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Parameter Sets (parameter + set)
Kinds of Parameter Sets Selected AbstractsEstimation and Confidence Regions for Parameter Sets in Econometric Models,ECONOMETRICA, Issue 5 2007Victor Chernozhukov This paper develops a framework for performing estimation and inference in econometric models with partial identification, focusing particularly on models characterized by moment inequalities and equalities. Applications of this framework include the analysis of game-theoretic models, revealed preference restrictions, regressions with missing and corrupted data, auction models, structural quantile regressions, and asset pricing models. Specifically, we provide estimators and confidence regions for the set of minimizers ,I of an econometric criterion function Q(,). In applications, the criterion function embodies testable restrictions on economic models. A parameter value ,that describes an economic model satisfies these restrictions if Q(,) attains its minimum at this value. Interest therefore focuses on the set of minimizers, called the identified set. We use the inversion of the sample analog, Qn(,), of the population criterion, Q(,), to construct estimators and confidence regions for the identified set, and develop consistency, rates of convergence, and inference results for these estimators and regions. To derive these results, we develop methods for analyzing the asymptotic properties of sample criterion functions under set identification. [source] Modelling of colloid leaching from unsaturated, aggregated soilEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 3 2007M. Laegdsmand Summary The migration of colloids in soils can enhance the leaching of strongly sorbing contaminants. We present a model for the simulation of colloid leaching from unsaturated, aggregated soil media under stationary flow. Transport in the intra-aggregate pores is simulated by convection,dispersion, and transport in the interaggregate pores, and a stagnant layer of water surrounding the aggregates, is simulated by diffusion. The model describes the release of colloids from soil aggregates, sorption and desorption processes at the air,water interfaces, and flocculation and subsequent straining from the flowing water. All three processes were simulated as functions of ionic strength. Transport of ions in intra-aggregate pores was simulated by Fickian diffusion. The model was calibrated against experimental results of colloid leaching from columns packed with natural soil aggregates. The aggregates were of two soils differing in organic matter content. On each soil a single calibrated parameter set could describe the experiments with the three ionic strengths. The parameters for release of colloids from the aggregate surface and the sorption properties of the air,water interface were different for the two soils. The key parameters for leaching were the thickness of the stagnant layer of water surrounding the aggregates, the mechanical dispersion, the maximum concentration of colloids at the surface of the aggregates, the sorption capacity and rate coefficient of the colloids at the air,water interface, and the colloid diffusion coefficient. Simulations were also done with two additional irrigation intensities at one ionic strength. Simulated leaching was greater than measured leaching at both irrigation intensities, but the diffusion-controlled release of colloids from the aggregates was simulated correctly. [source] A study on a new AVR parameter tuning concept using on-line measured data with the real-time simulatorEUROPEAN TRANSACTIONS ON ELECTRICAL POWER, Issue 3 2006Joong-Moon Kim Abstract Automatic voltage regulator (AVR) parameter tuning for voltage control of power system generators has generally been performed with the analytic methods and the simulation methods, which mostly depend on off-line linear mathematical models of power system. However, due to the nonlinear nature of power system, the mathematical models of the excitation system may not be correct. So the excitation control system performances with the parameter set that is tuned by using the mathematical model, may not be appropriate for some operating conditions. This paper presents an AVR parameter tuning method using on-line measured data of the excitation control system with parameter optimization technique. As this method utilizes on-line operating data, it can overcome the limitation of model uncertainty problems of conventional method. To validate the proposed tuning concept, a scaled model excitation system is connected to the real-time power system simulator, and the proposed tuning concept is tested. Copyright © 2006 John Wiley & Sons, Ltd. [source] Long-term investigations of the snow cover in a subalpine semi-forested catchmentHYDROLOGICAL PROCESSES, Issue 2 2006Manfred Stähli Abstract To improve spring runoff forecasts from subalpine catchments, detailed spatial simulations of the snow cover in this landscape is