TY - JOUR A1 - Deumer, J. A1 - Pauw, Brian Richard A1 - Marguet, S. A1 - Skroblin, D. A1 - Taché, O. A1 - Krumrey, M. A1 - Gollwitzer, C. T1 - Small-angle X-ray scattering: characterization of cubic Au nanoparticles using Debye’s scattering formula N2 - A versatile software package in the form of a Python extension, named CDEF (computing Debye’s scattering formula for extraordinary form factors), is proposed to calculate approximate scattering profiles of arbitrarily shaped nanoparticles for small-angle X-ray scattering (SAXS). CDEF generates a quasi-randomly distributed point cloud in the desired particle shape and then applies the open-source software DEBYER for efficient evaluation of Debye’s scattering formula to calculate the SAXS pattern (https://github.com/j-from-b/CDEF). If self-correlation of the scattering signal is not omitted, the quasi-random distribution provides faster convergence compared with a true-random distribution of the scatterers, especially at higher momentum transfer. The usage of the software is demonstrated for the evaluation of scattering data of Au nanocubes with rounded edges, which were measured at the four-crystal monochromator beamline of PTB at the synchrotron radiation facility BESSY II in Berlin. The implementation is fast enough to run on a single desktop computer and perform model fits within minutes. The accuracy of the method was analyzed by comparison with analytically known form factors and verified with another implementation, the SPONGE, based on a similar principle with fewer approximations. Additionally, the SPONGE coupled to McSAS3 allows one to retrieve information on the uncertainty of the size distribution using a Monte Carlo uncertainty estimation algorithm. KW - X-ray scattering KW - SAXS KW - Non-spherical nanoparticles KW - Nanoparticles KW - Nanomaterials KW - Debye scattering equation KW - Simulation KW - Data fitting PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-557652 DO - https://doi.org/10.1107/S160057672200499X VL - 55 IS - Pt 4 SP - 993 EP - 1001 PB - International Union of Crystallography CY - Chester, England AN - OPUS4-55765 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Chambers, M. S. A1 - Hunter, R. D. A1 - Hollamby, M. J. A1 - Pauw, Brian Richard A1 - Smith, A. J. A1 - Snow, T. A1 - Danks, A. E. A1 - Schnepp, Z. T1 - In Situ and Ex Situ X‑ray Diffraction and Small-Angle X‑ray Scattering Investigations of the Sol−Gel Synthesis of Fe3N and Fe3C N2 - Iron nitride (Fe3N) and iron carbide (Fe3C) nanoparticles can be prepared via sol−gel synthesis. While sol−gel methods are simple, it can be difficult to control the crystalline composition, i.e., to achieve a Rietveld-pure product. In a previous in situ synchrotron study of the sol−gel synthesis of Fe3N/Fe3C, we showed that the reaction proceeds as follows: Fe3O4 → FeOx → Fe3N → Fe3C. There was considerable overlap between the different phases, but we were unable to ascertain whether this was due to the experimental setup (side-on heating of a quartz capillary which could lead to thermal gradients) or whether individual particle reactions proceed at different rates. In this paper, we use in situ wide- and small-angle X-ray scattering (wide-angle X-ray scattering (WAXS) and small-angle X-ray scattering (SAXS)) to demonstrate that the overlapping phases are indeed due to variable reaction rates. While the initial oxide nanoparticles have a small range of diameters, the size range expands considerably and very rapidly during the oxide−nitride transition. This has implications for the isolation of Rietveld-pure Fe3N, and in an extensive laboratory study, we were indeed unable to isolate phasepure Fe3N. However, we made the surprising discovery that Rietveld-pure Fe3C nanoparticles can be produced at 500 °C with a sufficient furnace dwell time. This is considerably lower than the previous reports of the sol−gel synthesis of Fe3C nanoparticles. KW - Small-angle X-ray Scattering KW - SAXS KW - Diffraction KW - XRD KW - Scattering KW - Sol-gel KW - Iron nitride KW - Nanoparticles KW - Iron carbide KW - Catalyst KW - In-situ KW - Ex-situ KW - Synthesis KW - Synchrotron PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-548226 DO - https://doi.org/10.1021/acs.inorgchem.1c03442 VL - 61 IS - 18 SP - 6742 EP - 6749 PB - ACS Publications CY - Washington AN - OPUS4-54822 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hahn, Marc Benjamin T1 - Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations N2 - Radiation damage to DNA plays a central role in radiation therapy to cure cancer. The physico-chemical and biological processes involved encompass huge time and spatial scales. To obtain a comprehensive understanding on the nano and the macro scale is a very challenging tasks for experimental techniques alone. Therefore particle-scattering simulations are often applied to complement measurements and aide their interpretation, to help in the planning of