Calculations

Distribution by Scientific Domains
Distribution within Chemistry

Kinds of Calculations

  • First-principle calculation
  • Matthew coefficient calculation
  • ab initio calculation
  • ab initio mo calculation
  • ab initio molecular orbital calculation
  • ab-initio calculation
  • accurate calculation
  • am1 calculation
  • analytical calculation
  • annealing calculation
  • area calculation
  • b3lyp calculation
  • balance calculation
  • band structure calculation
  • benchmark calculation
  • carlo calculation
  • cd calculation
  • cfd calculation
  • chemical calculation
  • chemical shift calculation
  • chemistry calculation
  • coefficient calculation
  • computational calculation
  • constant calculation
  • cost calculation
  • density functional calculation
  • density functional theory calculation
  • density-functional calculation
  • density-functional theory calculation
  • dft calculation
  • direct calculation
  • docking calculation
  • dose calculation
  • dynamic calculation
  • dynamics calculation
  • efficiency calculation
  • efficient calculation
  • electronic structure calculation
  • element calculation
  • empirical calculation
  • energy calculation
  • engineering calculation
  • equilibrium calculation
  • exact calculation
  • example calculation
  • explicit calculation
  • fast calculation
  • field calculation
  • finite element calculation
  • first principle calculation
  • first-principle calculation
  • flow calculation
  • fock calculation
  • free energy calculation
  • free-energy calculation
  • frequency calculation
  • function calculation
  • functional calculation
  • functional theory calculation
  • giao calculation
  • high-level ab initio calculation
  • index calculation
  • initio calculation
  • initio mo calculation
  • initio molecular orbital calculation
  • iterative calculation
  • level calculation
  • load calculation
  • mass balance calculation
  • mechanic calculation
  • mechanical calculation
  • mm calculation
  • mo calculation
  • model calculation
  • modeling calculation
  • modelling calculation
  • molecular calculation
  • molecular dynamics calculation
  • molecular mechanic calculation
  • molecular modeling calculation
  • molecular orbital calculation
  • molecular-replacement calculation
  • monte carlo calculation
  • mp2 calculation
  • normal-mode calculation
  • numerical calculation
  • orbital calculation
  • pm3 calculation
  • power calculation
  • previous calculation
  • principle calculation
  • probability calculation
  • quantitative calculation
  • quantum calculation
  • quantum chemical calculation
  • quantum chemistry calculation
  • quantum mechanical calculation
  • quantum-chemical calculation
  • quantum-mechanical calculation
  • radiative transfer calculation
  • rate calculation
  • relativistic calculation
  • relativistic density functional calculation
  • risk calculation
  • sample size calculation
  • scattering calculation
  • self-consistent calculation
  • semiempirical calculation
  • sensitivity calculation
  • shift calculation
  • simple calculation
  • single-point calculation
  • size calculation
  • statistical calculation
  • structure calculation
  • test calculation
  • theoretical calculation
  • theory calculation
  • thermodynamic calculation
  • thermodynamic equilibrium calculation
  • time-dependent density functional theory calculation
  • total energy calculation
  • transfer calculation
  • trial calculation
  • variational calculation
  • volume calculation

  • Terms modified by Calculations

  • calculation method
  • calculation methods
  • calculation model
  • calculation models
  • calculation procedure
  • calculation process
  • calculation result
  • calculation scheme
  • calculation shows
  • calculation support
  • calculation time

  • Selected Abstracts


    TRUE WORLD INCOME DISTRIBUTION, 1988 AND 1993: FIRST CALCULATION BASED ON HOUSEHOLD SURVEYS ALONE

    THE ECONOMIC JOURNAL, Issue 476 2002
    Branko Milanovic
    The paper derives world income or expenditure distribution of individuals for 1988 and 1993. It is the first paper to calculate world distribution for individuals based entirely on household surveys from 91 countries, and adjusted for differences in purchasing power parity between countries. Measured by the Gini index, inequality increased from 63 in 1988 to 66 in 1993. The increase was driven more by differences in mean incomes between countries than by inequalities within countries. The most important contributors were rising urban-rural differences in China, and slow growth of rural incomes in South Asia compared to several large developed economies. [source]


    EFFECT OF ORIENTATION OF SPATIALLY DISTRIBUTED CURVE NUMBERS IN RUNOFF CALCULATIONS,

    JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 6 2000
    Glenn E. Moglen
    ABSTRACT: The NRCS curve number approach to runoff estimation has traditionally been to average or "lump" spatial variability into a single number for purposes of expediency and simplicity in calculations. In contrast, the weighted runoff curve number approach, which handles each individual pixel within the watershed separately, tends to result in larger estimates of runoff than the lumped approach. This work proposes further enhancements that consider not only spatial variability, but also the orientation of this variability with respect to the flow aggregation pattern of the drainage network. Results show that the proposed enhancements lead to much reduced estimates of runoff production. A revised model that considers overland flow lengths, consistent with existing NRCS concepts is proposed, which leads to only mildly reduced runoff estimates. Although more physically-based, this revised model, which accounts directly for spatially distributed curve numbers and flow aggregation, leads to essentially the same results as the original, lumped runoff model when applied to three study watersheds. Philosophical issues and implications concerning the appropriateness of attempting to disaggregate lumped models are discussed. [source]


