dataesr/scientific-paragraphs-categorization huggingface dataset:
DFT calculations Theoretical calculations were performed within plane-wave pseudopotential method based on density functional theory as implemented in the Vienna Ab initio Simulation Package (VASP). 38, 39 Ions are described by employing PAW pseudopotential for atomic core region. 40, 41 The exchange-correlation energy was calculated within the Perdew, Burke, and Ernzerhof formulation of the generalized-gradient approximation (GGA-PBE). 42, 43 After the extensive test calculations for the total energy convergence, the kinetic energy cut-off for plane wave expansion was set to 400 eV. Six Au surface orientations (111), (100), (110) (for low index surfaces) and (  221 ), (311), (331) (for high index surfaces) were considered. The Au surfaces were simulated by the (4 × 4) slab models containing 6 atom layers, in which the 2 bottom layers are fixed to mimic the bulk state.
Acknowledgements We gratefully acknowledge the help of  Yann Le Bouar  for the use of the Nanofabric Software Developed for the geometrical construction of free or supported crystalline nanoclusters. We also acknowledge the financial support of the  Region Ile-de-France  (convention SESAME E1845 for the JEOL ARM 200F electron microscope installed at the  University of Paris ), the  Labex SEAM , the  CNRS  and the  ANR  ( CYCLYS  project).
A Gatan 914 cryo-holder was used and the temperature was maintained below -160°C to prevent devitrification. The same Cryo-TEM procedure was used to measure Pt-NP densities at Pickering emulsion droplet interfaces. Pickering emulsion droplets were made binary in colour, manually using ArtStudio (5. 103). The binary images were then analysed for surface area coverage using ImageJ software and apparent nanoparticle surface densities were corrected for emulsion drop curvature. Both methods are described in a previous publication. [33]  Hexadecane core retention testing using gas chromatograpy (GC) 100% of the gold coated capsule dispersion was allowed to settle under gravity for 48 hours (Settling rates increase dramatically between the nano-Pickering emulsions and the corresponding thickest (15-20 nm) gold shell nanocapsules due to a combination of both a significant increase in mean density due to the gold (19.
s),   final radius of rotation (m),   initial radius of rotation (m),   nanoparticle metal core density (kg/m³),   emulsion drop oil density (kg/m³),   continuous phase density (kg/m³), ω is the angular velocity (radian/s),  time to sediment from   to   (s). Cryo-TEM was used in conjunction with particle counting software (imageJ) to measure the average Pt-NP core 2D densities on the surface of the Pickering emulsion droplets produced here and to verify that high Pt-NP densities are achieved. The mean Pt-NP core density was measured to be ~34% and was shown to be independent of Pickering emulsion drop size. High particle surface coverage is expected based on previously measured densities at liquid/solid interface. [33]  ,  [36]  Figure  7a  demonstrates the possibility of separating the Pickering emulsion droplets into two populations via centrifugation.
Many codes and software of elemental analysis and Monte Carlo simulation of atomic relaxation (softwares based on the AXIL package,  [1, 2]  PENELOPE,  [3] [4] [5]  PyMCA,  [6]  among many others) rely on the data available in literature regarding atomic relaxation, such as transition probabilities, fluorescence yields, partial fluorescence yields and radiationless transition yields. The accuracy of these codes and softwares are strongly related to the accuracy of the data used. GEometry ANd Tracking (Geant4) toolkit  [7, 8]  is widely employed for the simulation of the passage of the interaction of particles with matter. It includes a variety of packages for the simulation of the electromagnetic interactions of particles with matter using Monte Carlo methods. The Geant4 Low Energy Electromagnetic package  [9, 10]  handles physics in energy ranges that extend down to 100 eV, with a detailed description of particle interaction by taking into account the atomic structure of matter.
[11] To extend the use of the Geant4 to the simulation of experiments regarding X-ray, or Auger emission, the Low Energy Electromagnetic package incorporates a cascade model that handles atomic relaxation. [11] In the simulation of the atomic relaxation cascade, secondary photons or electrons are generated through radiative and radiationless transitions. The selection of the transitions is based on the respective partial transition yields and the energy of the emitted particles is calculated taking into account the atomic electron's binding energies. The transition yields and binding energies are tabulated in Geant4's library G4EMLOW and the values are derived from the Evaluated Atomic Data Library (EADL). [12] everal studies from Pia et al. [13] [14] [15]  present comparisons between partial fluorescence yield values of the radiative transitions from EADL tabulations with the values obtained from different references, namely Scofield's Dirac-Hartree-Slater calculations,  [16, 17]  Scofield's Dirac-Hartree-Fock calculations,  [18, 19]  and experimental values obtained from Salem et al.
