize, and even if digital resolution in an HD FT spectrum is very coarse compared with natural line widths.

  1. Comprehensive two-dimensional river ice model based on boundary-fitted coordinate transformation method

    Directory of Open Access Journals (Sweden)

    Ze-yu MAO

    2014-01-01

    Full Text Available River ice is a natural phenomenon in cold regions, influenced by meteorology, geomorphology, and hydraulic conditions. River ice processes involve complex interactions between hydrodynamic, mechanical, and thermal processes, and they are also influenced by weather and hydrologic conditions. Because natural rivers are serpentine, with bends, narrows, and straight reaches, the commonly-used one-dimensional river ice models and two-dimensional models based on the rectangular Cartesian coordinates are incapable of simulating the physical phenomena accurately. In order to accurately simulate the complicated river geometry and overcome the difficulties of numerical simulation resulting from both complex boundaries and differences between length and width scales, a two-dimensional river ice numerical model based on a boundary-fitted coordinate transformation method was developed. The presented model considers the influence of the frazil ice accumulation under ice cover and the shape of the leading edge of ice cover during the freezing process. The model is capable of determining the velocity field, the distribution of water temperature, the concentration distribution of frazil ice, the transport of floating ice, the progression, stability, and thawing of ice cover, and the transport, accumulation, and erosion of ice under ice cover. A MacCormack scheme was used to solve the equations numerically. The model was validated with field observations from the Hequ Reach of the Yellow River. Comparison of simulation results with field data indicates that the model is capable of simulating the river ice process with high accuracy.

  2. Improving the dimensional stability of natural fibers with the fiber polymer penetrant and electron beam method

    Science.gov (United States)

    Woods, Sean R.

    Cellulose-based material absorbs or releases moisture in relation to atmospheric conditions. This research looks to minimize dimensional change with the use of low molecular weight (LMW) monomers polymerized by electron beam (EB) ionizing radiation. Sisal, jute, coir, and hemp natural fibers with average natural swelling of 26.55%, 29.46%, 9.06%, and 32.69%, respectively, and glass fiber as control were used for analysis. Three LMW bulk monomers, hydroxyethyl acrylate (HEA), hydroxyethyl methacrylate (HEMA), and polyethylene glycol diacrylate (EGDA), as well as an encapsulating agent, isodecyl acrylate, and cross-linker, ethoxylated trimethylolpropane triacrylate, were evaluated for resin formulation. In total, 1015 specimens were measured for swelling. Moisture uptake characteristics of the specimens were analyzed. A new method of measuring specimen dimensional changes by a light microscope and image analysis software was used. Results indicate dimensional stability improvement of 39.34% - 91.46% for hemp with HEA and cross-linker, and sisal with HEMA and cross-linker respectively.

  3. Two-dimensional thermal analysis of a fuel rod by finite volume method

    Energy Technology Data Exchange (ETDEWEB)

    Costa, Rhayanne Y.N.; Silva, Mario A.B. da; Lira, Carlos A.B. de O., E-mail: ryncosta@gmail.com, E-mail: mabs500@gmail.com, E-mail: cabol@ufpe.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamaento de Energia Nuclear

    2015-07-01

    In a nuclear reactor, the amount of power generation is limited by thermal and physic limitations rather than by nuclear parameters. The operation of a reactor core, considering the best heat removal system, must take into account the fact that the temperatures of fuel and cladding shall not exceed safety limits anywhere in the core. If such considerations are not considered, damages in the fuel element may release huge quantities of radioactive materials in the coolant or even core meltdown. Thermal analyses for fuel rods are often accomplished by considering one-dimensional heat diffusion equation. The aim of this study is to develop the first paper to verify the temperature distribution for a two-dimensional heat transfer problem in an advanced reactor. The methodology is based on the Finite Volume Method (FVM), which considers a balance for the property of interest. The validation for such methodology is made by comparing numerical and analytical solutions. For the two-dimensional analysis, the results indicate that the temperature profile agree with expected physical considerations, providing quantitative information for the development of advanced reactors. (author)

  4. Solution of D dimensional Dirac equation for hyperbolic tangent potential using NU method and its application in material properties

    Energy Technology Data Exchange (ETDEWEB)

    Suparmi, A., E-mail: soeparmi@staff.uns.ac.id; Cari, C., E-mail: cari@staff.uns.ac.id; Pratiwi, B. N., E-mail: namakubetanurpratiwi@gmail.com [Physics Department, Faculty of Mathematics and Science, Sebelas Maret University, Jl. Ir. Sutami 36A Kentingan Surakarta 57126 (Indonesia); Deta, U. A. [Physics Department, Faculty of Science and Mathematics Education and Teacher Training, Surabaya State University, Surabaya (Indonesia)

    2016-02-08

    The analytical solution of D-dimensional Dirac equation for hyperbolic tangent potential is investigated using Nikiforov-Uvarov method. In the case of spin symmetry the D dimensional Dirac equation reduces to the D dimensional Schrodinger equation. The D dimensional relativistic energy spectra are obtained from D dimensional relativistic energy eigen value equation by using Mat Lab software. The corresponding D dimensional radial wave functions are formulated in the form of generalized Jacobi polynomials. The thermodynamically properties of materials are generated from the non-relativistic energy eigen-values in the classical limit. In the non-relativistic limit, the relativistic energy equation reduces to the non-relativistic energy. The thermal quantities of the system, partition function and specific heat, are expressed in terms of error function and imaginary error function which are numerically calculated using Mat Lab software.

  5. Fast Multipole Methods for Three-Dimensional N-body Problems

    Science.gov (United States)

    Koumoutsakos, P.

    1995-01-01

    We are developing computational tools for the simulations of three-dimensional flows past bodies undergoing arbitrary motions. High resolution viscous vortex methods have been developed that allow for extended simulations of two-dimensional configurations such as vortex generators. Our objective is to extend this methodology to three dimensions and develop a robust computational scheme for the simulation of such flows. A fundamental issue in the use of vortex methods is the ability of employing efficiently large numbers of computational elements to resolve the large range of scales that exist in complex flows. The traditional cost of the method scales as Omicron (N(sup 2)) as the N computational elements/particles induce velocities at each other, making the method unacceptable for simulations involving more than a few tens of thousands of particles. In the last decade fast methods have been developed that have operation counts of Omicron (N log N) or Omicron (N) (referred to as BH and GR respectively) depending on the details of the algorithm. These methods are based on the observation that the effect of a cluster of particles at a certain distance may be approximated by a finite series expansion. In order to exploit this observation we need to decompose the element population spatially into clusters of particles and build a hierarchy of clusters (a tree data structure) - smaller neighboring clusters combine to form a cluster of the next size up in the hierarchy and so on. This hierarchy of clusters allows one to determine efficiently when the approximation is valid. This algorithm is an N-body solver that appears in many fields of engineering and science. Some examples of its diverse use are in astrophysics, molecular dynamics, micro-magnetics, boundary element simulations of electromagnetic problems, and computer animation. More recently these N-body solvers have been implemented and applied in simulations involving vortex methods. Koumoutsakos and Leonard (1995

  6. Three-dimensional Reconstruction Method Study Based on Interferometric Circular SAR

    Directory of Open Access Journals (Sweden)

    Hou Liying

    2016-10-01

    Full Text Available Circular Synthetic Aperture Radar (CSAR can acquire targets’ scattering information in all directions by a 360° observation, but a single-track CSAR cannot efficiently obtain height scattering information for a strong directive scatter. In this study, we examine the typical target of the three-dimensional circular SAR interferometry theoryand validate the theory in a darkroom experiment. We present a 3D reconstruction of the actual tank metal model of interferometric CSAR for the first time, verify the validity of the method, and demonstrate the important potential applications of combining 3D reconstruction with omnidirectional observation.

  7. A 3-dimensional finite-difference method for calculating the dynamic coefficients of seals

    Science.gov (United States)

    Dietzen, F. J.; Nordmann, R.

    1989-01-01

    A method to calculate the dynamic coefficients of seals with arbitrary geometry is presented. The Navier-Stokes equations are used in conjunction with the k-e turbulence model to describe the turbulent flow. These equations are solved by a full 3-dimensional finite-difference procedure instead of the normally used perturbation analysis. The time dependence of the equations is introduced by working with a coordinate system rotating with the precession frequency of the shaft. The results of this theory are compared with coefficients calculated by a perturbation analysis and with experimental results.

  8. THREE-DIMENSIONAL ANALYSIS OF FUNCTIONALLY GRADED PLATE BASED ON THE HAAR WAVELET METHOD

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A three-dimensional analysis of a simply-supported functionally graded rectangular plate with an arbitrary distribution of material properties is made using a simple and effective method based on the Haar wavelet. With good features in treating singularities, Haar series solution converges rapidly for arbitrary distributions, especially for the case where the material properties change rapidly in some regions. Through numerical examples the influences of the ratio of material constants on the top and bottom surfaces and different material gradient distributions on the structural response of the plate to mechanical stimuli are studied.

  9. Three-dimensional hypersonic rarefied flow calculations using direct simulation Monte Carlo method

    Science.gov (United States)

    Celenligil, M. Cevdet; Moss, James N.

    1993-01-01

    A summary of three-dimensional simulations on the hypersonic rarefied flows in an effort to understand the highly nonequilibrium flows about space vehicles entering the Earth's atmosphere for a realistic estimation of the aerothermal loads is presented. Calculations are performed using the direct simulation Monte Carlo method with a five-species reacting gas model, which accounts for rotational and vibrational internal energies. Results are obtained for the external flows about various bodies in the transitional flow regime. For the cases considered, convective heating, flowfield structure and overall aerodynamic coefficients are presented and comparisons are made with the available experimental data. The agreement between the calculated and measured results are very good.

  10. Two dimensional density and its fluctuation measurements by using phase imaging method in GAMMA 10

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, M.; Negishi, S.; Shima, Y.; Hojo, H.; Imai, T. [Plasma Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 (Japan); Mase, A. [Kyushu University, 6-1 Kasuga-koen, Kasuga, Fukuoka 816-8580 (Japan); Kogi, Y. [Fukuoka Institute of Technology, 3-30-1 Wajiro-higashi, Higashiku, Fukuoka 811-0295 (Japan)

    2010-10-15

    Two dimensional (2D) plasma image analysis is useful to study the improvement of plasma confinement in magnetically confined fusion plasmas. We have constructed a 2D interferometer system with phase imaging method for studying 2D plasma density distribution and its fluctuation measurement in the tandem mirror GAMMA 10. 2D profiles of electron density and its fluctuation have been successfully obtained by using this 2D phase imaging system. We show that 2D plasma density and fluctuation profiles clearly depends on the axial confining potential formation with application of plug electron cyclotron heating in GAMMA 10.

  11. ARTIFICIAL BOUNDARY METHOD FOR THE THREE-DIMENSIONAL EXTERIOR PROBLEM OF ELASTICITY

    Institute of Scientific and Technical Information of China (English)

    Hou-de Han; Chun-xiong Zheng

    2005-01-01

    The exact boundary condition on a spherical artificial boundary is derived for thethree-dimensional exterior problem of linear elasticity in this paper. After this boundary condition is imposed on the artificial boundary, a reduced problem only defined in a bounded domain is obtained. A series of approximate problems with increasing accuracy can be derived if one truncates the series term in the variational formulation, which is equivalent to the reduced problem. An error estimate is presented to show how the error depends on the finite element discretization and the accuracy of the approximate problem.In the end, a numerical example is given to demonstrate the performance of the proposed method.

  12. THE OVERLAPPING DOMAIN DECOMPOSITION METHOD FOR HARMONIC EQUATION OVER EXTERIOR THREE-DIMENSIONAL DOMAIN

    Institute of Scientific and Technical Information of China (English)

    Ji-ming Wu; De-hao Yu

    2000-01-01

    In this paper, the overlapping domain decomposition method, which is based on the natural boundary reduction[1] and first suggested in [2], is applied to slove the exterior boundary value problem of harmonic equation over three-dimensional domain. The convergence and error estimates both for the continuous case and the discrete case are given. The contraction factor for the exterior spherical domain is also discussed. Moreover, numerical results are given which show that the accuracy and the convergence are in accord with the theoretical analyses.

  13. Spectral Methods for Linear and Non-Linear Semi-Supervised Dimensionality Reduction

    CERN Document Server

    Chatpatanasiri, Ratthachat

    2008-01-01

    We present a general framework of spectral methods for semi-supervised dimensionality reduction. Applying an approach called manifold regularization, our framework naturally generalizes existent supervised frameworks. Furthermore, by our two semi-supervised versions of the representer theorem, our framework can be kernelized as well. Using our framework, we give three examples of semi-supervised algorithms which are extended from three recent supervised algorithms, namely, ``discriminant neighborhood embedding'', ``marginal Fisher analysis'' and ``local Fisher discriminant analysis''. We also give three more semi-supervised examples of the kernel versions of these algorithms. Numerical results of the six semi-supervised algorithms compared to their supervised versions are presented.

  14. Cardiac motion estimation by using high-dimensional features and K-means clustering method

    Science.gov (United States)

    Oubel, Estanislao; Hero, Alfred O.; Frangi, Alejandro F.

