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The cowpea chlorotic mottle virus (CCMV) is a plant virus explored as a nanotechnological platform. The robust self-assembly mechanism of its capsid protein allows for drug encapsulation and targeted delivery. Additionally, the capsid nanoparticle can be used as a programmable platform to display different molecular moieties. In view of future applications, efficient production and purification of plant viruses are key steps. In established protocols, the need for ultracentrifugation is a significant limitation due to cost, difficult scalability, and safety issues. In addition, the purity of the final virus isolate often remains unclear. Here, an advanced protocol for the purification of the CCMV from infected plant tissue was developed, focusing on efficiency, economy, and final purity. The protocol involves precipitation with PEG 8000, followed by affinity extraction using a novel peptide aptamer. The efficiency of the protocol was validated using size exclusion chromatography, MALDI-TOF mass spectrometry, reversed-phase HPLC, and sandwich immunoassay. Furthermore, it was demonstrated that the final eluate of the affinity column is of exceptional purity (98.4%) determined by HPLC and detection at 220 nm. The scale-up of our proposed method seems to be straightforward, which opens the way to the large-scale production of such nanomaterials. This highly improved protocol may facilitate the use and implementation of plant viruses as nanotechnological platforms for in vitro and in vivo applications.
A few layer/multilayer graphene (MLG) with a specific surface area of BET ≥ 250 m2/g is proposed as an efficient multifunctional nanofiller for rubbers. The preparation method, i.e., ultrasonically-assisted solution or latex premixing of master batches followed by conventional two-roll milling, strongly influences the dispersion in the elastomeric matrix and is fundamental for the final properties. When homogenously dispersed, single stacks of only approximately 10 graphene sheets, with an aspect ratio of ca. 35, work at low loadings, enabling the replacement of large amounts of carbon black (CB), an increase in efficiency, and a reduction in filler load. The appropriate preparation yielded nanocomposites in which just 3 phr are sufficient to significantly improve the rheological, curing, gas barrier properties, electrical and thermal conductivity, as well as mechanical properties of different rubbers, as shown for chlorine-Isobutylene-Isoprene rubber (CIIR), nitrile-butadiene rubber (NBR), natural rubber (NR), and styrene-butadiene rubber (SBR).[1-5] 3 phr of MLG tripled the Young’s modulus of CIIR, an effect equivalent to 20 phr of CB. The stronger interactions between MLG and NR or SBR also resulted in a reduction in the elongation at break by 20% and 50%, respectively, while the same parameter was hardly changed for CIIR/MLG and NBR/MLG. CIIR/MLG and NBR/MLG were stiffer but just as defomable than CIIR and NBR. The strong reinforcing effect of 3 phr MLG was confirmed by the increase of greater than 10 Shore A in hardness. MLG reduces gas permeability, increases thermal and electrical conductivities, and retards flammability. We investigated MLG also as a synergist for reducing the aluminium trihydrate loading in flame retardant hydrogenated acrylonitrile-butadiene (HNBR), polybutadiene chloroprene (BR/CR), and chlorosulfonated polyethylene rubber(CSM).[6-8] The higher the nanofiller concentration is, the greater the improvement in the properties. For instance, the permeability decreased by 30% at 3 phr of MLG, 50% at 5 phr and 60% at 10 phr, respectively. Moreover, the MLG nanocomposites improve stability of mechanical properties against the effects of weathering. In key experiments an increase in UV-absorption and a pronounced radical scavenging were proved as stabilizing mechanisms. In a nutshell, MLG is an efficient multifunctional nanofiller ready to be used for innovative rubber development.
X-ray photoelectron spectroscopy (XPS) is widely used for characterising the chemistry of graphene-related two-dimensional materials (GR2M), however the careful preparation of the sample for analysis is important in obtaining representative quantifications. We report an investigation by three laboratories showing that the preparation method for oxygen-functionalised graphene nanoplatelet (GNP) powders has a significant effect on the homogeneous-equivalent elemental composition measured in XPS. We show that pressing GNP powders onto adhesive tapes, into recesses, or into solid pellets results in inconsistencies in the XPS quantification. The measured oxygen-to-carbon atomic ratio from GNP pellets depends upon the die pressure used to form them and the morphology of the GNPs themselves. We recommend that powder samples of GR2Ms are pelletised prior to XPS analysis to improve repeatability and reproducibility of measurements.
Comparative study of the co-assembly behaviour of 3-chloro-4-hydroxy-phenylazo dyes with DTAB
(2023)
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.
