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Scaling Factor (scaling + factor)
Selected AbstractsThree-Dimensional Protein,Ligand Interaction Scaling of Two-Dimensional FingerprintsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2009Lu Tan We introduce a computational scaling methodology that utilizes protein,ligand interaction information extracted from complex crystal structures to enrich similarity searching using structural fingerprints with compound class-specific information. Scaling factors are derived to emphasize fingerprint bit positions that result from interacting fragments of bound ligands and correspond to frequently occurring structural features. Through interaction-based scaling, this information is transferred to standard fingerprints of multiple reference compounds. In systematic search calculations, fingerprints scaled on the basis of three-dimensional information are found to produce higher recall rates of active compounds than alternative types of scaled and non-scaled fingerprints. [source] Perspective-aware cartoon clips synthesisCOMPUTER ANIMATION AND VIRTUAL WORLDS (PREV: JNL OF VISUALISATION & COMPUTER ANIMATION), Issue 3-4 2008Yueting Zhuang Abstract In this paper we propose an approach, which allows the users to synthesize cartoon clips according to the perspective of the background image. In order to construct the cartoons smoothly, the character's edge distance and motion direction distance are demonstrated to be the factors affecting the human perception in similarity evaluation, and utilized in cartoon clips synthesis. When applying the generated cartoons to the background image, in which the perspective exists, the size of the character is coordinated according to the scaling factor calculated from the vanishing line. The experiment results demonstrate that our approach can synthesize the cartoon clips more smoothly compared with other single frame reusing strategies. The generated cartoons, which are applied to the background image, can be accepted by the human perception well. Copyright © 2008 John Wiley & Sons, Ltd. [source] Gelifluction: viscous flow or plastic creep?EARTH SURFACE PROCESSES AND LANDFORMS, Issue 12 2003Charles Harris Abstract This paper reports results from two scaled centrifuge modelling experiments, designed to simulate thaw-related geli,uction. A planar 12° prototype slope was modelled in each experiment, using the same natural ,ne sandy silt soil. However two different scales were used. In Experiment 1, the model scale was 1/10, tested in the centrifuge at 10 gravities (g) and in Experiment 2, the scale was 1/30, tested at 30 g. Centrifuge scaling laws indicate that the time scaling factor for thaw consolidation between model and prototype is N2, where N is the number of gravities under which the model was tested. However, the equivalent time scaling for viscous ,ow is 1/1. If geli,uction is a viscosity-controlled ,ow process, scaling con,icts will therefore arise during centrifuge modelling of thawing slopes, and rates of displacement will not scale accurately to the prototype. If, however, no such scaling con,icts are observed, we may conclude that geli,uction is not controlled by viscosity, but rather by elasto-plastic soil deformation in which frictional shear strength depends on effective stress, itself a function of the thaw consolidation process. Models were saturated, consolidated and frozen from the surface downwards on the laboratory ,oor. The frozen models were then placed in the geotechnical centrifuge and thawed from the surface down. Each model was subjected to four freeze,thaw cycles. Soil temperatures and pore water pressures were monitored, and frost heave, thaw settlement and downslope displacements measured. Pore water pressures, displacement rates and displacement pro,les re,ecting accumulated shear strain, were all similar at the two model scales and volumetric soil transport per freeze,thaw cycle, when scaled to prototype, were virtually identical. Displacement rates and pro,les were also similar to those observed in earlier full-scale laboratory ,oor experiments. It is concluded therefore that the modelled geli,uction was not a time-dependent viscosity-controlled ,ow phenomenon, but rather elasto-plastic in nature. A ,rst approximation ,,ow' law is proposed, based on the ,Cam Clay' constitutive model for soils. Copyright © 2003 John Wiley & Sons, Ltd. [source] Size-dependent species-area relationships in benthos: is the world more diverse for microbes?ECOGRAPHY, Issue 3 2002Andrey I. Azovsky Using original and literature data on species richness, I compared the species-area relations for 5 different size classes of the Arctic benthos: macrofauna sensu lato, polychaetes, nematodes, ciliates and diatom algae. The data pool covered a wide range of areas from single samples to the whole seas. Both the slopes and intercepts of the curves depended significantly on the logarithm of the mean body size of the group. The number of small species (ciliates and diatom algae) showed relatively higher local