    Calculation of Posterior Probabilities for Bayesian Model Class Assessment and Averaging from Posterior Samples Based on Dynamic System Data

    COMPUTER-AIDED CIVIL AND INFRASTRUCTURE ENGINEERING, Issue 5 2010
    Sai Hung Cheung
    Because of modeling uncertainty, a set of competing candidate model classes may be available to represent a system and it is then desirable to assess the plausibility of each model class based on system data. Bayesian model class assessment may then be used, which is based on the posterior probability of the different candidates for representing the system. If more than one model class has significant posterior probability, then Bayesian model class averaging provides a coherent mechanism to incorporate all of these model classes in making probabilistic predictions for the system response. This Bayesian model assessment and averaging requires calculation of the evidence for each model class based on the system data, which requires the evaluation of a multi-dimensional integral involving the product of the likelihood and prior defined by the model class. In this article, a general method for calculating the evidence is proposed based on using posterior samples from any Markov Chain Monte Carlo algorithm. The effectiveness of the proposed method is illustrated by Bayesian model updating and assessment using simulated earthquake data from a ten-story nonclassically damped building responding linearly and a four-story building responding inelastically. [source]


    Increased Behavioral Variation and the Calculation of Release Numbers for Reintroduction Programs

    CONSERVATION BIOLOGY, Issue 3 2004
    M. ELSBETH McPHEE
    This increased variation can translate into decreased survivorship upon reintroduction to native habitats. Data show that captive populations of oldfield mice (Peromyscus polionotus subgriseus) exhibit such an increase in variation. Motivated by these results, we developed a series of calculations for a "release ratio" that can be used to determine the number of captive-bred animals needed to compensate for the increased variance. We present calculations of release ratios for behavioral and morphological variables with different distributions and illustrate the functional relationship between release numbers, increased variation, and change in average behavior and morphology. Our calculations indicated that the release of 130,150 captive-bred oldfield mice is equivalent to the release of 100 wildlike animals. Release ratios will vary among species, however, and perhaps among different populations of the same species and should be calculated separately for each situation. Development of the release ratio is the first rigorous effort to incorporate behavioral and morphological changes due to captivity into reintroduction planning. Release ratios will help conservation biologists ensure that the appropriate number of animals is released, thus increasing the success of reintroduction programs. Resumen:,Las poblaciones cautivas pueden exhibir mayor variación conductual que sus contrapartes silvestres como resultado del relajamiento de presiones selectivas en el ambiente de cautiverio. Esta variación incrementada puede traducirse en una disminución de la supervivencia en la reintroducción a hábitats nativos. Hay datos que muestran que poblaciones cautivas de ratones Peromyscus polionotus subgriseus exhiben tal incremento en la variación. Motivados por estos resultados, desarrollamos una serie de cálculos para un "índice de liberación" que pueda utilizarse para determinar el número de animales criados en cautiverio requerido para compensar la variación incrementada. Presentamos los cálculos de 2 índices de liberación para variables conductuales y morfológicas con distribuciones diferentes e ilustramos la relación funcional entre el número de liberaciones, la variación incrementada y el cambio en la conducta promedio y la morfología. Nuestros cálculos indicaron que la liberación de 130 a 150 ratones es equivalente a la liberación de 100 animales silvestres. Sin embargo, los índices de liberación varían entre especies y quizás entre poblaciones diferentes de la misma especie y deben calcularse por separado en cada situación. El desarrollo de índices de liberación es el primer esfuerzo riguroso para incorporar cambios conductuales y morfológicos debido al cautiverio en la planificación de reintroducciones. Los índices de liberación ayudarán a que los biólogos de la conservación se aseguren que el número de animales liberados es el apropiado, incrementando con ello el éxito de los programas de reintroducción. [source]


    Improvements in the 2D TEP Neutral Particle Transport Calculation in Edge Plasmas

    CONTRIBUTIONS TO PLASMA PHYSICS, Issue 7-9 2006
    D. Zhang
    Abstract Extensions of the 2D Transmission and Escape Probability neutral particle transport method in treating the spatial non-uniformity of collision sources and neutral energy effects are presented. These extensions have been tested by benchmarks against Monte Carlo calculations for specially designed models and for realistic DIII-D discharges. The comparisons indicate these extensions improve accuracy of the TEP method. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]


    Mechanisms of transjunctional transport of NaCl and water in proximal tubules of mammalian kidneys

    ACTA PHYSIOLOGICA, Issue 1 2002
    F. KIILArticle first published online: 30 APR 200
    ABSTRACT Tight junctions and the intercellular space of proximal tubules are not accessible to direct measurements of fluid composition and transport rates, but morphological and functional data permit analysis of diffusion and osmosis causing transjunctional NaCl and water transport. In the S2 segment NaCl diffuses through tight junctions along a chloride gradient, but against a sodium gradient. Calculation in terms of modified Nernst,Fick diffusion equation after eliminating electrical terms shows that transport rates (300,500 pmol min,1 mm,1 tubule length) and transepithelial voltage of +2 mV are in agreement with observations. Diffusion coefficients are Dtj=1500 ,m2 s,1 in the S1 segment, and Dtj=90,100 ,m2 s,1 in the S2 segment where apical intercellular NaCl concentration is 132 mM, 1 mM below complete stop (Dtj=0 and Donnan equilibrium). Tight junctions with gap distance 6 Å are impermeable to mannitol (effective molecular radius 4 Å); reflection coefficients are ,=0.92 for NaHCO3 and ,=0.28 for NaCl, because of difference in anion size. The osmotic force is provided by a difference in effective transjunctional osmolality of 10 mOsm kg,1 in the S1 segment and 30 mOsm kg,1 in the S2 segment, where differences in transjunctional concentration contribute with 21 mOsm kg,1 for NaHCO3 and ,4 mOsm kg,1 for NaCl. Transjunctional difference of 30 mOsm kg,1 causes a volume flow of 2 nL min,1 mm,1 tubule length. Luminal mannitol concentration of 30 mM stops all volume flow and diffusive and convective transport of NaCl. In conclusion, transjunctional diffusion and osmosis along gradients generated by transcellular transport of other solutes account for all NaCl transport in proximal tubules. [source]