Interactions between a polymer and a substrate interface play a vital role in understanding the improvement in thin film material properties as well as serving as a model for nanocomposites. For any non-repulsive polymer-substrate interactions, polymer segments form an irreversibly adsorbed layer and show a slowdown in the glassy dynamics and thus an increase in the thermal glass transition temperature compared to the bulk-like values. The growth kinetics of the adsorbed layer obey a two-step mechanism: formation of immobilized layer with flat segmental conformations and a loosely bound layer with stretched chains pinned to the surface. Here the adsorbed layer was studied for: poly (bisphenol-A carbonate) (PBAC) and polysulfone (PSU), two bulky polymers containing a functional group (phenyl ring) in the backbone and compared to poly (2-vinyl pyridine) (P2VP), where the backbone is a vinyl-derivative and the functional group (pyridine) is in the side chain. The growth kinetics for PBAC and PSU were found to deviate from the well-known mechanism, observed for polymers such as P2VP. Atomic force microscopy and ellipsometry were used for this investigation and was additionally supported by broadband dielectric spectroscopy.
Since its isolation, graphene has received growing attention from academia and industry due to its unique properties. Promising opportunities for applications are discussed in different field like electronics and optoelectronics, detection, and sensing devices, biosystems or chemical and environmental corrosion inhibition. Here, functionalization with elements like oxygen, nitrogen or fluorine can broaden the application, for example in composite materials. However, lack of generally accepted operation procedures hinders the commercialization, the so-called “what is my material” barrier. Therefore, first efforts were done to develop common, reliable, and reproducible ways to characterize the morphological and chemical properties of the industrially produced material.
In this contribution, our efforts in the development of reliable chemical characterizations protocols for functionalized graphene are presented. An ISO standard for the chemical characterization of graphene-related (GRM) is under development with X-ray photoelectron spectroscopy (XPS) having a prominent role. With its information depth of around 10 nm, which is the similar length scale as the thickness of particles of 2D materials consisting of a few monolayers, XPS seems to be highly suitable for the quantitative analysis of (functionalized) GRM. Thereby, different sample preparation methods like pressing the powders onto adhesive tapes, into recesses, or into solid pellets result in inconsistencies in the quantification. Furthermore, different morphologies like stacks of graphene layers (left figure) or irregular particles (right figure) lead to different analysis results for the chemical composition.
For the validation of the quantification with XPS and the further development of standards an international interlaboratory comparison was initiated under the head of the “Versailles Project on Advanced Materials and Standards” (VAMAS). First results are reported showing the suitability of the protocols. Finally, the XPS results are compared with the elemental composition results obtained after quantification with energy-dispersive X-ray spectroscopy (EDS) as a fast analytical method which is usually combined with electron microscopy.
Im Vortrag werden das Messprinzip einer Photozentrifuge erläutert und die Anforderungen der zugrundeliegenden Normen diskutiert. Die praktische Durchführung der Messung und insbesondere auch die vorbereitenden Arbeiten, sowie die Auswertung der Rohdaten bilden den Schwerpunkt des Vortrags. Gezeigt werden auch die Validierung sowie ein Beispiel zur regelmäßigen Verifizierung des Verfahrens. Nach Anwendungsbeispielen und Vergleichen zu Ergebnissen mit anderen Messverfahren, wird das Verfahren in einer Zusammenfassung bewertet.
Since there is a lack of knowledge about the effects of nanomaterials on human health and the environment, and in order to get safe- and sustainable-by-design nanomaterials, it is necessary to find an easy way to assess their properties, without having to perform time-consuming experiments each time. In the European project NanoSolveIT, the behavior of nanoparticles is to be derived from a nanomaterial fingerprint database with standardized physico-chemical properties of nanomaterials. The key element for these grouping and reading across approaches is the collection of standardized information about nanomaterials in combination with modelling and simulations. As parameters the particle size, particle shape, chemical composition and surface chemistry are discussed here.
Measurements of the shape and size were performed using scanning electron microscopy (SEM). For the chemical composition energy dispersive X-ray spectroscopy (EDS) and for the surface chemistry X-ray photoelectron spectroscopy (XPS) were used. As an additional method hard X-ray photoelectron spectroscopy (HAXPES) with a higher information depth than XPS was used, thus we were able to include information not only from the top surface, but also from deeper regions of about 30 nm. Therefore, this method is complementary to EDS.
All these methods have been correlatively used to study nanoparticles of different chemical composition that have been treated differently by sterilization. Such a sterilization step is common, before testing for toxicity. To date, the sterilization step has not been considered in establishing the structure-activity relationship of the nanomaterial.
The effects of sterilization are discussed on exemplary samples. The results demonstrate the influence of sterilization on all investigated properties, indicating a restructuring of the nanoparticles. This implies that samples that have been sterilized after synthesis, may show different toxicity from those used in applications without a sterilization step.
Acknowledgement: This research is part of the project “NanoSolveIT”, which has received funding from European Union Horizon 2020 Programme (H2020) under grant agreement no 814572. (https://nanosolveit.eu/)
Long seen as “a solution seeking a problem,” laser pulses are nowadays – more than 60 years after their first practical demonstration – paramount in shaping and structuring matter. Harnessing their capabilities to direct intense beams of light, the number of scientific and technological developments and daily-life applications is continuously increasing. Today, the presence of lasers is ubiquitous in all sites of scientific and technological interest, from the most advanced research laboratories to industrial factories and medical hospitals.
The directionality of the laser beam determines equally a local character on lightmatter interaction and as such a local modification to a material target. Furthermore, the coherence of laser radiation enables near-field or far-field scattering and interference effects that widen significantly the capabilities of controlling and tracking laser-matter interactions in space and time. Already with the advent of lasers, powerful beams of light have been directed at solid materials for a variety of purposes, making this application as old as the laser itself. The roots of the major applications for laser structuring were developed already in the 1960s, setting the base of both theoretical and experimental studies on laser ablation, with the number of publications expanding explosively during the next decades.
Within this dynamic context, laser processing of materials experienced an impressive development over the years. Laser processing means specifically the capability to structure and tailor a material on its surface or even within its volume, rendering new functions and properties that are impacting the mechanical, electrical, or optical characteristics of the material. These properties are scaledependent, generating thus over the years an equally impressive quest for spatial or temporal resolution. Therefore, the developments in laser engineering with major breakthroughs, notably in pulse duration and power, always closely accompanied the efforts in material structuring with two milestones in sight: (1) yield and (2) resolution. Every step in shrinking the laser pulse duration led to a subsequent strong-impact development in process precision – particularly when the ultrashort pulse durations surpassed the fundamental electron-phonon relaxation times. Thus, minimizing heat diffusion, the advent of pulses with duration smaller than molecular or lattice vibration times has managed to confine the spatial resolution to the optical diffraction limit and sometimes even beyond. The nanoscale was already in sight at the turn of the millennium. An important question may be raised now; is there any fundamental limit in the processing resolution, a barrier defined by the intrinsic properties of light and matter? The answer has an inherently multidisciplinary nature, following the conversion of free-propagating electromagnetic radiation into
material-confined energy potentially usable to drive or transform matter, and will be the focus of the present book.
Relying on the experience and expertise of the leading researchers in the field, the present book intends to explore the current efforts in achieving laser processing resolution beyond the diffraction limit, laying down a perspective towards extreme laser nanostructuring. Following the most recent advances and developments, it puts forward a concept of extreme processing scales enabled by optical pulses that are able to bypass diffraction limits and achieve structuring characteristic scales beyond 100 nm. This objective can be achieved by a comprehensive understanding on how light can change matter and how, in turn, matter can change light, allowing jointly for actively controlling light and material processes. In order to give an extended perspective on the current state-of-the-art in the field of precision laser structuring, the book is divided into three main parts.
The first part of the book (Part I: Fundamental Processes) offers a perspective into the fundamentals of laser-matter interaction on extreme spatial scales, with a description of the most advanced modeling efforts in understanding energy deposition in matter, a plethora of material-relaxation pathways, as well as advanced concepts for probing and observing matter in motion. Roadmaps for energy localization will be developed, and the atomistic perspective of laser ablation visualized. Theoretical modelling enables in-depth insights on ultrafast quantum processes at the nanoscale. Laser-driven self-organization at surfaces will be dissected regarding the question of how light drives material periodic patterns down to the nanoscale, explored and transmitted to its ultimate limits of an atomic printer, and immediately complemented by the unprecedented capabilities of ultrafast in-situ observation approaches for tracking the laser-induced material response with extreme spatial and temporal resolution.
In the second part of the book (Part II: Concepts of Extreme Nanostructuring), distinct concepts will be developed and explored that allow confinement of light and harnessing of a material response restricted to nano- or mesoscopic scales at surfaces or in the volume of irradiated materials. A special focus will be on optical near-field related approaches for localizing light on scales even below the optical diffraction limit and plasmonic printing. Spatial and temporal beam-shaping and tailored interference techniques are discussed in the context of ultrashort laser pulses, and insights into some extreme states of matter realized by the tight confinement of laser energy are presented. The ultimate limits of writing waveguides in the bulk of dielectrics and for manifesting 3D-nanolithography are elucidated. Plasma-based surface treatments can significantly enhance the vertical precision of surface processing through etching processes.
Finally, the third part of the book (Part III: Applications) leads us to a number of resuming applications, unveiling the tremendous capabilities of surface functionalization through laser micro- and nanostructuring, assessing the 3D-writing of waveguides in the bulk of dielectrics or semiconductors for enabling new branches of integrated photonics, and summarizing related applications ranging from nanophotonics to nanofluidics and from optical sensing to biomedical applications, including the latest capabilities of refractive eye surgery. This part will analyze the applications’ compatibility in yield and reproducibility with current industrial requirements, costs, and intellectual property aspects. It expands the involved spatial scales by more than eight orders of magnitude, when extending extremely small structures featuring sizes of few tens of nanometers to larger dimensions in the meter range.
