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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.

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., Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 161, 224905 (2024) and may be found at https://doi.org/10.1063/5.0236904

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., Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 161, 144904 (2024) and may be found at https://pubs.aip.org/aip/jcp/article/161/14/144904/3316214/Topological-comparison-of-flexible-and

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.

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.

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.

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., Comment: 9 pages, 11 figures

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., Comment: There were some errors in our manuscript such as mixing up data values from other published papers. Some clarifications were added

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.4380

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.

Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, 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., Comment: 5 pages, 3 figures

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., Comment: 8 pages, 5 figures; Authors to whom correspondence should be addressed: klaeui@uni-mainz.de, virnau@uni-mainz.de; Y.G. and J.R. contributed equally to this letter

Brownian computing exploits thermal motion of discrete signal carriers (tokens) for computations. In this paper we address two major challenges that hinder competitive realizations of circuits and application of Brownian token-based computing in actual devices for instance based on magnetic skyrmions. To overcome the problem that crossings generate for the fabrication of circuits, we design a crossing-free layout for a composite half-adder module. This layout greatly simplifies experimental implementations as wire crossings are effectively avoided. Additionally, our design is shorter to speed up computations compared to conventional designs. To address the key issue of slow computation based on thermal excitations, we propose to overlay artificial diffusion induced by an external excitation mechanism. For instance, if magnetic skyrmions are used as tokens, artificially induced diffusion by spin-orbit torques or other mechanisms increases the speed of computations by several orders of magnitude. Combined with conventional Brownian computing the latter could greatly enhance the application scenarios of token-based computing for instance for low power devices such as autonomous sensors with limited power that is harvested from the environment., Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Appl. Phys. Lett. 119, 132405 (2021) and may be found at https://doi.org/10.1063/5.0063584

We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. By performing simulations of single chains in a shear flow, we identify which of these phenomena are of collective nature and arise through interchain interactions and which are already present in dilute systems. Building upon these microscopic simulations we identify by means of the Irving-Kirkwood formula the corresponding macroscopic stress tensor for a non-Newtonian polymer fluid. Shear-thinning effects in oligomer melts are also demonstrated by macroscopic simulations of a channel flow. The latter have been obtained by the discontinuous Galerkin method approximating macroscopic polymer flows. Our study confirms the influence of microscopic details in the molecular structure of short polymers such as chain flexibility on macroscopic polymer flows.

Lattice models allow for a computationally efficient investigation of motility-induced phase separation (MIPS) compared to off-lattice systems. Simulations are less demanding and thus bigger systems can be accessed with higher accuracy and better statistics. In equilibrium, lattice and off-lattice models with comparable interactions belong to the same universality class. Whether concepts of universality also hold for active particles is still a controversial and open question. Here, we examine two recently proposed active lattice systems that undergo MIPS and investigate numerically their critical behaviour. In particular, we examine the claim that these systems and MIPS in general belong to the Ising universality class. We also take a more detailed look on the influence and role of rotational diffusion and active velocity in these systems.

Magnetic skyrmions are topological magnetic structures, which exhibit quasi-particle properties and can show enhanced stability against perturbation from thermal noise. Recently, thermal Brownian diffusion of these quasi-particles has been found in continuous films and applications in unconventional computing have received significant attention, which however require structured elements. Thus, as the next necessary step, we here study skyrmion diffusion in confined geometries and find it to be qualitatively different: The diffusion is governed by the interplay between the total number of skyrmions and the structure geometry. In particular, we ascertain the effect of circular and triangular geometrical confinement and find that for triangular geometries the behavior is drastically different for the cases when the number of skyrmions in the element is either commensurate or incommensurate with a symmetric filling of the element. This influence of commensurability is corroborated by simulations of a quasi-particle model., Comment: 21 pages, 3 figures

Phases of matter are ubiquitous with everyday examples including solids and liquids. In reduced dimensions, particular phases, such as the two-dimensional (2D) hexatic phase and corresponding phase transitions occur. A particularly exciting example of 2D ordered systems are skyrmion lattices, where in contrast to previously studied 2D colloid systems, the skyrmion size and density can be tuned by temperature and magnetic field. This allows us to drive the system from a liquid phase to a hexatic phase as deduced from the analysis of the hexagonal order. Using coarse-grained molecular dynamics simulations of soft disks, we determine the skyrmion interaction potentials and we find that the simulations are able to reproduce the full two-dimensional phase behavior. This shows that not only the static behavior of skyrmions is qualitatively well described in terms of a simple two-dimensional model system but skyrmion lattices are versatile and tunable two-dimensional model systems that allow for studying phases and phase transitions in reduced dimensions., Comment: Corrected Acknowledgements

We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics processing units. Chromosomes are represented by a string of connected beads, each of which corresponds to 100,000 base pairs, and contacts are mediated via a structure-based harmonic potential. We suggest and test two minimization protocols which consistently fold into conformationally similar low energy states. The latter are similar to previously published structures but are calculated in a fraction of the time. We find evidence that mere fulfillment of contact maps is insufficient to create experimentally relevant structures. Particularly, an excluded volume term is required in our model to induce the formation of chromosome territories. We also observe empirically that contact maps do not capture the chirality of the underlying structures. Depending on starting configurations and protocol details, one of two mirror images emerges. Finally, we analyze the occurrence of knots in a particular chromosome. The same knot appears in (almost) all structures irrespective of minimization protocols or even details of underlying potentials providing further evidence for the existence of knots in interphase chromatin., Comment: 18 pages, 7 figures. The updated submission contains additional explanations (for example) to the Go model and why we use this in the context of chromatin, we address the stopping criterion. References have been added as a result to an email received pointing us to publications we had not read before

Thermally activated processes are key to understanding the dynamics of physical systems. Thermal diffusion of (quasi-)particles for instance not only yields information on transport and dissipation processes but is also an exponentially sensitive tool to reveal emergent system properties and enable novel applications such as probabilistic computing. Here we probe the thermal dynamics of topologically stabilized magnetic skyrmion quasi-particles. We demonstrate in a specially tailored low pinning multilayer material system pure skyrmion diffusion that dominates the dynamics. Finally, we analyse the applicability to probabilistic computing by constructing a device, which uses the thermally excited skyrmion dynamics to reshuffle a signal. Such a skyrmion reshuffler is the key missing component for probabilistic computing and by evaluating its performance, we demonstrate the functionality of our device with high fidelity thus enabling probabilistic computing.

