Distribution by Scientific Domains
Distribution within Chemistry

Terms modified by Computational

  • computational advantage
  • computational algorithm
  • computational algorithms
  • computational analysis
  • computational application
  • computational approach
  • computational aspect
  • computational biology
  • computational burden
  • computational calculation
  • computational capability
  • computational challenge
  • computational chemistry
  • computational complexity
  • computational cost
  • computational demand
  • computational design
  • computational difficulty
  • computational domain
  • computational efficiency
  • computational effort
  • computational electromagnetic
  • computational environment
  • computational expense
  • computational experience
  • computational experiment
  • computational fluid dynamic
  • computational fluid dynamics
  • computational fluid dynamics code
  • computational fluid dynamics simulation
  • computational fluid dynamics study
  • computational framework
  • computational grid
  • computational investigation
  • computational issues
  • computational level
  • computational load
  • computational mechanic
  • computational mesh
  • computational method
  • computational methodology
  • computational methods
  • computational model
  • computational modeling
  • computational modelling
  • computational models
  • computational node
  • computational performance
  • computational physics
  • computational point
  • computational power
  • computational prediction
  • computational problem
  • computational procedure
  • computational process
  • computational program
  • computational property
  • computational requirement
  • computational resource
  • computational result
  • computational savings
  • computational scheme
  • computational science
  • computational simplicity
  • computational simulation
  • computational speed
  • computational strategy
  • computational studies
  • computational study
  • computational technique
  • computational techniques
  • computational test
  • computational time
  • computational tool
  • computational work

  • Selected Abstracts

    A Novel Bis(zinc,porphyrin),Oxoporphyrinogen Donor,Acceptor Triad: Synthesis, Electrochemical, Computational and Photochemical Studies

    Jonathan P. Hill
    Abstract The first example of a porphyrin-quinonoid donor,acceptor triad featuring (tetraphenylporphinato)zinc(II) moieties covalently attached to an oxoporphyrinogen through its macrocyclic nitrogen atoms is reported. This arrangement of chromophores results in an interesting interplay between the electron-donating zinc,porphyrin(s) and the electron/energy accepting oxoporphyrinogen. The optical absorption of the triad reveals features corresponding to both the donor and acceptor entities. The geometry and electronic structure of the triad deduced from B3LYP/3-21G(*) calculations reveal an absence of inter-chromophoric interactions and localization of the HOMO on one zinc,porphyrin group and the LUMO on the oxoporphyrinogen scaffold. The electrochemical redox states of the triad were established from a comparative electrochemistry of the triad and the reference compounds. Both steady-state and time-resolved emission studies revealed quenching of the singlet excited state of zinc,porphyrin in the triad, and the free-energy calculations performed using Weller's approach indicate the possibility of electron transfer from the singlet excited zinc,porphyrin group to the oxoporphyrinogen in polar solvents. Time-resolved fluorescence studies reveal excited state energy transfer from zinc,porphyrin to oxoporphyrinogen in nonpolar solvents, while nanosecond transient absorption studies combined with time-resolved fluorescence studies in polar solvents are indicative of the occurrence of photoinduced charge separation from the singlet excited zinc,porphyrin to the oxoporphyrinogen. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]

    Uncertainty Quantification in Computational and Prediction Science

    Roger G. Ghanem
    No abstract is available for this article. [source]

    Computational and experimental fluid dynamics of jet loop reactor

    AICHE JOURNAL, Issue 10 2009
    Channamallikarjun S. Mathpati
    Abstract A computational analysis using standard k-, model, RSM and LES has been carried out for jet loop reactors (JLR) to investigate the mean and turbulence quantities. These simulations have revealed that the flow in JLR was different from the self-similar round jets. RSM and LES showed better agreement with PIV measurements compared with standard k-, model. The modeled turbulence production and transport in k-, model overpredicted those estimated from LES data. To reduce the limitations, modified k-, models have been evaluated for JLR. Also, a hybrid k-, model has been suggested, which was found to perform better than other modified k-, models. This model was also found to hold for stirred tank reactors (STRs). Mixing time analysis has been carried out for JLR and STR at same power consumption. It has been shown that JLR can be inferior to STR if proper nozzle diameter is not selected. © 2009 American Institute of Chemical Engineers AIChE J, 2009 [source]

