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Field Parameters (field + parameter)
Kinds of Field Parameters Selected AbstractsEffects of urbanization on stream water quality in the city of Atlanta, Georgia, USA,HYDROLOGICAL PROCESSES, Issue 20 2009Norman E. Peters Abstract A long-term stream water quality monitoring network was established in the city of Atlanta, Georgia during 2003 to assess baseline water quality conditions and the effects of urbanization on stream water quality. Routine hydrologically based manual stream sampling, including several concurrent manual point and equal width increment sampling, was conducted ,12 times annually at 21 stations, with drainage areas ranging from 3·7 to 232 km2. Eleven of the stations are real-time (RT) stations having continuous measures of stream stage/discharge, pH, dissolved oxygen, specific conductance, water temperature and turbidity, and automatic samplers for stormwater collection. Samples were analyzed for field parameters, and a broad suite of water quality and sediment-related constituents. Field parameters and concentrations of major ions, metals, nutrient species and coliform bacteria among stations were evaluated and with respect to watershed characteristics and plausible sources from 2003 through September 2007. Most constituent concentrations are much higher than nearby reference streams. Concentrations are statistically different among stations for several constituents, despite high variability both within and among stations. Routine manual sampling, automatic sampling during stormflows and RT water quality monitoring provided sufficient information about urban stream water quality variability to evaluate causes of water quality differences among streams. Fecal coliform bacteria concentrations of most samples exceeded Georgia's water quality standard for any water-usage class. High chloride concentrations occur at three stations and are hypothesized to be associated with discharges of chlorinated combined sewer overflows, drainage of swimming pool(s) and dissolution and transport during rainstorms of CaCl2, a deicing salt applied to roads during winter storms. One stream was affected by dissolution and transport of ammonium alum [NH4Al(SO4)2] from an alum-manufacturing plant; streamwater has low pH (<5), low alkalinity and high metals concentrations. Several trace metals exceed acute and chronic water quality standards and high concentrations are attributed to washoff from impervious surfaces. Published in 2009 by John Wiley & Sons, Ltd. [source] Extensions of the 3-Dimensional Plasma Transport Code E3DCONTRIBUTIONS TO PLASMA PHYSICS, Issue 1-3 2004A. Runov Abstract One important aspect of modern fusion research is plasma edge physics. Fluid transport codes extending beyond the standard 2-D code packages like B2-Eirene or UEDGE are under development. A 3-dimensional plasma fluid code, E3D, based upon the Multiple Coordinate System Approach and a Monte Carlo integration procedure has been developed for general magnetic configurations including ergodic regions. These local magnetic coordinates lead to a full metric tensor which accurately accounts for all transport terms in the equations. Here, we discuss new computational aspects of the realization of the algorithm. The main limitation to the Monte Carlo code efficiency comes from the restriction on the parallel jump of advancing test particles which must be small compared to the gradient length of the diffusion coefficient. In our problems, the parallel diffusion coefficient depends on both plasma and magnetic field parameters. Usually, the second dependence is much more critical. In order to allow long parallel jumps, this dependence can be eliminated in two steps: first, the longitudinal coordinate x3 of local magnetic coordinates is modified in such a way that in the new coordinate system the metric determinant and contra-variant components of the magnetic field scale along the magnetic field with powers of the magnetic field module (like in Boozer flux coordinates). Second, specific weights of the test particles are introduced. As a result of increased parallel jump length, the efficiency of the code is about two orders of magnitude better. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Fatigue-relevant stress field parameters of welded lap joints: pointed slit tip compared with keyhole notchFATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 9 2009P. LAZZARIN ABSTRACT The notch stress intensity factor (NSIF) based analytical frame is applied to the slit tips (or weld roots) of welded joints with inclusion of the T-stress component. This T-stress can be determined from FE models evaluating the ligament stresses close to the pointed slit tip. An alternative analytical frame is presented for the corresponding keyhole notches based on analytical solutions from the literature, which are applied to the ligament stresses. In the slit tip models, the mean local strain energy density (SED) with inclusion of the T-stress effect is determined analytically and numerically in comparison, using two different fatigue-relevant control radii,,R0= 0.28 mm and,R0= 0.15 mm, the former value well proven for thick-sheet welded joints made of structural steel. The latter smaller value is tentatively proposed for thin-sheet welded joints, in the direction suggested in the recent literature where a reduction of the microstructural support length for laser beam welds and resistance spot welds is recommended. The FEM-based and analytical stress concentration factors (SCF) for the lap joint keyhole model and also the SED values for the corresponding pointed slit tips are found to be in good agreement. The,J -integral consisting of the first and second component (the latter containing the T-stress) is compared with the corresponding SED values. [source] Stability of hippocampal place cell activity across the rat estrous cycle,HIPPOCAMPUS, Issue 2 2005Jennifer Tropp Abstract Findings from both in vitro and in vivo