Miracle-dz/UniFAR-FTUs huggingface dataset:
Size-extensive calculations of static structure factors from the coupled cluster singles and doubles model

The x-ray incoherent scattering factor S(q), which is also called the static structure factor, is very sensitive to electron correlation. In this study a method for calculating S(q) based on coupled cluster singles and doubles (CCSD) approach is developed and the computed S(q) of H2O, CH3OH, CH3CN, C6H6, and C6H12 are compared with experimental results. It is shown that the CCSD method improves theoretical S(q) of large molecules significantly compared with those by configuration interaction singles and doubles (CISD) previously employed.The x-ray incoherent scattering factor S(q), which is also called the static structure factor, is very sensitive to electron correlation. In this study a method for calculating S(q) based on coupled cluster singles and doubles (CCSD) approach is developed and the computed S(q) of H2O, CH3OH, CH3CN, C6H6, and C6H12 are compared with experimental results. It is shown that the CCSD method improves theoretical S(q) of large molecules significantly compared with those by configuration interaction singles and doubles (CISD) previously employed.
Enzyme Electrode with Collagen-Immobilized Cholesterol Oxidase for the Microdetermination of Free Cholesterol

Abstract Cholesterol oxidase has been immobililzed on collagen films associated to an electrochemical sensor to form a “cholesterol electrode”. The electrode poised at a potential of + 650 my vs Ag/AgCl detects the hydrogen peroxide produced in the enzymatic reaction. This device presents a very high sensitivity and a wide range of linearity (10−7 M - 0.8.10−4 M). The use of a non enzymatic electrode associated with the enzymatic one allowed the detection and correction of electrochemical interferences when applied to human sera for free cholesterol determination.
Fourier transform fluorescence and phosphorescence of porphine in rare gas matrices

Matrix-isolated free-base porphine and its deuterated analogues show highly resolved intense fluorescence in neon, with evidence of strong b{sub 1g} vibronic activity, and highly resolved intense phosphorescence in xenon, dominated by totally symmetric vibrations. Triplet lifetimes were determined from T-T absorption decay, which revealed a new band at 310 nm. It was concluded that the heavy-atom enhancement of the T{sub 1} {yields} S{sub 0} radiative rate is dramatic. Both emissions exhibit site structure, and single-site spectra were obtained upon narrow-bandwidth excitation. The T{sub 1} {yields} S{sub 0} emission site pattern is identical with that of S{sub 1} {yields} S{sub 0} emission and S{sub 1} {l arrow} S{sub 0} absorption and totally different from that of S{sub 2} {l arrow} S{sub 0} absorption, suggesting that T{sub 1} and S{sub 1} are both Q{sub x} and have a common orbital origin, contrary to the currently accepted assignment. The implications of the results for the mechanism of the photoinduced double proton transfer in free-base porphine are considered. All the results are compatible with the proposal that the isomerization occurs in T{sub 1} in a stepwise fashion through the cis isomer. The advantages of interferometric recording of highly resolved visible and near-IR emission spectramore » are pointed out. « less
Accelerated aging test of hydrogenated nitrile butadiene rubber using the time–temperature–strain superposition principle

The effect of physical aging on the long-term performance of hydrogenated nitrile butadiene rubber (HNBR) is very important to its engineering applications. In this paper, aging tests of HNBR have been conducted systematically at different temperatures and levels of uniaxial tensile strain. Fracture strain was chosen as the index of the severity of aging. Applied strain shows an equivalent effect on aging acceleration to that of temperature; the higher the temperature and strain level are, the faster the aging is. A WLF-type time–temperature–strain superposition principle (TTSSP) is proposed to study the long-term aging performance of HNBR with short-term test data. With the constructed master curves, time and cost can be significantly reduced for the evaluation of the long-term aging behavior of the rubber materials.
Identification of the PcrA DNA helicase reaction pathway by applying advanced targeted molecular dynamic simulations