    2006-03-01

    Tagged Magnetic Resonance Imaging (MRI) is currently the reference modality for myocardial motion and strain analysis. Mutual Information (MI) based non rigid registration has proven to be an accurate method to retrieve cardiac motion and overcome many drawbacks present on previous approaches. In a previous work1, we used Wavelet-based Attribute Vectors (WAVs) instead of pixel intensity to measure similarity between frames. Since the curse of dimensionality forbids the use of histograms to estimate MI of high dimensional features, k-Nearest Neighbors Graphs (kNNG) were applied to calculate α-MI. Results showed that cardiac motion estimation was feasible with that approach. In this paper, K-Means clustering method is applied to compute MI from the same set of WAVs. The proposed method was applied to four tagging MRI sequences, and the resulting displacements were compared with respect to manual measurements made by two observers. Results show that more accurate motion estimation is obtained with respect to the use of pixel intensity.

  15. Semi-automatic computer construction of three-dimensional shapes for the finite element method.

    Science.gov (United States)

    Aharon, S; Bercovier, M

    1993-12-01

    Precise estimation of spatio-temporal distribution of ions (or other constitutives) in three-dimensional geometrical configuration plays a major role in biology. Since a direct experimental information regarding the free intracellular Ca2+ spatio-temporal distribution is not available to date, mathematical models have been developed. Most of the existing models are based on the classical numerical method of finite-difference (FD). Using this method one is limited when dealing with complicated geometry, general boundary conditions and variable or non-linear material properties. These difficulties are easily solved when the finite-element-method (FEM) is employed. The first step in the implementation of the FEM procedure is the mesh generation which is the single most tedious, time consuming task and vulnerable to mistake. In order to overcome these limitations we developed a new interface called AUTOMESH. This tool is used as a preprocessor program which generates two- and three-dimensional meshes for some known and often-used shapes in neurobiology. AUTOMESH creates an appropriate mesh by using the mesh generator commercial tool of FIDAP.

  16. The hydrogen tunneling splitting in malonaldehyde: A full-dimensional time-independent quantum mechanical method

    Science.gov (United States)

    Wu, Feng; Ren, Yinghui; Bian, Wensheng

    2016-08-01

    The accurate time-independent quantum dynamics calculations on the ground-state tunneling splitting of malonaldehyde in full dimensionality are reported for the first time. This is achieved with an efficient method developed by us. In our method, the basis functions are customized for the hydrogen transfer process which has the effect of greatly reducing the size of the final Hamiltonian matrix, and the Lanczos method and parallel strategy are used to further overcome the memory and central processing unit time bottlenecks. The obtained ground-state tunneling splitting of 24.5 cm-1 is in excellent agreement with the benchmark value of 23.8 cm-1 computed with the full-dimensional, multi-configurational time-dependent Hartree approach on the same potential energy surface, and we estimate that our reported value has an uncertainty of less than 0.5 cm-1. Moreover, the role of various vibrational modes strongly coupled to the hydrogen transfer process is revealed.

  17. An improved colony-PCR method for filamentous fungi for amplification of pcr-fragments of several kilobases

    NARCIS (Netherlands)

    Zeijl, C.M.J. van; Kamp, E.H.M. van de; Punt, P.J.; Selten, G.C.M.; Hauer, B.; Gorcom, R.F.M. van; Hondel, C.A.M.J.J. van den

    1998-01-01

    A method was developed to perform PCR directly on mycelial pellets or colonies treated with NOVOzym 234. The method allows rapid screening of large numbers of transformants of both sporulating and non-sporulating fungi for the presence of (co)transforming plasmid copies or for specific genetic

  18. An improved colony-PCR method for filamentous fungi for amplification of pcr-fragments of several kilobases

    NARCIS (Netherlands)

    Zeijl, C.M.J. van; Kamp, E.H.M. van de; Punt, P.J.; Selten, G.C.M.; Hauer, B.; Gorcom, R.F.M. van; Hondel, C.A.M.J.J. van den

    1998-01-01

    A method was developed to perform PCR directly on mycelial pellets or colonies treated with NOVOzym 234. The method allows rapid screening of large numbers of transformants of both sporulating and non-sporulating fungi for the presence of (co)transforming plasmid copies or for specific genetic modif

  19. An improved colony-PCR method for filamentous fungi for amplification of pcr-fragments of several kilobases

    NARCIS (Netherlands)

    Zeijl, C.M.J. van; Kamp, E.H.M. van de; Punt, P.J.; Selten, G.C.M.; Hauer, B.; Gorcom, R.F.M. van; Hondel, C.A.M.J.J. van den

    1998-01-01

    A method was developed to perform PCR directly on mycelial pellets or colonies treated with NOVOzym 234. The method allows rapid screening of large numbers of transformants of both sporulating and non-sporulating fungi for the presence of (co)transforming plasmid copies or for specific genetic modif

  20. SELF-ADAPTIVE STRATEGY FOR ONE-DIMENSIONAL FINITE ELEMENT METHOD BASED ON ELEMENT ENERGY PROJECTION METHOD

    Institute of Scientific and Technical Information of China (English)

    YUAN Si; HE Xue-feng

    2006-01-01

    Based on the newly-developed element energy projection (EEP) method for computation of super-convergent results in one-dimensional finite element method (FEM),the task of self-adaptive FEM analysis was converted into the task of adaptive piecewise polynomial interpolation. As a result, a satisfactory FEM mesh can be obtained, and further FEM analysis on this mesh would immediately produce an FEM solution which usually satisfies the user specified error tolerance. Even though the error tolerance was not completely satisfied, one or two steps of further local refinements would be sufficient.This strategy was found to be very simple, rapid, cheap and efficient. Taking the elliptical ordinary differential equation of second order as the model problem, the fundamental idea,implementation strategy and detailed algorithm are described. Representative numerical examples are given to show the effectiveness and reliability of the proposed approach.

  1. Polymerase chain reaction-restriction fragment length polymorphism method to distinguish three mealybug groups within the Planococcus citri-P. minor species complex (Hemiptera: Coccoidea: Pseudococcidae).

    Science.gov (United States)

    Rung, A; Miller, D R; Scheffer, S J

    2009-02-01

    The mealybug species Planococcus citri (Risso) and Planococcus minor (Maskell) (Hemiptera: Coccoidea: Pseudococcidae) have special significance to U.S. quarantine and U.S. agriculture. Commonly intercepted at U.S. ports-of-entry, they are difficult to identify based on morphological characters. This study presents a molecular method for distinguishing P. citri, P. minor, and a genetically distinct group that is morphologically identical to P. citri, from Hawaii. This method uses polymerase chain reaction (PCR) followed by restriction fragment polymorphism analysis (RFLP) using the restriction enzymes BspH1, BsmH1, and HpH1. The resulting band patterns can be visualized in a 2% agarose gel and are sufficient to differentiate between the three entities mentioned above. PCR-RFLP diagnostics can be used for all life stages and is cheaper and faster than DNA sequencing.

  2. SUPERCONVERGENCE OF DG METHOD FOR ONE-DIMENSIONAL SINGULARLY PERTURBED PROBLEMS

    Institute of Scientific and Technical Information of China (English)

    Ziqing Xie; Zhimin Zhang

    2007-01-01

    The convergence and superconvergence properties of the discontinuous Galerkin (DG) method for a singularly perturbed model problem in one-dimensional setting are studied.By applying the DG method with appropriately chosen numerical traces, the existence and uniqueness of the DG solution, the optimal order L2 error bounds, and 2p+1-order superconvergence of the numerical traces are established. The numerical results indicate that the DG method does not produce any oscillation even under the uniform mesh. Numerical experiments demonstrate that, under the uniform mesh, it seems impossible to obtain the uniform superconvergence of the numerical traces. Nevertheless, thanks to the implementation of the so-called Shishkin-type mesh, the uniform 2p + 1-order superconvergence is observed numerically.

  3. A Hybrid Nodal Method for Time-Dependent Incompressible Flow in Two-Dimensional Arbitrary Geometries

    Energy Technology Data Exchange (ETDEWEB)

    Toreja, A J; Uddin, R

    2002-10-21

    A hybrid nodal-integral/finite-analytic method (NI-FAM) is developed for time-dependent, incompressible flow in two-dimensional arbitrary geometries. In this hybrid approach, the computational domain is divided into parallelepiped and wedge-shaped space-time nodes (cells). The conventional nodal integral method (NIM) is applied to the interfaces between adjacent parallelepiped nodes (cells), while a finite analytic approach is applied to the interfaces between parallelepiped and wedge-shaped nodes (cells). In this paper, the hybrid method is formally developed and an application of the NI-FAM to fluid flow in an enclosed cavity is presented. Results are compared with those obtained using a commercial computational fluid dynamics code.

  4. Three-dimensional Extension of the Unit-Feature Spatial Classification Method for Cloud Type

    Institute of Scientific and Technical Information of China (English)

    ZHANG Chengwei; YU Fan; WANG Chenxi; YANG Jianyu

    2011-01-01

    We describe how the Unit-Feature Spatial Classification Method (UFSCM) can be used operationally to classify cloud types in satellite imagery efficiently and conveniently. By using a combination of Interactive Data Language (IDL) and Visual C++ (VC) code in combination to extend the technique in three dimensions (3-D), this paper provides an efficient method to implement interactive computer visualization of the 3-D discrimination matrix modification, so as to deal with the bi-spectral limitations of traditional two dimensional (2-D) UFSCM. The case study of cloud-type classification based on FY-2C satellite data (0600 UTC 18 and 0000 UTC 10 September 2007) is conducted by comparison with ground station data,and indicates that 3-D UFSCM makes more use of the pattern recognition information in multi-spectral imagery, resulting in more reasonable results and an improvement over the 2-D method.

  5. Three-dimensional registration methods for multi-modal magnetic resonance neuroimages

    CERN Document Server

    Triantafyllou, C

    2001-01-01

    automatically such measures in a reliable way. possible in principle, although the true accuracy of the method depends on the type of geometrical distortions present. These results also reveal that this class of algorithm is unable to solve more localised variations and higher order magnetic field distortions between the images. These facts motivate the development of a high-dimensional 3-D registration method capable of effecting a one-to-one correspondence by capturing the localised differences. This method was seen to account not only for topological differences but also for non-linear deformations in size and shape. Validation of the algorithm is carried out on geometrical objects, simulated data and real images to ensure that the important requirements for a topologically useful mapping; invertibility, smoothness of the deformation field and an almost perfect correspondence can be maintained between two image sequences. Finally, the performance of both approaches is compared by their application to clini...

  6. Finite element method for one-dimensional rill erosion simulation on a curved slope

    Directory of Open Access Journals (Sweden)

    Lijuan Yan

    2015-03-01

    Full Text Available Rill erosion models are important to hillslope soil erosion prediction and to land use planning. The development of rill erosion models and their use has become increasingly of great concern. The purpose of this research was to develop mathematic models with computer simulation procedures to simulate and predict rill erosion. The finite element method is known as an efficient tool in many other applications than in rill soil erosion. In this study, the hydrodynamic and sediment continuity model equations for a rill erosion system were solved by the Galerkin finite element method and Visual C++ procedures. The simulated results are compared with the data for spatially and temporally measured processes for rill erosion under different conditions. The results indicate that the one-dimensional linear finite element method produced excellent predictions of rill erosion processes. Therefore, this study supplies a tool for further development of a dynamic soil erosion prediction model.

  7. A General Method for Growing Two-Dimensional Crystals of Organic Semiconductors by "Solution Epitaxy".

    Science.gov (United States)

    Xu, Chunhui; He, Ping; Liu, Jie; Cui, Ajuan; Dong, Huanli; Zhen, Yonggang; Chen, Wei; Hu, Wenping

    2016-08-08

    Two-dimensional (2D) crystals of organic semiconductors (2DCOS) have attracted attention for large-area and low-cost flexible optoelectronics. However, growing large 2DCOS in controllable ways and transferring them onto technologically important substrates, remain key challenges. Herein we report a facile, general, and effective method to grow 2DCOS up to centimeter size which can be transferred to any substrate efficiently. The method named "solution epitaxy" involves two steps. The first is to self-assemble micrometer-sized 2DCOS on water surface. The second is epitaxial growth of them into millimeter or centimeter sized 2DCOS with thickness of several molecular layers. The general applicability of this method for the growth of 2DCOS is demonstrated by nine organic semiconductors with different molecular structures. Organic field-effect transistors (OFETs) based on the 2DCOS demonstrated high performance, confirming the high quality of the 2DCOS.

  8. (N+1)-dimensional fractional reduced differential transform method for fractional order partial differential equations

    Science.gov (United States)

    Arshad, Muhammad; Lu, Dianchen; Wang, Jun

    2017-07-01

    In this paper, we pursue the general form of the fractional reduced differential transform method (DTM) to (N+1)-dimensional case, so that fractional order partial differential equations (PDEs) can be resolved effectively. The most distinct aspect of this method is that no prescribed assumptions are required, and the huge computational exertion is reduced and round-off errors are also evaded. We utilize the proposed scheme on some initial value problems and approximate numerical solutions of linear and nonlinear time fractional PDEs are obtained, which shows that the method is highly accurate and simple to apply. The proposed technique is thus an influential technique for solving the fractional PDEs and fractional order problems occurring in the field of engineering, physics etc. Numerical results are obtained for verification and demonstration purpose by using Mathematica software.

  9. Discrete ordinates method for three-dimensional neutron transport equation based on unstructured-meshes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A discrete ordinates method for a threedimensional first-order neutron transport equation based on unstructured-meshes that avoids the singularity of the second-order neutron transport equation in void regions was derived.The finite element variation equation was obtained using the least-squares method.A three-dimensional transport calculation code was developed.Both the triangular-z and the tetrahedron elements were included.The numerical results of some benchmark problems demonstrated that this method can solve neutron transport problems in unstructuredmeshes very well.For most problems,the error of the eigenvalue and the angular flux is less than 0.3% and 3.0% respectively.

  10. Preparation of a Three-Dimensional Reduced Graphene Oxide Film by Using the Langmuir-Blodgett Method.

    Science.gov (United States)

    Jaafar, M Musoddiq; Ciniciato, Gustavo P M K; Ibrahim, S Aisyah; Phang, S M; Yunus, K; Fisher, Adrian C; Iwamoto, M; Vengadesh, P

    2015-09-29

    The Langmuir-Blodgett method has always been traditionally utilized in the deposition of two-dimensional structures. In this work, however, we employed the method to deposit three-dimensional reduced graphene oxide layers using an unconventional protocol for the first time. This was achieved by carrying out the dipping process after the collapse pressure or breaking point, which results in the formation of a highly porous three-dimensional surface topography. By varying the number of deposition layers, the porosity could be optimized from nanometer to micrometer dimensions. Employed as bioelectrodes, these three-dimensional reduced graphene oxide layers may allow improved adhesion and biocompatibility compared to the conventional two-dimensional surfaces. A larger number of pores also improves the mass transport of materials and therefore increases the charge-sustaining capacity and sensitivity. This could ultimately improve the performance of biofuel cells and other electrode-based systems.

  11. Application of Symmetry Adapted Function Method for Three-Dimensional Reconstruction of Octahedral Biological Macromolecules

    Directory of Open Access Journals (Sweden)

    Songjun Zeng

    2010-01-01

    Full Text Available A method for three-dimensional (3D reconstruction of macromolecule assembles, that is, octahedral symmetrical adapted functions (OSAFs method, was introduced in this paper and a series of formulations for reconstruction by OSAF method were derived. To verify the feasibility and advantages of the method, two octahedral symmetrical macromolecules, that is, heat shock protein Degp24 and the Red-cell L Ferritin, were utilized as examples to implement reconstruction by the OSAF method. The schedule for simulation was designed as follows: 2000 random orientated projections of single particles with predefined Euler angles and centers of origins were generated, then different levels of noises that is signal-to-noise ratio (S/N =0.1,0.5, and 0.8 were added. The structures reconstructed by the OSAF method were in good agreement with the standard models and the relative errors of the structures reconstructed by the OSAF method to standard structures were very little even for high level noise. The facts mentioned above account for that the OSAF method is feasible and efficient approach to reconstruct structures of macromolecules and have ability to suppress the influence of noise.

  12. How Many Political Parties Should Brazil Have? A Data-Driven Method to Assess and Reduce Fragmentation in Multi-Party Political Systems.

    Science.gov (United States)

    Vaz de Melo, Pedro O S

    2015-01-01

    In June 2013, Brazil faced the largest and most significant mass protests in a generation. These were exacerbated by the population's disenchantment towards its highly fragmented party system, which is composed by a very large number of political parties. Under these circumstances, presidents are constrained by informal coalition governments, bringing very harmful consequences to the country. In this work I propose ARRANGE, a dAta dRiven method foR Assessing and reduciNG party fragmEntation in a country. ARRANGE uses as input the roll call data for congress votes on bills and amendments as a proxy for political preferences and ideology. With that, ARRANGE finds the minimum number of parties required to house all congressmen without decreasing party discipline. When applied to Brazil's historical roll call data, ARRANGE was able to generate 31 distinct configurations that, compared with the status quo, have (i) a significant smaller number of parties, (ii) a higher discipline of partisans towards their parties and (iii) a more even distribution of partisans into parties. ARRANGE is fast and parsimonious, relying on a single, intuitive parameter.

  13. Experimental study on two-dimensional film flow with local measurement methods

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jin-Hwa, E-mail: evo03@snu.ac.kr [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Cho, Hyoung-Kyu [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Kim, Seok [Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Euh, Dong-Jin, E-mail: djeuh@kaeri.re.kr [Korea Atomic Energy Research Institute, 989-111, Daedeok-daero, Yuseong-gu, Daejeon 305-600 (Korea, Republic of); Park, Goon-Cherl [Nuclear Thermal-Hydraulic Engineering Laboratory, Seoul National University, Gwanak 599, Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of)

    2015-12-01

    Highlights: • An experimental study on the two-dimensional film flow with lateral air injection was performed. • The ultrasonic thickness gauge was used to measure the local liquid film thickness. • The depth-averaged PIV (Particle Image Velocimetry) method was applied to measure the local liquid film velocity. • The uncertainty of the depth-averaged PIV was quantified with a validation experiment. • Characteristics of two-dimensional film flow were classified following the four different flow patterns. - Abstract: In an accident condition of a nuclear reactor, multidimensional two-phase flows may occur in the reactor vessel downcomer and reactor core. Therefore, those have been regarded as important issues for an advanced thermal-hydraulic safety analysis. In particular, the multi-dimensional two-phase flow in the upper downcomer during the reflood phase of large break loss of coolant accident appears with an interaction between a downward liquid and a transverse gas flow, which determines the bypass flow rate of the emergency core coolant and subsequently, the reflood coolant flow rate. At present, some thermal-hydraulic analysis codes incorporate multidimensional modules for the nuclear reactor safety analysis. However, their prediction capability for the two-phase cross flow in the upper downcomer has not been validated sufficiently against experimental data based on local measurements. For this reason, an experimental study was carried out for the two-phase cross flow to clarify the hydraulic phenomenon and provide local measurement data for the validation of the computational tools. The experiment was performed in a 1/10 scale unfolded downcomer of Advanced Power Reactor 1400 (APR1400). Pitot tubes, a depth-averaged PIV method and ultrasonic thickness gauge were applied for local measurement of the air velocity, the liquid film velocity and the liquid film thickness, respectively. The uncertainty of the depth-averaged PIV method for the averaged

  14. Application of Corner Transfer Matrix Renormalization Group Method to the Correlation Function of a Two-Dimensional Ising Model

    Institute of Scientific and Technical Information of China (English)

    何春山; 李志兵

    2003-01-01

    The correlation function of a two-dimensionalIsing model is calculated by the corner transfer matrix renormalization group method.We obtain the critical exponent η= 0.2496 with few computer resources.

  15. The Use of Iterative Methods to Solve Two-Dimensional Nonlinear Volterra-Fredholm Integro-Differential Equations

    Directory of Open Access Journals (Sweden)

    shadan sadigh behzadi

    2012-03-01

    Full Text Available In this present paper, we solve a two-dimensional nonlinear Volterra-Fredholm integro-differential equation by using the following powerful, efficient but simple methods: (i Modified Adomian decomposition method (MADM, (ii Variational iteration method (VIM, (iii Homotopy analysis method (HAM and (iv Modified homotopy perturbation method (MHPM. The uniqueness of the solution and the convergence of the proposed methods are proved in detail. Numerical examples are studied to demonstrate the accuracy of the presented methods.

  16. Assessment of volumetric changes with a best-fit method in three-dimensional stereophotograms.

    Science.gov (United States)

    Ongkosuwito, E M; Goos, J A C; Wattel, E; van der Wal, K G H; van Adrichem, L N A; van Neck, J W

    2012-07-01

    Different three-dimensional stereophotogrammetry systems and analyzing methods exist that often use landmarks for comparison. Measurement errors in landmark or surface comparison are mostly within 1 mm, which seems clinically acceptable. The aim of this study was to validate a three-dimensional stereophotogrammetric best-fit method of assessing volumetric changes and to compare three devices. The validation of the best-fit method was at first done on a life-size dummy head. Scans were made in the ideal position, as well as in four additional positions, and a scan was made in which a soft putty specimen was added to the dummy head. The comparison was executed with a best-fit method using triangulation. Student's t tests were used to detect statistically significant differences. Second, comparisons were made among scans of a white man in the ideal position and with volume changes added. The different positions tested for the dummy head showed no significant volume differences within each system or among systems. The differences found when adding a soft putty specimen fell into the same range as the differences between various positions. The differences within a live situation were 10 times greater compared with the dummy-head situation. In a dummy-head situation, the different systems gave similar results when tested with a best-fit method. However, in live situations the differences may become 10 times greater, possibly due to different facial expressions. These differences may become clinically relevant and, therefore, further research in volumetric changes is needed.

  17. Comparison of Three Methods of Protein Extraction from Dermatophagoides Pteronyssinus for Two-dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Jin-lu Sun; Hong-yu Zhang; Zhi-yi Guo; Wan-tao Ying; Xiao-hong Qian; Jing-lan Wang

    2009-01-01

    Objective To explore an effective method of Dermatophagoides pteronyssinus protein extraction suitable for two-dimensional electrophoresis (2-DE) analysis. Methods The extracts of Dermatophagoides pteronyssinus were prepared with Coca's solution, lysis buffer of 2-DE, and Trizol reagent, respectively. Bicinchoninic acid (BCA) assay was used to determine the total protein concentration of the samples. The efficiency of different protein extraction methods were evaluated with 2-DE analysis. Results The concentrations of extracted protein by methods of Coca's solution, lysis buffer, and Trizol reagent were 0.63 g/L, 0.90 g/L, and 0.80 g/L, respectively. The 2-DE analysis results showed that some protein spots in low molecular weight (LMW) range could be detected with the Coca's solution method. With the lysis buffer of 2-DE method, more protein spots in LMW range could be detected, while the medium molecular weight (MMW) protein spots were absent. Several MMW protein spots (174-178 kD and 133 kD) and more LMW protein spots were detected with Trizol reagent method. Conclusions Among Coca's solution, lysis buffer of 2-DE, and Trizol reagent, the concentration of extracted protein of Dermatophagoides pteronyssinus by lysis buffer of 2-DE is the highest. However, most protein components of Dermatophagoides pteronyssinus purified mite bodies can be extracted by Trizol reagent, which may generally reflect the whole profile of Dermatophagoides pteronyssinus allergens.

  18. A new extrapolation cascadic multigrid method for three dimensional elliptic boundary value problems

    Science.gov (United States)

    Pan, Kejia; He, Dongdong; Hu, Hongling; Ren, Zhengyong

    2017-09-01

    In this paper, we develop a new extrapolation cascadic multigrid method, which makes it possible to solve three dimensional elliptic boundary value problems with over 100 million unknowns on a desktop computer in half a minute. First, by combining Richardson extrapolation and quadratic finite element (FE) interpolation for the numerical solutions on two-level of grids (current and previous grids), we provide a quite good initial guess for the iterative solution on the next finer grid, which is a third-order approximation to the FE solution. And the resulting large linear system from the FE discretization is then solved by the Jacobi-preconditioned conjugate gradient (JCG) method with the obtained initial guess. Additionally, instead of performing a fixed number of iterations as used in existing cascadic multigrid methods, a relative residual tolerance is introduced in the JCG solver, which enables us to obtain conveniently the numerical solution with the desired accuracy. Moreover, a simple method based on the midpoint extrapolation formula is proposed to achieve higher-order accuracy on the finest grid cheaply and directly. Test results from four examples including two smooth problems with both constant and variable coefficients, an H3-regular problem as well as an anisotropic problem are reported to show that the proposed method has much better efficiency compared to the classical V-cycle and W-cycle multigrid methods. Finally, we present the reason why our method is highly efficient for solving these elliptic problems.

  19. A parallel code base on discontinuous Galerkin method on three dimensional unstructured meshes for MHD equations

    Science.gov (United States)

    Li, Xujing; Zheng, Weiying

    2016-10-01

    A new parallel code based on discontinuous Galerkin (DG) method for hyperbolic conservation laws on three dimensional unstructured meshes is developed recently. This code can be used for simulations of MHD equations, which are very important in magnetic confined plasma research. The main challenges in MHD simulations in fusion include the complex geometry of the configurations, such as plasma in tokamaks, the possibly discontinuous solutions and large scale computing. Our new developed code is based on three dimensional unstructured meshes, i.e. tetrahedron. This makes the code flexible to arbitrary geometries. Second order polynomials are used on each element and HWENO type limiter are applied. The accuracy tests show that our scheme reaches the desired three order accuracy and the nonlinear shock test demonstrate that our code can capture the sharp shock transitions. Moreover, One of the advantages of DG compared with the classical finite element methods is that the matrices solved are localized on each element, making it easy for parallelization. Several simulations including the kink instabilities in toroidal geometry will be present here. Chinese National Magnetic Confinement Fusion Science Program 2015GB110003.

