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Simulated Annealing (simulated + annealing)
Terms modified by Simulated Annealing Selected AbstractsMultiobjective heuristic approaches to seismic design of steel frames with standard sectionsEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 11 2007M. Ohsaki Abstract Seismic design problem of a steel moment-resisting frame is formulated as a multiobjective programming problem. The total structural (material) volume and the plastic dissipated energy at the collapse state against severe seismic motions are considered as performance measures. Geometrically nonlinear inelastic time-history analysis is carried out against recorded ground motions that are incrementally scaled to reach the predefined collapse state. The frame members are chosen from the lists of the available standard sections. Simulated annealing (SA) and tabu search (TS), which are categorized as single-point-search heuristics, are applied to the multiobjective optimization problem. It is shown in the numerical examples that the frames that collapse with uniform interstorey drift ratios against various levels of ground motions can be obtained as a set of Pareto optimal solutions. Copyright © 2007 John Wiley & Sons, Ltd. [source] Using feedforward neural networks and forward selection of input variables for an ergonomics data classification problemHUMAN FACTORS AND ERGONOMICS IN MANUFACTURING & SERVICE INDUSTRIES, Issue 1 2004Chuen-Lung Chen A method was developed to accurately predict the risk of injuries in industrial jobs based on datasets not meeting the assumptions of parametric statistical tools, or being incomplete. Previous research used a backward-elimination process for feedforward neural network (FNN) input variable selection. Simulated annealing (SA) was used as a local search method in conjunction with a conjugate-gradient algorithm to develop an FNN. This article presents an incremental step in the use of FNNs for ergonomics analyses, specifically the use of forward selection of input variables. Advantages to this approach include enhancing the effectiveness of the use of neural networks when observations are missing from ergonomics datasets, and preventing overspecification or overfitting of an FNN to training data. Classification performance across two methods involving the use of SA combined with either forward selection or backward elimination of input variables was comparable for complete datasets, and the forward-selection approach produced results superior to previously used methods of FNN development, including the error back-propagation algorithm, when dealing with incomplete data. © 2004 Wiley Periodicals, Inc. Hum Factors Man 14: 31,49, 2004. [source] A modified X,,,Y methodACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2001Yan Chen The X,,,Y method seeks to solve the unknown phases of the X-ray reflections by minimizing a function (the X,,,Y function) of the phases. This cost function has been supplemented with a residual term. The total cost function is minimized by varying the positions of atoms. Simulated annealing is used to implement the minimization. Trial calculations for structures containing up to 176 non-H equal atoms have been carried out successfully. [source] Hybrid Meta-Heuristic Algorithm for the Simultaneous Optimization of the O,D Trip Matrix EstimationCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 6 2004Antony Stathopoulos These include a genetic algorithm (GA), a simulated annealing (SA) algorithm, and a hybrid algorithm (GASA) based on the combination of GA and SA. The computational performance of the three algorithms is evaluated and compared by implementing them on a realistic urban road network. The results of the simulation tests demonstrate that SA and GASA produce a more accurate final solution than GA, whereas GASA shows a superior convergence rate, that is, faster improvement from the initial solution, in comparison to SA and GA. In addition, GASA produces a final solution that is more robust and less dependent on the initial demand pattern, in comparison to that obtained from a greedy search algorithm. [source] Three-Dimensional Optimization of Urban Drainage SystemsCOMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 6 2000A. Freire Diogo A global mathematical model for simultaneously obtaining the optimal layout and design of urban drainage systems for foul sewage and stormwater is presented. The model can handle every kind of network, including parallel storm and foul sewers. It selects the optimal location for pumping systems and outfalls or wastewater treatment plants (defining the natural and artificial drainage basins), and it allows the presence of special structures and existing subsystems for optimal remodeling or expansion. It is possible to identify two basic optimization levels: in the first level, the generation and transformation of general layouts (consisting of forests of trees) until a convergence criterion is reached, and in the second level, the design and evaluation of each forest. The