arXiv subjects

Peter Virnau

Publications and source records attributed to Peter Virnau.

At least 19 recordsLinked to original sources

arXiv2026

Polymer Knots in Thin Films: Thickness Dependence, Local Effects, and Stiffness

We study how confinement affects topology and conformations in polymer films of varying thickness $h$. The knotting probability exhibits a maximum at intermediate thicknesses near the bulk radius of gyration $h \approx R_\mathrm{g,bulk}$, vanishes at small $h$ and approaches bulk values for large $h$. Close to walls, the entanglement length increases monotonically and conformations become flatter. A layer-resolved analysis of structural and topological properties allows us to reconstruct the explicit thickness dependencies by integrating layer-resolved properties of a thick film.

cond-mat.soft↗

arXiv2026

Liquid-vapor critical behavior of the TIP4P/2005 water model: effects of NaCl solutes and hydrophobic confinement

The liquid-vapor critical behavior of water is strongly influenced by both ionic solutes and confinement. Molecular dynamics simulations of aqueous NaCl solutions using the TIP4P/2005 water model and the Madrid-2019 ion parameters reveal a systematic increase in the liquid-vapor critical temperature and pressure with salt concentration, consistent with experimental trends. In contrast, confinement between parallel hydrophobic plates leads to a depression of the critical point. The critical temperature was determined from the Binder cumulant crossing in the NVT ensemble, using a recently developed method originally applied to an active Brownian particle system. The reliability of this approach was verified through complementary NPT simulations. We further demonstrate the pronounced sensitivity of the estimated critical point to the van der Waals cutoff distance, underscoring the importance of properly accounting for long-range interactions. Our framework, which employs and tests an adjusted subbox method, can be readily extended to other critical phenomena, including the liquid-liquid critical point of water.

physics.chem-ph↗

arXiv2025

Hybrid multiscale method for polymer melts: analysis and simulations

We model the flow behaviour of dense melts of flexible and semiflexible ring polymers in the presence of walls using a hybrid multiscale approach. Specifically, we perform molecular dynamics simulations and apply the Irving-Kirkwood formula to determine an averaged stress tensor for a macroscopic model. For the latter, we choose a Cahn-Hilliard-Navier-Stokes system with dynamic and no-slip boundary conditions. We present numerical simulations of the macroscopic flow that are based on a finite element method. In particular, we present detailed proofs of the solvability and the energy stability of our numerical scheme. Phase segregation under flow between flexible and semiflexible rings, as observed in the microscopic simulations, can be replicated in the macroscopic model by introducing effective attractive forces.

math.NA↗

arXiv2025

Real-Time Modeling of Skyrmion Dynamics in Arbitrary 2D Spatially Dependent Pinning Potential Landscapes

Non-flat energy landscapes leading to localized pinning of skyrmions pose an inherent and unavoidable challenge for studies of fundamental 2D spin structure dynamics as well as applications. Accounting for pinning is a key requirement for predictive modeling of skyrmion systems, as it impacts the systems' dynamics and introduces randomizing effects. In this article, we use magneto-optical Kerr microscopy to image skyrmions in a magnetic thin film system in real time and analyze their hopping dynamics within the non-flat energy landscape. To achieve a fully quantitative model, we utilize skyrmion diffusion and dwell times at pinning sites to extrapolate the pinning energy landscape into regions that cannot be sampled on reasonable experimental time scales. For evaluation with a coarse-grained Thiele model, we perform long-time measurements of skyrmion diffusion and then develop a two-step procedure to determine simulation parameters by comparing them to experimentally accessible behavior. This provides a direct conversion between simulation and experimental units, which is the missing key step that has previously prevented quantitative quasiparticle modeling. We demonstrate the predictive power of our approach by measuring the experimentally unexplored density dependence of skyrmion diffusion and show that it is in excellent agreement with simulation predictions. Our technique thus enables quantitative skyrmion simulations on experimental time and length scales, allowing for predictive in-silico prototyping of skyrmion devices.

cond-mat.stat-mech↗

arXiv2025

Skyrmion Lattice Order Controlled by Confinement Geometry

Magnetic skyrmions forming two-dimensional (2D) lattices provide a versatile platform for investigating phase transitions predicted by Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) theory. While 2D melting in skyrmion systems has been demonstrated, achieving controlled ordering in skyrmion lattices remains challenging due to pinning effects from a non-uniform energy landscape, which often results in polycrystalline structures. Skyrmions in thin films, however, offer thermal diffusion with high tunability and can be directly imaged via Kerr microscopy, enabling real-time observation of their dynamics. To regulate lattice order in such flexible systems, we introduce geometric confinements of varying shapes. Combining Kerr microscopy experiments with Thiele model simulations, we demonstrate that confinement geometry critically influences lattice order. Specifically, hexagonal confinements commensurate with the skyrmion lattice stabilize monodomain hexagonal ordering, while incommensurate geometries induce domain formation and reduce overall order. Understanding these boundary-driven effects is essential for advancing the study of 2D phase behavior and for the design of skyrmion-based spintronic applications, ranging from memory devices to unconventional computing architectures.