However, the partial fluorescence yields in these comparisons were normalized without taking into account the radiationless (or Auger) transition probabilities of the respective shell. These radiationless probabilities must be included because the partial transition yields presented in EADL library are normalized with these probabilities. Furthermore, codes and software where the simulation of radiationless transitions is relevant, use partial fluorescence yield values normalized taking into account the radiationless transitions. For these reasons, a comparison of comprehensive values of partial fluorescence yields obtained from different references is of significant importance for the context of improving data libraries. Such comparison can also complement the studies of Pia et al. [13] [14] [15]  We thus present an overview of the existing references that contain comprehensive values related to atomic transitions.
[21]  "fluorescence yield" -- Hubbell et al. [27]  "fluorescence yield" -- NIST database  [28]  "fluorescence yield" "relative intensity" -Kahoul et al. [29]  "fluorescence yield" "transition probability" - Daoudi et al. [30]  "fluorescence yield" -- method. In the Hartree-Slater, and Dirac-Hartree-Slater methods, it is considered that each electron is affected by an average field created by all other electrons, while in Hartree-Fock and Dirac-Hartree-Fock methods the average field is represented by the direct and exchange operators, J D and K ex , such that the average potential is given as: Γ Γ A + Γ CK * V HF (r) = V D (r) + V ex (r), (12) where V D is the direct potential, due to the electron repulsion, and V ex is the exchange potential, which accounts for the exchange of two electrons, due to the anti-symmetrization of the electron wave-functions.
Salem et al. experimental Kand L-shell X-ray transition ratios Salem et al. compiled selected experimental data for K-and L-shell transition rates, and through least-squares fitting, generated most probable values of K-and L-shell X-ray radiative transition rate ratios. [20] From these ratios, partial fluorescence yield values (normalized without accounting radiationless transitions)   (NA)  i can be obtained, as was performed in Pia et al. works,  [13] [14] [15]  and in NIST's Fundamental Parameters Database. [28].
Hubbell et al. 1994 semi-empirical fittings of experimental data In 1994, Hubbel et al. compiled the measured K-shell, L-shell, and higher atomic shell X-ray fluorescence yield data generated between the period 1978 -1993. [27] From the compiled data K-, L-and M-shell fluorescence yields were produced by fitting the selected data (the selection criteria and fitting procedure is explained in their work). They compared their fitted values with earlier fitted values and theoretical values. Hubbel et al. fits for K-shell fluorescence yields  K are presented in NIST Fundamental Parameters Database  [28]  even though an erratum  [42]  informs about extensive anomalies to their fitted values, and as such they advise that the values obtained from Bambynek's 1984 work  [41]  should be used instead, regarding K-shell fluorescence yield values.
NIST Fundamental Parameters Database Elam accomplished the compilation of a comprehensive database of atomic fundamental parameters relevant to X-ray spectroscopy,  [28]  which is available in the NIST's web-page. The radiative K-shell fluorescence yield  K , tabulated in the database were calculated from the fits to several experimental values by Hubbel et al. ,  [27]  discussed in the previous subsection. The radiative L-shell fluorescence yield tabulated in the database are from Krause's revision to experimental and theoretical values  [40]  with modifications proposed by Jitschin. [43] he database also presents partial fluorescence yield values (normalized without accounting radiationless transitions)   (NA)  for K-and L-shell transitions that were calculated using the emission rate ratios presented by Salem et al work  [20]  ; the fit process to the data is explained with detail in Elam et al.
works. In Scofield's Dirac-Fock work,  [18]  it is presented radiative transition probabilities A (R) for a limited number of transitions, and limited number of elements, as well as total radiative transition probability A  (TR). From this information, the partial fluorescence yields (normalized without accounting radiationless transitions)  (NA) can be obtained using Equation (6). As far as we know, the xraylib database  [26]  uses this method, with the exception that the values had to be normalized to satisfy Equation (  7 ). This method is limited to those transitions which are presented in Scofield's work. Pia et al. performed a different approach to obtain   (NA)  values from Scofield's Dirac-Fock work. [18] Since Scofield's work also present radiative transition probability ratios, Pia et al.