global strategy adopted combines and develops a sequence of optimal design and plan layout subproblems. Dynamic programming is used as a very powerful technique, alongside simulated annealing and genetic algorithms, in this discrete combinatorial optimization problem of huge dimension. [source] Synthesis and crystal structure determination of two dispiro compounds from laboratory x-ray powder diffraction dataCRYSTAL RESEARCH AND TECHNOLOGY, Issue 2 2008A. M. Moustafa Abstract The crystal structures of the dispiro compounds 1,3,4,8,10,11-Hexaphenyl-13-methyl-1,2,8,9,13-pentaazadispiro[4.1.4.3]tetradeca-2,9-dien-6-one (3a) and 4,11-Bis(4-methoxyphenyl)-13-methyl-1,3,8,10-tetraphenyl-1,2,8,9,13-pentaazadispiro-[4.1.4.3]tetradeca-2,9-dien-6-one (3b) have been determined at room temperature from X-ray powder diffraction data using the method of simulated annealing as implemented in the programs DASH and TOPAS. Subsequent Rietveld refinements using the data collected to 1.5 Å resolution yielded R-Bragg values of 2.2% for (3a) and 3.7% for (3b). It was found, that both compounds crystallize in the monoclinc space group P 21/n with lattice parameters of a = 17.1656(5) Å, b =13.8128(3) Å, c = 16.1016(5) Å, and , = 103.7330(2)° for (3a) and a = 17.2529(8) Å, b = 13.8729(5) Å, c =16.1287(10) Å, and , = 103.6910(3)° for (3b). Both compounds exhibit a distorted hexagonal close type of packing (hcp) of the molecular centers of gravity. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Optimal measurement placement for security constrained state estimation using hybrid genetic algorithm and simulated annealingEUROPEAN TRANSACTIONS ON ELECTRICAL POWER, Issue 2 2009T. Kerdchuen Abstract This paper proposes a hybrid genetic algorithm and simulated annealing (HGS) for solving optimal measurement placement for power system state estimation. Even though the minimum number of measurement pairs is N considering the single measurement loss, their positions are required to make the system observable. HGS algorithm is a genetic algorithm (GA) using the acceptance criterion of simulated annealing (SA) for chromosome selection. The P, observable concept is used to check the network observability with and without single measurement pair loss contingency and single branch outage. Test results of 10-bus, IEEE 14, 30, 57, and 118-bus systems indicate that HGS is superior to tabu search (TS), GA, and SA in terms of higher frequency of the best hit and faster computational time. Copyright © 2007 John Wiley & Sons, Ltd. [source] Optimal measurement of relative and absolute delay times by simulated annealingGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 1 2002S. Chevrot Summary Conventional approaches to determine relative arrival times of body waves recorded by a local or a regional array rely on cross-correlations between pairs of traces. This problem is better posed as a non-linear inverse problem, which involves the minimization of a cost function that measures the difference between a reference unknown waveform that can be time delayed, and the observed data. The unknown parameters that are solved for, are the amplitude values at each time sample of the optimal waveform and its time delay defined for each trace. The problem, which has a large number of unknown parameters, is solved with simulated annealing. The algorithm is very efficient and can be used for a routine analysis of seismic data. The application of this method to several earthquakes recorded during different PASSCAL experiments demonstrates that it provides accurate and robust differential traveltime measurements even with very noisy data. [source] Parameter identification for leaky aquifers using global optimization methodsHYDROLOGICAL PROCESSES, Issue 7 2007Hund-Der Yeh Abstract In the past, graphical or computer methods were usually employed to determine the aquifer parameters of the observed data obtained from field pumping tests. Since we employed the computer methods to determine the aquifer parameters, an analytical aquifer model was required to estimate the predicted drawdown. Following this, the gradient-type approach was used to solve the nonlinear least-squares equations to obtain the aquifer parameters. This paper proposes a novel approach based on a drawdown model and a global optimization method of simulated annealing (SA) or a genetic algorithm (GA) to determine the best-fit aquifer parameters for leaky aquifer systems. The aquifer parameters obtained from SA and the GA almost agree with those obtained from the extended Kalman filter and gradient-type method. Moreover, all results indicate that the SA and GA are robust and yield consistent results when dealing with the parameter identification problems. Copyright © 2006 John Wiley & Sons, Ltd. [source] A computer method based on simulated annealing to identify aquifer parameters using pumping-test dataINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 3 2008Yen-Chen Huang Abstract Conventional graphical or computer methods for identifying aquifer parameters have their own inevitable