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.

300-Times-Increased Diffusive Skyrmion Dynamics and Effective Pinning Reduction by Periodic Field Excitation.

Thermally induced skyrmion dynamics, as well as skyrmion pinning effects, in thin films have attracted significant interest. While pinning poses challenges in deterministic skyrmion devices and slows down skyrmion diffusion, for applications in non-conventional computing, both pinning of an appropriate strength and skyrmion diffusion speed are key. Here, periodic field excitations are employed to realize an increase of the skyrmion diffusion by more than two orders of magnitude. Amplifying the excitation, a drastic reduction of the effective skyrmion pinning, is reported, and a transition from pinning-dominated diffusive hopping to dynamics approaching free diffusion is observed. By tailoring the field oscillation frequency and amplitude, a continuous tuning of the effective pinning and skyrmion dynamics is demonstrated, which is a key asset and enabler for non-conventional computing applications. It is found that the periodic excitations additionally allow stabilization of skyrmions at different sizes for field values that are inaccessible in static systems, opening up new approaches to ultrafast skyrmion motion by transiently exciting moving skyrmions.

Brownian reservoir computing realized using geometrically confined skyrmion dynamics.

Reservoir computing (RC) has been considered as one of the key computational principles beyond von-Neumann computing. Magnetic skyrmions, topological particle-like spin textures in magnetic films are particularly promising for implementing RC, since they respond strongly nonlinearly to external stimuli and feature inherent multiscale dynamics. However, despite several theoretical proposals that exist for skyrmion reservoir computing, experimental realizations have been elusive until now. Here, we propose and experimentally demonstrate a conceptually new approach to skyrmion RC that leverages the thermally activated diffusive motion of skyrmions. By confining the electrically gated and thermal skyrmion motion, we find that already a single skyrmion in a confined geometry suffices to realize nonlinearly separable functions, which we demonstrate for the XOR gate along with all other Boolean logic gate operations. Besides this universality, the reservoir computing concept ensures low training costs and ultra-low power operation with current densities orders of magnitude smaller than those used in existing spintronic reservoir computing demonstrations. Our proposed concept is robust against device imperfections and can be readily extended by linking multiple confined geometries and/or by including more skyrmions in the reservoir, suggesting high potential for scalable and low-energy reservoir computing.

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, that is, knotting. Amongst others, we discovered a 71 -knot, the most topologically complex knot ever found in a protein, as well several six-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 51 -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.

Skyrmion pinning energetics in thin film systems.

A key issue for skyrmion dynamics and devices are pinning effects present in real systems. While posing a challenge for the realization of conventional skyrmionics devices, exploiting pinning effects can enable non-conventional computing approaches if the details of the pinning in real samples are quantified and understood. We demonstrate that using thermal skyrmion dynamics, we can characterize the pinning of a sample and we ascertain the spatially resolved energy landscape. To understand the mechanism of the pinning, we probe the strong skyrmion size and shape dependence of the pinning. Magnetic microscopy imaging demonstrates that in contrast to findings in previous investigations, for large skyrmions the pinning originates at the skyrmion boundary and not at its core. The boundary pinning is strongly influenced by the very complex pinning energy landscape that goes beyond the conventional effective rigid quasi-particle description. This gives rise to complex skyrmion shape distortions and allows for dynamic switching of pinning sites and flexible tuning of the pinning.