diversity but increased more slowly with the area than the number of larger ones. Thus, both ,- and ,-components of species diversity of the marine benthos were size-dependent. As a consequence, the actual relations between number of species and their physical size are spatially scale-dependent: there are many more species of smaller size classes in any one local community, but at a global scope the situation changes drastically. The possible reasons are discussed, including dispersal efficiency, rates of speciation and size-dependent perception of environmental heterogeneity. Body size is suggested to be the important scaling factor in manifestation of so-called "general ecological laws". [source] Estimation of the phosphorus sorption capacity of acidic soils in IrelandEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 3 2001R. O. Maguire Summary The test for the degree of phosphorus (P) saturation (DPS) of soils is used in northwest Europe to estimate the potential of P loss from soil to water. It expresses the historic sorption of P by soil as a percentage of the soil's P sorption capacity (PSC), which is taken to be , (Alox + Feox), where Alox and Feox are the amounts of aluminium and iron extracted by a single extraction of oxalate. All quantities are measured as mmol kg soil,1, and a value of 0.5 is commonly used for the scaling factor , in this equation. Historic or previously sorbed P is taken to be the quantity of P extracted by oxalate (Pox) so that DPS = Pox/PSC. The relation between PSC and Alox, Feox and Pox was determined for 37 soil samples from Northern Ireland with relatively large clay and organic matter contents. Sorption of P, measured over 252 days, was strongly correlated with the amounts of Alox and Feox extracted, but there was also a negative correlation with Pox. When PSC was calculated as the sum of the measured sorption after 252 days and Pox, the multiple regression of PSC on Alox and Feox gave the equation PSC = 36.6 + 0.61 Alox+,0.31 Feox with a coefficient of determination (R2) of 0.92. The regression intercept of 36.6 was significantly greater than zero. The 95% confidence limits for the regression coefficients of Alox and Feox did not overlap, indicating a significantly larger regression coefficient of P sorption on Alox than on Feox. When loss on ignition was employed as an additional variable in the multiple regression of PSC on Alox and Feox, it was positively correlated with PSC. Although the regression coefficient for loss on ignition was statistically significant (P <,0.001), the impact of this variable was small as its inclusion in the multiple regression increased R2 by only 0.028. Values of P sorption measured over 252 days were on average 2.75 (range 2.0,3.8) times greater than an overnight index of P sorption. Measures of DPS were less well correlated with water-soluble P than either the Olsen or Morgan tests for P in soil. [source] A geomorphological explanation of the unit hydrograph conceptHYDROLOGICAL PROCESSES, Issue 4 2004C. Cudennec Abstract The water path from any point of a basin to the outlet through the self-similar river network was considered. This hydraulic path was split into components within the Strahler ordering scheme. For the entire basin, we assumed the probability density functions of the lengths of these components, reduced by the scaling factor, to be independent and isotropic. As with these assumptions, we propose a statistical physics reasoning (similar to Maxwell's reasoning) that considers a hydraulic length symbolic space, built on the self-similar lengths of the components. Theoretical expressions of the probability density functions of the hydraulic length and of the lengths of all the components were derived. These expressions are gamma laws expressed in terms of simple geomorphological parameters. We validated our theory with experimental observations from two French basins, which are different in terms of size and relief. From the comparisons, we discuss the relevance of the assumptions and show how a gamma law structure underlies the river network organization, but under the influence of a strong hierarchy constraint. These geomorphological results have been translated into travel time probability density functions, through the hydraulic linear hypothesis. This translation provides deterministic explanations of some famous a priori assumptions of the unit hydrograph and the geomorphological unit hydrograph theories, such as the gamma law general shape and the exponential distribution of residence time in Strahler states. Copyright © 2004 John Wiley & Sons, Ltd. [source] Modeling and simulation of bioheat transfer in the human eye using the 3D alpha finite element method (,FEM)INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 8 2010Eric Li Abstract Computational modeling is an effective tool for the detection of eye abnormalities and a valuable assistant to hyperthermia treatments. In all these diagnoses and treatments, predicting the temperature distribution accurately is very important. However, the