studies have shown that estrogen exerts pronounced effects on hippocampal morphology and physiology. The degree to which these molecular findings influence hippocampal processing in freely behaving animals is unclear. The present study assessed the effect of the estrous cycle on hippocampal place cells in naturally cycling rats during two behavioral states. Female Sprague-Dawley rats were trained to alternate on a U-shaped runway for food reinforcement. Single-unit recordings of hippocampal CA1 cells were conducted under two conditions: (1) at rest on a holder, and (2) running on the maze. Spatial firing characteristics of the cells were examined at different stages of the estrous cycle (i.e., diestrus, proestrus, and estrus). Specifically, information was collected on (1) mean firing rates; (2) basic place field parameters; and (3) changes in the firing dynamics of these cells (e.g., burst properties). The findings showed a decrease in mean firing rate on the maze during proestrus. However, other basic measures of spatial tuning and burst properties were unchanged. The current study suggests that there is relative stability of hippocampal place cells across the estrous cycle during a well-trained task. © 2004 Wiley-Liss, Inc. [source] Effects of urbanization on stream water quality in the city of Atlanta, Georgia, USA,HYDROLOGICAL PROCESSES, Issue 20 2009Norman E. Peters Abstract A long-term stream water quality monitoring network was established in the city of Atlanta, Georgia during 2003 to assess baseline water quality conditions and the effects of urbanization on stream water quality. Routine hydrologically based manual stream sampling, including several concurrent manual point and equal width increment sampling, was conducted ,12 times annually at 21 stations, with drainage areas ranging from 3·7 to 232 km2. Eleven of the stations are real-time (RT) stations having continuous measures of stream stage/discharge, pH, dissolved oxygen, specific conductance, water temperature and turbidity, and automatic samplers for stormwater collection. Samples were analyzed for field parameters, and a broad suite of water quality and sediment-related constituents. Field parameters and concentrations of major ions, metals, nutrient species and coliform bacteria among stations were evaluated and with respect to watershed characteristics and plausible sources from 2003 through September 2007. Most constituent concentrations are much higher than nearby reference streams. Concentrations are statistically different among stations for several constituents, despite high variability both within and among stations. Routine manual sampling, automatic sampling during stormflows and RT water quality monitoring provided sufficient information about urban stream water quality variability to evaluate causes of water quality differences among streams. Fecal coliform bacteria concentrations of most samples exceeded Georgia's water quality standard for any water-usage class. High chloride concentrations occur at three stations and are hypothesized to be associated with discharges of chlorinated combined sewer overflows, drainage of swimming pool(s) and dissolution and transport during rainstorms of CaCl2, a deicing salt applied to roads during winter storms. One stream was affected by dissolution and transport of ammonium alum [NH4Al(SO4)2] from an alum-manufacturing plant; streamwater has low pH (<5), low alkalinity and high metals concentrations. Several trace metals exceed acute and chronic water quality standards and high concentrations are attributed to washoff from impervious surfaces. Published in 2009 by John Wiley & Sons, Ltd. [source] Modeling dioxygen binding to the non-heme iron-containing enzymesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2006A. V. Nemukhin Abstract The structures and properties of the complexes formed upon binding the oxygen molecule to the iron sites in non-heme 2-oxoglutarate-dependent enzymes are characterized by QM(CASSCF)/MM and density functional theory (DFT) calculations. Molecular models for the calculations are constructed following the crystal structure of hypoxia-inducible factor asparaginyl hydroxylase (FIH-1). DFT calculations for the 37-atomic cluster have been carried out at the B3LYP(LANL2DZdp) level. The flexible effective fragment potential method is used as a combined quantum mechanical,molecular mechanical (QM/MM) technique to characterize the fragment of the enzymatic system, including 1,758 atoms in the MM part and 27 atoms in the QM part. In these calculations, the CASSCF(LANL2DZdp) approach is applied in the QM subsystem, and AMBER force field parameters are used in the MM subsystem. With both approaches, equilibrium geometry configurations have been located for different spin states of the system. In DFT calculations, the order of the states is as follows: septet, triplet (+7.7 kcal/mol), quintet (+10.7 kcal/mol). Geometry configurations correspond to the end-on structures with no evidences of electron transfer from Fe(II) to molecular oxygen. In contrast, QM(CASSCF)/MM calculations predict the quintet state as the lowest one, while the septet structure has slightly (<2 kcal/mol) higher energy, and the triplet state is considerably more energetic. In QM/MM calculations, in both quintet and septet states, the electronic configurations show considerable electron charge transfer from iron to oxygen, and the oxidation state of iron in the metal binding site can be characterized as Fe(III). © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2010Benjamin Waldher Abstract The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy-to-use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Michio Iwaoka Abstract Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like ,-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Development of the force field parameters for phosphoimidazole and phosphohistidineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Yuri A. Kosinsky