Publications Repository - Helmholtz-Zentrum Dresden-Rossendorf

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39109 Publications

Influence of surface roughness on the sorption of Cm(III)

Demnitz, M.; Schymura, S.; Neumann, J.; Müller, K.; Schmidt, M.


Many countries will use deep geological repositories to dispose of their highly radioactive nuclear waste. With an international perspective, crystalline rock is a potential host rock because of its strong geotechnical stability, low permeability and low solubility. However, its inherent mineralogy is heterogeneous, consisting of a wide set of minerals in varying amounts. Therefore, there is a need for using sophisticated techniques that allow to characterize the nanostructure of such crystalline rock surfaces with spatial resolution and the molecular speciation of the actinides thereon. As a representative for trivalent actinides, such as Am(III), Np(III), and Pu(III), which are expected to be present due to the reducing conditions encountered in a deep geological repository, we have chosen the actinide Cm(III). It possesses excellent luminescence properties, allowing us to determine sorption uptake and molecular speciation of Cm(III) on the surface.


Investigations focused on cleaved orthoclase (K-feldspar) single crystals as well as different crystalline rocks stemming from various regions in Europe. Cleaved pieces of orthoclase or thin sections of the crystalline rocks were immersed in a sorption solution containing [Cm(III)] = 5∙10-7 – 10-5 M. The experiments were undertaken at selected pH values (5.0 and 6.9) and different inherent mineralogical complexity of the systems. Subsequently, we applied correlated spectroscopy to analyze the samples. We combined vertical scanning interferometry, calibrated autoradiography, and Raman microscopy coupled to µTRLFS. Thus, we were able to correlate mineralogy, topography, and grain boundary effects with radionuclide speciation, allowing us to identify important radionuclide retention processes and parameters. For experimental details, see [1].


We observed that Cm(III) sorption uptake and speciation depends not only on the mineral phase, but also the surface roughness. Already on single crystal orthoclase an increasing surface roughness leads to higher sorption uptake (see Fig. 1) and to a stronger coordination of the sorbed Cm(III).
Increasing the mineral complexity of the system further, we used thin sections of various crystalline rocks, consisting mainly of feldspar, quartz, and mica. We observed significant differences in sorption uptake on individual mineral phases as well as the resulting speciation. In case that one mineral phase dominates the sorption process, e.g. amphibole, sorption of Cm(III) on other mineral phases will only occur at strong binding sites, typically where surface roughness is high. Areas of feldspar and quartz with high surface roughness additionally showed the formation of sorption species with particularly high sorption strength that could either be interpreted as Cm(III) incorporation species or adsorbed ternary complexes on the mineral surface.[2]
At pH values of around 6.8 Cm(III) generally sorbs more weakly to the surface, while preferentially targeting mineral phases such as mica instead of feldspar or quartz. At a higher pH of 8.0 the sorption uptake on other mineral phases increases, with a general trend towards more strongly bound Cm(III) surface species.
We conclude that in addition to mineral composition, surface roughness needs to be considered adequately by reactive transport models to describe interfacial speciation of contaminants and respective retention patterns for the safety assessments of nuclear waste repositories.


This work has been developed in the frame of the iCross project. We gratefully acknowledge funding provided by the German Federal Ministry of Education and Research (BMBF, Grant 02NUK053) and the Helmholtz Association (Grant SO-093).


1. Molodtsov et al., “Sorption of Eu(III) on Eibenstock granite studied by µTRLFS: A novel spatially-resolved luminescence-spectroscopic technique” Scientific Reports, 9, Article Number 6287 (2019),

2. Demnitz et al., “Effects of surface roughness and mineralogy on the sorption of Cm(III) on crystalline rock” Journal of Hazardous Materials, (2021),

Keywords: luminescence; speciation; Cm; crystal; interface; crystalline; roughness; topography; microscopy; spatial

  • Poster (Online presentation)
    TransRet2020 - Workshop on Processes Influencing Radionuclide Transport and Retention, 12.04.-13.10.2021, Karlsruhe, Germany

Publ.-Id: 34516

Electronic pair alignment and roton feature in the warm dense electron gas

Dornheim, T.

The study of matter under extreme densities and temperatures as they occur e.g. in astrophysical objects and nuclear fusion applications has emerged as one of the most active frontiers in physics, material science, and related disciplines. In this context, a key quantity is given by the dynamic structure factor S(q,ω), which is probed in scattering experiments -- the most widely used method of diagnostics at these extreme conditions. In addition to its crucial importance for the study of warm dense matter, the modeling of such dynamic properties of correlated quantum many-body systems constitutes one of the most fundamental theoretical challenges of our time. Here we report a hitherto unexplained roton feature in S(q,ω) of the warm dense electron gas [1], and introduce a microscopic explanation in terms of a new electronic pair alignment model [2]. This new paradigm will be highly important for the understanding of warm dense matter, and has a direct impact on the interpretation of scattering experiments. Moreover, we expect our results to give unprecedented insights into the dynamics of a number of correlated quantum many-body systems such as ultracold helium, dipolar supersolids, and bilayer heterostructures.

  • Lecture (others)
    Theorie-Seminar am Insitut für Theoretische Physik und Astrophysik der Christian-Albrechts Universität zu Kiel., 12.04.2022, Kiel, Germany

Publ.-Id: 34515

Update of the Bunch Arrival Time Monitor at ELBE

Kuntzsch, M.; Maalberg, A.; Schwarz, A.; Zenker, K.; Czwalinna, M. K.; Kral, J.

The bunch arrival time monitor (BAM) at the radiation source ELBE has been upgraded twofold. In order to achieve a higher precision a new frontend has been designed, based on a development by DESY, that uses state of the art 50 GHz electro-optical modulators (EOMs). The frontend allows for thermal control of critical components and monitoring of system parameters. The modulated EOM signals and monitoring data are distributed to a new readout electronic. The new MicroTCA-based receiveris based on a dedicated FMC card developed at DESY that is installed on an FMC25 carrier board. The arrival time is calculated on a FPGA with low latency and can be used for machine diagnostic. The code has been adapted to enable the processing of a data stream of the continuous train of electron bunches, allowing for the implementation of a cw beam based feedback in a next step. The contribution will describe the BAM setup as well as the performance measured at the ELBE accelerator.

Keywords: BAM; ELBE; arrival time; synchronization

Related publications

  • Poster
    International Particle Accelerator Conference IPAC 2022, 12.-17.06.2022, Bangkok, Thailand

Publ.-Id: 34514

Identification of color pigments in wall paintings of Oscar Schlemmer

Hennig, C.

Residuals of wall paintings from Bauhaus artist Oscar Schlemmer have been re-discovered recently. The restauration strategy of these precious objects requires a phase identification of the color pigments. The study includes the identification of potential decomposition mechanisms, as the wall paintings were in contact with chemicals of the glue from overlaying wall paper. Some coloring minerals were identified by combining high-resolution powder diffraction (PXRD) and x-ray fluorescence spectroscopy (XRF) using the new diffractometers at the Rossendorf Beamline (ROBL).

The Bauhaus revolutionized creative and artistic thinking and work worldwide. Walter Gropius employed a series of acclaimed artists as professors, among them Oskar Schlemmer, Wassili Kandinsky, Lyonel Feininger and Paul Klee. Adolf Meier, head of the architectural office of Walter Gropius, commissioned Oskar Schlemmer with wall paintings in his apartment for the first Bauhaus exhibition in 1923. Oskar Schlemmer, who was 1922-1925 the head of the Bauhaus studio for wall paintings, performed the work with Werner Gilles. During the Nazi regime, Schlemmer’s work was classified as degenerate art. Many of his wall paintings were overpainted. The wall paintings in Meier’s former apartment fell into oblivion. It was in the 1990s that Bauhaus research became aware of the existence of these wall paintings, which are only documented by two black and white photos from the time they were created.

In 2018, the apartment became subject of restoration studies. For this purpose, a network of institutions was created to identify the color scheme of the wall paintings and to generate a detailed 3D model of the room. The identification of the original color substances of the paintings remains a demanding issue as there are only residuals available. Schlemmer used partly new organic color material which was identified by spectroscopic techniques. A part of the paints is based on natural or synthetic mineral phase. These substances appear usually in a crystalline form and were identified with XRD. Heavy metals were identified with XRF spectroscopy. The small size of the color fragments, which were released from the walls, have microscopic dimensions of 10-30µm. This makes it impossible to perform phase identi¬fication with conventional laboratory equipment. The results of the synchrotron based XRD and XRF measurements from ROBL will be presented.

Related publications

  • Invited lecture (Conferences)
    Das Raumkunstwerk Wohnraum Adolf Meyer in Weimar im Kontext der Entwicklung des Bauhauses, 20.04.2022, Weimar, Germany

Publ.-Id: 34513

Machine Learning Collaboration-as-a-service at Helmholtz

Steinbach, P.; Hoffmann, H.; Tanveer, M.; Schmerler, S.; Starke, S.

Machine Learning (ML) based methods are proliferating in industry, society, science and physics in particular in the last years. Not only do ML tools allow inferences from experimental data, but also have shown to be an inroads to previously unreachable theoretical or experimental domains. In this presentation, I'll introduce Helmholtz AI as a funded networking activity within Helmholtz to support matter research in using ML for science. I'll dive into how and why the program is split into research and collaboration-as-a-service staff. If time allows, I'll discuss how we approach ML projects with scientists from a consulting point of view.

Keywords: machine learning; consulting; academia; science; services; Helmholtz AI

  • Open Access Logo Invited lecture (Conferences) (Online presentation)
    Seminar des ORIGINS Data Science Laboratory Munich, Einladung durch Lukas Heinrich, 08.04.2022, virtuell, Germany
    DOI: 10.6084/m9.figshare.19550815.v1

Publ.-Id: 34512

Effects of electrically conductive walls on turbulent magnetohydrodynamic flow in a continuous casting mold

Blishchik, A.; Glavinic, I.; Wondrak, T.; van Odyck, D.; Kenjereš, S.

In the present study, we have performed a series of numerical simulations of the turbulent liquid metal flow in a laboratory-scale setup of the continuous casting. The liquid metal flow was subjected to an external non-uniform magnetic field reproducing a realistic electromagnetic brake (EMBr) effect. The focus of this research was on the effects of the finite electrical conductivity of Hartmann walls on the flow and turbulence in the mold. To be able to simulate distributions of the electric potential and current in both the fluid and solid wall domains, we applied our recently developed and validated in-house conjugate MHD solver based on the open-source code OpenFOAM. The dynamic Large Eddy Simulation (LES) method was used to simulate the turbulent flow. The results obtained for the neutral (non-MHD) and MHD cases over a range of the imposed EMBr strengths – all for the perfectly electrically insulated walls – were compared with the available Ultrasound Doppler Velocimetry (UDV) measurements. A good agreement between simulations and experiments was obtained for all simulated cases. Next, we completed a series of simulations including a wide range of the finite electric conductivities (ranging from a weakly to perfectly conducting wall conditions) of the Hartmann walls for a fixed value of the imposed EMBr. The obtained results demonstrated a significant influence of the electric wall conductivities on the flow and turbulence reorganization. It is expected that here provided insights can be applicable for the new generation of the laboratory- and real-scale continuous casting setups.

Keywords: MHD; Magnetic field; Lorentz force; OpenFOAM; Electrically conducting walls; Dynamic LES; Continuous casting

Publ.-Id: 34511

Depth-Adjustable Magnetostructural Phase Transition in Fe₆₀V₄₀Thin Films

Anwar, M. S.; Cansever, H.; Boehm, B.; Gallardo, R.; Hübner, R.; Zhou, S.; Kentsch, U.; Rauls, S.; Eggert, B.; Wende, H.; Potzger, K.; Faßbender, J.; Lenz, K.; Lindner, J.; Hellwig, O.; Bali, R.

Phase transitions occurring within spatially confined regions can be useful for generating nanoscale material property modulations. Here we describe a magneto-structural phase transition in a binary alloy, where a structural transition from short range order (SRO) to body centered cubic (bcc) results in the formation of depth-adjustable ferromagnetic layers, which reveal application-relevant magnetic properties of high saturation magnetitzation (Ms) and low Gilbert damping (α). Here we use Fe₆₀V₄₀ binary alloy films which transform from initially Ms = 17 kA/m (SRO structure) to 747 kA/m (bcc structure) driven by atomic displacements caused by penetrating ions. Simulations show that estimated ~1 displacement per atom triggers a structural transition, forming homogeneous ferromagnetic layers. The thickness of ferromagnetic layer increases as a step-like function of the ion-fluence. Microwave excitations of the ferromagnetic/non-ferromagnetic layered system reveals an α = 0.0027 ± 0.0001. The combination of nanoscale spatial confinement, low α and high Ms provide a pathway for the rapid patterning of magnetic and microwave device elements.

Keywords: Magneto-structural correlations; Phase transitions; Magnetic thin films; Ion-irradiation; Short-range order

Related publications

Publ.-Id: 34510

Spatially-resolved sorption of Cm(III)/Eu(III) on heterogeneous crystalline rocks

Molodtsov, K.; Schymura, S.; Schierz, A.; Müller, K.; Stumpf, T.; Schmidt, M.

Many countries will use deep geological repositories (DGR) to store their heat generating high-level radioactive waste. Crystalline rock is one of the potential host rocks, but possesses high inherent mineralogical heterogeneity. Since the molecular retardation reactions of radionuclides at water-mineral interfaces depend mainly on the availability of reactive sites, heterogeneity is expected to play a major role for contaminant transport in a DGR. The fundamental understanding and transferrability of this heterogeneity into modeling different transport scenarios is of urgent need for a reliable safety assessment of a repository. Through correlation of spectroscopic information with spatial resolution we characterized the nanostructure of crystalline rock surfaces and the surface speciation of selected radionuclides, namely Eu(III) and Cm(III) thereon. We utilized vertical scanning interferometry, autoradiography, and Raman microscopy in combination with µTRLFS – microfocus time-resolved laser-induced fluorescence spectrsocopy.[1] Using these novel techniques the surface speciation of Eu(III) and Cm(III) can be qualified and quantified. Moreover, we were able to correlate mineralogy, topography, and grain boundary effects with radionuclide speciation, allowing us to draw conclusions about radionuclide retention mechanisms on mineral surfaces.
Our work focussed on granite from Eibenstock (Germany) and migmatised gneiss from the Bukov URL (Czech Republic). We characterized the sorption of Cm(III) and Eu(III) on feldspar, mica, quartz and accessory mineral areas on both rocks. [1-3] Using autoradiography and µTRLFS we linked the sorption uptake on the heterogeneous surface with the mineralogy and the surface roughness, showing that surface roughness within the same mineral phase has an impact not only on the amount of sorption uptake, but also the radionuclide surface speciation and thus bond strengths and reversibility.
Using µTRLFS we identified how the speciation correlates to mineral phases and surface roughness. A higher surface roughness induces more binding sites available to Eu(III) and Cm(III) resulting in strongly bound trivalent radionuclide surface complexes and a higher sorption uptake. On quartz and feldspar high surface roughness leads to ternary Cm(III) complex formation on the surface presumably with silicate and carbonate ions avaliable in solution.
In comparison to Eibenstock granite, Bukov gneiss inherently contained a greater number of accessory minerals. We observed that some of them seem to dominate the sorption process, lowering the sorption of Eu(III) on the major components feldspar and quartz in comparison to Eibenstock granite.[2] The leftover Cm(III)/Eu(III) sorb on stronger and preferential sorption sites, which are located in regions exhibiting a high surface roughness.[3] This could be clearly proven for Cm(III)/Eu(III) surface complexes being stronger on feldspar. With this work we demonstrated a successful upscaling approach to derive molecular understanding of radionuclide retention processes from the nm to the cm sacle.

[1] Molodtsov, Sorption of Eu(III) on Eibenstock granite studied by µTRLFS: A novel spatially-resolved luminescence-spectroscopic technique, Scientific Reports, 9, 6287 (2019).
[2] Molodtsov, A µTRLFS investigation on the sorption of Eu3+ on Bukov migmatised gneiss on the molecular level, Environmental Science & Technology, submitted.
[3] Demnitz, A spatially-resolved study on the sorption of Cm(III) on different crystalline rocks using surface investigation techniques, in preparation.

Keywords: luminescence; trlfs; surface; mineralogy; topography; interface; curium; europium; correlative; spectroscopy

  • Open Access Logo Lecture (Conference) (Online presentation)
    2. Tage der Standortauswahl, 11.-12.02.2021, Freiberg, Germany

Publ.-Id: 34509

Contemporary environment and historical legacy explain functional diversity of freshwater fishes in the world rivers

Su, G.; Tedesco, P. A.; Toussaint, A.; Villéger, S.; Brosse, S.

Regional taxonomic diversity (species richness) is strongly influenced by a joint effect of the current processes (habitat and energy availability) and historical legacies (past climate and geography), but it is still unclear how those historical and current environmental drivers have shaped the functional diversity of species assemblages.

Major taxa studied
Freshwater fish.


Time period

We combined the spatial occurrences over 2,400 river basins world-wide and the functional traits measured on 10,682 freshwater fish species to quantify the relative role of the habitat, climate and historical processes on the current global fish functional diversity. To avoid any correlation between taxonomic diversity and functional diversity, we controlled for differences in the number of species (species richness) between rivers. Functional diversity was considered through three complementary facets: functional richness, functional dispersion and functional identity.

The habitat-related variables explained most of the gradient in functional richness, verifying the habitat size–diversity hypothesis. In contrast, the historical climate–geography legacies markedly imprinted the functional dispersion and functional identity patterns, leading to a balanced influence of the current and historical processes. Indeed, the distribution of morphological traits related to fish dispersal was explained largely by the glaciation events during the Quaternary, leading to strong latitudinal gradients.

Main conclusions
This study provides new insights into the role of historical and current environmental determinants on the functional structure of fish assemblages and strengthens the proposal that the independence of facets of functional diversity from the species richness makes them essential biodiversity variables to understand the structure of communities and their responses to global changes.

Publ.-Id: 34508

FISHMORPH: A global database on morphological traits of freshwater fishes

Brosse, S.; Charpin, N.; Su, G.; Toussaint, A.; Herrera-R, G. A.; Tedesco, P. A.; Villéger, S.

Global freshwater fish biodiversity and the responses of fishes to global changes have been explored intensively using taxonomic data, whereas functional aspects remain understudied owing to the lack of knowledge for most species. To fill this gap, we compiled morphological traits related to locomotion and feeding for the world freshwater fish fauna based on pictures and scientific drawings available from the literature.

Main types of variables contained
The database includes 10 morphological traits measured on 8,342 freshwater fish species, covering 48.69% of the world freshwater fish fauna.

Spatial location and grain

Major taxa and level of measurement
The database considers ray-finned fishes (class Actinopterygii). Measurements were made at the species level.

Software format

Main conclusion
The FISHMORPH database provides the most comprehensive database on fish morphological traits to date. It represents an essential source of information for ecologists and environmental managers seeking to consider morphological patterns of fish faunas throughout the globe, and for those interested in current and future impacts of human activities on the morphological structure of fish assemblages. Given the high threat status of freshwater environments and the biodiversity they host, we believe this database will be of great interest for future studies on freshwater ecology research and conservation.


Publ.-Id: 34507

Spatially resolved sorption of Cm(III) on crystalline rock: influence of surface roughness and mineralogy

Demnitz, M.; Molodtsov, K.; Schymura, S.; Schierz, A.; Müller, K.; Schmidt, M.

Many countries will use deep geological repositories to dispose of their highly active nuclear waste. Crystalline rock is a potential host rock because of its high stability, heat resistance and low solubility. However, it possesses a high inherent mineralogical heterogeneity. Using sophisticated techniques that allow spatial resolution we characterized the nanostructure of such crystalline rock surfaces and the speciation of the actinide Cm(III) thereon.