experiments, to predict their outcome and to test damage models. In the last years, powerful multipurpose particle-scattering framework based on the Monte-Carlo simulation (MCS) method, such as Geant4 and Geant4-DNA, were extended by user friendly interfaces such as TOPAS and TOPAS-nBio. This shifts their applicability from the realm of dedicated specialists to a broader range of scientists. In the present review we aim to give an overview over MCS based approaches to understand radiation interaction on a broad scale, ranging from cancerous tissue, cells and their organelles including the nucleus, mitochondria and membranes, over radiosensitizer such as metallic nanoparticles, and water with additional radical scavenger, down to isolated biomolecules in the form of DNA, RNA, proteins and DNA-protein complexes. Hereby the degradation of biomolecules by direct damage from inelastic scattering processes during the physical stage, and the indirect damage caused by radicals during the chemical stage as well as some parts of the early biological response is covered. Due to their high abundance the action of hydroxyl radicals (•OH) and secondary low energy electrons (LEE) as well as prehydrated electrons are covered in additional detail. Applications in the prediction of DNA damage, DNA repair processes, cell survival and apoptosis, influence of radiosensitizer on the dose distribution within cells and their organelles, the study of linear energy transfer (LET), the relative biological effectiveness (RBE), ion beam cancer therapy, microbeam radiation therapy (MRT), the FLASH effect, and the radiation induced bystander effect are reviewed. KW - DNA KW - Protein KW - G5P KW - OH KW - Au KW - AuNP KW - Radiation KW - SSB KW - DSB KW - Beta decay KW - Brachytherapy KW - Cancer treatment KW - Clustered nanoparticles KW - DNA damage KW - Dosimetry KW - Energy deposit KW - Geant4 KW - Geant4-DNA KW - Gold Nanoparticles KW - Livermore model KW - Low energy electrons KW - MCS KW - Microdosimetry KW - Monte-Carlo simulation KW - NP KW - OH radical KW - Particle scattering KW - Penelope model KW - Proteins KW - Radiation damage KW - Radiation therapy KW - Radiationtherapy KW - Radioactive decay KW - Radiolysis KW - Radiotherapy KW - Simulation KW - TOPAS KW - TOPAS-nbio KW - Base damage KW - Base loss KW - DNA radiation damage KW - Direct damage KW - Dissociative electron attachment (DEA) KW - Dissociative electron transfer (DET) KW - Double-strand break (DSB) KW - ESCA KW - Hydrated DNA KW - Hydrated electron KW - Hydration shell KW - Hydroxyl radical KW - Indirect damage KW - Ionization KW - Ionisation KW - NAP-XPS KW - Near ambient pressure xray photo electron spectroscopy KW - Net-ionization reaction KW - Prehydrated electron KW - Presolvated electron KW - Quasi-direct damage KW - ROS KW - Radical KW - Reactive oxygen species KW - Single-strand break (SSB) KW - XPS KW - Xray KW - Xray photo electron spectrocopy KW - Cosolute KW - Ectoin KW - Ectoine KW - GVP KW - Gene five protein KW - Hydroxyectoine KW - Ionizing radiation damage KW - OH radical scavenger KW - Monte-Carlo simulations KW - Nanodosimetry KW - Osmolyte KW - Particle scattering simulations KW - Protein unfolding KW - Radical Scavenge KW - Radical scavenger KW - Single-stranded DNA-binding proteins KW - SAXS KW - Bio-SAXS KW - X-ray scattering KW - ssDNA KW - dsDNA KW - FLASH effect KW - Bystander effect KW - Ion beam therapy KW - Bragg peak KW - LET KW - MCNP KW - Photons KW - Electrons KW - Carbon ions KW - MRT KW - RNA KW - RBE KW - base loss KW - abasic side KW - DMSO KW - Cells PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-573240 DO - https://doi.org/10.1088/2399-6528/accb3f SN - 2399-6528 VL - 7 IS - 4 SP - 042001 PB - Institute of Physics (IOP) Publishing CY - London AN - OPUS4-57324 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Laskina, Sofya T1 - Computing the forward and inverse problem of X-ray scattering N2 - Continuing progress in the field of X-ray scattering methods empowers scientists with new possibilities to capture the most important piece of information about the structure of the sample - its 3D electron density. Although the first methods appeared almost a century ago, recovering the density structure of a sample is still very problematic. Most avail-able imaging techniques transform a 3D electron density of a realspace structure into the 2D Fourier Transform of the intensity of scattered waves in the reciprocal space. This process causes a loss of information. Firstly, instead of a 3D sample, a 2D image is created, and secondly, the phase information of the scattered waves is lost. The latter is known as the ”phase problem” and poses a serious obstacle on a way to recover a 3D electron density. In this work, we draw attention to the problem of forward and inverse Small Angle X-Ray Scattering. In the first, forward, part, we rethink the existing pipelines to computationally simulate such scattering