bluuebunny/crossref_metadata_2025_split huggingface dataset:
Calibration of an oscillating nozzle‐type rainfall simulator
Authors: Yu Bofu , Ciesiolka Cyril A. A. , Langford Paul 
Published: December 2003

AbstractNozzle‐type rainfall simulators are commonly used in hydrologic and soil erosion research. Simulated rainfall intensity, originating from the nozzle, increases as the distance between the point of measurement and the source is decreased. Hence, rainfall measured using rain gauges would systematically overestimate the rainfall received at the ground level. A simple model was developed to adjust rainfall measured anywhere under the simulator to plot‐wide average rainfall at the ground level. Nozzle height, plot width, gauge diameter and height, and gauge location are required to compute this adjustment factor. Results from 15 runs at different rain intensities and durations, and with different rain gauge layouts, showed that a simple average of measured rain would overestimate the plot‐wide rain by about 20 per cent. Using the adjustment factor to convert measured rainfall for individual gauges before averaging improved the estimate of plot‐wide rainfall considerably. For the 15 runs considered, overall discrepancy between actual and measured rain is reduced to less than 1 per cent with a standard error of 0·97 mm. This model can be easily tested in the ﬁeld by comparing rainfall depths of different sized gauges. With the adjustment factor they should all give very similar values. Copyright © 2003 John Wiley & Sons, Ltd.
A contemporary winter ground thermal profile in the Lesotho highlands and implications for active and relict soil frost phenomena
Authors: Sumner Paul 
Published: December 2003

AbstractA 2 m deep ground thermal proﬁle is constructed from temperature data collected over the winter and spring of 2000 at 3220 m a.s.l. near the Thabana Ntlenyana summit (3482 m) in Lesotho, southern Africa. The zero isotherm is found to have penetrated to 0·16 m soil depth. Ground remained frozen at 0·05 m for a total of 79 days and for shorter periods at 0·02 m and 0·10 m. Diurnal freezing and thawing is restricted to the upper 0·10 m and conforms to the observed depth of active micro‐patterned ground found in the region. Holocene temperature depressions projected along the thermal proﬁle can account for freezing down to 0·45 to 0·65 m. Deeper sorting to 1 m, evident from relict patterned ground near the logger site, corresponds to at least a 2·5 °C temperature depression and such landforms are evidently pre‐Holocene. Projections indicate a seasonal freezing depth exceeding 2 m during the Pleistocene Last Glacial Maximum although the existence of permafrost appears unlikely. Copyright © 2003 John Wiley & Sons, Ltd.
Weathering control over geomorphology of supermature Proterozoic Delhi quartzites of India
Authors: Tripathi Jayant K. , Rajamani V. 
Published: December 2003

AbstractQuartz and quartzite are thought to be resistant as a mineral and a rock respectively; however, we have shown that the presence of small amounts of pyrite in the quartzites makes them vulnerable to weathering. We observe that weathering of Proterozoic quartzite in the semi‐arid conditions around Delhi proceeded from fractures towards the inside and produced weathering rinds. The chemical index of alteration (CIA), which is actually a measure of weathering of aluminosilicate minerals, increases from the core outwards, through the rinds. Although aluminosilicate minerals occur only as minor phases (<2 per cent), their weathering indicates a movement of the weathering front from the periphery towards the core. We have suggested a coupled mechanism in which the dissolution of pyrites by moving water produced a sulphate‐bearing acidic solution and ferrous iron, which reacted with aluminosilicate minerals and quartz, respectively. This initially makes the Delhi quartzite porous and subsequently friable. The total disintegration of grain to grain contacts imparted friability to this quartzite to produce silica sand. Subsequent physical erosion of loose sand, produced during rind development in the outermost zones, has given rise to features like tors, spheroids, gullies, cavities and small‐scale caves on these quartzites. Thus, the terrain has acquired ruggedness in semi‐arid conditions. Copyright © 2003 John Wiley & Sons, Ltd.
The causes of bedload pulses in a gravel channel: the implications of bedload grain‐size distributions
Authors: Cudden Judith R. , Hoey Trevor B. 
Published: December 2003

