Multicrystal approach to crystal structure solution and refinement

2004 ◽  
Vol 219 (12) ◽  
Author(s):  
Gavin B. M. Vaughan ◽  
Soeren Schmidt ◽  
Henning F. Poulsen
Keyword(s):  
Single Crystal ◽  
Polycrystalline Sample ◽  
Test Case ◽  
Data Sets ◽  
Data Set ◽  
Structure Solution ◽  
The Individual ◽  
Integrated Intensities ◽  
Subsequent Integration

AbstractWe present a method in which the contributions from the individual crystallites in a polycrystalline sample are separated and treated as essentially single crystal data sets. The process involves the simultaneous determination of the orientation matrices of the individual crystallites in the sample, the subsequent integration of the individual peaks, and filtering and summing of the subsequent integrated intensities, in order to arrive at a single-crystal like data set which may be treated normally. In order to demonstrate the method, we consider as a test case a small molecule structure, cupric acetate monohyrade. We show that it is possible to obtain a single-crystal quality structure solution and refinement, in which accurate anisotropic thermal parameters and hydrogen atom positions are obtained.

scholarly journals Making a difference in multi-data-set crystallography: simple and deterministic data-scaling/selection methods

2020 ◽  
Vol 76 (7) ◽  
pp. 636-652 ◽  
Author(s):  
Greta M. Assmann ◽  
Meitian Wang ◽  
Kay Diederichs
Keyword(s):  
Simulated Data ◽  
Test Case ◽  
Data Sets ◽  
Selection Methods ◽  
Data Set ◽  
Partial Data ◽  
Structure Solution ◽  
Making A Difference ◽  
Data Scaling ◽  
Anomalous Signal

Phasing by single-wavelength anomalous diffraction (SAD) from multiple crystallographic data sets can be particularly demanding because of the weak anomalous signal and possible non-isomorphism. The identification and exclusion of non-isomorphous data sets by suitable indicators is therefore indispensable. Here, simple and robust data-selection methods are described. A multi-dimensional scaling procedure is first used to identify data sets with large non-isomorphism relative to clusters of other data sets. Within each cluster that it identifies, further selection is based on the weighted ΔCC1/2, a quantity representing the influence of a set of reflections on the overall CC1/2 of the merged data. The anomalous signal is further improved by optimizing the scaling protocol. The success of iterating the selection and scaling steps was verified by substructure determination and subsequent structure solution. Three serial synchrotron crystallography (SSX) SAD test cases with hundreds of partial data sets and one test case with 62 complete data sets were analyzed. Structure solution was dramatically simplified with this procedure, and enabled solution of the structures after a few selection/scaling iterations. To explore the limits, the procedure was tested with much fewer data than originally required and could still solve the structure in several cases. In addition, an SSX data challenge, minimizing the number of (simulated) data sets necessary to solve the structure, was significantly underbid.

Single crystal structure determination of cetylpyridiniumammonium bromide and Rietveld structure determination of cetylquinuclidinium bromide

1998 ◽  
Vol 213 (2) ◽  
Author(s):  
P. Ballirano ◽  
R. Caminiti ◽  
C. Sadun ◽  
V. M. Coiro ◽  
G. Mancini ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Structure Determination ◽  
Single Crystal Structure ◽  
Crystal Structure Determination ◽  
Tetraalkylammonium Bromide ◽  
Structure Solution

AbstractThe structures of cetylpyridiniumammonium bromide (CPyB) and cetylquinuclidinium bromide (CQB), two tetraalkylammonium bromide surfactants, are reported. In particular, whereas the structure solution of CPyB was carried out through conventional single-crystal diffractometry, the structure of CQB has been determined by means of powder diffractometry. CPyB crystallizes in

scholarly journals The GTC exoplanet transit spectroscopy survey

2019 ◽  
Vol 622 ◽  
pp. A172 ◽  
Author(s):  
F. Murgas ◽  
G. Chen ◽  
E. Pallé ◽  
L. Nortmann ◽  
G. Nowak
Keyword(s):  
Transmission Spectrum ◽  
Rayleigh Scattering ◽  
Extrasolar Planets ◽  
Light Curves ◽  
Data Sets ◽  
Transmission Spectra ◽  
Data Set ◽  
Systematic Effects ◽  
The Individual ◽  
Spectrum Slope