cond-mat.mes-hall↗

arXiv2025

Skyrmion Lattice Domain Formation in a Non-Flat Energy Landscape

Magnetic skyrmions are chiral spin structures with non-trivial topology that comprise two-dimensional quasi-particles and are promising information carriers for data storage and processing devices. Skyrmion lattices in magnetic thin films exhibit Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) phase transitions and have garnered significant interest for studying emergent 2D phase behavior. In experimental skyrmion lattices, the main factor limiting the quasi-long-range order in thin films has been the non-flat energy landscape - often referred to as pinning effects. We demonstrate direct control of the skyrmion lattice order by effectively tuning the energy landscape employing magnetic field oscillations. By quantifying lattice order and dynamics, we explore how domain boundaries form and evolve due to pinning effects in Kerr microscopy experiments and in Brownian dynamics simulations, offering a pathway to control and study emergent skyrmion lattice properties and 2D phase behavior.

cond-mat.mes-hall↗

arXiv2025

Realizing Quantitative Quasiparticle Modeling of Skyrmion Dynamics in Arbitrary Potentials

We demonstrate fully quantitative Thiele model simulations of magnetic skyrmion dynamics on previously unattainable experimentally relevant large length and time scales by ascertaining the key missing parameters needed to calibrate the experimental and simulation time scales and current-induced forces. Our work allows us to determine complete spatial pinning energy landscapes that enable quantification of experimental studies of diffusion in arbitrary potentials within the Lifson-Jackson framework. Our method enables us to ascertain the time scales, and by isolating the effect of ultra-low current density (order $10^6 A/m^2$) generated torques we directly infer the total force acting on the skyrmion for a quantitative modelling.

cond-mat.stat-mech↗

arXiv2025

Imaging Topological Defect Dynamics Mediating 2D Skyrmion Lattice Melting

Topological defects are the key feature mediating 2D phase transitions. However, both resolution and tunability have been lacking to access the dynamics of the transitions. With dynamic Kerr microscopy, we directly capture the melting of a confined 2D magnetic skyrmion lattice with high resolution in real-time and -space. Skyrmions in magnetic thin films are two-dimensional, topologically non-trivial quasi-particles that provide rich dynamics as well as unique tunability as an essential ingredient for controlling phase behavior: We tune the skyrmion size and effective temperature on the fly to drive the two-step melting through an intermediate hexatic regime between the solid lattice and the isotropic liquid. We quantify the characteristic occurrence of topological defects mediating the transitions and reveal the so-far inaccessible dynamics of the lattice dislocations. The full real-time and -space imaging reveals the diffusion coefficient of the dislocations, which we find to be orders of magnitudes higher than that of the skyrmions.

cond-mat.stat-mech↗

arXiv2024

Effect of simple shear on knotted polymer coils and globules

We explore the effect of Couette flow on knotted linear polymer chains with extensive Molecular Dynamics (MD) simulations. Hydrodynamic interactions are accounted for by means of Multi-Particle Collision Dynamics (MPCD). The polymer chain, containing originally a simple trefoil knot at rest, is described by a coarse-grained bead-spring model in a coil or globular state. We demonstrate that under shear existing loosely localized knots in polymer coils typically tighten to several segments beyond a certain shear rate threshold. At large shear rates the polymer undergoes a tumbling-like motion during which knot sizes can fluctuate. In contrast, sheared knotted globules unwind into a convoluted pearl-necklace structure of sub-globules that folds back onto itself and in which knot types change over time.

cond-mat.soft↗

arXiv2024

Topological comparison of flexible and semiflexible chains in polymer melts with $\theta$-chains

A central paradigm of polymer physics states that chains in melts behave like random walks as intra- and interchain interactions effectively cancel each other out. Likewise, $\theta$-chains, i.e., chains at the transition from a swollen coil to a globular phase, are also thought to behave like ideal chains, as attractive forces are counterbalanced by repulsive entropic contributions. While the simple mapping to an equivalent Kuhn chain works rather well in most scenarios with corrections to scaling, random walks do not accurately capture the topology and knots particularly for flexible chains. In this paper, we demonstrate with Monte Carlo and molecular dynamics simulations that chains in polymer melts and $\theta$-chains not only agree on a structural level for a range of stiffnesses, but also topologically. They exhibit similar knotting probabilities and knot sizes, both of which are not captured by ideal chain representations. This discrepancy comes from the suppression of small knots in real chains, which is strongest for very flexible chains because excluded volume effects are still active locally and become weaker with increasing semiflexibility. Our findings suggest that corrections to ideal behavior are indeed similar for the two scenarios of real chains and that structure and topology of a chain in a melt can be approximately reproduced by a corresponding $\theta$-chain.