    Semi-quantitative and structural metabolic phenotyping by direct infusion ion trap mass spectrometry and its application in genetical metabolomics

    Albert Koulman
    The identification of quantitative trait loci (QTL) for plant metabolites requires the quantitation of these metabolites across a large range of progeny. We developed a rapid metabolic profiling method using both untargeted and targeted direct infusion tandem mass spectrometry (DIMSMS) with a linear ion trap mass spectrometer yielding sufficient precision and accuracy for the quantification of a large number of metabolites in a high-throughput environment. The untargeted DIMSMS method uses top-down data-dependent fragmentation yielding MS2 and MS3 spectra. We have developed software tools to assess the structural homogeneity of the MS2 and MS3 spectra hence their utility for phenotyping and genetical metabolomics. In addition we used a targeted DIMS(MS) method for rapid quantitation of specific compounds. This method was compared with targeted LC/MS/MS methods for these compounds. The DIMSMS methods showed sufficient precision and accuracy for QTL discovery. We phenotyped 200 individual Loliumperenne genotypes from a mapping population harvested in two consecutive years. Computational and statistical analyses identified 246 nominal m/z bins with sufficient precision and homogeneity for QTL discovery. Comparison of the data for specific metabolites obtained by DIMSMS with the results from targeted LC/MS/MS analysis showed that quantitation by this metabolic profiling method is reasonably accurate. Of the top 100 MS1 bins, 22 ions gave one or more reproducible QTL across the 2 years. Copyright © 2009 John Wiley & Sons, Ltd. [source]

    Robust Generation of Lead Compounds for Protein,Protein Interactions by Computational and MCR Chemistry: p53/Hdm2 Antagonists,

    ANGEWANDTE CHEMIE, Issue 31 2010
    Anna Czarna Dr.
    Eine Antagonistensammlung durch Mehrkomponenten-Reaktionen: Die hier vorgestellte parallele Entdeckung unterschiedlicher Gerüste, die als Antagonisten der krebsrelevanten Protein-Protein-Wechselwirkung p53/Hdm2 in Frage kommen, nutzt das Wechselspiel zwischen Mehrkomponenten-Reaktionen, Strukturbiologie, Computerchemie und NMR-basiertem Screening. [source]

    A Computational and Experimental Study of the Structure and Raman and 77Se NMR Spectra of SeX3+ and SeX2 (X: Cl, Br, I): FT-Raman Spectrum of (SeI3)[AsF6].

    CHEMINFORM, Issue 23 2005
    J. Mikko Rautiainen
    Abstract For Abstract see ChemInform Abstract in Full Text. [source]

    On Mercury(I) Oxo Compounds , Quasi-Relativistic Computational and Experimental Studies

    CHEMINFORM, Issue 49 2003
    S. G. Wang
    Abstract For Abstract see ChemInform Abstract in Full Text. [source]

    Reaction Mechanism for the LiCl-Mediated Directed Zinc Insertion: A Computational and Experimental Study

    Ching-Yuan Liu Dr.
    Tired of wondering about the role of LiCl in the DoI reaction of zinc? Kinetic/thermodynamic competitive experiments and DFT calculations were performed to clarify the regioselectivity and reaction mechanism/pathways of lithium chloride-promoted directed zinc insertion into bromobenzenes. The results strongly suggest that the LiCl-containing "push,pull form" transition state (TSb) is formed at an early stage, thus accelerating the reaction rate of zinc insertion. (DoI=directed ortho insertion.) [source]

    On the Dichotomic Reactivity of Lithiated Styrene Oxide: A Computational and Multinuclear Magnetic Resonance Investigation

