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" JF - Physical chemistry chemical physics (PCCP) 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 - 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 JF - Physical chemistry chemical physics (PCCP) 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 - Hahn, Marc Benjamin T1 - Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations JF - Journal of Physics Communications 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 - 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 JF - ACS Applied Materials & Interfaces 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 - 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 JF - Soft Matter 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 - Pauw, Brian Richard A1 - Laskina, Sofya A1 - Naik, Aakash Ashok A1 - Smales, Glen Jacob A1 - George, Janine A1 - Breßler, Ingo A1 - Benner, Philipp T1 - "Ultima Ratio": Simulating wide-range X-ray scattering and diffraction JF - ArXiv N2 - We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated patterns can be used to test holistic analysis models, and, since the diffraction intensity is on the same scale as the scattering intensity, may offer a novel pathway for determining the degree of crystallinity. The "Ultima Ratio" strategy is demonstrated on a 64-nm Metal Organic Framework (MOF) particle, calculated from Q < 0.01 1/nm up to Q < 150 1/nm, with a resolution of 0.16 Angstrom. The computations exploit a modified 3D Fast Fourier Transform (3D-FFT), whose modifications enable the transformations of matrices at least up to 8000^3 voxels in size. Multiple of these modified 3D-FFTs are combined to improve the low-Q behaviour. The resulting curve is compared to a wide-range scattering pattern measured on a polydisperse MOF powder. While computationally intensive, the approach is expected to be useful for simulating scattering from a wide range of realistic, complex structures, from (poly-)crystalline particles to hierarchical, multicomponent structures such as viruses and catalysts. KW - X-ray KW - Simulation KW - 3D Fourier Transform KW - High resolution KW - XRD KW - SAXS KW - PDF KW - Total scattering KW - X-ray scattering KW - Metal organic framework KW - Electron density map KW - FFT PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-572067 DO - https://doi.org/10.48550/arXiv.2303.13435 VL - Cornell University SP - 1 EP - 12 PB - Ithaca, NY AN - OPUS4-57206 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Abram, Sarah-Luise A1 - Mrkwitschka, Paul A1 - Thünemann, Andreas A1 - Radnik, Jörg A1 - Häusler, I. A1 - Bresch, Harald A1 - Hodoroaba, Vasile-Dan A1 - Resch-Genger, Ute T1 - Iron Oxide Nanocubes as a New Certified Reference Material for Nanoparticle Size Measurements JF - Analytical chemistry N2 - The rational design and increasing industrial use of nanomaterials require a reliable characterization of their physicochemical key properties like size, size distribution, shape, and surface chemistry. This calls for nanoscale reference materials (nanoRMs) for the validation and standardization of commonly used characterization methods closely matching real-world nonspherical nano-objects. This encouraged us to develop a nonspherical nanoRM of very small size consisting of 8 nm iron oxide nanocubes (BAM-N012) to complement spherical gold, silica, and polymer nanoRMs. In the following, the development and production of this nanoRM are highlighted including the characterization by transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) as complementary methods for size and shape parameters, homogeneity and stability studies, and calculation of a complete uncertainty budget of the size features. The determination of the nanocubes’ edge length by TEM and SAXS allows a method comparison. In addition, SAXS measurements can also provide the mean particle number density and the mass concentration. The certified size parameters, area equivalent circular diameter and square edge length, determined by TEM with a relative expanded uncertainty below 9%, are metrologically traceable to a natural constant for length, the very precisely known (111) lattice spacing of silicon. Cubic BAM-N012 qualifies as a certified nanoRM for estimating the precision and trueness, validation, and quality assurance of particle size and shape measurements with electron microscopy and SAXS as well as other sizing methods suitable for nanomaterials. The production of this new iron oxide nanocube RM presents an important achievement for the nanomaterial community, nanomaterial manufacturers, and regulators. KW - Certification KW - SAXS KW - Homogeneity KW - Nano KW - Particle KW - Iron oxide KW - Quality assurance KW - Reference material KW - Size KW - Electron microscopy KW - Stability KW - Shape PY - 2023 DO - https://doi.org/10.1021/acs.analchem.3c00749 SN - 0003-2700 VL - 95 IS - 33 SP - 12223 EP - 12231 PB - American Chemical Society CY - Columbus, Ohio AN - OPUS4-58176 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hildebrandt, Jana A1 - Taubert, Andreas A1 - Thünemann, Andreas T1 - Synthesis and Characterization of Ultra‐Small Gold Nanoparticles in the Ionic Liquid 1‐Ethyl‐3‐methylimidazolium Dicyanamide, [Emim][DCA] JF - ChemistryOpen N2 - AbstractWe report on gold clusters with around 62 gold atoms and a diameter of 1.15±0.10 nm. Dispersions of the clusters are long‐term stable for two years at ambient conditions. The synthesis was performed by mixing tetrachloroauric acid (HAuCl4 ⋅ 3 H2O) with the ionic liquid 1‐ethyl‐3‐methylimidazolium dicyanamide ([Emim][DCA]) at temperatures of 20 to 80 °C. Characterization was performed with small‐angle X‐ray scattering (SAXS), UV‐Vis spectroscopy, and MALDI‐TOF mass spectrometry. A three‐stage model is proposed for the formation of the clusters, in which cluster growth from gold nuclei takes place according to the Lifshitz‐Slyozov‐Wagner (LSW) model followed by oriented attachment to form colloidal stable clusters. KW - Reference materials KW - SAXS KW - Gold KW - Nanoparticle KW - Small-angle X-ray scattering KW - Ionic liquid PY - 2023 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-588203 DO - https://doi.org/10.1002/open.202300106 SN - 2191-1363 VL - 44 SP - 1 EP - 19 PB - Wiley AN - OPUS4-58820 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -