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Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations
(2023)
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.
The ionic liquid 1,3-dimethyl-imidazolium-dimethylphosphate ([MMIM]+[DMP]−) was analyzed using (hard) x-ray photoelectron spectroscopy.
Here, XPS and HAXPES spectra are shown in comparison. For the acquisition of the XPS spectra, monochromatic Al Kα radiation at 1486.6 eV was used, while for the acquisition of the HAXPES spectra, monochromatic Cr Kα radiation at 5414.8 eV was applied. Here, survey scans and high-resolution spectra of P 2p, P 2s, C 1s, O 1s, and N 1s for both methods and P 1s, P KL2,3L2,3, and P KL1L2,3 for HAXPES are shown.
This work presents the determination of the corrosion characteristics of CrCoNi (medium entropy alloy) and CrMnFeCoNi (high entropy alloy) in 0.1 M NaCl and 0.1 M H2SO4. The morphology and chemical composition of the oxide layers formed on CrCoNi and CrMnFeCoNi were comparatively analyzed by scanning Kelvin probe microscopy (SKPFM) and scanning electron microscopy (SEM) and supported with chemical analysis by means of inductively coupled plasma mass spectrometry (ICP-MS) and X-Ray photoelectron spectroscopy (XPS). The analysis of the 3p core level peaks showed that the oxide layer (native and after anodic passivation) on CrCoNi consisted mainly of Cr oxides, while the oxide layer on CrMnFeCoNi was primarily composed of a mixture of Cr and Fe oxides. In addition, XPS was utilized to assess the oxide layer thicknesses. These results were compared to the thicknesses obtained by means of electrochemical impedance spectroscopy (EIS), with both approaches yielding values up to about 4 nm depending on the electrolyte and the alloy. Cyclic polarization measurements indicated superior corrosion resistance of CrCoNi in both aqueous environments compared to CrMnFeCoNi, as well as to AISI 304 stainless steel.
In order to bridge the gap between lab-scale and industrial-scale production of graphene it is necessary to develop processes, equipment and measurement procedures to control the material features. One of the crucial reasons of graphene’s limited commercialization is the lack of standard procedures to properly characterize and define the material chemical and structural properties down to the nanometer level. This leads to many issues regarding material synthesis repeatability, inappropriateness choice of measurands and measurement reproducibility which heavily affect the consistency of the material performance.
In our study, a comparative analysis is performed on two different series (G5 and G6) of industrial graphene powders, each series produced with four types of functionalization: raw graphene, oxygen-functionalized, nitrogen-functionalized and fluorine-functionalized. All the 8 sample variants were analyzed from a chemical and morphological point of view in the form of powders prepared as slightly pressed in metallic sample holders.
The results of the comparative chemical analyses XPS and EDS show a good agreement in the concentration values for all the elements present in the samples, despite the different analysis volumes addressed by the two techniques. For this reason, the samples can be considered homogeneous in both lateral and vertical direction.
A clear influence of the morphology on the composition is evident. Therefore, such correlative measurements of morphology and composition are necessary for a comprehensive characterization of industrial graphene flakes.
Nanosafety is becoming increasingly important as nanomaterials are widely used in industrial processes and consumer products. For nanotoxicity measurements prior sterilization of the samples is necessary, but as structure activity relationships are made with properties of pristine particles, the question arises, if the sterilization process has an impact on the physico-chemical properties of nanoparticles and thus on the biological behavior.
This question will be addressed in this talk. For this purpose, results from SEM and EDS measurements are combined with those of a novel lab-based HAXPES spectrometer in order to obtain a more complete picture. At the end, an influence of sterilization will be evident, which indicates a restructuring of the nanoparticles owing to sterilization.