    Vito Capriati Prof.
    Abstract A multinuclear magnetic resonance investigation, supported by density functional theory calculations, has been synergically used to investigate the configurational stability, reactivity and aggregation states of ,-lithiated styrene oxide in THF at 173,K. NMR studies on ,-lithiated [,,,- 13C2]styrene oxide (also in an enantiomerically enriched form) proved that in THF this oxiranyllithium is mainly present as a solvated monomeric species in equilibrium with a complex mixture of stereoisomeric dimeric aggregates, as well as with bridged and tetrameric aggregates. The fact that some C,Li bonds are partially broken in some stereoisomers reduces their symmetry and complicates the NMR spectra: two diastereoisomers each having a pair of diastereotopic carbon atoms slowly inverting at the lithium atom in absence of tetramethylethylenediamine (TMEDA) have been detected. A (13C,7Li)-HMQC experiment to correlate 7Li and 13C resonances of the various aggregates has been performed for the first time. From natural bond analysis, the monomeric aggregate was proven to have a lower carbenoid character with respect to bridged O-coordinated dimeric aggregates. The employment of suitable experimental conditions in terms of concentration, temperature and the presence or not of TMEDA are crucial to mitigate at the best the "carbene-like" reactivity of lithiated styrene oxide toward intermolecular CLi insertions, eliminative dimerisation reactions and ring-opening reactions. A two-step mechanism for the deprotonation of styrene oxide by sBuLi in THF has been proposed and discussed as well as competitive side reactions. [source]

    ,-Carbonyl Substituent Effect on the Lifetimes of Triplet 1,4-Biradicals from Norrish-Type-II Reactions

    Xichen Cai Dr.
    Abstract Triplet 1,4-biradicals were generated by Norrish-Type-II hydrogen transfer from ,-heteroatom-substituted ,-branched butyrophenones 1,6 and detected by laser flash absorption measurements. For three oxy-substituted compounds 2,4 (R,=OH, OCOMe, OCOOEt) comparable lifetimes were determined in acetonitrile (roughly 1.5 ,s). In benzene, divergent trends were observed: for the hydroxy compound 2 a lower lifetime of 790 ns was determined, whereas for 3 and 4 the lifetimes increased to 4.9 ,s. Photolyses of the ,-amino-substituted compounds 1 and 6 resulted in transient species with significant lower lifetimes (for 1 160 ns in benzene and 450 ns in acetonitrile; for 6 <100 ns in both solvents). The mesyloxy substrate 5 undergoes rapid CO bond cleavage upon photolysis and no transient triplet species were detected. Computational (UB3,LYP/6,31G* and natural don orbital (NBO) analyses) results supported the assumption of a negative hyperconjugative interaction strongly stabilizing ,-oxy-substituted over ,-amino-substituted radicals. [source]

    Computational and Structural Approaches to Drug Discovery: Ligand,Protein Interactions.

    CHEMMEDCHEM, Issue 7 2008
    Edited by Robert M. Stroud, Janet Finer-Moore.
    No abstract is available for this article. [source]

    Combining Computational and Biochemical Studies for a Rationale on the Anti-Aromatase Activity of Natural Polyphenols

    CHEMMEDCHEM, Issue 12 2007
    Abstract Aromatase, an enzyme of the cytochrome,P450 family, is a very important pharmacological target, particularly for the treatment of breast cancer. The anti-aromatase activity of a set of natural polyphenolic compounds was evaluated in,vitro. Strong aromatase inhibitors including flavones, flavanones, resveratrol, and oleuropein, with activities comparable to that of the reference anti-aromatase drug aminoglutethimide, were identified. Through the application of molecular modeling techniques based on grid-independent descriptors and molecular interaction fields, the major physicochemical features associated with inhibitory activity were disclosed, and a putative virtual active site of aromatase was proposed. Docking of the inhibitors into a 3D homology model structure of the enzyme defined a common binding mode for the small molecules under investigation. The good correlation between computational and biological results provides the first rationalization of the anti-aromatase activity of polyphenolic compounds. Moreover, the information generated in this approach should be further exploited for the design of new aromatase inhibitors. [source]