Namely, we combined vertical scanning interferometry, calibrated autoradiography, and Raman microscopy coupled to µTRLFS (micro-focus time-resolved laser-induced spectroscopy).[1] Thus we were able to correlate mineralogy, topography, and grain boundary effects with radionuclide speciation, allowing us to identify important radionuclide retention processes and parameters.

Investigations focussed on granite from Eibenstock (Germany) and migmatised gneiss from Bukov (Czech Republic). Cm(III) sorption on the rock’s constituing minerals - primarily feldspar, mica and quartz - was analyzed quantitatively and qualitatively. We observed that Cm(III) sorption uptake and speciation depends not only on the mineral phase, but also the surface roughness. An increasing surface roughness leads to higher sorption uptake and a stronger coordination of the sorbed Cm(III). On the same mineral grains sorption differed significantly depending if an area exhibits a low or high surface roughness. In case that one mineral phase dominates the sorption process, sorption of Cm(III) on other mineral phases will only occur at strong binding sites, typically where surface roughness is high. Areas of feldspar and quartz with high surface roughness additionally showed the formation of sorption species with particularly high sorption strength that could either be interpreted as Cm(III) incorporation species or ternary complexes on the mineral surface.

We conclude that in addition to mineral composition, surface roughness needs to be considered adequately to describe interfacial speciation of contaminants and respective retention patterns for the safety assessments of nuclear waste repositories.

[1] Molodtsov, Schymura, Rothe, Dardenne & Schmidt (2019), Scientific Reports 9, 6287.

  • Open Access Logo Lecture (Conference) (Online presentation)
    Goldschmidt Virtual 2021, 08.07.2021, Lyon, France
    DOI: 10.7185/gold2021.3156

Publ.-Id: 34506

Mechanistic understanding of Curium(III) sorption on natural K feldspar surfaces

Demnitz, M.; Schymura, S.; Neumann, J.; Schmidt, M.; Schäfer, T.; Stumpf, T.; Müller, K.

To assess a reliable safety case for future deep underground repositories for highly active nuclear waste the retention of radionuclides by the surrounding host rock must be understood comprehensively. Retention is influenced by several parameters such as mineral heterogeneity and surface roughness, as well as pore water chemistry (e.g., pH). However, the interplay between those parameters is not yet well understood. Therefore, we present a correlative spectromicroscopic approach to investigate sorption of the actinide Cm(III) on: 1) bulk K-feldspar crystals to determine the effect of surface roughness and pH (5.5 and 6.9) and 2) a large feldspar grain as part of a complex crystalline rock system to observe how sorption is influenced by the surrounding heterogeneous mineralogy. Our findings show that rougher K-feldspar surfaces exhibit increased Cm(III) uptake and stronger complexation. Similarly, increasing pH leads to higher surface loading and stronger Cm(III) binding to the surface. Within a heterogeneous mineralogical system sorption is further affected by neighboring mineral dissolution and competitive sorption between mineral phases such as mica and feldspar. The obtained results express a need for investigating relevant processes on multiple scales of dimension and complexity to better understand trivalent radionuclide retention by a potential repository host rock.

Keywords: luminescence; speciation; Cm; host rock; interface; crystalline; roughness; topography; microscopy; spatial


  • Secondary publication expected from 15.10.2023

Publ.-Id: 34505

BIM - Biomedical Image analysis Models survey

Li, R.; Sharma, V.; Thangamani, S.; Yakimovich, A.

This is meta-analysis repository for the program code and meta-data collected on open-source biomedical image analysis models. This repository is maintained as a continuous survey of published open-source models. Code is aimed at obtaining statistical summary of the meta-data.

Keywords: open source; machine learning; bioimage analysis; deep learning

  • Software in external data repository
    Publication year 2022
    Programming language: Python
    System requirements: Python 3.9.7 seaborn 0.11.2 pandas 1.3.4 matplotlib 3.5.0
    License: MIT (Link to license text)
    Hosted on GitHub: Link to location

Publ.-Id: 34504

GUI Flow data

Döß, A.; Schubert, M.

- english version below -

Diese grafische Nutzeroberfläche in Form einer installirbaren standalone-Anwendung dient zur Visualisierung aus der Literatur bekannter experimenteller Datensätze und Strömungskarten für horizontal strömende Luft/Wasser-Systeme. Weiterhin sind Modelle und Strömungskarten aus der Literatur integriert, die für beliebige Stoffsysteme eine Vorhersage über die zu erwartenden Strömungsformen treffen. Zusätzlich erlauben Schnitstellen in Form von .txt-Dateien das Importieren eigener Datensätze, bzw. das Exportieren der visualisierten Inhalte.

Für die Richtigkeit der dargestellten Inhalte wird keine Haftung übernommen. Das Urheberrecht für die zugrundeliegenden Datensätze und Berechnungen liegt bei den Autoren der referenzierten Primärliteratur.

This graphical user interface in the form of an installable standalone application is used to visualize experimental data sets and flow maps known from the literature for horizontally flowing air/water systems. Furthermore, models and flow maps from the literature are integrated to predict the flow patterns for any fluid system. Additionally, data interfaces in the form of .txt files allow the import of own data sets, respectively the export of the visualized contents.

No liability is assumed for the correctness of the displayed contents. The copyright for the underlying data sets and calculations is held by the authors of the referenced primary literature.

Keywords: GUI; Interface; Flow data; flow regime maps; Strömungsdaten; Strömungskarten


Publ.-Id: 34503

Fully encapsulated and stable black phosphorus field-effect transistors

Arora, H.; Fekri, Z.; Vekariya, Y. N.; Chava, P.; Watanabe, K.; Taniguchi, T.; Helm, M.; Erbe, A.

Black phosphorus (BP) has quickly gained popularity in the scientific community owing to its interesting semiconducting properties, such as direct bandgap, high mobility, and intrinsic ambipolar behavior. However, its sensitivity to oxygen, moisture, and other air species has restricted its integration into active devices. Here, we employ lithography-free via-encapsulation scheme to fabricate fully-encapsulated BP-based field-effect transistors (FETs). The full encapsulation is achieved by sandwiching the BP layers between top and bottom hexagonal boron nitride (hBN) layers; top hBN passivating the BP layer from the environment and bottom hBN acting as a spacer and suppressing charge transfer to the BP layer from the SiO2 substrate. The embedded via-metal-electrodes allow us to perform reliable electrical measurements of the BP FETs. Based on our results, we find that the electronic properties of the via-encapsulated BP FETs are significantly improved compared to unencapsulated devices and a clear metal–insulator transition is observed which remained missing in the latter. We further establish that the via-contacting scheme leads to superior results compared to graphene-hBN heterostructures and bare hBN layers combined with evaporated metal contacts (both use top and bottom hBN to encapsulate BP) by revealing a higher mobility, lower hysteresis, and long-term ambient-stability in BP FETs.

Keywords: two-dimensional semiconductors; black phosphorus; field-effect transistors; hexagonal boron nitride; encapsulation

Related publications

Publ.-Id: 34502

Open-Source Biomedical Image Analysis Models: a Meta-analysis and Continuous Survey

Li, R.; Sharma, V.; Thangamani, S.; Yakimovich, A.

Open-source research software has proven indispensable in modern biomedical image analysis. A multitude of open-source platforms drive image analysis pipelines and help disseminate novel analytical approaches and algorithms. Recent advances in machine learning allow for unprecedented improvement in these approaches. However, these novel algorithms come with new requirements in order to remain open source. To understand how these requirements are met, we have collected 50 biomedical image analysis models and performed meta-analysis of their respective paper, source code, dataset and trained model parameters. We concluded that while there are many positive trends in openness, only a fraction of all publications makes all necessary elements available to the research community.

Keywords: deep learning; machine learning; bioimage analysis; open source

Publ.-Id: 34501

Sequencing meets machine learning to fight emerging pathogens: A preview

Yakimovich, A.

In searching for SARS-CoV variants-of-concern, pathogen sequencing is generating an impressive amount of data. However, beyond epidemiological use, these data contain cues fundamental to our understanding of pathogen evolution in the human population. Yet, to harness them, further development of computational methodology, such as machine learning, may be required. This preview discusses updates in machine learning to understand emerging pathogens.

Keywords: SARS-CoV2; machine learning; sequencing

Publ.-Id: 34497

A tandem segmentation-classification approach for the localization of morphological predictors of C. elegans lifespan and motility

Galimov, E.; Yakimovich, A.

C. elegans is an established model organism for studying genetic and drug effects on aging, many of which are conserved in humans. It is also an important model for basic research, and C. elegans pathologies is a new emerging field. Here we develop a proof-of-principal convolutional neural network-based platform to segment C. elegans and extract features that might be useful for lifespan prediction. We use a dataset of 734 worms tracked throughout their lifespan and classify worms into long-lived and short-lived. We designed WormNet - a convolutional neural network (CNN) to predict the worm lifespan class based on young adult images (day 1 – day 3 old adults) and showed that WormNet, as well as, InceptionV3 CNN can successfully classify lifespan. Based on U-Net architecture we develop HydraNet CNNs which allow segmenting worms accurately into anterior, mid-body and posterior parts. We combine HydraNet segmentation, WormNet prediction and the class activation map approach to determine the segments most important for lifespan classification. Such a tandem segmentation-classification approach shows the posterior part of the worm might be more important for classifying long-lived worms. Our approach can be useful for the acceleration of anti-aging drug discovery and for studying C. elegans pathologies.

Keywords: aging; deep learning; Caenorhabditis elegans; interpretable machine learning; convolutional neural networks

Publ.-Id: 34496

PaN Training Catalogue

Knodel, O.; Padovani, A.

The source code of the training catalogue for the PaN community developed in the ExPaNDS and PaNOSC projects. The initial code was developed for the training portal TeSS developed in the ELIXIR project.

Keywords: data management; photon and neutron community; training catalogue

  • Open Access Logo Software in external data repository
    Publication year 2022
    Programming language: Ruby on Rails
    System requirements: ruby-2.7.4
    License: BSD 3-Clause License (Link to license text)
    Hosted on Link to location


Publ.-Id: 34495

Model-independent determination of the dipole response of 66Zn using quasimonoenergetic and linearly polarized photon beams

Savran, D.; Isaak, J.; Schwengner, R.; Massarczyk, R.; Scheck, M.; Tornow, W.; Battaglia, G.; Beck, T.; Finch, S. W.; Fransen, C.; Friman-Gayer, U.; Gonzalez, R.; Hoemann, E.; Janssens, R. V. F.; Johnson, S.; Jones, M. D.; Kelly, N.; Kleemann, J.; Krishichayan, D. R. L.; O'Donnell, D.; Papst, O.; Sinclair, J.; Werner, V.; Wieland, O.; Wilhelmy, J.

Photon strength functions are an important ingredient in calculations relevant for the nuclear synthesis of heavy elements. The relation to the photo-absorption cross section allows to experimentally constrain photon strength functions by investigating the photo-response of atomic nuclei.
We determine the photoresponse of 66Zn in the energy region of 5.6 MeV to 9.9 MeV and analyze the contribution of the decay channel back to the ground state. In addition, for the elastic channel electric and magnetic dipole transitions can be separated.
Nuclear resonance fluorescence experiments were performed using a linearly-polarized quasimonoenergetic photon beam at the High Intensity Gamma-ray Source. Photon beam energies in the energy range from 5.6 MeV to 9.9 MeV with an energy spread of about 3 % were selected in steps of 200 - 300 keV.
Two High-Purity Germanium detectors were used for the subsequent gamma-ray spectroscopy.
Full photo absorption cross sections are extracted from the data making use of the mono-energetic character of the photon beam. For the ground-state decay channel the average contribution of electric and magnetic dipole strength is disentangled. The average branching ratio back to the ground state is determined as well.
The new results show lower cross sections compared to the values extracted from experiments using bremsstrahlung. In the latter the average branching ratio to the ground state needs to be estimated from statistical model calculations in order to analyze the data. The calculations underestimate this branching ratio
compared to the values extracted within the present analysis, which would partly explain the high cross sections determined from the bremsstrahlung data.

Keywords: Nuclear structure; electromagnetic transitions; photon scattering; nuclear resonance fluorescence; polarized photon beams

Related publications


Publ.-Id: 34493

Evaluation of raw data from THz source.

Gruber, T.

The radiation source ELBE (Electron Linac for beams with high Brilliance and low Emittance) at the Helmholtz Centre Dresden Rossendorf (HZDR) can produce several kinds of secondary radiations. THz radiation is one of them and can be used with a typical pulse frequency of 100 kHz as a stimulation source for elementary low-energy degrees of freedom in matter. It was used in the "Phase-resolved Higgs response in superconducting cuprates" publication (DOI: 10.1038/s41467-020-15613-1). The raw data for this publication can be accessed on RODARE (DOI: 10.14278/rodare.277) and will be used to reproduce the figures from the publication. This Jupyter notebook enables the user to handle the raw data from an TELBE THz experiment. To sample the whole THz wave the laser path length is modified by moving specific mirrors. The raw data contains for each mirror position a binary file storing the signal spectra and a folder with gray scaled tiff files storing the jitter timing. Parts of the code are parallelized and can run on multiple cores. The execution time on a single core is roughly 15 min after downloading and extracting a 20 GB zip file.

Keywords: Jupyter Notebook; Thz

Related publications


Publ.-Id: 34492

Data publication: Caenorhabditis elegans microscopy dataset with lifespan, movement and segmentation annotations.

Galimov, E.; Pincus, Z.; Yakimovich, A.

The nematode Caenorhabditis elegans (C. elegans) is an established model for studying various interventions into the ageing process, which allowed to find numerous genes and drugs interfering with agein. This dataset of widefield time-lapse (days 1 to 3) micrographs of C. elegans was initially obtained in the Pincus lab (Pincus et al. 2011, Zhang et al. 2016). Here, the dataset was annotated for lifespan, movement and segmentation of C. elegans, and was employed for developing a machine learning framework (Yakimovich et al. 2021). All files are in 8-bit PNG format. Movement and lifespan annotations are provided using folder structure. Segmentation annotation is provided by the accompanying masks.

Keywords: C. elegans; Caenorhabditis elegans; lifespan; movement; segmentation; microscopy

Publ.-Id: 34491

Review on zigzag air classifier

Kaas, A.; Mütze, T.; Peuker, U. A.

The zigzag (ZZ) classifier is a sorting and classification device with a wide range of applications (e.g. recycling, food industry [1, 2]). Due to the possible variation of geometry and process settings, the apparatus is used for various windows of operation regarding the specifications of the separation (e.g. cut sizes from 100 μm to several decimetres, compact and fluffy materials as well as foils). Since the ZZ-classifier gains more and more interest in recycling applications, it is discussed in this paper, regarding its design, mode of operation, influencing parameters and the research to date. Research on the ZZ-classifier has been going on for more than 50 years and can be divided into mainly experimental studies and modelling approaches.

Keywords: zigzag; classifier; separation; modelling; design

Publ.-Id: 34489

Development of Proton Bunch Monitors for Prompt Gamma-Ray Timing Based Treatment Verification

Makarevich, K.; Franke, A.; Pausch, G.; Permatasari, F.; Römer, K.; Schellhammer, S.; Stach, D.; Tiebel, J.; Wagner, A.; Weinberger, D.; Werner, R.-D.; Kögler, T.

Particle therapy emerged as a principal innovative technology for tumor treatment. However, it requires verification to exploit its full potential. Various approaches based on prompt gamma radiation were developed for range verification. Prompt gamma-ray timing (PGT), which determines the range of the therapeutic particles from time distributions of produced secondary gamma-rays, is a promising candidate for this as it is collimator-free and can be easily integrated into existing clinical beam deliveries [1]. However, phase instabilities between the accelerating radio frequency (RF) and the actual proton arrival time make phase monitoring indispensable [2]. In recent years, different concepts for proton bunch monitors (PBM) were developed [3,4]. The two most promising candidates are presented here.

Materials and Methods
A diamond detector with high radiation hardness and excellent time resolution was positioned close to the beam degrader. Protons scattered there were used to determine the phase correlation between RF and proton arrival time under realistic clinical conditions. The second monitor is a direct phasing tap on the low-level RF module of the IBA Proteus®C230 isochronous cyclotron. The correlation of both PBMs to the actual phase was checked in a scattering setup where protons from a pencil beam scattered in a thin polythene foil and then were coincidentally detected by CeBr₃-scintillators. The kinematics of this reaction makes the determination of the proton arrival time independent of the beam's bunch time spread.

Both PBMs strongly correlate with the phase shift between the arrival time of the proton bunch and the RF. A model based on an over-damped, harmonic oscillator was able to describe the time-dependent change in the phase position and its correction by a control circuit with sufficient accuracy. Thus, the phase instabilities in the PGT data could be successfully corrected, enabling the improved measurement accuracy.

The phase instability of the proton bunch is the source of the greatest uncertainty of the PGT method [2]. Two PBMs were studied to correct these instabilities. PBM(s) complement the measurement setup, which should increase the sensitivity of the method and facilitate the translation of the PGT approach into clinical application.

[1] C. Golnik et al.: Range assessment in particle therapy based on prompt γ-ray timing measurements, Phys. Med. Biol. 59 (2014) 5399.
[2] T. Werner et al.: Processing of prompt gamma-ray timing data for proton range measurements at a clinical beam delivery, Phys. Med. Biol. 64 (2019) 105023.
[3] F. Permatasari: Development of a Clinically Applicable Technique for Range Verification in Proton Therapy Based on the PGT Method, PhD thesis, TU Dresden, in preparation.
[4] R.-D. Werner: Charakterisierung eines schnellen Diamantdetektors als PBM für die Reichweiteverifikation in der Protonentherapie, Masterarbeit, Universität Halle-Wittenberg, 2021.

Keywords: proton range verification; prompt gamma timing; proton bunch monitor; particle range verification; prompt gamma-ray timing; range verification; proton therapy; PGT

Related publications

  • Lecture (Conference)
    53. Jahrestagung der Deutschen Gesellschaft für Medizinische Physik, 21.-24.09.2022, Aachen, Deutschland

Publ.-Id: 34488

2-Phosphonobutane-1,2,4,-Tricarboxylic Acid (PBTC): pH-Dependent Behavior Studied by Means of Multinuclear NMR Spectroscopy

Kretzschmar, J.; Wollenberg, A.; Tsushima, S.; Schmeide, K.; Acker, M.

Although 2-phosphonobutane-1,2,4,-tricarboxylic acid, PBTC, has manifold industrial applications, relevant and reliable data on the protonation of PBTC are poor. However, these data are critical parameters for ascertaining PBTC speciation, especially with regard to a sound structural and thermodynamic characterization of its metal ion complexes. A rigorous evaluation of pH-dependent 1H, 13C, and 31P chemical shifts along with accessible scalar spin–spin coupling constants (J) was performed in order to determine the pKa values of PBTC in 0.5 molal NaCl aqueous solution by means of nuclear magnetic resonance (NMR) spectroscopy. The phosphonate group revealed pKa values of 0.90 ± 0.02 and 9.79 ± 0.02, and the pKa values associated with the carboxylic groups are 3.92 ± 0.02, 4.76 ± 0.03, and 6.13 ± 0.03. Supported by DFT-calculated structures revealing strong intramolecular hydrogen bonding, the sequence of deprotonation could be unambiguously determined.

Keywords: PBTC; NMR; DFT; speciation; Thermodynamic constant; protolysis

Publ.-Id: 34485

The RODARE Data Repository (InvenioRDM) and why we need a separate Metadata Catalogue

Knodel, O.