    Using Design Effects From Previous Cluster Surveys to Guide Sample Size Calculation in Emergency Settings

    DISASTERS, Issue 2 2006
    Reinhard Kaiser
    Abstract A good estimate of the design effect is critical for calculating the most efficient sample size for cluster surveys. We reviewed the design effects for seven nutrition and health outcomes from nine population-based cluster surveys conducted in emergency settings. Most of the design effects for outcomes in children, and one-half of the design effects for crude mortality, were below two. A reassessment of mortality data from Kosovo and Badghis, Afghanistan revealed that, given the same number of clusters, changing sample size had a relatively small impact on the precision of the estimate of mortality. We concluded that, in most surveys, assuming a design effect of 1.5 for acute malnutrition in children and two or less for crude mortality would produce a more efficient sample size. In addition, enhancing the sample size in cluster surveys without increasing the number of clusters may not result in substantial improvements in precision. [source]


    Impact of Body Mass Index on Markers of Left Ventricular Thickness and Mass Calculation: Results of a Pilot Analysis

    ECHOCARDIOGRAPHY, Issue 3 2005
    Ranjini Krishnan M.D.
    Specific correlations between body mass index (BMI) and left ventricular (LV) thickness have been conflicting. Accordingly, we investigated if a particular correlation exists between BMI and echocardiographic markers of ventricular function. Methods: A total of 122 patients, referred for routine transthoracic echocardiography, were included in this prospective pilot study using a 3:1 randomization approach. Patient demographics were obtained using a questionnaire. Results: Group I consisted of 80 obese (BMI was >30 kg/m2), Group II of 16 overweight (BMI between 26 and 29 kg/m2), and Group III of 26 normal BMI (BMI < 25 kg/m2) individuals. No difference was found in left ventricular wall thickness, LV end-systolic cavity dimension, fractional shortening (FS), or pulmonary artery systolic pressure (PASP) among the groups. However, mean LV end-diastolic cavity dimension was greater in Group I (5.0 ± 0.9 cm) than Group II (4.6 ± 0.8 cm) or Group III (4.4 ± 0.9 cm; P < 0.006). LV mass indexed to height2.7 was also significantly larger in Group I (61 ± 21) when compared to Group III (48 ± 19; P < 0.001). Finally, left atrial diameter (4.3 ± 0.7 cm) was also larger (3.8 ± 0.6 and 3.6 ± 0.7, respectively; P < 0.00001).Discussion: We found no correlation between BMI and LV wall thickness, FS, or PASP despite the high prevalence of diabetes and hypertension in obese individuals. However, obese individuals had an increased LV end-diastolic cavity dimension, LV mass/height2.7, and left atrial diameter. These findings could represent early markers in the sequence of cardiac events occurring with obesity. A larger prospective study is needed to further define the sequence of cardiac abnormalities occurring with increasing BMI. [source]


    Proximal Isovelocity Surface Area (PISA) in the Evaluation of Fixed Membranous Subaortic Stenosis

    ECHOCARDIOGRAPHY, Issue 2 2002
    Gregory M. Goodkin M.D.
    The evaluation of the severity of subaortic stenosis is usually expressed by the magnitude of the subvalvular gradient. Calculation of the membrane orifice area noninvasively is difficult by the standard means. We present a patient in whom the area was calculated using the proximal isovelocity surface area (PISA) method. This method should have clinical applicability because it is not flow dependent and can be used in patients with normal, reduced, or increased stroke volume. [source]


    Do dams increase genetic diversity in brown trout (Salmo trutta)?

    ECOLOGY OF FRESHWATER FISH, Issue 4 2006
    Microgeographic differentiation in a fragmented river
    Abstract , Local genetic differentiation may potentially arise in recently fragmented populations. Brown trout is a polytypic species exhibiting substantial genetic differentiation, which may evolve in few generations. Movement (semi-)barriers in rivers may cause fragmentation, isolation and genetic differentiation in fish. In the Måna River (28 km) flowing from the alpine Lake Møsvatn to the boreal Lake Tinnsjø, construction of four hydropower dams during the period 1906,1957 have fragmented the previously (since last Ice Age) continuous wild resident brown trout population. Samples from the two lakes (N = 40) and six sites in the river (N = 30) isolated at different times were analysed at nine microsatellite loci. All populations showed substantial genetic variation (mean number of alleles per locus 5.3,8.9, observed heterozygosity 0.57,0.65 per population, overall Fst = 0.032). Pairwise multilocus Fst estimates indicated no significant differentiation between populations in the two lakes, and no or little differentiation in the lower river (Fst = 0.0035,0.0091). The microgeographic differentiation among wild resident trout at these sites was less than expected based on similar previous studies. However, results from the upper river, in particular the site immediately below the Lake Møsvatn outlet and dam, indicated isolation (Fst > 0.035). Calculation of genetic distances and assignment tests corroborated these results, as did a significant correlation between years of isolation (since dam construction) and Fst. The population structuring is most likely a result of fragmentation by dams, which has increased overall genetic diversity. This increased local differentiation may be caused by natural selection, but more likely by genetic drift in small, recently fragmented populations. Increased local genetic diversity by genetic drift does not justify conservation measures aiming at preserving genetic diversity. [source]