Context. Rayleigh scattering in a hydrogen-dominated exoplanet atmosphere can be detected using ground- or space-based telescopes. However, stellar activity in the form of spots can mimic Rayleigh scattering in the observed transmission spectrum. Quantifying this phenomena is key to our correct interpretation of exoplanet atmospheric properties. Aims. We use the ten-meter Gran Telescopio Canarias (GTC) telescope to carry out a ground-based transmission spectra survey of extrasolar planets to characterize their atmospheres. In this paper we investigate the exoplanet HAT-P-11b, a Neptune-sized planet orbiting an active K-type star. Methods. We obtained long-slit optical spectroscopy of two transits of HAT-P-11b with the Optical System for Imaging and low-Intermediate-Resolution Integrated Spectroscopy (OSIRIS) on August 30, 2016 and September 25, 2017. We integrated the spectrum of HAT-P-11 and one reference star in several spectroscopic channels across the λ ~ 400–785 nm region, creating numerous light curves of the transits. We fit analytic transit curves to the data taking into account the systematic effects and red noise present in the time series in an effort to measure the change of the planet-to-star radius ratio (Rp∕Rs) across wavelength. Results. By fitting both transits together, we find a slope in the transmission spectrum showing an increase of the planetary radius towards blue wavelengths. Closer inspection of the transmission spectrum of the individual data sets reveals that the first transit presents this slope while the transmission spectrum of the second data set is flat. Additionally, we detect hints of Na absorption on the first night, but not on the second. We conclude that the transmission spectrum slope and Na absorption excess found in the first transit observation are caused by unocculted stellar spots. Modeling the contribution of unocculted spots to reproduce the results of the first night we find a spot filling factor of δ = 0.62−0.17+0.20 and a spot-to-photosphere temperature difference of ΔT = 429−299+184 K.

A classification approach based on variable precision rough sets and cluster validity index function

2014 ◽  
Vol 31 (8) ◽  
pp. 1778-1789
Author(s):  
Hongkang Lin
Keyword(s):  
Optimal Number ◽  
Data Sets ◽  
Cluster Validity ◽  
Cluster Validity Index ◽  
Index Method ◽  
Data Set ◽  
Content Type ◽  
The Individual ◽  
Variable Precision Rough Sets ◽  
Optimal Number Of Clusters

Purpose – The clustering/classification method proposed in this study, designated as the PFV-index method, provides the means to solve the following problems for a data set characterized by imprecision and uncertainty: first, discretizing the continuous values of all the individual attributes within a data set; second, evaluating the optimality of the discretization results; third, determining the optimal number of clusters per attribute; and fourth, improving the classification accuracy (CA) of data sets characterized by uncertainty. The paper aims to discuss these issues. Design/methodology/approach – The proposed method for the solution of the clustering/classifying problem, designated as PFV-index method, combines a particle swarm optimization algorithm, fuzzy C-means method, variable precision rough sets theory, and a new cluster validity index function. Findings – This method could cluster the values of the individual attributes within the data set and achieves both the optimal number of clusters and the optimal CA. Originality/value – The validity of the proposed approach is investigated by comparing the classification results obtained for UCI data sets with those obtained by supervised classification BPNN, decision-tree methods.

scholarly journals Improved retrieval of nitrogen dioxide (NO<sub>2</sub>) column densities by means of MKIV Brewer spectrophotometers

2014 ◽  
Vol 7 (11) ◽  
pp. 4009-4022 ◽  
Author(s):  
H. Diémoz ◽  
A. M. Siani ◽  
A. Redondas ◽  
V. Savastiouk ◽  
C. T. McElroy ◽  
...  
Keyword(s):  
Nitrogen Dioxide ◽  
Ad Hoc ◽  
Absorption Spectrometry ◽  
Atmospheric Composition ◽  
Data Sets ◽  
Data Set ◽  
Noise Interference ◽  
Atmospheric Species ◽  
Mass Factor