Presentations from the Workshop on Metadata Catalogues, which took place virtually via Zoom on the 4th April 2022. Rodare was presented to introduce a data publication repository in contrast to the metadata catalogues SciCAT and ICAT. A recording of the event can be found on the ExPaNDS website:

Keywords: Data Management; Metadata Catalogue; ExPaNDS

  • Open Access Logo Invited lecture (Conferences) (Online presentation)
    ExPaNDS Workshop on Metadata Catalogues, 04.04.2022, online, online


Publ.-Id: 34484

Novel Mixing Relations for Determining the Effective Thermal Conductivity of Open-Cell Foams

Nain Camacho Hernandez, J.; Link, G.; Schubert, M.; Hampel, U.

This paper proposes a new approach to relate the effective thermal conductivity of open-cell solid foams to their porosity. It is based on a recently published approach for estimating the dielectric permittivity of isotropic porous media. A comprehensive assessment was performed comparing the proposed mixing relation with published experimental data for thermal conductivity and with numerical data from state-of-the-art relations. The mixing relation for the estimation of thermal conductivities based on dodecahedrons as building blocks shows good agreement with experimental data over a wide range of porosity.

Keywords: open-cell foams; effective permittivity; thermal conductivity; platonic solids

Publ.-Id: 34483

Analysis of Low-Temperature Magnetotransport Properties of NbN Thin Films Grown by Atomic Layer Deposition

Vegesna, S. V.; Lanka, S. V.; Bürger, D.; Li, Z.; Linzen, S.; Schmidt, H.

Superconducting niobium nitride (NbN) films with nominal thicknesses of 4 nm, 5 nm, 7 nm, and 9 nm were grown on
sapphire substrates using atomic layer deposition (ALD). We observed probed Hall resistance (HR) (Rxy) in external out-ofplane magnetic fields up to 6 T and magnetore-sistance (MR) (Rxx) in external in-plane and out-of-plane magnetic fields up
to 6 T on NbN thin films in Van der Pauw geometry. We also observed that positive MR dominated. Our study focused on the
analysis of interaction and localisation effects on electronic disorder in NbN in the normal state in temperatures that ranged
from 50 K down to the superconducting transition temperature. By modelling the temperature and magnetic field
dependence of the MR data, we extracted the temperature-dependent Coulomb interaction constants, spin–orbit scattering
lengths, localisation lengths, and valley degeneracy factors. The MR model allowed us to distinguish between interaction
effects (positive MR) and localisation effects (negative MR) for in-plane and out-of-plane magnetic fields. We showed that
anisotropic dephasing scattering due to lattice non-idealities in NbN could be neglected in the ALD-grown NbN thin films.

Keywords: Atomic layer deposition; Coulomb interaction constant; Magnetoresistance; NbN thin films; Supercondutor; Valley degeneracy

Related publications

Publ.-Id: 34481

Liquid Metal Alloy Ion Sources for FIB Applications in Nano – Technology

Bischoff, L.; Klingner, N.; Hlawacek, G.; Pablo Navarro, J.; Lenz, K.; Lindner, J.; Mazarov, P.; Pilz, W.; Meyer, F.

Focused Ion Beam (FIB) processing has been established as a well-suited and promising technique in R&D in nearly all fields of nanotechnology for patterning and prototyping on the μm-scale and below. Liquid Metal Alloy Ion Sources (LMAIS) represent an alternative to expand the FIB application fields beside all other source concepts. Here we present in the frame of two industrial related projects (ZIM) the development of different special LMAIS for FIB applications in nano–technology. So among others the alloys CoNd, CoNdB, AuGeB, AuGeBNi, AuSiCr, GaBiLi, CoDy, CuDy and AuSiDy are investigated and tested with regard to their use in modern mass separated FIB systems due to mass resolution, ion beam current of the certain ion species and the available spot size. The light ions like B, Li or Si dedicated for ion beam lithography systems. The transition metal elements Co, Fe and Ni are important for the modification and the adjustment of magnetic properties of nanomagnetic structures, presented in detail with a Co – FIB on a permalloy nanowire. Rare earth elements, especially Dy can tune the magnetic damping in nanometric dimensions. The latter is shown on magnonic stripe pattern of one mm² in size on a thin permalloy film made by a VELION FIB.

Keywords: Focused Ion Beam; Liquid Metal Alloy Ion Sources; nanomagnetic structures; magnetic damping

Related publications

  • Lecture (Conference)
    Ion Beam Workshop 2022, 31.03.-01.04.2022, Jena, Germany

Publ.-Id: 34480

Technological assessments on recent developments in fine and coarse particle flotation systems

Ahmad, H.; Mehdi, S.; Hoang, D. H.; Hamid, K.; Boris, A.; Przemyslaw, B. K.

After more than a century applying flotation to the mining industry, two completely different strategies have been introduced for processing purposes. One is the classical approach viz. grinding ores to a certain extent (fine particles) and floating them via conventional mechanical and pneumatic cells i.e., Jameson, Imhoflot™ and Reflux™. This strategy continues because mines face declining cut-off grades, complex and poly-mineralized ores, and they are required to achieve an acceptable degree of mineral liberation. The other school of thought deals with coarse particle processes mainly owing to the low energy requirements, that includes SkimAir® flash, fluidized bed and HydroFloat™ cells. There is no study in the literature to comparatively present the recent developments of flotation apparatuses versus the conventional mechanical cells. To cover this knowledge gap in the literature, the present paper endeavors to critically evaluate these concepts from several points of view, including existing technological advancements, water and energy usage, kinetics, and circuit design. A brief introduction of advanced technologies, along with their applications is presented. The data from literature and case studies showed that the Jameson, Imhoflot™ and recently developed Reflux™ flotation cells can be very effective for recovering fine particles owing to their specific hydrodynamic designs, intensive energy dissipation rate and generation of micron-sized bubbles (100–700 μm). Very low (less than a few minutes) mean particle residence time, high gas-hold up (ca. 50–70 %), no agitation and high efficiency of particle-bubble collision were identified as their main advantages compared to traditional mechanical flotation cells. In addition to their common applications in cleaner stage, these cells were used in pre-flotation and scalping (producing final concentrate from the rougher feed) duties. Their main challenges were recognized as relatively unclear procedure on their scale up/down, optimization and simulation. The HydroFloat™ cell was indicated as a promising technology for recovering coarse particle fraction sizes by taking advantage of the fluidized-bed concept with plug-flow dispersion regime, high particle residence time, and limited cell turbulence. We finally concluded that fine particle flotation may remain as the main focus of re-processing tailings dams, while coarse particle treatment should be the focus of this century to reduce total energy consumptions.

Keywords: Pneumatic flotation cells; Slurry retention time; Technological development; Flotation kinetics; Micron-sized bubbles


  • Secondary publication expected from 22.03.2023

Publ.-Id: 34479

Teaching on Software Carpentry (Virtual) (2022-03-28-upr-online)

Shao, Z.

Teaching "Programming with Python" for the workshop.
Workshop recordings are available on .

Keywords: Python

  • Software in external data repository
    Publication year 2022
    Programming language: Python
    System requirements: Python, jupyter
    License: Creative Commons Attribution license (Link to license text)
    Hosted on Link to location

Publ.-Id: 34478

Rhodium-decorated nanoconical nickel electrode synthesis and characterization as an electrochemical active cathodic material for hydrogen production

Skibińska, K.; Kutyła, D.; Yang, X.; Krause, L.; Marzec, M. M.; Żabiński, P.

Noble metals in form of bulk materials are rarely used as catalysts in industrial applications due to their price and limited accessibility. However, the surface of commonly-used materials can be modified with an exceptionally low amount of platinoids to enhance their electrochemical activity. In this work, the surface of the free-standing nanoconical Ni structures was modified with a thin metallic rhodium layer with a spontaneous galvanic displacement process. It emerged that Rh-decorated Ni nanoconical electrodes exhibited higher catalytic activity in a model hydrogen evolution reaction in an alkaline environment in comparison to the unmodified electrode. Furthermore, the proposed synthesis protocol is high-speed and straightforward,
making it promising in application on a semi and industrial scale. Linear Sweep Voltammetry measurements were used to test the catalytic activity in 1 M NaOH electrolyte. The nanoconical structures were highly-hydrophobic, what has been observed by dedicated camera-based equipment. In addition, the electrochemically-active surface area (ECSA) of tested electrodes were estimated and confirmed in atomic force microscope AFM measurements. The durability of coatings was tasted in 1 M NaOH for 14 days.

Keywords: one-step method; crystal modifier; surface modification; noble metal; hydrogen evolution reaction

Publ.-Id: 34477

EZ: An Efficient, Charge Conserving Current Deposition Algorithm for Electromagnetic Particle-In-Cell Simulations

Steiniger, K.; Widera, R.; Bastrakov, S.; Bussmann, M.; Chandrasekaran, S.; Hernandez, B.; Hübl, A.; Juckeland, G.; Kelling, J.; Leinhauser, M.; Pausch, R.; Rogers, D.; Schramm, U.; Young, J.; Debus, A.

We present EZ, a novel Current Deposition algorithm for particle-in-cell simulations, which calculates the current density field due to macro-particle motion within a time step by solving the electrodynamic continuity equation.
Being a charge conserving hybridization of \textbf{E}sirkepov's method and \textbf{Z}igZag, we refer to it as ``EZ'' as shorthand for ``Esirkepov meets ZigZag''.
EZ achieves the same level of charge conservation as the commonly used method by Esirkepov, yet reaches higher performance for macro-particle assignment-functions up to third-order.
Key considerations of its implementation in PIConGPU, an open source, C++, performance portable, fully relativistic 3D3V particle-in-cell code, are outlined in addition to the detailed description of EZ along with remarks on its optimization and customization.

Keywords: EZ; particle-in-cell; current deposition; PIConGPU; high-performance computing

  • Invited lecture (Conferences)
    Advanced Accelerators Concepts Workshops 2022, 06.-11.11.2022, Hauppauge, New York, United States of America

Publ.-Id: 34476

EZ publication: source code, profiling, analysis and simulation data

Steiniger, K.; Widera, R.; Young, J.

Data of the PIConGPU simulations as used in the publication: EZ: An Efficient, Charge Conserving Current Deposition Algorithm for Electromagnetic Particle-In-Cell Simulations

Data overview:

    • source code forked from the PIConGPU mainline version 0.7.0-dev
    • used input set `share/picongpu/examples/PaperThermal`
    • output including hdf5 dumps to validate charge conservation property for the PaperThermal setup (warm plasma)
    • simulation timings output for Spock CPU, Spock GPU and Summit GPU runs
    • profile data for Spock GPU and Summit GPU runs
    • output including hdf5 dumps to validate charge conservation property for the single particle test
    • jupyter notebooks for setup and analysis of PaperThermal setup
    • python script to plot charge conservation from hdf5 simulation output over time
    • bash script for statistical analysis of performance runs

Keywords: EZ; charge conservation; current deposition; PIConGPU; particle-in-cell; profiling; CUDA; HIP; NVIDIA; AMD; Spock; Summit; HPC


Publ.-Id: 34475

Modeling Inhomogeneous Warm Dense Matter

Moldabekov, Z.

The results of the analysis of the accuracy of the commonly used ground-state exchange-correlation (XC) functionals (LDA, PBE, PBEsol, AM05, SCAN) at warm dense matter conditions are presented [1,2]. We considered both unpolarized and polarized electrons. The analysis is performed by comparing to the available path-integral quantum Monte-Carlo (QMC) data. The relative deviation of the total density from the reference data is reported for different XC functionals in the case of the inhomogeneous electron gas. As a key finding of our evaluation, we emphasize that the overall performance of the ground-state XC functionals worsens with increasing the wavenumber of density perturbation.
Finally, the non-linear static density response of electrons is investigated using KS-DFT approach [3]. The results are verified by comparing to the QMC data when thermal temperature is equal to the Fermi temperature. New results for partially and strongly degenerate electrons are presented.


[1] Z. Moldabekov, T.Dornheim, M. Böhme, J. Vorberger, A. Cangi, The relevance of electronic perturbations in the warm dense electron gas. The Journal of Chemical Physics 155, 124116 (2021).
[2] Z. Moldabekov, T.Dornheim, J. Vorberger, A. Cangi, Benchmarking Exchange-Correlation Functionals in the Spin-Polarized Inhomogeneous Electron Gas under Warm Dense Conditions. Physical Review B, accepted for publication (2022), arXiv:2110.06708 .
[3] Z.Moldabekov, T. Dornheim, J. Vorberger, Density-Functional-Theory Perspective on the Non-Linear Response of Correlated Electrons Across Temperature Regimes, arXiv:2201.01623 (2022)

  • Open Access Logo Invited lecture (Conferences)
    Matter in Extreme Conditions: from MATerial science to Plasmas for Laboratory Astropohysics (MECMATPLA), 12.-19.03.2022, Montgenèvre, FRANCE

Publ.-Id: 34474

Enzymatic Hydrolysis of Triglycerides at the Water–Oil Interface Studied via Interfacial Rheology Analysis of Lipase Adsorption Layers

Javadi, A.; Dowlati, S.; Shourni, S.; Rusli, S.; Eckert, K.; Miller, R.; Kraume, M.

The enzymatic hydrolysis of sunflower oil occurs at the water–oil interface. Therefore, the characterization of dynamic interfacial phenomena is essential for understanding the related mechanisms for process optimizations. Most of the available studies for this purpose deal with averaged interfacial properties determined via reaction kinetics and dynamic surface tension measurements. In addition to the classical approach for dynamic surface tension measurements, here, the evolution of the dilational viscoelasticity of the lipase adsorbed layer at the water–oil interface is characterized using profile analysis tensiometry. It is observed that lipase exhibits nonlinear dilational rheology depending on the concentration and age of the adsorbed layer. For reactive water–oil interfaces, the response of the interfacial tension to the sinusoidal area perturbations becomes more asymmetric with time. Surface-active products of the enzymatic hydrolysis of triglycerides render the interface less elastic during compression compared to the expansion path. The lipolysis products can facilitate desorption upon compression while inhibiting adsorption upon expansion of the interface. Lissajous plots provide an insight into how the hysteresis effect leads to different interfacial tensions along the expansion and compression routes. Also, the droplet shape increasingly deviates from a Laplacian shape, demonstrating an irreversible film formation during aging and ongoing hydrolysis reaction, which supports our findings via interfacial elasticity analysis.

Keywords: Enzymatic reaction at the water oil interface; Hydrolysis of triglycerides in sunflower oil; Biodiesel; Dynamic surface phenomena; Interfacial elasticity; Protein adsorption at interface

Publ.-Id: 34473

CTAB-Silica nanoparticle complexes - dynamic surface tension measurements and modeling

Javadi, A.; Jafarlou, A.; Eckert, K.; Miller, R.

The adsorption dynamics of silica nanoparticles (NP) and cetyltrimethylammonium bromide (CTAB) complexes is studied via dynamic surface properties characterization by the drop Profile Analysis Tensiometry (PAT). Considering the hypothesis that a nanoparticle with a certain number of attached surfactant molecules can be considered as a unified surface-active complex, the equilibrium surface tension for fixed CTAB/NP mixing ratios were considered to construct respective adsorption isotherms. The results can be well described by the Frumkin adsorption model. The fitting parameters of the Frumkin model for different mixing ratios demonstrate that complexes with higher mixing ratios occupy less space at the interface and show weaker interaction with each other.

Keywords: Surfactant-nanoparticle interactions; CTAB silica complexes; Diffusion kinetics controlled adsorption; Drop profile analysis tensiometry; Stokes-Einstein equation; Dynamic surface phenomena

Publ.-Id: 34472

Influence of Cell Opening Methods on Electrolyte Removal during Processing in Lithium-Ion Battery Recycling

Werner, D. M.; Mütze, T.; Peuker, U. A.

Lithium-Ion batteries (LIBs) are an important pillar for the sustainable transition of the mobility and energy storage sector. LIBs are complex devices for which waste management must incorporate different recycling technologies to produce high-quality secondary (raw) materials at high recycling efficiencies (RE). This contribution on LIB recycling investigated the influence of different pretreatment strategies on the subsequent processing. The experimental study combined different dismantling depths and depollution temperatures with subsequent crushing and thermal drying. Therein, the removal of organic solvent is quantified during liberation and separation. This allows to evaluate the safety of cell opening according to the initial depollution status. These process steps play a key role in the recycling of LIBs when using the low temperature route. Therefore, combinations of pretreatment and processing steps regarding technical and economic feasibility are discussed. Moreover, the process medium and equipment properties for a safe cell opening, the technical recycling efficiencies and their consequences on future industrial LIB waste management are pointed out.

Keywords: Lithium-ion battery; recycling; battery cells; processing; crushing; thermal drying; process routes

Publ.-Id: 34471

Data publication: Characterization of protein corona formation on nanoparticles via dynamic interfacial properties analysis: Bovine serum albumin - silica particle case study

Shourni, S.; Javadi, A.; Hosseinpour, N.; Bahramian, A.; Raoufi, M.

Dynamic surface tension and elasticity values of BSA proteins and silica nanoparticles, in separated and also mixed solutions, measured via drop profile analysis tensiometry.

Keywords: Protein corona on nanoparticle (PCN); Bovine serum albumin (BSA); SiO2 nanoparticles; Dynamic surface tension; Kinetics of adsorption; Interfacial elasticity; Drug delivery

Related publications


Publ.-Id: 34470

Isotopic cross sections of fragmentation residues produced by light projectiles on carbon near 400A MeV

Boillos, J. M.; Cortina-Gil, D.; Benlliure, J.; Rodríguez-Sánchez, J. L.; Alvarez-Pol, H.; Atar, L.; Aumann, T.; Avdeichikov, V. V.; Beceiro-Novo, S.; Bemmerer, D.; Bertulani, C. A.; Boretzky, K.; Borge, M. J. G.; Caamaño, M.; Caesar, C.; Casarejos, E.; Catford, W.; Cederkall, J.; Chartier, M.; Chulkov, L.; Cravo, E.; Crespo, R. N. P.; Dillmann, I.; Díaz Fernández, P.; Elekes, Z.; Enders, J.; Ershova, O.; Estrade, A.; Farinon, F.; Fraile, L. M.; Freer, M.; Galaviz Redondo, D.; Geissel, H.; Gernhäuser, R.; Golubev, P.; Göbel, K.; Hagdahl, J.; Heftrich, T.; Heil, M.; Heine, M.; Heinz, A.; Henriques, A.; Holl, M.; Hufnagel, A.; Ignatov, A.; Johansson, H. T.; Jonson, B.; Kahlbow, J.; Kalantar-Nayestanaki, N.; Kanungo, R.; Kelic-Heil, A.; Knyazev, A.; Kröll, T.; Kurz, N.; Labiche, M.; Langer, C.; Le Bleis, T.; Lemmon, R.; Lindberg, S.; Machado, J. F. D. C.; Marganiec, J.; Movsesyan, A.; Nacher, E.; Najafi, M. A.; Nilsson, T.; Nociforo, C.; Panin, V.; Paschalis, S.; Perea, A.; Petri, M.; Pietri, S.; Plag, R.; Reifarth, R.; Ribeiro, G.; Rigollet, C.; Rossi, D. M.; Röder, M.; Savran, D.; Scheit, H.; Simon, H.; Sorlin, O.; Syndikus, I. J.; Taylor, J. T.; Tengblad, O.; Thies, R.; Togano, Y.; Vandebrouck, M.; Velho, P. J. F.; Volkov, V.; Wagner, A.; Wamers, F.; Weick, H.; Wheldon, C.; Wilson, G. L.; Winfield, J. S.; Woods, P.; Yakorev, D.; Zhukov, M.; Zilges, A.; Zuber, K.

We measured 135 cross sections of residual nuclei produced in fragmentation reactions of 12C, 14N, and 13−16,20,22O projectiles impinging on a carbon target at kinetic energies of near 400A MeV, most of them for the first time, with the R 3B/LAND setup at the GSI facility in Darmstadt (Germany). The use of this state-of-the-art experimental setup in combination with the inverse kinematics technique gave the full identification in atomic and mass numbers of fragmentation residues with a high precision. The cross sections of these residues were determined with uncertainties below 20% for most of the cases. These data are compared to other previous measurements with stable isotopes and are also used to benchmark different model calculations.

Keywords: low and intermediate energy heavy-ion collisions; nuclear fragmentation; nuclear reactions; unstable nuclear induced reactions; nuclear physics

Publ.-Id: 34468

Probing charged lepton flavor violation with the Mu2e experiment

Müller, S.; Ferrari, A.; Knodel, O.; Rachamin, R.

Presentation a 2022 DPG spring meeting (section "Hadrons & Nuclei"), March 31, 2022

Keywords: MU2E; Charged Lepton Flavor Violation; DPG

Related publications

  • Lecture (Conference) (Online presentation)
    DPG Spring meeting 2022, Section "Hadrons & Nuclei", 28.03.-01.04.2022, virtual, Germany

Publ.-Id: 34467

High Energy Resolution X-ray Spectroscopy for Actinide Science

Kvashnina, K. O.

In recent years, scientists have progressively recognized the role of electronic structure in the characterization of chemical and physical properties for actinide containing materials. High-energy resolution X-ray spectroscopy at the actinide M4,5 edges emerged as a promising direction because this method can probe actinide properties at the atomic level through the possibility of reducing the experimental spectral width below the natural core-hole life time broaden-ing.

In this lecture, I will describe the latest progress in the field of high-energy resolution X-ray spectroscopy at the acti-nide M4,5 edges1. More than 10 years passed after the first X-ray spectroscopy experiment in the high-energy resolu-tion mode on uranium systems at the U M4 edge (~3728 eV) in 20092. Quite a bit is known for the moment and X-ray absorption spectroscopy (XAS) or X-ray absorption near edge structure (XANES) in the high-energy resolution fluo-rescence detection (HERFD) mode together with resonant inelastic X-ray scattering (RIXS) or resonant X-ray emission spectroscopy (RXES) are now common techniques for studying the physics and chemistry of the f-block elements. I will show that the methods are able to a) provide fingerprint information on the actinide oxidation state and ground state character b) probe 5f occupancy, non-stoichiometry, defects c) investigate the local symmetry and effects of the crystal field3–12

Related publications

  • Lecture (Conference)
    Actinides Revisited 2022, 21.-23.09.2022, Dresden, Germany

Publ.-Id: 34466

Electrical Conductivity of Iron in Earth's Core from Microscopic Ohm's Law (DFT4MEC)

Ramakrishna, K.; Lokamani, M.; Baczewski, A.; Vorberger, J.; Cangi, A.

Understanding the electronic transport properties of materials under high temperatures and pressures is essential for constraining geophysical processes and provides indispensable insights useful for novel materials discovery. The difficulty of measuring the electrical conductivity of iron under Earth-core conditions reliably in experiments calls for sophisticated theoretical methods that can support diagnostics. We present results of the electrical conductivity in iron within the pressure and temperature ranges found in Earth's core by simulating microscopic Ohm's law using time-dependent density functional theory. Our predictions are independent of previous studies, which primarily used the Kubo-Greenwood formula, and therefore provide a new perspective on resolving discrepancies in recent experiments.

Keywords: TDDFT; Computational Physics; High-performance Computing; Planetary Physics

  • Invited lecture (Conferences)
    DFT Methods for Matter under Extreme Conditions, 22.02.2022, Görlitz, Germany

Publ.-Id: 34465

Electrical Conductivity of Iron under Earth-Core Conditions from Time-Dependent Density Functional Theory (APS)

Ramakrishna, K.; Lokamani, M.; Baczewski, A.; Vorberger, J.; Cangi, A.

Time-dependent density functional theory (TDDFT) enables calculating electronic transport properties in the warm dense matter (WDM) and is an alternative to present state-of-the-art approaches. In the real-time formalism of TDDFT (RT-TDDFT), the electrical conductivity is directly computed from the time evolution of the electronic current density and provides direct means to assess the validity of Ohm's law in WDM. Without relying on the methods of diagonalization, the method is computationally fast compared to linear-response TDDFT (LR-TDDFT). We present TDDFT calculations of the electrical conductivity in iron within the pressure and temperature ranges found in Earth's core and discuss the ramifications of using TDDFT for calculating the electrical conductivity in contrast to the Kubo-Greenwood (KG) formalism and dielectric models.

  • Lecture (Conference) (Online presentation)
    APS March meeting 2022 (Session: Matter at Extreme Conditions: Planetary Materials I), 14.03.2022, Chicago, USA

Publ.-Id: 34464

Design und Synthese von hochpotenten und spezifischen Histondeacetylase 1- und 2-Inhibitoren mit dem Ziel der Herstellung geeigneter Radiotracer zur bildgebenden Darstellung der Enzyme in Tumoren des Menschen

Clauß, O.

Störungen in der Regulation der Expression von Genen in Zellen sind von großer Bedeutung für die Entstehung von Krebserkrankungen. Die Transkription von Genen wird u. a. durch den Grad der Acetylierung von bestimmten DNA-bindenden Proteinen, den Histonen, reguliert. Damit kommt den Histondeacetylasen (HDACs), die enzymatisch Acetylgruppen u. a. von Histonmolekülen abspalten, eine besondere Bedeutung bei der transkriptionellen Regulation von tumorrelevanten Genen, wie bspw. Tumorsuppressorgenen, zu. HDAC-Inhibitoren werden daher als aussichtsreiche Medikamente für die Krebstherapie untersucht. Mit Hilfe des nicht-invasiven Bildgebungsverfahrens Positronen-Emissions-Tomographie könnte es möglich sein, die Rolle von einzelnen Histondeacetylasen für die Entstehung und Progression neuroonkologischer Erkrankungen, wie bspw. Gliome, zu untersuchen.
Das Ziel dieser Arbeit ist es, neuartige hochpotente, spezifische und fluorhaltige Inhibitoren für die besonders tumorrelevanten Histondeacetylasen HDACs1/2 auf der Grundlage der Leitstrukturen BRD8951, Cpd-60 und Cpd-4 zu entwickeln. Nach der pharmakologischen Charakterisierung der HDAC-Inhibitoren gegenüber humaner, rekombinanter HDAC1/2 und der Bestimmung der Spezifität gegenüber humaner HDAC3 und HDAC6, wurde die potente und HDAC1/2-spezifische Verbindung N-[2-Amino-5-(thiophen-3-yl)phenyl]-4-[(2-fluorpropanamido)methyl]benzamid (BA3) ausgewählt und als Radiotracer weiterentwickelt. Durch die Herstellung eines geeigneten Präkursors wurde das Radionuklid Fluor-18 durch eine nukleophile Substitution eingeführt und der entsprechende Radioligand [18F]BA3 generiert. Anschließend wurde eine automatisierte Radiosynthese entwickelt. Erste biologische Experimente in der Maus zeigten jedoch, dass der Radiotracer eine geringe Hirnaufnahme aufweist, die u. a. auf die Interaktion mit P-Glykoprotein als Effluxtransporter zurückzuführen ist. Zusätzlich wurde ein hoher Anteil radioaktiver Metabolite im Hirn 30 min p.i. nachgewiesen, sodass das detektierte radioaktive Signal nicht allein dem Radioliganden [18F]BA3 zugeordnet werden kann. Die erhaltenen Daten sprechen gegen eine Verwendung dieses Radiotracers in der In-Vivo-Bildgebung der HDACs1/2. Daraufhin sollten die vermutlich metabolisch stabileren HDAC-Inhibitoren N-[2-Amino-5-(thiophen-2-yl)phenyl]-4-[(3-fluor-2,2-dimethylpropanamido)-methyl]benzamid (BA15) und N-(4-Amino-4'-fluor-[1,1'-biphenyl]-3-yl)-4-(pivalamidomethyl)-benzamid (BA17) radiofluoriert werden. Unabhängig von den In-vivo-Untersuchungen wurde das toxikologische Potential von BA3, BA15 und BA17 gegenüber ausgewählten Tumorzelllinien untersucht. Die HDAC-Liganden weisen eine vergleichbare Toxizität gegenüber etablierten HDAC-Inhibitoren auf.

Keywords: Histondeacetylasen; HDAC1/2; Inhibitor; Tacedinalin; Benzamid; Fluor-18; Radiotracer; Positronen-Emissions-Tomographie

  • Doctoral thesis
    Universität Leipzig, 2022

Publ.-Id: 34463

Multivariate statistische Modellierung von Prompt Gamma-Ray Timing Spektren für die Behandlungsverifikation der Protonentherapie

Schellhammer, S.; Wiedkamp, J.; Löck, S.; Kögler, T.


Aufgrund der steilen Dosisgradienten und der Variabilität des Bremsvermögens kann die Präzision der Protonentherapie durch Bewegungen und anatomische Veränderungen stark kompromittiert werden. Hieraus resultiert ein hoher Bedarf für eine Online-Verifizierung der Behandlung. Als leichtes, kollimatorfreies System, das einfach in bestehende Anlagen integriert werden kann, ist die Prompt Gamma-Ray Timing (PGT) Methode eine vielversprechende Kandidatin für diese Anwendung. Die Entwicklung eines solchen Systems stellt jedoch eine Herausforderung dar, da die im Patienten applizierte Protonenreichweite mit hoher Genauigkeit aus der zeitlichen Verteilung einer limitierten Anzahl von Gammaquanten rekonstruiert werden muss. Bisher basierte diese Rekonstruktion auf dem arithmetischen Mittel und der Standardabweichung der Verteilung, aber die Genauigkeit dieser Methode erwies sich als begrenzt. Ziel dieser Studie war deshalb die Entwicklung multivariater statistischer Modelle auf Basis weiterer Histogramm-Merkmale und somit eine Optimierung der Verifikationsgenauigkeit der PGT-Methode.

Material & Methoden

Es wurden PGT-Verteilungen analysiert, die während einer statischen Pencil-Beam-Bestrahlung eines Acrylglasphantoms mit unterschiedlich dicken Lufthohlräumen aufgenommen wurden. Relevante Histogramm-Merkmale wurden aus den Empfehlungen der Image Biomarker Standardisation Initiative abgeleitet und automatisiert mittels Vorwärtsauswahl (Forward Selection) sowie der Least Absolute Shrinkage and Selection Operator (LASSO) Methode ausgewählt. Diese Merkmale wurden anschließend in multivariaten linearen Regressionsmodellen genutzt um die Hohlraumdicke vorherzusagen. Die Güte der Modelle wurde anhand ihres Bestimmtheitsmaßes R2 und ihres mittleren quadratischen Fehlers RMSE an einem unabhängigen Datensatz bewertet. Abschließend wurde ein homogenes Bestrahlungsfeld im Pencil-Beam-Scanning-Verfahren appliziert und die Modellvorhersage anhand von zweidimensionaler Bildgebung verglichen.


Die neu entwickelten Modelle zeigen eine stark verbesserte Vorhersagekraft (R2 > 0,6) im Vergleich zur bisherigen Methodik (R2 < 0,1, s. Abbildung 1). Beide Selektionsmethoden erreichen eine ähnliche Vorhersagekraft. Die Modelle erzielen ihre maximale Vorhersagekraft ab etwa vier kombinierten Histogramm-Merkmalen, wobei sich insbesondere die robuste mittlere Abweichung und die Kurtosis als starke Prädiktoren erweisen. Die neu entwickelten Modelle ermöglichen die Identifizierung der eingebrachten Lufthohlräume im gescannten Bestrahlungsfeld (Abbildung 2).


Diese Ergebnisse zeigen, dass die statistische Modellierung ein wertvolles Instrument zur Optimierung der Prompt Gamma-Ray Timing Methode ist und demonstrieren ihr Potential zur Anwendung für die Behandlungsverifikation der Protonentherapie.

Keywords: proton therapy; treatment verification; prompt gamma-ray timing; statistical modelling

  • Lecture (Conference)
    53. Jahrestagung der Deutschen Gesellschaft für Medizinische Physik (DGMP), 21.-24.09.2022, Aachen, Deutschland

Publ.-Id: 34462

Tuning of Curie temperature in Mn5Ge3 films

Xie, Y.; Birowska, M.; Simon Funk, H.; Anita Fischer, I.; Schwarz, D.; Schulze, J.; Zeng, Y.-J.; Helm, M.; Zhou, S.; Prucnal, S.

We report a change in the structural and magnetic properties of epitaxial Mn5Ge3 on a Ge-on-Si (111) substrate by applying strain engineering through ms-range flash lamp annealing (FLA). X-ray diffraction results demonstrate that during FLA for 20 ms, the formation of nonmagnetic MnxGey secondary phases is suppressed, while the in-plane expansion of the lattice increases with increasing annealing temperature. Temperature-dependent magnetization results indicate that the Curie temperature of Mn5Ge3 rises from 287 K in the as-prepared sample to above 400 K after FLA, making Mn5Ge3 an attractive material for spintronics. Experimental results together with theoretical Monte Carlo simulations allow us to conclude that the expansion of the in-plane lattice causes the increase of the Curie temperature due to enhancement of the ferromagnetic interaction between Mn atoms.

Keywords: Strain engineering; flash lamp annealing (FLA); Curie temperature; ferromagnetic material; epitaxial film

Related publications

Publ.-Id: 34461

Optimized activation for quantum-inspired self-supervised neural network based fully automated brain lesion segmentation

Konar, D.; Bhattacharyya, S.; Dey, S.; Panigrahi, B. K.

Due to the lack of appropriate tailoring of the inter-connection weights, the segmentation performance of the recently suggested Quantum-inspired Self-supervised Neural Network models suffers from the slow convergence problem. As a result, using quantum-inspired meta-heuristics in Quantum-Inspired Self-supervised Neural Network models improves their hyper-parameters and inter-connection weights. The goal of this paper is to propose an improved version of a Quantum-Inspired Self-supervised Neural Network (QIS-Net) model for brain lesion segmentation. The proposed Optimized Quantum-Inspired Self-supervised Neural Network (Opti-QISNet) model is based on the QIS-Net architecture, and its operations are used to get the best segmentation results. A Quantum-Inspired Optimized Multi-Level Sigmoidal (Opti-QSig) activation is the optimized activation function used in the described model. Three quantum-inspired meta-heuristics improve the Opti-QSig activation function, with fitness evaluated using Otsu’s multi-level thresholding. Experiments were carried out using brain MR images from the Cancer Imaging Archive (TCIA) in the Nature data repository. The results show that the proposed self-supervised Opti-QISNet model outperforms our recently established QIBDS Net and QIS-Net models in brain lesion segmentation, and it is a potential candidate to extensively supervised neural network based architectures (UNet and FCNNs).

Keywords: Quantum computing; U-Net; QIBDS Net; MR Images

Publ.-Id: 34460

Mu2e-II: Muon to electron conversion with PIP-II

Byrum, K.; Corrodi, S.; Oksuzian, Y.; Winter, P.; Xia, L.; Edmonds, A. W. J.; Miller, J. P.; Mott, J.; Marciano, W. J.; Szafron, R.; Bonventre, R.; Brown, D. N.; Kolomensky, Y. G.; Ning, O.; Singh, V.; Prebys, E.; Borrel, L.; Echenard, B.; Hitlin, D. G.; Hu, C.; Lin, D. X.; Middleton, S.; Porter, F. C.; Zhang, L.; Zhu, R.-Y.; Ambrose, D.; Badgley, K.; Bernstein, R. H.; Boi, S.; Casey, B. C. K.; Culbertson, R.; Gaponenko, A.; Glass, H. D.; Glenzinski, D.; Goodenough, L.; Hocker, A.; Kargiantoulakis, M.; Kashikhin, V.; Kiburg, B.; Kutschke, R. K.; Murat, P. A.; Neuffer, D.; Pronskikh, V. S.; Pushka, D.; Rakness, G.; Strauss, T.; Yucel, M.; Bloise, C.; Diociaiuti, E.; Giovannella, S.; Happacher, F.; Miscetti, S.; Sarra, I.; Martini, M.; Ferrari, A.; Müller, S.; Rachamin, R.; Barlas-Yucel, E.; Artikov, A.; Atanov, N.; Davydov, Y. I.; Glagolev, V.; Vasilyev, I. I.; Brown, D. N.; Uesaka, Y.; Denisov, S. P.; Evdokimov, V.; Kozelov, A. V.; Popov, A. V.; Vasilyev, I. A.; Tassielli, G.; Teubner, T.; Chislett, R. T.; Hesketh, G. G.; Lancaster, M.; Campbell, M.; Ciampa, K.; Heller, K.; Messerly, B.; Cummings, M. A. C.; Calibbi, L.; Blazey, G. C.; Syphers, M. J.; Zutshi, V.; Kampa, C.; Mackenzie, M.; Di Falco, S.; Donati, S.; Gioiosa, A.; Giusti, V.; Morescalchi, L.; Pasciuto, D.; Pedreschi, E.; Spinella, F.; Hedges, M. T.; Jones, M.; You, Z. Y.; Zanetti, A. M.; Valetov, E. V.; Dukes, E. C.; Ehrlich, R.; Group, R. C.; Heeck, J.; Hung, P. Q.; Demers, S. M.; Pezzullo, G.; Lynch, K. R.; Popp, J. L.

An observation of Charged Lepton Flavor Violation (CLFV) would be unambiguous evidence for
physics beyond the Standard Model. The Mu2e and COMET experiments, under construction, are
designed to push the sensitivity to CLFV in the μ → e conversion process to unprecedented levels.
Whether conversion is observed or not, there is a strong case to be made for further improving
sensitivity, or for examining the process on additional target materials. Mu2e-II is a proposed
upgrade to Mu2e, with at least an additional order of magnitude in sensitivity to the conversion
rate over Mu2e. The approach and challenges for this proposal are summarized. Mu2e-II may be
regarded as the next logical step in a continued high-intensity muon program at FNAL.

Keywords: Charged Lepton Flavor Violation; Muon to Electron conversion; Mu2e; FLUKA

Related publications

  • Open Access Logo Contribution to proceedings
    Particle Physics Community Planning Exercise (SNOWMASS), 17.-26.07.2022, Seattle, USA
    DOI: 10.48550/arXiv.2203.07569

Publ.-Id: 34459

A user-friendly R Platform for Optimizing Mineral Processing

Ben Said, B.; Pereira, L.; Tolosana Delgado, R.; Rudolph, M.

An open-source and user-friendly platform for using design of experiments for optimizing mineral processing. No specific knowledge of programming languages is required for using the platform. Depending on the user needs, the platform suggests the optimal experimental strategy with a minimum number of runs required. Different types of experimental designs such as screening, full factorial and central composite designs are currently available. The R shiny app can be accessed via:

Keywords: Design of experiments; Plant optimization; Mineral processing; Shiny R; Process Modelling


Publ.-Id: 34457

Developing Accelerator Mass Spectrometry Capabilities for Anthropogenic Radionuclide Analysis to Extend the Set of Oceanographic Tracers

Hain, K.; Martschini, M.; Gülce, F.; Honda, M.; Lachner, J.; Kern, M.; Pitters, J.; Quinto, F.; Sakaguchi, A.; Steier, P.; Wiederin, A.; Wieser, A.; Yokoyama, A.; Golser, R.

