### Recent Submissions

• Journal Article

#### A minimalist model to measure interactions between proteins and synaptic vesicles ﻿

Scientific Reports 2020; 10(1)
Protein dynamics in the synaptic bouton are still not well understood, despite many quantitative studies of synaptic structure and function. The complexity of the synaptic environment makes investigations of presynaptic protein mobility challenging. Here, we present an in vitro approach to create a minimalist model of the synaptic environment by patterning synaptic vesicles (SVs) on glass coverslips. We employed fluorescence correlation spectroscopy (FCS) to measure the mobility of monomeric enhanced green fluorescent protein (mEGFP)-tagged proteins in the presence of the vesicle patterns. We observed that the mobility of all eleven measured proteins is strongly reduced in the presence of the SVs, suggesting that they all bind to the SVs. The mobility observed in these conditions is within the range of corresponding measurements in synapses of living cells. Overall, our simple, but robust, approach should enable numerous future studies of organelle-protein interactions in general.
• Journal Article

#### Observation of electron-induced characteristic x-ray and bremsstrahlung radiation from a waveguide cavity ﻿

We demonstrate x-ray generation based on direct emission of spontaneous x-rays into waveguide modes. Photons are generated by electron impact onto a structured anode target, which is formed as an x-ray waveguide or waveguide array. Both emission of characteristic radiation and bremsstrahlung are affected by the changes in mode density induced by the waveguide structure. We investigate how the excited modal pattern depends on the positions of the metal atoms and the distance of the focused electron beam with respect to the waveguide exit side. We compare the results to synchrotron-excited fluorescence. We then discuss how x-ray generation in waveguides can be used to increase the brilliance and directional emission of tabletop x-ray sources, with a corresponding increase in the spatial coherence. On the basis of the Purcell effect, we lastly show that the gain of emission into waveguide modes is governed by the quality factor of the waveguide.
• Journal Article

#### Using enriched semantic event chains to model human action prediction based on (minimal) spatial information ﻿

PLOS ONE 2020; 15(12)
Predicting other people’s upcoming action is key to successful social interactions. Previous studies have started to disentangle the various sources of information that action observers exploit, including objects, movements, contextual cues and features regarding the acting person’s identity. We here focus on the role of static and dynamic inter-object spatial relations that change during an action. We designed a virtual reality setup and tested recognition speed for ten different manipulation actions. Importantly, all objects had been abstracted by emulating them with cubes such that participants could not infer an action using object information. Instead, participants had to rely only on the limited information that comes from the changes in the spatial relations between the cubes. In spite of these constraints, participants were able to predict actions in, on average, less than 64% of the action’s duration. Furthermore, we employed a computational model, the so-called enriched Semantic Event Chain (eSEC), which incorporates the information of different types of spatial relations: (a) objects’ touching/untouching, (b) static spatial relations between objects and (c) dynamic spatial relations between objects during an action. Assuming the eSEC as an underlying model, we show, using information theoretical analysis, that humans mostly rely on a mixed-cue strategy when predicting actions. Machine-based action prediction is able to produce faster decisions based on individual cues. We argue that human strategy, though slower, may be particularly beneficial for prediction of natural and more complex actions with more variable or partial sources of information. Our findings contribute to the understanding of how individuals afford inferring observed actions’ goals even before full goal accomplishment, and may open new avenues for building robots for conflict-free human-robot cooperation.
• Journal Article

#### Analysis of signal to noise ratio in coronagraph observations of coronal mass ejections ﻿

Journal of Space Weather and Space Climate 2021; 11
We establish a baseline signal-to-noise ratio (SNR) requirement for the European Space Agency (ESA)-funded Solar Coronagraph for OPErations (SCOPE) instrument in its field of view of 2.5–30 solar radii based on existing observations by the Solar and Heliospheric Observatory (SOHO). Using automatic detection of coronal mass ejections (CMEs), we anaylse the impacts when SNR deviates significantly from our previously established baseline. For our analysis, SNR values are estimated from observations made by the C3 coronagraph on the Solar and Heliospheric Observatory (SOHO) spacecraft for a number of different CMEs. Additionally, we generate a series of artificial coronagraph images, each consisting of a modelled coronal background and a CME, the latter simulated using the graduated cylindrical shell (GCS) model together with the SCRaytrace code available in the Interactive Data Language (IDL) SolarSoft library. Images are created with CME SNR levels between 0.5 and 10 at the outer edge of the field of view (FOV), generated by adding Poisson noise, and velocities between 700 km s−1 and 2800 km s−1. The images are analysed for the detectability of the CME above the noise with the automatic CME detection tool CACTus. We find in the analysed C3 images that CMEs near the outer edge of the field of view are typically 2% of the total brightness and have an SNR between 1 and 4 at their leading edge. An SNR of 4 is defined as the baseline SNR for SCOPE. The automated detection of CMEs in our simulated images by CACTus succeeded well down to SNR = 1 and for CME velocities up to 1400 km s−1. At lower SNR and higher velocity of ≥ 2100 km s−1 the detection started to break down. For SCOPE, the results from the two approaches confirm that the initial design goal of SNR = 4 would, if achieved, deliver a comparable performance to established data used in operations today, with a more compact instrument design, and a margin in SNR before existing automatic detection produces significant false positives.
• Journal Article

#### One-Shot Multi-Path Planning Using Fully Convolutional Networks in a Comparison to Other Algorithms ﻿

Frontiers in Neurorobotics 2021; 14
Path planning plays a crucial role in many applications in robotics for example for planning an arm movement or for navigation. Most of the existing approaches to solve this problem are iterative, where a path is generated by prediction of the next state from the current state. Moreover, in case of multi-agent systems, paths are usually planned for each agent separately (decentralized approach). In case of centralized approaches, paths are computed for each agent simultaneously by solving a complex optimization problem, which does not scale well when the number of agents increases. In contrast to this, we propose a novel method, using a homogeneous, convolutional neural network, which allows generation of complete paths, even for more than one agent, in one-shot, i.e., with a single prediction step. First we consider single path planning in 2D and 3D mazes. Here, we show that our method is able to successfully generate optimal or close to optimal (in most of the cases <10% longer) paths in more than 99.5% of the cases. Next we analyze multi-paths either from a single source to multiple end-points or vice versa. Although the model has never been trained on multiple paths, it is also able to generate optimal or near-optimal (<22% longer) paths in 96.4 and 83.9% of the cases when generating two and three paths, respectively. Performance is then also compared to several state of the art algorithms.
• Journal Article

#### Absolute quantum yield measurements of fluorescent proteins using a plasmonic nanocavity ﻿

Communications Biology 2020; 3(1)
One of the key photophysical properties of fluorescent proteins that is most difficult to measure is the quantum yield. It describes how efficiently a fluorophore converts absorbed light into fluorescence. Its measurement using conventional methods become particularly problematic when it is unknown how many of the proposedly fluorescent molecules of a sample are indeed fluorescent (for example due to incomplete maturation, or the presence of photophysical dark states). Here, we use a plasmonic nanocavity-based method to measure absolute quantum yield values of commonly used fluorescent proteins. The method is calibration-free, does not require knowledge about maturation or potential dark states, and works on minute amounts of sample. The insensitivity of the nanocavity-based method to the presence of non-luminescent species allowed us to measure precisely the quantum yield of photo-switchable proteins in their on-state and to analyze the origin of the residual fluorescence of protein ensembles switched to the dark state.
• Journal Article

#### Spectral µCT with an energy resolving and interpolating pixel detector ﻿

Optics Express 2020; 28(7) p.9842-9859
A main challenge in x-ray µCT with laboratory radiation derives from the broad spectral content, which in contrast to monochromatic synchrotron radiation gives rise to reconstruction artifacts and impedes quantitative reconstruction. Due to the low spectral brightness of these sources, monochromatization is unfavorable and parallel recording of a broad bandpath is practically indispensable. While conventional CT sums up all spectral components into a single detector value, spectral CT discriminates the data in several spectral bins. Here we show that a new generation of charge integrating and interpolating pixel detectors is ideally suited to implement spectral CT with a resolution in the range of 10 µm. We find that the information contained in several photon energy bins largely facilitates automated classification of materials, as demonstrated for of a mouse cochlea. Bones, soft tissues, background and metal implant materials are discriminated automatically. Importantly, this includes taking a better account of phase contrast effects, based on tailoring reconstruction parameters to specific energy bins.
• Journal Article

#### Multi-scale X-ray phase-contrast tomography of murine heart tissue ﻿

Biomedical Optics Express 2020; 11(5) p.2633-2651
The spatial organization of cardiac muscle tissue exhibits a complex structure on multiple length scales, from the sarcomeric unit to the whole organ. Here we demonstrate a multi-scale three-dimensional imaging (3d) approach with three levels of magnification, based on synchrotron X-ray phase contrast tomography. Whole mouse hearts are scanned in an undulator beam, which is first focused and then broadened by divergence. Regions-of-interest of the hearts are scanned in parallel beam as well as a biopsy by magnified cone beam geometry using a X-ray waveguide optic. Data is analyzed in terms of orientation, anisotropy and the sarcomeric periodicity via a local Fourier transformation.
• Journal Article