experiments. Although there are efficient implementations of fast Fourier transformation, they often have some drawbacks. For instance, to calculate a 3D fast Fourier transform it is required to place its density in the RAM. For high-resolution structures of size > 1024 3 , this becomes very problematic, as the whole density structure requires more than 16 GB of memory. CUDA solution allows for a very fast and parallelizable implementation of high-resolution data on hundreds of last-generation machines. Such computations are very pricy and inaccessible for most scientists. To bypass this limitation, we propose a solution for a split-up 3D fast Fourier transform, which is implemented as a sequence of 2D and 1D operations. We compare our implementation on the simulated 3D shapes and show the result of a proof-of-concept on 4096 3 Metallorganic framework density structure. In the second, inverse problem, we train an invertible neural network, that given scattering data can predict the shape and its parameters. The architecture is built such, that the inverse problem is learned together with the forward process - the Fourier Transformation. We achieved very good results with this architecture, nonetheless, further testing is required, as the current training set only encompasses three simple shapes: sphere, hard sphere and cylinder. All code to reproduce and analyze the results is available at https: //github.com/sofyalaski/SAXS-simulations. KW - Machine Learning KW - SAXS KW - DFT PY - 2023 SP - 1 EP - 76 PB - Freie Universität Berlin CY - Berlin AN - OPUS4-56798 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Iannuzzi, Maurizio A1 - Chowdhary, Suvrat A1 - Fiedler, Holly A1 - Haoues, Kilian A1 - Schade, Boris A1 - Thünemann, Andreas A1 - Quaas, Elisa A1 - Koksch, Beate T1 - Rational design of polyfluorinated peptide-based materials: Self-assembly of an amphiphilic motif N2 - Generation of a pH sensitive amphiphilic block oligopeptide containing the bioactive function RGD and a library of derivatives varying the length of the hydrophobic core and the degree of side chain fluorination. Peptide rational design enables us to obtain desired features (pH sensitivity etc.). The introduction of fluorine alters a wide range of peptide properties such as secondary structure propensity, folding, thermal and metabolic stability and proteolytic resistance. The RGD function is highly effective at promoting the attachment of numerous cell types to a plethora of materials. This small sequence is the principal integrin-binding domain present within ECM proteins such as fiobronectin, vibronectin and fibrinogen. For this reason, RGD containing peptides offer several advantages for biomaterials applications. The use of RGD compared with native ECM proteins, minimized the risk of immune reactivity or pathogen transfer. Herein in this work, we present the peptide motif X6RGD and its fluoro-derivates for prospective receptor-specific drug delivery in cancer theraphy. Overall, our results demonstrate that high degree of fluorination achieved triggers a selective modification of peptide self-assembly dramatically improving the structural properties, the carrier suitability, enzimatic degradation profiles and cytotoxic features of the fluoropeptide conjugate(s). T2 - 37th European Peptide Symposium CY - Florence, Italy DA - 25.08.2024 KW - Nanostructure KW - SAXS KW - Small-angle X-ray scattering PY - 2024 SN - 1099-1387 VL - 30 IS - S2 SP - 247 EP - 248 PB - Wiley CY - New York, NY AN - OPUS4-62191 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Müller, W. A1 - Schweins, R. A1 - Nöcker, B. A1 - Kohlbrecher, J. A1 - Smales, Glen Jacob A1 - Huber, K. T1 - Comparative study of the co-assembly behaviour of 3-chloro-4-hydroxy-phenylazo dyes with DTAB N2 - The co-assembly of three one-fold negatively charged 3-chloro-4-hydroxy-phenylazo dyes (Yellow, Blue and Red) with the cationic surfactant dodecyltrimethylammoniumbromide (DTAB) was studied to probe dye–DTAB binding stoichiometry and assembly morphology. For each dye, phase separation was observed above a given dye : DTAB ratio with the ratio depending on the dye. While Yellow and DTAB showed liquid/liquid phase separation above Yellow : DTAB = 1 : 1.67, crystalline dye–DTAB complexes were observed for Blue–DTAB and Red–DTAB above Blue : DTAB = 1 : 2.56 and Red : DTAB = 1 : 2.94 respecively. In homogeneous solution, UV/vis spectroscopic investigations suggest stochiometries of Yellow : DTAB = 1 : 2, Blue : DTAB = 1 : 3 and Red : DTAB = 1 : 4. It was concluded, that Yellow exhibits the highest dye : DTAB binding stoichiometry in both, dye–surfactant complexes in the 2-phase region and in solution, whereas the lowest dye : DTAB binding stoichiometry was observed for Red–DTAB in both cases. The observed stoichiometries are inversely correlated to the impact dye addition has on the morphology of DTAB micelles. Generally, addition of dye to DTAB micelles leads to