standard finite element method (FEM) currently used for such purposes has strong reliance on element meshes and the discretized system exhibits the so-called ,overly stiff' behavior. To overcome this shortcoming, this paper formulates an alpha finite element method (,FEM) to compute two-dimensional (2D) and three-dimensional (3D) bioheat transfer in the human eyes. The ,FEM can produce much more accurate results using triangular (2D) and tetrahedron (3D) elements that can be generated automatically for complicated domains and hence is particularly suited for modeling human eyes. In the ,FEM, a scaling factor ,,[0, 1] is introduced to combine the ,overly stiff' FEM model and ,overly soft' node-based finite element method (NS-FEM) model. With a properly chosen ,, the ,FEM can produce models with very ,close-to-exact' stiffness of the continuous system. Numerical results have shown that the present method gives much more accurate results compared with the standard FEM and the NS-FEM. Copyright © 2010 John Wiley & Sons, Ltd. [source] Estimating time dependent O-D trip tables during peak periodsJOURNAL OF ADVANCED TRANSPORTATION, Issue 3 2000Srinivas S. Pulugurtha Intelligent transportation systems (ITS) have been used to alleviate congestion problems arising due to demand during peak periods. The success of ITS strategies relies heavily on two factors: 1) the ability to accurately estimate the temporal and spatial distribution of travel demand on the transportation network during peak periods, and, 2) providing real-time route guidance to users. This paper addresses the first factor. A model to estimate time dependent origin-destination (O-D) trip tables in urban areas during peak periods is proposed. The daily peak travel period is divided into several time slices to facilitate simulation and modeling. In urban areas, a majority of the trips during peak periods are work trips. For illustration purposes, only peak period work trips are considered in this paper. The proposed methodology is based on the arrival pattern of trips at a traffic analysis zone (TAZ) and the distribution of their travel times. The travel time matrix for the peak period, the O-D trip table for the peak period, and the number of trips expected to arrive at each TAZ at different work start times are inputs to the model. The model outputs are O-D trip tables for each time slice in the peak period. 1995 data for the Las Vegas metropolitan area are considered for testing and validating the model, and its application. The model is reasonably robust, but some lack of precision was observed. This is due to two possible reasons: 1) rounding-off, and, 2) low ratio of total number of trips to total number of O-D pair combinations. Hence, an attempt is made to study the effect of increasing this ratio on error estimates. The ratio is increased by multiplying each O-D pair trip element with a scaling factor. Better estimates were obtained. Computational issues involved with the simulation and modeling process are discussed. [source] Assessing impacts of large herbivores on shrubs: tests of scaling factors for utilization rates from shoot-level measurementsJOURNAL OF APPLIED ECOLOGY, Issue 1 2007DANIELLE M. BILYEU Summary 1Accurate methods for estimating the intensity of browsing by herbivores are fundamental to understanding the ecology of shrub communities. Quantifying browse utilization on shrubs at large scales is difficult because shrubs have complex, spatially variable growth forms. Most existing methods estimate browsing rate at the scale of linear current-year shoots or twigs. How such fine-scale estimates relate to the proportion of current-year growth consumed from whole plants or plots is often unknown. The relationship is likely to be complex because herbivores selectively browse more productive plants and plant parts. 2Using a clipping experiment designed to mimic elk Cervus elaphus browsing, we quantified how utilization estimates at the scale of individual current-year shoots of two willow species, Salix bebbiana and Salix geyeriana, relate to actual mass removed at the scale of rooted stems. Three approaches to scaling were examined: (i) taking an average, (ii) multiplying by the proportion of shoots clipped and (iii) multiplying by a novel scaling factor that weights utilization by productivity. To address how to scale-up from stems to plots, we applied the most accurate stem-level method to elk-browsed willow and compared plot-level estimates by two scaling approaches. 3In scaling from shoots to stems, the novel scaling factor was most successful and resulted in accurate estimates for up to c. 45% of current annual growth clipped. In scaling from the stem to the plot, elk preference for more productive stems caused a simple average of stem-level utilization to differ from a productivity-weighted average by 15%. 