  20. Study of a new method for three-dimensional restoration from single image

    Institute of Scientific and Technical Information of China (English)

    XIE Ming-hong

    2009-01-01

    The aim of three-dimensional recovery technology from the image is to recover the relative height of each point on the surface from the light variations in the single image and carry out the recovery. A new method that recovers three-dimensional is presented object based on radius basis function for the image from the unknown light source direction, which constructs a surface equation by the network, uses the reflectivity function as a constraint, continuonsly estimates the light source direction in the self-learning process of the network from the bright spots around the spread of the image, and eventually obtains a satisfactory surface equation. This method makes the resumption of surface good continuity and smoothness, and can recover the height value of each network point of the image and be automatically inserted in any point the among the network. It is suitable for the image of Lambert reflection model and the image of the Specular reflection model and the mixed-reflex model.

  1. Four-dimensional measurement by a single-frame structured light method.

    Science.gov (United States)

    Sitnik, Robert

    2009-06-20

    A four-dimensional [4D--three-dimensional (3D) shape varying in time] shape measurement system is described. A single 3D shape of an object is calculated from only one frame. The projected pattern is composed of sinusoidal intensity fringes and one color-encoded stripe, the analysis of which allows us to find the absolute coordinates of the measured object. During measurement, the position of the stripe changes due to the improvement of the quality of spatiotemporal unwrapping. The fringes deformed by the shape of the object are captured by a CCD camera and processed by an adaptive spatial carrier phase-shifting algorithm. The use of an algorithm based on fast Fourier transformation is proposed to approximate the local period of fringes. A new phase-unwrapping routine based on the spatiotemporal information is presented as well. All these features make the 3D shape measurement of an object in motion possible with the additional advantage of using a low-cost system. Experimental results of the developed method together with a preliminary assessment of measurement uncertainty are presented to show the validity of the method.

  2. Electroeluting DNA fragments.

    Science.gov (United States)

    Zarzosa-Alvarez, Ana L; Sandoval-Cabrera, Antonio; Torres-Huerta, Ana L; Bermudez-Cruz, Rosa M

    2010-09-05

    Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The electroelution procedure allows one to purify very clean DNA to be used in a large number of applications (sequencing, radiolabeling, enzymatic restriction, enzymatic modification, cloning etc). This procedure consists in placing DNA band-containing agarose or acrylamide slices into sample wells of the electroeluter, then applying current will make the DNA fragment to leave the agarose and thus be trapped in a cushion salt to be recovered later by ethanol precipitation.

  3. Energy-loss distributions of fission fragments

    Energy Technology Data Exchange (ETDEWEB)

    Demidovich, N.N.; Nakhutin, I.E.; Shatunov, V.G.

    1976-03-05

    The f-f coincidence method was used to investigate the change in the form of the energy-loss distributions of Cf/sup 252/ fission fragments in air, down to fragment energies approx.0.8 MeV. A theoretical model is considered for the estimate of the mean-squared deviations of the fragment energy-loss distributions. (AIP)

  4. Integral three-dimensional television with video system using pixel-offset method.

    Science.gov (United States)

    Arai, Jun; Kawakita, Masahiro; Yamashita, Takayuki; Sasaki, Hisayuki; Miura, Masato; Hiura, Hitoshi; Okui, Makoto; Okano, Fumio

    2013-02-11

    Integral three-dimensional (3D) television based on integral imaging requires huge amounts of information. Previously, we constructed an Integral 3D television using Super Hi-Vision (SHV) technology, with 7680 pixels horizontally and 4320 pixels vertically. We report on improved image quality through the development of video system with an equivalent of 8000 scan lines for use with Integral 3D television. We conducted experiments to evaluate the resolution of 3D images using an experimental setup and were able to show that by using the pixel-offset method we have eliminated aliasing produced by full-resolution SHV video equipment. We confirmed that the application of the pixel-offset method to integral 3D television is effective in increasing the resolution of reconstructed images.

  5. Multi-Dimensional High Order Essentially Non-Oscillatory Finite Difference Methods in Generalized Coordinates

    Science.gov (United States)

    Shu, Chi-Wang

    1998-01-01

    This project is about the development of high order, non-oscillatory type schemes for computational fluid dynamics. Algorithm analysis, implementation, and applications are performed. Collaborations with NASA scientists have been carried out to ensure that the research is relevant to NASA objectives. The combination of ENO finite difference method with spectral method in two space dimension is considered, jointly with Cai [3]. The resulting scheme behaves nicely for the two dimensional test problems with or without shocks. Jointly with Cai and Gottlieb, we have also considered one-sided filters for spectral approximations to discontinuous functions [2]. We proved theoretically the existence of filters to recover spectral accuracy up to the discontinuity. We also constructed such filters for practical calculations.

  6. Viscosity of confined two-dimensional Yukawa liquids: A nonequilibrium method

    Energy Technology Data Exchange (ETDEWEB)

    Landmann, S. [Universität Leipzig, Institut für Theoretische Physik, Brüderstr. 16, 04103 Leipzig (Germany); Kählert, H.; Thomsen, H.; Bonitz, M. [Christian-Albrechts-Universität zu Kiel, Institut für Theoretische Physik und Astrophysik, Leibnizstr. 15, 24098 Kiel (Germany)

    2015-09-15

    We present a nonequilibrium method that allows one to determine the viscosity of two-dimensional dust clusters in an isotropic confinement. By applying a tangential external force to the outer parts of the cluster (e.g., with lasers), a sheared velocity profile is created. The decay of the angular velocity towards the center of the confinement potential is determined by a balance between internal (viscosity) and external friction (neutral gas damping). The viscosity can then be calculated from a fit of the measured velocity profile to a solution of the Navier-Stokes equation. Langevin dynamics simulations are used to demonstrate the feasibility of the method. We find good agreement of the measured viscosity with previous results for macroscopic Yukawa plasmas.

  7. Three-dimensional multi-mesh material point method for solving collision problems

    CERN Document Server

    Pan, Xiaofei; Zhang, Guangcai; Zhu, Jianshi; Ma, Shang; Zhang, Xiong

    2007-01-01

    Contact algorithm between different bodies plays an important role in solving collision problems. Usually it is not easy to be treated very well. Several ones for material point method were proposed by Bardenhangen, Brackbill, and Sulsky\\cite{Bardenhagen2000,Bardenhagen2001}, Hu and Chen\\cite{Hu_Chen2003}. An improved one for three-dimensional material point method is presented in this paper. The improved algorithm emphasizes the energy conservation of the system and faithfully recovers opposite acting forces between contacting bodies. Contrasted to the one by Bardenhagen, both the normal and tangential contacting forces are more appropriately applied to the contacting bodies via the contacting nodes of the background mesh; Contrasted to the one by Hu and Chen, not only the tangential velocities but also the normal ones are handled separately in respective individual mesh. This treatment ensures not only the contact/sliding/separation procedure but also the friction between contacting bodies are recovered. Th...

  8. A quasi-3-dimensional simulation method for a high-voltage level-shifting circuit structure

    Institute of Scientific and Technical Information of China (English)

    Liu Jizhi; Chen Xingbi

    2009-01-01

    A new quasi-three-dimensional (quasi-3D) numeric simulation method for a high-voltage level-shifting circuit structure is proposed. The performances of the 3D structure are analyzed by combining some 2D device structures; the 2D devices are in two planes perpendicular to each other and to the surface of the semiconductor. In comparison with Davinci, the full 3D device simulation tool, the quasi-3D simulation method can give results for the potential and current distribution of the 3D high-voltage level-shifting circuit structure with appropriate accuracy and the total CPU time for simulation is significantly reduced. The quasi-3D simulation technique can be used in many cases with advantages such as saving computing time, making no demands on the high-end computer terminals, and being easy to operate.

  9. Energy method for multi-dimensional balance laws with non-local dissipation

    KAUST Repository

    Duan, Renjun

    2010-06-01

    In this paper, we are concerned with a class of multi-dimensional balance laws with a non-local dissipative source which arise as simplified models for the hydrodynamics of radiating gases. At first we introduce the energy method in the setting of smooth perturbations and study the stability of constants states. Precisely, we use Fourier space analysis to quantify the energy dissipation rate and recover the optimal time-decay estimates for perturbed solutions via an interpolation inequality in Fourier space. As application, the developed energy method is used to prove stability of smooth planar waves in all dimensions n2, and also to show existence and stability of time-periodic solutions in the presence of the time-periodic source. Optimal rates of convergence of solutions towards the planar waves or time-periodic states are also shown provided initially L1-perturbations. © 2009 Elsevier Masson SAS.

  10. Method for the determination of the three-dimensional structure of ultrashort relativistic electron bunches

    CERN Document Server

    Geloni, Gianluca; Saldin, Evgeni; Schneidmiller, Evgeni; Yurkov, Mikhail

    2009-01-01

    We describe a novel technique to characterize ultrashort electron bunches in X-ray Free-Electron Lasers. Namely, we propose to use coherent Optical Transition Radiation to measure three-dimensional (3D) electron density distributions. Our method relies on the combination of two known diagnostics setups, an Optical Replica Synthesizer (ORS) and an Optical Transition Radiation (OTR) imager. Electron bunches are modulated at optical wavelengths in the ORS setup. When these electron bunches pass through a metal foil target, coherent radiation pulses of tens MW power are generated. It is thereafter possible to exploit advantages of coherent imaging techniques, such as direct imaging, diffractive imaging, Fourier holography and their combinations. The proposed method opens up the possibility of real-time, wavelength-limited, single-shot 3D imaging of an ultrashort electron bunch.

  11. Reconstruction of three-dimensional grain structure in polycrystalline iron via an interactive segmentation method

    Science.gov (United States)

    Feng, Min-nan; Wang, Yu-cong; Wang, Hao; Liu, Guo-quan; Xue, Wei-hua

    2017-03-01

    Using a total of 297 segmented sections, we reconstructed the three-dimensional (3D) structure of pure iron and obtained the largest dataset of 16254 3D complete grains reported to date. The mean values of equivalent sphere radius and face number of pure iron were observed to be consistent with those of Monte Carlo simulated grains, phase-field simulated grains, Ti-alloy grains, and Ni-based super alloy grains. In this work, by finding a balance between automatic methods and manual refinement, we developed an interactive segmentation method to segment serial sections accurately in the reconstruction of the 3D microstructure; this approach can save time as well as substantially eliminate errors. The segmentation process comprises four operations: image preprocessing, breakpoint detection based on mathematical morphology analysis, optimized automatic connection of the breakpoints, and manual refinement by artificial evaluation.

  12. A minimum action method for small random perturbations of two-dimensional parallel shear flows

    Science.gov (United States)

    Wan, Xiaoliang

    2013-02-01

    In this work, we develop a parallel minimum action method for small random perturbations of Navier-Stokes equations to solve the optimization problem given by the large deviation theory. The Freidlin-Wentzell action functional is discretized by hp finite elements in time direction and spectral methods in physical space. A simple diagonal preconditioner is constructed for the nonlinear conjugate gradient solver of the optimization problem. A hybrid parallel strategy based on MPI and OpenMP is developed to improve numerical efficiency. Both h- and p-convergence are obtained when the discretization error from physical space can be neglected. We also present preliminary results for the transition in two-dimensional Poiseuille flow from the base flow to a non-attenuated traveling wave.

  13. Vibration band-gap properties of three-dimensional Kagome lattices using the spectral element method

    Science.gov (United States)

    Wu, Zhi-Jing; Li, Feng-Ming; Zhang, Chuanzeng

    2015-04-01

    The spectral element method (SEM) is extended to investigate the vibration band-gap properties of three-dimensional (3D) Kagome lattices. The dynamic stiffness matrix of the 3D element which contains bending, tensional and torsional components is derived. The spectral equations of motion of the whole 3D Kagome lattice are then established. Comparing with frequency-domain solutions calculated by the finite element method (FEM), the accuracy and the feasibility of the SEM solutions are verified. It can be shown that the SEM is suitable for analyzing the vibration band-gap properties. Due to the band-gap characteristics, the periodic 3D Kagome lattice has the performance of vibration isolation. The influences of the structural and material parameters on the vibration band-gaps are discussed and a new type of 3D Kagome lattice is designed to obtain the improved vibration isolation capability.

  14. A Ternary Solvent Method for Large-Sized Two-Dimensional Perovskites.

    Science.gov (United States)

    Chen, Junnian; Gan, Lin; Zhuge, Fuwei; Li, Huiqiao; Song, Jizhong; Zeng, Haibo; Zhai, Tianyou

    2017-02-20

    Recent reports demonstrate that a two-dimensional (2D) structural characteristic can endow perovskites with both remarkable photoelectric conversion efficiency and high stability, but the synthesis of ultrathin 2D perovskites with large sizes by facile solution methods is still a challenge. Reported herein is the controlled growth of 2D (C4 H9 NH3 )2 PbBr4 perovskites by a chlorobenzene-dimethylformide-acetonitrile ternary solvent method. The critical factors, including solvent volume ratio, crystallization temperature, and solvent polarity on the growth dynamics were systematically studied. Under optimum reaction condition, 2D (C4 H9 NH3 )2 PbBr4 perovskites, with the largest lateral dimension of up to 40 μm and smallest thickness down to a few nanometers, were fabricated. Furthermore, various iodine doped 2D (C4 H9 NH3 )2 PbBrx I4-x perovskites were accessed to tune the optical properties rationally.