obligatory. For more than 30 years, the Swiss Federal Research Institute WSL has been conducting extensive snow cover observations in the subalpine watershed Alptal (central Switzerland). This paper summarizes the conclusions from past snow studies in the Alptal valley and presents an analysis of 14 snow courses located at different exposures and altitudes, partly in open areas and partly in forest. The long-term performance of a physically based numerical snow,vegetation,atmosphere model (COUP) was tested with these snow-course measurements. One single parameter set with meteorological input variables corrected to the prevailing local conditions resulted in a convincing snow water equivalent (SWE) simulation at most sites and for various winters with a wide range of snow conditions. The snow interception approach used in this study was able to explain the forest effect on the SWE as observed on paired snow courses. Finally, we demonstrated for a meadow and a forest site that a successful simulation of the snowpack yields appropriate melt rates. Copyright © 2006 John Wiley & Sons, Ltd. [source] Kinetics and mechanism of the hydrolytic disproportionation of iodineINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 11 2004Krisztina Seb, k-Nagy Kinetics of the hydrolytic disproportionation of I2 was studied by UV,VIS spectrophotometry at 298 K and at the ionic strength 0.2 M (NaClO4) in buffered solutions in the pH range 8.91,10.50 at different initial iodide concentrations. The characterization of this reaction is fundamental for modeling oscillatory and front reactions in the presence of iodine as reactant or intermediate as well as for drinking water treatment. A matrix rank analysis confirmed three absorbing species in the beginning of the reaction, whereas later assumption of two species is enough to describe the experimental data in the visible part of the spectrum. A reaction mechanism was proposed for disproportionation by using fitting/simulation with a multipurpose program package ZiTa, by simultaneous evaluation of 17,906 points in 79 experimental curves. A parameter set was suggested, which was obtained by absolute, relative, and orthogonal fittings of the experimental data. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36: 596,602, 2004 [source] A molecular mechanics force field for biologically important sterolsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Zoe Cournia Abstract A parameterization has been performed of the biologically important sterols cholesterol, ergosterol, and lanosterol for the CHARMM27 all-atom molecular mechanics force field. An automated parameterization method was used that involves fitting the potential to vibrational frequencies and eigenvectors derived from quantum-chemical calculations. The partial charges were derived by fitting point charges to quantum-chemically calculated electrostatic potentials. To model the dynamics of the hydroxyl groups of the sterols correctly, the parameter set was refined to reproduce the energy barrier for the rotation of the hydroxyl group around the carbon connected to the hydroxyl of each sterol. The frequency-matching plots show good agreement between the CHARMM and quantum chemical normal modes. The parameters are tested in a molecular dynamics simulation of the cholesterol crystal structure. The experimental geometry and cell dimensions are well reproduced. The force field derived here is also useful for simulating other sterols such as the phytosterols sigmasterol, and campesterol, and a variety of steroids. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1383,1399, 2005 [source] A new GROMOS force field for hexopyranose-based carbohydratesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005Roberto D. Lins Abstract A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) 4C1 chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (,- and ,-D-glucose, ,- and ,-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400,1412, 2005 [source] An improved nucleic acid parameter set for the GROMOS force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2005Thereza A. Soares Abstract Over the past decades, the GROMOS force field for biomolecular simulation has primarily been developed for performing molecular dynamics (MD) simulations of polypeptides and, to a lesser extent, sugars. When applied to DNA, the 43A1 and 45A3 parameter sets of the years 1996 and 2001 produced rather flexible double-helical structures, in which the Watson,Crick hydrogen-bonding content was more limited than expected. To improve on the currently available parameter sets, the nucleotide backbone torsional-angle parameters and the charge distribution of the nucleotide bases are reconsidered based on quantum-chemical data. The new 45A4 parameter set resulting from this refinement appears to perform well in terms of reproducing solution NMR data and canonical hydrogen bonding. The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 725,737, 2005 [source] PM3-compatible