cond-mat.soft↗

arXiv2024

Influence of Topology on Rheological Properties of Polymer Ring Melts

We investigate with numerical simulations the influence of topology and stiffness on macroscopic rheological properties of polymer melts consisting of unknotted, knotted or concatenated rings. While melts of flexible, knotted oligomer rings tend to be significantly more viscous than their unknotted counterparts, differences vanish in a low shear rate scenario with increasing degree of polymerization. Melts of catenanes consisting of two rings on the other hand are consistently more viscous than their unconcatenated counterparts. These topology-based differences in rheological properties can be exploited to segregate mixtures of otherwise chemically similar polymers, e.g., in microfluidic devices, which is demonstrated by exposing a blend of flexible knotted and unknotted oligomer rings to channel flow.

cond-mat.soft↗

arXiv2024

Skyrmion flow in periodically modulated channels

Magnetic skyrmions, topologically stabilized chiral magnetic textures with particle-like properties have so far primarily been studied statically. Here, we experimentally investigate the dynamics of skyrmion ensembles in metallic thin film conduits where they behave as quasi-particle fluids. By exploiting our access to the full trajectories of all fluid particles by means of time-resolved magneto-optical Kerr microscopy, we demonstrate that boundary conditions of skyrmion fluids can be tuned by modulation of the channel geometry. We observe as a function of channel width deviations from classical flow profiles even into the no- or partial-slip regime. Unlike conventional colloids, the skyrmion Hall effect can also introduce transversal flow-asymmetries and even local motion of single skyrmions against the driving force which we explore with particle-based simulations, demonstrating the unique properties of skyrmion liquid flow that uniquely deviates from previously known behavior of other quasi-particles.

cond-mat.mes-hall↗

arXiv2023

Viscosity of flexible and semiflexible ring melts -- molecular origins and flow-induced segregation

We investigate with numerical simulations the molecular origin of viscosity in melts of flexible and semiflexible oligomer rings in comparison to corresponding systems with linear chains. The strong increase of viscosity with ring stiffness is linked to the formation of entangled clusters, which dissolve under shear. This shear-induced breakup and alignment of rings in the flow direction lead to pronounced shear-thinning and non-Newtonian behavior. In melts of linear chains, the viscosity can be associated with the (average) number of entanglements between chains, which also dissolve under shear. While blends of flexible and semiflexible rings are mixed at rest, the two species separate under flow. This phenomenon has potential applications in microfluidic devices to segregate ring polymers of similar mass and chemical composition by their bending rigidity.

cond-mat.soft↗

arXiv2022

Influence of ionic conditions on knotting in a coarse-grained model for DNA

We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers. We find that the occurrence of knots in DNA can be reinforced considerably by high salt conditions and confinement between plates. Likewise, knots can almost be dissolved completely in a low salt scenario. Comparisons with recent experiments confirm that the coarse-grained model is able to capture and quantitatively predict topological features of DNA and can be used for guiding future experiments on DNA knots.

cond-mat.soft↗

arXiv2022

Growth and aging in a few phase-separating active matter systems

Via computer simulations we study evolution dynamics in systems of continuously moving Active Brownian Particles. The obtained results are discussed against those from the passive 2D Ising case. Following sudden quenches of uniform configurations to state points lying within the miscibility gaps and to the critical points, we investigate the far-from-steady-state dynamics by calculating quantities associated with structure and characteristic length scales. We also study aging for quenches into the miscibility gap and provide a quantitative picture for the scaling behavior of the two-time order-parameter correlation function. The overall structure and dynamics are consistent with expectations from the Ising model. This remains true for certain active lattice models as well for which we present results for quenches to the critical points.

cond-mat.soft↗

arXiv2022

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.

q-bio.BM↗

arXiv2022

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 quasi particles evolving according to the Thiele equation. Interaction potentials are the key missing parameters for predictive modeling of experiments. We apply the Iterative Boltzmann Inversion technique commonly used in soft matter simulations 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. We find that the two interactions are purely repulsive and can be described by an exponential function for experimentally relevant skyrmions. This captures the physics on experimental time and length scales that are of interest for most skyrmion applications and typically inaccessible to atomistic or micromagnetic simulations.

cond-mat.mtrl-sci↗

arXiv2022

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 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.

cond-mat.mtrl-sci↗