    Adding Depth to Cartoons Using Sparse Depth (In)equalities

    D. Sıkora
    Abstract This paper presents a novel interactive approach for adding depth information into hand-drawn cartoon images and animations. In comparison to previous depth assignment techniques our solution requires minimal user effort and enables creation of consistent pop-ups in a matter of seconds. Inspired by perceptual studies we formulate a custom tailored optimization framework that tries to mimic the way that a human reconstructs depth information from a single image. Its key advantage is that it completely avoids inputs requiring knowledge of absolute depth and instead uses a set of sparse depth (in)equalities that are much easier to specify. Since these constraints lead to a solution based on quadratic programming that is time consuming to evaluate we propose a simple approximative algorithm yielding similar results with much lower computational overhead. We demonstrate its usefulness in the context of a cartoon animation production pipeline including applications such as enhancement, registration, composition, 3D modelling and stereoscopic display. [source]

    Artificial Animals and Humans: From Physics to Intelligence

    Demetri Terzopoulos
    The confluence of virtual reality and artificial life, an emerging discipline that spans the computational and biological sciences, has yielded synthetic worlds inhabited by realistic, artificial flora and fauna. Artificial animals are complex synthetic organisms that possess functional biomechanical bodies, sensors, and brains with locomotion, perception, behavior, learning, and cognition centers. Artificial humans and other animals are of interest in computer graphics because they are self-animating characters that dramatically advance the state of the art of production animation and interactive game technologies. More broadly, these biomimetic autonomous agents in their realistic virtual worlds also foster deeper, computationally oriented insights into natural living systems. [source]

    Applying content management to automated provenance capture

    Karen L. Schuchardt
    Abstract Workflows and data pipelines are becoming increasingly valuable to computational and experimental sciences. These automated systems are capable of generating significantly more data within the same amount of time compared to their manual counterparts. Automatically capturing and recording data provenance and annotation as part of these workflows are critical for data management, verification, and dissemination. We have been prototyping a workflow provenance system, targeted at biological workflows, that extends our content management technologies and other open source tools. We applied this prototype to the provenance challenge to demonstrate an end-to-end system that supports dynamic provenance capture, persistent content management, and dynamic searches of both provenance and metadata. We describe our prototype, which extends the Kepler system for the execution environment, the Scientific Annotation Middleware (SAM) content management software for data services, and an existing HTTP-based query protocol. Our implementation offers several unique capabilities, and through the use of standards, is able to provide access to the provenance record with a variety of commonly available client tools. Copyright © 2007 John Wiley & Sons, Ltd. [source]

    GridBLAST: a Globus-based high-throughput implementation of BLAST in a Grid computing framework

    Arun KrishnanArticle first published online: 24 JUN 200
    Abstract Improvements in the performance of processors and networks have made it feasible to treat collections of workstations, servers, clusters and supercomputers as integrated computing resources or Grids. However, the very heterogeneity that is the strength of computational and data Grids can also make application development for such an environment extremely difficult. Application development in a Grid computing environment faces significant challenges in the form of problem granularity, latency and bandwidth issues as well as job scheduling. Currently existing Grid technologies limit the development of Grid applications to certain classes, namely, embarrassingly parallel, hierarchical parallelism, work flow and database applications. Of all these classes, embarrassingly parallel applications are the easiest to develop in a Grid computing framework. The work presented here deals with creating a Grid-enabled, high-throughput, standalone version of a bioinformatics application, BLAST, using Globus as the Grid middleware. BLAST is a sequence alignment and search technique that is embarrassingly parallel in nature and thus amenable to adaptation to a Grid environment. A detailed methodology for creating the Grid-enabled application is presented, which can be used as a template for the development of similar applications. The application has been tested on a ,mini-Grid' testbed and the results presented here show that for large problem sizes, a distributed, Grid-enabled version can help in significantly reducing execution times. Copyright © 2005 John Wiley & Sons, Ltd. [source]

