## Case Study: small angle scattering ### Paper 1: Phase behavior of colloidal silica rods Paper link: [[Phase behavior of colloidal silica rods]] - **How was the data collected? Is there information on exposure time, sample container, sample transmission, sample thickness, detector distance and so on?** The authors did not mention the exposure time or the sample transmission in the paper. The samples were placed in flat glass capillaries (Vitrocom) with internal dimensions of $0.1 \times 1 \times 100\ mm^{3}$. The glass thickness is $100\ \mu m$. The wavelength of the X-rays used was 0.095 nm. The beam size at the sample position was 0.3 mm. The distance between the sample and the detector was 7.4 meters. - **Do they mention the type of detector used?** A CCD detector by Photonic Science Ltd was used, with a pixel size of $9 \times 9\ \mu m$. - **What corrections were applied?** The paper does not detail any corrections made to the data, including background subtraction or ensuring the data are on an absolute scale. The integration was performed by integrating over a circular sector containing the area of interest in the scattering patterns. - **What type of integration was applied?** The integration was performed by radial integration for different phases (isotropic, nematic phase, smectic-C phase, etc.) in horizontal and vertical directions. - **Is the data shown in absolute scale?** The paper does not provide information to confirm whether the data is shown on an absolute scale. The authors did not mention any intensity values in numerical form, or any corrections that would indicate the data is on an absolute scale. All comparisons and extractions in the paper are given qualitatively. - **Is the data background subtracted? How did the assure a proper subtraction?** The paper does not mention if the data was background subtracted, nor does it provide details on how a proper background subtraction was ensured. - **How was the data interpreted? Did they use modelling? Which one?** the SAXS data in the paper was interpreted qualitatively without the use of explicit modeling. TEM measurements are combined with SAXS by checking the minimum interparticle distance to estimate effective dimensions of the rods, and these effective values aids to establish the phase diagram, but they are not the typical modelling method for SAXS. - **Did they indicate the structure and form factor contributions?** The structure factor and form factor from SAXS are not explicitly discussed in the paper. Although one can clearly notice the intensity profile shows a structure factor induced fluctuation in horizontal direction (perpendicular to gravity) for selected phases. The radial distribution function $g(r)$ and 2D local hexagonal bond orientational order parameter $\psi_{6}$ were obtained, but from confocal scanning. - **Did they indicate the sample concentration? Is a structure factor visible?** Yes, the paper does indicate the sample concentration. The concentration is expressed in terms of volume fraction, which varies due to sedimentation. The volume fractions are provided for different systems of silica rods (e.g., systems B31, B35, B36, B48, and N51) in Table 1 of the paper. However, due to the experiments undergoes sedimentation, the actual concentration characterized by SAXS and confocal scanning could be much more dense than the values reported here. The structure factor is visible from most SAXS plot provided in the paper, this is reasonable considering the high packing density. - **Did the fit the data? What’s the estimated error?** No, they did not provide any model and doing fitting. - **What software was used for the fitting?** The did not do fitting. - **Discuss the good and bad examples of documentation from the manuscripts.** Real space structure is obtained from the scattering experiments, also confocal measurements. This enables the phase behavior due to special arrangement of particles being much convincing. However, very little information on intensity value was given. The paper did not even show normalized intensity. Data analysis and interpretation relays mainly on confocal data, and SAXS seems only being an a less important auxiliary methods. More analysis could be done in principal based on the raw scattering data. - **Are any of the model-free methods used in the model manuscripts? Which one? Why?** Yes, correlation analysis was performed. Due to the close-packed nature of the system, the authors determined the interparticle distances from the intensity profile directly. - **Do the model manuscripts detail the method used?** The paper did not discuss how they analyze the correlation for SAXS in detail, since the $g(r)$ in the paper is provided by confocal scanning rather than scattering. - **Do you think you could replicate the analysis?** Yes, it's possible. - **Could any of the model-free methods be used for your research? Which one? Why?** - **Do you indentify the Gunier, Fourier or Porod region in your model manuscripts? If so, select the figure and describe it.** Yes. - **What type of radius of gyration would you use for the sample of interest?** For the particles described in this paper, radius of gyration for elongated cylinder would be the best. - **Which method for the calculation of molecular weight could be possible for your sample of interest?** Due to the close-packed nature of the system, the molecular weight estimation is almost impossible. Considering the particles are silica rods and typically have pre-known molecular weight, this should not be a big issue. ### Paper 2: A New Insight into Growth Mechanism and Kinetics of Mesoporous Silica Nanoparticles by in Situ Small Angle X‑ray Scattering Paper link: [[A New Insight into Growth Mechanism and Kinetics of Mesoporous Silica Nanoparticles by in Situ Small Angle X‑ray Scattering]] - **How was the data collected? Is there information on exposure time, sample container, sample transmission, sample thickness, detector distance and so on?** The sample container (or measurement setup) is a combined system with a quartz capillary (20 mm length, 2.5 mm outside diameter, 0.01 mm thickness) and a circulating setup with a pump, tubes, and a beaker with stirring. Total exposure time is different for selected temperatures. At 30 °C, 2 seconds every 28 seconds for 150 minutes (total 300 patterns); at 95 °C, measurements were completed in 1 hour. Sample-detector distance is 1.6 m. Energy adjusted to 9 keV, covering a Q range of 0.008−0.45 Å−1. - **Do they mention the type of detector used?** The detector applied is Pilatus 1M. - **What corrections were applied?** They applied beam masking, hot pixel and gap averaging, and radial averaging using Scatterbrain software. Background subtraction and absolute intensity calibration using Milli-Q water. (2.3. Setup of time-resolved synchrotron SAXS) - **What type of integration was applied?** The type of integration applied was radial averaging. The isotropic counts on the Pilatus detector were radially averaged around the direction of the primary beam to convert the data to intensity versus Q, using the measurement geometry of the beamline software (Scatterbrain). - **Is the data shown in absolute scale?** Yes, the data was shown in absolute scale. The scattering intensity was normalized using Milli-Q water as the standard. - **Is the data background subtracted? How did the assure a proper subtraction?** Yes, the data was background subtracted. Proper subtraction was assured by collecting an appropriate background from capillary tubes filled with the reaction solution (phosphate buffer or ammonium hydroxide) and subtracting this from each scattering curve. - **How was the data interpreted? Did they use modelling? Which one?** Yes, the author did modelling for the data. The ellipsoid core-shell model was applied before TEOS addition, and a sphere core-shell model was used after TEOS addition. - **Did they indicate the structure and form factor contributions?** Yes, and they explicitly stated that the intensity satisfies $I(Q)=P(Q)\cdot S(Q)+\textrm{background}$ in 2.4. Modelling of CTAB micelles. The form factor for CATB micelles both with and without TEOS addition was calculated and shown. The form factors for both models are provided in the supplementary material (Figure S3). - **Did they indicate the sample concentration? Is a structure factor visible?** Yes, they indicated the sample concentration. The CTAB concentration was 80 mM, and the TEOS concentration was also 80 mM for all samples. But due to this is a time dependent reaction, the concentration of structures of interest might vary during the measurement. A structure factor was visible in the scattering patterns. The presence of a peak related to the structure factor of CTAB micelles at around 0.075 Å⁻¹ was observed, which disappeared during the growth of MSNs due to the condensation of silica changing the interaction between micelles. The time that this peak becomes invisible indicates the formation of mesoporous silica and completion of the MSN growth reaction. - **Did the fit the data? What’s the estimated error?** Yes, they fitted the data with the model mentioned previously. The estimated error was not explicitly mentioned. But from the plot the authors provided in Figure 4, the fitting is very good. Although $q$ less than 0.03 Å⁻¹ was not fitted. - **What software was used for the fitting?** They use SASview. - **Discuss the good and bad examples of documentation from the manuscripts.** This paper provided most information required to repeat the experiment. The data reduction, modelling and fitting was extensively discussed. The experiment setup is relatively complicated since this is a time-resolved measurement, and the paper shows detailed setup for the experiment. Overall, the documentation is good and does not have noticeable drawbacks to be improved. - **Are any of the model-free methods used in the model manuscripts? Which one? Why?** Yes, the paper uses a model-free method. The authors calculated the Porod invariant as a representation of the volume fraction of each component (for this paper, volume fraction of silica is of the interest), consequently determine the MSN growth and gain an estimation of the silica growth kinetics. - **Do the model manuscripts detail the method used?** Yes, they used a three-component Porod invariant, and consider the growth follows the Avrami equation. This enables them to fit the fraction of invariant and time. This is discussed in 3.1. Growth kinetics of MSNs. The invariant is $\text{Invariant} = 2\pi^2 (\rho_1 \varphi_1 \Delta_1^2 + \rho_2 \varphi_2 \Delta_2^2 + \rho_3 \varphi_3 \Delta_3^2)$ - **Do you think you could replicate the analysis?** It's possible, but quite difficult. The fitting of this time-dependent measurement can be complicated considering the multiple-components core-shell system and ellipsoid shape of the particle. Scattering invariant is also a more complicated case compared with the typically two-component systems. To get reasonable analysis, good measurements and data reduction would be required. - Could any of the model-free methods be used for your research? Which one? Why? - **Do you indentify the Gunier, Fourier or Porod region in your model manuscripts? If so, select the figure and describe it.** Yes. - **What type of radius of gyration would you use for the sample of interest?** For this sample, $R_{g}$ for core-shell system can be applied. But considering the porosity or ellipsoid shape, modification would be a must. Such 3-compnent system with different SLD makes radius of gyration less reasonable to be applied. - **Which method for the calculation of molecular weight could be possible for your sample of interest?