Abstract. A new algorithm to retrieve nitrogen dioxide (NO2) column densities using MKIV ("Mark IV") Brewer spectrophotometers is described. The method includes several improvements, such as a more recent spectroscopic data set, the reduction of measurement noise, interference by other atmospheric species and instrumental settings, and a better determination of the zenith sky air mass factor. The technique was tested during an ad hoc calibration campaign at the high-altitude site of Izaña (Tenerife, Spain) and the results of the direct sun and zenith sky geometries were compared to those obtained by two reference instruments from the Network for the Detection of Atmospheric Composition Change (NDACC): a Fourier Transform Infrared Radiometer (FTIR) and an advanced visible spectrograph (RASAS-II) based on the differential optical absorption spectrometry (DOAS) technique. To determine the extraterrestrial constant, an easily implementable extension of the standard Langley technique for very clean sites without tropospheric NO2 was developed which takes into account the daytime linear drift of stratospheric nitrogen dioxide due to photochemistry. The measurement uncertainty was thoroughly determined by using a Monte Carlo technique. Poisson noise and wavelength misalignments were found to be the most influential contributors to the overall uncertainty, and possible solutions are proposed for future improvements. The new algorithm is backward-compatible, thus allowing for the reprocessing of historical data sets.

scholarly journals Tsallis Entropy for Assessing Spatial Uncertainty Associated with Mean Annual Runoff of Quaternary Catchments of the Middle Vaal Basin in South Africa

Entropy ◽  
2020 ◽  
Vol 22 (9) ◽  
pp. 1050
Author(s):  
Masengo Ilunga
Keyword(s):  
South Africa ◽  
Shannon Entropy ◽  
Annual Runoff ◽  
Spatial Uncertainty ◽  
Data Sets ◽  
Data Set ◽  
Information Index ◽  
Surface Water Resources ◽  
Convergence Point

This study assesses mainly the uncertainty of the mean annual runoff (MAR) for quaternary catchments (QCs) considered as metastable nonextensive systems (from Tsalllis entropy) in the Middle Vaal catchment. The study is applied to the surface water resources (WR) of the South Africa 1990 (WR90), 2005 (WR2005) and 2012 (WR2012) data sets. The q-information index (from the Tsalllis entropy) is used here as a deviation indicator for the spatial evolution of uncertainty for the different QCs, using the Shannon entropy as a baseline. It enables the determination of a (virtual) convergence point, zone of positive and negative uncertainty deviation, zone of null deviation and chaotic zone for each data set. Such a determination is not possible on the basis of the Shannon entropy alone as a measure for the MAR uncertainty of QCs, i.e., when they are viewed as extensive systems. Finally, the spatial distributions for the zones of the q-uncertainty deviation (gain or loss in information) of the MAR are derived and lead to iso q-uncertainty deviation maps.

An Improved Classification Analysis on Utility Aware K-Anonymized Dataset

2019 ◽  
Vol 16 (2) ◽  
pp. 445-452
Author(s):  
Kishore S. Verma ◽  
A. Rajesh ◽  
Adeline J. S. Johnsana
Keyword(s):  
Data Mining ◽  
Analytical Approach ◽  
Value Added ◽  
Data Sets ◽  
Data Set ◽  
Privacy Preserving Data Mining ◽  
Privacy Leakage ◽  
Anonymized Data ◽  
Null Values ◽  
The Individual

K anonymization is one of the worldwide used approaches to protect the individual records from the privacy leakage attack of Privacy Preserving Data Mining (PPDM) arena. Typically anonymized dataset will impact the effectiveness of data mining results. Anyhow, currently researchers of PPDM progress in driving their efforts in finding out the optimum trade-off between privacy and utility. This work tends in bringing out the optimum classifier from a set of best classifiers of data mining approaches that are capable enough in generating value-added classifying results on utility aware k-anonymized data set. We performed the analytical approach on the data set that are anonymized in sense of accompanying the anonymity utility factors like null values count and transformation pattern loss. The experimentation is done with three widely used classifiers HNB, PART and J48 and these classifiers are analysed with Accuracy, F-measure, and ROC-AUC which are literately proved to be the perfect measures of classification. Our experimental analysis reveals the best classifiers on the utility aware anonymized data sets of Cell oriented Anonymization (CoA), Attribute oriented Anonymization (AoA) and Record oriented Anonymization (RoA).