    Mechanical computation in neurons

    Jummi Laishram
    Abstract Growth cones are the main motile structures located at the tip of neurites and are composed of a lamellipodium from which thin filopodia emerge. In this article, we analyzed the kinetics and dynamics of growth cones with the aim to understand two major issues: first, the strategy used by filopodia and lamellipodia during their exploration and navigation; second, what kind of mechanical problems neurons need to solve during their operation. In the developing nervous system and in the adult brain, neurons constantly need to solve mechanical problems. Growth cones must decide how to explore the environment and in which direction to grow; they also need to establish the appropriate contacts, to avoid obstacles and to determine how much force to exert. Here, we show that in sparse cultures, filopodia grow and retract following statistical patterns, nearly optimal for an efficient exploration of the environment. In a dense culture, filopodia exploration is still present although significantly reduced. Analysis on 1271, 6432, and 185 pairs of filopodia of DRG, PC12 and Hippocampal neurons respectively showed that the correlation coefficient |,| of the growth of more than 50% of filopodia pairs was >0.15. From a computational point of view, filopodia and lamellipodia motion can be described by a random process in which errors are corrected by efficient feedback loops. This article argues that neurons not only process sensory signals, but also solve mechanical problems throughout their entire lifespan, from the early stages of embryogenesis to adulthood. © 2009 Wiley Periodicals, Inc. Develop Neurobiol, 2009 [source]

    Flow reversal over a natural pool,riffle sequence: a computational study

    Zhixian Cao
    Abstract A computational study is presented on the hydraulics of a natural pool,rif,e sequence composed of mixed cobbles, pebbles and sand in the River Lune, northern England. A depth-averaged two-dimensional numerical model is employed, calibrated with observed data at the ,eld site. From the computational outputs, the occurrence of longitudinally double peak zones of bed shear stress and velocity is found. In particular, at low discharge there exists a primary peak zone of bed shear stress and velocity at the rif,e tail in line with the local maximum energy slope, in addition to a secondary peak at the pool head. As discharge increases, the primary peak at the rif,e tail at low ,ow moves toward the upstream side of the rif,e along with the maximum energy slope, showing progressive equalization to the surrounding hydraulic pro,les. Concurrently, the secondary peak, due to channel constriction, appears to stand at the pool head, with its value increasing with discharge and approaching or exceeding the primary peak over the rif,e. The existence of ,ow reversal is demonstrated for this speci,c case, which is attributable to channel constriction at the pool head. A dynamic equilibrium model is presented to reconstruct the pool,rif,e morphology. A series of numerical modelling exercises demonstrates that the pool,rif,e morphology is more likely produced by shallow ,ows concentrated with coarse sediments than deep ,ows laden with low concentrations of ,ne sediments. It is concluded that channel constriction can, but may not necessarily, lead to competence reversal, depending on channel geometry, ,ow discharge and sediment properties. Copyright © 2003 John Wiley & Sons, Ltd. [source]

    Computer-assisted 2-D agarose electrophoresis of Haemophilus influenzae type B meningitis vaccines and analysis of polydisperse particle populations in the size range of viruses: A review

    ELECTROPHORESIS, Issue 4 2007
    Dietmar Tietz Dr.
    Abstract When protein,polysaccharide conjugated vaccines were first developed for the immunization of small children against meningitis caused by infection with Haemophilus influenzae type b (Hib), the vaccine preparations varied in immunogenicity. Testing for immunogenicity was time-consuming and alternative analytical procedures for determining vaccine quality were unsatisfactory. For example, due to the very high molecular weight of the vaccine particles, immunogens could only be physically characterized as a fraction in the void volume of Sepharose gel filtration. In search of better analytical methods, a computer-assisted electrophoretic technique for analyzing such vaccines was developed in the period from 1983 to 1995. This new approach made it possible to analyze highly negatively charged particles as large as or larger than intact viruses. 2-D gel patterns were generated that varied depending on the conditions of the particular vaccine preparation and were therefore characteristic of each vaccine sample. Thus, vaccine particle populations with a continuous size variation over a wide range (polydisperse) could be characterized according to size and free mobility (related to particle surface net charge density). These advances are reviewed in this article, since the developed methods are still a promising tool for vaccine quality control and for predicting immunogen effectiveness in the production of vaccines. The technique is potentially beneficial for Hib immunogens and other high-molecular-mass vaccines. Additional biomedical applications for this nondenaturing electrophoretic technique are briefly discussed and detailed information about computational and mathematical procedures and theoretical aspects is provided in the Appendices. [source]

