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Computational Methodology (computational + methodology)
Selected AbstractsIntraprotein electrostatics derived from first principles: Divide-and-conquer approaches for QM/MM calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2003Pablo A. Molina Two divide-and-conquer (DAQ) approaches for building multipole-based molecular electrostatic potentials of proteins are presented and evaluated for use in QM/MM calculations. One approach is a further development of the neutralization method of Bellido and Rullmann (J Comput Chem 1989, 10, 479,487) while the other is based on removing part of the electron density before performing the multipole expansion. Both methods create systems with integer charges without using charge renormalization. To determine their performance in terms of location of cuts and distance to QM region, the new DAQ approaches are tested in calculations of the proton affinity of N, of Lys55 in the inhibitor turkey ovomucoid third domain. Finally, the two methods are used to build a variety of MM regions, applied to calculations of the pKa of Lys55, and compared to other computational methodologies in which force field charges are employed. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1971,1979, 2003 [source] Generalized X-ray and neutron crystallographic analysis: more accurate and complete structures for biological macromoleculesACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Paul D. Adams X-ray and neutron crystallographic techniques provide complementary information on the structure and function of biological macromolecules. X-ray and neutron (XN) crystallographic data have been combined in a joint structure-refinement procedure that has been developed using recent advances in modern computational methodologies, including cross-validated maximum-likelihood target functions with gradient-based optimization and simulated annealing. The XN approach for complete (including hydrogen) macromolecular structure analysis provides more accurate and complete structures, as demonstrated for diisopropyl fluorophosphatase, photoactive yellow protein and human aldose reductase. Furthermore, this method has several practical advantages, including the easier determination of the orientation of water molecules, hydroxyl groups and some amino-acid side chains. [source] A diffusion model with cubic drift: statistical and computational aspects and application to modelling of the global CO2 emission in SpainENVIRONMETRICS, Issue 1 2007R. Gutiérrez Abstract The aim of this work is the study of a new stochastic diffusion model with a cubic-type drift coefficient. The model is considered as the solution of an Ito stochastic differential equation. Using the Ito's stochastic calculus and properties of the Kummer function, the trend functions and steady-state distribution for the process are obtained. Statistical estimation and corresponding computational methodology are established. Finally, the model is applied to modelling and prediction of the global CO2 emission in Spain. Copyright © 2006 John Wiley & Sons, Ltd. [source] Comparison of waveform inversion, part 2: phase approachGEOPHYSICAL PROSPECTING, Issue 4 2007J. B. Bednar ABSTRACT In this paper, we take advantage of the natural separation into amplitude and phase of a logarithmic-based approach to full-wavefield inversion and concentrate on deriving purely kinematic approaches for both conventional and logarithmic-based methods. We compare the resulting algorithms theoretically and empirically. To maintain consistency between this and the previous paper in this series, we continue with the same symbolism and notation and apply our new algorithms to the same three data sets. We show that both of these new techniques, although different in implementation style, share the same computational methodology. We also show that reverse-time back-propagation of the residuals for our new kinematic methods continues to be the basis for calculation of the steepest-descent vector. We conclude that the logarithmic phase-based method is more practical than its conventionally based counterpart, but, in spite of the fact that the conventional algorithm appears unstable, differences are not great. [source] Efficient modal analysis of systems with local stiffness uncertaintiesINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 6-7 2009S. F. Wojtkiewicz Abstract The characterization of the uncertainty in modal quantities of an uncertain linear structural system is essential to the rapid determination of its response to arbitrary loadings. Although the size of many computational structural models used is extremely large, i.e. thousands of equations, the uncertainty to be analyzed is oftentimes localized to very small regions of the model. This paper addresses the development of an efficient, computational methodology for the modal analysis of linear structural systems with local stiffness uncertainties. The newly developed methodology utilizes an enriched basis that consists of the sub-spectrum of a nominal structural system augmented with additional basis vectors generated from a knowledge of the structure of the stiffness uncertainty. In addition, methods for determining bounds on the approximate modal frequencies and mode shapes are discussed. Numerical results demonstrate that the algorithm produces highly accurate results with greatly reduced computational effort. Copyright © 2009 John Wiley & Sons, Ltd. [source] Computational form-finding of tension membrane structures,Non-finite element approaches: Part 1.INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 5 2003Use of cubic splines in finding minimal surface membranes Abstract This paper, presented in three parts, discusses a computational methodology for form-finding of tension membrane structures (TMS), or fabric structures, used as roofing forms. The term ,form-finding' describes a process of finding the shape of a TMS under its initial tension. Such a shape is neither known a priori, nor can it be described by a simple mathematical function. The work is motivated by the need to provide an efficient numerical tool, which will allow a better integration of the design/analysis/manufacture of TMS. A particular category of structural forms is considered, known as minimal surface membranes (such as can be reproduced by soap films). The numerical method adopted throughout is dynamic relaxation (DR) with kinetic damping. Part 1 describes a new form-finding approach, based on the Laplace,Young equation and cubic spline fitting to give a full, piecewise, analytical description of a minimal surface. The advantages arising from the approach, particularly with regard to manufacture of cutting patterns for a membrane, are highlighted. Part 2 describes an alternative and novel form-finding approach, based on a constant tension field and faceted (triangular mesh) representation of the minimal surface. It presents techniques for controlling mesh distortion and discusses effects of mesh control on the accuracy and computational efficiency of the solution, as well as on the subsequent stages in design. Part 3 gives a comparison of the performance of the initial method (Part 1) and the faceted approximations (Part 2). Functional relations, which encapsulate the numerical efficiency of each method, are presented. Copyright © 2002 John Wiley & Sons, Ltd. [source] Computational form-finding of tension membrane structures,Non-finite element approaches: Part 2.INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 5 2003Triangular mesh discretization, control of mesh distortion in modelling minimal surface membranes Abstract This paper, presented in three parts, discusses a computational methodology for form-finding of tension membrane structures (TMS), or fabric structures, used as roofing forms. The term ,form-finding' describes a process of finding the shape of a TMS under its initial tension. Such a shape is neither known a priori, nor can it be described by a simple mathematical function. The work is motivated by the need to provide an efficient numerical tool, which will allow a better integration of the design/analysis/manufacture of TMS. A particular category of structural forms is considered, known as minimal surface membranes (such as can be reproduced by soap films). The numerical method adopted throughout is dynamic relaxation (DR) with kinetic damping. Part 1 gave a background to the problem of TMS design, described the DR method, and presented a new form-finding methodology, based on the Laplace,Young equation and cubic spline fitting to give a full, piecewise, analytical description of the surface. Part 2 describes an alternative and novel form-finding method, based on a constant tension field and faceted (triangular mesh) representation of the minimal surface. Techniques for controlling mesh distortion are presented, and their effects on the accuracy and computational efficiency of the solution, as well as on the subsequent stages in design, are examined. Part 3 gives a comparison of the performance of the initial method (Part 1) and the faceted approximations (Part 2). Functional relations, which encapsulate the numerical efficiency of each method, are presented. Copyright © 2002 John Wiley & Sons, Ltd. [source] Microstructure,property,quality-correlated paint design: An LMC-based approachAICHE JOURNAL, Issue 1 2009Jie Xiao Abstract Paint is designed to offer various chemical and physical properties for surface protection, styling, and appearance. Nevertheless, the anticipated quality of the surface coating is frequently unsatisfactory, which is often attributed to paint formulation. As new demands on coating performance continuously emerge, paint formulation design becomes much more challenging than ever. It is recognized that paint design can be significantly improved with the help of advanced computational methods, as they can provide great freedom and control over the investigation of paint formulation through any number of in silico experiments virtually under any application conditions. This article introduces a lattice Monte Carlo based computational methodology for paint formulation design. By this methodology and structural analysis techniques, a variety of correlations among paint material, curing condition, coating microstructure, and coating qualities can be generated, which are critical for the development of superior paint formulations. A comprehensive study on acrylic-melamine-based paint design and analysis demonstrates the methodological efficacy. © 2008 American Institute of Chemical Engineers AIChE J, 2009 [source] Methodology for the optimal component selection of electronic devices under reliability and cost constraintsQUALITY AND RELIABILITY ENGINEERING INTERNATIONAL, Issue 8 2007E. P. Zafiropoulos Abstract The objective of this paper is to present an efficient computational methodology for the reliability optimization of electronic devices under cost constraints. The system modeling for calculating the reliability indices of the electronic devices is based on Bayesian networks using the fault tree approach, in order to overcome the limitations of the series,parallel topology of the reliability block diagrams. Furthermore, the Bayesian network modeling for the reliability analysis provides greater flexibility for representing multiple failure modes and dependent failure events, and simplifies fault diagnosis and reliability allocation. The optimal selection of components is obtained using the simulated annealing algorithm, which has proved to be highly efficient in complex optimization problems where