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Computational Techniques (computational + techniques)
Selected AbstractsCall for Papers: Special Issue on ,Recent Advances in Computational Techniques for Biomedical Imaging' Communications in Numerical Methods in Engineering (CNM)INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 2 2008Prof. Guo-Wei Wei Submitting Editor Guest Editor No abstract is available for this article. [source] A Three-Dimensional Quanititative Structure-Activity Relationship (3D-QSAR) Model for Predicting the Enantioselectivity of Candida antarctica Lipase BADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 9 2009Paolo Braiuca Abstract Computational techniques involving molecular modeling coupled with multivariate statistical analysis were used to evaluate and predict quantitatively the enantioselectivity of lipase B from Candida antarctica (CALB). In order to allow the mathematical and statistical processing of the experimental data largely available in the literature (namely enantiomeric ratio E), a novel class of GRID-based molecular descriptors was developed (differential molecular interaction fields or DMIFs). These descriptors proved to be efficient in providing the structural information needed for computing the regression model. Multivariate statistical methods based on PLS (partial least square , projection to latent structures), were used for the analysis of data available from the literature and for the construction of the first three-dimensional quanititative structure-activity relationship (3D-QSAR) model able to predict the enantioselectivity of CALB. Our results indicate that the model is statistically robust and predictive. [source] Computational techniques applied to the study of the oxidation kinetics of iron and molybdenum cyanocomplexes by peroxynitrous acidJOURNAL OF CHEMOMETRICS, Issue 10 2008H. Herrero Abstract The oxidation kinetics of iron and molybdenum cyanocomplexes by peroxynitrous acid were studied by computational techniques. The rate constants of ONOOH decomposition and substrate oxidation were calculated by fitting the experimental data to the solution of the ordinary differential equations mechanism. There is a linear relationship between the rate constants which is solved by varying the initial concentration of one of the reactive species. The rate constants of the steps involved in ONOOH decomposition were also determined following the same procedure and considering a linear relationship between the rate constants. The results are consistent with the values previously found using the conventional method of integration, and they validate the prior steady state assumption. Copyright © 2008 John Wiley & Sons, Ltd. [source] Detecting corpus callosum abnormalities in autism subtype using planar conformal mappingINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 2 2010Ye Duan Abstract A number of studies have documented that autism has a neurobiological basis, but the anatomical extent of these neurobiological abnormalities is largely unknown. In this paper, we apply advanced computational techniques to extract 3D models of the corpus callosum (CC) and subsequently analyze local shape variations in a homogeneous group of autistic children. Besides the traditional volumetric analysis, we explore additional phenotypic traits based on the oriented bounding rectangle of the CC. In shape analysis, a new conformal parameterization is applied in our shape analysis work, which maps the surface onto a planar domain. Surface matching among different individual meshes is achieved by aligning the planar domains of individual meshes. Shape differences of the CC between autistic patients and the controls are computed using Hotelling T2 two-sample metric followed by a permutation test. The raw and corrected p -values are shown in the results. Additional visualization of the group difference is provided via mean difference map. Copyright © 2009 John Wiley & Sons, Ltd. [source] FOIST: Fluid,object interaction subcomputation techniqueINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 9 2009V. Udoewa Abstract Our target is to develop computational techniques for studying aerodynamic interactions between multiple objects. The computational challenge is to predict the dynamic behavior and path of the object, so that separation (the process of objects relatively falling or moving away from each other) is safe and effective. This is a very complex problem because it has an unsteady, 3D nature and requires the solution of complex equations that govern the fluid dynamics (FD) of the object and the aircraft together, with their relative positions changing in time. Large-scale 3D FD simulations require a high computational cost. Not only must one solve the time-dependent Navier,Stokes equations governing the fluid flow, but also one must handle the equations of motion of the object as well as the treatment of the moving domain usually treated as a type of pseudo-solid. These costs include mesh update methods, distortion-limiting techniques, and remeshing and projection tactics. To save computational costs, point force calculations have been performed in the past. This paper presents a hybrid between full mesh-moving simulations and the point force calculation. This mesh-moving alternative is called FOIST: fluid,object subcomputation interaction technique. Copyright © 2009 John Wiley & Sons, Ltd. [source] Special issue on recent advances in computational techniques for biomedical imaging,INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 6 2009Guo-Wei Wei Guest Editor Abstract A total of 12 papers in the area of mathematical methods and computational techniques for biomedical imaging and image analysis are presented in this special issue. Copyright © 2009 John Wiley & Sons, Ltd. [source] Multiscale modeling of impact on heterogeneous viscoelastic