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.

Can Polymer Helicity Affect Topological Chirality of Polymer Knots?

We investigate the effect of helicity in isolated polymers on the topological chirality of their knots with computer simulations. Polymers are described by generic worm-like chains (WLC), where helical conformations are promoted by chiral coupling between segments that are neighbors along the chain contour. The sign and magnitude of the coupling coefficient u determine the sense and strength of helicity. The corrugation of the helix is adjusted via the radius R of a spherical, hard excluded volume around each WLC segment. Open and compact helices are, respectively, obtained for R that is either zero or smaller than the length of the WLC bond, and R that is a few times larger than the bond length. We use a Monte Carlo algorithm to sample polymer conformations for different values of u, spanning the range from achiral polymers to chains with well-developed helices. Monitoring the average helix torsion and fluctuations of chiral order as a function of u, for two very different chain lengths, demonstrates that the coil-helix transition in this model is not a phase transition but a crossover. Statistical analysis of conformations forming the simplest chiral knots, 31, 51, and 52, demonstrates that topological mirror symmetry is broken─knots formed by helices with a given sense prefer one handedness over the other. For the 31 and 51 knots, positive helical sense favors positive handedness. Intriguingly, an opposite trend is observed for 52 knots, where positive helical sense promotes negative handedness. We argue that this special coupling between helicity and topological chirality stems from a generic mechanism: conformations where some of the knot crossings are found in "braids" formed by two tightly interwoven sections of the polymer.

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.

Knot formation of dsDNA pushed inside a nanochannel.

Recent experiments demonstrated that knots in single molecule dsDNA can be formed by compression in a nanochannel. In this manuscript, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment in silico, where an equilibrated coarse-grained double-stranded DNA confined in a square channel is pushed by a piston. The probability of forming knots is a non-monotonic function of the persistence length and can be enhanced significantly by increasing the piston speed. Under compression knots are abundant and delocalized due to a backfolding mechanism from which chain-spanning loops emerge, while knots are less frequent and only weakly localized in equilibrium. Our in silico study thus provides insights into the formation, origin and control of DNA knots in nanopores.