a reduction in spontaneous curvature of these micelles and to the formation of triaxial ellipsoidal or cylindrical micelles from oblate ellipsoidal DTAB micelles. At a DTAB concentration of 30 mM and a dye concentration of 5 mM, this effect was most pronounced for Red and least pronounced for Yellow, whilst Blue showed an intermediate effect. KW - Dye KW - DTAB KW - SAXS KW - Small-angle X-ray scattering KW - X-ray scattering KW - Data analysis KW - Micelle PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-576978 DO - https://doi.org/10.1039/D3SM00501A SN - 1744-683X VL - 19 IS - 24 SP - 4588 EP - 4598 PB - Royal Society of Chemistry AN - OPUS4-57697 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kool, L. A1 - Dekker, F. A1 - Bunschoten, A. A1 - Smales, Glen Jacob A1 - Pauw, Brian Richard A1 - Velders, A. H. A1 - Saggiomo, V. T1 - Gold and silver dichroic nanocomposite in the quest for 3D printing the Lycurgus cup N2 - The Lycurgus cup is an ancient glass artefact that shows dichroism as it looks green when a white light is reflected on it and a red colouring appears when a white light is transmitted through it. This peculiar dichroic effect is due to silver and gold nanoparticles present in the glass. In this research we show the synthesis of dichroic silver nanoparticles and their embedding in a 3D printable nanocomposite. The addition of gold nanoparticles to the silver nanoparticle composite, gave a 3D printable nanocomposite with the same dichroism effect of the Lycurgus cup. KW - SAXS KW - Au KW - Ag KW - Nanocomposite KW - 3D printing PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-501831 DO - https://doi.org/10.3762/bjnano.11.2 SP - 16 EP - 23 AN - OPUS4-50183 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hunter, R. D. A1 - Rowlandson, J. L. A1 - Smales, Glen Jacob A1 - Pauw, Brian Richard A1 - Ting, V. P. A1 - Kulak, A. A1 - Schnepp, Z. T1 - The effect of precursor structure on porous carbons produced by iron-catalyzed graphitization of biomass N2 - This paper reports a systematic study into the effect of different biomass-derived precursors on the structure and porosity of carbons prepared via catalytic graphitization. Glucose, starch and cellulose are combined with iron nitrate and heated under a nitrogen atmosphere to produce Fe3C nanoparticles, which catalyze the conversion of amorphous carbon to graphitic nanostructures. The choice of organic precursor provides a means of controlling the catalyst particle size, which has a direct effect on the porosity of the material. Cellulose and glucose produce mesoporous carbons, while starch produces a mixture of micro- and mesopores under the same conditions and proceeds via a much slower graphitization step, generating a mixture of graphitic nanostructures and turbostratic carbon. Porous carbons are critical to energy applications such as batteries and electrocatalytic processes. For These applications, a simple and sustainable route to those carbons is essential. Therefore, the ability to control the precise structure of a biomass-derived carbon simply through the choice of precursor will enable the production of a new generation of energy materials. KW - SAXS KW - Porous carbons KW - Graphitization KW - Iron nanoparticles KW - Catalysis KW - Gas sorption PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-515531 DO - https://doi.org/10.1039/d0ma00692k VL - Royal Society of Chemistry SP - 1 EP - 11 AN - OPUS4-51553 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Pauw, Brian Richard T1 - How to manage a modern X-ray scattering lab – a modest example N2 - Introduction A good laboratory organization can help address the reproducibility crisis in science, and easily multiply the scientific output of a laboratory, while greatly elevating the quality of the measurements. We have demonstrated this for small- and wide-angle X-ray scattering in the MOUSE project (Methodology Optimization for Ultrafine Structure Exploration). In the MOUSE, we have combined: a) a comprehensive laboratory workflow with b) a heavily modified, highly automated X-ray scattering instrument. This combination allows us to collect fully traceable scattering data, with a well-documented data flow (akin to what is found at the more automated beamlines). With two full-time researchers, the lab collects and interprets thousands of datasets, on hundreds of samples for dozens of projects per year, supporting many users along the entire process from sample selection and preparation, to the analysis of the resulting data. While these numbers do not light a candle to those achieved by our hardworking compatriots at the synchrotron beamlines, the laboratory approach does allow us to continually modify and fine-tune the integral methodology. So for the last three years, we have incorporated e.g. FAIR principles, traceability, automated processing, data curation strategies, as well as a host of good scattering practices into the MOUSE system. We have concomitantly expanded our purview as specialists to include an increased responsibility for the entire scattering aspect of the resultant publications. This ensures full exploitation of the data quality, whilst avoiding common pitfalls. Talk scope This talk will present the MOUSE project as implemented to date, and will introduce foreseeable upgrades and changes. These upgrades include better pre-experiment sample scattering predictions to filter projects on the basis of their suitability, exploitation of the measurement database for detecting long-term changes and automated flagging of datasets, extending the measurement range through an Ultra-SAXS module, and enhancing MC fitting with sample scattering simulations for better matching of odd-shaped scatterers. T2 - 2021 joint virtual meeting of the African Light Source (AfLS), the African Physical Society (AfPS), and Pan African Conference on Crystallography (ePCCr) CY - Online meeting DA - 15.11.2021 KW - X-ray scattering KW - MOUSE KW - Instrumentation KW - SAXS KW - Methodology KW - Laboratory management KW - Databases KW - Data management KW - Data catalog KW - Scicat PY - 2021 UR - https://events.saip.org.za/event/170/contributions/7619/ AN - OPUS4-53811 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Smales, Glen Jacob A1 - Pauw, Brian Richard T1 - The MOUSE project - A meticulous approach for obtaining traceable, wide-range X-ray scattering information N2 - Herein, we provide a "systems architecture"-like overview and detailed discussions of the methodological and instrumental components that, together, comprise the "MOUSE" project (Methodology Optimization for UltrafineStructure Exploration). The MOUSE project provides scattering information on a wide variety of samples, with traceable dimensions for both the scattering vector (q) and the absolute scattering cross-section (I). The measurable scattering vector-range of 0.012≤ q (nm-1) ≤ 92, allows information across a hierarchy of structures with dimensions ranging from ca. 0.1 to 400 nm. In addition to details that comprise the MOUSE project, such as the organisation and traceable aspects, several representative examples are provided to demonstrate its flexibility. These include measurements on alumina membranes, the tobacco mosaic virus, and dual-source information that overcomes fluorescence limitations on ZIF-8 and iron-oxide-containing carbon catalyst materials. KW - X-ray scattering KW - MOUSE KW - Instrumentation KW - SAXS KW - Methodology KW - Traceability KW - Wide-range KW - Data curation KW - FAIR KW - Uncertainties KW - Nanomaterials KW - Nanometrology PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-528669 DO - https://doi.org/10.1088/1748-0221/16/06/P06034 VL - 16 IS - 6 SP - 1 EP - 50 PB - IOP CY - Bristol, UK AN - OPUS4-52866 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Pauw, Brian Richard T1 - X-ray Scattering for Nanostructure Quantification, and the Quest for the Perfect Experiment N2 - Compared to the clear, real-space images you can get from electron microscopy, X-ray scattering patterns are rather featureless. These patterns, however, contain structural information from all of the material structure illuminated by the X-ray beam. With this technique, you can measure nanoparticle dispersions, catalysts, composites, MOF powders, battery materials, light metal alloys and gels to reveal information on the structural features found within these materials. We have even measured many such materials for several research groups from the University of Birmingham, revealing structure features in the sub-nm to the micrometer range. Measuring an X-ray scattering pattern is relatively easy, but measuring a high-quality, useful pattern requires significant effort and good laboratory organization. Such laboratory organization can help address the reproducibility crisis in science, and easily multiply the scientific output of a laboratory, while greatly elevating the quality of the measurements. We have demonstrated this for small- and wide-angle X-ray scattering in the MOUSE project (Methodology Optimization for Ultrafine Structure Exploration) [1]. With the MOUSE, we have combined: a) a comprehensive and highly automated laboratory workflow with b) a heavily modified X-ray scattering instrument. This combination allows us to collect fully traceable scattering data, within a well-documented, FAIR-compliant data flow (akin to what is found at the more automated synchrotron beamlines). With two full-time researchers, our lab collects and interprets thousands of datasets, on hundreds of samples, for dozens of projects per year, supporting many users along the entire process from sample selection and preparation, to the analysis of the resulting data. T2 - School of Chemistry Seminars CY - Birmingham, UK DA - 10.11.2021 KW - X-ray scattering KW - MOUSE KW - Instrumentation KW - SAXS KW - Methodology KW - Nanostructure PY - 2021 UR - https://www.youtube.com/watch?v=N2kY4wbqeM4 AN - OPUS4-53810 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hallier, Dorothea C. A1 - Smales, Glen Jacob A1 - Seitz, H. A1 - Hahn, Marc Benjamin T1 - Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine N2 - Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL−1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies. KW - BioSAXS KW - Bio-SAXS KW - Cosolute KW - Ectoine KW - G5P KW - GVP KW - Radiation damage KW - Radical Scavenger KW - Single-stranded DNA-binding proteins KW - X-ray scattering KW - DNA KW - ssDNA KW - Protein KW - SAXS KW - Small-angle xray scattering KW - McSAS3 KW - Dosimetry KW - Microdosimetry KW - Geant4 KW - Geant4-DNA KW - Topas KW - Topas-MC KW - Monte-Carlo simulations KW - Particle scattering simulations KW - Topas-nBio KW - OH Radical KW - OH radical scavenger KW - LEE KW - Ionizing radiation damage KW - Protein unfolding KW - Ectoin PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-568909 DO - https://doi.org/10.1039/d2cp05053f SN - 1463-9076 SN - 1463-9084 VL - 25 IS - 7 SP - 5372 EP - 5382 PB - Royal Society of Chemistry CY - Cambridge AN - OPUS4-56890 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hallier, Dorothea C. A1 - Smales, Glen Jacob A1 - Seitz, H. A1 - Hahn, Marc Benjamin T1 - Inside back cover for the article "Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine" N2 - Showcasing research from the Federal Institute for Material Research and Testing Berlin and Fraunhofer Institute for Celltherapy and Immunology Branch Bioanalytics and Bioprocesses Potsdam. Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine. We aimed to increase the possible undisturbed exposure time during bio-SAXS measurements of single-stranded DNA-binding proteins. Therefore small angle X-ray scattering was performed on Gene-V Protein (G5P/GVP), which is involved in DNA repair processes. To achieve this, irradiations were performed in presence and absence of the hydroxyl-radical scavenger and osmolyte Ectoine, which showed efficient radiation protection and prevented protein aggregation, thus allows for a non-disturbing way to improve structure-determination of biomolecules. KW - Bio-SAXS KW - BioSAXS KW - Cosolute KW - DNA KW - Dosimetry KW - Ectoin KW - Ectoine KW - G5P KW - GVP KW - Geant4 KW - Geant4-DNA KW - Ionizing radiation damage KW - LEE KW - McSAS3 KW - Microdosimetry KW - Monte-Carlo simulations KW - OH Radical KW - OH radical scavenger KW - Protein KW - Protein unfolding KW - Radiation damage KW - Radical Scavenger KW - SAXS KW - Single-stranded DNA-binding proteins KW - Small-angle xray scattering KW - Topas-MC KW - Topas-nBio KW - TopasMC KW - X-ray scattering KW - Particle scatterin simulations KW - ssDNA PY - 2023 DO - https://doi.org/10.1039/D3CP90056H SN - 1463-9076 SN - 1463-9084 VL - 25 IS - 7 SP - 5889 PB - Royal Society of Chemistry CY - Cambridge AN - OPUS4-57006 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Hahn, Marc Benjamin T1 - Extending Bio-SAXS measurements of Single-Stranded DNA-Binding Proteins: Radiation Protection of G5P by Cosolutes N2 - Small-angle X-ray scattering (SAXS) can be used for structural de- termination of biological macromolecules and polymers in their na- tive states. To improve the reliability of such experiments, the re- duction of radiation damage occurring from exposure to X-rays is needed.One method, is the use of scavenger molecules that protect macromolecules against radicals produced by radiation exposure.In this study we investigate the feasibility to apply the compatible solute, osmolyte and radiation protector Ectoine (THP(B)) as a scavenger throughout SAXS measurements of single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). Therefore we monitor the radiation induced changes of G5P during bio-SAXS. The resulting microscopic energy-damage relation was determined by particle scattering simu- lations with TOPAS/Geant4. The results are interpreted in terms of radical scavenging as well as post-irradiation effects, related to preferential-exclusion from the protein surface. Thus, Ectoine provides an non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies. T2 - MultiChem Conference 2023 CY - Prague, Czech Republic DA - 26.04.2023 KW - Bio-SAXS KW - BioSAXS KW - Compatible solute KW - Cosolute KW - DNA KW - Dosimetry KW - Ectoin KW - Ectoine KW - Ectoin KW - G5P KW - GVP KW - Geant4 KW - Geant4-DNA KW - Gene five protein KW - Hydroxyectoine KW - Ionizing radiation damage KW - LEE KW - McSAS3 KW - Microdosimetry KW - Monte-Carlo simulations KW - OH Radical KW - OH radical scavenger KW - Osmolyte KW - Particle scattering simulations KW - Protein KW - Protein unfolding KW - Proteins KW - ROS KW - Radiation damage KW - Radical Scavenger KW - Radical scavenger KW - SAXS KW - Single-stranded DNA-binding proteins KW - Small-angle xray scattering KW - Topas KW - Topas-MC KW - Topas-nBio KW - X-ray scattering KW - ssDNA KW - Median lethal