  15. Dimensional accuracy of acrylic resin maxillary denture base polymerized by a new injection pressing method.

    Science.gov (United States)

    Ono, Takahiro; Kita, Seiichi; Nokubi, Takashi

    2004-09-01

    The purpose of this study was to confirm the dimensional accuracy of a newly developed injection pressing method for resin polymerization by making use of the internal electric resistance of resin to determine the optimal timing for resin injection. A new injection pressing polymerization pot with a built-in system to measure the internal electric resistance of resin was used for resin polymerization. Fluid-type resin was injected into the mold of a maxillary complete denture base under nine different conditions: three different timings for resin injection according to the electric resistance of resin dough (early stage: 11 Mohms; intermediate stage: 16 Mohms; final stage: 21 Mohms) and three different motor powers for resin injection (2000 N, 4000 N, and 6000 N). In the best polymerization condition (injected during the early stage of resin dough under a motor power of 6000 N), the adaptation of the denture base showed a statistically significant improvement compared with the conventional pouring method.

  16. Three-dimensional shape measurement of a highly reflected, specular surface with structured light method.

    Science.gov (United States)

    Zhang, Hongwei; Ji, Lishuan; Liu, Shugui; Li, Shaohui; Han, Shujian; Zhang, Xiaojie

    2012-11-01

    This paper proposes a mathematical measurement model of a highly reflected, specular surface with structured light method. In the measurement, an auxiliary fringe pattern named amplitude perturbation is adopted to be projected onto the measured surface. The amplitude perturbation can ease the procedure of searching the corresponding points between the phase map of the measured surface and that of the reference plane by locking up the most reliable point as the starting unwrapping point whose true phase can be calculated accurately. The proposed method is also suitable for measuring the step surfaces such as gauge blocks with different heights. Furthermore, the image segmentation technology is introduced in the phase unwrapping procedure to increase the speed. Based on the unwrapped phase map, zonal wave-front reconstruction algorithm is implemented to realize three-dimensional, highly reflected, specular surface reconstruction. Experimental studies show that the developed methodology displays accuracy and high stability for highly reflected, specular surface measurement.

  17. INTERVAL FINITE VOLUME METHOD FOR UNCERTAINTY SIMULATION OF TWO-DIMENSIONAL RIVER WATER QUALITY

    Institute of Scientific and Technical Information of China (English)

    HE Li; ZENG Guang-ming; HUANG Guo-he; LU Hong-wei

    2004-01-01

    Under the interval uncertainties, by incorporating the discretization form of finite volume method and interval algebra theory, an Interval Finite Volume Method (IFVM) was developed to solve water quality simulation issues for two-dimensional river when lacking effective data of flow velocity and flow quantity. The IFVM was practically applied to a segment of the Xiangjiang River because the Project of Hunan Inland Waterway Multipurpose must be started working after the environmental impact assessment for it. The simulation results suggest that there exist rather apparent pollution zones of BOD5 downstream the Dongqiaogang discharger and that of COD downstream Xiaoxiangjie discharger, but the pollution sources have no impact on the safety of the three water plants located in this river segment. Although the developed IFVM is to be perfected, it is still a powerful tool under interval uncertainties for water environmental impact assessment, risk analysis, and water quality planning, etc. besides water quality simulation studied in this paper.

  18. The PLSI Method of Stabilizing Two-Dimensional Nonsymmetric Half-Plane Recursive Digital Filters

    Directory of Open Access Journals (Sweden)

    Gangatharan N

    2003-01-01

    Full Text Available Two-dimensional (2D recursive digital filters find applications in image processing as in medical X-ray processing. Nonsymmetric half-plane (NSHP filters have definitely positive magnitude characteristics as opposed to quarter-plane (QP filters. In this paper, we provide methods for stabilizing the given 2D NSHP polynomial by the planar least squares inverse (PLSI method. We have proved in this paper that if the given 2D unstable NSHP polynomial and its PLSI are of the same degree, the PLSI polynomial is always stable, irrespective of whether the coefficients of the given polynomial have relationship among its coefficients or not. Examples are given for 2D first-order and second-order cases to prove our results. The generalization is done for the th order polynomial.

  19. Method for the determination of the three-dimensional structure of ultrashort relativistic electron bunches

    Energy Technology Data Exchange (ETDEWEB)

    Geloni, Gianluca; Ilinski, Petr; Saldin, Evgeni; Schneidmiller, Evgeni; Yurkov, Mikhail

    2009-05-15

    We describe a novel technique to characterize ultrashort electron bunches in Xray Free-Electron Lasers. Namely, we propose to use coherent Optical Transition Radiation to measure three-dimensional (3D) electron density distributions. Our method relies on the combination of two known diagnostics setups, an Optical Replica Synthesizer (ORS) and an Optical Transition Radiation (OTR) imager. Electron bunches are modulated at optical wavelengths in the ORS setup.When these electron bunches pass through a metal foil target, coherent radiation pulses of tens MW power are generated. It is thereafter possible to exploit advantages of coherent imaging techniques, such as direct imaging, diffractive imaging, Fourier holography and their combinations. The proposed method opens up the possibility of real-time, wavelength-limited, single-shot 3D imaging of an ultrashort electron bunch. (orig.)

  20. Assessing the accuracy and reliability of ultrasonographic three-dimensional parathyroid volume measurement in a patient with secondary hyperparathyroidism: a comparison with the two-dimensional conventional method

    Directory of Open Access Journals (Sweden)

    Sung-Hye You

    2017-01-01

    Full Text Available Purpose The purpose of this study was to investigate the accuracy and reliability of the semi-automated ultrasonographic volume measurement tool, virtual organ computer-aided analysis (VOCAL, for measuring the volume of parathyroid glands. Methods Volume measurements for 40 parathyroid glands were performed in patients with secondary hyperparathyroidism caused by chronic renal failure. The volume of the parathyroid glands was measured twice by experienced radiologists by two-dimensional (2D and three-dimensional (3D methods using conventional sonograms and the VOCAL with 30°angle increments before parathyroidectomy. The specimen volume was also measured postoperatively. Intraclass correlation coefficients (ICCs and the absolute percentage error were used for estimating the reproducibility and accuracy of the two different methods. Results The ICC value between two measurements of the 2D method and the 3D method was 0.956 and 0.999, respectively. The mean absolute percentage error of the 2D method and the 3D VOCAL technique was 29.56% and 5.78%, respectively. For accuracy and reliability, the plots of the 3D method showed a more compact distribution than those of the 2D method on the Bland-Altman graph. Conclusion The rotational VOCAL method for measuring the parathyroid gland is more accurate and reliable than the conventional 2D measurement. This VOCAL method could be used as a more reliable follow-up imaging modality in a patient with hyperparathyroidism.

  1. Assessing the accuracy and reliability of ultrasonographic three-dimensional parathyroid volume measurement in a patient with secondary hyperparathyroidism: a comparison with the two-dimensional conventional method

    Science.gov (United States)

    2017-01-01

    Purpose The purpose of this study was to investigate the accuracy and reliability of the semi-automated ultrasonographic volume measurement tool, virtual organ computer-aided analysis (VOCAL), for measuring the volume of parathyroid glands. Methods Volume measurements for 40 parathyroid glands were performed in patients with secondary hyperparathyroidism caused by chronic renal failure. The volume of the parathyroid glands was measured twice by experienced radiologists by two-dimensional (2D) and three-dimensional (3D) methods using conventional sonograms and the VOCAL with 30°angle increments before parathyroidectomy. The specimen volume was also measured postoperatively. Intraclass correlation coefficients (ICCs) and the absolute percentage error were used for estimating the reproducibility and accuracy of the two different methods. Results The ICC value between two measurements of the 2D method and the 3D method was 0.956 and 0.999, respectively. The mean absolute percentage error of the 2D method and the 3D VOCAL technique was 29.56% and 5.78%, respectively. For accuracy and reliability, the plots of the 3D method showed a more compact distribution than those of the 2D method on the Bland-Altman graph. Conclusion The rotational VOCAL method for measuring the parathyroid gland is more accurate and reliable than the conventional 2D measurement. This VOCAL method could be used as a more reliable follow-up imaging modality in a patient with hyperparathyroidism. PMID:27457337

  2. Novel method for producing hypoallergenic wheat flour by enzymatic fragmentation of the constituent allergens and its application to food processing.

    Science.gov (United States)

    Watanabe, M; Watanabe, J; Sonoyama, K; Tanabe, S

    2000-12-01

    A novel method is proposed to produce hypoallergenic wheat flour suitable for patients allergic to wheat. Wheat flour was mixed with a cellulase solution, and the mixture was incubated at 50 degrees C for 1 h to hydrolyze the carbohydrate allergens. The hydrolysate was further incubated with actinase at 40 degrees C for 1 h while gently stirring to decompose the proteinaceous allergens. The product was evaluated for its allergenicity by an enzyme-linked immunosorbent assay, the results of which suggested negative allergenicity in most cases. The product changed to a batter state that was difficult to process by the usual methods. Gelatinization of the starch in the product and the addition of a surfactant were beneficial for food processing.

  3. Validation of a Novel 3-Dimensional Sonographic Method for Assessing Gastric Accommodation in Healthy Adults.

    Science.gov (United States)

    Buisman, Wijnand J; van Herwaarden-Lindeboom, Maud Y A; Mauritz, Femke A; El Ouamari, Mourad; Hausken, Trygve; Olafsdottir, Edda J; van der Zee, David C; Gilja, Odd Helge

    2016-07-01

    A novel automated 3-dimensional (3D) sonographic method has been developed for measuring gastric volumes. This study aimed to validate and assess the reliability of this novel 3D sonographic method compared to the reference standard in 3D gastric sonography: freehand magneto-based 3D sonography. A prospective study with 8 balloons (in vitro) and 16 stomachs of healthy volunteers (in vivo) was performed. After a 500-mL liquid meal, 1 preprandial and 3 postprandial volume scans of the stomachs were performed by the novel 3D sonographic method and the current reference-standard 3D sonographic method. The in vitro study showed a mean volume difference between the novel method and the true balloon volume of -1.3 mL; limits of agreement (LoA) were small (-39.3 to12.3 mL), with an intraclass correlation coefficient (ICC) of 0.998. The in vivo study showed a mean gastric volume of 321 mL between the novel method and the freehand magneto-based method, with a mean volume difference of -4.4 mL; LoA were -40.1 to 31.2 mL, and the ICC was 0.991. The intraobserver and interobserver variability rates were low, at 0.8 mL (LoA, -24.0 to 25.6 mL), with an ICC of 0.995, and 0.5 mL (LoA, of -26.8 to 27.8 mL), with an ICC of 0.999, respectively. The novel 3D sonographic method with automated acquisition showed good agreement with the current reference-standard gastric 3D sonographic method, with low intraobserver and interobserver variability. This novel 3D sonographic method is a valid and reliable technique for determining gastric accommodation.

  4. A Three-Dimensional Satellite Retrieval Method for Atmospheric Temperature and Moisture Profiles

    Institute of Scientific and Technical Information of China (English)

    ZHANG Lei; QIU Chongjian; HUANG Jianping

    2008-01-01

    A three-dimensional variational method iS proposed to simultaneously retrieve the 3-D atmospheric temperature and moisture profiles from satellite radiance measurements.To include both vertical structure and the horizontal patterns of the atmospheric temperature and moisture.an EOF technique iS used to decompose the temperature and moisture field in a 3-D space.A number of numerical simulations are conducted and they demonstrate that the 3-D method iS less sensitive to the observation errors compared to the 1-D method.When the observation error iS more than 2.0 K.to get the best results.the truncation number for the EOF'S expansion have to be restricted to 2 in the 1-D method.while it can be set as large as 40 in a 3-D method.This results in the truncation error being reduced and the retrieval accuracy being improved in the 3-D method.Compared to the 1-D method.the rlTLS errors of the 3-D method are reduced by 48%and 36%for the temperature and moisture retrievals,respectively.Using the real satellite measured brightness temperatures at 0557 UTC 31 July 2002,the temperature and moisture profiles are retrieved over a region(20°-45°N,100°-125°E)and compared with 37 collocated radiosonde observations.The results show that the retrieval accuracy with a 3-D method iS significantly higher than those with the 1-D method.

  5. Fragment size for calculations on alkaline-earth oxides by the crystal cluster SCF-X/sub approx. /-RW method

    Energy Technology Data Exchange (ETDEWEB)

    Lobach, V.A.; Sobolev, A.B.; Shul' gin, B.V.

    1987-05-01

    Calculations have been performed on the clusters (A/sub x/B/sub y/) (x = 1, 13; y = 6, 14), corresponding to perfect crystals of the alkaline-earth oxides (AEO) MgO, CaO, and SrO by means of methods involving molecular clusters (MC) and crystalline clusters (CC) in the SCF-X/sub approx./-RW method. It is found that MC is unsuitable for describing perfect AEO, because they have a long-range Coulomb interaction and a potential cluster effect. Even in the CC method, the nonstoichiometric composition of (A/sub x/B/sub y/) for x < 13 and y < 14 does not allow one to obtain satisfactory agreement with the observed optical and x-ray spectra. The (A/sub 13/B/sub 14/) and (B/sub 13/A/sub 14/) clusters reproduce satisfactorily the partial composition of the valence band (VB) and the conduction band (CB), as well as the widths of those bands, the fine structure of the K emission spectrum for oxygen in MgO, and the observed electron-density distribution. A study is made of the effects of varying the radii of the spheres on the error from the region between the spheres with muffin-tin averaging.

  6. A Generalized Variable-Coefficient Algebraic Method Exactly Solving (3+1)-Dimensional Kadomtsev-Petviashvilli Equation

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A generalized variable-coefficient algebraic method is applied to construct several new families of exact solutions of physical interestfor (3+1)-dimensional Kadomtsev-Petviashvilli (KP) equation. Among them, the Jacobi elliptic periodic solutions exactly degenerate to the soliton solutions at a certain limit condition. Compared with the existing tanh method, the extended tanh method, the Jacobi elliptic function method, and the algebraic method, the proposed method gives new and more general solutions.

  7. Assessing the accuracy and reliability of ultrasonographic three-dimensional parathyroid volume measurement in a patient with secondary hyperparathyroidism: a comparison with the two-dimensional conventional method

    Energy Technology Data Exchange (ETDEWEB)

    You, Sung Hye; Son, Gyu Ri; Lee, Nam Joon [Dept. of Radiology, Korea University Anam Hospital, Seoul (Korea, Republic of); Suh, Sangil; Ryoo, In Seon; Seol, Hae Young [Dept. of Radiology, Korea University Guro Hospital, Seoul (Korea, Republic of); Lee, Young Hen; Seo, Hyung Suk [Dept. of Radiology, Korea University Ansan Hospital, Ansan (Korea, Republic of)

    2017-01-15

    The purpose of this study was to investigate the accuracy and reliability of the semi-automated ultrasonographic volume measurement tool, virtual organ computer-aided analysis (VOCAL), for measuring the volume of parathyroid glands. Volume measurements for 40 parathyroid glands were performed in patients with secondary hyperparathyroidism caused by chronic renal failure. The volume of the parathyroid glands was measured twice by experienced radiologists by two-dimensional (2D) and three-dimensional (3D) methods using conventional sonograms and the VOCAL with 30°angle increments before parathyroidectomy. The specimen volume was also measured postoperatively. Intraclass correlation coefficients (ICCs) and the absolute percentage error were used for estimating the reproducibility and accuracy of the two different methods. The ICC value between two measurements of the 2D method and the 3D method was 0.956 and 0.999, respectively. The mean absolute percentage error of the 2D method and the 3D VOCAL technique was 29.56% and 5.78%, respectively. For accuracy and reliability, the plots of the 3D method showed a more compact distribution than those of the 2D method on the Bland-Altman graph. The rotational VOCAL method for measuring the parathyroid gland is more accurate and reliable than the conventional 2D measurement. This VOCAL method could be used as a more reliable follow-up imaging modality in a patient with hyperparathyroidism.

  8. A meshless local radial basis function method for two-dimensional incompressible Navier-Stokes equations

    KAUST Repository

    Wang, Zhiheng

    2014-12-10

    A meshless local radial basis function method is developed for two-dimensional incompressible Navier-Stokes equations. The distributed nodes used to store the variables are obtained by the philosophy of an unstructured mesh, which results in two main advantages of the method. One is that the unstructured nodes generation in the computational domain is quite simple, without much concern about the mesh quality; the other is that the localization of the obtained collocations for the discretization of equations is performed conveniently with the supporting nodes. The algebraic system is solved by a semi-implicit pseudo-time method, in which the convective and source terms are explicitly marched by the Runge-Kutta method, and the diffusive terms are implicitly solved. The proposed method is validated by several benchmark problems, including natural convection in a square cavity, the lid-driven cavity flow, and the natural convection in a square cavity containing a circular cylinder, and very good agreement with the existing results are obtained.

  9. An Ant Colony Optimization Based Dimension Reduction Method for High-Dimensional Datasets

    Institute of Scientific and Technical Information of China (English)

    Ying Li; Gang Wang; Huiling Chen; Lian Shi; Lei Qin

    2013-01-01

    In this paper,a bionic optimization algorithm based dimension reduction method named Ant Colony Optimization -Selection (ACO-S) is proposed for high-dimensional datasets.Because microarray datasets comprise tens of thousands of features (genes),they are usually used to test the dimension reduction techniques.ACO-S consists of two stages in which two well-known ACO algorithms,namely ant system and ant colony system,are utilized to seek for genes,respectively.In the first stage,a modified ant system is used to filter the nonsignificant genes from high-dimensional space,and a number of promising genes are reserved in the next step.In the second stage,an improved ant colony system is applied to gene selection.In order to enhance the search ability of ACOs,we propose a method for calculating priori available heuristic information and design a fuzzy logic controller to dynamically adjust the number of ants in ant colony system.Furthermore,we devise another fuzzy logic controller to tune the parameter (q0) in ant colony system.We evaluate the performance of ACO-S on five microarray datasets,which have dimensions varying from 7129 to 12000.We also compare the performance of ACO-S with the results obtained from four existing well-known bionic optimization algorithms.The comparison results show that ACO-S has a notable ability to generate a gene subset with the smallest size and salient features while yielding high classification accuracy.The comparative results generated by ACO-S adopting different classifiers are also given.The proposed method is shown to be a promising and effective tool for mining high-dimension data and mobile robot navigation.

  10. Predicting the Dynamic Behavior of Asphalt Concrete Using Three-dimensional Discrete Element Method

    Institute of Scientific and Technical Information of China (English)

    CHEN Jun; PAN Tongyan; CHEN Jingya; HUANG Xiaoming; LU Yang

    2012-01-01

    A user-defined three-dimensional (3D) discrete element model was presented to predict the dynamic modulus and phase angle of asphalt concrete (AC).The 3D discrete element method (DEM) model of AC was constructed employing a user-defined computer program developed using the "Fish" language in PFC3D.Important microstructural features of AC were modeled,including aggregate gradation,air voids and mastic.The irregular shape of aggregate particle was modeled using a clump of spheres.The developed model was validated through comparing with experimental measurements and then used to simulate the cyclic uniaxial compression test,based on which the dynamic modulus and phase angle were calculated from the output stressstrain relationship.The effects of air void content,aggregate stiffness and volumetric fraction on AC modulus were further investigated.The experimental results show that the 3D DEM model is able to accurately predict both dynamic modulus and phase angle of AC across a range of temperature and loading frequencies.The userdefined 3D model also demonstrated significant improvement over the general existing two-dimensional models.

  11. Three-dimensional electro-floating display system using an integral imaging method.

    Science.gov (United States)

    Min, Sung-Wook; Hahn, Minsoo; Kim, Joohwan; Lee, Byoungho

    2005-06-13

    A new-type of three-dimensional (3D) display system based on two different techniques, image floating and integral imaging, is proposed. The image floating is an antiquated 3D display technique, in which a large convex lens or a concave mirror is used to display the image of a real object to observer. The electro-floating system, which does not use a real object, requires a volumetric display part in order to present 3D moving pictures. Integral imaging is an autostereoscopic technique consisting of a lens array and a two-dimensional display device. The integral imaging method can be adapted for use in an electro-floating display system because the integrated image has volumetric characteristics within the viewing angle. The proposed system combines the merits of the two techniques such as an impressive feel of depth and the facility to assemble. In this paper, the viewing characteristics of the two techniques are defined and analyzed for the optimal design of the proposed system. The basic experiments for assembling the proposed system were performed and the results are presented. The proposed system can be successfully applied to many 3D applications such as 3D television.

  12. Dimensional accuracy optimization of the micro-plastic injection molding process using the Taguchi design method

    Directory of Open Access Journals (Sweden)

    Chil-Chyuan KUO KUO

    2015-06-01

    Full Text Available Plastic injection molding is an important field in manufacturing industry because there are many plastic products that produced by injection molding. However, the time and cost required for producing a precision mold are the most troublesome problems that limit the application at the development stage of a new product in precision machinery industry. This study presents an approach of manufacturing a hard mold with microfeatures for micro-plastic injection molding. This study also focuses on Taguchi design method for investigating the effect of injection parameters on the dimensional accuracy of Fresnel lens during plastic injection molding. It was found that the dominant factor affecting the microgroove depth of Fresnel lens is packing pressure. The optimum processing parameters are packing pressure of 80 MPa, melt temperature of 240 °C, mold temperature of 90 °C and injection speed of 50 m/s. The dimensional accuracy of Fresnel lens can be controlled within ±3 µm using the optimum level of process parameters through the confirmation test. The research results of this study have industrial application values because electro-optical industries are able to significantly reduce a new optical element development cycle time.DOI: http://dx.doi.org/10.5755/j01.ms.21.2.5864

  13. A Method for Geometry Optimization in a Simple Model of Two-Dimensional Heat Transfer

    CERN Document Server

    Peng, Xiaohui; Protas, Bartosz

    2013-01-01

    This investigation is motivated by the problem of optimal design of cooling elements in modern battery systems. We consider a simple model of two-dimensional steady-state heat conduction described by elliptic partial differential equations and involving a one-dimensional cooling element represented by a contour on which interface boundary conditions are specified. The problem consists in finding an optimal shape of the cooling element which will ensure that the solution in a given region is close (in the least squares sense) to some prescribed target distribution. We formulate this problem as PDE-constrained optimization and the locally optimal contour shapes are found using a gradient-based descent algorithm in which the Sobolev shape gradients are obtained using methods of the shape-differential calculus. The main novelty of this work is an accurate and efficient approach to the evaluation of the shape gradients based on a boundary-integral formulation which exploits certain analytical properties of the sol...

  14. Novel Method of Detecting Movement of the Interference Fringes Using One-Dimensional PSD

    Directory of Open Access Journals (Sweden)

    Qi Wang

    2015-06-01

    Full Text Available In this paper, a method of using a one-dimensional position-sensitive detector (PSD by replacing charge-coupled device (CCD to measure the movement of the interference fringes is presented first, and its feasibility is demonstrated through an experimental setup based on the principle of centroid detection. Firstly, the centroid position of the interference fringes in a fiber Mach-Zehnder (M-Z interferometer is solved in theory, showing it has a higher resolution and sensitivity. According to the physical characteristics and principles of PSD, a simulation of the interference fringe’s phase difference in fiber M-Z interferometers and PSD output is carried out. Comparing the simulation results with the relationship between phase differences and centroid positions in fiber M-Z interferometers, the conclusion that the output of interference fringes by PSD is still the centroid position is obtained. Based on massive measurements, the best resolution of the system is achieved with 5.15, 625 μm. Finally, the detection system is evaluated through setup error analysis and an ultra-narrow-band filter structure. The filter structure is configured with a one-dimensional photonic crystal containing positive and negative refraction material, which can eliminate background light in the PSD detection experiment. This detection system has a simple structure, good stability, high precision and easily performs remote measurements, which makes it potentially useful in material small deformation tests, refractivity measurements of optical media and optical wave front detection.

  15. Faults simulations for three-dimensional reservoir-geomechanical models with the extended finite element method

    Science.gov (United States)

    Prévost, Jean H.; Sukumar, N.

    2016-01-01

    Faults are geological entities with thicknesses several orders of magnitude smaller than the grid blocks typically used to discretize reservoir and/or over-under-burden geological formations. Introducing faults in a complex reservoir and/or geomechanical mesh therefore poses significant meshing difficulties. In this paper, we consider the strong-coupling of solid displacement and fluid pressure in a three-dimensional poro-mechanical (reservoir-geomechanical) model. We introduce faults in the mesh without meshing them explicitly, by using the extended finite element method (X-FEM) in which the nodes whose basis function support intersects the fault are enriched within the framework of partition of unity. For the geomechanics, the fault is treated as an internal displacement discontinuity that allows slipping to occur using a Mohr-Coulomb type criterion. For the reservoir, the fault is either an internal fluid flow conduit that allows fluid flow in the fault as well as to enter/leave the fault or is a barrier to flow (sealing fault). For internal fluid flow conduits, the continuous fluid pressure approximation admits a discontinuity in its normal derivative across the fault, whereas for an impermeable fault, the pressure approximation is discontinuous across the fault. Equal-order displacement and pressure approximations are used. Two- and three-dimensional benchmark computations are presented to verify the accuracy of the approach, and simulations are presented that reveal the influence of the rate of loading on the activation of faults.

  16. Novel method of detecting movement of the interference fringes using one-dimensional PSD.

    Science.gov (United States)

    Wang, Qi; Xia, Ji; Liu, Xu; Zhao, Yong

    2015-06-02

    In this paper, a method of using a one-dimensional position-sensitive detector (PSD) by replacing charge-coupled device (CCD) to measure the movement of the interference fringes is presented first, and its feasibility is demonstrated through an experimental setup based on the principle of centroid detection. Firstly, the centroid position of the interference fringes in a fiber Mach-Zehnder (M-Z) interferometer is solved in theory, showing it has a higher resolution and sensitivity. According to the physical characteristics and principles of PSD, a simulation of the interference fringe's phase difference in fiber M-Z interferometers and PSD output is carried out. Comparing the simulation results with the relationship between phase differences and centroid positions in fiber M-Z interferometers, the conclusion that the output of interference fringes by PSD is still the centroid position is obtained. Based on massive measurements, the best resolution of the system is achieved with 5.15, 625 μm. Finally, the detection system is evaluated through setup error analysis and an ultra-narrow-band filter structure. The filter structure is configured with a one-dimensional photonic crystal containing positive and negative refraction material, which can eliminate background light in the PSD detection experiment. This detection system has a simple structure, good stability, high precision and easily performs remote measurements, which makes it potentially useful in material small deformation tests, refractivity measurements of optical media and optical wave front detection.