    Computational significance of transient dynamics in cortical networks

    Daniel Durstewitz
    Abstract Neural responses are most often characterized in terms of the sets of environmental or internal conditions or stimuli with which their firing rate are correlated increases or decreases. Their transient (nonstationary) temporal profiles of activity have received comparatively less attention. Similarly, the computational framework of attractor neural networks puts most emphasis on the representational or computational properties of the stable states of a neural system. Here we review a couple of neurophysiological observations and computational ideas that shift the focus to the transient dynamics of neural systems. We argue that there are many situations in which the transient neural behaviour, while hopping between different attractor states or moving along ,attractor ruins', carries most of the computational and/or behavioural significance, rather than the attractor states eventually reached. Such transients may be related to the computation of temporally precise predictions or the probabilistic transitions among choice options, accounting for Weber's law in decision-making tasks. Finally, we conclude with a more general perspective on the role of transient dynamics in the brain, promoting the view that brain activity is characterized by a high-dimensional chaotic ground state from which transient spatiotemporal patterns (metastable states) briefly emerge. Neural computation has to exploit the itinerant dynamics between these states. [source]

    Resolution of Racemic N -Benzyl ,-Amino Acids by Liquid-Liquid Extraction: A Practical Method Using a Lipophilic Chiral Cobalt(III) Salen Complex and Mechanistic Studies

    Pawel Dzygiel
    Abstract The efficient resolution of racemic N -benzyl ,-amino acids (N -Bn-AA) has been achieved by a liquid-liquid extraction process using the lipophilic chiral salen,cobalt(III) complex [CoIII(3)(OAc)]. As a result of the resolution by extraction, one enantiomer (S) of the N -benzyl ,-amino acid predominated in the aqueous phase, while the other enantiomer (R) was driven into the organic phase by complexation to cobalt. The complexed amino acid (R) was then quantitatively released by a reductive (CoIII,,,CoII) counter-extraction with aqueous sodium dithionite or L -ascorbic acid in methanol. Thereductive cleavage allowed to recover the [CoII(3)] complex in good yield, which could be easily re-oxidized to[CoIII(3)(OAc)] with air/AcOH and reused with essentially no loss of reactivity and selectivity. Investigation on the nitrogen substitution indicates that the presence of a single benzyl group on the amino acid nitrogen is important to obtain high enantioselectivity in the extraction process. The kinetic vs. thermodynamic nature of the resolution process was also investigated with an enantiomeric exchange experiment, which shows that the liquid-liquid extraction with [CoIII(3)(OAc)] is an equilibrium process operating under thermodynamic control. In the absence of a suitable crystal structure of the [CoIII(3)(N -Bn-AA)] complexes, computational and spectroscopic studies were used to investigate how the N -benzyl ,-amino acids are accommodated in the "binding pocket" of the chiral cobalt complex. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source]

    Closure of plane-strain cracks under large-scale yielding conditions

    C. H. Wang
    Abstract ,This paper presents computational and theoretical investigations of the plasticity-induced crack-closure of a plane-strain crack under large-scale yielding conditions. Solutions of the crack-tip opening displacements for a stationary crack and a growing fatigue crack have been obtained using the finite element method. The self-similar crack-closure model has been extended to the plane strain case by introducing two plastic constraint factors: one for tension yielding and the other for compression yielding. These two plastic constraint factors are identified by matching the model predictions with the computational results. It is shown that the first constraint factor decreases rapidly with the applied stress while the second constraint factor is approximately equal to unity. The findings of this study allow the cohesive-zone based crack-closure model to be extended to plane-strain cracks, especially under large-scale yielding conditions. [source]

    Experimental and computational investigation of three-dimensional mixed-mode fatigue