Thus, from surfaces to the bulk, from subtractive to additive manufacturing approaches, from advanced theoretical frames to practical technological processes – we invite the readers here to an exciting journey into the varicolored landscape of extreme laser nanostructuring.
The idea of this book project was seeded in early 2020. We were delighted about the numerous and extremely positive responses from the laser-processing community, quickly receiving commitments for more than 30 individual book chapters. About 2500 communications later, the book is published. We would like to thank all authors of this book project for their insightful and detailed chapters, reviewing and reporting on this fascinating topic of the pursuit of extreme scales in ultrafast laser nanostructuring. Moreover, we would like to acknowledge the professional help and guidance of the staff of Springer Nature. Finally, we hope you will enjoy reading this book as much as we have enjoyed putting it together.
Saint Etienne, France Razvan Stoian
Berlin, Germany Jörn Bonse
December 2022
Surface nanostructures provide the possibility to create and tailor surface functionalities mainly via controlling their topography along with other chemical and physical material properties. One of the most appealing technologies for surface functionalization via micro- and nanostructuring is based on laser processing. This can be done either via direct contour-shaping of the irradiated material using a tightly focused laser beam or in a self-ordered way that allows employing larger laser beam diameters along with areal scanning to create a variety of laser-induced periodic surface structures (LIPSS). For the latter approach, particularly ultrashort pulsed lasers have recently pushed the borders across long-lasting limitations regarding the minimum achievable feature sizes and additionally boosted up the production times. This chapter reviews the plethora of recently investigated applications of LIPSS—for example, via imposing diffractive or plasmonic structural colors, the management of liquids and surface wetting properties, biomedical and bioinspired functionalities, beneficial effects in tribology for reducing friction and wear, the manipulation of optical scattering and absorption in photovoltaics, or the modification of magnetic or superconducting surface properties in other energy applications. The footprint of the LIPSS-based technology is explored in detail regarding the current state of industrialization, including an analysis of the market and associated LIPSS production costs.
Irradiation of solid surfaces with intense ultrashort laser pulses represents a unique way of depositing energy into materials. It allows to realize states of extreme electronic excitation and/or very high temperature and pressure and to drive materials close to and beyond fundamental stability limits. As a consequence, structural changes and phase transitions often occur along unusual pathways and under strongly nonequilibrium conditions. Due to the inherent multiscale nature—both temporally and spatially—of these irreversible processes, their direct experimental observation requires techniques that combine high temporal resolution with the appropriate spatial resolution and the capability to obtain good quality data on a single pulse/event basis. In this respect, fourth-generation light sources, namely, short wavelength and short pulse free electron lasers (FELs), are offering new and fascinating possibilities. As an example, this chapter will discuss the results of scattering experiments carried out at the FLASH free electron laser at DESY (Hamburg, Germany), which allowed us to resolve laser-induced structure formation at surfaces on the nanometer to submicron length scale and in temporal regimes ranging from picoseconds to several nanoseconds with sub-picosecond resolution.
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.
While the synthesis of Metal-Organic Framework (MOF) particles can be as easy as adding two solutions together, reproducibly obtaining the same particles, time and time again, is a lot harder. As laboratory-independent reproducibility is a cornerstone of the scientific method, we must put effort into finding and controlling all necessary parameters to achieve this.
An open-source Python/EPICS-controlled robotic platform (see picture) was adapted to systematically explore this for a 20 ml MOF synthesis of the Zeolitic Imidazole Framework-8 (ZIF-8) chemistry in methanol. Parameters that were explored included: 1) addition sequence, 2) addition speeds, 3) reaction times, 4) source chemicals, 5) stirring speeds, 6) stirring bar choice, 7) starting concentrations, and 8) workup methodologies. It was found that, by controlling these parameters, highly reproducible syntheses are obtained. Secondly, the variation of these parameters alone led to a dramatic difference in volume-weighted particle size means, which exceeds an order of magnitude as investigated by our in-house X-ray scattering instrument [1].
The syntheses are thoroughly documented in an automated fashion, and the synthesis libraries as well as analyses libraries will become available in batches soon. With this library, it will be possible to extract previously unknown correlations, and other laboratories can produce specific particles by following the exact procedures of the particles of their choice.
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.
Elemental composition and thickness determination of thin films by electron probe microanalysis
(2023)
Electron probe microanalysis (EPMA) applies to solid samples of homogenous (bulk) chemical composition and can usually not be applied to structures which are inhomogeneous in the micrometer range such as thin film systems down to a few nm. However, in combination with the established thin film software Stratagem, the thickness as well as the elemental composition of thin films on a substrate can be determined. This has been recently successfully demonstrated for Fe-Ni on Si and Si-Ge on Al2O3 thin film systems. For both systems five samples of different elemental composition and a reference were produced and characterised by inductively coupled plasma mass spectrometry (ICP-MS), Rutherford backscattering (RBS), and transmission electron microscopy (TEM) as reference values. Last year, a new and open-source thin film evaluation programme called BadgerFilm has been released. It can also be used to determine thin film composition and thickness from intensity ratios of the unknown sample and standards (k-ratios). In this contribution, we reevaluated the data acquired for the Fe-Ni and Si-Ge systems using the BadgerFilm software package and compared the obtained elemental compositions and thickness values with the results of the Stratagem software and the reference methods. The conclusion is that the BadgerFilm software shows good agreement with the elemental composition and thickness calculated by Stratagem (mostly <2% for both composition and thickness) and with the reference values for two representative thin film systems (<1%–2% for composition and <10%–20% for thickness).
The growth kinetics of the adsorbed layer of poly(2-vinylpiridine) on silicon oxide is studied using a leaching technique which is based on the Guiselin brushes approach. The adsorbed layer is grown from a 200 nm thick P2VP film for several annealing time periods at different annealing temperatures. Then the film is solvent-leached, and the height of the remaining adsorbed layer is measured by atomic force microscopy. At the lowest annealing temperature only a linear growth regime is observed, followed by a plateau. Here, the molecular mobility of segments is too low to allow for a logarithmic growth. At higher annealing temperatures, both linear and logarithmic growth regimes are observed, followed by a plateau. At even higher annealing temperatures, the growth kinetics of the adsorbed layer changes.
A linear growth followed by logarithmic growth kinetics is observed for short annealing time periods. For longer annealing time periods, an upturn of the growth kinetics is observed. At the highest annealing temperature, only a logarithmic growth regime is found. The change in the growth kinetics is discussed by an alteration in the structure of the adsorbed layer. Moreover, the interaction between the polymer segments and the substrate becomes weaker due to both enthalpic and entropic effects. Therefore, at high annealing temperatures the polymer segments might more easily desorb from the substrate.
McSAS3 is a refactored software package for fitting large batches of (X-ray or Neutron) scattering data. It uses a Monte-Carlo acceptance-rejection algorithm to optimize model parameters - ideal for analysis of size-disperse scatterers.
The refactored code can exploit multiprocessing, traceably stores (multiple) results in the output file, and allows for re-histogramming of previous optimizations. Besides analysis of large batches, it can also be integrated in automated data processing pipelines.
The live demonstration will show how to use the software, what its limitations are, and what outcomes can look like for batches of results.
Ratiometric green–red fluorescent nanosensors for fluorometrically monitoring pH in the acidic range were designed from 80 nm-sized polystyrene (PS) and silica (SiO2) nanoparticles (NPs), red emissive reference dyes, and a green emissive naphthalimide pH probe, analytically and spectroscopically characterized, and compared regarding their sensing performance in aqueous dispersion and in cellular uptake studies. Preparation of these optical probes, which are excitable by 405 nm laser or LED light sources, involved the encapsulation of the pH-inert red-fuorescent dye Nile Red (NR) in the core of self-made carboxylated PSNPs by a simple swelling procedure and the fabrication of rhodamine B (RhB)-stained SiO2-NPs from a silane derivative of pH-insensitive RhB. Subsequently, the custom-made naphthalimide pH probe, that utilizes a protonation-controlled photoinduced electron transfer process, was covalently attached to the carboxylic acid groups at the surface of both types of NPs. Fluorescence microscopy studies with the molecular and nanoscale optical probes and A549 lung cancer cells confirmed the cellular uptake of all probes and their penetration into acidic cell compartments, i.e., the lysosomes, indicated by the switching ON of the green naphthalimide fluorescence. This underlines their suitability for intracellular pH sensing, with the SiO2-based nanosensor revealing the best performance regarding uptake speed and stability.
Laser-induced Periodic Surface Structures (LIPSS, ripples) are a universal phenomenon and can be generated in a contactless, single-step process on almost any type of solid upon irradiation with intense laser pulses. They represent a (quasi-)periodic modulation of the surface topography in the form of a linear grating and are typically formed in a “self-ordered” way in the focus of a laser beam. Thus, they are often accompanying laser material processing applications. The structural sizes of LIPSS typically range from several micrometers down to less than 100 nanometers – far beyond the optical diffraction limit – while their orientations exhibit a clear correlation with the local polarization direction of the laser radiation.