** Getting absolute scaled $I(0)$ and using Porod volume should both work in theory. $I(0)$ may be extracted rather easy with the fitted model (though not sure how well is the fitting for low $q$ region). Porod invariant is already calculated in this paper. ### Paper 3: Temperature-Dependent Nanostructure of an End-Tethered Octadecane Brush in Tetradecane and Nanoparticle Phase Behavior Paper link: [[Temperature-Dependent Nanostructure of an End-Tethered Octadecane Brush in Tetradecane and Nanoparticle Phase Behavior]] Direct investigation of slope at Porod region shows a gel behavior (with fractal dimension 2.2) at 20 degrees and fluid state at 40 degrees. Indicating that nanoparticle aggregation is related to phase transition of octadecane brushes. The authors extracted the shell thickness, grafting density, tilt angle of octadecane chains by fitting the SANS data to a polydisperse core-shell model. - **How was the data collected? Is there information on exposure time, sample container, sample transmission, sample thickness, detector distance and so on?** Information about brushes are collected using SANS and NR (neutron reflectometry). Exposure time is not specified. Sample container is demountable titanium cells with 1mm path length. The author did not mention the transmission data and sample thickness, but normalization is performed and the authors claimed that they are measured. Detector distance is selected as 1, 4, 13 m. - **Do they mention the type of detector used?** No, the detector is not explicitly mentioned in the paper. But the experiment is done on the NG3 30 m SANS instrument, which is shown on NIST website (https://www.nist.gov/ncnr/ngb-30m-sans-small-angle-neutron-scattering). On current website, the detector is described as "640 mm x 640 mm 3He position-sensitive proportional counter with a 5.08 mm x 5.08 mm resolution". - **What corrections were applied?** The author did not specify which corrections are applied, though the author did state that data reduction was performed. - **What type of integration was applied?** From the plot, radial integration was applied. - **Is the data shown in absolute scale?** Yes. Normalization and background substruction was performed. Data reduction was done using the program IGOR Pro. Although no detailed information was given. - **Is the data background subtracted? How did they assure a proper subtraction?** Yes, the author used a linear fit to a Porod plot ($I(Q)\cdot Q^{4}$ versus $Q^{4}$) to determine low-Q intensity $I_{0}$, and consider it as the incoherent background. - **How was the data interpreted? Did they use modelling? Which one?** The intensity profile was fitted to a hard sphere model and core-shell model, then temperature-dependent behavior was suggested. The uncoated particle were modeled as a polydisperse hard sphere model (Schulz distribution). The coated silica particles ware modeled as a polydisperse core-shell model (Schulz distribution). - **Did they indicate the structure and form factor contributions?** No, these two factors are not discussed explicitly. But a fractal like behavior with a slope being -2.2 is shown for coated particles at low temperature, implicitly showing its contribution. - **Did they indicate the sample concentration? Is a structure factor visible?** Yes, concentration was provided in the paper. For uncoated silica nanoparticles used in contrast matching experiments, particle volume faction is less than 0.008. For octadecyl coated particles, concentration is $\phi=0.05$. Structure factor is only implicitly shown in the $\phi=0.05$ case to suggest fractal structure. - **Did they fit the data? What’s the estimated error?** Yes, as stated above the data was fitted to a polydisperse hard sphere model for uncoated particles and polydisperse core-shell model for coated particles. The paper did not provide $\chi^{2}$ like parameters to show how well is the fitting. The ranges of fitted parameters are provided, though. - **What software was used for the fitting?** They used IGOR Pro. - **Discuss the good and bad examples of documentation from the manuscripts** The paper provided comprehensive analysis for the studied systems at different temperatures and for coated and uncoated particles. Particle size and polydispersity were pre-studied using fiber optics quasi-elastic light scattering. NR was applied as a cross validation method to investigate the coated polymer behavior. Methodology is overall clear. However, the data reduction steps are not described, and the background subtraction was only done by a low-Q limit, rather than a separate empty cell. These information could be added in an appendix. - **Are any of the model-free methods used in the model manuscripts? Which one? Why?** This paper perform model free analysis on Guinier region, for octadecyl coated particle at low temperature, a fractal dimension of 2.2 can be extracted. And Porod plot was mentioned during the background reduction process. - **Do the model manuscripts detail the method used?** No, the model-free method is merely mentioned and not explicitly discussed. - **Do you think you could replicate the analysis?** Yes, for the SANS part it's possible. The analysis (not only the model free part) is straightforward. - **Could any of the model-free methods be used for your research? Which one? Why?** - **Do you identify the Gunier, Fourier or Porod region in your model manuscripts? If so, select the figure and describe it.**** Yes. - **What type of radius of gyration would you use for the sample of interest?** For silica particles (coated and uncoated), spherical one or core-shell one would be the best. - **Which method for the calculation of molecular weight could be possible for your sample of interest?** Using $I_{0}$ to calculate $M$ could be possible. But for such well-defined systems, molecular weight could be obtained rather simple in synthesis steps. ### Proposal writing