#### Coherent control of a surface structural phase transition. ﻿

Nature 2020; 583(7815) p.232-236
The desire to exert active optical control over matter is a unifying theme across multiple scientific disciplines, as exemplified by all-optical magnetic switching, light-induced metastable or exotic phases of solids and the coherent control of chemical reactions. Typically, these approaches dynamically steer a system towards states or reaction products far from equilibrium. In solids, metal-insulator transitions are an important target for optical manipulation, offering dramatic and ultrafast changes of the electronic and lattice properties. In this context, essential questions concern the role of coherence in the efficiencies and thresholds of such transitions. Here, we demonstrate coherent control over a metal-insulator structural phase transition in a quasi-one-dimensional solid-state surface system. A femtosecond double-pulse excitation scheme is used to drive the system from the insulating to a metastable metallic state, and the corresponding structural changes are monitored by ultrafast low-energy electron diffraction. We harness vibrational coherence in key structural modes to govern the transition, as evidenced by delay-dependent oscillations in the double-pulse switching efficiency. Mode-selective coherent control of solids and surfaces could open new routes to switching chemical and physical functionalities, facilitated by metastable and non-equilibrium states.
• Journal Article

#### Pinacolone-Alcohol Gas-Phase Solvation Balances as Experimental Dispersion Benchmarks ﻿

Molecules 2020; 25(21) p.1-14: Art. 5095
The influence of distant London dispersion forces on the docking preference of alcohols of different size between the two lone electron pairs of the carbonyl group in pinacolone was explored by infrared spectroscopy of the OH stretching fundamental in supersonic jet expansions of 1:1 solvate complexes. Experimentally, no pronounced tendency of the alcohol to switch from the methyl to the bulkier tert-butyl side with increasing size was found. In all cases, methyl docking dominates by at least a factor of two, whereas DFT-optimized structures suggest a very close balance for the larger alcohols, once corrected by CCSD(T) relative electronic energies. Together with inconsistencies when switching from a C4 to a C5 alcohol, this points at deficiencies of the investigated B3LYP and in particular TPSS functionals even after dispersion correction, which cannot be blamed on zero point energy effects. The search for density functionals which describe the harmonic frequency shift, the structural change and the energy difference between the docking isomers of larger alcohols to unsymmetric ketones in a satisfactory way is open.
• Journal Article

#### 3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography ﻿

eLife 2020; 9 p.1-25: Art. e60408
We present a three-dimensional (3D) approach for virtual histology and histopathology based on multi-scale phase contrast x-ray tomography, and use this to investigate the parenchymal architecture of unstained lung tissue from patients who succumbed to Covid-19. Based on this first proof-of-concept study, we propose multi-scale phase contrast x-ray tomography as a tool to unravel the pathophysiology of Covid-19, extending conventional histology by a third dimension and allowing for full quantification of tissue remodeling. By combining parallel and cone beam geometry, autopsy samples with a maximum cross section of 8 mm are scanned and reconstructed at a resolution and image quality, which allows for the segmentation of individual cells. Using the zoom capability of the cone beam geometry, regions-of-interest are reconstructed with a minimum voxel size of 167 nm. We exemplify the capability of this approach by 3D visualization of diffuse alveolar damage (DAD) with its prominent hyaline membrane formation, by mapping the 3D distribution and density of lymphocytes infiltrating the tissue, and by providing histograms of characteristic distances from tissue interior to the closest air compartment.
• Journal Article

#### Time-continuous and time-discrete SIR models revisited: theory and applications ﻿

Advances in Difference Equations. 2020 Oct 07;2020(1):556
Since Kermack and McKendrick have introduced their famous epidemiological SIR model in 1927, mathematical epidemiology has grown as an interdisciplinary research discipline including knowledge from biology, computer science, or mathematics. Due to current threatening epidemics such as COVID-19, this interest is continuously rising. As our main goal, we establish an implicit time-discrete SIR (susceptible people–infectious people–recovered people) model. For this purpose, we first introduce its continuous variant with time-varying transmission and recovery rates and, as our first contribution, discuss thoroughly its properties. With respect to these results, we develop different possible time-discrete SIR models, we derive our implicit time-discrete SIR model in contrast to many other works which mainly investigate explicit time-discrete schemes and, as our main contribution, show unique solvability and further desirable properties compared to its continuous version. We thoroughly show that many of the desired properties of the time-continuous case are still valid in the time-discrete implicit case. Especially, we prove an upper error bound for our time-discrete implicit numerical scheme. Finally, we apply our proposed time-discrete SIR model to currently available data regarding the spread of COVID-19 in Germany and Iran.
• Journal Article

#### Cavitation bubble dynamics and sonochemiluminescence activity inside sonicated submerged flow tubes ﻿

Chemical Engineering and Processing - Process Intensification 2020; 150
• Journal Article

#### Structure of Nanocrystalline, Partially Disordered MoS$_{2+δ}$ Derived from HRTEM—An Abundant Material for Efficient HER Catalysis ﻿

Catalysts 2020; 10(8) p.1-16: Art. 856
Molybdenum sulfides (MoS$_x$, x > 2) are promising catalysts for the hydrogen evolution reaction (HER) that show high hydrogen evolution rates and potentially represent an abundant alternative to platinum. However, a complete understanding of the structure of the most active variants is still lacking. Nanocrystalline MoS$_{2+δ}$ was prepared by a solvothermal method and immobilized on graphene. The obtained electrodes exhibit stable HER current densities of 3 mA cm$^{−2}$ at an overpotential of ~200 mV for at least 7 h. A structural analysis of the material by high-resolution transmission electron microscopy (HRTEM) show partially disordered nanocrystals of a size between 5–10 nm. Both X-ray and electron diffraction reveal large fluctuations in lattice spacing, where the average c-axis stacking is increased and the in-plane lattice parameter is locally reduced in comparison to the layered structure of crystalline MoS$_2$. A three-dimensional structural model of MoS$_{2+δ}$ could be derived from the experiments, in which [Mo$_2$S$_{12}$]$^{2−}$ and [Mo$_3$S$_{13}$]$^{2−}$ clusters as well as disclinations represent the typical defects in the ideal MoS$_2$ structure. It is suggested that the partially disordered nanostructure leads to a high density of coordinatively modified Mo sites with lower Mo–Mo distances representing the active sites for HER catalysis, and, that these structural features are more important than the S:Mo ratio for the activity.
• Journal Article

#### Environmental transmission electron microscopy study of hydrogen charging effect on a Cu-Zr metallic glass ﻿

Materials Research Letters 2020; 8(12) p.439-445
Hydrogen induced plasticity has been found in metallic glasses; however, the underlying mechanism remains unclear. Herein, we studied a Cu-Zr metallic glass charged in a hydrogen atmosphere inside an environmental transmission electron microscope. Compression tests of hydrogen charged nanopillars show more controllable deformation compared to uncharged ones. A variable resolution fluctuation electron microscopy study of the hydrogen charged samples reveals an increase in the correlation length of the medium-range order. Our results provide experimental evidence for hydrogen-induced heterogeneity and support the idea that increasing the degree of heterogeneity leads to multiple local shear events and suppresses catastrophic shear banding.
• Journal Article

#### Towards full surface Brillouin zone mapping by coherent multi-photon photoemission ﻿

New Journal of Physics 2020; 22(7) p.1-6: Art. 073035
We report a novel approach for coherent multi-photon photoemission in the entire Brillouin zone with infrared light that is readily implemented in a laboratory setting. We excite a solid state material, Ag(110), with intense femtosecond laser pulses to excite higher-order multi-photon photoemission; angle-resolved electron spectroscopic acquisition records photoemission at large in-plane momenta involving optical transitions from the occupied to unoccupied bands of the sample that otherwise might remain hidden by the photoemission horizon. We propose this as a complementary ultrafast method to time- and angle-resolved two-color, e.g. infrared pump and extreme ultraviolet probe, photoemission spectroscopy, with the advantage of being able to measure and control the coherent electron dynamics.
• Journal Article

#### Upconversion photoluminescence of Ho$^{3+}$-Yb$^{3+}$ doped barium titanate nanocrystallites: Optical tools for structural phase detection and temperature probing ﻿