limitations. This paper proposes a computer method based on a drawdown model and a heuristic approach of simulated annealing (SA) to determine the best-fit aquifer parameters of the confined and unconfined aquifer systems. The drawdown model for the confined aquifer is the Theis solution and the unconfined aquifer is the Neuman solution. The estimated results of proposed method have better accuracy than those of the graphical methods and agree well with those of the computer methods based on the extended Kalman filter and Newton's method. Finally, the sensitivity analyses for the control parameters of SA indicate that the proposed method is very robust and stable in parameter identification procedures. Copyright © 2007 John Wiley & Sons, Ltd. [source] Design techniques of two-layer architectures for WDM optical networksINTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS, Issue 2 2001Andrea Borella Abstract A general method for designing multilayered WDM optical networks, based on the combined use of single-and multi-hop connection modes, is presented. It takes into account variable values for the number of users and wavelengths in each cluster. Closed form expressions are derived for the transmission capacity and the optimum number of channels for intra-cluster communications, either in the case of uniform or non-uniform traffic distribution. The analytical approach is particularly useful in the presence of constraints on the number of wavelengths, due to technological limits or non-linear phenomena, when sub-optimal solutions must be necessarily addressed. The proposed method is integrated with the adoption of well-known selection procedures, like simulated annealing or genetic algorithms, to reduce the computational effort. Copyright © 2001 John Wiley & Sons, Ltd. [source] A new parameter extraction method for accurate modeling of PEM fuel cellsINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 11 2009M. T. Outeiro Abstract In this paper, a new parameter extraction method for accurate modeling of proton exchange membrane (PEM) fuel cell systems is presented. The main difficulty in obtaining an accurate PEM fuel cell dynamical model is the lack of manufacturer information about the exact values of the parameters needed for the model. In order to obtain a realistic dynamic model of the PEM system, the electrochemical considerations of the system are incorporated into the model. Although many models have been reported in the literature, the parameter extraction issue has been neglected. However, model parameters must be precisely identified in order to obtain accurate simulation results. The main contribution of the present work is the application of the simulated annealing (SA) optimization algorithm as a method for identification of PEM fuel cell model parameter identification. The major advantage of SA is its ability to avoid becoming trapped in local minimum, as well as its flexibility and robustness. The parameter extraction and performance validation are carried out by comparing experimental and simulated results. The good agreement observed confirms the usefulness of the proposed extraction approach together with adopted PEM fuel cell model as an efficient tool to help design of power fuel cell power systems. Copyright © 2009 John Wiley & Sons, Ltd. [source] Integral evaluation in semiconductor device modelling using simulated annealing with Bose,Einstein statisticsINTERNATIONAL JOURNAL OF NUMERICAL MODELLING: ELECTRONIC NETWORKS, DEVICES AND FIELDS, Issue 4 2007E.A.B. Cole Abstract Fermi integrals arise in the mathematical and numerical modelling of microwave semiconductor devices. In particular, associated Fermi integrals involving two arguments arise in the modelling of HEMTs, in which quantum wells form at the material interfaces. The numerical evaluation of these associated integrals is time consuming. In this paper, these associated integrals are replaced by simpler functions which depend on a small number of optimal parameters. These parameters are found by optimizing a suitable cost function using a genetic algorithm with simulated annealing. A new method is introduced whereby the transition probabilities of the simulated annealing process are based on the Bose,Einstein distribution function, rather than on the more usual Maxwell,Boltzmann statistics or Tsallis statistics. Results are presented for the simulation of a four-layer HEMT, and show the effect of the approximation for the associated Fermi integrals. A comparison is made of the convergence properties of the three different statistics used in the simulated annealing process. Copyright © 2007 John Wiley & Sons, Ltd. [source] Searching the global minimum of a peptide/bilayer potential energy surface by fast heating and cooling cycles of simulated annealingINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2008C. A. Fuzo Abstract The total time reached by molecular dynamics simulation in the study of the interactions between hydrated bilayers and peptides is still very short. A scheme of fast heating and cooling cycles of simulated annealing (FHCCSA) is proposed to improve the efficiency of the search for the global minimum of the peptide/bilayer potential energy surface. In FHCCSA, the high temperatures facilitate the transitions between stable configurations; i.e., heating and cooling cycles make easier the escape of the system outside the local energy minimum. The FHCCSA efficiency is confirmed by comparing its results with conventional NpT simulations. The new scheme saves more than 90% of the total cpu time compared with ordinary NpT simulations. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Chlorartinite, a volcanic exhalation product also found in industrial magnesia screedJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 5 2006Kunihisa Sugimoto The volcanic exhalation product chlorartinite, [Mg2(CO3)(H2O)(OH)]Cl·H2O, has recently been found to be a minor, and in some samples a major, component of magnesia floors for industrial use. In order to be able to perform quantitative phase analysis using the Rietveld method, its crystal structure was determined from high-resolution synchrotron powder diffraction data by the global optimization technique of simulated annealing and Rietveld refinement. The final Rp and Rwp values are 5.23% and 6.56%, respectively. Chlorartinite crystallizes in the rhombohedral space group R3c (No. 161), with a = 23.14422,(16),Å, c = 7.22333,(5),Å, V = 3350.84,(5),Å3, Z = 18. The building units of chlorartinite consist of MgO6 octahedra forming 15-membered puckered rings which are interconnected by CO3 triangular moieties. The rings are stacked to form a honeycomb-like three-dimensional framework structure with large isolated channels. Within the channels, free chlorine atoms and disordered water molecules are located. [source] Abinitio structure determination of m -toluidine by powder X-ray diffractionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3 2004Mwaffak Rukiah The powder X-ray diffraction pattern of the crystalline phase of m -toluidine has been recorded with a sensitive curved detector (CPS120) at 150,K. The structure has been solved by real-space methods (simulated annealing) followed by Rietveld refinements with phenyl rings as rigid bodies and with soft constraints on bond lengths for peripheral atoms. The cell is monoclinic with space group P21/c and Z = 8. Equivalent molecules form chains along c. The crystalline cohesion is achieved by N,H,N hydrogen bonds between neighbouring chains of non-equivalent molecules and by van der Waals interactions of neighbouring chains of equivalent molecules. The hydrogen-bonding network has been confirmed by lattice-energy minimization. Anisotropic strain effects of the cell have been calculated. The directions of the minimal strains correspond to the directions of the hydrogen bonds. An explanation of the difficulty to crystallize the metastable phase is given. [source] FOX, `free objects for crystallography': a modular approach to ab initio structure determination from powder diffractionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2002Vincent Favre-Nicolin A new program has been developed for ab initio crystal structure determination from powder diffraction data (X-ray and neutron). It uses global-optimization algorithms to solve the structure by performing trials in direct space. It is a modular program, capable of using several criteria for evaluating each trial configuration (e.g. multi-pattern). It is also modular in the description of the crystal content, with the possibility of describing building blocks in the sample, such as polyhedra or molecules, and with automatic adaptive handling of special positions and sharing of identical atoms between neighbouring building blocks. It can therefore find the correct structure without any assumption about the connectivity of the building blocks and is suitable for any kind of material. Several optimization algorithms (simulated annealing, parallel tempering) are available, with the possibility of choosing the convergence criterion as a combination of available cost functions. This program is freely available for Linux and Windows platforms; it is also fully `open source', which, combined with an object-oriented design and a complete developer documentation, ensures its future evolution. [source] Wavelength selection with Tabu SearchJOURNAL OF CHEMOMETRICS, Issue 8-9 2003J. A. Hageman Abstract This paper introduces Tabu Search in analytical chemistry by applying it to wavelength selection. Tabu Search is a deterministic global optimization technique loosely based on concepts from artificial intelligence. Wavelength selection is a method which can be used for improving the quality of calibration models. Tabu Search uses basic, problem-specific operators to explore a search space, and memory to keep track of parts already visited. Several implementational aspects of wavelength selection with Tabu Search will be discussed. Two ways of memorizing the search space are investigated: storing the actual solutions and storing the steps necessary to create them. Parameters