Recent major advances in Accelerator Mass Spectrometry (AMS) at the Vienna Environmental Research Accelerator (VERA) regarding detection efficiency and isobar suppression have opened possibilities for the analysis of additional long-lived radionuclides at ultra-low environmental concentrations. These radionuclides, including 233U, 135Cs, 99Tc, and 90Sr, will become important for oceanographic tracer application due to their generally conservative behavior in ocean water. In particular, the isotope ratios 233U/236U and 137Cs/135Cs have proven to be powerful fingerprints for emission source identification as they are not affected by elemental fractionation. Improved detection efficiencies allowed us to analyze all major long-lived actinides, i.e., 236U, 237Np, 239,240Pu, 241Am as well as the very rare 233U, in the same 10 L water samples of a depth profile from the northwest Pacific Ocean. For this purpose, a simplified and very flexible chemical purification procedure based on extraction chromatography (a single UTEVA® column) was implemented which can be extended by a DGA® column for Am purification. The procedure was validated with the reference materials IAEA-381/385. With the additional increase in ionization efficiency expected for the extraction of actinides as fluoride molecules from the AMS ion source, a further reduction of chemical processing may become possible. This method was successfully applied to an exemplary set of air filter samples. In order to determine the quantitative 237Np concentration reliably, a 236Np spike material is being developed in collaboration with the University of Tsukuba, Japan. Ion-Laser Interaction Mass Spectrometry (ILIAMS), a novel technique for the efficient suppression of stable isobaric background, has been developed at VERA and provides unprecedented detection sensitivity for the fission fragments 135Cs, 99Tc, and 90Sr. The corresponding setup is fully operational now and the isobar suppression factors of >105 achieved, in principle, allow for the detection of the mentioned radionuclides in the environment. Especially for 90Sr analysis, this new approach has already been validated for selected reference materials (e.g., IAEA-A-12) and is ready for application in oceanographic studies. We estimate that a sample volume of only (1–3) L ocean water is sufficient for 90Sr as well as for 135Cs analysis, respectively.

Publ.-Id: 34456

HERMES: HMC supported automated software publications

Knodel, O.; Druskat, S.; Bertuch, O.; Juckeland, G.; Schlauch, T.

To satisfy the principles of FAIR software, software sustainability and software citation, research software must be formally published. Publication repositories make this possible and provide published software versions with unique and persistent identifiers. However, software publication is still a tedious, mostly manual process. To streamline software publication, HERMES, a project funded by the Helmholtz Metadata Collaboration, develops automated workflows to publish research software with rich metadata.
This talk presents the progress of the first year and summarises the interaction with the Helmholtz Association and beyond.

Keywords: HMC; Metadata; Software publication

  • Open Access Logo Invited lecture (Conferences) (Online presentation)
    HMC Projects | Welcome Meeting Projects 2021, 30.03.2022, Berlin, Deutschland

Publ.-Id: 34455

N-Donor Ligands as Versatile Actinide Complexation Agents

Köhler, L.; Patzschke, M.; März, J.; Schmidt, M.; Stumpf, T.

Actinide coordination chemistry has attracted chemists´ interest for decades in terms of nuclear safety, catalysis, or radiopharmaceutical research. Especially the early actinides exhibit an unusually large range of oxidation states, which originates in the near degeneracy of the 5f, 6d and 7s energy levels. This offers unique chemical and physical properties, not yet fully understood. Schiff bases like the mixed N, O donor ligands of the salen (Bis(salicyliden)ethylendiamine) family are frequently chosen systems for complexation studies, because of their advantageous ability to stabilize a large number of metals including actinides, as well as their tuneable electronical and sterical properties. Based on pyrrole structural relatives of salen can be constructed, which only exhibit N-donor functionalities. This provides the possibility to investigate and compare the binding situation between early actinides and N atoms in different environments.
In this study a complex series with Th and U as well as the transuranic elements Np and Pu with the pyrrole-based ligand 1,2-ethylenediamine-N,N’-bis(1H-pyrrol-2-yl)methylene (H2pyren) H2L1 was synthesized. Characterization in solid state (via SC-XRD) shows an 8-fold coordination at the metal centre, where all N donors participate. Moreover, the An−Npyrrolide bond distance is in all cases shorter, compared to the An−Nimine bond. Quantum chemical calculations, including Pa(IV) prove not only the bond shortening, but also an increased bond strength for An−Npyrrolide over An−Nimine. Comparison to the salen system shows preference of the mixed N,O donor ligand over its pure N,N donor relative for Th as well as U-Pu. For Pa, however, the pyren ligand is preferred over salen, pointing to a special role of the f 1 electron configuration in actinide(IV) coordination chemistry. Synthesis of a mixed pyren salen complex shows a significant expansion of the 1H NMR shift range and altered signal position compared to the bis complexes. This indicates a possible reorientation of the easy axis of magnetization upon ligand exchange. Further investigations on the influence of ligand substitution is achived by synthesis of the mono pyren complex [UCl2(py)(pyren)] and comparison to the analogous salen complex.

Keywords: N-Donor Ligands; actinides; coordination chemistry

  • Invited lecture (Conferences) (Online presentation)
    Angular Momentum - Symposium on f-Element Chemistry, 29.03.2022, Dresden, Deutschland

Publ.-Id: 34454

Software publication: Modeling COVID-19 optimal testing strategies in long-term care facilities: An optimization-based approach

Davoodi Monfared, M.; Batista German, A. C.; Senapati, A.; Schlechte-Welnicz, W.; Wagner, B.; Calabrese, J.

Algorithm for computing the optimal testing strategy and reproducing the figures.

Keywords: Testing strategy; Retirement home; COVID-19; Long-term care; Nursing home; Symmetry proper; Pandemic

Related publications


Publ.-Id: 34453

Efficient DNA Repair Mitigates Replication Stress Resulting in Less Immunogenic Cytosolic DNA in Radioresistant Breast Cancer Stem Cells

Meyer, F.; M. Engel, A.; K. Krause, A.; Wagner, T.; Poole, L.; Dubrovska, A.; Peitzsch, C.; Rothkamm, K.; Petersen, C.; Borgmann, K.

Cancer stem cells (CSCs) are a major cause of tumor therapy failure. This is mainly attributed to increased DNA repair capacity and immune escape. Recent studies have shown that functional DNA repair via homologous recombination (HR) prevents radiation-induced accumulation of DNA in the cytoplasm, thereby inhibiting the intracellular immune response. However, it is unclear whether CSCs can suppress radiation-induced cytoplasmic dsDNA formation. Here, we show that the increased radioresistance of ALDH1-positive breast cancer stem cells (BCSCs) in S phase is mediated by both enhanced DNA double-strand break repair and improved replication fork protection due to HR. Both HR-mediated processes lead to suppression of radiation-induced replication stress and consequently reduction of cytoplasmic dsDNA. The amount of cytoplasmic dsDNA correlated significantly with BCSC content (p=0.0002). This clearly indicates that HR-dependent avoidance of radiation-induced replication stress mediates radioresistance and contributes to its immune evasion. Consistent with this, enhancement of replication stress by inhibition of ataxia telangiectasia and RAD3 related (ATR) resulted in significant radiosensitization (SER37 increase 1.7-2.8 Gy, p<0.0001). Therefore, disruption of HR-mediated processes, particularly in replication, opens a CSC-specific radiosensitization option by enhancing their intracellular immune response.

Keywords: ATR inhibition; DNA repair; breast cancer stem cells (BCSCs); cellular immuneresponse; homologous recombination; immunogenic cytosolic dsDNA; radioresistance; replication stress

Publ.-Id: 34452

Accurate and efficient calculations of mean ionization states with an average-atom model

Callow, T. J.; Kraisler, E.; Cangi, A.

The mean ionization state (MIS) is a critical property in dense plasma and warm dense matter research. It is used (for example) as an input parameter in various models, including for example the calculation of adiabats in inertial confinement fusion; it is also used to help interpret and fit experimental results. Unfortunately however, theoretical predictions of the MIS are often inconsistent with each other and experimental data. In this presentation, I will compute the MIS using a variety of approaches in an average-atom model and compare results with higher-fidelity simulations and experimental benchmarks [1]. I will show that the canonical approach for computing the MIS is usually insufficient; I will also discuss a novel approach based on the electron localization function, which yields improved results but tends to systematically under-estimate the MIS. Finally, I will adapt a recently-proposed Kubo–Greenwood method [2] to our computationally efficient average-atom model, which shows very promising agreement with all the benchmarks considered, with one example shown in Fig. 1 below.

[1] Callow, Kraisler and Cangi, arXiv:2203.05863 (2022)
[2] Bethkenhagen et al., Phys. Rev. Research 2, 023260 (2020)

  • Lecture (Conference)
    Strongly Coupled Coulomb Systems 2022, 24.-29.07.2022, Görlitz, Deutschland

Publ.-Id: 34451

Optimal workplace occupancy strategies during the COVID-19 pandemic

Davoodi Monfared, M.; Senapati, A.; Mertel, A.; Schlechte-Welnicz, W.; Calabrese, J.

During the COVID-19 pandemic, many organizations (e.g. businesses, companies, government facilities, etc.) have attempted to reduce infection risk by employing partial home office strategies. However, working from home can also reduce productivity for certain types of work and particular employees. Over the long term, many organizations therefore face a need to balance infection risk against productivity. Motivated by this trade-off, we model this situation as a bi-objective optimization problem and propose a practical approach to find trade-off (Pareto optimal) solutions. We present a new probabilistic framework to compute the expected number of infected employees as a function of key parameters including: the incidence level in the neighborhood of the organization, the COVID-19 transmission rate, the number of employees, the percentage of vaccinated employees, the testing frequency, and the contact rate among employees.We implement the model and the optimization algorithm and perform several numerical experiments with different parameter settings. Furthermore, we provide an online application based on the models and algorithms developed in this paper, which can be used to identify the optimal workplace occupancy rate for real-world organizations.

Keywords: COVID-19; Pandemic; Optimal Presence Strategy; Productivity\sep Infection


Publ.-Id: 34450

Magnetic Configuration Driven Femtosecond Spin Dynamics in Synthetic Antiferromagnets

de Anulekha, S. S. P. K. A.; Koch, L.; Samad, F.; Surya, N. P.; Benny, B.; Hellwig, O.; Anjan, B.

Ultrafast demagnetization in diverse materials has sparked
immense research activities due to its captivating richness and contested
underlying mechanisms. Among these, the two most celebrated mechanisms
have been the spin-flip scattering (SFS) and spin transport (ST) of optically
excited carriers. In this work, we have investigated femtosecond laser-induced
ultrafast demagnetization in perpendicular magnetic anisotropy-based synthetic
antiferromagnets (p-SAFs) where [Co/Pt]n−1/Co multilayer blocks are separated
by Ru or Ir spacers. Our investigation conclusively shows that the ST of optically
excited carriers can have a significant contribution to the ultrafast demagnetization
in addition to SFS processes. Moreover, we have also achieved an active control
over the individual mechanisms by specially designing the SAF samples and
altering the external magnetic field and excitation fluence. Our study provides a
vital understanding of the underlying mechanism of ultrafast demagnetization in
synthetic antiferromagnets, which will be crucial in future research and
applications of antiferromagnetic spintronics.

Keywords: synthetic antiferromagnets; magnetic multilayers; ultrafast demagnetization; spin transport

Publ.-Id: 34449

Mechanism of femtosecond laser induced ultrafast demagnetization in ultrathin film magnetic multilayers

Pan, S.; Ganss, F.; Panda, S.; Sellge, G.; Banerjee, C.; Sinha, J.; Hellwig, O.; Barman, A.

Ever since its discovery ultrafast demagnetization has remained one of the most
intriguing research areas in magnetism. Here, we demonstrate that in [Co (tCo )/
Pd (0.9 nm)] 8 multilayers, the characteristic decay time in femtosecond time-
scale varies non-monotonically with tCo in the range 0.07 nm B tCo B 0.75 nm.
Further investigation reveals higher spin fluctuation at higher ratio of electron to
Curie temperature to be responsible for this. Microscopic three-temperature
modelling unravels a similar trend in the spin–lattice interaction strength, which
strongly supports our experimental observation. The knowledge of the fem-
tosecond magnetization decay mechanism in ultrathin ferromagnetic films is
unique and important for the advancement of fundamental magnetism besides
their potential applications in ultrahigh speed spintronic devices.

Publ.-Id: 34448

High-energy resolution X-ray spectroscopy at actinide M4,5 edges: what we know, what we want to know, what we can know

Kvashnina, K. O.

In recent years, scientists have progressively recognized the role of electronic structure in the characterization of chemical and physical properties for actinide containing materials. High-energy resolution X-ray spectroscopy at the actinide M4,5 edges emerged as a promising direction because this method can probe actinide properties at the atomic level through the possibility of reducing the experimental spectral width below the natural core-hole life time broadening [1].

In this lecture, I will describe the latest progress in the field of high-energy resolution X-ray spectroscopy at the actinide M4,5 edges [2]. More than 10 years passed after the first X-ray spectroscopy experiment in the high-energy resolution mode on uranium systems at the U M4 edge (~3728 eV) [1] at ESRF in 2009 [3,4]. Quite a bit is known for the moment and X-ray absorption spectroscopy (XAS) or X-ray absorption near edge structure (XANES) in the high-energy resolution fluorescence detection (HERFD) mode (also known as HR-XANES) together with resonant inelastic X-ray scattering (RIXS) or resonant X-ray emission spectroscopy (RXES) are now common techniques for studying the physics and chemistry of the f-block elements [5]. I will show that the methods are able to a) provide fingerprint information on the actinide oxidation state and ground state character b) probe 5f occupancy, non-stoichiometry, defects c) investigate the local symmetry and effects of the crystal field [6–14].

Related publications

  • Open Access Logo Lecture (Conference)
    JdA 51 - Journées des Actinides, 10.-14.04.2022, Santa Margherita Ligure (Genova), Italy

Publ.-Id: 34447

Plutonium Chemistry by Innovative Synchrotron Methods

Kvashnina, K. O.

Over the past several years, our understanding of plutonium chemistry at the atomic level was greatly improved. This is partly due to the expansion of advanced analytical techniques, developed at the large-scale synchrotron facilities, which recently become available for the investigation of radioactive materials. This contribution will give an overview of those experimental methods available at various synchrotrons and applicable to studying physico-chemical processes of radionuclides behaviour in the environment.

I will mainly focus on high energy resolution fluorescence detected (HERFD) X-ray absorption spectroscopy and Resonant Inelastic X-ray Scattering (RIXS) methods1, which probe the local and electronic structure of actinide materials at the L3 and M4 actinide absorption edges. HERFD and RIXS techniques have high sensitivity towards oxidation state detection and can provide unprecedented information on the ground state configuration, electron-electron interactions, and hybridization between molecular orbitals. I will show the results of recently performed studies on plutonium oxide nanoparticles2–5, which were achieved by the combination of HERFD, RIXS, EXAFS, XRD, HEXS (PDF) synchrotron methods together with results on thorium6,7 and uranium8 oxide nanoparticles. The experimental results were analyzed using electronic structure calculations 9,10. It might be of interest for fundamental research in chemistry and physics of actinides as well as for applied science.

Related publications

  • Invited lecture (Conferences)
    Plutonium Futures -The Science 2022, 26.-29.09.2022, Avignon, France

Publ.-Id: 34446

High Energy Resolution X-ray Spectroscopy for Actinide Science

Kvashnina, K. O.

In recent years, scientists have progressively recognized the role of electronic structure in the characterization of chemical and physical properties for actinide containing materials. High-energy resolution X-ray spectroscopy at the actinide M4,5 edges emerged as a promising direction because this method can probe actinide properties at the atomic level through the possibility of reducing the experimental spectral width below the natural core-hole life time broadening.

In this lecture, I will describe the latest progress in the field of high-energy resolution X-ray spectroscopy at the actinide M4,5 edges1. More than 10 years passed after the first X-ray spectroscopy experiment in the high-energy resolution mode on uranium systems at the U M4 edge (~3728 eV) in 20092–4. Quite a bit is known for the moment and X-ray absorption spectroscopy (XAS) or X-ray absorption near edge structure (XANES) in the high-energy resolution fluorescence detection (HERFD) mode together with resonant inelastic X-ray scattering (RIXS) or resonant X-ray emission spectroscopy (RXES) are now common techniques for studying the physics and chemistry of the f-block elements. I will show that the methods are able to a) provide fingerprint information on the actinide oxidation state and ground state character b) probe 5f occupancy, non-stoichiometry, defects c) investigate the local symmetry and effects of the crystal field5-15.

Related publications

  • Open Access Logo Invited lecture (Conferences)
    18th International Conference on X-Ray Absorption and Fine Structure (XAFS2022), 10.-15.07.2022, Sydney, Australia

Publ.-Id: 34445

Terahertz charge and spin transport in metallic ferromagnets: The role of crystalline and magnetic order

Neeraj, K.; Sharma, A.; Almeida, M.; Matthes, P.; Samad, F.; Salvan, G.; Hellwig, O.; Bonetti, S.

We study the charge and spin dependent scattering in a set of CoFeB thin films whose crystalline order is systematically enhanced and
controlled by annealing at increasingly higher temperatures. Terahertz conductivity measurements reveal that charge transport closely
follows the development of the crystalline phase, with the increasing structural order leading to higher conductivity. The terahertz-induced
ultrafast demagnetization, driven by spin-flip scattering mediated by the spin–orbit interaction, is measurable in the pristine amorphous sam-
ple and much reduced in the sample with the highest crystalline order. Surprisingly, the largest demagnetization is observed at intermediate
annealing temperatures, where the enhancement in spin-flip probability is not associated with an increased charge scattering. We are able to
correlate the demagnetization amplitude with the magnitude of the in-plane magnetic anisotropy, which we characterize independently, sug-
gesting a magnetoresistance-like description of the phenomenon.

Publ.-Id: 34444

Nanoscaled LiMn2O4 for extended cycling stability in the 3 V plateau

Siller, V.; Carlos Gonzalez-Rosillo, J.; Nuñez Eroles, M.; Baiutti, F.; Liedke, M. O.; Butterling, M.; Elsherif, A. G. A.; Hirschmann, E.; Wagner, A.; Morata, A.; Tarancón, A.

Extending the potential window towards the 3V plateau below the typically used range could boost the effective capacity of LiMn2O4 spinel cathodes. . This usually leads to an “overdischarge” of the cathode, which can cause severe material damage due to manganese dissolution into the electrolyte and a critical volume expansion (induced by Jahn-Teller distortions). As those factors determine the stability and cycling lifetime for all-solid-state batteries, the operational window of LiMn2O4 is usually limited to 3.5 – 4.5 V vs. Li/Li+ in common battery cells. However, it has been reported that nano-shaped particles and thin films can potentially mitigate these detrimental effects. We report here that porous LiMn2O4 thin film cathodes with a certain level in off-stoichiometry show improved cycling stability for the extended cycling range of 2.0 – 4.5 V vs. Li/Li+. We argue through operando Spectroscopic Ellipsometry that the origin of this stability lies in the surprisingly small volume change in the layer during lithiation.

Keywords: LMO; battery; Li; solid state; cathode; positron annihilation spectroscopy

Related publications

  • Open Access Logo ACS Applied Materials and Interfaces 14(2022)29, 33438-33446
    Online First (2022) DOI: 10.1021/acsami.2c10798

Publ.-Id: 34443

Fundamental investigations of actinide immobilization by incorporation into solid phases relevant for final disposal

Huittinen, N. M.; Braga Ferreira Dos Santos, L.; Gilson, S.; Hennig, C.; Lender, T.; Marquardt, J.; Murphy, G.; Nießen, J.; Peters, L.; Svitlyk, V.; Tonnesen, T.; Winkler, B.