solids containing evolving microcracksINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 4 2010Flavio V. Souza Abstract Multiscale computational techniques play a major role in solving problems related to viscoelastic composites due to the complexities inherent to these materials. In this paper, a numerical procedure for multiscale modeling of impact on heterogeneous viscoelastic solids containing evolving microcracks is proposed in which the (global scale) homogenized viscoelastic incremental constitutive equations have the same form as the local-scale viscoelastic incremental constitutive equations, but the homogenized tangent constitutive tensor and the homogenized incremental history-dependent stress tensor at the global scale depend on the amount of damage accumulated at the local scale. Furthermore, the developed technique allows the computation of the full anisotropic incremental constitutive tensor of viscoelastic solids containing evolving cracks (and other kinds of heterogeneities) by solving the micromechanical problem only once at each material point and each time step. The procedure is basically developed by relating the local-scale displacement field to the global-scale strain tensor and using first-order homogenization techniques. The finite element formulation is developed and some example problems are presented in order to verify the approach and demonstrate the model capabilities. Copyright © 2009 John Wiley & Sons, Ltd. [source] Sliding mesh algorithm for CFD analysis of helicopter rotor,fuselage aerodynamicsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 5 2008R. Steijl Abstract The study of rotor,fuselage interactional aerodynamics is central to the design and performance analysis of helicopters. However, regardless of its significance, rotor,fuselage aerodynamics has so far been addressed by very few authors. This is mainly due to the difficulties associated with both experimental and computational techniques when such complex configurations, rich in flow physics, are considered. In view of the above, the objective of this study is to develop computational tools suitable for rotor,fuselage engineering analysis based on computational fluid dynamics (CFD). To account for the relative motion between the fuselage and the rotor blades, the concept of sliding meshes is introduced. A sliding surface forms a boundary between a CFD mesh around the fuselage and a rotor-fixed CFD mesh which rotates to account for the movement of the rotor. The sliding surface allows communication between meshes. Meshes adjacent to the sliding surface do not necessarily have matching nodes or even the same number of cell faces. This poses a problem of interpolation, which should not introduce numerical artefacts in the solution and should have minimal effects on the overall solution quality. As an additional objective, the employed sliding mesh algorithms should have small CPU overhead. The sliding mesh methods developed for this work are demonstrated for both simple and complex cases with emphasis placed on the presentation of the inner workings of the developed algorithms. Copyright © 2008 John Wiley & Sons, Ltd. [source] A segregated method for compressible flow computation Part I: isothermal compressible flowsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 4 2005Guillermo Hauke Abstract Traditionally, coupled methods have been employed for the computation of compressible flows, whereas segregated methods have been preferred for the computation of incompressible flows. Compared to coupled methods, segregated solvers present the advantage of reduced computer memory and CPU time requirements, although at the cost of an inferior robustness. Therefore, in a series of papers we present unified computational techniques to compute compressible and incompressible flows with segregated stabilized methods. The proposed algorithms have an increased robustness compared to existing techniques, while possessing additional benefits such as employing standard pressure boundary conditions. In this first part, the thermodynamics of isothermal, thermally perfect compressible flows is set up in the framework of symmetric systems and the corresponding segregated algorithms are introduced. Copyright © 2005 John Wiley & Sons, Ltd. [source] Importance of O(3P) atoms and OH radicals in hydrocarbon oxidation during the nonthermal plasma treatment of diesel exhaust inferred using relative-rate methods,INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 6 2003John Hoard The consumption of acetylene and propene during passage of simulated diesel exhaust through a nonthermal plasma at 453 K and atmospheric pressure was studied using experimental and computational techniques. Experimental observations of the relative decay rates of acetylene and propene and computer modeling of the chemical and physical processes in the plasma suggest that O(3P) atoms and, to a lesser extent, OH radicals are the dominant species responsible for initiating hydrocarbon oxidation in this system. Results are discussed in terms of the gas-phase chemistry occurring during the nonthermal plasma treatment of diesel exhaust. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 231,238, 2003 [source] On blends R32/R134a and R32/R125: Thermodynamic and heat transfer aspectsINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 9 2001A. Stegou-SagiaArticle first published online: 4 JUN 200 Abstract In this paper the author develops an algorithm on the basis of heat and thermodynamics theory, to predict data for film condensation on horizontal integral,fin tubes for R32/R134a and R32/R125 mixtures in 25/75, 50/50 per cent compositions by mass correspondingly. Emphasis is focused on the presentation of thermophysical properties of the blends involved in the process considered, i.e. liquid density, viscosity, surface tension, thermal conductivity and latent heat of vaporization. The main point of this work is to define with computational techniques the blend with the most favourable composition, as an environmentally acceptable solution for R22 replacement in some shell-side condensers. Copyright © 2001 John Wiley & Sons, Ltd. [source] An efficient triplet-based algorithm for evidential reasoning,INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS, Issue 4 2008Yaxin Bi Linear-time computational techniques based on the structure of an evidence space have been developed for combining multiple pieces of evidence using Dempster's rule (orthogonal sum), which is available on a number of contending hypotheses. They offer a means of making the computation-intensive calculations involved more efficient in certain circumstances. Unfortunately, they restrict the orthogonal sum of evidential functions to the dichotomous structure that applies only to elements and their complements. In this paper, we present a novel evidence structure in terms of a triplet and a set of algorithms for evidential reasoning. The merit of this structure is that it divides a set of evidence into three subsets, distinguishing the trivial evidential elements from the important ones,focusing particularly on some elements of an evidence space. It avoids the deficits of the dichotomous structure in representing the preference of evidence and estimating the basic probability assignment of evidence. We have established a formalism for this structure and the general formulae for combining pieces of evidence in the form of the triplet, which have been theoretically and empirically justified. © 2008 Wiley Periodicals, Inc. [source] Computational techniques applied to the study of the oxidation kinetics of iron and molybdenum cyanocomplexes by peroxynitrous acidJOURNAL OF CHEMOMETRICS, Issue 10 2008H. Herrero Abstract The oxidation kinetics of iron and molybdenum cyanocomplexes by peroxynitrous acid were studied by computational techniques. The rate constants of ONOOH decomposition and substrate oxidation were calculated by fitting the experimental data to the solution of the ordinary differential equations mechanism. There is a linear relationship between the rate constants which is solved by varying the initial concentration of one of the reactive species. The rate constants of the steps involved in ONOOH decomposition were also determined following the same procedure and considering a linear relationship between the rate constants. The results are consistent with the values previously found using the conventional method of integration, and they validate the prior steady state assumption. Copyright © 2008 John Wiley & Sons, Ltd. [source] Analyzing single-molecule manipulation experimentsJOURNAL OF MOLECULAR RECOGNITION, Issue 5 2009Christopher P. Calderon Abstract Single-molecule manipulation studies can provide quantitative information about the physical properties of complex biological molecules without ensemble artifacts obscuring the measurements. We demonstrate computational techniques which aim at more fully utilizing the wealth of information contained in noisy experimental time series. The "noise" comes from multiple sources e.g., inherent thermal motion, instrument measurement error, etc. The primary focus of this paper is a methodology that uses time domain based methods to extract the effective molecular friction from single-molecule pulling data. We studied molecules composed of eight tandem repeat titin I27 domains, but the modeling approaches have applicability to other single-molecule mechanical studies. The merits and challenges associated with applying such a computational approach to existing single-molecule manipulation data are also discussed. Copyright © 2009 John Wiley & Sons, Ltd. [source] A theoretical study of pentacyclo-undecane cage peptides of the type [Ac-X-Y-NHMe]JOURNAL OF PEPTIDE SCIENCE, Issue 2 2006Krishna Bisetty Abstract The conformational preferences of peptides of the type, Ac-X-Y-NHMe, where X and Y = Ala, cage and Pro, were studied by means of computational techniques within the framework of a molecular mechanics approach. For each of the eight peptide analogues, extensive conformational searches were carried out using molecular dynamics (MD) and simulated annealing (SA) protocols in an iterative fashion. Both results are in good agreement and complement each other. The conformational search indicates that the cage residue restricts the conformational freedom of the dipeptide considerably in comparison with the other model residues used. This study revealed that proline exhibits a greater tendency in promoting reverse-turn characteristics in comparison to the cage peptides, which show promising ,-turn characteristics. It was also found that 300,500 K is not sufficient to overcome rotational barriers for cage peptides. In all cases, the low-energy conformers have a tendency to form bent structures. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd. [source] A General Misspecification Test for Spatial Regression Models: Dependence, Heterogeneity, and NonlinearityJOURNAL OF REGIONAL SCIENCE, Issue 2 2001Thomas De Graaff There is an increasing awareness of the potentials of nonlinear modeling in regional science. This can be explained partly by the recognition of the limitations of conventional equilibrium models in complex situations, and also by the easy availability and accessibility of sophisticated computational techniques. Among the class of nonlinear models, dynamic variants based on, for example, chaos theory stand out as an interesting approach. However, the operational significance of such approaches is still rather limited and a rigorous statistical-econometric treatment of nonlinear dynamic modeling experiments is lacking. Against this background this paper is concerned with a methodological and empirical analysis