associated with Tabu Search are configured with a Plackett,Burman design. In addition, two extension schemes for Tabu Search, intensification and diversification, have been implemented and are applied with good results. Eventually, two implementations of wavelength selection with Tabu Search are tested, one which searches for a solution with a constant number of wavelengths and one with a variable number of wavelengths. Both implementations are compared with results obtained by wavelength selection methods based on simulated annealing (SA) and genetic algorithms (GAs). It is demonstrated with three real-world data sets that Tabu Search performs equally well as and can be a valuable alternative to SA and GAs. The improvements in predictive abilities increased by a factor of 20 for data set 1 and by a factor of 2 for data sets 2 and 3. In addition, when the number of wavelengths in a solution is variable, measurements on the coverage of the search space show that the coverage is usually higher for Tabu Search compared with SA and GAs. Copyright © 2003 John Wiley & Sons, Ltd. [source] Lattice models of peptide aggregation: Evaluation of conformational search algorithmsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2005Mark T. Oakley Abstract We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa,Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1638,1646, 2005 [source] Molecular dynamic simulations of nanomechanic chaperone peptide and effects of in silico His mutations on nanostructured functionJOURNAL OF PEPTIDE SCIENCE, Issue 11 2008Abolfazl Barzegar Abstract The nanoscale peptide YSGVCHTDLHAWHGDWPLPVK exhibits molecular chaperone activity and prevents protein aggregation under chemical and/or thermal stress. Here, His mutations of this peptide and their impact on chaperone activity were evaluated using theoretical techniques. Molecular dynamic (MD) simulations with simulated annealing (SA) of different mutant nanopeptides were employed to determine the contribution of the scaffolding His residues (H45, H49, H52), when mutated to Pro, on chaperone action in vitro. The in silico mutations of His residues to Pro (H45P, H49P, H52P) revealed loss of secondary ordered strand structure. However, a small part of the strand conformation was formed in the middle region of the native chaperone peptide. The His-to-Pro mutations resulted in decreased gyration radius (Rg) values and surface accessibility of the mutant peptides under the simulation times. The invariant dihedral angle (,) values and the disrupting effects of the Pro residues indicated the coil conformation of mutant peptides. The failure of the chaperone-like action in the Pro mutant peptides was consistent with their decreased effective accessible surfaces. The high variation of , value for His residues in native chaperone peptide leads to high flexibility, such as a minichaperone acting as a nanomachine at the molecular level. Our findings demonstrate that the peptide strand conformation motif with high flexibility at nanoscale is critical for chaperone activity. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. [source] Search-based refactoring: an empirical studyJOURNAL OF SOFTWARE MAINTENANCE AND EVOLUTION: RESEARCH AND PRACTICE, Issue 5 2008Mark O'Keeffe Abstract Object-oriented systems that undergo repeated addition of functionality commonly suffer a loss of quality in their underlying design. This problem must often be remedied in a costly refactoring phase before further maintenance programming can take place. Recently search-based approaches to automating the task of software refactoring, based on the concept of treating object-oriented design as a combinatorial optimization problem, have been proposed. However, because search-based refactoring is a novel approach it is yet to be established as to which search techniques are most suitable for the task. In this paper we report the results of an empirical comparison of simulated annealing (SA), genetic algorithms (GAs) and multiple ascent hill-climbing (HCM) in search-based refactoring. A prototype automated refactoring tool is employed, capable of making radical changes to the design of an existing program in order that it conforms more closely to a contemporary quality model. Results show HCM to outperform both SA and GA over a set of five input programs. Copyright © 2008 John Wiley & Sons, Ltd. [source] Near-optimal designs for dual channel microarray studiesJOURNAL OF THE ROYAL STATISTICAL SOCIETY: SERIES C (APPLIED STATISTICS), Issue 5 2005Ernst Wit Summary., Much biological and medical research employs microarray studies to monitor gene expression levels across a wide range of organisms and under many experimental conditions. Dual channel microarrays are a common platform and allow two samples to be measured simultaneously. A frequently used design uses a common reference sample to make conditions across different arrays comparable. Our aim is to formulate microarray experiments in the experimental design context and to use simulated annealing to search for near-optimal designs. We identify a subclass of designs, the so-called interwoven loop designs, that seems to have good optimality properties compared with the near-optimal designs that are found by simulated annealing. Commonly used reference designs and dye swap designs are shown to be highly inefficient. [source] Anfis models for the quasistatic analysis of coplanar strip line structuresMICROWAVE AND OPTICAL TECHNOLOGY LETTERS, Issue 9 2010Mustafa Turkmen Abstract In this work, computer-aided design models based on adaptive-network-based fuzzy inference system (ANFIS) for the quasistatic analysis of three different coplanar strip line structures are presented. These strip line structures are conventional coplanar strip lines, asymmetrical coplanar strip lines with infinitely wide strip, and asymmetrical coplanar strip lines with infinitely thick dielectric substrate. The design parameters of the proposed ANFIS models are optimally determined by using four different optimization algorithms, hybrid learning, simulated annealing, least-squares, and genetic algorithm. When the performances of ANFIS models are compared with each other, the best results for training and test are obtained from the models trained with hybrid learning algorithm. There is a good agreement among the results of ANFIS models, quasistatic analysis, a full-wave electromagnetic simulator IE3D, and experimental works realized in this study. © 2010 Wiley Periodicals, Inc. Microwave Opt Technol Lett 52: 1990,1996, 2010; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.25372 [source] Molecular shapes from small-angle X-ray scattering: extension of the theory to higher scattering anglesACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2009V. L. Shneerson A low-resolution shape of a molecule in solution may be deduced from measured small-angle X-ray scattering I(q) data by exploiting a Hankel transform relation between the coefficients of a multipole expansion of the scattered amplitude and corresponding coefficients of the electron density. In the past, the radial part of the Hankel transform has been evaluated with the aid of a truncated series expansion of a spherical Bessel function. It is shown that series truncation may be avoided by analytically performing the radial integral over an entire Bessel function. The angular part of the integral involving a spherical harmonic kernel is performed by quadrature. Such a calculation also allows a convenient incorporation of a molecular hydration shell of constant density intermediate between that of the protein and the solvent. Within this framework, we determine the multipole coefficients of the shape function by optimization of the agreement with experimental data by simulated annealing. [source] A Genetic Algorithm Hybrid for Constructing Optimal Response Surface DesignsQUALITY AND RELIABILITY ENGINEERING INTERNATIONAL, Issue 7 2004David Drain Abstract Hybrid heuristic optimization methods can discover efficient experiment designs in situations where traditional designs cannot be applied, exchange methods are ineffective, and simple heuristics like simulated annealing fail to find good solutions. One such heuristic hybrid is GASA (genetic algorithm,simulated annealing), developed to take advantage of the exploratory power of the genetic algorithm, while utilizing the local optimum exploitive properties of simulated annealing. The successful application of this method is demonstrated in a difficult design problem with multiple optimization criteria in an irregularly shaped design region. Copyright © 2004 John Wiley & Sons, Ltd. [source] Structure determination of seven phases and solvates of Pigment Yellow 183 and Pigment Yellow 191 from X-ray powder and single-crystal dataACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2009Svetlana N. Ivashevskaya The crystal structures of two industrially produced laked yellow pigments, Pigment Yellow 183 [P.Y. 183, Ca(C16H10Cl2N4O7S2), , phase] and Pigment Yellow 191 [P.Y. 191, Ca(C17H13ClN4O7S2), , and , phases], were determined from laboratory X-ray powder diffraction data. The coordinates of the molecular fragments of the crystal structures were found by means of real-space methods (simulated annealing) with the program DASH. The coordinates of the calcium ions and the water molecules were determined by combining real-space methods (DASH and MRIA) and repeated Rietveld refinements (TOPAS) of the partially finished crystal structures. TOPAS was also used for the final Rietveld refinements. The crystal structure of ,-P.Y. 183 was determined from single-crystal data. The , phases of the two pigments are isostructural, whereas the , phases are not. All four phases exhibit a double-layer structure, built from nonpolar layers containing the C/N backbone and polar layers containing the calcium ions, sulfonate groups and water molecules. Furthermore, the crystal structures of an N,N -dimethylformamide solvate of P.Y. 183, and of P.Y. 191 solvates with N,N -dimethylformamide and N,N -dimethylacetamide were determined by single-crystal X-ray analysis. [source] Structure of lithium benzilate hemihydrate solved by simulated annealing and difference Fourier synthesis from powder dataACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2003Asiloé J. Mora The crystal structure of lithium benzilate hemihydrate (C14H11OLi+·0.5H2O) was solved from synchrotron powder diffraction data. This compound crystallizes in the monoclinic space group P21/a. The structure was solved via the direct space search for two benzilate fragments using the simulated-annealing program DASH, localization of the lithium ions and water molecule from a difference Fourier map, and a restrained Rietveld refinement (Rwp = 0.0687). The structure is a coordination polymer of [Li2(C14H11O3)2·H2O]2 tetramers building helical fourfold one-dimensional channels parallel to [010]. Inside the channels the tetrahedral coordination spheres of the lithium ions contain hydroxyl and carbonyl groups, and water molecules. The water molecule functions as the cohesive entity forming extended hydrogen-bonded chains running along [010], and bifurcated donor hydrogen bonds with the two nearest carboxylates. At the outer edge of the channels, weaker intermolecular C,H,Ph hydrogen bonds along [100] and [001] contribute to the supramolecular aggregation of the structure. [source] A LOTTO SYSTEMS PROBLEMAUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS, Issue 3 2005K.G. Russell Summary A Lotto Systems bet allows the player to nominate n numbers from which (s)he believes the winning six numbers will be drawn, and to bet on all combinations of six of these n numbers. Assume that the winning six numbers come from the nominated n. How many combinations must be entered to guarantee that one combination will include at least five of the winning six numbers? The problem is generalized in this paper, and the method of simulated annealing is used to find solutions for various situations. The case where two supplementary numbers are drawn after the initial six winning numbers is also considered. [source] Structure of buffalo lactoferrin at 3.3,Å resolution at 277,KACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2000S. Karthikeyan The three-dimensional structure of diferric buffalo lactoferrin has been determined at 3.3,Å resolution. The structure was solved by molecular replacement using the coordinates of diferric human lactoferrin as a search model and was refined by simulated annealing (X-PLOR). The final model comprises 5316 protein atoms for all 689 residues, two Fe3+ and two CO ions. The final R factor was 21.8% for 11,711 reflections in the resolution range 17.0,3.3,Å. The folding of buffalo lactoferrin is essentially similar to that of the other members of the transferrin family. The significant differences are found in the dimensions of the binding cleft and the interlobe orientation. The interlobe interactions are predominantly hydrophobic in nature, thus facilitating the sliding of two lobes owing to external forces. The interdomain interactions are comparable in the N and C lobes. [source] Computational design of proteins stereochemically optimized in size, stability, and folding speedBIOPOLYMERS, Issue 2 2006Sadhna Joshi Abstract Artificial proteins potentially barrier-free in the folding kinetics are approached computationally under the guidance of protein-folding theories. The smallest and fastest folding globular protein triple-helix-bundle (THB) is so modified as to minimize or eliminate its presumed barriers in folding speed. As the barriers may reside in the ordering of either secondary or tertiary structure, the elements of both secondary and tertiary structure in the protein are targeted for prenucleation with suitable stereochemically constrained amino acid residues. The required elements of topology and sequence for the THB are optimized independently; first the topology is optimized with simulated annealing in polypeptides of highly simplified alphabet; next, the sequence in side chains is optimized using the standard inverse design methods. The resultant three best-adapted THBs, variable in topology and distinctive in sequences, are assessed by comparing them with a few benchmark proteins. The results of mainly molecular dynamics (MD) comparisons, undertaken in explicit water at different temperatures, show that the designed sequences are favorably placed against the chosen benchmarks as THB proteins potentially thermostable in the native folds. Folding simulation experiments with MD establish that the designed sequences are rapid in the folding of individual helices, but not in the evolution of tertiary structure; energetic cum topological frustrations remain but could be the artifacts of the starting conformations that were chosen in the THBs in the folding simulations. Overall, a practical high-throughput approach for de novo protein design has been developed that may have fruitful application for any type of tertiary structure. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 122,134, 2006 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] | |||||||||||||||||||