AbstractUnsteady bedload transport was measured in two c. 5 m wide anabranches of a gravel‐bed braided stream draining the Haut Glacier d'Arolla, Switzerland, during the 1998 and 1999 melt seasons. Bedload was directly sampled using 152 mm square Helley–Smith type samplers deployed from a portable measuring bridge, and independent transport rate estimates for the coarser size fractions were obtained from the dispersion of magnetically tagged tracer pebbles. Bedload transport time series show pulsing behaviour under both marginal (1998) and partial (1999) transport regimes. There are generally weak correlations between transport rates and shear stresses determined from velocity data recorded at the measuring bridge. Characteristic parameters of the bedload grain‐size distributions (D50, D84) are weakly correlated with transport rates. Analysis of full bedload grain‐size distributions reveals greater structure, with a tendency for transport to become less size selective at higher transport rates. The bedload time series show autoregressive behaviour but are difﬁcult to distinguish by this method. State–space plots, and associated measures of time‐series separation, reveal the structure of the time series more clearly. The measured pulses have distinctly different time‐series characteristics from those modelled using a one‐dimensional sediment routing model in which bed shear stress and grain size are varied randomly. These results suggest a mechanism of pulse generation based on irregular low‐amplitude bedforms, that may be generated in‐channel or may represent the advection of material supplied by bank erosion events. Copyright © 2003 John Wiley & Sons, Ltd.
Mineral accumulations induced by biological activity on granitic rocks in Qinghai Plateau, China
Authors: Arocena J. M. , Zhu L. P. , Hall K. 
Published: December 2003

AbstractFragments of weathered granitic rocks from the Kunlun Shan, Qinghai Plateau (China) were investigated to elucidate the inﬂuence of biotic crusts on the breakdown of granitic rocks in an alpine environment. Scanning electron microscopy with energy dispersive system and X‐ray diffractometry were used to describe the nature and properties of mineral accumulations on the rock surface. Results showed that organic salts such as calcium oxalate and calcium formate are associated with Aspicilia caesiocinera (Nyl.ex Malbr.) Arnold, Caloplaca sp., Xanthoria elegans (Link) Th.Fr., and Lecidea plana (Lahm) Nyl. Secondary accumulations of 2 : 1 clays minerals are found in A. caesiocinera while oxides of manganese are associated with X. elegans. Coatings of goethite (iron oxides) are believed to form from biological activity associated with the presence of hyphae and rodlet structures on the ﬂakes. Calcium oxalate crystallizes into several morphologies such as druse, hexagonal plates, and lenticular containing between 20 and 48 per cent calcium by weight. Calcium formate and iron oxide (goethite) occur together in the form of ‘red’ desert varnish. Observed ‘black’ coatings contain as much as 37 per cent manganese and 22 per cent iron. Clay accumulations have plate‐like morphology and contain c. 2 : 1 silicon to aluminium contents. We argue that organic acids from the activities of biotic crusts contribute to the breakdown of granitic rocks. Fungi accelerate the breakdown of granitic rocks through the growth of fungal hyphae along the 001 cleavage planes in primary chloritic minerals. Copyright © 2003 John Wiley & Sons, Ltd.
Resolution of the flow in clarifiers by using a stabilized finite element method
Authors: Vellando P. , Puertas J. , Colominas I. 
Published: December 2003

AbstractThe description of the flow that takes place in clarifiers and other wastewater treatment basins may be a powerful tool to attain an optimum design of these structures, in order to make the most of the wastewater treatment plant resources. Some authors have attempted so by making use of the potential flow or the Stokes equations. When these simplifications are used, an approximation of the flow for slow creeping conditions is obtained, but only the resolution of the all‐term‐including Navier–Stokes equations will allow us to detect the real streamlines and the vortices that show up for even very slow water flows. The use of the Navier–Stokes formulae as the governing equations involves the appearance of complex stability problems that do not show up for the previously mentioned simplifications. In the present work a stable finite element method for the resolution of the Navier–Stokes equations is presented, verified, and used in the resolution of some wastewater treatment flow problems with very interesting results. Copyright © 2004 John Wiley & Sons, Ltd.
Indirect boundary element method for unsteady linearized flow over prolate and oblate spheroids and hemispheroidal protuberances
Authors: Shatz Lisa F. 
Published: December 2003

AbstractThe indirect boundary element method was used to study the hydrodynamics of oscillatory viscous flow over prolate and oblate spheroids, and over hemispheroidal bodies hinged to a plate. Analytic techniques, such as spheroidal coordinates, method of images, and series representations, were used to make the numerical methods more efficient. A novel method for computing the hydrodynamic torque was used, since for oscillatory flow the torque cannot be computed directly from the weightings. Instead, a Green's function for torque was derived to compute the torque indirectly from the weightings. For full spheroids, the method was checked by comparing the results to exact solutions at low and high frequencies, and to results computed using the singularity method. For hemispheroids hinged to a plate, the method for low frequencies was checked by comparing the results to previous results, and to exact solutions at high frequencies. Copyright © 2004 John Wiley & Sons, Ltd.
Implementation and validation of a slender vortex filament code: Its application to the study of a four‐vortex wake model
Authors: Margerit D. , Brancher P. , Giovannini A. 
Published: December 2003