zinc parameters optimized for metalloenzyme active sitesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2004Edward N. Brothers Abstract Recent studies have shown that semiempirical methods (e.g., PM3 and AM1) for zinc-containing compounds are unreliable for modeling structures containing zinc ions with ligand environments similar to those observed in zinc metalloenzymes. To correct these deficiencies a reparameterization of zinc at the PM3 level was undertaken. In this effort we included frequency corrected B3LYP/6-311G* zinc metalloenzyme ligand environments along with previously utilized experimental data. Average errors for the heats of formation have been reduced from 46.9 kcal/mol (PM3) to 14.2 kcal/mol for this new parameter set, termed ZnB for "Zinc, Biological." In addition, the new parameter sets predict geometries for the Bacillus fragilis active site model and other zinc metalloenzyme mimics that are qualitatively in agreement with high-level ab initio results, something existing parameter sets failed to do. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1677,1692, 2004 [source] A backoff strategy for model-based experiment design under parametric uncertaintyAICHE JOURNAL, Issue 8 2010Federico Galvanin Abstract Model-based experiment design techniques are an effective tool for the rapid development and assessment of dynamic deterministic models, yielding the most informative process data to be used for the estimation of the process model parameters. A particular advantage of the model-based approach is that it permits the definition of a set of constraints on the experiment design variables and on the predicted responses. However, uncertainty in the model parameters can lead the constrained design procedure to predict experiments that turn out to be, in practice, suboptimal, thus decreasing the effectiveness of the experiment design session. Additionally, in the presence of parametric mismatch, the feasibility constraints may well turn out to be violated when that optimally designed experiment is performed, leading in the best case to less informative data sets or, in the worst case, to an infeasible or unsafe experiment. In this article, a general methodology is proposed to formulate and solve the experiment design problem by explicitly taking into account the presence of parametric uncertainty, so as to ensure both feasibility and optimality of the planned experiment. A prediction of the system responses for the given parameter distribution is used to evaluate and update suitable backoffs from the nominal constraints, which are used in the design session to keep the system within a feasible region with specified probability. This approach is particularly useful when designing optimal experiments starting from limited preliminary knowledge of the parameter set, with great improvement in terms of design efficiency and flexibility of the overall iterative model development scheme. The effectiveness of the proposed methodology is demonstrated and discussed by simulation through two illustrative case studies concerning the parameter identification of physiological models related to diabetes and cancer care. © 2009 American Institute of Chemical Engineers AIChE J, 2010 [source] QUADRATIC TERM STRUCTURE MODELS FOR RISK-FREE AND DEFAULTABLE RATESMATHEMATICAL FINANCE, Issue 4 2004Li Chen In this paper, quadratic term structure models (QTSMs) are analyzed and characterized in a general Markovian setting. The primary motivation for this work is to find a useful extension of the traditional QTSM, which is based on an Ornstein,Uhlenbeck (OU) state process, while maintaining the analytical tractability of the model. To accomplish this, the class of quadratic processes, consisting of those Markov state processes that yield QTSM, is introduced. The main result states that OU processes are the only conservative quadratic processes. In general, however, a quadratic potential can be added to allow QTSMs to model default risk. It is further shown that the exponent functions that are inherent in the definition of the quadratic property can be determined by a system of Riccati equations with a unique admissible parameter set. The implications of these results for modeling the term structure of risk-free and defaultable rates are discussed. [source] Calculation of the Energy of Explosives with a Partial Reaction Model.PROPELLANTS, EXPLOSIVES, PYROTECHNICS, Issue 1 2006Comparison with Cylinder Test Data Abstract The energy delivered by explosives is described by means of the useful expansion work along the isentrope of the detonation products. A thermodynamic code (W-DETCOM) is used, in which a partial reaction model has been implemented. In this model, the reacted fraction of the explosive in the detonation state is used as a fitting factor so that the calculated detonation velocity meets the experimental value. Calculations based on such a model have been carried out for a number of commercial explosives of ANFO