    If cannabis caused schizophrenia,how many cannabis users may need to be prevented in order to prevent one case of schizophrenia?

    ADDICTION, Issue 11 2009
    England, Wales calculations
    ABSTRACT Background We consider how many cannabis users may need to be prevented in order to prevent one case of schizophrenia or psychosis [defined as number needed to prevent (NNP)]. Method Calculation for England and Wales using best available estimates of: incidence of schizophrenia; rates of heavy and light cannabis use; and risk that cannabis causes schizophrenia. Results In men the annual mean NNP for heavy cannabis and schizophrenia ranged from 2800 [90% confidence interval (CI) 2018,4530] in those aged 20,24 years to 4700 (90% CI 3114,8416) in those aged 35,39. In women, mean NNP for heavy cannabis use and schizophrenia ranged from 5470 (90% CI 3640,9839) in those aged 25,29 to 10 870 (90% CI 6786,22 732) in 35,39-year-olds. Equivalent mean NNP for heavy cannabis use and psychosis were lower, from 1360 (90% CI 1007,2124) in men aged 20,24 and 2480 (90% CI 1408,3518) in women aged 16,19. The mean and median number of light cannabis users that would need to be prevented in order to prevent one case of schizophrenia or psychosis per year are four to five times greater than among heavy users. Conclusions The number of young people who need to be exposed to an intervention to generate NNP and prevent one case of schizophrenia will be even larger. The public health importance of preventing cannabis to reduce schizophrenia or psychosis remains uncertain. More attention should be given to testing the hypothesis that cannabis is related causally to psychotic outcomes, and to considering what strategies will be the most effective in reducing heavy cannabis use among young people. [source]


    What changes in health-related quality of life matter to multiple myeloma patients?

    EUROPEAN JOURNAL OF HAEMATOLOGY, Issue 4 2010
    A prospective study
    Abstract Objective: To determine the clinical significance of changes in quality-of-life scores in patients with multiple myeloma (MM), we have estimated the minimal important difference (MID) for the health-related quality-of-life instrument, the European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30. The MID is the smallest change in a quality-of-life score considered important to patients. Methods: Between 2006 and 2008, 239 patients with MM completed the EORTC QLQ-C30 at inclusion (T1) and after 3 months (T2). At T2, a structured quality-of-life interview was also performed. MIDs were calculated by using mean score changes (T2,T1) for patients who in the interview stated they had improved, deteriorated or were unchanged. MIDs were also estimated by the receiver-operating characteristic (ROC) curve method as well as by calculation effect sizes using standard deviations of baseline scores. Results: MIDs varied slightly depending on the method used. Patients stating in the interview that they had ,improved' or ,deteriorated' had a corresponding change in EORTC QLQ-C30 score ranging from 6 to15 (improvement) and from 9 to17 (deterioration) (scale range 0,100). The ROC analysis indicated that changes in score from 7 to17 represent clinically important changes to patients. The effect size method suggested 5,6 to be a small and 11,15 to be a medium change. Conclusion: Calculation of MIDs as mean score changes or by ROC analysis suggested that a change in the EORTC QLQ-C30 score in the range of approximately 6,17 is considered important by patients with MM. These MIDs are closer to a medium effect size than to a small effect size. Our findings imply that mean score changes smaller than 6 are unlikely to be important to the patients, even if these changes are statistically significant. [source]


    Density-Functional Calculation of the 183W and 17O NMR Chemical Shifts for Large Polyoxotungstates

    EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 6 2006
    Jose Gracia
    Abstract A phosphane sulfate relativistic DFT method (ZORA)has been used to calculate the 183W and 17O NMR chemicalshifts for large polyoxotungstates, including W6O192,,CH3OTiW5O183,, W5O18WIINO3,, W10O324,, ,-,-,-XW12O40n,, ,-PW9O28Br63,, P2W18O626,, PW2O143,, and W7O246,, based on their optimized molecular structures. Despite sizeable deviations between the calculated and experimental values, the calculations correctly reproduce the trends in the change of the chemical shift for both nuclei. As expected, the diamagnetic term is almost constant throughout the whole series. The change in the chemical shifts is shown to be determined by the paramagnetic term, which depends on the electronic structure of the whole anion under study and, in particular, on the local geometry around a given tungsten atom. On the other hand, there is no correlation between the chemical shift and HOMO,LUMO gap, showing that deeper occupied levels and several unoccupied orbitals play an important role in the paramagnetic term. However, analysis of the components of the paramagnetic shielding has shown that the most significant transitions determining the change of both 183W and 17O NMR chemical shifts for anions consisting of tungsten and oxygen atoms are the occupied,occupied and not the occupied,virtual ones.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006) [source]