From a theoretical point of view, a controversial debate has emerged during the last decades, whether LIPSS originate from electromagnetic effects (seeded already during the laser irradiation) – or whether they emerge from matter-reorganization processes (distinctly after the laser irradiation). From a practical point of view, however, LIPSS represent a simple and robust way for the nanostructuring of solids that allows creating a wide range of different surface functionalities featuring applications in optics, tribology, medicine, energy technologies, etc.
This presentation reviews the currently existent theories of LIPSS. A focus is laid on the historic development of the fundamental ideas behind the LIPSS, their corresponding mathematical descriptions and numerical implementations, along with a comparison and critical assessment of the different approaches.
Fourth generation light sources, namely short wavelength, short pulse free electron lasers (FELs) are offering new and fascinating possibilities to resolve laser-induced structure formation at surfaces on the sub-micrometer to nanometer length scale and in temporal regimes ranging from picoseconds to several nanoseconds with sub-picosecond resolution. This unique spatio-temporal resolution allows to reveal early signatures of coherent/plasmonic electromagnetic scattering effects followed by the excitation of hydrodynamic capillary waves – providing new insights to the above-mentioned debate.
Finally, some unsolved scientific problems related to LIPSS are identified and the pending technological limitations are discussed. While the currently available laser and scanner technology already allows large area surface processing with rates at the m2/min level, industrial applications of LIPSS are sometimes limited by the complex interplay between the nanoscale surface topography and the specific surface chemistry. This typically manifests in difficulties to control the processing of LIPSS and in limitations to ensure the long-term stability of the created surface functions. Strategies for overcoming such limitations are outlined.
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.
This is a remote presentation I gave at the 2022 Small-angle Scattering conference in Campinas, Brazil. The video has been obtained from the conference organisers with their explicit permission for use on YouTube. I've tried to spruce up the audio from the remote recording the best I could.
The conference abstract for this talk was:
"How much do we, the small-angle scatterers, influence the results of an investigation? What uncertainty do we add by our human diversity in thoughts and approaches, and is this significant compared to the uncertainty from the instrumental measurement factors?
After our previous Round Robin on data collection, we know that many laboratories can collect reasonably consistent small-angle scattering data on easy samples[1]. To investigate the next, human component, we compiled four existing datasets from globular (roughly spherical) scatterers, each exhibiting a common complication, and asked the participants to apply their usual methods and toolset to the quantification of the results (https://lookingatnothing.com/index.ph....
Accompanying the datasets was a modicum of accompanying information to help with the interpretation of the data, similar to what we normally receive from our collaborators. More than 30 participants reported back with volume fractions, mean sizes and size distribution widths of the particle populations in the samples, as well as information on their self-assessed level of experience and years in the field.
While the Round Robin is still underway (until the 25th of April, 2022), the initial results already show significant spread in the results. Some of these are due to the variety in interpretation of the meaning of the requested parameters, as well as simple human errors, both of which are easy to correct for. Nevertheless, even after correcting for these differences in understanding, a significant spread remains. This highlights an urgent challenge to our community: how can we better help ourselves and our colleagues obtain more reliable results, how could we take the human factor out of the equation, so to speak?
In this talk, we will introduce the four datasets, their origins and challenges. Hot off the press, we will summarize the anonymized, quantified results of the Data Analysis Round Robin. (Incidentally, we will also see if a correlation exists between experience and proximity of the result to the median). Lastly, potential avenues for improving our field will be offered based on the findings, ranging from low-effort yet somehow controversial improvements, to high-effort foundational considerations."
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.
Simulates X-ray and Neutron scattering patterns from arbitrary shapes defined by STL files.
Features:
- Uses multithreading to compute a number of independent solutions, then uses the variance of the results to estimate an uncertainty on the output.
- Can be launched from the command line using an excel sheet to define settings, or from a jupyter notebook.
- Outputs scattering patterns in absolute units if the contrast is set.
- A Gaussian size distribution is available, where the relative scaling of objects for each repetion can be varied. Recommended to be used with limited width (max. 10%) to avoid artefacts.
- Writes results with settings to an archival HDF5 file.
Application examples:
This software has been used in several studies to date. For example, it has been used here to simulate a model scattering pattern for a cuboid shape, which was then fed forward into the McSAS3 analysis program for analyzing scattering patterns of polydisperse cuboids. A second use is here, where it was used for the modeling of flattened helices. In this paper, scattering pattern features could be matched with particular morphological changes in the structure. Lastly, this paper has an example where it was used to validate the analytical analysis model, and explore the realistic limits of application of the analytical model.
McSAS3
(2023)
McSAS3 is a refactored version of the original McSAS (see DOI 10.1107/S1600576715007347). This software fits scattering patterns to obtain size distributions without assumptions on the size distribution form. The refactored version has some neat features:
- Multiprocessing is included, spread out over as many cores as number of repetitions!