AbstractA computational code EZ‐vortex is developed for the motion of slender vortex filaments of closed or open shape. The integro‐differential equations governing the motion of the vortex centre lines are either the Callegari and Ting equations, which are the leading order solution of a matched asymptotic analysis, or equivalent forms of these equations. They include large axial velocity and nonsimilar profiles in the vortical cores. The fluid may be viscous or inviscid. This code is validated both against known solutions of these equations and results from linear stability analyses. The linear and non‐linear stages of a perturbed two‐vortex wake and of a four‐vortex wake model are then computed. Copyright © 2004 John Wiley & Sons, Ltd.
Euler solutions for aerodynamic inverse shape design
Authors: de Bortoli A. L. , de Quadros R. 
Published: December 2003

AbstractContributions to the aerodynamics development have to be involved to achieve an increase in quality, reducing time and computer costs. Therefore, this work develops an optimization method based on the finite volume explicit Runge–Kutta multi‐stage scheme with central spatial discretization in combination with multigrid and preconditioning. The multigrid approach includes local time‐stepping and residual smoothing. Such a method allows getting the goal of compressible and almost incompressible solution of fluid flows, having a rate of convergence almost independent from the Mach number. Numerical tests are carried out for the NACA 0012 and 0009 airfoils and three‐dimensional wings based on NACA profiles for Mach‐numbers ranging from 0.8 to 0.002 using the Euler equations. These calculations are found to compare favorably with experimental and numerical data available in the literature. Besides, it is worth pointing out that these results build on earlier ones when finding appropriate new three‐dimensional aerodynamical geometries. Copyright © 2004 John Wiley & Sons, Ltd.
Finite element analysis of filling stage in die‐casting process using marker surface method and adaptive grid refinement technique
Authors: Jeong J. H. , Yang D. Y. 
Published: December 2003

AbstractThe marker surface method and the adaptive grid refinement technique have been applied to the three‐dimensional (3‐D) finite element analysis of the filling stage in the die‐casting process. Especially, the marker surface plugging technique and the marker surface regeneration technique incorporated in the marker surface method have been proposed for the efficient analysis of 3‐D practical problems. Through the marker surface plugging technique, new parts of marker surface are effective lycreated in order to eliminate the gaps between the parts of marker surface or between the edge of marker surface and cavity wall. By using the marker surface regeneration technique, the marker surface including a great number of marker elements is recreated on the basis of its original shape in order to decrease the number of marker elements and computational time. A3‐D example used as the benchmark test and a typical industrial problem of the die‐casting process have been analysed. The numerical results have been in good agreement with the experimental results and the efficiency of the adaptive grid refinement technique has been verified. It has been shown that the proposed techniques incorporated in the marker surface method and the adaptive grid refinement technique can be effectively applied to general industrial problems. Copyright © 2004 John Wiley & Sons, Ltd.
Krylov subspace accelerated inexact Newton method for linear and nonlinear equations
Authors: Harrison Robert J. 
Published: December 2003

AbstractA Krylov subspace accelerated inexact Newton (KAIN) method for solving linear and nonlinear equations is described, and its relationship to the popular direct inversion in the iterative subspace method [DIIS; Pulay, P., Chem Phys Lett 1980, 393, 73] is analyzed. The two methods are compared with application to simple test equations and the location of the minimum energy crossing point of potential energy surfaces. KAIN is no more complicated to implement than DIIS, but can accommodate a wider variety of preconditioning and performs substantially better with poor preconditioning. With perfect preconditioning, KAIN is shown to be very similar to DIIS. For these reasons, KAIN is recommended as a replacement for DIIS. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 328–334, 2004
A simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function
Authors: Bachler Vinzenz 
Published: December 2003

AbstractWe devise and apply a simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function. These bonding schemes are close to resonance structures drawn by chemists. Firstly, a CASSCF wave function is computed. Secondly, the CASSCF computation is repeated but now the delocalized complete active space MOs are substituted by Weinhold's localized natural atomic orbitals. In this way the original CASSCF wave function is represented by a sequence of Slater determinants composed of localized natural atomic orbitals. Thus, a standard CASSCF wave function can be reinterpreted in terms of a local picture. To test the method we obtain localized bonding schemes and their weights for the ground and the π–π* excited state of ethylene. Moreover, bonding schemes and their weights are derived for the ground, the 11Bu, and the 21Ag π–π* excited states oftrans‐butadiene. The large weight bonding schemes are shown to be a qualitative indicator for the known photochemistry of butadiene. The remarkable stability of the Arduengo carbene is discussed by obtaining bonding schemes that indicate a stabilizing delocalization of the π electrons. We illustrate that the large weight bonding schemes are in line with the observed reactivity of the Arduengo carbene. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 343–367, 2004
New developments in the symmetry‐adapted algorithm of the Polarizable Continuum Model
Authors: Frediani Luca , Cammi Roberto , Pomelli Christian S. , Tomasi Jacopo , Ruud Kenneth 
Published: December 2003