Combination of semi-empirical or empirical K-shell fluorescence yield values with Salem et al. values From the references regarding semi-empirical or empirical fittings presented so far ("Bambynek1972  [22]  ", "Krause1979  [40]  ", "Bambynek1984  [41]  ", "NIST  [28]  ", "Kahoul2012  [29]  " and "Daoudi2015  [30]  "), semi-empirical and empirical values regarding K-shell fluorescence yield  K were obtained. In the present work, we calculate partial fluorescence yields  K-L 2 ,  K-L 3 ,  K-M 2 ,  K-M 3 for each of these references using using Equation (8), where the partial fluorescence yield values (normalized without accounting radiationless transitions)   (NA)  are those obtained from Salem et al. work,  [20]  which are tabulated in NIST Fundamental Parameters Database. As an example, to derive the K-L 2 partial fluorescence yield  K-L 2 from Daoudi et al.
radiationless Diroc-Fock calculations  [25]  and Scofield's radiative Dirac-Fock calculations. [18] EADL": values obtained from the Evaluated Atomic Data Library. [12]  FIGURE 2 "Bambynek1972": Values from Bambynek et al. earlier semi-empirical fit. [22] Krause1979": values from Krause's semi-empirical fit. [40]  "Bambynek1984": values from Bambynek et al. later semi-empirical fit. [41]  "NIST": semi-empirical fit values presented in NIST's Fundamental Parameters Database. [28]  "Kahoul": values from Kahoul et al. empirical fit. [29] Daoudi": values from Daoudi et al. empirical fit. [30]  number Z, and a radiative transition ij, the relative difference of the partial fluorescence yield from reference 1 and reference 2 is given as: Δ𝜔 ref1,ref2 i𝑗 (Z) = ( 𝜔 ref1 i𝑗 (Z) -𝜔 ref2 i𝑗 (Z) ) × 100% 𝜔 ref1 i𝑗 (Z)+𝜔 ref2 i𝑗 (Z) 2.
radiationless Diroc-Fock calculations  [25]  and Scofield's radiative Dirac-Slater calculations. [17] "DF": values obtained from the combination of Chen et al. radiationless Diroc-Fock calculations  [25]  and Scofield's radiative Dirac-Fock calculations. [18] "EADL": values obtained from the Evaluated Atomic Data Library. [12] IGURE 4 "Bambynek1972": Values from Bambynek et al. earlier semi-empirical fit. [22] "Krause1979": values from Krause's semi-empirical fit. [40] "Bambynek1984": values from Bambynek et al. later semi-empirical fit  [41]. "NIST": semi-empirical fit values presented in NIST's Fundamental Parameters Database. [28] "Kahoul": values from Kahoul et al. empirical fit. [29] "Daoudi": values from Daoudi et al. empirical fit. [30] creases, better agreement is generally found between the different references.
[41] "NIST": semi-empirical fit values presented in NIST's Fundamental Parameters Database. [28] "Kahoul": values from Kahoul et al. empirical fit. [29] "Daoudi": values from Daoudi et al. empirical fit. [30] uorescence yields exhibit significantly high differences between each other, especially at low atomic numbers. In the range 3 ≤ Z < 20 some references present 10% to 100% difference to other references. As the atomic number increases better agreement is observed between all references. In the range 20 < Z < 80, the values are comprised within 10% difference from each other, and in the range 80 < Z < 96, differences are lower than 2%. The  K-M 2 and  K-M 3 semi-empirical and empirical values are normalized with the respective "DF" theoretical values in Figure  6c, d , and with the respective theoretical "DF,DS" values in Figure  6e ,f.
CONCLUSIONS The comparisons between all theoretical, empirical, and semi-empirical K-shell fluorescence yield values,  K , from the different references exhibit that NIST's Fundamental Parameters Database values disagree with the other references, especially in the atomic number range 60 ≤ Z ≤ 80. As such, we suggest a change to values obtained from other references. The  K ,  K-L 2 ,  K-L 3 ,  K-M 2 ,  K-M 3 partial fluorescence yields values from EADL and from Dirac-Fock/Dirac-Slater calculations ("DF,DS") exhibit some disagreement even though they were obtained from the same references. Pia et al. [13] [14] [15]  had already pointed out this disagreement in their comparisons of partial fluorescence yields (normalized without accounting for radiationless transitions). Part of this disagreement can be due to the fact EADL includes a correction to the radiationless transition probabilities that we do not included in the present work.
ACKNOWLEDGEMENTS This work was supported by the research center grant  UID/FIS/04559/2013  to  LIBPhys-UNL , from the  FCT/MCTES /PIDDAC, Portugal. Laboratoire Kastler Brossel is Unité Mixte de Recherche du CNRS, de l'ENS et de l'UPMC  No. 8552. JPS and PI acknowledge the sup-.
Synchrotron-radiation circular dichroism. 25 µL of collagen solutions in 3 mM HCl were loaded in quartz cells (Hellma) with a path length of 0. 01 cm. The measurements were performed on the DISCO Beamline at SOLEIL synchrotron (Saint Aubin, France). 31, 32 Melting temperatures were obtained by increasing temperature from 20 to 74°C with steps of 3°C and an equilibration time of 5 min. Raw spectra were acquired from 320 to 170 nm with a 1 nm spectral resolution. Spectra were treated with the CDTool software. 33 They are the average of three spectra. A background (HCl 3 mM acquired in the same conditions) was subtracted from them. Intensity calibration was obtained with a CSA sample. Second harmonic generation / 2-photon excited fluorescence. We used a custom-built laserscanning multiphoton microscope and recorded Second Harmonic Generation (SHG) and 2-photon excited fluorescence (2PEF) images in parallel as previously described.
Characterization techniques and numerical calculations 2. 3. 1. AFM microscopy Atomic Force Microscopy (AFM) was used to investigate the morphological, adhesive and mechanical properties of electrodeposited thin films. The physico-chemical and mechanical nanoscale features of the samples were measured using a Bruker Multimode 8 AFM with the Peakforce Quantitative Nanomechanics (PeakForce QNM) mode. Peak-Force QNM mode is a recent advancement in AFM method providing quantitative nanomechanical mapping mode with the simultaneous measurement of the sample's adhesion between tip and sample surface, Young's modulus (according to either DMT or Sneddon model), deformation and energy dissipation along with the surface topography. The imaging scan size was (5 µm × 5 µm). The average adhesion and the DMT Modulus were determined using the Gwydion software.
QNM etched silicon probes (RTESPA-300 probes presenting a nominal spring constant k ≈ 40 N/m) were provided by Bruker. All used tips were calibrated according to Bruker's recommendations. The results were analyzed by both Nanoscope analysis 1. 9 software provided by Bruker and Gwyddion. The adhesion and DMT modulus parameters were measured for at least three representative AFM images from different areas of each bead, and at least three different samples for each film were studied.
As exhibited in Fig. 1c  & d , the spacing between the final tip apex and the irradiated surface plane can be controlled at each step. It is equal to (450±150 nm). The location of the GB or interface appearing in the needle is controlled with TKD imaging between the final steps of annular milling. These procedures ensure that the analyzed feature from a depth of 300-600 nm beneath the irradiated surface is finally located in the first 100 nm of the needle. reconstruction, both the commercial IVAS software (CAMECA, v. 3. 6. 6) and the GPM 3D software (from GPM lab, v. 6. 3) were used.
Acknowledgement This work was performed on the GENESIS platform, financially supported by  Centre National de la Recherche Scientifique (CNRS)  belonging to the project entitled " Investissements d'avenir " with a reference number  ANR-11-EQPX-0020. This work is part of the  EM2VM Joint Laboratory Study and Modeling of the Microstructure for Ageing of Materials. This work was supported by the  MAI-sn  ( Materials Ageing Institute-Scientific Network , http://themai. org/scientific-network). The authors also owe their sincere gratitude to  Prof. Didier Blavette  for the fruitful discussions.
040-0. 063 mm, Merck and eluents are indicated for each particular case. Gel permeation chromatography (GPC) was performed using Bio-Beads S-X1 (200400 mesh, Bio-Rad, Hercules, CA, USA). NMR spectra were recorded on a Bruker Ascend 400 spectrometer. 1 H and 13 C NMR spectra were recorded using Bruker DPX 600 at 600 and 150 MHz, respectively, while for oxidized complex, the NMR spectra were recorded on a Bruker Ascend 400 spectrometer. The IR spectra were obtained using Jasco 6300 FTIR. UV-Vis spectra were recorded with a Varian Cary 5 or Shimadzu UV-2600 spectrophotometer. MALDI-TOF MS was performed on a Bruker ultrafleXtreme using RP 700-3500-Da LP-700-3500-Da methods and 2, 5-dihydroxybenzoic acid (DHB) as the matrix on a ground steel plate. The MALDI-TOF mass data for Pcs are presented as the mass of the most intense peak in the cluster instead of exact mass.
Computational Details The starting geometries of Pz tCzZnPc1 were optimized using CAM-B3LYP/LANL2DZ  [31, 32]  for all atoms. Frequency calculation was used to confirm the energy minima in optimized geometry. Chloroform was used as a solvent in all of the single point DFT-PCM and TDDFT-DCM calculations were performed using the polarizable continuum model (PCM) to study the solvation effects  [34]. The first 100 excited states of each compound were calculated in all TDDFT-PCM calculations. All DFT calculations were conducted using the Gaussian 09 software package  [35] , and the GaussView program  [36]  was used for the molecular orbital analysis. 2 ),  [37]  have been prepared according to published procedures.