4Synthesis and applications. In order to reflect accurately the proportion of biomass consumed at a whole-plant level, fine-scale estimates of utilization should be weighted by an estimate of pre-browse productivity, as this is mathematically equivalent to summing pre-browse and post-browse mass before calculating the proportion consumed. In developing methods to estimate utilization at plot scales, an important consideration is the choice of sampling unit, which should be both amenable to unbiased sampling and tractable in terms of measuring productivity. [source] Ontogenic changes in the allometric scaling of the mass and length relationship in Sprattus sprattusJOURNAL OF FISH BIOLOGY, Issue 3 2005M. A. Peck An analysis of mass (M) and standard length (LS) data for larval, juvenile and adult sprat (Sprattus sprattus; Clupeidae) revealed marked changes in the allometric scaling factor (b in ). For sprat <44 mm LS, b was 5·0, whereas in larger juveniles and adults, b was c. 3·4 indicating a relatively protracted metamorphic period for this species. [source] Growth of Self-Similar GraphsJOURNAL OF GRAPH THEORY, Issue 3 2004B. Krön Abstract Locally finite self-similar graphs with bounded geometry and without bounded geometry as well as non-locally finite self-similar graphs are characterized by the structure of their cell graphs. Geometric properties concerning the volume growth and distances in cell graphs are discussed. The length scaling factor , and the volume scaling factor , can be defined similarly to the corresponding parameters of continuous self-similar sets. There are different notions of growth dimensions of graphs. For a rather general class of self-similar graphs, it is proved that all these dimensions coincide and that they can be calculated in the same way as the Hausdorff dimension of continuous self-similar fractals: . © 2004 Wiley Periodicals, Inc. J Graph Theory 45: 224,239, 2004 [source] Prediction of human pharmacokinetics , improving microsome-based predictions of hepatic metabolic clearanceJOURNAL OF PHARMACY AND PHARMACOLOGY: AN INTERNATI ONAL JOURNAL OF PHARMACEUTICAL SCIENCE, Issue 10 2007Urban Fagerholm Physiologically based methods generally perform poorly in predicting in-vivo hepatic CL (CLH) from intrinsic clearance (CLint) in microsomes in-vitro and unbound fraction in blood (fu,bl). Various strategies to improve the predictability have been developed, and inclusion of an empirical scaling factor (SF) seems to give the best results. This investigation was undertaken to evaluate this methodology and to find ways to improve it further. The work was based on a diverse data set taken from Ito and Houston (2005). Another objective was to evaluate whether rationalization of CLH predictions can be made by replacing blood/plasma-concentration ratio (Cbl/Cpl) measurements with SFs. There were apparently no or weak correlations between prediction errors and lipophilicity, permeability (compounds with low permeability missing in the data set) and main metabolizing CYP450s. The use of CLint class (high/low) and drug class (acid/base/neutral) SFs (the CD-SF method) gives improved and reasonable predictions: 1.3-fold median error (an accurate prediction has a 1-fold error), 76% within 2-fold-error, and a median absolute rank ordering error of 2 for CLH (n = 29). This approach is better than the method with a single SF. Mean (P < 0.05) and median errors, fraction within certain error ranges, higher percentage with most accurate predictions, and ranking were all better, and 76% of predictions were more accurate with this new method. Results are particularly good for bases, which generally have higher CLH and the potential to be incorrectly selected/rejected as candidate drugs. Reasonable predictions of fu,bl can be made from plasma fu (fu,pl) and empirical blood cell binding SFs (B-SFs; 1 for low fu,pl acids; 0.62 for other substances). Mean and median fu,bl prediction errors are negligible. The use of the CD-SF method with predicted fu,bl (the BCD-SF method) also gives improved and reasonable results (1.4-fold median error; 66% within 2-fold-error; median absolute rank ordering error = 1). This new empirical approach seems sufficiently good for use during the early screening; it gives reasonable estimates of CLH and good ranking, which allows replacement of Cbl/Cpl measurements by a simple equation. [source] Spectroscopic and computational studies on self-assembly complexes of bis(pyrrol-2- ylmethyleneamine) ligands linked by alkyl spacers with Cu(II)JOURNAL OF RAMAN SPECTROSCOPY, Issue 5 2007Wei Li Abstract Bis(pyrrol-2-ylmethyleneamine) ligands and their mononuclear monomeric and dinuclear dimeric self-assembly complexes with Cu(II) were investigated by means of IR and Raman spectroscopies and density functional theory. The ground-state geometries were calculated by using the BeckeLeeYangParr composite exchange-correlation functional (B3LYP) and a combined basis set (LanL2DZ for Cu; 6,31G(d) for C, H, N), and they were compared with the single-crystal X-ray diffraction (XRD) structures. The DFT-calculated CuN bond lengths are generally higher by 0.001,0.040 Å than those determined through XRD. The vibrational spectra were also calculated at the same level of theory for the