  17. Angular Correlations Between Fragment Spin and Prompt Neutron Evaporation in Spontaneous Fission of 252Cf: CORA-Demon Experiment

    Science.gov (United States)

    Prokhorova, E.; Gönnenwein, F.; Kopatch, Yu.; Mutterer, M.; Hanappe, F.; Kinnard, V.; Stuttgé, L.; Dorvaux, O.; Wollersheim, H.-J.

    2007-05-01

    A novel method to search for the anisotropic emission of prompt neutrons in the center-of-mass system of fission fragments is presented. The anisotropy is conjectured to be due to the large spins of fission fragments are known to carry. Triple neutron- neutron-fragment correlations in spontaneous fission of 252Cf were investigated in an exploratory experiment dubbed CORA-DEMON experiment. Fission fragments were intercepted in a double ionization chamber while neutrons were spotted in 2 two-dimensional cylindrical walls of Demon detectors with the target on the vertical cylinder axis. A new method of analysis of triple angular correlations between 2 neutrons and a fission fragment was applied. Preliminary results are reported.

  18. Improved non-dimensional dynamic influence function method for vibration analysis of arbitrarily shaped plates with clamped edges

    Directory of Open Access Journals (Sweden)

    Sang-Wook Kang

    2016-03-01

    Full Text Available A new formulation for the non-dimensional dynamic influence function method, which was developed by the authors, is proposed to efficiently extract eigenvalues and mode shapes of clamped plates with arbitrary shapes. Compared with the finite element and boundary element methods, the non-dimensional dynamic influence function method yields highly accurate solutions in eigenvalue analysis problems of plates and membranes including acoustic cavities. However, the non-dimensional dynamic influence function method requires the uneconomic procedure of calculating the singularity of a system matrix in the frequency range of interest for extracting eigenvalues because it produces a non-algebraic eigenvalue problem. This article describes a new approach that reduces the problem of free vibrations of clamped plates to an algebraic eigenvalue problem, the solution of which is straightforward. The validity and efficiency of the proposed method are illustrated through several numerical examples.

  19. Two-dimensional Phase Unwrapping Method Using Cost Function of L0 Norm

    Science.gov (United States)

    GAO, J.; LI, L.; SHI, L.

    2017-02-01

    Considering cost model and convergence speed of the minimum norm unwrapping, a highly efficient two-dimensional global phase unwrapping method optimized with L0 norm is proposed. As analysing features of cost model in phase unwrapping with minimum norm, a cost function definition is provided in line with the L0 norm, which impose a stronger constraint in the tangent direction of phase discontinuity boundary than that in normal direction, in order to preserve integrity of discontinuity during iterative unwrapping processing for continuous phase. For the sake of slow speed of low-frequency error convergence during linear solving, a data partitioning strategy is introduced into unwrapping processing. Due to independence of minimum norm method in blocks, linear solving only focus on high-frequency information and improve efficiency of iterative work, and the low-frequency processing part is transferred to offsetting-aligning between blocks. With experiments and analysis, reliability and efficiency of the novel phase unwrapping method are certified comparing to existing methods.

  20. Two-dimensional cylindrical thermal cloak designed by implicit transformation method

    Science.gov (United States)

    Yuan, Xuebo; Lin, Guochang; Wang, Youshan

    2016-07-01

    As a new-type technology of heat management, thermal metamaterials have attracted more and more attentions recently and thermal cloak is a typical case. Thermal conductivity of thermal cloak designed by coordinate transformation method is usually featured by inhomogeneity, anisotropy and local singularity. Explicit transformation method, which is commonly used to design thermal cloak with the coordinate transformation known in advance, has insufficient flexibility, making it hard to proactively reduce the difficulty of device fabrication. In this work, we designed the thermal conductivity of two-dimensional (2D) cylindrical thermal cloak using the implicit transformation method without knowledge of the coordinate transformation in advance. With two classes of generation functions taken into consideration, this study adopted full-wave simulations to analyze the thermal cloaking performances of designed thermal cloaks. Material distributions and simulation results showed that the implicit transformation method has high flexibility. The form of coordinate transformation not only influences the homogeneity and anisotropy but also directly influences the thermal cloaking performance. An improved layered structure for 2D cylindrical thermal cloak was put forward based on the generation function g(r) = r15, which reduces the number of the kinds of constituent materials while guaranteeing good thermal cloaking performance. This work provides a beneficial guidance for reducing the fabrication difficulty of thermal cloak.

  1. Three-dimensional morphological analysis method for geologic bodies and its parallel implementation

    Science.gov (United States)

    Mao, Xiancheng; Zhang, Bin; Deng, Hao; Zou, Yanhong; Chen, Jin

    2016-11-01

    It has been found that the spatial locations and distributions of orebodies, especially for certain hydrothermal mineral deposits, are closely related to the shape of intrusive geologic bodies. For complex and large-scale geologic bodies, however, it is challenging to achieve rigorous and quantitative morphological analysis by standard geological surface reconstruction and trend-surface analysis methods. This paper presents a novel, quantitative morphological analysis method for general geologic bodies of closed 2-manifold surface based on mathematical morphology. Through the processes of morphological filtering, set operations and three-dimensional Euclidean distance transform (3D-EDT), the global trend shape, local convex and concave zones as well as degree of surface undulation of a geologic body are extracted respectively. All of the three analysis phases are speeded up via parallel algorithms implemented by using the message passing interface (MPI) standard. The proposed method is tested with a case study of the Xinwuli intrusion with complex shape in Fenghuangshan deposit of the Tongling district, China. The results demonstrate that the method is an effective and efficient way to achieve quantitative morphological analysis, thereby decreasing the time necessary to find the association between morphological parameters of geologic bodies and mineralization.

  2. A method for two-dimensional characterization of animal vibrational signals transmitted along plant stems.

    Science.gov (United States)

    McNett, Gabriel D; Miles, Ronald N; Homentcovschi, Dorel; Cocroft, Reginald B

    2006-12-01

    Conventional approaches to measuring animal vibrational signals on plant stems use a single transducer to measure the amplitude of vibrations. Such an approach, however, will often underestimate the amplitude of bending waves traveling along the stem. This occurs because vibration transducers are maximally sensitive along a single axis, which may not correspond to the major axis of stem motion. Furthermore, stem motion may be more complex than that of a bending wave propagating along a single axis, and such motion cannot be described using a single transducer. Here, we describe a method for characterizing stem motion in two dimensions by processing the signals from two orthogonally positioned transducers. Viewed relative to a cross-sectional plane, a point on the stem surface moves in an ellipse at any one frequency, with the ellipse's major axis corresponding to the maximum amplitude of vibration. The method outlined here measures the ellipse's major and minor axes, and its angle of rotation relative to one of the transducers. We illustrate this method with measurements of stem motion during insect vibrational communication. It is likely the two-dimensional nature of stem motion is relevant to insect vibration perception, making this method a promising avenue for studies of plant-borne transmission.

  3. Tuning of Feedback Decoupling Controller for Two-Dimensional Heat Plate by Using VRFT Method

    Science.gov (United States)

    Matsunaga, Nobutomo; Nakano, Masahiko; Okajima, Hiroshi; Kawaji, Shigeyasu

    In manufacturing processes, inappropriate thermal distribution, which is observed in both steady and transient states of the thermal plant, leads to inferior quality. For a plant with strong thermal interaction, decoupling control is effective in precisely tuning the control system. We proposed the decoupling controller based on the temperature-difference feedback model. However, no parameter-identification method of thermal interaction has been presented so far. Traditionally, iterative tuning by trial and error has been used to tune the controller parameters. In the case of an industrial plant, the tuning time would be long because of the large time constants of the plant. Recently, the virtual reference feedback tuning (VRFT) method, which can be used for off-line tuning of the controller parameters using a set of I/O data, has been studied to examine the possibility of shortening the tuning time. In this paper, a VRFT method for the feedback decoupling controller is proposed for a two-dimensional heat plate by taking consideration the thermal interaction property. The effectiveness of this VRFT method is evaluated by performing an experimental simulation.

  4. Guided Autotransplantation of Teeth: A Novel Method Using Virtually Planned 3-dimensional Templates.

    Science.gov (United States)

    Strbac, Georg D; Schnappauf, Albrecht; Giannis, Katharina; Bertl, Michael H; Moritz, Andreas; Ulm, Christian

    2016-12-01

    The aim of this study was to introduce an innovative method for autotransplantation of teeth using 3-dimensional (3D) surgical templates for guided osteotomy preparation and donor tooth placement. This report describes autotransplantation of immature premolars as treatment of an 11-year-old boy having suffered severe trauma with avulsion of permanent maxillary incisors. This approach uses modified methods from guided implant surgery by superimposition of Digital Imaging and Communications in Medicine files and 3D data sets of the jaws in order to predesign 3D printed templates with the aid of a fully digital workflow. The intervention in this complex case could successfully be accomplished by performing preplanned virtual transplantations with guided osteotomies to prevent bone loss and ensure accurate donor teeth placement in new recipient sites. Functional and esthetic restoration could be achieved by modifying methods used in guided implant surgery and prosthodontic rehabilitation. The 1-year follow-up showed vital natural teeth with physiological clinical and radiologic parameters. This innovative approach uses the latest diagnostic methods and techniques of guided implant surgery, enabling the planning and production of 3D printed surgical templates. These accurate virtually predesigned surgical templates could facilitate autotransplantation in the future by full implementation of recommended guidelines, ensuring an atraumatic surgical protocol. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  5. Three-dimensional reconstruction method of Tang Dynasty building based on point clouds

    Science.gov (United States)

    Wang, Yinghui; Zhang, Huanhuan; Zhao, Yanni; Hao, Wen; Ning, Xiaojuan; Shi, Zhenghao; Zhao, Minghua

    2015-12-01

    We present a method to reconstruct the three-dimensional (3-D) Tang Dynasty building model from raw point clouds. Different from previous building modeling techniques, our method is developed for the Tang Dynasty building which does not exhibit planar primitives, facades, and repetitive structural elements as residential low- or high-rise buildings. The proposed method utilizes the structural property of the Tang Dynasty building to process the original point clouds. First, the raw point clouds are sliced into many parallel layers to generate a top-bottom hierarchical structure, and each layer is resampled to achieve a subset purification of 3-D point clouds. In addition, a series of different building components of the building are recognized by clustering these purifications of 3-D point clouds. In particular, we get the tree-structured topology of these different building components during slicing and clustering. Second, different solutions are explored to reconstruct its 3-D model for different building components. The overall model of building can be gotten based on the building components and tree-structured topology. Experimental results demonstrate that the proposed method is more efficient for generating a high realistic 3-D model of the Tang Dynasty building.

  6. Comparison of Cox Model Methods in A Low-dimensional Setting with Few Events

    Institute of Scientific and Technical Information of China (English)

    Francisco M Ojeda; Christian Muller; Daniela Bornigen; David-Alexandre Tregouet; Arne Schillert; Matthias Heinig; Tanja Zeller; Renate B Schnabel

    2016-01-01

    Prognostic models based on survival data frequently make use of the Cox proportional hazards model. Developing reliable Cox models with few events relative to the number of predictors can be challenging, even in low-dimensional datasets, with a much larger number of observations than variables. In such a setting we examined the performance of methods used to estimate a Cox model, including (i) full model using all available predictors and estimated by standard tech-niques, (ii) backward elimination (BE), (iii) ridge regression, (iv) least absolute shrinkage and selec-tion operator (lasso), and (v) elastic net. Based on a prospective cohort of patients with manifest coronary artery disease (CAD), we performed a simulation study to compare the predictive accu-racy, calibration, and discrimination of these approaches. Candidate predictors for incident cardio-vascular events we used included clinical variables, biomarkers, and a selection of genetic variants associated with CAD. The penalized methods, i.e., ridge, lasso, and elastic net, showed a compara-ble performance, in terms of predictive accuracy, calibration, and discrimination, and outperformed BE and the full model. Excessive shrinkage was observed in some cases for the penalized methods, mostly on the simulation scenarios having the lowest ratio of a number of events to the number of variables. We conclude that in similar settings, these three penalized methods can be used interchangeably. The full model and backward elimination are not recommended in rare event scenarios.