of a general misspecification test for spatial regression models that is expected to have power against nonlinearity, spatial dependence, and heteroskedasticity. The paper seeks to break new research ground by linking the classical diagnostic tools developed in spatial econometrics to a misspecification test derived directly from chaos theory,the BDS test, developed by Brock, Dechert, and Scheinkman (1987). A spatial variant of the BDS test is introduced and applied in the context of two examples of spatial process models, one of which is concerned with the spatial distribution of regional investments in The Netherlands, the other with spatial crime patterns in Columbus, Ohio. [source] Solid-State Ionics: Roots, Status, and Future ProspectsJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 7 2002Philippe Knauth This review represents the authors' view of the evolution of solid-state ionics over approximately the past 100 years. A brief history, introducing milestones of the development of this discipline, is followed by a short summary of the theory of ionic conduction in the bulk and the more recently developed theory of ionic conduction at interfaces. The central part of the article gives examples of ionic-conducting materials systems with structures ranging from one- to three-dimensional disorder. Important experimental techniques for analyzing ionic conduction, including alternating-current impedance spectroscopy, direct-current coulometry, and direct-current current-voltage measurements with blocking electrodes, are also summarized. The main technological applications, that is, batteries, solid-oxide fuel cells, electrochemical sensors, electrochromic windows, and oxygen-separation membranes, are reviewed. Finally, new concepts in solid-state ionics are presented, including the investigation of new materials (such as nanostructured phases), the study of boundaries (for example, using microelectrodes), the development of computational techniques, and the connections with other classes of materials (notably magnetic and semiconducting materials). [source] Importance of interpolation when constructing double-bootstrap confidence intervalsJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES B (STATISTICAL METHODOLOGY), Issue 2 2000Peter Hall We show that, in the context of double-bootstrap confidence intervals, linear interpolation at the second level of the double bootstrap can reduce the simulation error component of coverage error by an order of magnitude. Intervals that are indistinguishable in terms of coverage error with theoretical, infinite simulation, double-bootstrap confidence intervals may be obtained at substantially less computational expense than by using the standard Monte Carlo approximation method. The intervals retain the simplicity of uniform bootstrap sampling and require no special analysis or computational techniques. Interpolation at the first level of the double bootstrap is shown to have a relatively minor effect on the simulation error. [source] Tutorial on Computational Linguistic PhylogenyLINGUISTICS & LANGUAGE COMPASS (ELECTRONIC), Issue 5 2008Johanna Nichols Over the last 10 or more years, there has been a tremendous increase in the use of computational techniques (many of which come directly from biology) for estimating evolutionary histories (i.e., phylogenies) of languages. This tutorial surveys the different methods and different types of linguistic data that have been used to estimate phylogenies, explains the scientific and mathematical foundations of phylogenetic estimation, and presents methodologies for evaluating a phylogeny estimation method. [source] Selection criteria for drug-like compoundsMEDICINAL RESEARCH REVIEWS, Issue 3 2003Ingo Muegge Abstract The fast identification of quality lead compounds in the pharmaceutical industry through a combination of high throughput synthesis and screening has become more challenging in recent years. Although the number of available compounds for high throughput screening (HTS) has dramatically increased, large-scale random combinatorial libraries have contributed proportionally less to identify novel leads for drug discovery projects. Therefore, the concept of ,drug-likeness' of compound selections has become a focus in recent years. In parallel, the low success rate of converting lead compounds into drugs often due to unfavorable pharmacokinetic parameters has sparked a renewed interest in understanding more clearly what makes a compound drug-like. Various approaches have been devised to address the drug-likeness of molecules employing retrospective analyses of known drug collections as well as attempting to capture ,chemical wisdom' in algorithms. For example, simple property counting schemes, machine learning methods, regression models, and clustering methods have been employed to distinguish between drugs and non-drugs. Here we review computational techniques to address the drug-likeness of compound selections and offer an outlook for the further development of the field. © 2003 Wiley Periodicals, Inc. Med Res Rev, 23, No. 3, 302-321, 2003 [source] Status of HTS Data Mining ApproachesMOLECULAR INFORMATICS, Issue 4 2004Alexander Böcker Abstract High-throughput screening of large compound collections results in large sets of data. This review gives an overview of the most frequently employed computational techniques for the analysis of such data and the establishment of first QSAR models. Various methods for descriptor selection, classification and data mining are discussed. Recent trends include the application of kernel-based machine learning methods for the design of focused libraries and compilation of target-family biased compound collections. [source] On the solution of an initial-boundary value problem that combines Neumann and integral condition for the wave equation,NUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS, Issue 