optimized geometries. The calculated wavenumbers were scaled by a uniform scaling factor and compared with the experimental fundamentals. The predicted spectra are in good agreement with the experimental ones with the deviations generally less than 30 cm,1. In comparison with the spectra of the ligands, the coordination effect shifts the ,(CN) wavenumber by about 50 cm,1 toward a lower value. Because of the weak intermolecular CH···Cu hydrogen bond, the CuN stretching mode is shifted toward a lower wavenumber. Copyright © 2006 John Wiley & Sons, Ltd. [source] Scaling of one-shot oscillation images with a reference data setJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2004Kunio Hirata By combining a least-squares procedure with the program MOSFLM, a program SCLONE has been developed which processes diffraction images that do not contain serial oscillation images and may have a few or no full reflections. After each image was processed by MOSFLM, the partialities and structure amplitudes of the reflections were estimated using a least-squares method to refine the scaling factor, the relative temperature factor, the mosaic spread, cell constants, and missetting angles for each independent image. The SCLONE calculation significantly improved the quality of the intensities from the reflections obtained by the initial MOSFLM calculation and crystal structural refinement confirmed the improvement. The SCLONE calculation indicated that the reflection of the present crystal had a rocking curve that was steeper at the middle of the profile and more gradual at both ends of the profile than that assumed in the program MOSFLM. [source] A stabilized Hermite spectral method for second-order differential equations in unbounded domainsNUMERICAL METHODS FOR PARTIAL DIFFERENTIAL EQUATIONS, Issue 5 2007Heping Ma Abstract A stabilized Hermite spectral method, which uses the Hermite polynomials as trial functions, is presented for the heat equation and the generalized Burgers equation in unbounded domains. In order to overcome instability that may occur in direct Hermite spectral methods, a time-dependent scaling factor is employed in the Hermite expansions. The stability of the scheme is examined and optimal error estimates are derived. Numerical experiments are given to confirm the theoretical results.© 2007 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007 [source] Multiresolution of quasicrystal diffraction spectraACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009Avi Elkharrat A method for analyzing and classifying two-dimensional pure point diffraction spectra (i.e. a set of Bragg peaks) of certain self-similar structures with scaling factor , > 1, such as quasicrystals, is presented. The two-dimensional pure point diffraction spectrum , is viewed as a point set in the complex plane in which each point is assigned a positive number, its Bragg intensity. Then, by using a nested sequence of self-similar subsets called ,-lattices, we implement a multiresolution analysis of the spectrum ,. This analysis yields a partition of , simultaneously in geometry, in scale and in intensity (the `fingerprint' of the spectrum, not of the diffracting structure itself). The method is tested through numerical explorations of pure point diffraction spectra of various mathematical structures and also with the diffraction pattern of a realistic model of a quasicrystal. [source] Reliable State Feedback Control Synthesis For Uncertain Linear SystemsASIAN JOURNAL OF CONTROL, Issue 2 2003Guang-Hong Yang ABSTRACT This paper is concerned with the problem of designing reliable state- feedback control for a class of uncertain linear systems with norm bounded uncertainty. A procedure for designing reliable state-feedback control is presented for the case of actuator faults that can be modeled by a scaling factor. In the design, the performance of the normal system (without fault) is optimized, as the considered system operates under the normal condition most of the time. In addition, when actuator faults occur, the closed-loop system retains robust stability and satisfies a known quadratic performance bound. A numerical example is provided to illustrate the effectiveness of the proposed design method. [source] Scaling of spectral displacement ordinates with damping ratiosEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 2 2005Julian J. Bommer Abstract The next generation of seismic design codes, especially those adopting the framework of performance-based design, will include the option of design based on displacements rather than forces. For direct displacement-based design using the substitute structure approach, the spectral ordinates of displacement need to be specified for a wide range of response periods and for several levels of damping. The code displacement spectra for damping values higher than the nominal value of 5% of critical will generally be obtained, as is the case in Eurocode 8 and other design codes, by applying scaling factors to the 5% damped ordinates. These scaling factors are defined as