  7. Comparison of Cox Model Methods in A Low-dimensional Setting with Few Events

    Directory of Open Access Journals (Sweden)

    Francisco M. Ojeda

    2016-08-01

    Full Text Available Prognostic models based on survival data frequently make use of the Cox proportional hazards model. Developing reliable Cox models with few events relative to the number of predictors can be challenging, even in low-dimensional datasets, with a much larger number of observations than variables. In such a setting we examined the performance of methods used to estimate a Cox model, including (i full model using all available predictors and estimated by standard techniques, (ii backward elimination (BE, (iii ridge regression, (iv least absolute shrinkage and selection operator (lasso, and (v elastic net. Based on a prospective cohort of patients with manifest coronary artery disease (CAD, we performed a simulation study to compare the predictive accuracy, calibration, and discrimination of these approaches. Candidate predictors for incident cardiovascular events we used included clinical variables, biomarkers, and a selection of genetic variants associated with CAD. The penalized methods, i.e., ridge, lasso, and elastic net, showed a comparable performance, in terms of predictive accuracy, calibration, and discrimination, and outperformed BE and the full model. Excessive shrinkage was observed in some cases for the penalized methods, mostly on the simulation scenarios having the lowest ratio of a number of events to the number of variables. We conclude that in similar settings, these three penalized methods can be used interchangeably. The full model and backward elimination are not recommended in rare event scenarios.

  8. Two-grain nanoindentation using the quasicontinuum method: Two-dimensional model approach

    Energy Technology Data Exchange (ETDEWEB)

    Iglesias, Rodrigo A. [Instituto de Investigaciones en Fisicoquimica de Cordoba (INFIQC), Consejo Nacional de Investigaciones, Cientificas y Tecnicas (CONICET), Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Edificio Integrador, Ciudad Universitaria, Cordoba, CP 5000 (Argentina)]. E-mail: riglesias@mail.fcq.unc.edu.ar; Leiva, Ezequiel P.M. [Instituto de Investigaciones en Fisicoquimica de Cordoba (INFIQC), Consejo Nacional de Investigaciones, Cientificas y Tecnicas (CONICET), Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Edificio Integrador, Ciudad Universitaria, Cordoba, CP 5000 (Argentina)

    2006-06-15

    The quasicontinuum method (two-dimensional) developed by Tadmor et al. [Tadmor EB, Ortiz M, Phillips R. Philos Mag 1996;73:1529] is applied to an indentation process taking account of the atomic structure of the indenter and the substrate subject to indentation. Slip vectors, dislocation nucleation and nanostructure formation are analyzed for different indenter materials (Ag, Cu and Pd) and indenter crystal orientations. Slip vectors near to the contact region show that, depending on the material and orientation of the indenter, plastic deformations occur either inside the indenter or the substrate. Long-range material deformations appear during the indentation or retraction of the indenter. All of these aspects mainly dictate the formation of nanoclusters or nanoholes on the substrate surface.

  9. A method of boundary parameter estimation for a two-dimensional diffusion system under noisy observations

    Science.gov (United States)

    Sunahara, Y.; Kojima, F.

    1988-01-01

    The purpose of this paper is to establish a method for identifying unknown parameters involved in the boundary state of a class of diffusion systems under noisy observations. A mathematical model of the system dynamics is given by a two-dimensional diffusion equation. Noisy observations are made by sensors allocated on the system boundary. Starting with the mathematical model mentioned above, an online parameter estimation algorithm is proposed within the framework of the maximum likelihood estimation. Existence of the optimal solution and related necessary conditions are discussed. By solving a local variation of the cost functional with respect to the perturbation of parameters, the estimation mechanism is proposed in a form of recursive computations. Finally, the feasibility of the estimator proposed here is demonstrated through results of digital simulation experiments.

  10. A solution of two-dimensional magnetohydrodynamic flow using the finite volume method

    Directory of Open Access Journals (Sweden)

    Naceur Sonia

    2014-01-01

    Full Text Available This paper presents the two dimensional numerical modeling of the coupling electromagnetic-hydrodynamic phenomena in a conduction MHD pump using the Finite volume Method. Magnetohydrodynamic problems are, thus, interdisciplinary and coupled, since the effect of the velocity field appears in the magnetic transport equations, and the interaction between the electric current and the magnetic field appears in the momentum transport equations. The resolution of the Maxwell's and Navier Stokes equations is obtained by introducing the magnetic vector potential A, the vorticity z and the stream function y. The flux density, the electromagnetic force, and the velocity are graphically presented. Also, the simulation results agree with those obtained by Ansys Workbench Fluent software.

  11. Three-dimensional analysis of elastic stress distribution of indented ceramic surface by finite element method

    Institute of Scientific and Technical Information of China (English)

    Tatsuyuki NEZU

    2006-01-01

    The three-dimensional stress distributions in the area surrounding indentation pattern for three different materials,Al2O3,Si3N4 and SiC were analyzed by finite element method(FEM). Those theoretical results were also compared with the experimental ones by Rockwell hardness test. The effect of loading stress on the plastic deformation in specimens,surface was investigated on the assumption of shear strain energy theory by Huber-Mises when the materials were indented. The distributions of nomal stress,shear stress,and Mises stress were analysed with variations of loading conditions. It is clear that the analytical results for the stress distributions,the crack length and its density of probability are in good agreement with the experimental results.

  12. The complex Jacobi iterative method for three-dimensional wide-angle beam propagation.

    Science.gov (United States)

    Le, Khai Q; Godoy-Rubio, R; Bienstman, Peter; Hadley, G Ronald

    2008-10-13

    A new complex Jacobi iterative technique adapted for the solution of three-dimensional (3D) wide-angle (WA) beam propagation is presented. The beam propagation equation for analysis of optical propagation in waveguide structures is based on a novel modified Padé(1,1) approximant operator, which gives evanescent waves the desired damping. The resulting approach allows more accurate approximations to the true Helmholtz equation than the standard Padé approximant operators. Furthermore, a performance comparison of the traditional direct matrix inversion and this new iterative technique for WA-beam propagation method is reported. It is shown that complex Jacobi iteration is faster and better-suited for large problems or structures than direct matrix inversion.

  13. Moiré-reduction method for slanted-lenticular-based quasi-three-dimensional displays

    Science.gov (United States)

    Zhuang, Zhenfeng; Surman, Phil; Zhang, Lei; Rawat, Rahul; Wang, Shizheng; Zheng, Yuanjin; Sun, Xiao Wei

    2016-12-01

    In this paper we present a method for determining the preferred slanted angle for a lenticular film that minimizes moiré patterns in quasi-three-dimensional (Q3D) displays. We evaluate the preferred slanted angles of the lenticular film for the stripe-type sub-pixel structure liquid crystal display (LCD) panel. Additionally, the sub-pixels mapping algorithm of the specific angle is proposed to assign the images to either the right or left eye channel. A Q3D display prototype is built. Compared with the conventional SLF, this newly implemented Q3D display can not only eliminate moiré patterns but also provide 3D images in both portrait and landscape orientations. It is demonstrated that the developed slanted lenticular film (SLF) provides satisfactory 3D images by employing a compact structure, minimum moiré patterns and stabilized 3D contrast.

  14. Three-Dimensional Water-Quality Simulation for River Based on VOF Method

    Institute of Scientific and Technical Information of China (English)

    敖雪菲; 王晓玲; 宋明瑞; 邓韶辉; 李松敏

    2016-01-01

    In the present study, considering the transport and transformation processes of variables, a three-dimensional water quality model for the river system was established, which coupled the volume of fluid(VOF) method with thek-ε turbulence mathematical model. Then, the water hydrodynamic characteristics and transport processes for BOD5, NH3-N and TP were analyzed. The results showed that the water surface of convex bank was a little lower than that of concave bank due to the centrifugal force near the bend, and most concentrations were infe-rior to the typeⅤ standard indexes of surface water environmental quality. The model validation indicated that the errors between the simulated and monitored values were comparatively small, satisfying the application demands and providing scientific basis and decision support for the restoration and protection of water quality.

  15. Cardiac dimensional analysis by use of biplane cineradiography: description and validation of method.

    Science.gov (United States)

    Lipscomb, K

    1980-01-01

    Biplane cineradiography is a potentially powerful tool for precise measurement of intracardiac dimensions. The most systematic approach to these measurements is the creation of a three-dimensional coordinate system within the x-ray field. Using this system, interpoint distances, such as between radiopaque clips or coronary artery bifurcations, can be calculated by use of the Pythagoras theorem. Alternatively, calibration factors can be calculated in order to determine the absolute dimensions of a structure, such as a ventricle or coronary artery. However, cineradiography has two problems that have precluded widespread use of the system. These problems are pincushion distortion and variable image magnification. In this paper, methodology to quantitate and compensate for these variables is presented. The method uses radiopaque beads permanently mounted in the x-ray field. The position of the bead images on the x-ray film determine the compensation factors. Using this system, measurements are made with a standard deviation of approximately 1% of the true value.

  16. Three-Dimensional Dynamic Topology Optimization with Frequency Constraints Using Composite Exponential Function and ICM Method

    Directory of Open Access Journals (Sweden)

    Hongling Ye

    2015-01-01

    Full Text Available The dynamic topology optimization of three-dimensional continuum structures subject to frequency constraints is investigated using Independent Continuous Mapping (ICM design variable fields. The composite exponential function (CEF is selected to be a filter function which recognizes the design variables and to implement the changing process of design variables from “discrete” to “continuous” and back to “discrete.” Explicit formulations of frequency constraints are given based on filter functions, first-order Taylor series expansion. And an improved optimal model is formulated using CEF and the explicit frequency constraints. Dual sequential quadratic programming (DSQP algorithm is used to solve the optimal model. The program is developed on the platform of MSC Patran & Nastran. Finally, numerical examples are given to demonstrate the validity and applicability of the proposed method.

  17. Three-Dimensional Multi-mesh Material Point Method for Solving Collision Problems

    Institute of Scientific and Technical Information of China (English)

    YANG Zhan-Ying; PAN Xiao-Fei; XUE Pan-Pan; XU Ai-Guo; ZHAO Liu; ZHANG Guang-Cai; SHI Kang-Jie; ZHANG Ping; ZHU Jian-Shi; MA Shang; ZHANG Xiong

    2008-01-01

    A new multi-mesh contact algorithm for three-dimensional material point method is presented. The contact algorithm faithfully recovers the opposite acting forces between colliding bodies. Collision procedures between regular bodies and/or rigid bodies are treated within the same framework. Multi-value of momentum and mass are defined on every node to describe the contact/sliding/separation procedure. Both normal and tangential velocities of each particle at the contact surface are calculated in respective individual mesh. A Coulomb friction is applied to describe the sliding or slipping between the contacting bodies. The efficiency of the contact algorithm is linearly related to the number of the contacting bodies because the overlapped nodes are labeled by sweeping the material particles of a11 bodies when the nodal momentum and mass are formed at every time step. Numerical simulation shows that our contact algorithm possesses high accuracy and low numerical energy dissipation, which is very important for solving collision problems.

  18. A comparison of dimensionality reduction methods for retrieval of similar objects in simulation data

    Energy Technology Data Exchange (ETDEWEB)

    Cantu-Paz, E; Cheung, S S; Kamath, C

    2003-09-23

    High-resolution computer simulations produce large volumes of data. As a first step in the analysis of these data, supervised machine learning techniques can be used to retrieve objects similar to a query that the user finds interesting. These objects may be characterized by a large number of features, some of which may be redundant or irrelevant to the similarity retrieval problem. This paper presents a comparison of six dimensionality reduction algorithms on data from a fluid mixing simulation. The objective is to identify methods that efficiently find feature subsets that result in high accuracy rates. Our experimental results with single- and multi-resolution data suggest that standard forward feature selection produces the smallest feature subsets in the shortest time.

  19. An Inverse Electromagnetic Scattering Method for One-Dimensional Inhomogeneous Media

    Institute of Scientific and Technical Information of China (English)

    LIN Zhi-Wei; XU Xin; ZHANG Xiao-Juan; FANG Guang-You

    2011-01-01

    A frequency-domain inversion scheme for reconstructing the permittivity profile of one-dimensional inhomogeneous media is proposed. The generalized reflection coefficients and the generalized transmission coefficients of the inhomogeneous media are used as the input data of the inverse model. A Newton-like iterative algorithm known as the generalized pulse-spectrum technique with the Tikhonov regularization is applied to solve the inverse problem. Novel boundary conditions are proposed for the inverse problem and therefore the permittivity at the boundary of the inhomogeneous media is not required as prior knowledge. The choice of frequency points of the frequency-domain method is also investigated. Numerical examples are carried out to validate the inversion technique. Good agreements between the reconstructed profiles and the true profiles are shown.

  20. Finite difference method and analysis for three-dimensional semiconductor device of heat conduction

    Institute of Scientific and Technical Information of China (English)

    袁益让

    1996-01-01

    The mathematical model of the three-dimensional semiconductor devices of heat conduction is described by a system of four quasilinear partial differential equations for initial boundary value problem. One equation in elliptic form is for the electric potential; two equations of convection-dominated diffusion type are for the electron and hole concentration; and one heat conduction equation is for temperature. Characteristic finite difference schemes for two kinds of boundary value problems are put forward. By using the thick and thin grids to form a complete set and treating the product threefold-quadratic interpolation, variable time step method with the boundary condition, calculus of variations and the theory of prior estimates and techniques, the optimal error estimates in L2 norm are derived in the approximate solutions.