This contribution provides an overview of a current research network funded by the German Federal Ministry of Education and Research (BMBF), entitled “Fundamental investigations of actinide immobilization by incorporation into solid phases relevant for final disposal” – AcE. The AcE project aims at understanding the incorporation and immobilization of actinides (An) in crystalline, repository-relevant solid phases, such as zirconia (ZrO2) and UO2, but also in zircon (ZrSiO4), pyrochlores (Ln2Zr2O7) and orthophosphates of the monazite type (LnPO4), which may find use as host matrices for the immobilization and safe disposal of high-level waste streams.
The main objectives of the AcE project are (i) the development of synthesis strategies for An(IV)-doped solid phases, (ii) understanding their associated structural and physical properties using combined modelling and experimental approaches and (iii) determining their performance after irradiation with particular regard to an assessment of their long-term stability, dissolution behavior, and suitability for An matrix incorporation.

Recent results obtained for ZrO2, the main corrosion product of the Zircaloy cladding material surrounding nuclear fuel rods, will also be discussed. ZrO2 is monoclinic phase (P2(1)/c) at ambient conditions, and transforms into tetragonal (P4(2)/nmc) and cubic phases (Fm3 ̅m) at high temperatures of around 1200 °C and 2370 °C, respectively. However, particle size effects, the incorporation of foreign ions such as the actinides, as well as high radiation fields are known to also influence the stability fields of the polymorphs. A short overview of experimental studies conducted by the AcE partners, addressing both the ZrO2 bulk structure, irradiation-induced changes, as well as the An environment during and after such structural transformations, will be given.

Related publications

  • Poster
    19th Radiochemical Conference, 15.-20.05.2022, Mariánské Lázně, Czech Republic

Publ.-Id: 34442

ExPaNDS - Data Analysis Services

Konrad, U.; Knodel, O.; Barty, A.; Buteau, A.; Manzi, A.; Millar, P.; Minotti, C.; Moge, E.; Ounsy, M.; Matej, Z.; Pozsa, K.; Reynolds, C.; Schoen, S.; Fuhrmann, P.; Soler, N.; Jover-Manas, G.

We present the deliverables achieved for a summarization of the prototyped remote data analysis services and the derived outcomes that have been realised in the process at each ExPaNDS partner facility to align with the PanOSC project and to proceed towards onboarding services into the EOSC portal. The work represents the achievement of deliverable D4.4 of the Horizon 2020 ExPaNDS project. ExPaNDS is the EU Project: European Open Science Cloud Photon and Neutron Data Services

Keywords: Photon Science; Neutron Science; Data Services; EOSC Portal; Data Analysis; ELBE; Teraherz Spectroscopy

Related publications

Publ.-Id: 34441

Complexation of Cm(III) with aqueous phosphates at elevated temperatures: a luminescence, thermodynamic, and ab initio study

Jordan, N.; Huittinen, N.; Jessat, I.; Réal, F.; Vallet, V.

The incorporation of actinides in lanthanide phosphate matrices crystallizing in the monazite structure has been intensely investigated in the past decades due to the relevance of these monazites as potential ceramic host phases for the immobilization of specific high level radioactive waste (HLW) streams [1-3]. In recent years, understanding the incorporation behaviour of trivalent dopants in the LnPO4•xH2O rhabdophane structure has been given more attention [4,5]. Rhabdophane is the hydrated phosphate precursor in the synthesis of monazites through precipitation routes and a potential secondary mineral controlling actinide solubility in dissolution and re-precipitation reactions of monazite host-phases. Despite the large interest in lanthanide phosphates and the interaction of actinides with these solids, very little data [6-8] is available on the complexation of lanthanides and actinides with aqueous phosphates, even though these complexation reactions precede any aqueous synthesis of monazite ceramics and are expected to occur in natural waters as well as in the proximity of monazite-containing HLW repositories. In many cases, an independent spectroscopic validation of the stoichiometry of the proposed complexes, is also missing. Both from the perspective of aqueous rhabdophane synthesis, which is often carried out at elevated temperatures, and heat-generating HLW immobilization in monazites, the lanthanide and actinide complexation reactions with aqueous phosphates under ambient conditions should be complemented with data obtained at higher temperatures.

In the present work, laser-induced luminescence spectroscopy was used to study the complexation of Cm(III) (1.15×10−8 to 1.15×10−7 M) as a function of total phosphate concentration (0 to 0.08 M) in the temperature regime 25-90 °C, using NaClO4 as a background electrolyte (I = 0.5 to 3.0 M). These studies have been conducted in the acidic pH-range (−log10 [H+] = 1.00, 2.52, 3.44, and 3.65) to avoid precipitation of solid Cm rhabdophane. For the first time, in addition to the presence of CmH2PO42+ already evidenced before [6,7], the formation of Cm(H2PO4)2+ was unambiguously established from the luminescence spectroscopic data collected at the various H+ concentrations previously mentioned [8].
The conditional complexation constants of both aqueous complexes were found to increase upon rising ionic strength and temperature. Extrapolation of the obtained complexation constants to infinite dilution at 25 °C was performed by applying the Specific Ion Interaction Theory (SIT) [9]. The obtained log β° values for CmH2PO42+ and Cm(H2PO4)2+ were 0.45 ± 0.04 and 0.08 ± 0.07 [8], respectively, for reactions 1 and 2 below:

Cm3+ + H3PO4 ⇌ CmH2PO42+ + H+ (1)
Cm3+ + 2 H3PO4 ⇌ Cm(H2PO4)2+ + 2 H+ (2)

The ion interaction coefficients ε(CmH2PO42+;ClO4−) = 0.17 ± 0.04 and ε(Cm(H2PO4)2+;ClO4−) = −0.10 ± 0.06 were derived at 25 °C [8].

Temperature-dependent conditional complexation constants for the identified species were obtained from the recorded luminescence emission spectra. They were subsequently extrapolated to I =0 M, assuming that the ion interaction parameters obtained at 25 °C are not significantly impacted by the temperature increase from 25 °C to 90 °C [6]. Using the integrated van´t Hoff equation, both the molar enthalpy of reaction ΔrHm° and entropy of reaction ΔrSm° values were found to be positive for the two complexes, namely CmH2PO42+ and Cm(H2PO4)2+ [8].

Relativistic quantum chemical investigations revealed a monodentate binding of the H2PO4− ligand to the central Cm3+ ion to be the most stable configuration for both complexes. By combining ab initio calculations with a thorough analysis of the obtained luminescence spectroscopic data, both CmH2PO42+ and Cm(H2PO4)2+ complexes with an overall CN of 9 were shown to be stable in solution at 25 °C. However, a different temperature-dependent evolution of the coordination of the Cm3+ ion to hydration water molecules could be derived from the electronic structure of the Cm(III)-phosphate complexes. More specifically, an overall coordination number of 9 was retained for the CmH2PO42+ complex in the investigated temperature range (25 to 90 °C), while a coordination change from 9 to 8 was established for the Cm(H2PO4)2+ species with increasing temperature [8]. This change of coordination upon increasing temperature, which has not been investigated in detail in the past, might also be relevant in the complexation of other f-elements with inorganic and/or organic ligands and deserves further exploration.

[1] R. C. Ewing, Proc. Natl. Acad. Sci. USA 96, 3432 (1999).
[2] D. Bregiroux et al., J. Nucl. Mater. 366, 52 (2007).
[3] N. Huittinen et al., J. Nucl. Mater. 486, 148 (2017).
[4] E. Du Fou de Kerdaniel, J. Nucl. Mater. 362, 451 (2007).
[5] N. Huittinen et al., Inorg. Chem. 57, 6252−6265 (2018).
[6] H. Moll et al., Radiochim. Acta, 99, 775−782 (2011).
[7] N. Jordan et al., Inorg. Chem. 57, 7015-7024 (2018).
[8] N. Huittinen et al., Inorg. Chem. 60, 10656−10673 (2021).
[9] I. Grenthe et al., Second update on the chemical thermodynamics of uranium, neptunium, plutonium, americium and technetium, OECD Nuclear Energy Agency Data Bank, Eds., OECD Publications, Paris, France, (2020).

  • Contribution to proceedings
    Plutonium Futures – The Science 2022, 26.-29.09.2022, Avignon, France
  • Lecture (Conference)
    Plutonium Futures – The Science 2022, 26.-29.09.2022, Avignon, France

Publ.-Id: 34440

Passive magnetische Abschirmung für 0,22T In-Beam-MR-Bildgebung bei Protonen-Pencil Beam Scanning-Bestrahlung

Semioshkina, E.; Bradley, M. O.; Aswin, L. H.

Zum ersten Mal wurde ein MR-Scanner (0,22 T) mit einer horizontalen Protonen Pencil Beam Scanning (PBS) Strahlführung integriert. Die Herausforderung hierbei ist die elektromagnetische Wechselwirkung zwischen magnetischen Streufeldern, erzeugt von Strahlsteuermagneten (SSM), und dem statischen Magnetfeld (B0) des MR-Scanners. Diese führt zu Geisterbildartefakten in den MR-Bildern, wie in Abbildung 1 gezeigt[1]. Passive magnetische Abschirmung ist eine mögliche Lösung zur Beseitigung dieser Artefakte. In dieser Studie bestimmen wir den magnetischen Abschirmungsfaktor (MAF), der für eine artefaktfreie MR-Bildgebung während der PBS-Bestrahlung erforderlich ist. Außerdem untersuchen wir die Auswirkung von Design-Parametern einer passiven magnetischen Abschirmung, die um die SSMs positioniert ist, auf die Reduzierung der Stärke ihrer Streufelder.
Material & Methoden
Eine Magnetfeldkamera (MFK) wurde im MR-Isozentrum positioniert um Änderungen vom B0-Feld (ΔB0) aufgrund des Streufelds der SSMs zu messen. Variiert wurden dabei sowohl die Strahlfeldgröße als auch der Abstand zwischen MR-Isozentrum und PBS-Isozentrum. Für verschiedene Parameterkombinationen wurden Bilder des ACR Small Phantoms während der Bestrahlung aufgenommen, und die prozentuale Signal Ghosting Ratio (PSGR) berechnet, um den maximalen ΔB0-Wert zu bestimmen, für welchen das ACR-Kriterium von PSGR ≤ 0,025 noch erfüllt wurde[2].
Finite-Elemente-Modell (FEM) Simulationen der PBS-Strahlführung wurden durchgeführt, um die von den SSMs erzeugten magnetischen Streufelder zu berechnen. Für eine magnetische Abschirmung wurden verschiedene Parameter untersucht, wie Geometrie, Materialdicke, Anzahl der Schichten und Größe dazwischenliegenden Luftspalts. Der MAF wurde an der Position des MR-Isozentrums berechnet.
Die MFK-Messungen ergaben, dass der maximale ΔB0-Wert 5,66 μT betrug. Der PSGR-Test wurde nur bei Feldgrößen von 1,2, 4 und 12 cm und bei Abständen von 0,3, 1,3 bzw. 2,3 m zwischen dem PBS- und MR-Isozentrum bestanden. In diesen Fällen betrug der maximale ΔB0-Wert 0,27 μT. Daher ist für eine artefaktfreie MR-Bildgebung während der PBS-Dosisabgabe ein Mindestabschirmungsfaktor von 20,22 erforderlich.
Auf der Grundlage von FEM-Simulationen lässt sich dieser MAF am effektivsten durch eine mehrschichtige zylindrische Abschirmung erreichen. Ein MAF von 21 wurde durch die Verwendung von zwei konzentrischen Schichten mit einer Dicke von jeweils 10 mm und einem Luftspaltabstand von 10 mm erreicht.
Der magnetische Abschirmungsfaktorwurde experimentell für den 0,22-T-In-Beam-MR-Scanner Beamline bestimmt. Computersimulationen zeigten, dass dieser Abschirmungsfaktor mit einer passiven magnetischen Abschirmung erreicht werden kann, wobei eine mehrschichtige konzentrische Geometrie aus Kohlenstoffstahl mit einem Luftspalt zwischen den Schichten verwendet wird.

[1] S. Gantz et al. 2020 Phys. Med. Biol.
[2] Small Phantom Guide, American College of Radiology

  • Contribution to proceedings
    53. Jahrestagung der Deutschen Gesellschaft für Medizinische Physik 24. Jahrestagung der Deutschen Sektion der ISMRM, 21.09.2022, Aachen, Deutschland

Publ.-Id: 34439

First Experiences in Performance Benchmarking with the New SPEChpc 2021 Suites

Brunst, H.; Chandrasekaran, S.; Ciorba, F. M.; Hagerty, N.; Henschel, R.; Juckeland, G.; Li, J.; Vergara, V. G. M.; Wienke, S.; Zavala, M.

Modern High Performance Computing (HPC) systemsare built with innovative system architectures and novelprogramming models to further push the speed limit of computing.The increased complexity poses challenges for performanceportability and performance evaluation. The Standard PerformanceEvaluation Corporation (SPEC) has a long history ofproducing industry-standard benchmarks for modern computersystems. SPEC’s newly released SPEChpc 2021 benchmark suites,developed by the High Performance Group, are a bold attempt toprovide a fair and objective benchmarking tool designed for state-HPC, SPEC, HPG, SPEChpc 2021, benchmarks,performance benchmarking and analysis, heterogeneity, offloading,MPI, MPI+X, OpenMP, OpenACCof-the-art HPC systems. With the support of multiple host andaccelerator programming models, the suites are portable acrossboth homogeneous and heterogeneous architectures. Differentworkloads are developed to fit system sizes ranging from a fewcompute nodes to a few hundred compute nodes. In this work wepresent our first experiences in performance benchmarking thenew SPEChpc2021 suites and evaluate their portability and basicperformance characteristics on various popular and emergingHPC architectures, including x86 CPU, NVIDIA GPU, and AMDGPU. This study provides a first-hand experience of executingthe SPEChpc 2021 suites at scale on production HPC systems,discusses real-world use cases, and serves as an initial guidelinefor using the benchmark suites

Keywords: HPC; SPEC; SPEChpc 2021; Benchmarks

  • Contribution to proceedings
    22nd International Symposium on Cluster, Cloud and Internet Computing (CCGrid), 16.-19.05.2022, Taormina (Messina), Italy: IEEE Press
    DOI: 10.1109/CCGrid54584.2022.00077

Publ.-Id: 34438

Production of Nb-95 at the cyclotron Cyclone 18/9

Franke, K.

Nb-94 is a constituent of the radioactive waste in the dismantling process of nuclear power plants. It has a half-life of 20300 a and has to be considered in the risk assessment [1]. This motivates the need for a suitable Nb-radiotracer, which allows to investigate the interaction of Nb in future waste repositories. Half-life and decay mode suggest the isotope Nb-95 as promising candidate.

  • Contribution to proceedings
    WTTC18 - 18th Workshop on Targetry and Target Chemistry, 21.-26.08.2022, Whistler, Canada

Publ.-Id: 34437

Establishment of experimental possibilities for separation experiments on gaseous H-isotope mixtures

Becker, A.; Lippold, H.; Fischer, C.

Hydrogen isotopes are studied in many research areas to clarify fundamental and applied aspects of their physicochemical behavior. Besides deuterium, the isotope tritium has become the focus of current investigations. One important application is the separation of hydrogen isotopes. Currently available methods have low separation efficiency and high energy consumption. Therefore, approaches to increase efficiency are presently being explored, with a focus on gaseous deuterium.
In our work we will investigate two types of materials, on the one hand membrane materials (graphene and Nafion) and on the other hand nanoporous materials (metal-organic frameworks) with respect to tritium separation. For these studies, we needed to establish an analytical routine for working with gaseous tritium, from access to quantification methods. For this purpose, we employed a tritium manifold that uses heat to release gaseous tritium from a reservoir in a defined manner. The tritium gas under defined pressure and, in the future, mixtures of hydrogen isotopes will be used for separation experiments in flow cells. The gas will eventually be converted to HTO, which will be analyzed by liquid scintillation counting (LSC), where the measured activity directly corresponds to the concentration of tritium in the analyzed sample. To assess the quality of the proposed analytical method, the data obtained from the LSC measurements were compared with the calculated values and with the pressures applied during tritium dosing from the manifold. The measured values correspond directly to the applied pressures and agree well with the calculated data. These results indicate the proficiency of the established analytical approach, which allows to explore the proposed separation methods with high precision.

Keywords: tritium; isotope separation; hydrogen isotopes

  • Open Access Logo Lecture (Conference)
    RadChem 2022, 15.-20.05.2022, Mariánské Lázně, Tschechische Republik


Publ.-Id: 34436

Environmental drivers of body size in North American bats

Alston, J.

Bergmann’s Rule—which posits that larger animals live in colder areas—is thought to influence variation in body size within species across space and time, but evidence for this claim is mixed. We tested four competing hypotheses for spatio-temporal variation in body size within bat species during the past two decades across North America: (1) the heat conservation hypothesis, which posits that increased body size facilitates body heat conservation (and which is the traditional explanation for the mechanism underlying Bergmann’s Rule); (2) the heat mortality hypothesis, which posits that increased body size increases susceptibility to acute heat stress; (3) the resource availability hypothesis, which posits that increased body size is enabled in areas with more abundant food; and (4) the starvation resistance hypothesis, which posits that increased body size reduces susceptibility to starvation during acute food shortages. Bayesian hierarchical models revealed that spatial variation in body mass was most consistently (and negatively) correlated with mean annual temperature, supporting the heat conservation hypothesis. Across time, variation in body mass was most consistently (and positively) correlated with net primary productivity, supporting the resource availability hypothesis. Climate change could influence body size in animals through both changes in mean annual temperature and in resource availability. Rapid reductions in body size associated with increasing temperatures have occurred in short-lived, fecund species, but such reductions likely transpire more slowly in longer-lived species.

Keywords: bats

  • Open Access Logo Invited lecture (Conferences) (Online presentation)
    Mississippi Bat Working Group Annual Meeting, 24.03.2022, Jackson, MS, USA

Publ.-Id: 34435

Constraints on the dipole photon strength for the odd uranium isotopes

Moreno-Soto, J.; Valenta, S.; Berthoumieux, E.; Chebboubi, A.; Diakaki, M.; Dridi, W.; Dupont, E.; Gunsing, F.; Krticka, M.; Litaize, O.; Serot, O.; Aberle, O.; Alcayne, V.; Amaducci, S.; Andrzejewski, J.; Audouin, L.; Bécares, V.; Babiano-Suarez, V.; Bacak, M.; Barbagallo, M.; Benedikt, T.; Bennett, S.; Billowes, J.; Bosnar, D.; Brown, A.; Busso, M.; Caamaño, M.; Caballero-Ontanaya, L.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Casanovas, A.; Cerutti, F.; Chiaveri, E.; Colonna, N.; Cortés, G.; Cortés-Giraldo, M. A.; Cosentino, L.; Cristallo, S.; Damone, L. A.; Davies, P. J.; Dietz, M.; Domingo-Pardo, C.; Dressler, R.; Ducasse, Q.; Durán, I.; Eleme, Z.; Fernández-Domínguez, B.; Ferrari, A.; Finocchiaro, P.; Furman, V.; Göbel, K.; Gawlik-Ramiga, A.; Gilardoni, S.; Gonçalves, I. F.; González-Romero, E.; Guerrero, C.; Heinitz, S.; Heyse, J.; Jenkins, D. G.; Junghans, A.; Käppeler, F.; Kadi, Y.; Kimura, A.; Knapová, I.; Kokkoris, M.; Kopatch, Y.; Kurtulgil, D.; Ladarescu, I.; Lampoudis, C.; Lederer-Woods, C.; Lonsdale, S. J.; Macina, D.; Manna, A.; Martínez, T.; Masi, A.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Michalopoulou, V.; Milazzo, P. M.; Mingrone, F.; Musumarra, A.; Negret, A.; Nolte, R.; Ogállar, F.; Oprea, A.; Patronis, N.; Pavlik, A.; Perkowski, J.; Piersanti, L.; Petrone, C.; Pirovano, E.; Porras, I.; Praena, J.; Quesada, J. M.; Ramos-Doval, D.; Rauscher, T.; Reifarth, R.; Rochman, D.; Sabaté-Gilarte, M.; Saxena, A.; Schillebeeckx, P.; Schumann, D.; Sekhar, A.; Smith, A. G.; Sosnin, N. V.; Sprung, P.; Stamatopoulos, A.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tassan-Got, L.; Torres-Sánchez, P.; Tsinganis, A.; Ulrich, J.; Urlass, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vescovi, D.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Woods, P. J.; Wright, T.; Žugec, P.