gradient-based methods can not be applied. The reliability modeling and optimization methodology was implemented into a computer program in Matlab using a Bayesian network toolbox. The methodology was applied for the optimal selection of components for an electrical switch of power installations under reliability and cost constraints. The full enumeration of the solution space was calculated in order to demonstrate the efficiency of the proposed optimization algorithm. The results obtained are excellent since a near optimum solution was found in a small fraction of the time needed for the complete enumeration (3%). All the optimum solutions found during consecutive runs of the optimization algorithm lay in the top 0.3% of the solutions that satisfy the reliability and cost constraints. Copyright © 2007 John Wiley & Sons, Ltd. [source] Numerical Simulation of Thrombus Aspiration in Two Realistic Models of Catheter TipsARTIFICIAL ORGANS, Issue 4 2010Giancarlo Pennati Abstract Thrombus aspiration catheters are devices used to remove a blood clot from a vessel, usually prior to angioplasty or stent implantation. However, in vitro results showed that the use of different commercial devices could produce very different thrombus removals, suggesting a primary dependence on the distal tip configuration of the catheter. A computational methodology based on realistic catheter tip modeling was developed to investigate the factors affecting the thrombus suction. Two different designs were considered, either with a single central lumen or a combination of central and side holes. First, steady-state aspiration of distilled water from a reservoir was simulated and compared with experimental tests. Subsequently, the aspiration of a totally occlusive thrombus, modeled as a high viscous fluid, was simulated solving a complex two-phase (blood and thrombus) problem. In particular, the benefit of additional openings was investigated. Good matching between the steady-state experimental and numerically simulated hydraulic behaviors allowed a validation of the numerical models. Numerical results of thrombus aspiration showed that the catheter with central and side holes had a worse performance if compared with the single central lumen catheter. Indeed, the inlets in contact with both blood and thrombus preferentially aspirate blood due to its much lower viscosity. This effect hindered the aspiration of thrombus. The amount of aspirated thrombus highly depends on the complex, two-phase fluid dynamics occurring across the catheter tips. Results suggested that location of additional holes is crucial in the catheter aspiration performance. [source] Minimum sequence requirements for the binding of paromomycin to the rRNA decoding site ABIOPOLYMERS, Issue 2 2007Peter C. Anderson Abstract We have recently introduced a computational methodology that combines molecular dynamics (MD) simulations, free-energy calculations, and in vitro binding assays to predict the minimum RNA structural requirements for selective, high-affinity RNA binding to small-molecule ligands. Here, we show that this methodology can be applied to the conformationally flexible aminoglycoside antibiotic paromomycin. A RNA consisting of an 11-mer:10-mer duplex that contains one 16S ribosome RNA decoding A-site bound to paromomycin was simulated for 4 ns. The methodology predicts that the 11-mer:10-mer duplex binds to paromomycin with high affinity, whereas smaller RNA duplexes lose complex stability and the ability to bind paromomycin. The predicted high-affinity binding to paromomycin of the 11-mer:10-mer duplex was confirmed experimentally (EC50 = 0.28 ,M), as well as the inability of smaller complexes to bind. Our simulations show good agreement with experiment for dynamic and structural properties of the isolated A-site, including hydrogen-bonding networks and RNA structural rearrangements upon ligand binding. The results suggest that MD simulations can supplement in vitro methods as a tool for predicting minimum RNA-binding motifs for both small, rigid ligands, and large, flexible ligands when structural information is available. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 95,111, 2007. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Reliability of capacitive RF MEMS switches at high and low temperaturesINTERNATIONAL JOURNAL OF RF AND MICROWAVE COMPUTER-AIDED ENGINEERING, Issue 4 2004Yong Zhu Abstract Some applications of RF MEMS switches, such as aircraft condition monitoring and distributed satellite communication, present a unique challenge for device design and reliability. This article examines these switches when operational temperatures in the range ,60°C to 100°C are envisioned. The basic operation of a capacitive MEMS switch is described and two tools for examining device reliability, modeling, and on-chip experimentation, are discussed in the case of capacitive MEMS switches. 1D, 2D, and 3D models are presented with emphasis on 3D coupled-field finite-element analysis, including temperature effects. Results and findings from the 3D simulations are reported. In particular, the advantages of employing corrugated membranes in the design of RF MEMS switches are assessed. Their performance in terms of reliability as a function of temperature is quantified. The effects of corrugation on the geometric parameters are discussed in the context of device-design optimization. In order to assess reliability experimentally, the M-test and the membrane deflection experiment (MDE) are reviewed due to their on-chip characteristic and simplicity. Ways in which these experimental/computational methodologies can be combined for identifying material properties and device performance is also highlighted. © 2004 Wiley Periodicals, Inc. Int J RF and Microwave CAE 14: 317,328, 2004. [source] | |||||||||||||