    An Ab Initio Molecular Dynamics Study of Bioactive Phosphate Glasses,

    ADVANCED ENGINEERING MATERIALS, Issue 7 2010
    Emilia Tang
    First principles molecular dynamics simulations of ternary phosphate-based glasses P2O5CaONa2O (PBGs) have been carried out in order to provide an accurate description of the local structure and properties of these important materials for biomedical applications. The structures of PBGs with compositions (P2O5)0.45(CaO)x(Na2O)0.55,,,x (x,=,0.30, 0.35, and 0.40) were generated using a full ab initio molecular dynamics melt-and-quench procedure. The analysis of the structure of the glasses at 300,K shows the prevalence of the metaphosphate Q2 and pyrophosphate Q1 species, whereas the number of Q3 units, which constitute the three-dimensional phosphate network, significantly decreases with the increase in calcium content in the glass. Calculation of the pair and angular distribution functions suggests that the rigidity of the phosphate tetrahedral glass network increases with the concentration of calcium, an observation which is interpreted in terms of the tendency of Ca2+ to be a stronger coordinator than sodium. [source]


    The role of NGF uptake in selective vulnerability to cell death in ageing sympathetic neurons

    EUROPEAN JOURNAL OF NEUROSCIENCE, Issue 11 2004
    Kliment P. Gatzinsky
    Abstract We have examined the hypothesis that differences in nerve growth factor (NGF) uptake and transport determine vulnerability to age-related neurodegeneration. Neurons projecting to cerebral blood vessels (CV) in aged rats are more vulnerable to age-related degeneration than those projecting to the iris. Uptake of NGF was therefore examined in sympathetic neurons projecting from the superior cervical ganglion (SCG) to CV and iris in young and old rats by treating the peripheral processes of these neurons with different doses of I125 -NGF. Total uptake of I125 -NGF was reduced in old CV-projecting, but not iris-projecting, neurons. Numbers of radiolabelled neurons projecting to each target were counted in sectioned ganglia. The data showed age-related reductions in numbers of labelled neurons projecting to CV, but no change in numbers of neurons projecting to the iris. Calculation of uptake of I125 -NGF per neuron unexpectedly showed no major age-related differences in either of the two neuron populations. However, uptake per neuron was considerably lower for young and old CV-projecting, compared to iris-projecting, SCG neurons. We hypothesized that variations in NGF uptake might affect neuronal survival in old age. Counts of SCG neurons using a physical disector following retrograde tracing with Fluorogold confirmed the selective vulnerability of CV-projecting neurons by showing a significant 37% loss of these neurons in the period between 15 and 24 months. In contrast, there was no significant loss of iris-projecting neurons. We conclude that vulnerability to, or protection from, age-related neurodegeneration and neuronal cell death are associated with life-long low, or high, levels of NGF uptake, respectively. [source]


    "PHYBAL" a Short-Time Procedure for a Reliable Fatigue Life Calculation

    ADVANCED ENGINEERING MATERIALS, Issue 4 2010
    Peter Starke
    Abstract The reliable calculation of the fatigue life of high-strength steels and components requires the systematic investigation of the cyclic deformation behaviour and the comprehensive evaluation of proceeding fatigue damage. Besides mechanical stress-strain hysteresis measurements, temperature and electrical resistance measurements were used for the detailed characterisation of the fatigue behaviour of the steel SAE 4140 in one quenched and tempered, one normalised, one bainitic and one martensitic condition. To guarantee optimal operation conditions the new fatigue life calculation method "PHYBAL" on the basis of generalised Morrow and Basquin equations was developed. It is a short-time procedure which requires the data of only three fatigue tests for a rapid and nevertheless precise determination of S-N (Woehler) curves. Consequently, "PHYBAL" provides the opportunity to reduce significantly experimental time and costs compared to conventional test methods. [source]


    A comparison of the urea-induced unfolding of apoflavodoxin and flavodoxin from Desulfovibrio vulgaris

    FEBS JOURNAL, Issue 1 2002
    Brian Ó Nuallain
    The kinetics and thermodynamics of the urea-induced unfolding of flavodoxin and apoflavodoxin from Desulfovibrio vulgaris were investigated by measuring changes in flavin and protein fluorescence. The reaction of urea with flavodoxin is up to 5000 times slower than the reaction with the apoprotein (0.67 s,1 in 3 m urea in 25 mm sodium phosphate at 25 °C), and it results in the dissociation of FMN. The rate of unfolding of apoflavodoxin depends on the urea concentration, while the reaction with the holoprotein is independent of urea. The rates decrease in high salt with the greater effect occurring with apoprotein. The fluorescence changes fit two-state models for unfolding, but they do not exclude the possibility of intermediates. Calculation suggests that 21% and 30% of the amino-acid side chains become exposed to solvent during unfolding of flavodoxin and apoflavodoxin, respectively. The equilibrium unfolding curves move to greater concentrations of urea with increase of ionic strength. This effect is larger with phosphate than with chloride, and with apoflavodoxin than with flavodoxin. In low salt the conformational stability of the holoprotein is greater than that of apoflavodoxin, but in high salt the relative stabilities are reversed. It is calculated that two ions are released during unfolding of the apoprotein. It is concluded that the urea-dependent unfolding of flavodoxin from D. vulgaris occurs because apoprotein in equilibrium with FMN and holoprotein unfolds and shifts the equilibrium so that flavodoxin dissociates. Small changes in flavin fluorescence occur at low concentrations of urea and these may reflect binding of urea to the holoprotein. [source]