Background: The photon strength functions (PSFs) and nuclear level density (NLD) are key ingredients for
calculation of the photon interaction with nuclei, in particular the reaction cross sections. These cross sections are
important especially in nuclear astrophysics and in the development of advanced nuclear technologies.
Purpose: The role of the scissors mode in the M1 PSF of (well-deformed) actinides was investigated by several
experimental techniques. The analyses of different experiments result in significant differences, especially on the
strength of the mode. The shape of the low-energy tail of the giant electric dipole resonance is uncertain as well.
In particular, some works proposed a presence of the E1 pygmy resonance just above 7 MeV. Because of these
inconsistencies additional information on PSFs in this region is of great interest.
Methods: The γ -ray spectra from neutron-capture reactions on the 234U, 236U, and 238U nuclei have been
measured with the total absorption calorimeter of the n_TOF facility at CERN. The background-corrected
sum-energy and multi-step-cascade spectra were extracted for several isolated s-wave resonances up to about
140 eV.
Results: The experimental spectra were compared to statistical model predictions coming from a large selection
of models of photon strength functions and nuclear level density. No combination of PSF and NLD models from
literature is able to globally describe our spectra. After extensive search we were able to find model combinations
with modified generalized Lorentzian (MGLO) E1 PSF, which match the experimental spectra as well as the total
radiative widths.
Conclusions: The constant temperature energy dependence is favored for a NLD. The tail of giant electric dipole
resonance is well described by the MGLO model of the E1 PSF with no hint of pygmy resonance. The M1 PSF
must contain a very strong, relatively wide, and likely double-resonance scissors mode. The mode is responsible
for about a half of the total radiative width of neutron resonances and significantly affects the radiative cross

Publ.-Id: 34434

Nuclear astrophysics with accelerator mass spectrometry

Rugel, G.

Nuclear astrophysics with accelerator mass spectrometry

Related publications

  • Invited lecture (Conferences)
    17th Rußbach School on Nuclear Astrophysics, 13.-19.03.2022, Rußbach, Österreich

Publ.-Id: 34433

Validation of CD98hc as a therapeutic target for a combination of radiation and immunotherapies in head and neck squamous cell carcinoma

Köseer, A. S.; Rodrigues Loureiro, L. R.; Jureczek, J.; Mitwasi, N.; González Soto, K. E.; Aepler, J.; Bartsch, T.; Feldmann, A.; Kunz-Schughart, L. A.; Linge, A.; Krause, M.; Bachmann, M.; Arndt, C.; Dubrovska, A.

Most patients with head and neck squamous cell carcinomas (HNSCC) are diagnosed at a locally advanced stage and show heterogeneous treatment responses. Low SLC3A2 (solute carrier family 3 member 2) mRNA and protein (CD98hc) expression levels are associated with higher locoregional control in HNSCC patients treated with primary radiochemotherapy or postoperative radiochemotherapy, suggesting that CD98hc could be a target for HNSCC radiosensitization. One of the targeted strategies for tumor radiosensitization is precision immunotherapy, e.g., the use of chimeric antigen receptor (CAR) T cells. This study aimed to define the potential clinical value of new treatment approaches combining conventional radiotherapy with CD98hc-targeted immunotherapy. To address this question, we analyzed the antitumor activity of the combination of fractionated irradiation and switchable universal CAR (UniCAR) system against radioresistant HNSCC cells in 3D culture. CD98hc-redirected UniCAR T cells showed the ability to destroy radioresistant HNSCC spheroids. Also, the infiltration rate of the UniCAR T cells was enhanced in the presence of the CD98hc target module. Furthermore, sequential treatment with fractionated irradiation followed by CD98hc-redirected UniCAR T treatment showed a synergistic effect. Taken together, our obtained data underline the improved antitumor effect of the combination of radiotherapy with CD98hc-targeted immunotherapy. Such a combination presents an attractive approach for the treatment of high-risk HNSCC patients.

Keywords: HNSCC; radiotherapy; immunotherapy; CD98hc; SLC3A2; chimeric antigen receptor; radioimmunotherapy; combination therapy; biomarker

Publ.-Id: 34432

Tunable metal hydroxide–organic frameworks for catalysing oxygen evolution

Yuan, S.; Peng, J.; Cai, B.; Huang, Z.; Garcia-Esparza, A. T.; Sokaras, D.; Zhang, Y.; Giordano, L.; Akkiraju, K.; Guang Zhu, Y.; Hübner, R.; Zou, X.; Román-Leshkov, Y.; Shao-Horn, Y.

The oxygen evolution reaction is central to making chemicals and energy carriers using electrons. Combining the great tunability of enzymatic systems with known oxide-based catalysts can create breakthrough opportunities to achieve both high activity and stability. Here we report a series of metal hydroxide–organic frameworks (MHOFs) synthesized by transforming layered hydroxides into two-dimensional sheets crosslinked using aromatic carboxylate linkers. MHOFs act as a tunable catalytic platform for the oxygen evolution reaction, where the π–π interactions between adjacent stacked linkers dictate stability, while the nature of transition metals in the hydroxides modulates catalytic activity. Substituting Ni-based MHOFs with acidic cations or electron-withdrawing linkers enhances oxygen evolution reaction activity by over three orders of magnitude per metal site, with Fe substitution achieving a mass activity of 80 A gcatalyst -1 at 0.3 V overpotential for 20 h. Density functional theory calculationscorrelate the enhanced oxygen evolution reaction activity with the MHOF-based modulation of Ni redox and the optimized binding of oxygenated intermediates.

Related publications

Publ.-Id: 34431

Data synchronizator of Where2test pipeline

Abdussalam, W.

Software to synchonise the data between various data sources and casus database server. For Unix users please use and for WIndows users please use In order to use the scripts, please use the following instructions:


1. Create the postgreq sql database and set the port 5432 

2. Create folder C:\Workspaces and unzip the unix file. 

3. Create folder in workspaces,\COM_CASUS_WHERE2TEST_MIGRATION and then unzip the source file inside COM_CASUS_WHERE2TEST_MIGRATION. 

4. Set run Develop and run the .bat file on the folder MigrateWhere2test_0.7Unix to run in localhost.


1. Create PostgreSQL with port 32771.
2. Create folder /home/wildan/Workspaces and unzip the unix file. 

3. Create folder in workspaces, and then unzip the source file inside COM_CASUS_WHERE2TEST_MIGRATION. 

4. Set run Develop and run the .sh file on the folder MigrateWhere2test_0.7Unix to run in localhost.

Keywords: data pipeline


Publ.-Id: 34430

Size transferability of machine-learning based density functional theory surrogates

Fiedler, L.; Popoola, G. A.; Modine, N. A.; Thompson, A. P.; Cangi, A.; Rajamanickam, S.

Density Functional Theory (DFT) is the most common tool for investigating materials under extreme conditions, yet its scaling behavior with respect to both system size and temperature prohibits large scale simulations in such regimes. Progress in this regard would enable accurate modeling of planetary interiors or radiation damage in fusion reactor walls.
One possible route to alleviate these scaling problems is through the use of surrogate models, i.e., machine-learning models. These are trained on DFT data and are able to reproduce DFT predictions of energies and forces at comparable accuracy, but negligible computational cost.
Yet, in order to avoid repeated costly training data generation, models need to be able to transfer across length scales. Here, we present such transferability results. They show how learning local information can allow models to extrapolate to length scales that are not attainable with standard DFT methods. The models are based upon the Materials Learning Algorithms (MALA) package [1] and the therein implemented LDOS based machine learning workflow [2].

[2]: J. A. Ellis et al., Phys. Rev. B 104, 035120, 2021

Keywords: Density Functional Theory; Machine Learning

  • Lecture (Conference)
    APS March Meeting, 14.-18.03.2022, Chicago, United States of America

Publ.-Id: 34429

Hyperparameter optimization for automated DFT surrogate model creation

Fiedler, L.; Cangi, A.

While the high efficiency of Density Functional Theory (DFT) calculations have enabled many important materials science application over the past decades, modern scientific problems require accurate electronic structure data beyond the scales attainable with DFT. For instance, the modeling of materials at extreme conditions across multiple length and time scales, which is important for the understanding for physical phenomena such as radiation damages in fusion reactor walls, evades ab-initio treatment.
One possible method to obtain such models at near ab-initio accuracy are DFT surrogate models, that, based on machine learning (ML) algorithms, reproduce DFT results at a fraction of the cost. One drawback of the ML workflow is the need for hyperparameter optimization, i.e., the need to tune the employed ML algorithm in order to best perform on the given dataset. Manually performing this optimization becomes prohibitive if a wide range of materials and conditions is eventually to be treated. Here, we present results of an hyperparameter study in an effort to find optimal surrogate models for aluminium at ambient conditions [1], that investigates how modern hyperparameter optimization techniques can be used to automate large parts of the model selection process and eventually move towards automated surrogate model creation. The models are based upon the Materials Learning Algorithms (MALA) package [2] and the therein implemented LDOS based machine learning workflow [3].

Keywords: Density Functional Theory; Machine Learning

  • Lecture (Conference)
    DFT Methods for Matter under Extreme Conditions, 21.-22.02.2022, Görlitz, Deutschland
  • Lecture (Conference)
    Helmholtz AI 2022, 02.-03.06.2022, Dresden, Deutschland

Publ.-Id: 34428

Laser-induced ionization with liquid metal ion sources and two-color sculpted laser fields

Machalett, F.; Ying, B.; Wustelt, P.; Bischoff, L.; Klingner, N.; Pilz, W.; Kübel, M.; Sayler, A. M.; Stöhlker, T.; Paulus, G. G.

We have successfully employed high-brightness liquid metal ion sources (LMIS) for the investigation of the
interaction of metal and metalloid ions with strong field laser beams. The gold and silicon ions, generated in the
LMIS by electrostatic field ionization, can be further ionized up to Au11+ and Si4+ with Thales laser (1 kHz)
at intensities of up to 4e16 W/cm2. Furthermore, we employed the fiber laser with 100 kHz to manipulate
the recoil momenta with subcycle resolution.

Keywords: Liquid Metal Alloy Ion Sources; Laser-induced ionization; Au11+ and Si4+ ions

Related publications

  • Contribution to external collection
    in: Jahresbericht Helmholtz-Institut Jena 2021, Jena: Helmholtz-Institut Jena, Fröbelstieg, 2022, 60-60

Publ.-Id: 34427

Sustainable development of case setups in OpenFOAM_RCS

Lehnigk, R.; Bruschewski, M.; Lucas, D.; Rehm, M.; Schlegel, F.

Due to the growing importance of Computational Fluid Dynamics (CFD) for reactor safety research, there have been activities aimed at qualifying the associated methods for many years. This entails the development and validation of models on the basis of detailed experimental data, generated in comprehensive projects. There was and is a need for development, among other things, for multiphase flows, in particular for accident scenarios in the reactor coolant system (RCS). In order to be able to use the model developments and validation data generated throughout the various projects funded by the German Federal Ministry for Economic Affairs and Energy in the long term, these are carried out using the reference code OpenFOAM, which is thereby qualified for application. The OpenFOAM_RCS project includes the OpenFOAM_RCS Addon for the C++ library OpenFOAM from the OpenFOAM Foundation, which gathers additional software that is relevant for the simulation of the reactor cooling system. This entails solvers, physical models, functionObjects, boundary conditions as well as pre- and post-processing utilities. The associated simulation setups are maintained along with the code.

Keywords: OpenFOAM; CFD; Multiphase flows; Nuclear reactor safety

  • Lecture (Conference) (Online presentation)
    33rd German CFD Network Meeting, 22.-23.03.2022, Online, Online

Publ.-Id: 34426

Personalized drug testing in human pheochromocytoma/paraganglioma primary cultures

Wang, K.; Schütze, I.; Gulde, S.; Bechmann, N.; Richter, S.; Helm, J.; Lauseker, M.; Maurer, J.; Reul, A.; Spöttl, G.; Klink, B.; William, D.; Knösel, T.; Friemel, J.; Bihl, M.; Weber, A.; Fankhauser, M.; Schober, L.; Vetter, D.; Broglie Däppen, M.; Ziegler, C. G.; Ullrich, M.; Pietzsch, J.; Bornstein, S. R.; Lottspeich, C.; Kroiß, M.; Fassnacht, M.; Wenter, V.; Ladurner, R.; Hantel, C.; Reincke, M.; Eisenhofer, G.; Grossman, A. B.; Pacak, K.; Beuschlein, F.; Auernhammer, C. J.; Pellegata, N.; Nölting, S.

Aggressive pheochromocytomas and paragangliomas (PPGLs) are difficult to treat, and molecular targeting is being increasingly considered, but with variable results. This study investigates established and novel molecular-targeted drugs and chemotherapeutic agents for the treatment of PPGLs in human primary cultures and murine cell line spheroids. In PPGLs from 33 patients, including 7 metastatic PPGLs, we identified germline or somatic driver-mutations in 82% of cases, allowing us to assess potential differences in drug responsivity between pseudohypoxia-associated cluster 1- (n=11) and kinase signaling-associated cluster 2-related (n=14) PPGL primary cultures. Single anti-cancer drugs were either more effective in cluster 1 (cabozantinib, selpercatinib, 5-FU) or similarly effective in both clusters (everolimus, sunitinib, alpelisib, trametinib, niraparib, gemcitabine, AR-A014418, high-dose zoledronic acid). Estrogen and low-dose zoledronic acid were the only single substances more effective in cluster 2. Neither cluster 1- nor cluster 2-related patient primary cultures responded to HIF-2α inhibitors, temozolomide, dabrafenib, or octreotide. We showed particular efficacy of targeted combination treatments (cabozantinib/everolimus, alpelisib/everolimus, alpelisib/trametinib) in both clusters, with higher efficacy in cluster 2 and overall synergistic effects (cabozantinib/everolimus, lpelisib/trametinib) or synergistic effects in cluster 2 (alpelisib/everolimus). Cabozantinib/everolimus combination therapy, gemcitabine, and high-dose zoledronic acid appear to be the very promising treatment options with particularly high efficacy in SDHB-mutant and metastatic tumors. In conclusion, only minor differences regarding drug responsivity were found between cluster 1 and cluster 2: Some single anti-cancer drugs were more effective in cluster 1 and targeted combination treatments were more effective in cluster 2.

Keywords: Personalized drug testing; pheochromocytoma/paraganglioma; human primary cultures; 3D spheroid models; somatic mutations

Publ.-Id: 34425

Redox-Active Metaphosphate-Like Terminals Enable High-Capacity MXene Anodes for Ultrafast Na-Ion Storage

Sun, B.; Lu, Q.; Chen, K.; Zheng, W.; Liao, Z.; Lopatik, N.; Li, D.; Hantusch, M.; Zhou, S.; Wang, H. I.; Sofer, Z.; Brunner, E.; Zschech, E.; Bonn, M.; Dronskowski, R.; Mikhailova, D.; Liu, Q.; Zhang, D.; Yu, M.; Feng, X.

2D transition metal carbides and/or nitrides, so-called MXenes, are noted as ideal fast-charging cation-intercalation electrode materials, which nev-ertheless suffer from limited specific capacities. Herein, it is reported that constructing redox-active phosphorus−oxygen terminals can be an attractive strategy for Nb4C3 MXenes to remarkably boost their specific capacities for ultrafast Na+ storage. As revealed, redox-active terminals with a stoichio-metric formula of PO2- display a metaphosphate-like configuration with each P atom sustaining three PO bonds and one PO dangling bond. Compared with conventional O-terminals, metaphosphate-like terminals empower Nb4C3 (denoted PO2-Nb4C3) with considerably enriched carrier density (four-fold), improved conductivity (12.3-fold at 300 K), additional redox-active sites, boosted Nb redox depth, nondeclined Na+-diffusion capability, and buffered internal stress during Na+ intercalation/de-intercalation. Consequently, com-pared with O-terminated Nb4C3, PO2-Nb4C3 exhibits a doubled Na+-storage capacity (221.0 mAh g-1), well-retained fast-charging capability (4.9 min at 80% capacity retention), significantly promoted cycle life (nondegraded capacity over 2000 cycles), and justified feasibility for assembling energy−power-balanced Na-ion capacitors. This study unveils that the molecular-level design of MXene terminals provides opportunities for developing simulta-neously high-capacity and fast-charging electrodes, alleviating the energy−power tradeoff typical for energy-storage devices.

Publ.-Id: 34424

Electronic pair alignment and roton feature in the warm dense electron gas

Dornheim, T.; Moldabekov, Z.; Vorberger, J.; Kählert, H.; Bonitz, M.

The study of matter under extreme densities and temperatures as they occur e.g. in astrophysical
objects and nuclear fusion applications has emerged as one of the most active frontiers in physics,
material science, and related disciplines. In this context, a key quantity is given by the dynamic
structure factor S(q, ω), which is probed in scattering experiments—the most widely used method
of diagnostics at these extreme conditions. In addition to its crucial importance for the study of
warm dense matter, the modelling of such dynamic properties of correlated quantum many-body
systems constitutes one of the most fundamental theoretical challenges of our time. Here we report
a hitherto unexplained roton feature in S(q, ω) of the warm dense electron gas, and introduce a
microscopic explanation in terms of a new electronic pair alignment model. This new paradigm
will be highly important for the understanding of warm dense matter, and has a direct impact on
the interpretation of scattering experiments. Moreover, we expect our results to give unprecedented
insights into the dynamics of a number of correlated quantum many-body systems such as ultracold
helium, dipolar supersolids, and bilayer heterostructures.

Publ.-Id: 34423

Band transport by large Fröhlich polarons in MXenes

Zheng, W.; Sun, B.; Li, D.; Gali, S. M.; Zhang, H.; Fu, S.; Di Virgilio, L.; Li, Z.; Yang, S.; Zhou, S.; Beljonne, D.; Yu, M.; Feng, X.; Wang, H. I.; Bonn, M.

MXenes are emerging layered materials that are promising for electrochemical energy storage and (opto-)electronic applications. A fundamental understanding of charge transport in MXenes is essential for such applications, but has remained under debate. While theoretical studies pointed to efficient band transport, device measurements have revealed thermally activated, hopping-type transport. Here we present a unifying picture of charge transport in two model MXenes by combining ultrafast terahertz and static electrical transport measurements to distinguish the short- and long-range transport characteristics. We find that band-like transport dominates short-range, intra-flake charge conduction in MXenes, whereas long-range, inter-flake transport occurs through thermally activated hopping, and limits charge percolation across the MXene flakes. Our analysis of the intra-flake charge carrier scattering rate shows that it is dominated by scattering from longitudinal optical phonons with a small coupling constant (α ≈ 1), for both semiconducting and metallic MXenes. This indicates the formation of large polarons in MXenes. Our work therefore provides insight into the polaronic nature of free charges in MXenes, and unveils intra- and inter-flake transport mechanisms in the MXene materials, which are relevant for both fundamental studies and applications.

Publ.-Id: 34422

Abnormal quantum moment of inertia and structural properties of electrons in 2D and 3D quantum dots: an ab initio path-integral Monte Carlo study

Dornheim, T.; Yan, Y.