Spectral analysis and inversion of experimental codas

Geophysics ◽  
1993 ◽  
Vol 58 (3) ◽  
pp. 408-418 ◽  
Author(s):  
L. R. Jannaud ◽  
P. M. Adler ◽  
C. G. Jacquin
Keyword(s):  
Spectral Analysis ◽  
Characteristic Length ◽  
Gaussian Model ◽  
Seismic Survey ◽  
Data Sets ◽  
Data Set ◽  
Anisotropic Elastic ◽  
And Inversion ◽  
Good Agreement

A method developed for the determination of the characteristic lengths of an heterogeneous medium from the spectral analysis of codas is based on an extension of Aki’s theory to anisotropic elastic media. An equivalent Gaussian model is obtained and seems to be in good agreement with the two experimental data sets that illustrate the method. The first set was obtained in a laboratory experiment with an isotropic marble sample. This sample is characterized by a submillimetric length scale that can be directly observed on a thin section. The spectral analysis of codas and their inversion yields an equivalent correlation length that is in good agreement with the observed one. The second data set is obtained in a crosshole experiment at the usual scale of a seismic survey. The codas are recorded, analysed, and inverted. The analysis yields a vertical characteristic length for the studied subsurface that compares well with the characteristic length measured by seismic and stratigraphic logs.

Determination of site occupancies by the intermeasurement minimization method. I. Anomalous scattering usage for noncentrosymmetric crystals

2008 ◽  
Vol 41 (1) ◽  
pp. 83-95 ◽  
Author(s):  
Alexander Dudka
Keyword(s):  
Site Occupancy ◽  
Anomalous Scattering ◽  
Data Sets ◽  
Minimization Method ◽  
Data Set ◽  
Occupancy Factor ◽  
Site Occupancy Factor ◽  
Three Samples ◽  
Scattering Contribution

New methods for the determination of site occupancy factors are described. The methods are based on the analysis of differences between intensities of Friedel reflections in noncentrosymmetric crystals. In the first method (Anomalous-Expert) the site occupancy factor is determined by the condition that it is identical for two data sets: (1) initial data without averaging of Friedel intensities and (2) data that are averaged on Friedel pairs after the reduction of the anomalous scattering contribution. In the second method (anomalous anisotropic intermeasurement minimization method, Anomalous-AniMMM) the site occupancy factor is refined to satisfy the condition that the differences between the intensities of Friedel reflections that are reduced on the anomalous scattering contribution must be minimal. The methods were checked for three samples of RbTi1−xZrxOPO4crystals (A,BandC) with KTiOPO4structure, at 295 and 105 K (five experimental data sets). Microprobe measurements yield compositionsxA,B= 0.034 (5) andxC= 0.022 (4). The corresponding site occupancy factors areQA,B= 0.932 (10) andQC= 0.956 (8). Using Anomalous-AniMMM and three independent refinements for the first and second samples, the initial occupancy factor ofQA,B= 0.963 (15) was improved toQA,B= 0.938 (7). Of the three room-temperature data sets, one was improved toQA,B= 0.934 (2). For the third sample and one data set, the initial occupancy factor ofQC= 1.000 was improved toQC= 0.956 (1). The methods improve the Hirshfeld rigid-bond test. It is discussed how the description of chemical bonding influences the site occupancy factor.

scholarly journals Crystalline perfection of an aluminium single crystal determined by neutron diffraction

2011 ◽  
Vol 44 (4) ◽  
pp. 681-687
Author(s):  
Sabrina Metairon ◽  
Carlos Benedicto Ramos Parente ◽  
Vera Lucia Mazzocchi ◽  
Thierry Jacques Lemaire
Keyword(s):  
Neutron Diffraction ◽  
Single Crystal ◽  
Relative Intensity ◽  
Three Dimensional ◽  
Point Of View ◽  
Crystalline Perfection ◽  
Contour Map ◽  
The Individual ◽  
Crystalline Domains

In this work, a study of the crystalline perfection of an aluminium single crystal is presented. The study shows that, from three-dimensional neutron diffraction rocking curves, it is possible to characterize the individual crystalline domains of a multidomain crystal. From a macroscopic point of view, the determination of the domains allows an evaluation of the crystalline perfection of the crystal under study. Three-dimensional rocking curves have been obtained by neutron diffraction from a large mosaic aluminium crystal. Construction of a contour map of individual domains made it easier to determine the breadth and relative intensity of each domain. The angular distances between domains were also determined.

Sign in / Sign up

Export Citation Format

Share Document