AbstractWe present recent developments in the symmetry implementation of the Polarizable Continuum Model (PCM). The structure of the matrix, which defines the PCM solvent response, is examined, and we demonstrate how this matrix can be transformed to a block diagonal form where each block belongs to different irreducible representations of the molecular point group. This development is especially important at the Multi‐configurational Self‐Consistent Field (MCSCF) level where symmetry is needed to avoid problems with symmetry breaking in the wave function and facilitate the optimization of electronic excited states. Moreover, although only the totally symmetric part of the solvent interaction is needed for energy calculations, in response or perturbation theory calculations of molecular properties, other irreps play an important role and the classification of solvent interaction terms by irrep is, therefore, desirable. In addition, the use of symmetry reduces the computational cost. The implementation presented here is illustrated with a series of calculations of absorption and emission processes in solution on the diazines pyrazine, pyrimidine, and pyridazine. These calculations allow us to illustrate both formal aspects of the implementation such as the choice of active spaces based on orbital symmetry as well as practical aspects such as the speed‐up of the calculation. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 375–385, 2004
QM/MM study of aqueous solvation of the uranyl fluoride [UO2F] complex
Authors: Infante Ivan , Visscher Lucas 
Published: December 2003

AbstractThe aqueous solvation of the uranylfluoride complex [UO2F] was studied using full quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methods. Inclusion of a complete first solvation shell was found necessary to reproduce the experimentally observed heptacoordination of uranium. An efficient and accurate computational model is proposed that consists of structure optimization of the coordinated uranium complex as QM region, followed by single‐point full QM calculations to compute relative energies. This method is proven feasible for studies of large solvated actinide complexes. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 386–392, 2004
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment
Authors: Cecchini Marco , Kolb Peter , Majeux Nicolas , Caflisch Amedeo 
Published: December 2003

AbstractAn improved version of the fragment‐based flexible ligand docking approach SEED–FFLD is tested on inhibitors of human immunodeficiency virus type 1 protease, human α‐thrombin and the estrogen receptor β. The docking results indicate that it is possible to correctly reproduce the binding mode of inhibitors with more than ten rotatable bonds if the strain in their covalent geometry upon binding is not large. A high degree of convergence towards a unique binding mode in multiple runs of the genetic algorithm is proposed as a necessary condition for successful docking. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 412–422, 2004
Time‐reversible always stable predictor–corrector method for molecular dynamics of polarizable molecules
Authors: Kolafa Jiří 
Published: December 2003

AbstractAn improved method for classic molecular dynamics of polarizable molecules is proposed. The method uses a predictor, one evaluation of the electrostatic field per integration step, and relaxation (damping). The self‐consistent solution is approximated with error of the second order (with respect to the timestep). The time reversibility (long‐time energy conservation) error is of the (2n − 1)th order, where n is the predictor length. The method is easy to implement, efficient, accurate, and suitable for any model of polarizability. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 335–342, 2004
Calculation of affinities of peptides for proteins
Authors: Donnini Serena , Juffer André H. 
Published: December 2003

AbstractSeveral methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein–ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein–ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein–ligand complexes were employed for an all‐atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all‐atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all‐atom approach to preserve electroneutrality. The various methods are further judged upon their merits. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 393–411, 2004
Class I ribonucleotide reductase revisited: The effect of removing a proton on Glu441
Authors: Pelmenschikov Vladimir , Cho Kyung‐Bin , Siegbahn Per E. M. 
Published: December 2003

AbstractThe substrate mechanism of class I ribonucleotide reductase has been revisited using the hybrid density functional B3LYP method. The molecular model used is based on the X‐ray structure and includes all the residues of the R1 subunit commonly considered in the RNR substrate conversion scheme: Cys439 initiating the reaction as a thiyl radical, the redox‐active cysteines Cys225 and Cys462, and the catalytically important Glu441 and Asn437. In contrast to previous theoretical studies of the overall mechanism, Glu441 is added as an anion. All relevant transition states have been optimized, including one where an electron is transferred 8 Å from the disulfide to the substrate simultaneously with a proton transfer from Glu441. The calculated barrier for this step is 19.1 kcal/mol, which can be compared to the rate‐limiting barrier indicated by experiments of about 17 kcal/mol. Even though the calculated barrier is somewhat higher than the experimental limit, the discrepancy is within the normal error bounds of B3LYP. The suggestion from the present modeling study is thus that a protonated Glu441 does not need to be present at the active site from the beginning of the catalytic cycle. However, the previously suggested mechanism with an initial protonation of Glu441 cannot be ruled out, because even with the cost added for protonation of Glu441 with a typical pKa of 4, the barrier for that mechanism is lower than the one obtained for the present mechanism. The results are compared to experimental results and suggestions. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 311–321, 2004