- Full state of the optimization is stored in an organized HDF5 state file.
- Histogramming is separate from optimization and a result can be re-histogrammed as many times as desired.
- SasModels allow a wide range of models to be used
- If SasModels does not work (e.g. because of gcc compiler issues on Windows or Mac), an internal sphere model is supplied
- Simulated data of the scattering of a special shape can also be used as a McSAS fitting model. Your models are infinite!
- 2D fitting also works.
As virus outbreaks continue to pose a challenge, a nonspecific viral inhibitor can provide significant benefits, especially against respiratory viruses. Polyglycerol sulfates recently emerge as promising agents that mediate interactions between cells and viruses through electrostatics, leading to virus inhibition.
Similarly, hydrophobic C60 fullerene can prevent virus infection via interactions with hydrophobic cavities of surface proteins. Here, two strategies are combined to inhibit infection of SARS-CoV-2 variants in vitro. Effective inhibitory concentrations in the millimolar range highlight the significance of bare fullerene’s hydrophobic moiety and electrostatic interactions of polysulfates with surface proteins of SARS-CoV-2. Furthermore, microscale thermophoresis measurements support that fullerene linear polyglycerol sulfates interact with the SARS-CoV-2 virus via its spike protein, and highlight importance of electrostatic interactions within it. All-atom molecular dynamics simulations reveal that the fullerene binding site is situated close to the receptor binding domain, within 4 nm of polyglycerol sulfate binding sites, feasibly allowing both portions of the material to interact simultaneously.
Laser-induced periodic surface structures (LIPSS) have gained remarkable attention as they represent a universal phenomenon that is often accompanying laser-processing. Such LIPSS enable a plethora of different surface functionalizations for applications in the fields of optics, fluidics, tribology, or medicine. Due to the inherent multiscale nature of processes involved in LIPSS formation, their in-situ observation requires experimental techniques that combine high temporal resolution with the appropriate spatial resolution. In this respect fourth generation light sources, namely short wavelength, short pulse free electron lasers (FELs) are offering new and fascinating possibilities. This work contribution will discuss the results of scattering experiments carried at the FLASH free electron laser at DESY (Hamburg, Germany), which allowed us to resolve laser-induced structure formation at surfaces on the nm to sub-µm length scale and in temporal regimes ranging from ps to several ns with sub-ps resolution. A ps-optical pump / fs-XUV scattering probe scheme was employed to 100 nm thick laser-excited silicon films, while recording snapshots of the transmitted XUV scattering patterns at various delay times after the laser pulse impact. On timescales ranging from hundred ps until several ns almost quantitative agreement was observed between certain features of the recorded scattering patterns and predictions of the first-principles theory of J.E. Sipe and coworkers. Other scattering features appearing with a delay of ~100 ps and lasting for ~1 ns are attributed to capillary surface waves being excited at the laser-melted film material while ablation proceeds. Our superior spatio-temporal resolution experiments allow to uniquely reveal and distinguish early signatures of coherent/plasmonic electromagnetic scattering effects, separately followed by hydrodynamic matter reorganization.
Photodynamic therapy (PDT) used for treating cancer relies on the generation of highly reactive oxygen species, for example, singlet oxygen 1O2, by light-induced excitation of a photosensitizer (PS) in the presence of molecular oxygen, inducing DNA damage in close proximity of the PS. Although many precious metal complexes have been explored as PS for PDT and received clinical approval, only recently, the potential of photoactive complexes of nonnoble metals as PS has been discovered. Using the DNA origami technology that can absolutely quantify DNA strand break cross sections, we assessed the potential of the luminescent transition metal complex [Cr(ddpd)2]3+ (ddpd=N,N’-dimethyl-N,N’-dipyridine-2-ylpyridine-2,6-diamine) to damage DNA in an air-saturated aqueous environment upon UV/Vis illumination. The quantum yield for strand breakage, that is, the ratio of DNA strand breaks to the number of absorbed photons, was determined to 1–4%, indicating efficient transformation of photons into DNA strand breaks by [Cr(ddpd)2]3+.
Inorganic nanocrystals with linear and nonlinear luminescence in the ultraviolet, visible, near infrared and short-wave infrared like semiconductor quantum dots and spectrally shifting lanthanide-based nanophosphors have meanwhile found many applications in the life and material sciences. This includes optical reporters for bioimaging and sensing, security and authentication barcodes, solid state lighting, converter materials, and photovoltaics. The identification of optimum particle structures requires quantitative spectroscopic studies under application-relevant conditions, focusing on the key performance parameter photoluminescence quantum yield, ideally flanked by single particle studies to assess spectroscopic inhomogeneities on a particle-to-particle level for typical preparation methods. In this context, methods to quantify the photoluminescence of these different nanoscale emitters are shown and utilized as a basis for a profound mechanistic understanding of the nonradiative deactivation pathways in semiconductor and upconversion nanocrystals of different size and particle architecture in different environments. Exemplary for the application potential of such nanomaterials, in addition, the design of optical sensors from different nanomaterials and functional organic dyes is briefly summarized.
Suppressed Transition and Dynamic self-asembly of ionic superdiscs in cylindrical nanochannels
(2023)
Liquid crystalline mesophases in nanoconfinement exhibit intriguing phase transition behaviors and relaxation dynamics. Here, we investigate the molecular mobility and electrical conductivity of a columnar ionic liquid crystal confined in self-ordered nanoporous alumina oxide membranes of pore size ranging from 180 nm down to 25 nm. We use nano-broadband dielectric spectroscopy (BDS) and calorimetry to study the dynamics and phase behavior. Calorimetric investigation reveals a complete suppression of the columnar – isotropic transition, while the plastic crystalline – columnar transition temperature decreases with inverse pore size and deviates from the Gibbs – Thomson equation.
For the bulk case, BDS detects two relaxation modes in the crystalline phase, the γ relaxation and the α1 relaxation, and two relaxation modes in the columnar phase, the α2 and α3 relaxation. All relaxation modes slow down for the confined case compared to the bulk. However, a new relaxation mode reflecting the interfacial layer emerges for the 80 and 25 nm. We discuss the possible molecular origins of the different relaxation modes observed. For the bulk ILC, a clear jump of 4 orders of magnitude in the absolute values of DC conductivity occurs at the transition from the plastic crystalline to hexagonal columnar phase, for the confined ILC, this transition is smooth. DC conductivity is reduced for the confined case, except for the 25nm, where the values are similar to the bulk.
We report the dielectric and calorimetric investigations of an homologous series of Janus polynorbornenes with rigid main backbone and flexible -Si(OR)3 side groups, of differing length alkyl chains (R = Propyl, Butyl, Hexyl, Octyl, Decyl). Dielectric dispersion reveals two active processes at low temperatures, denoted as β- and α- relaxation. The former can be assigned to localized fluctuations, whilst the latter relates to the glassy dynamics of the flexible -Si(OR)3 side groups, that creates a nanophase separation in both the alkyl chain rich and backbone rich domains. Temperature modulated DSC measurements and X-ray scattering experiment confirm the nanophase separation. Fast Scanning Calorimetry employing both fast heating and cooling rates detects the glass transition temperatures of the backbone rich domains, which are beyond or near to their degradation temperatures in terms of conventional DSC. The cooperative length scale of glass transition and the size of the alkyl chain rich domains increases with chain length. Alongside these results, a significant conductivity contribution was observed for all Poly(tricyclononenes) with Si(OR)3 side groups, which is interpreted in terms of a percolation model.
Suppressed Transition and Dynamic self-asembly of ionic superdiscs in cylindrical nanochannels
(2023)
Liquid crystalline mesophases in nanoconfinement exhibit intriguing phase transition behaviors and relaxation dynamics. Here, we investigate the molecular mobility and electrical conductivity of a columnar ionic liquid crystal confined in self-ordered nanoporous alumina oxide membranes of pore size ranging from 180 nm down to 25 nm. We use nano-broadband dielectric spectroscopy (BDS) and calorimetry to study the dynamics and phase behavior. Calorimetric investigation reveals a complete suppression of the columnar – isotropic transition, while the plastic crystalline – columnar transition temperature decreases with inverse pore size and deviates from the Gibbs – Thomson equation.
For the bulk case, BDS detects two relaxation modes in the crystalline phase, the γ relaxation and the α1 relaxation, and two relaxation modes in the columnar phase, the α2 and α3 relaxation. All relaxation modes slow down for the confined case compared to the bulk. However, a new relaxation mode reflecting the interfacial layer emerges for the 80 and 25 nm. We discuss the possible molecular origins of the different relaxation modes observed. For the bulk ILC, a clear jump of 4 orders of magnitude in the absolute values of DC conductivity occurs at the transition from the plastic crystalline to hexagonal columnar phase, for the confined ILC, this transition is smooth. DC conductivity is reduced for the confined case, except for the 25nm, where the values are similar to the bulk.
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.
## Summary:
This notebook and associated datasets (including VASP details) accompany a manuscript available on the ArXiv (https://doi.org/10.48550/arXiv.2303.13435) and hopefully soon in a journal as short communication as well. Most of the details needed to understand this notebook are explained in that paper with the same title as above. For convenience, the abstract is repeated here:
## Paper abstract:
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 presented coupled to 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 $Q<0.01$\,$\mathrm{nm}^{-1}$ up to $Q\approx150$\,$\mathrm{nm}^{-1}$, with a resolution of 0.16\,\AA. 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.