energy deposit PY - 2023 AN - OPUS4-57407 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Pauw, Brian Richard T1 - X-ray Scattering USAXS/SAXS/WAXS (/XRD/PDF) N2 - A ten minute introduction to the technique of X-ray scattering. This talk discusses the foundation and the resulting morphological parameters that can be obtained from the technique. The talk is prepared for discussion within the framework of the OECD REACH guideline for nanomaterials. T2 - Digitaler Info-Tag "Nano or not Nano" CY - Berlin, Germany DA - 16.02.2023 KW - X-ray scattering KW - BAM Academy KW - SAXS KW - XRD KW - WAXS KW - Nanomaterial KW - REACH KW - OECD KW - Guideline PY - 2023 AN - OPUS4-57013 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Aliyah, K. A1 - Prehal, C. A1 - Diercks, J. S. A1 - Diklić, N. A1 - Xu, L. A1 - Ünsal, S. A1 - Appel, C. A1 - Pauw, Brian Richard A1 - Smales, Glen Jacob A1 - Guizar-Sicairos, M. A1 - Herranz, J. A1 - Gubler, L. A1 - Büchi, F. N. A1 - Eller, J. T1 - Quantification of PEFC Catalyst Layer Saturation via In Silico, Ex Situ, and In Situ Small-Angle X-ray Scattering N2 - The complex nature of liquid water saturation of polymer electrolyte fuel cell (PEFC) catalyst layers (CLs) greatly affects the device performance. To investigate this problem, we present a method to quantify the presence of liquid water in a PEFC CL using small-angle X-ray scattering (SAXS). This method leverages the differences in electron densities between the solid catalyst matrix and the liquid water filled pores of the CL under both dry and wet conditions. This approach is validated using ex situ wetting experiments, which aid the study of the transient saturation of a CL in a flow cell configuration in situ. The azimuthally integrated scattering data are fitted using 3D morphology models of the CL under dry conditions. Different wetting scenarios are realized in silico, and the corresponding SAXS data are numerically simulated by a direct 3D Fourier transformation. The simulated SAXS profiles of the different wetting scenarios are used to interpret the measured SAXS data which allows the derivation of the most probable wetting mechanism within a flow cell electrode. KW - Polymer electrolyte fuel cell KW - Water management KW - Catalyst layer KW - Representative morphology modeling KW - Small-angle X-ray scattering KW - MOUSE KW - SAXS PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-575973 DO - https://doi.org/10.1021/acsami.3c00420 SN - 1944-8244 VL - 15 IS - 22 SP - 26538 EP - 26553 PB - ACS Publications AN - OPUS4-57597 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Pauw, Brian Richard A1 - Smales, Glen Jacob T1 - Small-angle scattering data analysis round robin dataset - Original for participants N2 - These are four datasets that were made available to the participants of the Small-angle Scattering data analysis round robin. The intent was to find out how comparable results from different researchers are, who analyse exactly the same processed, corrected dataset. In this repository, there are: 1) a PDF document with more details for the study, 2) the datasets for people to try and fit, 3) an Excel spreadsheet to document the results. Datasets 1 and 2 were modified from: Deumer, Jerome, & Gollwitzer, Christian. (2022). npSize_SAXS_data_PTB (Version 5) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5886834 Datasets 3 and 4 were collected in-house on the MOUSE instrument. KW - Round robin KW - SAXS KW - Small angle scattering KW - SANS KW - X-ray KW - Neutron KW - Human factor KW - Data analysis KW - Data fitting KW - Human influence PY - 2023 DO - https://doi.org/10.5281/zenodo.7506365 PB - Zenodo CY - Geneva AN - OPUS4-56799 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Pauw, Brian Richard T1 - X-ray scattering for nanostructure quantification, and the quest for the perfect experiment N2 - Measuring an X-ray scattering pattern is relatively easy, but measuring a steady stream of high-quality, useful patterns requires significant effort and good laboratory organization. Such laboratory organization can help address the reproducibility crisis in science, and easily multiply the scientific output of a laboratory, while greatly elevating the quality of the measurements. We have demonstrated this for small- and wide-angle X-ray scattering in the MOUSE project (Methodology Optimization for Ultrafine Structure Exploration). With the MOUSE, we have combined a comprehensive and highly automated laboratory workflow with a heavily modified X-ray scattering instrument. This combination allows us to collect fully traceable scattering data, within a well-documented, FAIR-compliant data flow (akin to what is found at the more automated synchrotron beamlines). With two full-time researchers, our lab collects and interprets thousands of datasets, on hundreds of samples, for dozens of projects per year, supporting many users along the entire process from sample selection and