PcrA DNA helicase uses the free energy of hydrolysis and binding of ATP to unwind double-stranded DNA (ds-DNA). There are two states of PcrA, termed the substrate and product complexes and, through the conformational changes between these two states, PcrA moves along ds-DNA and separates the two strands. In this study, two different methods, namely chain minimisation (CM, less reliable method) and auto targeted molecular dynamic (TMD) simulation (more reliable), were performed to generate two different initial reaction pathways between these two states, and then fixed root mean square distance (RMSD) TMD simulation was performed to optimise these two initial pathways. In general, the two optimised pathways share very similar major conformational changes, but are different in the minor motions. The potential energy profiles of the two improved pathways are generally similar, but the one generated by the improved TMD path is slightly lower. Considering the poor reliability of the initial path generated by CM and insignificant improvements of the auto-TMD path, our study suggests that fixed RMSD TMD simulation can generate reliable reaction pathways, but the different initial paths still have some influence on the detailed conformational analysis.
Tissue analysis using X-ray scattering

Scattered radiation in medicine is usually regarded as a problem. It either degrades image contrast or increases absorbed dose. However, if monitored correctly it can provide additional information in diagnostic procedures. It is shown that both coherent and incoherent scattering have a useful role to play. Incoherent or Compton scattering can be used to estimate the density of internal structures. In the study of osteoporosis it has been shown that Compton scatter densitometry leads to better estimates of trabecular bone density than dual-energy absorptiometry. Coherent scattering leads to diffraction effects. These have been used in the study of both archeological and clinical osteoporosis and have been shown to have greater precision than currently accepted procedures. However, the greatest impact for coherent scattering techniques is in the study of breast cancer. Tumour detection can be significantly increased.
Surface characterization of polyaniline-coated polystyrene latexes

The surface compositions of seven polyaniline (PAni)-coated polystyrene (PS) latexes have been investigated by X-ray photoelectron spectroscopy. This technique was used to assess the uniformity of the PAni overlayers deposited onto micrometer-sized, poly(N-vinylpyrrolidone) (PNVP)-stabilized PS latex particles under various synthesis conditions. Peak fitting of the N(1s) core-line spectra provided evidence for the presence of both PAni and the PNVP stabilizer at the surface of the PS latex. Nonuniform PAni coatings were obtained using conventional aniline polymerization conditions (aniline monomer, ammonium persulfate, 1.2 M HCl at 25 °C). In contrast, more homogeneous PAni coatings were obtained when polymerizing aniline hydrochloride at 0 °C in water. The relative proportion of PAni at the surface of the PS latex was estimated by comparing the surface nitrogen contents of the coated and uncoated PS latexes to that of a PAni “bulk powder” prepared in the absence of any latex. It was shown that the relati.
Surface Composition of the CoPd Alloys Studied by Electron Spectroscopies

Palladium-based alloys and bimetallic systems are of importance in heterogeneous catalysis. Recently, attention was devoted to studies of the catalytic properties of the Co-Pd binary system. An important issue to consider is the surface composition of this alloy. The aim of the present work was to determine the surface composition of the polycrystalline CoPd alloys in a wide range of constituent concentrations (Co30Pd70 at.%, Co50Pd50 at.% and Co70Pd30 at.%) at temperatures up to 900°C. Quantitative AES and XPS analyses were used for this purpose. To determine the surface composition, the values of the inelastic mean free path (IMFP) for the studied alloys are necessary. These were derived from the elastic peak intensity. The reported values of the IMFP for Pd are in agreement with the data available in the literature. Reasonable consistency of the IMFP values for CoPd alloys and Co was also observed. The surface compositions of the CoPd alloys at room temperature determined by AES and XPS are in good agreement. It has been found that Pd segregates to surfaces of the Co30Pd70 and Co50Pd50 alloys at temperatures above 300 °C.
Direct Electron Transfer at Cellobiose Dehydrogenase Modified Anodes for Biofuel Cells