Abstract Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule,a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1313,1321, 2004 [source] Specific force field parameters determination for the hybrid ab initio QM/MM LSCF methodJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2002Nicolas Ferré Abstract The pure quantum mechanics method, called Local Self-Consistent Field (LSCF), that allows to optimize a wave function within the constraint that some predefined spinorbitals are kept frozen, is discussed. These spinorbitals can be of any shape, and their occupation numbers can be 0 or 1. Any post-Hartree,Fock method, based on the restricted or unrestricted Hartree,Fock Slater determinant, and Kohn,Sham-based DFT method are available. The LSCF method is easily applied to hybrid quantum mechanics/molecular mechanics (QM/MM) procedure where the quantum and the classical parts are covalently bonded. The complete methodology of our hybrid QM/MM scheme is detailed for studies of macromolecular systems. Not only the energy but also the gradients are derived; thus, the full geometry optimization of the whole system is feasible. We show that only specific force field parameters are needed for a correct description of the molecule, they are given for some general chemical bonds. A careful analysis of the errors induced by the use of molecular mechanics in hybrid computation show that a general procedure can be derived to obtain accurate results at low computation effort. The methodology is applied to the structure determination of the crambin protein and to Menshutkin reactions between primary amines and chloromethane. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 610,624, 2002 [source] Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2001Tran Trung Tran Abstract When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high-resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least-square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X-ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010,1025, 2001 [source] Crystal field parameters of praseodymium in oxidesPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 9 2007P. Novák Abstract The crystal field parameters of the Pr4+ ion in PrO2 and PrBaO3 are calculated using the density of states projected on the 4f states of the Pr4+ ion. The orbital-dependent potential is used and the procedure involves an adjustable parameter ,f that determines the relative position of the center of the 4f levels. ,f can be estimated using the LDA + U method. For reasonable values of ,f the calculated crystal field parameters give a splitting close to the one observed. It is shown that the hybridization of the 4f states is important. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] In search of the Royal Ptolemaic Cemetery in central Alexandria, Egypt,the first contactARCHAEOLOGICAL PROSPECTION, Issue 3 2003St. P. Papamarinopoulos Abstract At Chatby in central Alexandria, Egypt, a team from the University of Patras conducted a detailed geophysical study as part of an investigation for locating the Royal Ptolemaic Cemetery. The exploration site is located in the Latin and Greek cemeteries in the southeast corner of the modern cemeteries of Alexandria. An area of 10,000,m2 was investigated down to a depth of 10,m. Gravity, electromagnetic prospecting, electrical, ground-penetrating radar and seismic methods were applied. The use of various methods allowed as much information from the subsurface as possible to be obtained and comparison of the data in order to enhance interpretation. Despite the increased geophysical noise present in such a highly urbanized environment, intelligent selection of field parameters, use of advanced processing techniques and specialized software made it possible to reveal important information from the subsurface data. Interpreted geophysical features may be related to buried archaeological structures at some locations of the area explored. Copyright © 2003 John Wiley & Sons, Ltd. [source] Brief exposure to a 50 Hz, 100 ,T magnetic field: Effects on reaction time, accuracy, and recognition memoryBIOELECTROMAGNETICS, Issue 3 2002John Podd Abstract The present study investigated both the direct and delayed effects of a 50 Hz, 100 ,T magnetic field on human performance. Eighty subjects completed a visual duration discrimination task, half being exposed to the field and the other half sham exposed. The delayed effects of this field were also examined in a recognition memory task that followed immediately upon completion of the discrimination task, Unlike our earlier studies, we were unable to find any effects of the field on reaction time and accuracy in the visual discrimination task. However, the field had a delayed effect on memory, producing a decrement in recognition accuracy. We conclude that after many years of experimentation, finding a set of magnetic field parameters and human performance measures that reliably yield magnetic field effects is proving elusive. Yet the large number of significant findings suggests that further research is warranted. Bioelectromagnetics 23:189,195, 2002. © 2002 Wiley-Liss, Inc. [source] Investigation of the Adsorption and Self Assembly of Isocyanide Derivatives on Au(111) SurfaceCHINESE JOURNAL OF CHEMISTRY, Issue 9 2007Jun-Hong Zhou Abstract The adsorption and self-assembly of isocyanide derivatives on Au(111) surface were investigated by density functional theory (DFT) and molecular dynamics simulation. The calculation for phenyl isocyanide by DFT was based on cluster and slab models. The self-assembled monolayers of 2-isocyanoazulene and 1,3-diethoxycarbonyl- 2-isocyanoazulene on Au(111) were simulated using Au-C force field parameters developed by us. It was found that the top site was the most preferred position, and the isocyanoazulene and its derivatives could form the ordered face to edge self-assembled monolayer on gold surface indeed, and the molecules stood on the gold surface vertically. [source] | ||||||||||||||||