    Calculation of IBD probabilities with dense SNP or sequence data

    GENETIC EPIDEMIOLOGY, Issue 6 2008
    Jonathan M. Keith
    Abstract The probabilities that two individuals share 0, 1, or 2 alleles identical by descent (IBD) at a given genotyped marker locus are quantities of fundamental importance for disease gene and quantitative trait mapping and in family-based tests of association. Until recently, genotyped markers were sufficiently sparse that founder haplotypes could be modelled as having been drawn from a population in linkage equilibrium for the purpose of estimating IBD probabilities. However, with the advent of high-throughput single nucleotide polymorphism genotyping assays, this is no longer a reasonable assumption. Indeed, the imminent arrival of individual sequencing will enable high-density single nucleotide polymorphism genotyping on a scale for which current algorithms are not equipped. In this paper, we present a simple new model in which founder haplotypes are modelled as a Markov chain. Another important innovation is that genotyping errors are explicitly incorporated into the model. We compare results obtained using the new model to those obtained using the popular genetic linkage analysis package Merlin, with and without using the cluster model of linkage disequilibrium that is incorporated into that program. We find that the new model results in accuracy approaching that of Merlin with haplotype blocks, but achieves this with orders of magnitude faster run times. Moreover, the new algorithm scales linearly with number of markers, irrespective of density, whereas Merlin scales supralinearly. We also confirm a previous finding that ignoring linkage disequilibrium in founder haplotypes can cause errors in the calculation of IBD probabilities. Genet. Epidemiol. 2008. © 2008 Wiley-Liss, Inc. [source]


    The geochemical evolution of very dilute CO2 -rich water in Chungcheong Province, Korea: processes and pathways

    GEOFLUIDS (ELECTRONIC), Issue 1 2008
    K. KIM
    Abstract A geochemical study was carried out on the CO2 -rich water occurring in granite areas of Chungcheong Province, Korea. In this area, very dilute and acidic CO2 -rich waters [62,242 mg l,1 in total dissolved solid (TDS), 4.0,5.3 in pH; group I) occur together with normal CO2 -rich waters (317,988 mg l,1 in TDS, 5.5,6.0 in pH; group II). The concentration levels and ages of group I water are similar to those of recently recharged and low-mineralized groundwater (group III). Calculation of reaction pathways suggests that group I waters are produced by direct influx of CO2 gas into group III type waters. When the groundwater is injected with CO2, it develops the capacity to accept dissolved solids and it can evolve into water with very high solute concentrations. Whether the water is open or closed to the CO2 gases becomes less important in controlling the reaction pathway of the CO2 -rich groundwater when the initial pco2 is high. Our data show that most of the solutes are dissolved in the CO2 -rich groundwater at pH > 5 where the weathering rates of silicates are very slow or independent of pH. Thus, groundwater age is likely more important in developing high solute concentrations in the CO2 -rich groundwaters than accelerated weathering kinetics because of acidic pH caused by high pco2. [source]


    Calculation of the wave propagation angle in complex media: application to turning wave simulations

    GEOPHYSICAL JOURNAL INTERNATIONAL, Issue 3 2009
    Xiaofeng Jia
    SUMMARY The wave propagation angle is one of the key factors in seismic processing methods. For the dual-domain propagators, it is sometimes necessary to acquire the wave propagation angle in the space-frequency domain instead of the wavenumber domain or the angle domain. We propose a method dealing with this problem, in which the wavefield gradient is used for the calculation of the wave propagation angle. The wavefield gradient can be directly obtained by either the finite difference approximation or the marching expression of the propagator. This method is not applicable in the case of extremely low frequency due to the comparability between the wavelength and the grid interval. Combined with the superwide-angle one-way propagator, this approach is instrumental in simulating the turning wave, which is hard to be handled by the traditional one-way propagator. Numerical examples show the good performance of the superwide-angle one-way propagator with our approach involved. The turning wave is modelled accurately; as a result, a high-quality image of the overhanging salt flank can be obtained. [source]


    Calculation of Elapsed Decimal Time for Tracing Studies

    GROUND WATER, Issue 1 2008
    Malcolm S. Field
    Calculation of time of travel from tracing studies in hydrologic systems is critical to establishing pollutant arrival times from points of inflow to points outflow, calculating subsurface flow velocities, and determining other important transport parameters such as longitudinal dispersion. In addition, breakthrough curve modeling demands accurate time of travel calculations if model results are to have any realistic meaning. However, accurate time of travel calculations are very difficult for long tracer tests in which sampling schedules are not consistent, or when there are major disruptions such as may occur when adverse weather conditions cause automatic sampling equipment to fail. Long and inconsistent sampling times may be accurately converted to decimal times of travel by converting the conventionally recorded Coordinated Universal Time for sampling date and time event to a baseline time standard. By converting to a baseline time standard, all recorded dates and times are linked to the established baseline standard so that each succeeding sampling date and time are correctly determined relative to the previous sampling date and time and to the injection date and time. [source]