Cellobiose dehydrogenases (CDHs, EC 1.1.99.18) contain a larger flavin-associated (dehydrogenase) domain and a smaller heme-binding (cytochrome) domain. CDHs from basidiomycete fungi oxidize at an appreciable level cellobiose, cellodextrins, and lactose, and those from ascomycetes may additionally oxidize some monosaccharides to their corresponding lactones at the flavin domain. CDHs are able to communicate directly with an electrode via their heme domain. In this work, different types of CDHs have been adsorbed on graphite electrodes and studied with respect to their direct electron transfer (DET) properties. Electrochemical studies were performed in the presence and absence of single-walled carbon nanotubes (SWCNTs) using lactose as substrate. In the presence of SWCNTs, the electrocatalytic current for substrate oxidation based on DET between enzyme and electrode was significantly increased. Furthermore, the onset of the electrocatalytic current was at lower potential than in the absence of SWCNTs. The highest electrocatalytic activity toward oxidation of lactose was found for CDH from the basidiomycete Phanerochaete sordida. Based on CDH from Phanerochaete sordida, an anode for biofuel cells was developed. This anode using lactose as substrate was combined with a Pt black cathode for oxygen reduction as a model for a membrane-less biofuel cell in which the processes at both electrodes occur by DET.
Characteristics of the terahertz radiation from single crystals of N-substituted 2-methyl-4-nitroaniline

Terahertz (THz) radiation was generated via optical rectification from organic single crystals, i.e. N-substituted (N-benzyl, N-diphenylmethyl, and N-2-naphthylmethyl) derivatives of 2-methyl-4-nitroaniline (MNA), and it was detected by means of the electro-optic sampling method. The intensity and the spectrum of the THz radiation were compared with those of ZnTe and DAST (N, N-dimethylamino-N'-methylstilbazolium p-toluenesulphonate) crystals. The integrated intensity of the THz radiation from the N-benzyl-MNA crystal was two thirds of that for the ZnTe crystal, the best-known practical THz emitter, and was as intense as that for the DAST crystal, the best organic THz emitter ever studied. The spectrum of the ZnTe crystal extended to 3 THz, while that of the N-benzyl MNA and DAST crystals dropped off around 2.5 THz. The THz radiation intensities from all of the organic crystals were compared quantitatively, on the basis of the consideration of molecular arrangements in the crystals. It was suggested that the absorption due to low-frequency phonon modes affected both the intensity and the spectral band shape of the THz radiation.
Characterization of Hydrogenated Fullerene Mixture of C60Hx and C70Hx

A commercially available hydrogenated mixture of fullerenes (HMF) composed of 77% C60Hx and 22% C70Hx has been analyzed by liquid chromatographic analysis (HPLC), electronic absorption, FT-IR spectroscopy, solubility and by thermal analysis (TGA). The results confirm that the HMF is composed by a mixture of C60Hx and C70Hx with a high degree of hydrogenation. The hydrogen content of the HMF was found 6.12% by combustion elemental analysis, suggesting that hydrogenated fullerenes are mixed with hydrogenated fullerene fragments derived from the cage breakdown due to the forcing conditions used in the synthesis (high pressure and high temperature hydrogenation). The HMF is stable in air for a relatively long time of exposure. Under N2, it starts to decompose at 478°C. The maximum decomposition rate under N2 occurs at 522°C. An attempt was made to resolve the C-H stretching band of HMF by recording the FT-IR spectrum at -180°C.
Theoretical and experimental study of electronic transport and structure in atomic-sized contacts