functions of the damping ratio and, in some cases, the response period, but are independent of the nature of the expected ground shaking. Using both predictive equations for spectral ordinates at several damping levels and stochastic simulations, it is shown that the scaling factors for different damping levels vary with magnitude and distance, reflecting a dependence of the scaling on the duration of shaking that increases with the damping ratio. The options for incorporating the influence of this factor into design code specifications of displacement response spectra are discussed. Copyright © 2004 John Wiley & Sons, Ltd. [source] A geometrically and materially non-linear piezoelectric three-dimensional-beam finite element formulation including warping effectsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 5 2008A. Butz Abstract This paper is concerned with a three-dimensional piezoelectric beam formulation and its finite element implementation. The developed model considers geometrically and materially non-linear effects. An eccentric beam formulation is derived based on the Timoshenko kinematics. The kinematic assumptions are extended by three additional warping functions of the cross section. These functions follow from torsion and piezoelectrically induced shear deformations. The presented beam formulation incorporates large displacements and finite rotations and allows the investigation of stability problems. The finite element model has two nodes with nine mechanical and five electrical degrees of freedom. It provides an accurate approximation of the electric potential, which is assumed to be linear in the direction of the beam axis and quadratic within the cross section. The mechanical degrees of freedom are three displacements, three rotations and three scaling factors for the warping functions. The latter are computed in a preprocess by solving a two-dimensional in-plane equilibrium condition with the finite element method. The gained warping patterns are considered within the integration through the cross section of the beam formulation. With respect to material non-linearities, which arise in ferroelectric materials, the scalar Preisach model is embedded in the formulation. This model is a mathematical model for the general description of hysteresis phenomena. Its application to piezoelectric materials leads to a phenomenological model for ferroelectric hysteresis effects. Here, the polarization direction is assumed to be constant, which leads to unidirectional constitutive equations. Some examples demonstrate the capability of the proposed model. Copyright © 2008 John Wiley & Sons, Ltd. [source] Improvement of scale factors for harmonic vibrational frequency calculations using new polarization functionsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2008Anibal Sierraalta Abstract Density functional calculations were carried to improve the calculated CO vibrational frequencies for transition metal carbonyls. Two types of density functionals were studied, hybrid and generalized-gradient methods. Using the simplex optimization method, new polarization functions for C and O atoms were obtained. With these new optimized functions, new scaling factors were obtained. The results reveal that, with the new polarization functions, the agreement between the calculated and the experimental values improves considerably. In general, the new scaling factors are very close to unit, with standard uncertainties close to ±0.006 cm,1. The use of the new polarization functions allows more precise calculations of the transition metal carbonyl CO vibrational frequencies. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Benzonitriles: Survey of their importance and scaling of their vibrational frequenciesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2003M. Alcolea Palafox Abstract This work provides a short survey of the studies carried out on benzonitrile and its derivatives, with special attention on a spectroscopic point of view. The importance and main applications of these molecules are also briefly indicated. For an accurate assignment of their vibrational spectra, the scaling procedures for the wave numbers are described. For this purpose, the performance of semiempirical, ab initio, and density functional methods, with different basis sets, is determined. A "resume" of the main scaling factors to be used in the calculated wave numbers is shown. The results obtained for several benzene derivatives, and in particular for four benzonitriles, are analyzed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 189,204, 2003 [source] Accuracy of free energies of hydration using CM1 and CM3 atomic chargesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Blagovi, Marina Udier Abstract Absolute free energies of hydration (,Ghyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard,Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute ,Ghyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N -methylacetamide in water. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1322,1332, 2004 [source] An improved OPLS,AA force field for carbohydratesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2002D. Kony Abstract This work describes an improved version of the original OPLS,all atom (OPLS,AA) force field for carbohydrates (Damm et al., J Comp Chem 1997, 18, 1955). The improvement is achieved by applying additional scaling factors for the electrostatic interactions between 1,5- and 1,6-interactions. This new model is tested first for improving the conformational energetics of 1,2-ethanediol, the smallest polyol. With a 1,5-scaling factor of 1.25 the force field calculated relative energies are in excellent agreement with the ab initio -derived data. Applying the new 1,5-scaling makes it also necessary to use a 1,6-scaling factor for the interactions between the C4 and C6 atoms in hexopyranoses. After torsional parameter fitting, this improves the conformational energetics in comparison to the OPLS,AA force field. The set of hexopyranoses included in the torsional parameter derivation consists of the two anomers of D -glucose, D -mannose, and D -galactose, as well as of the methyl-pyranosides of D -glucose, D -mannose. Rotational profiles for the rotation of the exocyclic group and of different hydroxyl groups are also compared for the two force fields and at the ab initio level of theory. The new force field reduces the overly high barriers calculated using the OPLS,AA force field. This leads to better sampling, which was shown to produce more realistic conformational behavior for hexopyranoses in liquid simulation. From 10-ns molecular dynamics (MD) simulations of ,- D -glucose and ,- D -galactose the ratios for the three different conformations of the hydroxymethylene group and the average 3JH,H coupling constants are derived and compared to experimental values. The results obtained for OPLS,AA,SEI force field are in good agreement with experiment whereas the properties derived for the OPLS,AA force field suffer from sampling problems. The undertaken investigations show that the newly derived OPLS,AA,SEI force field will allow simulating larger carbohydrates or polysaccharides with improved sampling of the hydroxyl groups. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1416,1429, 2002 [source] Integration of Life Cycle Assessment Into Agent-Based ModelingJOURNAL OF INDUSTRIAL ECOLOGY, Issue 2 2009Toward Informed Decisions on Evolving Infrastructure Systems Summary A method is presented that allows for a life cycle assessment (LCA) to provide environmental information on an energy infrastructure system while it evolves. Energy conversion facilities are represented in an agent-based model (ABM) as distinct instances of technologies with owners capable of making decisions based on economic and environmental information. This simulation setup allows us to explore the dynamics of assembly, disassembly, and use of these systems, which typically span decades, and to analyze the effect of using LCA information in decision making. We were able to integrate a simplified LCA into an ABM by aligning and connecting the data structures that represent the energy infrastructure and the supply chains from source to sink. By using an appropriate database containing life cycle inventory (LCI) information and by solving the scaling factors for the technology matrix, we computed the contribution to global warming in terms of carbon dioxide (CO2) equivalents in the form of a single impact indicator for each instance of technology at each discrete simulation step. These LCAs may then serve to show each agent the impact of its activities at a global level, as indicated by its contribution to climate change. Similar to economic indicators, the LCA indicators may be fed back to the simulated decision making in the ABM to emulate the use of environmental information while the system evolves. A proof of concept was developed that is illustrated for a simplified LCA and ABM used to generate and simulate the evolution of a bioelectricity infrastructure system. [source] A design tool for planning emulsified oil-injection systemsREMEDIATION, Issue 4 2008Aaron M. Weispfenning Emulsified oils have been used to stimulate anaerobic bioremediation at hundreds of sites contaminated with chlorinated solvents, perchlorate, heavy metals, and nitrate. A simple spreadsheet-based tool has been developed to assist in the design of injection-only systems for distributing emulsified oils in barriers and area treatments. This tool allows users to quickly compare the relative costs and performance of different injection alternatives and identify a design that is best suited to site-specific conditions. Contact efficiency is estimated using results of prior numerical model simulations and dimensionless scaling factors that relate the volume of oil and water injected to treatment-zone dimensions. Sensitivity analysis results indicate that maximum oil retention is one of the most important factors controlling system performance and cost. © 2008 Wiley Periodicals, Inc. [source] | |||||||||||||||||||||||||