preparation, to the analysis of the resulting data. This talk will briefly introduce the foundations of X-ray scattering, present the MOUSE project, and will highlight the proven utility of the methodology for materials science. Upgrades to the methodology will also be discussed, as well as possible avenues for transferring this holistic methodology to other instruments T2 - SNI 2022 CY - Berlin, Germany DA - 05.09.2022 KW - Methodology KW - X-ray scattering KW - Laboratory management KW - Instrumentation utilization KW - MOUSE KW - SAXS KW - WAXS KW - Automation PY - 2022 AN - OPUS4-55760 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Smales, Glen Jacob A1 - Hahn, Marc Benjamin A1 - Hallier, Dorothea C. A1 - Seitz, H. T1 - X-ray scattering datasets and simulations associated with the publication "Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine" N2 - This dataset contains the processed and analysed small-angle X-ray scattering data associated with all samples from the publications "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine" (https://doi.org/10.1039/D2CP05053F). Files associated with McSAS3 analyses are included, alongside the relevant SAXS data, with datasets labelled in accordance to the protein (G5P), its concentration (1, 2 or 4 mg/mL), and if Ectoine is present (Ect) or absent (Pure). PEPSIsaxs simulations of the GVP monomer (PDB structure: 1GV5 ) and dimer are also included. TOPAS-bioSAXS-dosimetry extension for TOPAS-nBio based particle scattering simulations can be obtained from https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry which is further described in https://doi.org/10.26272/opus4-55751. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant number 442240902 (HA 8528/2-1 and SE 2999/2-1). We acknowledge Diamond Light Source for time on Beamline B21 under Proposal SM29806. This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 program of the European Commission. KW - SAXS KW - Radiation protection KW - Microdosimetry KW - G5P KW - Ectoine KW - DNA-Binding protein PY - 2023 DO - https://doi.org/10.5281/zenodo.7515394 PB - Zenodo CY - Geneva AN - OPUS4-56811 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Deumer, J. A1 - Andresen, Elina A1 - Gollwitzer, C. A1 - Schürmann, R. A1 - Resch-Genger, Ute T1 - Adding More Shape to Nanoscale Reference Materials-LiYF4:Yb,Tm Bipyramids as Standards for Sizing Methods and Particle Number Concentration N2 - The increasing industrial use of nanomaterials calls for the reliable characterization of their physicochemical key properties like size, size distribution, shape, and surface chemistry, and test and reference materials (RMs) with sizes and shapes, closely matching real-world nonspheric nano-objects. An efficient strategy to minimize efforts in producing nanoscale RMs (nanoRMs) for establishing, validating, and standardizing methods for characterizing nanomaterials are multimethod nanoRMs. Ideal candidates are lanthanide-based, multicolor luminescent, and chemically inert nanoparticles (NPs) like upconversion nanoparticles (UCNPs), which can be prepared in different sizes, shapes, and chemical composition with various surface coatings. This makes UCNPs interesting candidates as standards not only for sizing methods, but also for element-analytical methods like laser ablation-inductively coupled plasma mass spectrometry (LA-ICP-MS), quantitative bioimaging methods like X-ray fluorescence computed tomography (XFCT), and luminescence methods and correlative measurements. Here, we explore the potential of two monodisperse LiYF4:Yb,Tm bipyramids with peak-to-peak distances of (43 ± 2) nm and (29 ± 2) nm as size standards for small-angle X-ray scattering (SAXS) and tools for establishing and validating the sophisticated simulations required for the analysis of SAXS data derived from dispersions of nonspheric nano-objects. These SAXS studies are supplemented by two-dimensional (2D)-transmission electron microscopy measurements of the UCNP bipyramids. Additionally, the particle number concentration of cyclohexane dispersions of these UCNP bipyramids is determined by absolute SAXS measurements, complemented by gravimetry, thermogravimetric analysis (TGA), and inductively coupled plasma optical emission spectrometry (ICP-OES). This approach enables traceable particle number concentration measurements of ligand-capped nonspheric particles with unknown chemical composition. KW - Fluorescence KW - Upconversion nanoparticles KW - SAXS KW - Particle number concentration KW - Reference material KW - Traceability KW - Quality assurance KW - Quantum yield KW - Spectroscopy KW - Synthesis KW - Quantification KW - NanoRM KW - Nano KW - Particle KW - Bipyramid KW - Reference data KW - Simulation PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-617940 DO - https://doi.org/10.1021/acs.analchem.4c03641 SP - 1 EP - 8 PB - ACS Publications AN - OPUS4-61794 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -