Reversing the training effect in exchange biased CoO/Co bilayers

We performed a detailed study of the training effect in exchange biased CoO/Co bilayers. High-resolution measurements of the anisotropic magnetoresistance (AMR) are consistent with nucleation of magnetic domains in the antiferromagnetic CoO layer during the first magnetization reversal. This accounts for the enhanced spin rotation observed in the ferromagnetic Co layer for all subsequent reversals. Surprisingly, the AMR measurements as well as magnetization measurements reveal that it is possible to partially reinduce the untrained state by performing a hysteresis measurement with an in plane external field perpendicular to the cooling field. Indeed, the next hysteresis loop obtained in a field parallel to the cooling field resembles the initial asymmetric hysteresis loop, but with a reduced amount of spin rotation occurring at the first coercive field. This implies that the antiferromagnetic domains, which are created during the first reversal after cooling, can be partially erased.Comment: 4 pages, 4 figure

AlphaFold predicts the most complex protein knot and composite protein knots

The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands of proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these predictions for cases where the protein backbone exhibits rare topological complexity, i.e. knotting. Amongst others, we discovered a $7_1$-knot, the most topologically complex knot ever found in a protein, as well several 6-crossing composite knots comprised of two methyltransferase or carbonic anhydrase domains, each containing a simple trefoil knot. These deeply embedded composite knots occur evidently by gene duplication and interconnection of knotted dimers. Finally, we report two new five-crossing knots including the first $5_1$-knot. Our list of analyzed structures forms the basis for future experimental studies to confirm these novel knotted topologies and to explore their complex folding mechanisms.Comment: This article appeared openly accessible in M. A. Brems et al., Protein Science. 2022; 31( 8):e4380 and may be found at https://doi.org/10.1002/pro.438

Coarse-graining collective skyrmion dynamics in confined geometries

Magnetic skyrmions are magnetic quasi-particles with enhanced stability and different manipulation mechanisms using external fields and currents making them promising candidates for future applications for instance in neuromorphic computing. Recently, several measurements and simulations have shown that thermally activated skyrmions in confined geometries, as they are necessary for device applications, arrange themselves predominantly based on commensurability effects. In this simulational study, based on the Thiele model, we investigate the enhanced dynamics and degenerate non-equilibrium steady state of a system in which the intrinsic skyrmion-skyrmion and skyrmion-boundary interaction compete with thermal fluctuations as well as current-induced spin-orbit torques. The investigated system is a triangular-shaped confinement geometry hosting four skyrmions, where we inject spin-polarized currents between two corners of the structure. We coarse-grain the skyrmion states in the system to analyze the intricacies of skyrmion arrangements of the skyrmion ensemble. In the context of neuromorphic computing, such methods address the key challenge of optimizing read-out positions in confined geometries and form the basis to understand collective skyrmion dynamics in systems with competing interactions on different scales.Comment: 11 pages, 4 figure

Perspective on unconventional computing using magnetic skyrmions

Learning and pattern recognition inevitably requires memory of previous events, a feature that conventional CMOS hardware needs to artificially simulate. Dynamical systems naturally provide the memory, complexity, and nonlinearity needed for a plethora of different unconventional computing approaches. In this perspective article, we focus on the unconventional computing concept of reservoir computing and provide an overview of key physical reservoir works reported. We focus on the promising platform of magnetic structures and, in particular, skyrmions, which potentially allow for low-power applications. Moreover, we discuss skyrmion-based implementations of Brownian computing, which has recently been combined with reservoir computing. This computing paradigm leverages the thermal fluctuations present in many skyrmion systems. Finally, we provide an outlook on the most important challenges in this field.Comment: 19 pages and 3 figure

Constructing coarse-grained skyrmion potentials from experimental data with Iterative Boltzmann Inversion

In an effort to understand skyrmion behavior on a coarse-grained level, skyrmions are often described as 2D quasiparticles evolving according to the Thiele equation. Interaction potentials are the key missing parameters for predictive modeling of experiments. Here, the Iterative Boltzmann Inversion technique commonly used in soft matter simulations is applied to construct potentials for skyrmion-skyrmion and skyrmion-magnetic material boundary interactions from a single experimental measurement without any prior assumptions of the potential form. It is found that the two interactions are purely repulsive and can be described by an exponential function for micrometer-sized skyrmions in a ferromagnetic thin film multilayer stack. This captures the physics on experimental length and time scales that are of interest for most skyrmion applications and typically inaccessible to atomistic or micromagnetic simulations

Constructing coarse-grained skyrmion potentials from experimental data with Iterative Boltzmann Inversion

In an effort to understand skyrmion behavior on a coarse-grained level, skyrmions are often described as 2D quasiparticles evolving according to the Thiele equation. Interaction potentials are the key missing parameters for predictive modeling of experiments. Here, the Iterative Boltzmann Inversion technique commonly used in soft matter simulations is applied to construct potentials for skyrmion-skyrmion and skyrmion-magnetic material boundary interactions from a single experimental measurement without any prior assumptions of the potential form. It is found that the two interactions are purely repulsive and can be described by an exponential function for micrometer-sized skyrmions in a ferromagnetic thin film multilayer stack. This captures the physics on experimental length and time scales that are of interest for most skyrmion applications and typically inaccessible to atomistic or micromagnetic simulations

Reconstructing diploid 3D chromatin structures from single cell Hi-C data with a polymer-based approach

Detailed understanding of the 3D structure of chromatin is a key ingredient to investigate a variety of processes inside the cell. Since direct methods to experimentally ascertain these structures lack the desired spatial fidelity, computational inference methods based on single cell Hi-C data have gained significant interest. Here, we develop a progressive simulation protocol to iteratively improve the resolution of predicted interphase structures by maximum-likelihood association of ambiguous Hi-C contacts using lower-resolution predictions. Compared to state-of-the-art methods, our procedure is not limited to haploid cell data and allows us to reach a resolution of up to 5,000 base pairs per bead. High resolution chromatin models grant access to a multitude of structural phenomena. Exemplarily, we verify the formation of chromosome territories and holes near aggregated chromocenters as well as the inversion of the CpG content for rod photoreceptor cells

ISPY – NaCo imaging survey for planets around young stars : a young companion candidate embedded in the R CrA cloud

Context Within the NaCo-ISPY exoplanet imaging program, we aim at detecting and characterizing the population of low-mass companions at wide separations (≳10 AU), focusing in particular on young stars either hosting a known protoplanetary disk or a debris disk. Aims R CrA is one of the youngest (1-3 Myr) and most promising objects in our sample because of two previous studies that suggested the presence of a close companion. Our aim is to directly image and characterize the companion for the first time. Methods We observed R CrA twice with the NaCo instrument at the Very Large Telescope (VLT) in the L' filter with a one year time baseline in between. The high-contrast imaging data were reduced and analyzed and the companion candidate was detected in both datasets. We used artificial negative signals to determine the position and brightness of the companion and the related uncertainties. Results The companion is detected at a separation of 196.8 ± 4.5/196.6 ± 5.9 mas (18.7 ± 1.3/18.7 ± 1.4 AU) and position angle of 134.7 ± 0.5 ° /133.7 ± 0.7° in the first/second epoch observation. We measure a contrast of 7.29 ± 0.18/6.70 ± 0.15 mag with respect to the primary. A study of the stellar proper motion rejects the hypothesis that the signal is a background object. The companion candidate orbits in the clockwise direction and, if on a face-on circular orbit, its period is ˜43 - 47 yr. This value disagrees with the estimated orbital motion and therefore a face-on circular orbit may be excluded. Depending on the assumed age, extinction, and brightness of the primary, the stellar companion has a mass between 0.10 ± 0.02 M⊙ and 1.03-0.18+0.20 M⊙ range, if no contribution from circumsecondary material is taken into account. Conclusions As already hypothesized by previous studies, we directly detected a low-mass stellar companion orbiting the young Herbig Ae/Be star R CrA. Depending on the age assumptions, the companion is among the youngest forming companions imaged to date, and its presence needs to be taken into account when analyzing the complex circumstellar environment of R CrA