    S. C. Forth
    Experimental and computational methods were developed to model three-dimensional (3-D) mixed-mode crack growth under fatigue loading with the objective of evaluating proposed 3-D fracture criteria. The experiments utilized 7075-T73 aluminium forgings cut into modified ASTM E740 surface crack specimens with pre-cracks orientated at angles of 30, 45 and 60° in separate tests. The progress of the evolving fatigue crack was monitored in real time using an automated visualization system. In addition, the amplitude of the loading was increased at prescribed intervals to mark the location of the 3-D crack front for post-test inspection. In order to evaluate proposed crack growth equations, computer simulations of the experiments were conducted using a 3-D fracture model based on the surface integral method. An automatic mesher advanced the crack front by adding a ring of elements consistent with local application of fracture criteria governing rate and direction of growth. Comparisons of the computational and experimental results showed that the best correlation was obtained when KII and KIII were incorporated in the growth rate equations. [source]

    Numerical aspects of a real-time sub-structuring technique in structural dynamics

    R. Sajeeb
    Abstract A time domain coupling technique, involving combined computational and experimental modelling, for vibration analysis of structures built-up of linear/non-linear substructures is developed. The study permits, in principle, one or more of the substructures to be modelled experimentally with measurements being made only on the interfacial degrees of freedom. The numerical and experimental substructures are allowed to communicate in real time within the present framework. The proposed strategy involves a two-stage scheme: the first is iterative in nature and is implemented at the initial stages of the solution in a non-real-time format; the second is non-iterative, employs an extrapolation scheme and proceeds in real time. Issues on time delays during communications between different substructures are discussed. An explicit integration procedure is shown to lead to solutions with high accuracy while retaining path sensitivity to initial conditions. The stability of the integration scheme is also discussed and a method for numerically dissipating the temporal growth of high-frequency errors is presented. For systems with non-linear substructures, the integration procedure is based on a multi-step transversal linearization method; and, to account for time delays, we employ a multi-step extrapolation scheme based on the reproducing kernel particle method. Numerical illustrations on a few low-dimensional vibrating structures are presented and these examples are fashioned after problems of seismic qualification testing of engineering structures using real-time substructure testing techniques. Copyright © 2007 John Wiley & Sons, Ltd. [source]

    Defining and optimizing algorithms for neighbouring particle identification in SPH fluid simulations

    G. Viccione
    Abstract Lagrangian particle methods such as smoothed particle hydrodynamics (SPH) are very demanding in terms of computing time for large domains. Since the numerical integration of the governing equations is only carried out for each particle on a restricted number of neighbouring ones located inside a cut-off radius rc, a substantial part of the computational burden depends on the actual search procedure; it is therefore vital that efficient methods are adopted for such a search. The cut-off radius is indeed much lower than the typical domain's size; hence, the number of neighbouring particles is only a little fraction of the total number. Straightforward determination of which particles are inside the interaction range requires the computation of all pair-wise distances, a procedure whose computational time would be unpractical or totally impossible for large problems. Two main strategies have been developed in the past in order to reduce the unnecessary computation of distances: the first based on dynamically storing each particle's neighbourhood list (Verlet list) and the second based on a framework of fixed cells. The paper presents the results of a numerical sensitivity study on the efficiency of the two procedures as a function of such parameters as the Verlet size and the cell dimensions. An insight is given into the relative computational burden; a discussion of the relative merits of the different approaches is also given and some suggestions are provided on the computational and data structure of the neighbourhood search part of SPH codes. Copyright © 2008 John Wiley & Sons, Ltd. [source]

    Non-equilibrium behaviour of equilibrium reservoirs in molecular simulations

    Martin W. Tysanner
    Abstract We explore two widely used algorithms for fluid reservoirs in molecular simulations and demonstrate that they may induce non-physical non-equilibrium effects, even in systems that should be at equilibrium. For example, correlations of momentum and density fluctuations lead to a bias in the mean fluid velocity when measured as the mean over samples of instantaneous fluid velocity. The non-physical behaviour is entirely computational in origin and is an instance of a more general issue in molecular simulations: a failure to correctly model stochastic properties may induce non-equilibrium behaviour that does not exist in the corresponding physical system. Finally, we demonstrate that simple algorithm corrections eliminate this artifact. Copyright © 2005 John Wiley & Sons, Ltd. [source]

    Online pattern recognition based on a generalized hidden Markov model for intraoperative vital sign monitoring