The spatial distribution and concentration of lanthanide activator and sensitizer dopant ions are of key importance for the luminescence color and efficiency of upconverting nanoparticles (UCNPs). Quantifying dopant ion distributions and intermixing, and correlating them with synthesis methods require suitable analytical techniques. Here, X-ray photoelectron spectroscopy depth-profiling with tender X-rays (2000–6000 eV), providing probe depths ideally matched to UCNP sizes, is used to measure the depth-dependent concentration ratios of Er3+ to Yb3+, [Er3+]/[Yb3+], in three types of UCNPs prepared using different reagents and synthesis methods. This is combined with data simulations and inductively coupled plasma-optical emission spectroscopy (ICP-OES) measurements of the lanthanide ion concentrations to construct models of the UCNPs’ dopant ion distributions. The UCNP sizes and architectures are chosen to demonstrate the potential of this approach. Core-only UCNPs synthesized with XCl3·6H2O precursors (β-phase) exhibit a homogeneous distribution of lanthanide ions, but a slightly surface-enhanced [Er3+]/[Yb3+] is observed for UCNPs prepared with trifluroacetate precursors (α-phase). Examination of Yb-core@Er-shell UCNPs reveals a co-doped, intermixed region between the single-doped core and shell. The impact of these different dopant ion distributions on the UCNP's optical properties is discussed to highlight their importance for UCNP functionality and the design of efficient UCNPs.
Recent developments of X-ray photoelectron spectroscopy using excitation energies different from the usual lab-sources Mg Kα and Al Kα, thus covering larger and different kinetic energy ranges, require more flexible approaches for determining the transmission function than the well-established ones using reference spectra. Therefore, the approach using quantified peak areas (QPA) was refined allowing a more precise estimation of the transmission function. This refinement was tested by comparing the results obtained with the new version with former calculations. Furthermore, the obtained transmission function was validated by comparing the results with a transmission function using the reference spectrum of polyethylene. Additionally, an ionic liquid was used as reference for estimating the transmission function at the energy resolved HE-SGM beamline at BESSY II. Comparison between the measured and stoichiometric composition shows that a transmission function was determined, which allows a reasonable quantification.
Here, we present a study on agarose thin-film samples that represent a model system for the exopolysaccharide matrix of biofilms. Povidone-iodide (PVP-I) was selected as an antibacterial agent to evaluate our x-ray photoelectron spectroscopy (XPS)-based methodology to trace specific marker elements, here iodine, commonly found in organic matrices of antibiotics. The in-depth distribution of iodine was determined by XPS analyses with variable excitation energies and in combination with argon gas cluster ion beam sputter cycles. On mixed agarose/PVP-I nanometer-thin films, both methods were found to solve the analytical task and deliver independently comparable results. In the mixed agarose/PVP-I thin film, we found the outermost surface layer depleted in iodine, whereas the iodine is homogeneously distributed in the depth region between this outermost surface layer and the interface between the thin film and the substrate. Depletion of iodine from the uppermost surface in the thin-film samples is assumed to be caused by ultrahigh vacuum exposure resulting in a loss of molecular iodine (I2) as reported earlier for other iodine-doped polymers.
ISO Technical Report 23173 describes methods by which electron spectroscopies, including X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and synchrotron techniques, can be employed to calculate the Coating thicknesses and compositions of nanoparticles. The document has been developed to review and outline the current state-of-the-art for such measurements. Such analyses of core–shell nanoparticles are common within the literature, however the
methods employed are varied; the relative advantages and disadvantages of These methods, and the optimal usage of each may not be clear to the general analyst. ISO Technical Report 23173 aims to clarify the methods that are available, describe them in clear terms, exhibit examples of their use, and highlight potential issues users may face. The information provided should allow analysts of electron spectroscopy data to make clear choices regarding the appropriate analysis of electron spectroscopy data from coated nanoparticle systems and provide a basis for understanding and comparing results from different methods and systems.
Ionizing radiation damage to DNA plays a fundamental role in cancer therapy. X-ray photoelectron-spectroscopy (XPS) allows simultaneous irradiation and damage monitoring. Although water radiolysis is essential for radiation damage, all previous XPS studies were performed in vacuum. Here we present near-ambient-pressure XPS xperiments to directly measure DNA damage under water atmosphere. They permit in-situ monitoring of the effects of radicals on fully hydrated double-stranded DNA. The results allow us to distinguish direct damage, by photons and secondary low-energy electrons (LEE), from damage by hydroxyl radicals or hydration induced modifications of damage pathways. The exposure of dry DNA to x-rays leads to strand-breaks at the sugar-phosphate backbone, while deoxyribose and nucleobases are less affected. In contrast, a strong increase of DNA damage is observed in water, where OH-radicals are produced. In consequence, base damage and base release become predominant, even though the number of strand-breaks increases further.