and emulsion types. The BKW (Becker-Kistiakowsky-Wilson) equation of state is used for the detonation gases with the Sandia parameter set (BKWS). The energy delivered in the expansion (useful work) is calculated, and the values obtained are compared with the Gurney energies from cylinder test data at various expansion ratios. The expansion work values obtained are much more realistic than those from an ideal detonation calculation and, in most cases, the values predicted by the calculation are in good agreement with the experimental ones. [source] A statistically derived parameterization for the collagen triple-helixPROTEIN SCIENCE, Issue 11 2002Jan K. Rainey Abstract The triple-helix is a unique secondary structural motif found primarily within the collagens. In collagen, it is a homo- or hetero-tripeptide with a repeating primary sequence of (Gly-X-Y)n, displaying characteristic peptide backbone dihedral angles. Studies of bulk collagen fibrils indicate that the triple-helix must be a highly repetitive secondary structure, with very specific constraints. Primary sequence analysis shows that most collagen molecules are primarily triple-helical; however, no high-resolution structure of any entire protein is yet available. Given the drastic morphological differences in self-assembled collagen structures with subtle changes in assembly conditions, a detailed knowledge of the relative locations of charged and sterically bulky residues in collagen is desirable. Its repetitive primary sequence and highly conserved secondary structure make collagen, and the triple-helix in general, an ideal candidate for a general parameterization for prediction of residue locations and for the use of a helical wheel in the prediction of residue orientation. Herein, a statistical analysis of the currently available high-resolution X-ray crystal structures of model triple-helical peptides is performed to produce an experimentally based parameter set for predicting peptide backbone and C, atom locations for the triple-helix. Unlike existing homology models, this allows easy prediction of an entire triple-helix structure based on all existing high-resolution triple-helix structures, rather than only on a single structure or on idealized parameters. Furthermore, regional differences based on the helical propensity of residues may be readily incorporated. The parameter set is validated in terms of the predicted bond lengths, backbone dihedral angles, and interchain hydrogen bonding. [source] PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2008Miha Andreja The number and variety of macromolecular structures in complex with `hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh,Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/. [source] A Geometric Approach to Comparing Treatments for Rapidly Fatal DiseasesBIOMETRICS, Issue 1 2006Peter F. Thall Summary In therapy of rapidly fatal diseases, early treatment efficacy often is characterized by an event, "response," which is observed relatively quickly. Since the risk of death decreases at the time of response, it is desirable not only to achieve a response, but to do so as rapidly as possible. We propose a Bayesian method for comparing treatments in this setting based on a competing risks model for response and death without response. Treatment effect is characterized by a two-dimensional parameter consisting of the probability of response within a specified time and the mean time to response. Several target parameter pairs are elicited from the physician so that, for a reference covariate vector, all elicited pairs embody the same improvement in treatment efficacy compared to a fixed standard. A curve is fit to the elicited pairs and used to determine a two-dimensional parameter set in which a new treatment is considered superior to the standard. Posterior probabilities of this set are used to construct rules for the treatment comparison and safety monitoring. The method is illustrated by a randomized trial comparing two cord blood transplantation methods. [source] Force Field Evaluation for Biomolecular Simulation: Free Enthalpies of Solvation of Polar and Apolar Compounds in Various SolventsCHEMPHYSCHEM, Issue 3 2006Daan P. Geerke Abstract Recently, the GROMOS biomolecular force field parameter set 53A6,which has been parametrized to reproduce experimentally determined free enthalpies of hydration and solvation in cyclohexane of amino acid side-chain analogs,was presented. To investigate the transferability of the new parameter set, we calculated free enthalpies of solvation of a range of polar and apolar compounds in different solvents (methanol, dimethyl sulfoxide (DMSO), acetonitrile, and acetone) from molecular dynamics simulations using the GROMOS 53A6 force field. For methanol and DMSO, parameters were used that are available in the 53A6 parameter set. For acetonitrile, a recently developed model was taken and for acetone, two models available in literature were used. We found that trends in and values for the solvation free enthalpies are in satisfactory agreement with experiment, except for the solvation in acetone for which deviations from experiment can be explained in terms of the properties of the models used. [source] Phylogeny of Nerillidae (Polychaeta, Annelida) as inferred from combined 18S rDNA and morphological dataCLADISTICS, Issue 2 2005Katrine Worsaae A phylogeny of the meiofaunal polychaete family Nerillidae based on morphological, molecular and combined data is presented here. The data sets comprise nearly complete sequences of 18S rDNA and 40 morphological characters of 17 taxa. Sequences were analyzed simultaneously with the morphological data by direct optimization in the program POY, with a variety of parameter sets (costs of gaps: transversions: transitions). Three outgroups were selected from the major polychaete group Aciculata and one from Scolecida. The 13 nerillid species from 11 genera were monophyletic in all analyses with very high support, and three new apomorphies for Nerillidae are identified. The topology of the ingroup varied according to the various parameter settings. Reducing the number of outgroups to one decreased the variance among the phylogenetic hypotheses. The congruence among these was tested and a parameter set, with equal weights (222) and extension gap weighted 1, yielded minimum incongruence (ILD). Several terminal clades of the combined analysis were highly supported, as well as the position of Leptonerilla prospera as sister terminal to the other nerillids. The evolution of morphological characters such as segment numbers, chaetae, appendages and ciliation are traced and discussed. A regressive pathway within Nerillidae is indicated for several characters, however, generally implying several convergent losses. Numerous genera are shown to require revision. © The Willi Hennig Society 2005. [source] Vadose Zone Flow Model Uncertainty as Conditioned on Geophysical DataGROUND WATER, Issue 2 2003Andrew Binley An approach to estimating the uncertainty in model descriptions based on a landscape space to model space mapping concept is described. The approach is illustrated by an application making use of plot scale geophysical estimates of changes in water content profiles to condition a model of recharge to the Sherwood Sandstone Aquifer in the United Kingdom. It is demonstrated that the mapping is highly uncertain and that many different parameter sets give acceptable simulations of the observations. Multiple profile measurements over time offer only limited additional constraints on the mapping. The resulting mapping weights may be used to evaluate uncertainty in the predictions of vadose zone flow dynamics for the site. [source] Diagnostic evaluation of conceptual rainfall,runoff models using temporal clusteringHYDROLOGICAL PROCESSES, Issue 20 2010N. J. de Vos Abstract Given the structural shortcomings of conceptual rainfall,runoff models and the common use of time-invariant model parameters, these parameters can be expected to represent broader aspects of the rainfall,runoff relationship than merely the static catchment characteristics that they are commonly supposed to quantify. In this article, we relax the common assumption of time-invariance of parameters, and instead seek signature information about the dynamics of model behaviour and performance. We do this by using a temporal clustering approach to identify periods of hydrological similarity, allowing the model parameters to vary over the clusters found in this manner, and calibrating these parameters simultaneously. The diagnostic information inferred from these calibration results, based on the patterns in the parameter sets of the various clusters, is used to enhance the model structure. This approach shows how diagnostic model evaluation can be used to combine information from the data and the functioning of the hydrological model in a useful manner. Copyright © 2010 John Wiley & Sons, Ltd. [source] Detecting the effects of spatial variability of rainfall on hydrological modelling within an uncertainty analysis frameworkHYDROLOGICAL PROCESSES, Issue 14 2009P. M. Younger Abstract Spatial patterns of rainfall are known to cause differences in observed flow. In this paper, the effects of perturbations in rainfall patterns on changes in parameter sets as well as model output are explored using the hydrological model Dynamic TOPMODEL for the Brue catchment (135 km2) in southwest England. Overall rainfall amount remains the same at each time step so the perturbations act as effectively treated errors in the spatial pattern. The errors were analysed with particular emphasis on when they could be detected under an uncertainty framework. Higher rainfall perturbations (multipliers of × 4 and greater) in the low lying and high areas of the catchment resulted in changes to event peaks and accompanying compensation in the baseflow. More significantly, changes in the effective model parameter values required by the best models to take account of the more extreme patterns were able to be detected by noting when distributions of parameters change under uncertainty. Copyright © 2009 John Wiley & Sons, Ltd. [source] Modelling the chloride signal at Plynlimon, Wales, using a modified dynamic TOPMODEL incorporating conservative chemical mixing (with uncertainty)HYDROLOGICAL PROCESSES, Issue 3 2007T. Page Abstract The application of a modified version of dynamic TOPMODEL for two subcatchments at Plynlimon, Wales is described. Conservative chemical mixing within mobile and immobile stores has been added to the hydrological model in an attempt to simulate observed stream chloride concentrations. The model was not fully able to simulate the observed behaviour, in particular the short- to medium-term dynamics. One of the primary problems highlighted by the study was the representation of dry deposition and cloud-droplet-deposited chloride, which formed a significant part of the long-term chloride mass budget. Equifinality of parameter sets inhibited the ability to determine the effective catchment mixing volumes and coefficients or the most likely partition between occult mass inputs and chloride mass inputs determined by catchment immobile-store antecedent conditions. Some success was achieved, in as much as some aspects of the dynamic behaviour of the signal were satisfactorily simulated, although spectral analysis showed that the model could not fully reproduce the 1/f power spectra of observed stream chloride concentrations with its implications of a wide distribution of residence times for water in the catchment. Copyright © 2006 John Wiley & Sons, Ltd. [source] How to model shallow water-table depth variations: the case of the Kervidy-Naizin catchment, FranceHYDROLOGICAL PROCESSES, Issue 4 2005Jérôme Molénat Abstract The aim of this work is threefold: (1) to identify the main characteristics of water-table variations from observations in the Kervidy-Naizin catchment, a small catchment located in western France; (2) to confront these characteristics with the assumptions of the Topmodel concepts; and (3) to analyse how relaxation of the assumptions could improve the simulation of distributed water-table depth. A network of piezometers was installed in the Kervidy-Naizin catchment and the water-table depth was recorded every 15 min in each piezometer from 1997 to 2000. From these observations, the Kervidy-Naizin groundwater appears to be characteristic of shallow groundwaters of catchments underlain by crystalline bedrock, in view of the strong relation between water distribution and topography in the bottom land of the hillslopes. However, from midslope to summit, the water table can attain a depth of many metres, it does not parallel the topographic surface and it remains very responsive to rainfall. In particular, hydraulic gradients vary with time and are not equivalent to the soil surface slope. These characteristics call into question some assumptions that are used to model shallow lateral subsurface flow in saturated conditions. We investigate the performance of three models (Topmodel, a kinematic model and a diffusive model) in simulating the hourly distributed water-table depths along one of the hillslope transects, as well as the hourly stream discharge. For each model, two sets of parameters are identified following a Monte Carlo procedure applied to a simulation period of 2649 h. The performance of each model with each of the two parameter sets is evaluated over a test period of 2158 h. All three models, and hence their underlying assumptions, appear to reproduce adequately the stream discharge variations and water-table depths in bottom lands at the foot of the hillslope. To simulate the groundwater depth distribution over the whole hillslope, the steady-state assumption (Topmodel) is quite constraining and leads to unacceptable water-table depths in midslope and summit areas. Once this assumption is relaxed (kinematic model), the water-table simulation is improved. A subsequent relaxation of the hydraulic gradient (diffusive model) further improves water-table simulations in the summit area, while still yielding realistic water-table depths in the bottom land. Copyright © 2004 John Wiley & Sons, Ltd. [source] Use of caesium-137 data to evaluate SHETRAN simulated long-term erosion patterns in arable landsHYDROLOGICAL PROCESSES, Issue 10 2004Y. Norouzi Banis Abstract The caesium-137 method of quantifying soil erosion is used to provide field data for validating the capability of the SHETRAN modelling system for predicting long-term (30-year) erosion rates and their spatial variability. Simulations were carried out for two arable farm sites (area 3,5 ha) in central England for which average annual erosion rates of 6·5 and 10·4 t ha,1 year,1 had already been determined using caesium-137 measurements. These rates were compared with a range of simulated values representing the uncertainty in model output derived from uncertainty in the evaluation of model parameters. A successful validation was achieved in that the simulation range contained the measured rate at both sites, whereas the spatial variability was reproduced excellently at one site and partially at the other. The results indicate that, as the caesium-137 technique measures the erosion caused by all the processes acting at a site, it is relevant to hydrologically based models such as SHETRAN only if erosion by wind, agricultural activities and other processes not represented in the model are insignificant. The results also indicate a need to reduce the uncertainty in model parameter evaluation. More generally, the caesium-137 technique is shown to provide field data that improve the severity of the validation procedure (accounting for internal as well as outlet conditions) and that add spatial variability to magnitude as a condition for identifying unrealistic parameter sets when seeking to reduce simulation uncertainty. Copyright © 2004 John Wiley & Sons, Ltd. [source] Assessment of algorithms for the no-slip boundary condition in the lattice Boltzmann equation of BGK modelINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 12 2008Yong Kweon Suh Abstract Three kinds of algorithms for the lattice Boltzmann equation of the BGK model in the implementation of the no-slip boundary condition on the wall are assessed by using the analytical formula for the slip velocity of the fully developed pressure-driven channel flow. It is shown that the bounce-back algorithm results in the spatial accuracy of 1st order, except for the case when the wall is located at half way between the two grid lines. The interpolation scheme proposed by Yu et al. (Prog. Aerospace Sci. 2003; 39:329,367) and the similar one by Bouzidi et al. (Phys. Fluids 2001; 13(11):3452,3459) are of 2nd order, but the error increases quadratically with the relaxation time. The extrapolation scheme of Guo et al. (Phys. Fluids 2002; 14(6):2007,2010) is also shown to be of 2nd order, and the error level increases linearly with the relaxation time, but it turns out that this scheme is unstable for a certain range of parameter values. Numerical experiments with various parameter sets have been performed to obtain the stability diagram. Three algorithms are then applied to a circular-Couette flow and their performance is also studied in terms of the numerical accuracy and stability. Copyright © 2008 John Wiley & Sons, Ltd. [source] Performance analysis of an improved multi-carrier CDMA system under frequency-selective Rayleigh fading channelsINTERNATIONAL JOURNAL OF COMMUNICATION SYSTEMS, Issue 7 2003Hsiao-Hwa Chen Abstract In this article, an analytical method is proposed to study an improved orthogonal multi-carrier DS/CDMA system, which uses QPSK for both spreading and carrier modulations without redundant sub-carriers and time interleavers in each sub-channel. The article concerns in particular such a system and its performance under frequency-selective Rayleigh fading channels with various delay-power profiles. The bit error probabilities under varying multipath-diversity orders (using maximal ratio combing RAKE reception) and different numbers of resolvable multipaths are derived. It has been shown that the system, despite of its structural simplicity, performs well in mitigating frequency-selective fading. The performance is also evaluated taking into account various other parameter sets, such as numbers of users and sub-carriers, lengths of PN codes and the number of fingers in an RAKE receiver, etc. Copyright © 2003 John Wiley & Sons, Ltd. [source] Rules-of-thumb of implementing short electric band heaters (length to diameter ratio <1.5) for external heating of pipe flowsINTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 2 2002X. D. Chen Abstract Short electric band heaters (L/Di<1.5) are constructed for the ease of implementation in small scale heating applications. They are usually mounted side-by-side in series along the external wall of a pipe for heating the fluid within the pipe. There are no rules-of-thumb available about designing such a system to achieve good uniformity of the temperature profile at the pipe inner surface beforehand. Non-uniformity can cause preferential fouling at hotter spots. This study focuses on the axial uniformity of heating along a pipe inside which the heated fluid if flowing. The situation has been simplified a great deal in mathematical terms from the corresponding conventional conjugate problem considered previously due to the small temperature rise in the fluid flow through one section of the pipe which is heated by one band heater. Similarity parameter sets have been deduced and verified by numerical simulations. The worst scenario of non-uniformity for such short band heaters, that is when L/Di=1.5, is presented in this paper. This may be used for designing a system to minimize the non-uniformity in terms of choosing the right pipe material, percentage of heater wire coverage in the band heater, etc. Copyright © 2002 John Wiley & Sons, Ltd. [source] An improved nucleic acid parameter set for the GROMOS force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2005Thereza A. Soares Abstract Over the past decades, the GROMOS force field for biomolecular simulation has primarily been developed for performing molecular dynamics (MD) simulations of polypeptides and, to a lesser extent, sugars. When applied to DNA, the 43A1 and 45A3 parameter sets of the years 1996 and 2001 produced rather flexible double-helical structures, in which the Watson,Crick hydrogen-bonding content was more limited than expected. To improve on the currently available parameter sets, the nucleotide backbone torsional-angle parameters and the charge distribution of the nucleotide bases are reconsidered based on quantum-chemical data. The new 45A4 parameter set resulting from this refinement appears to perform well in terms of reproducing solution NMR data and canonical hydrogen bonding. The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 725,737, 2005 [source] A force-field description of short-range repulsions for high density alkane molecular dynamics simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2004Joseph M. Hayes Abstract The use of Buckingham (exp-6) van der Waals potentials in molecular dynamics (MD) simulations can quite successfully reproduce experimental thermodynamic data at low densities. However, they are less successful in producing a description of the repulsive regions of the potential energy surface (PES) that is in accord with the results of high-level ab initio computations. We show that Morse potentials can be parameterized to give excellent fits to both the attractive and repulsive regions of the PES. The best set of alkane van der Waals Morse function parameters reported to date for the description of nonbond repulsive interactions is presented, as determined by comparison with both ab initio and experimental results. C,C, H,H and C,H atom-pair potentials employing parameter sets based on the use of the geometric mean in the fitting procedure are found to be portable from methane to n- butane. Fitting to a combination of methane dimer interaction energies and forces from ab initio calculations yields parameter sets whose performance is superior to those determined from the interaction energies alone. Used in MD simulations, our newly developed parameter sets predict thermodynamic functions that show better agreement with experiment than those based on parameter sets in common use. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1953,1966, 2004 [source] PM3-compatible zinc parameters optimized for metalloenzyme active sitesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2004Edward N. Brothers Abstract Recent studies have shown that semiempirical methods (e.g., PM3 and AM1) for zinc-containing compounds are unreliable for modeling structures containing zinc ions with ligand environments similar to those observed in zinc metalloenzymes. To correct these deficiencies a reparameterization of zinc at the PM3 level was undertaken. In this effort we included frequency corrected B3LYP/6-311G* zinc metalloenzyme ligand environments along with previously utilized experimental data. Average errors for the heats of formation have been reduced from 46.9 kcal/mol (PM3) to 14.2 kcal/mol for this new parameter set, termed ZnB for "Zinc, Biological." In addition, the new parameter sets predict geometries for the Bacillus fragilis active site model and other zinc metalloenzyme mimics that are qualitatively in agreement with high-level ab initio results, something existing parameter sets failed to do. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1677,1692, 2004 [source] Molecular dynamics simulation of the hydrocarbon region of a biomembrane using a reduced representation modelJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2001Lewis Whitehead Abstract The development of a coarse-grained reduced-representation model of the hydrocarbon region of a biological membrane is reported. The potential is based on the popular Gay,Berne model of liquid crystals, and involves the linking of individual Gay,Berne ellipsoids by harmonic springs to form each hydrocarbon chain. Diffusion coefficients and order parameters have been calculated by molecular dynamics computer simulations for a range of parameter sets. The results clearly demonstrate the presence of a phase transition from an ordered low-temperature solid phase reminiscent of the L,, phase of phospholipids, to a high-temperature disordered phase reminiscent of the L, phase. Order parameters calculated for each layer of the model are consistent with the experimental segmental order parameters reported for dipalmitoyl phosphatidylcholine. The application of this model to the study of small molecule diffusion within the membrane core is proposed. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1622,1633, 2001 [source] | ||||||||||||||||