Scientific Reports 2020; 10(1) p.1-12: Art. 8775
Authors have explored the photo-physical properties of Ho$^{3+}$-Yb$^{3+}$ doped BaTiO$_3$ nanocrystals and proposed an intuitive method to probe temperature and crystal phase structure of the matrix. Structural phase change of doped crystals was analyzed in terms of their X-ray diffraction, and it was confirmed through second harmonic generation. We give insights on upconversion of energy of light-emission in Ho$^{3+}$-Yb$^{3+}$: BaTiO$_3$ nanocrystals upon a 980 nm laser-light excitation and subsequently, the excited state dynamics were studied with the help of dependence of upconversion luminescence on excitation power and measuring-temperature. To understand the nature of occupancies of the Ho$^{3+}$ ions at the Ti- and Ba-sites, we performed site-selective, time-resolved spectroscopic measurements at various crystal phases. Based on the lifetime analysis, it is inferred that the Ho$^{3+}$ ions are present at two types of sites in barium titanate lattice. One of those is the 6-coordinated Ti-site of low symmetry, while the other one is the 12-coordinated Ba-site of higher symmetry. The upconversion emission of the nanocrystals are found to be temperature-sensitive (12 to 300 K), indicating possible use as a self-referenced temperature probe. An analysis of the temperature dependent emissions from $^5$F$_4$ and $^5$S$_2$ levels of Ho$^{3+}$ ions, gives a maximum value of temperature sensitivity ~ 0.0095 K$^{−1}$ at 12 K. Furthermore, we observe a sharp change in the luminescence intensity at ~180 K due to a ferroelectric phase change of the sample. The correlation of upconversion luminescence with the results of X-ray diffraction and second harmonic generation at different crystal phases implies that the frequency upconversion may be used as a probe of structural change of the lattice.
• Journal Article

#### Hey, look over there: Distraction effects on rapid sequence recall ﻿

PLOS ONE 2020; 15(4) p.1-22: Art. e0223743
In the course of everyday life, the brain must store and recall a huge variety of representations of stimuli which are presented in an ordered or sequential way. The processes by which the ordering of these various things is stored and recalled are moderately well understood. We use here a computational model of a cortex-like recurrent neural network adapted by a multitude of plasticity mechanisms. We first demonstrate the learning of a sequence. Then, we examine the influence of different types of distractors on the network dynamics during the recall of the encoded ordered information being ordered in a sequence. We are able to broadly arrive at two distinct effect-categories for distractors, arrive at a basic understanding of why this is so, and predict what distractors will fall into each category.
• Journal Article

#### Modeling the Shape of Synaptic Spines by Their Actin Dynamics ﻿

Frontiers in Synaptic Neuroscience 2020; 12 p.1-19: Art. 9
Dendritic spines are the morphological basis of excitatory synapses in the cortex and their size and shape correlates with functional synaptic properties. Recent experiments show that spines exhibit large shape fluctuations that are not related to activity-dependent plasticity but nonetheless might influence memory storage at their synapses. To investigate the determinants of such spontaneous fluctuations, we propose a mathematical model for the dynamics of the spine shape and analyze it in 2D—related to experimental microscopic imagery—and in 3D. We show that the spine shape is governed by a local imbalance between membrane tension and the expansive force from actin bundles that originates from discrete actin polymerization foci. Experiments have shown that only few such polymerization foci co-exist at any time in a spine, each having limited life time. The model shows that the momentarily existing set of such foci pushes the membrane along certain directions until foci are replaced and other directions may now be affected. We explore these relations in depth and use our model to predict shape and temporal characteristics of spines from the different biophysical parameters involved in actin polymerization. Approximating the model by a single recursive equation we finally demonstrate that the temporal evolution of the number of active foci is sufficient to predict the size of the model-spines. Thus, our model provides the first platform to study the relation between molecular and morphological properties of the spine with a high degree of biophysical detail.
• Journal Article

#### Thermophysical properties of a Si$_{50}$Ge$_{50}$ melt measured on board the International Space Station ﻿

npj Microgravity 2020; 6(1) p.1-9: Art. 10
Thermophysical properties of highly doped Si$_{50}$Ge$_{50}$ melt were measured contactlessly in the electromagnetic levitation facility ISSEML on board the International Space Station. The sample could be melted, overheated by about 375 K, and cooled down in 350 mbar Argon atmosphere. A large undercooling of about 240 K was observed and a quasi-homogeneous nucleation on the droplet surface occurred. During the cooling phase, high-resolution videos were taken from the side and the top. The density and thermal expansion were evaluated with digital image processing; the viscosity and the surface tension were measured by means of the oscillating drop technique. Inductive measurements of the electrical resistivity were conducted by a dedicated electronics. All data were taken as a function of temperature T from the overheated melt down to the undercooled range. We found a nonlinear thermal expansion, suggesting a many body effect in the liquid beyond the regular pair interaction, an enhanced damping of surface oscillations likely related to an internal turbulent flow, and an increment of the electrical resistivity with decreased T in the undercooled range regarding a demixing of the components.