    , -Cyclodextrin as Inhibitor of the Precipitation Reaction between Berberine and Glycyrrhizin in Decoctions of Natural Medicines: Interaction Studies of Cyclodextrins with Glycyrrhizin and Glycyrrhetic Acid by 1H-NMR Spectroscopy and Molecular-Dynamics Calculation

    HELVETICA CHIMICA ACTA, Issue 9 2008
    Miyoko Kamigauchi
    Abstract To prevent the precipitation reaction between glycyrrhizin (1) and berberine (3) in the decoctions of Glycyrrhiza/Coptis rhizome or Glycyrrhiza/Phellodendron bark, the presence of cyclodextrin (CD) in the mixture was proven to be effective. The preventing effect decreased in the order , -CD>, -CD, and no effect was observed for , -CD. On the other hand, the extraction degree of 1 from the natural medicine Glycyrrhia was considerably increased in the presence of , -CD, , -CD being much more effective than , - or , -CD. Thus, the blocking effect of CD on the precipitate formation between 1 and 3 is suggested to be primarily dependent on the stability of the inclusion complex of the CD with 1. To establish the structure of such a preferred inclusion complex, the interactions of 1 with , - and , -CDs were investigated by 1H-NMR spectroscopy and molecular-dynamics (MD) calculations. The 1H-NMR measurements showed that the increase in solubility of 1 in H2O is dependent on the degree of its inclusion into the CD, which depends on the molecular size of the CD. The MD calculations suggested that the H-bond interactions are sufficiently strong to form a stable [1/, -CD] complex, in which the lipophilic rings C, D, and E of 1 are fully inserted into the molecular cavity of , -CD, thus forming a kind of structure covered by a hydrophilic molecular capsule, while such an interaction mode is impossible for , - or , -CD. [source]


    Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flow

    INSECT MOLECULAR BIOLOGY, Issue 5 2002
    J. Martin
    Abstract Phylogenetic analysis of DNA sequences from mitochondrial (mt) genes (Cytochrome b and Cytochrome oxidase I) and one nuclear gene (globin 2b) was used for the investigation of Nearctic and Palearctic populations representing four Chironomus species of the subgenus Camptochironomus, namely C. biwaprimus, C. pallidivittatus, C. tentans sensu stricto and C. dilutus (the last two species constitute Holarctic C. tentans sensu lato). Phenograms constructed on the basis of mt sequences were not congruent with trees based on nuclear genes, or with morphological and cytological data. The mt tree divided the populations by continental region, rather than by the species groupings recognized by the other data sets. The incongruence is explained by mt gene flow resulting from hybridization between the sympatric species on each continent. Calculation of divergence times, based on the sequence data, suggest that C. tentans (s.l.) and C. pallidivittatus have both been in North America for about 2.5 My. [source]


    Calculation of nonlinear aerodynamic characteristics of a wing using a 3-D panel method

    INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 1 2008
    Jeonghyun Cho
    Abstract The nonlinear aerodynamic characteristic of a wing is investigated using the frequency-domain panel method. To calculate the nonlinear aerodynamic characteristics of a three-dimensional wing, the iterative decambering approach is introduced into the frequency-domain panel method. The decambering approach uses the known nonlinear aerodynamic characteristic of airfoil and calculates two-variable decambering function to take into consideration the boundary-layer separation effects for the each section of the wing. The multidimensional Newton iteration is used to account for the coupling between the different sections of wing. The nonlinear aerodynamic analyses for a rectangular wing, a tapered wing, and a wing with the control surface are performed. Present results are given with experiments and other numerical results. Computed results are in good agreement with other data. This method can be used for any wing having different nonlinear aerodynamic characteristics of airfoil. The present method will contribute to the analysis of aircraft in the conceptual design because the present method can predict the nonlinear aerodynamic characteristics of a wing with a few computing resources and significant time. Copyright © 2007 John Wiley & Sons, Ltd. [source]


    Calculation of turbulent fluid flow and heat transfer in ducts by a full Reynolds stress model

    INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 2 2003
    Masoud Rokni
    Abstract A computational method has been developed to predict the turbulent Reynolds stresses and turbulent heat fluxes in ducts by different turbulence models. The turbulent Reynolds stresses and other turbulent flow quantities are predicted with a full Reynolds stress model (RSM). The turbulent heat fluxes are modelled by a SED concept, the GGDH and the WET methods. Two wall functions are used, one for the velocity field and one for the temperature field. All the models are implemented for an arbitrary three-dimensional channel. Fully developed condition is achieved by imposing cyclic boundary conditions in the main flow direction. The numerical approach is based on the finite volume technique with a non-staggered grid arrangement. The pressure,velocity coupling is handled by using the SIMPLEC-algorithm. The convective terms are treated by the van Leer scheme while the diffusive terms are handled by the central-difference scheme. The hybrid scheme is used for solving the , equation. The secondary flow generation using the RSM model is compared with a non-linear k,, model (non-linear eddy viscosity model). The overall comparison between the models is presented in terms of the friction factor and Nusselt number. Copyright © 2003 John Wiley & Sons, Ltd. [source]


    Modeling the Effects of Reactor Inlet Configuration on Isothermal CVI Process of C/SiC Composites