1 2005Mehdi Dehghan Abstract Numerical solution of hyperbolic partial differential equation with an integral condition continues to be a major research area with widespread applications in modern physics and technology. Many physical phenomena are modeled by nonclassical hyperbolic boundary value problems with nonlocal boundary conditions. In place of the classical specification of boundary data, we impose a nonlocal boundary condition. Partial differential equations with nonlocal boundary specifications have received much attention in last 20 years. However, most of the articles were directed to the second-order parabolic equation, particularly to heat conduction equation. We will deal here with new type of nonlocal boundary value problem that is the solution of hyperbolic partial differential equations with nonlocal boundary specifications. These nonlocal conditions arise mainly when the data on the boundary can not be measured directly. Several finite difference methods have been proposed for the numerical solution of this one-dimensional nonclassic boundary value problem. These computational techniques are compared using the largest error terms in the resulting modified equivalent partial differential equation. Numerical results supporting theoretical expectations are given. Restrictions on using higher order computational techniques for the studied problem are discussed. Suitable references on various physical applications and the theoretical aspects of solutions are introduced at the end of this article. © 2004 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2005 [source] Genome-wide association studies and the genetic dissection of complex traits,AMERICAN JOURNAL OF HEMATOLOGY, Issue 8 2009Paola Sebastiani The availability of affordable high throughput technology for parallel genotyping has opened the field of genetics to genome-wide association studies (GWAS), and in the last few years hundreds of articles reporting results of GWAS for a variety of heritable traits have been published. What do these results tell us? Although GWAS have discovered a few hundred reproducible associations, this number is underwhelming in relation to the huge amount of data produced, and challenges the conjecture that common variants may be the genetic causes of common diseases. We argue that the massive amount of genetic data that result from these studies remains largely unexplored and unexploited because of the challenge of mining and modeling enormous data sets, the difficulty of using nontraditional computational techniques and the focus of accepted statistical analyses on controlling the false positive rate rather than limiting the false negative rate. In this article, we will review the common approach to analysis of GWAS data and then discuss options to learn more from these data. We will use examples from our ongoing studies of sickle cell anemia and also GWAS in multigenic traits. Am. J. Hematol., 2009. © 2009 Wiley-Liss, Inc. [source] Binding of Warfarin Influences the Acid-Base Equilibrium of H242 in Sudlow Site I of Human Serum AlbuminPHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 5 2006Jennifer L. Perry ABSTRACT Sudlow Site I of human serum albumin (HSA) is located in subdomain IIA of the protein and serves as a binding cavity for a variety of ligands. In this study, the binding of warfarin (W) is examined using computational techniques and isothermal titration calorimetry (ITC). The structure of the docked warfarin anion (W,) to Site I is similar to that revealed by X-ray crystallography, with a calculated binding constant of 5.8 × 105M,1. ITC experiments (pH 7.13 and I = 0.1) carried out in three different buffers (MOPs, phosphate and Tris) reveal binding of W, is accompanied by uptake of 0.30 ± 0.02 protons from the solvent. This measurement suggests that the binding of W, is stabilized by an ion-pair interaction between protonated H242 and the phenoxide group of W,. [source] Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 , HisPROTEIN SCIENCE, Issue 5 2009Blaine H. M. Mooers Abstract Mutant R96H is a classic temperature-sensitive mutant of bacteriophage T4 lysozyme. It was in fact the first variant of the protein to be characterized structurally. Subsequently, it has been studied extensively by a variety of experimental and computational techniques, but the reasons for the loss of stability of the mutant protein remain controversial. In the crystallographic refinement of the mutant structure at 1.9 Å resolution one of the bond angles at the site of substitution appeared to be distorted by about 11°, and it was suggested that this steric strain was one of the major factors in destabilizing the mutant. Different computationally-derived models of the mutant structure, however, did not show such distortion. To determine the geometry at the site of mutation more reliably, we have extended the resolution of the data and refined the wildtype (WT) and mutant structures to be better than 1.1 Å resolution. The high-resolution refinement of the structure of R96H does not support the bond angle distortion seen in the 1.9 Å structure determination. At the same time, it does confirm other manifestations of strain seen previously including an unusual rotameric state for His96 with distorted hydrogen bonding. The rotamer strain has been estimated as about 0.8 kcal/mol, which is about 25% of the overall reduction in stability of the mutant. Because of concern that contacts from a neighboring molecule in the crystal might influence the geometry at the site of mutation we also constructed and analyzed supplemental mutant structures in which this crystal contact was eliminated. High-resolution refinement shows that the crystal contacts have essentially no effect on the conformation of Arg96 in WT or on His96 in the R96H mutant. [source] | ||||||||||||||||||||||