We present extensive new direct path-integral Monte Carlo results for electrons in quantum dots in two and three dimensions. This allows us to investigate the nonclassical rotational inertia (NCRI) of the system, and we find an abnormal negative superfluid fraction [Phys. Rev. Lett. 112, 235301 (2014)] under some conditions. In addition, we study the structural properties by computing a sophisticated center-two particle correlation function. Remarkably, we find no connection between the spatial structure and the NCRI, since the former can be nearly identical for Fermi- and Bose-statistics for parameters where the superfluid fraction is diverging towards negative infinity.

Publ.-Id: 34421

The uniform electron gas at high temperatures: ab initio path integral Monte Carlo simulations and analytical theory

Dornheim, T.; Vorberger, J.; Moldabekov, Z.; Röpke, G.; Kraeft, W.-D.

We present extensive new ab initio path integral Monte Carlo (PIMC)
simulations of the uniform electron gas (UEG) in the high-temperature regime,
8 ≤ θ = kBT /EF ≤ 128. This allows us to study the convergence of different
properties towards the classical limit. In particular, we investigate the classical relation
between the static structure factor S(q) and the static local field correction G(q),
which is only fulfilled at low densities. Moreover, we compare our new results for
the interaction energy to the parametrization of the UEG by Groth et al. [PRL 119,
135001 (2017)], which interpolates between PIMC results for θ ≤ 8 and the Debye-
H ̈uckel limit, and to higher order analytical virial expansions. Finally, we consider the
momentum distribution function n(q) and find an interaction-induced increase in the
occupation of the zero-momentum state even for θ & 32. All PIMC data are freely
available online, and can be used as input for improved parametrizations and as a
rigorous benchmark for approximate methods.


Publ.-Id: 34420

Electronic Density Response of Warm Dense Hydrogen: Ab initio Path Integral Monte Carlo Simulations

Böhme, M.; Moldabekov, Z.; Vorberger, J.; Dornheim, T.

The properties of hydrogen under extreme conditions are important for many applications, including inertial confinement fusion and astrophysical models. A key quantity is given by the electronic density response to an external perturbation, which is probed in X-ray Thomson scattering (XRTS) experiments -- the state of the art diagnostics from which system parameters like the free electron density , the electronic temperature , and the charge state can be inferred. In this work, we present highly accurate path integral Monte Carlo (PIMC) results for the electronic density response of hydrogen. We obtain the exchange-correlation (XC) kernel , which is of central relevance for many applications, such as time-dependent density functional theory (TD-DFT). This gives us a first unbiased look into the electronic density response of hydrogen in the warm-dense matter regime, thereby opening up a gamut of avenues for future research.

Publ.-Id: 34419

Ab initio path integral Monte Carlo simulations of hydrogen snapshots at warm dense matter conditions

Böhme, M.; Moldabekov, Z.; Vorberger, J.; Dornheim, T.

We combine ab initio path integral Monte Carlo (PIMC) simulations with fixed ionic configurations, obtained by DFT-MD simulations, in order to solve the electronic problem for hydrogen under warm dense matter conditions. To solve the divergence problem in the Ewald-sum for attractive potentials we employ the pair-approximation. This approach is compared against the much simpler Kelbg pair-potential. We find very favorable convergence behavior towards the latter. Since PIMC does not require any further assumptions regarding exchange and correlations of the many-body system, we then compare electronic densities obtained from our snapshot PIMC calculations with DFT calculations in the metallic regime. Furthermore, we investigate the manifestation of the resulting fermionic sign problem in our snapshot PIMC simulations. This gives us the unique capability to study the properties of warm dense hydrogen from ab initio simulations without any further assumptions, like the functional form of the exchange-correlation effects or fixed fermionic nodes. Thus, snapshot PIMC enables us to obtain the exact density response of warm dense hydrogen. This is extremely valuable to both experiments, like X-Ray Thomson scattering, as well as the development of new XC-functionals.

Keywords: Warm Dense Matter; Path-Intergral Monte-Carlo; Hydrogen; Electronic structure

  • Open Access Logo Poster
    Matter in Extreme Conditions : from MATerial science to Plasmas for Laboratory Astropohysics (MECMATPLA), 13.-19.03.2022, Montgenèvre, Frankreich
  • Open Access Logo Lecture (Conference)
    13th International Conference on High Energy Density Laboratory Astrophysics, 23.-27.05.2022, Lissabon, Portugal
  • Open Access Logo Physical Review E (2023)
  • Open Access Logo Contribution to WWW
    DOI: 10.48550/arXiv.2207.14716
  • Open Access Logo Poster
    8th annual meeting of the programme "Matter and Technologies", 26.-27.09.2022, Hamburg, Deutschland
  • Open Access Logo Poster
    Big data analytical methods for complex systems, 06.-07.10.2022, Wroclaw, Polen
  • Open Access Logo Poster
    Strongly Coupled Coulomb Systems 2022, 24.-29.07.2022, Görlitz, Deutschland
  • Open Access Logo Lecture (Conference) (Online presentation)
    64th Annual Meeting of the APS Division of Plasma Physics, 17.-21.10.2022, Spokane Washington, USA
  • Open Access Logo Lecture (Conference)
    10th International Symposium "Optics & its applications", 05.-9.12.2022, Cali und Armenia, Kolumbien


Publ.-Id: 34418

Modeling COVID-19 optimal testing strategies in long-term care facilities: An optimization-based approach

Davoodi Monfared, M.; Batista German, A. C.; Senapati, A.; Schlechte-Welnicz, W.; Wagner, B.; Calabrese, J.

Long-term care facilities have been widely affected by the COVID-19 pandemic. Retirement homes are particularly vulnerable due to the higher mortality risk of infected elderly individuals. Once an outbreak is happening, suppressing the spread of the virus in retirement homes is challenging because the residents are in contact with each other and isolation measures cannot be widely enforced. Regular testing strategies, on the other hand, have been shown to effectively prevent outbreaks in retirement homes. However, high frequency testing may consume substantial staff working time, which results a trade-off between the time invested in testing, and the time spent providing essential care to residents.
Thus, developing an optimal testing strategy is crucial to proactively detect infections while guaranteeing efficient use of limited staff time in these facilities.
Although numerous efforts have been made to prevent the virus from spreading in long-term care facilities, this is the first study to develop testing strategies based on formal optimization methods.
This paper proposes two novel optimization models for testing schedules. The models aim to minimize the risk of infection in retirement homes, considering the trade-off between the probability of infection and staff workload. We employ a probabilistic approach in conjunction with the optimization models, to compute the risk of infection, including contact rates, incidence status, and the probability of infection of the residents.
To solve the models, we propose an enhanced local search algorithm by leveraging the \textit{symmetry property} of the optimal solution. We perform several experiments with realistically sized instances and show that the proposed approach can derive optimal testing strategies.

Keywords: Testing strategy; Retirement home; COVID-19; Long-term care; Nursing home; Symmetry proper; Pandemic


Publ.-Id: 34417

Data of Covid-19 Death and Infections in all counties of Germany

Abdussalam, W.

We provide post-processing data of daily dead and infected COVID-19 cases for a county (Landkreise) and a state (Bundesland) level. The data are extracted from the following link the data source, and subsequently transferred to the Casus-HZDR database server (see Fig above). The age-based and gender-based data are then aggregated and prepared in csv file.

The current data for county level is prepared on Germany_Counties_COVID19_Death_Infections.csv and its daily version is stored in Archive folder. Likewise, the actual data for state level is prepared on Germany_States_COVID19_Death_Infections.csv and its daily version is stored in Archive folder. The file consists of six columns such as region, name, date, dead, infected and population. The region denotes the ID of a county/state followed by its name in the next column. The inserted date of data is prepared in the third column followed by the number of dead and infected cases. Last but not least, the population of the county is provided in the last column.


Publ.-Id: 34416

Computing the mean ionization state with average-atom models

Callow, T. J.; Kraisler, E.; Cangi, A.

Average-atom (AA) models are an important tool in the modelling of warm dense matter, being both a computationally cheap and conceptually straightforward alternative to full DFT MD simulations. AA models are typically based on a common premise - namely, an atom immersed in a plasma environment - but use a range of different assumptions and approximations, which can cause inconsistent predictions for various properties. In this talk, I will compare results across several models, differing for example in their choice of boundary conditions and exchange-correlation functional. I will focus on the mean ionization state (MIS), an important property in WDM. I will compare different methods for computing the MIS, including methods which are historically popular and still widely-used in AA codes, and also consider more novel approaches using the electron localization function and Kubo-Greenwood formalism. If time permits, these results with also be compared with results from full DFT-MD simulations.

  • Lecture (Conference)
    DFT Methods for Matter under Extreme Conditions, 21.02.2022, Görlitz, Deutschland

Publ.-Id: 34415

Comparisons of density-functional average-atom models and measures of the mean ionization state

Callow, T. J.; Rahat, N.; Kraisler, E.; Cangi, A.

Density-functional average-atom (AA) models are an important tool in simulations of the warm dense matter (WDM) regime, because they account for quantum interactions at favourable computational cost. AA models are typically based on a common premise - namely, an atom immersed in a plasma environment - but use a range of different assumptions and approximations, leading to inconsistent predictions for various properties. We compare results across several models, differing for example in their choice of boundary conditions and exchange-correlation functional, focussing on the mean ionization state (MIS), an important property in WDM. Furthermore, we compare different methods for evaluating the MIS: a simple energy threshold, and approaches based on the inverse participation function and electron localization function. We evaluate the relative merits of these approaches and, time-permitting, compare our AA results with full Kohn-Sham density-functional theory calculations.

  • Lecture (Conference)
    APS March Meeting 2022, 15.03.2022, Chicago, USA

Publ.-Id: 34414

Reserach Data: THz-induced structural phase transition in hybrid perovskites (March 2022)

Deinert, J.-C.; Kovalev, S.; Kim, H.

Research data measured during the TELBE beamtime in March 2022 for the proposal 21202600 (THz-induced structural phase transition in hybrid perovskites). PI: Heejae Kim, experimental team: Jaco Geuchies, Sheng Qu, and the TELBE team

Keywords: Terahertz; phase transition; ultrafast; transient absorption; perovskite

Related publications


Publ.-Id: 34413

Self-Supported Three-Dimensional Quantum Dot Aerogels as a Promising Photocatalyst for CO2 Reduction

Jiang, G.; Wang, J.; Li, N.; Hübner, R.; Georgi, M.; Cai, B.; Li, Z.; Lesnyak, V.; Gaponik, N.; Eychmüller, A.

With the merits of quantum dots (QDs) (e.g., high molar extinction coefficient, strong visible light absorption, large specific surface area, and abundant functional surface active sites) and aerogels (e.g., self-supported architectures, porous network), semiconductor QD aerogels show great prospect in photocatalytic applications. However, typical gelation methods rely on oxidative treatments of QDs. Moreover, the remaining organic ligands (e.g., mercaptoacids) are still present on the surface of gels. Both these factors inhibit the activity of such photocatalysts, hampering their widespread use.
Herein, we present a facile 3D assembly of II−VI semiconductor QDs capped with inorganic (NH4)2S ligands into aerogels using H2O as a dispersion solvent. Without any sacrificial agents, the resulting CdSe QD aerogels achieve a high CO generation rate of 15 μmol g-1 h-1, which is 12-fold higher than that of pristine-aggregated QD powders. Our work not only provides a facile strategy to fabricate QD aerogels but also offers a platform for designing advanced aerogel-based photocatalysts.

Related publications

Publ.-Id: 34412

Dataset: spatially resolved temperature distribution in a rare-earth-doped transparent glass-ceramic

Podlipec, R.; Sedmak, I.

Dataset of glass-ceramic temperature-dependent fluorescence emission used for the calibration of the time measurements of spatially resolved temperature distribution in rare-earth-doped glass-ceramic materials for the studies of thermal processes within optically transparent materials.   

Related publications


Publ.-Id: 34411

Application of a fluorescence anisotropy-based assay to quantify transglutaminase 2 activity in cell lysates

Hauser, S.; Sommerfeld, P.; Wodtke, J.; Hauser, C.; Schlitterlau, P.; Pietzsch, J.; Löser, R.; Pietsch, M.; Wodtke, R.

Transglutaminase 2 (TGase 2) represents a multifunctional protein, which is involved in various physiological and pathophysiological processes. The latter also include its participation in the development and progression of malignant neoplasms, which is often accompanied by an in-creased protein synthesis. Besides the elucidation of the molecular functions of TGase 2 in tumor cells, knowledge of its concentration that is available for targeting by theranostic agents repre-sents a valuable information. Herein, we describe the application of a recently developed fluo-rescence anisotropy (FA)-based assay for the quantitative expression profiling of TGase 2 by means of transamidase-active enzyme in cell lysates. The assay is based on the incorporation of rhodamine B‑isonipecotyl‑cadaverine (R-I-Cad) into N,N-dimethylated casein (DMC), which results in an increase of FA signal over time. It was shown that this reaction is not only catalyzed by TGase 2 but also by TGases 1, 3, and 6 and factor XIIIa using recombinant proteins. Therefore, control measurements in the presence of a selective irreversible TGase 2 inhibitor were manda-tory to ascertain the specific contribution of TGase 2 to the overall FA rate. To validate the assay regarding the quality of quantification, spike/recovery and linearity of dilution experiments were performed. A total of 25 cancer and 5 non-cancer cell lines were characterized with this as-say method in terms of their activatable TGase 2 concentration (fmol/µg protein lysate) and the results were compared to protein synthesis data obtained by western blotting. Moreover, com-plementary protein quantification methods using a biotinylated irreversible TGase 2 inhibitor as activity-based probe and a commercially available ELISA were applied for selected cell lines to further validate the results obtained by the FA-based assay. Overall, the present study demonstrates that the FA-based assay using the substrate pair R-I-Cad and DMC represents a facile, homogenous and continuous method for quantifying TGase 2 activity in cell lysates.

Keywords: activity-based protein profiling; cancer; ELISA; enzyme assay; transamidase activity

Publ.-Id: 34410

Laser-proton acceleration in the near-critical regime using density tailored cryogenic hydrogen jets

Rehwald, M.

Modern particle accelerators are a key component of today’s research landscape and indispensable in industry and medicine. In special application areas, the portfolio of these facilities will be expanded by laser-driven compact plasma accelerators that generate short, high-intensity pulses of ions with unique beam properties. Though intensely explored by the community, scaling the maximum beam energies of laser-driven ion accelerators to the required level is one of the most significant challenges of this field. This endeavor is inherently linked to a fundamental understanding of the underlying acceleration processes. The prospect to effciently increase the beam energy relies on the ability to control the accelerating field structures beyond the well-established acceleration from the stationary target rear side. However, manipulating the interaction in such micrometer-sized accelerators proves to be challenging due to the transient nature of the plasma fields and requires precise tuning of the temporal laser pulse shape and the volumetric density distribution of the plasma target to a level that could so far not be achieved.
This thesis investigates laser-proton acceleration using a cryogenic hydrogen target that combines the capabilities of predictive three-dimensional simulation and the in-situ realtime monitoring of the density distribution in the experiment to explore the fundamental physical principles of plasma based acceleration mechanisms. The corresponding experiments were performed at the DRACO laser facility at the Helmholtz-Zentrum Dresden-Rossendorf. The key to the success of these studies was the advancement of the cryogenic target system that generates a self-replenishing pure hydrogen jet. Using a mechanical chopping device, which protects the target system from the disruptive influence originating from the high-intensity interaction, allowed, for the first time, systematic experiments with a large number of laser shots in the harsh environment of the ultra-short pulse DRACO petawatt laser. The performance of a cylindrical hydrogen jet can be substantially optimized by a flexible all-optical tailoring of the target profile. Guided by real-time multi-color probing, the target density, the decisive parameter of the interaction, was scanned over two orders of magnitude allowing the exploration of different advanced acceleration regimes in a controlled manner. This approach led to the experimental realization of proton beams with energies up to 80 MeV and application relevant high particle yield from advanced acceleration mechanisms occurring in near-critical density plasmas, a regime so far mostly investigated in numerical studies. Besides cylindrical jets, the formation of thin hydrogen sheets was studied to gain insight into the fluid and crystallization dynamics that can be used to tailor the target shape for laser-proton acceleration. Using these jets, the onset of target transparency was explored, a regime that promises increased proton energies when optimized. Furthermore, after irradiation of the hydrogen jet with a high-intensity laser pulse, an unexpected axial modulation in the plasma density distribution was observed that can play a role in structuring the proton beam profile. This modulation is caused by instabilities that originate from the laser-plasma interaction, for example due to laser-driven return currents or the plasma expansion dynamics.

  • Open Access Logo Wissenschaftlich-Technische Berichte / Helmholtz-Zentrum Dresden-Rossendorf; HZDR-120 2022
    ISSN: 2191-8708, eISSN: 2191-8716
  • Doctoral thesis
    TU Dresden, 2022
    Mentor: Dr. Karl Zeil
    147 Seiten
  • Lecture (others)
    Verteidigungsvortrag, 17.03.2022, Dresden, Deutschland


Publ.-Id: 34409

alpaka, LLAMA and More - Solutions for Exascale Performance Portability

Stephan, J.

Heterogeneous hardware landscapes will define the Exascale era. At the same time, keeping scientific libraries and applications portable across different hardware setups while maintaining high performance is no trivial matter. Vendor-provided programming platforms often cannot target accelerators from other vendors, and different hardware types like CPUs, GPUs and FPGAs require differently tuned algorithms for optimal performance.

A solution to these issues can be found in abstraction layers that provide the user with a single programming interface while still maintaining portability and performance. In this talk, we introduce the Caravan HPC ecosystem. With the alpaka abstraction library for accelerator programming at its core and many sibling libraries for related use cases --- such as the memory access abstraction layer LLAMA or the C++ primitives library vikunja --- the Caravan ecosystem is an ideal choice for scientists and programmers setting out to tackle the challenges of the Exascale era.

Keywords: alpaka; LLAMA; bactria; vikunja; cupla; C++; heterogeneous computing; RedGrapes; GPU programming; OpenMP

  • Open Access Logo Lecture (Conference) (Online presentation)
    SIAM Conference on Parallel Processing for Scientific Computing 2022, 23.-26.02.2022, Seattle, WA, United States of America

Publ.-Id: 34407

Evaluating GPU Programming Models for the LUMI Supercomputer

Markomanolis, G. S.; Alpay, A.; Young, J.; Klemm, M.; Malaya, N.; Esposito, A.; Heikonen, J.; Bastrakov, S.; Debus, A.; Kluge, T.; Steiniger, K.; Stephan, J.; Widera, R.; Bussmann, M.

It is common in the HPC community that the achieved performance with just CPUs is limited for many computational cases. The EuroHPC pre-exascale and the coming exascale systems are mainly focused on accelerators, and some of the largest upcoming supercomputers such as LUMI and Frontier will be powered by AMD Instinct™ accelerators. However, these new systems create many challenges for developers who are not familiar with the new ecosystem or with the required programming models that can be used to program for heterogeneous architectures. In this paper, we present some of the more well-known programming models to program for current and future GPU systems. We then measure the performance of each approach using a benchmark and a mini-app, test with various compilers, and tune the codes where necessary. Finally, we compare the performance, where possible, between the NVIDIA Volta (V100), Ampere (A100) GPUs, and the AMD MI100 GPU.

Keywords: GPU; Programming Models; HIP; CUDA; OpenMP; hipSYCL; Kokkos; Alpaka

  • Open Access Logo Contribution to proceedings
    Supercomputing Frontiers Asia 2022, 01.-03.03.2022, Singapore, Republic of Singapore
    Supercomputing Frontiers, Cham, Schweiz: Springer Nature, 978-3-031-10418-3, 79-101
    DOI: 10.1007/978-3-031-10419-0_6

Publ.-Id: 34406

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