    INTERNATIONAL JOURNAL OF APPLIED CERAMIC TECHNOLOGY, Issue 6 2007
    Xi Wei
    Two comparative models were proposed to simulate the effects of the reactor configuration on the isothermal chemical vapor infiltration (ICVI) process of C/SiC composites. The difference in the two models is that there is an expansion zone near the reactor inlet in one model while no expansion zone exists in another model. Calculation results show that the existence of the expansion zone has rather negligible effects on the ICVI process. It is accordingly suggested that the simplification of the reactor configuration by neglecting the expansion zone of the reactor is reasonable and acceptable for the ICVI process of C/SiC composites. [source]


    Parameter optimization for a PEMFC model with a hybrid genetic algorithm

    INTERNATIONAL JOURNAL OF ENERGY RESEARCH, Issue 8 2006
    Zhi-Jun Mo
    Abstract Many steady-state models of polymer electrolyte membrane fuel cells (PEMFC) have been developed and published in recent years. However, models which are easy to be solved and feasible for engineering applications are few. Moreover, rarely the methods for parameter optimization of PEMFC stack models were discussed. In this paper, an electrochemical-based fuel cell model suitable for engineering optimization is presented. Parameters of this PEMFC model are determined and optimized by means of a niche hybrid genetic algorithm (HGA) by using stack output-voltage, stack demand current, anode pressure and cathode pressure as input,output data. This genetic algorithm is a modified method for global optimization. It provides a new architecture of hybrid algorithms, which organically merges the niche techniques and Nelder,Mead's simplex method into genetic algorithms (GAs). Calculation results of this PEMFC model with optimized parameters agreed with experimental data well and show that this model can be used for the study on the PEMFC steady-state performance, is broader in applicability than the earlier steady-state models. HGA is an effective and reliable technique for optimizing the model parameters of PEMFC stack. Copyright © 2005 John Wiley & Sons, Ltd. [source]


    Haemoglobinometry in general practice

    INTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 6 2003
    S. M. Lewis
    Summary Haemoglobinometry as a primary point-of-care test is well established. This study was undertaken to assess whether haemoglobinometry by itself provides an adequate haematological screening procedure in general practice. In a series of 500 sequential blood counts received by the central hospital laboratory from local doctors, 405 (81%) had a normal haemoglobin. Full blood counts on these samples showed 15% with one or more blood count parameters outside 2SD of normal reference values, including increased MCV, low MCV with low MCH and MCHC, leucocytosis with neutrophilia, a few cases with neutropenia, lymphopenia, monocytosis or eosinophilia. When the limits were set at 3SD, these abnormalities were found in only 7.6% of the cases. Calculation of test utility gave a positive predictive value of 0.83, a negative predictive value of 0.85, with a likelihood ratio of 14.3 and an overall diagnostic reliability of 84%. It was concluded that haemoglobin alone is a valuable primary screening test and a full blood count is required only when anaemia is present or when the patient's history and clinical signs indicate the need for such further investigation. Using this protocol it is unlikely that any serious error will be made in diagnosing a clinically significant condition; the main limitation is failure to diagnose pre-anaemic iron deficiency. [source]


    Calculation of the electronic structure of AmO2 and Pr6O11 for XANES analysis with redox property

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2009
    Chikashi Suzuki
    Abstract We calculated X-ray absorption near-edge structure (XANES) of Am LIII of AmO2 and Pr LIII of Pr6O11 using the relativistic discrete-variational (DV)-X, method based on the Dirac,Slater method, and compared it with the experimental spectra. These spectra were calculated on a model of AmO2 ([AmO8]12,) and Pr6O11 ([PrO8]12,). In spite of using small cluster models, the calculated spectra were in good agreement with the experiment ones. Besides, we calculated the electronic structure of AmO2 and Pr6O11 to analyze the peak structures of XANES. From this calculation, it was found that O s, p, and f components had influence on the specific peak structures but that O d component had influence on various peak structures for AmO2 and Pr6O11. From this result, it was suggested that the change of the electronic structure of actinide 6d and O d or f was important for actinide LIII XANES corresponding to oxygen to metal ratio in the oxide nuclear fuel. On the basis of these results, we calculated the fine structures of densities of states and the transition energy from the HOMO to the white line of AmO2, UO2, and Pr6O11 and investigated redox properties of Am and U in the oxide nuclear fuel with the evaluation of validity of Pr as simulant materials of Am. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source]


    Calculation of proton affinity using the CR-CCSD[T]/ECP method

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2006
    Nelson H. Morgon
    Abstract High-level calculations of proton and electron affinities (PA and EA) of CH2X, and CH2CHCHX, (with X = F, Cl, Br, and I) systems were obtained. The methodology employed in the PA and EA calculations is based on CR-CCSD[T]/B1//MP2/B0 and CCSD(T)/B1//MP2/B0 levels, respectively. B0 is a (small) valence basis set developed by Stevens and colleagues (SBKJC), and B1 is a larger basis set, with extra diffuse and polarization functions (B0 + s, p, d, and f functions). This scheme has been tested on systems containing H, C, and X atoms, and is shown to give good results. The differences between calculated results of PA and EA and the experimental values are in the range of 0.2,4.5 kJ · mol,1 and 0.01 to 0.10 eV, respectively. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source]