    Ping Yang
    Abstract The trend patterns of vital signs provide significant insight into the interpretation of intraoperative physiological measurements. We have modeled the trend signal of a vital sign parameter as a generalized hidden Markov model (also known as a hidden semi-Markov model). This model treats a time series as a sequence of predefined patterns and describes the transition between these patterns as a first-order Markov process and the intra-segmental variations as different dynamic linear systems. Based on this model, a switching Kalman smoother combines a Bayesian inference process with a fixed-point Kalman smoother in order to estimate the unconditional true signal values and generates the probability of occurrence for each pattern online. The probabilities of pattern transitions are tested against a threshold to detect change points. A second-order generalized pseudo-Bayesian algorithm is used to summarize the state propagation over time and reduces the computational overhead. The memory complexity is reduced using linked tables. The algorithm was tested on 30 simulated signals and 10 non-invasive-mean-blood-pressure trend signals collected at a local hospital. In the simulated test, the algorithm achieved a high accuracy of signal estimation and pattern recognition. In the test on clinical data, the change directions of 45 trend segments, out of the 54 segments annotated by an expert, were correctly detected with the best performing threshold, and with the introduction of only 8 false-positive detections. The proposed method can detect the changes of trend patterns in a time series online, while generating quantitative evaluation of the significance of detection. This method is promising for physiological monitoring as the method not only generates early alerts, but also summarizes the temporal contextual information for a high-level decision support system. Copyright © 2009 John Wiley & Sons, Ltd. [source]

    When has estimation reached a steady state?

    The Bayesian sequential test
    Abstract This paper is concerned with distributions of time series, which (i) are influenced by initial conditions (ii) are stimulated by an exogenous signal or (iii) are obtained by recursive estimation of underlying parameters and thus undergo a transient period. In computer intensive applications, it is desirable to stop the processing when the transient period is practically over. This aspect is addressed here from a Bayesian perspective. Under an often met assumption that the model of a system's time series is recursively estimated anyway, the computational overhead of the constructed stopping rule is negligible. Algorithmic details are presented for important normal ARX models (auto-regression with exogenous variable) and models of discrete-valued, independent, identically distributed data. The latter case provides non-parametric Bayesian estimation of credibility interval with sequential stopping. Copyright © 2004 John Wiley & Sons, Ltd. [source]

    Real-time identification of vehicle chassis dynamics using a novel reparameterization based on sensitivity invariance

    S. Brennan
    Abstract This work presents a novel methodology to identify model parameters using the concept of sensitivity invariance. Within many classical system representations, relationships between Bode parameter sensitivities may exist that are not explicitly accounted for by the formal system model. These relationships, called sensitivity invariances, will explicitly limit the possible parameter variation of the system model to a small subspace of the possible parameter gradients. By constraining the parameter identification or adaptation to a model structure with uncoupled parameter sensitivities, a more efficient identification can be obtained at a reduced computational and modelling cost. As illustration, an identification method of using sensitivity invariance is demonstrated on an experimental problem to identify, in real time, a time-varying tire parameter associated with the chassis dynamics of passenger vehicles at highway speeds. The results are validated with simulations as well as an experimental implementation on a research vehicle driven under changing road conditions. Copyright © 2004 John Wiley & Sons, Ltd. [source]

    Adaptive least mean squares block Volterra filters

    Tarek I. Haweel
    Abstract Adaptive filtering has found many applications in situations where the underlying signals are changing or unknown. While linear filters are simple from implementation and conceptual points of view, many signals are non-linear in nature. Non-linear filters based on truncated Volterra expansions can effectively model a large number of systems. Unfortunately, the resulting input auto-moment matrix is ill conditioned, which results in a slow convergence rate. This paper proposes a class of block adaptive Volterra filters in which the input sequences are Hadamard transformed to improve the condition number of the input auto-moment matrix and consequently improve the convergence rate. This is achieved by the decorrelation effect produced by the orthogonality of the transform. Since Hadamard transformation employs only ±1's, the additional required computational and implementation burdens are few. The effect of additive white Gaussian noise is introduced. Simulation experiments are given to illustrate the improved performance of the proposed method over the conventional Volterra LMS method. Copyright © 2001 John Wiley & Sons, Ltd. [source]