Funding: This work was financially supported by the  Kuwait Foundation for the Advancement of Science  (Grant Number  PN18-12-SC01 ) and the  RSP unit general facilities of the Faculty of Science GFS  ( GS 01/01 ,  GS 03/01 ,  GS 01/03 ,  GS 01/05 , and  GS 02/13 ) (S. M. ). T. T. thanks  MINECO  (project  CTQ2017-85393-P ) and  ERA-NET/European Commission/MINECO , ( UNIQUE ,  SOLAR-ERA. NET Cofund 2 N • 008/PCI2019-111889-2 ). R. D. acknowledges  ANR  for funding through  ODYCE project. (Grant agreement No  ANR-14-OHRI-0003-01 ). RD thanks  European Research Council (ERC)  for funding. This project has received funding from the  European Union 's  Horizon 2020 research and innovation program  (grant agreement No  832606 )-Project  PISCO.
Humidity-dependent spectroscopic ellipsometry (SE) The porosity and pore size of alteration layers formed on ISG samples were characterized using a rotating compensator spectroscopic ellipsometer (Alpha-SE, J. A. Woollam Co. ) equipped with a sample cell and an airflow system that allow to control the RH within the cell during the SE measurements. The ellipsometer has a wavelength range of 381-893 nm with a wavelength increment of ~6 nm. The RH value in the cell was monitored using an RH meter with its probe inserted into the cell. The water isotherm was determined for both adsorption and desorption processes. Detailed experimental procedure and data analysis can be found in ref. 40  Molecular dynamics (MD) simulations of hydrogen bonding interactions of hydrous species in nano-porous silica gels LAMMPS  117  software was used to perform all MD simulations using a Diffuse Charge Reactive potential initially developed by Mahadevan and Garofalini for the simulation of bulk water  118  and later parameterized for sodium  119  and other elements.
The resultant nano-porous structures (named Gel298, Gel598, and Gel998 for the 298, 598, and 998 K processed gels, respectively) had poresize distributions as shown in Fig. 9. The average pore sizes were 6. 95, 9. 98, and 17. 53 Å for the gels obtained by processing at 298, 598, and 998 K, respectively. Thus, higher equilibration temperature led to porous structures with larger sized pores, which are due to higher available thermal energy to rearrange the pore structures. Following the pore structure generations, water molecules at a density of ~1 g/cm  3  were inserted into the pore areas of the gels using the "regions" feature in the LAMMPS software. The resultant gel-water system was run under NVT conditions for ~2 ns to study the hydrogen bonding interactions and the structural information.
Attenuated total reflection infrared (ATR-IR) spectroscopy The amount of hydrous species (Si-OH and molecular water) in the alteration layer was measured using a Fourier transform infrared spectrometer equipped with a 20x objective and a Germanium crystal (Bruker Hyperion 3000). The incident angle of the IR beam was 37°and an area of 70 × 70 μm 2 was examined. Each spectrum was an average of 100 scans and a spectral resolution of 4 cm -1 was set for the data collection. The experiments were performed at room relative humidity (~37%). A spectrum of air at room RH was used as the reference.
9  Relative distribution of pore size in the glasses processed at different temperatures, normalized to the volume fraction of the largest pores. The average pore sizes were 6. 95, 9. 98, and 17. 53 Å for the gels obtained by processing at 298, 598, and 998 K, respectively. respectively. The step scan in SFG experiments was 10 cm -1 in the frequency range of 3000-4000 cm -1 and each data point was an average of 300 pulses. The SFG spectra were collected with a polarization combination of ssp (s-polarized SFG, s-polarized 532 nm, p-polarized IR) and normalized to IR and visible beam intensities to account for the laser power fluctuation. The spectra obtained were then fitted using non-linear curve fittings in Matlab (see the Supplementary Information). The relative humidity during the SFG measurements was controlled by mixing a dry nitrogen flow and a water vapor-saturated nitrogen flow.
ACKNOWLEDGEMENTS This work was supported as part of the  Center for Performance and Design of Nuclear Waste Forms and Containers , an  Energy Frontier Research Center  funded by the  U. S. Department of Energy, Office of Science, Basic Energy Sciences  under Award #  DE-SC0016584. We thank  Dr. Michael A. Hickner  ( The Pennsylvania State University ) for the access to the spectroscopic ellipsometry set-up in his lab, and  Dr. Nicholas J. Smith  ( Corning, Inc. ) for providing the porous Vycor glass used in this study.