We can summarize the main achievements in this thesis work as follows: a) The first stage of the formation of an atomic-sized contact and the process of its breakage have been studied and modeled for different materials. These two phenomena are shown to undergo respectively through a Jump to contact and a Jump out of contact process. Our studies provide information on the influence on both processes of the geometries of the nanocontacts before the contact and before breaking the contact. Moreover, a relationship between these atomic scale processes and the macroscopic properties of the materials have been provided through a systematic study for different materials. b) We show that it is possible to create stable and atomically well-defined tips through a ``mechanical annealing'' process involving the repeated indentation of an electrode into a surface as long as the indentation is limited to a few conductance quanta (approx 5G0) in the case of gold). Simulations provide an explanation showing how, under repeated indentations, two pyramidal tips with (111) faces form. c) We provide experimental evidence for the formation of diatomic long chains in gold. These diatomic chains have been confirmed in MD simulations and their conductance, as obtained by DFT, is in agreement with the experimentally measured values. Moreover, we show that there is a relationship between the formation of long monoatomic chains and diatomic chains in gold since normally these double stranded chains evolve to form the monoatomic ones d) Finally, our experiments show that a nanocontact between two Bismuth electrodes at room conditions presents an almost constant conductance close to 1G0 when stretched. We can understand this phenomena as a result of pulling a single bilayer of Bi(111) when such bilayer conducts a constant conductance of a quantum. Tight-Binding calculations on these structures show that these results can be understood as a manifestation of topological insulator behavior. This result provides a possible path to create topological insulators at room temperature. Therefore, we can say that this work has improved our understanding on how two metals connect at the atomic scale, as well as how a nanocontact breaks also at an atomic level.
TOPOS3.2: a new version of the program package for multipurpose crystal- chemical analysis

The principal features of the package are as follows. (i) Management of crystal structure information with DBMS (database management system) which has gateways to the CSD and ICSD databases. (ii) Comprehensive analysis of geometrical and topological properties of crystal structures (employing the programs Dirichlet, AutoCN, ADS, DiAn, IsoCryst and IsoTest). (iii) Special facilities for statistical analysis of large sets of crystal structures (the program StatPack). In addition to the programs contained in the previous version (Blatov et al., 1999), version 3.2 includes the following two programs. (a) IsoTest, which provides an automatic search for the topological similarity (isotypism) in large groups of stoichiometrically and structurally different compounds, on three levels: the whole topological and geometrical similarity (crystal-chemical isotypism; Lima-deFaria et al., 1990); only the whole or partial topological similarity of crystal structures (topological isotypism; Blatov, 2000); topological similarity of separate atomic subnets and packings. (b) HSite, which searches for hydrogen positions in crystal structures of organic, organometallic and inorganic compounds. Besides traditional methods of geometrical and statistical analysis, and graphical representation of crystal structures (the programs DiAn, IsoCryst and StatPack), there are two novel concepts used in TOPOS algorithms: the concept of an atomic domain represented as a Voronoi±Dirichlet polyhedron (the program Dirichlet; Blatov et al., 1995) and the concept of a periodic net described as a contracted graph (the programs ADS, AutoCN and IsoTest; Blatov, 2000). The program IsoTest automatically enumerates all variants of topological representation of crystal structures and ®nds similar ones through a given list of compounds by comparing coordination sequences (Brunner & Laves, 1971) of corresponding atomic subnets (Blatov, 2000). The program HSite uses characteristics of Voronoi±Dirichlet polyhedra to predict the optimal positions of hydrogen atoms and orientation of atomic groups.
Effect of Short-Term Temperature Increase on the Performance of a Mesophilic UASB Reactor

A study was carried out to assess the effects of short-term temperature increments on the treatment efficiency and methane production of UASB reactors at a working temperature of 37-39°C. Two different substrates were used to determine the effects on the several bacterial groups involved in the digestion process. One reactor was fed with defined synthetic acidified wastewater the other with unacidified wastewaler from a distillery process. Shocks of 5-24 hrs were applied at temperatures in the range of 45 to 61°C. Up to 45°C no detrimental effects were noticeable. Higher temperatures led to a sharp decrease of the activity of the different microbial populations as a result of elevated decay rates. Propionate oxidation turned out to be the most sensitive for temperature increments, whereas the acidogenic bacteria were least affected. Temperature shocks of 55 and 61°C led to a decrease of 50% of the overall efficiency after 10 and 3 hrs, respectively. By means of batch experiments decay rates of 0.44 and > 10 hr −1 of the methanogenic bacteria were estimated at 55 and 65°C respectively. As temporary inactivation of the mesophilic bacteria during a temperature shock was found to be unlikely, reactor recovery is dependent on the bacterial growth and the biomass retention capacity of the reactor. When unacidified wastewater is treated, a pH decrease has to be considered during a temperature shock.
Diamagnetic susceptibility changes in apple tissue after bruising

In nuclear magnetic resonance images of bruised apples, the bruised tissue regions appear brighter than intact tissue regions. The cause for the contrast was investigated. The spin-spin relaxation rates (1/T 2 ) of the bruised regions were found to be greater than those of firm tissue regions ruling out this mechanism as a cause for the contrast. By comparing spin-echo images (with echo delays of 14 ms and 50 ms) with gradient-recalled-echo images (with echo delay of 5.5 ms) it was concluded that the contrast may be attributed to the decrease in the diamagnetic susceptibility variations within the bruised regions as a result of the partial destruction of the cellular structure caused by bruising. Images of a bruised apple were acquired before bruising, immediately after bruising and approximately every 4 h thereafter, and showed that the contrast between bruised and non-bruised regions increased with time
Recognizing Events in Spatiotemporal Soccer Data

Spatiotemporal datasets based on player tracking are widely used in sports analytics research. Common research tasks often require the analysis of game events, such as passes, fouls, tackles, and shots on goal. However, spatiotemporal datasets usually do not include event information, which means it has to be reconstructed automatically. We propose a rule-based algorithm for identifying several basic types of events in soccer, including ball possession, successful and unsuccessful passes, and shots on goal. Our aim is to provide a simple procedure that can be used for practical soccer data analysis tasks, and also serve as a baseline model for algorithms based on more advanced approaches. The resulting algorithm is fast, easy to implement, achieves high accuracy on the datasets available to us, and can be used in similar scenarios without modification.
60 keV beam transport line and switch-yard for ISAC

The ISAC project under construction at TRIUMF is to consist of radioactive ion sources, a high resolution mass separator, a low-energy (60 keV) experimental area, RFQ and DTL linacs to reach 1.5 MeV per atomic mass unit (amu), and a high-energy experimental area. Additionally, there will be a stable off-line source primarily for commissioning the linacs but also for use by the low-energy experimental program. The transport line which connects these elements therefore includes a switch which allows either the radioactive beam to supply the low energy area simultaneously with the off-line source supplying the RFQ, or the radioactive beam supplying beam to the RFQ simultaneously with the off-line source supplying beam to the low-energy experiments. The maximum ion source voltage is 60 kV. The RFQ accepts particles with 2 keV per amu, so masses less than 30 must have lower energy and masses larger than 30 can only be accelerated if they are multiply-charged.
Twist and shear in β-sheets and β-ribbons

The structures of the beta-sheets and the beta-ribbons have been analysed using high-resolution protein structure data. Systematic asymmetries measured in both parallel and antiparallel beta-structures include the sheet twist and the strand shear. In order to determine the origin of these asymmetries, numerous interactions and correlations were examined. The strongest correlations are observed for residues in antiparallel beta-sheets and beta-ribbons that form non-H-bonded pairs. For these residues, the sheet twist is correlated to the backbone phi angle but not to the psi angle. Our analysis supports the existence of an inter-strand C(alpha)H(alpha). O weak H-bond, which, together with the CO.HN H-bond, constitutes a bifurcated H-bond that links neighbouring beta-strands. Residues of beta-sheets and beta-ribbons in high-resolution protein structures form a distinct region of the Ramachandran plot, which is determined by the formation of the bifurcated H-bond, the formation of an intra-strand O.H(alpha) non-bonded polar interaction, and an intra-strand O.C(beta) steric clash. Using beta-strands parameterised by phi-psi values from the allowed beta-sheet region of the Ramachandran plot, the shear and the right-hand twist can be reproduced in a simple model of the antiparallel and parallel beta-ribbon that models the bifurcated H-bonds specifically. The conformations of interior residues of beta-sheets are shown to be subsets of the conformations of residues of beta-ribbons.