Results from Monte Carlo simulations of wall-attached droplets in the three-dimensional Ising lattice gas model and in a symmetric binary Lennard-Jones fluid, confined by antisymmetric walls, are analyzed, with the aim to estimate the dependence of the contact angle $(\Theta)$ on the droplet radius $(R)$ of curvature. Sphere-cap shape of the wall-attached droplets is assumed throughout. An approach, based purely on "thermodynamic" observables, e.g., chemical potential, excess density due to the droplet, etc., is used, to avoid ambiguities in the decision which particles belong (or do not belong, respectively) to the droplet. It is found that the results are compatible with a variation $[\Theta(R)-\Theta_{\infty}] \propto 1/R$, $\Theta_{\infty}$ being the contact angle in the thermodynamic limit ($R=\infty$). The possibility to use such results to estimate the excess free energy related to the contact line of the droplet, namely the line tension, at the wall, is discussed. Various problems that hamper this approach and were not fully recognized in previous attempts to extract the line tension are identified. It is also found that the dependence of wall tensions on the difference of chemical potential of the droplet from that at the bulk coexistence provides effectively a change of the contact angle of similar magnitude. The simulation approach yields precise estimates for the excess density due to wall-attached droplets and the corresponding free energy excess, relative to a system without a droplet at the same chemical potential. It is shown that this information suffices to estimate nucleation barriers, not affected by ambiguities on droplet shape, contact angle and line tension., Comment: 18 pages, 11 figures

We study active Brownian particles as a paradigm for genuine non-equilibrium phase transitions. Access to the critical point in computer simulations is obstructed by the fact that the density is conserved. We propose a modification of sampling finite-size fluctuations and successfully test this method for the 2D Ising model. Using this model allows us to determine accurately the critical point of two dimensional active Brownian particles at $\text{Pe}_{\text{cr}}=40(2)$, $\phi_{\text{cr}}=0.597(3)$. Based on this estimate, we study the corresponding critical exponents $\beta$, $\gamma/\nu$, and $\nu$. Our results are incompatible with the 2D-Ising exponents, thus raising the question whether there exists a corresponding non-equilibrium universality class.

In polymer physics it is typically assumed that excluded volume interactions are effectively screened in polymer melts. Hence, chains could be described by an effective random walk without excluded volume interactions. In this letter, we show that this mapping is problematic by analyzing the occurrence of knots, their spectrum and sizes in polymer melts, corresponding random walks and chains in dilute solution. The effective random walk severely overrates the occurrence of knots and their complexity, particularly when compared to melts of flexible chains, indicating that non-trivial effects due to remnants of self-avoidance still play a significant role for the chain lengths considered in this numerical study. For melts of semiflexible chains, the effect is less pronounced. In addition, we find that chains in a melt are very similar in structure and topology to dilute single chains close to the collapse transition, which indicates that the latter are also not well-represented by random walks. We finally show that typical equilibration procedures are well-suited to relax the topology in melts.

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We also propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations., Comment: 14 pages, 15 figures

Monte Carlo simulations of crystal nuclei coexisting with the fluid phase in thermal equilibrium in finite volumes are presented and analyzed, for fluid densities from dense melts to the vapor. Generalizing the lever-rule for two-phase coexistence in the canonical ensemble to finite volume, "measurements" of the nucleus volume together with the pressure and chemical potential of the surrounding fluid allows to extract the surface free energy of the nucleus. Neither the knowledge of the (in general non-spherical) nucleus shape nor of the angle-dependent interface tension is required for this task. The feasibility of the approach is demonstrated for a variant of the Asakura-Oosawa model for colloid-polymer mixtures, which form face-centered cubic colloidal crystals. For a polymer to colloid size ratio of $0.15$, the colloid packing fraction in the fluid phase can be varied from melt values to zero by the variation of an effective attractive potential between the colloids. It is found that the approximation of spherical crystal nuclei often underestimates actual nucleation barriers significantly. Nucleation barriers are found to scale as $\Delta F^*=(4\pi/3)^{1/3}\bar{\gamma}(V^*)^{2/3}+const.$ with the nucleus volume $V^*$, and the effective surface tension $\bar{\gamma}$ that accounts implicitly for the nonspherical shape can be precisely estimated., Comment: 17 pages, 17 figures

In this paper we provide high precision estimates of the phase diagram of active Brownian particles. We extract coexisting densities from simulations of phase separated states in an elongated box (slab geometry) which minimizes finite-size effects and allows for precise determination of points on the binodal lines. Using this method, we study the influence of both shape and dimensionality on the two-phase region. Active spheres and dumbbells of active particles are compared to the known phase diagram of active Brownian disks. In the case of dimers, both correlated and uncorrelated propulsion of the two beads are studied. The influence of correlation is discussed through a simple mapping.

We study numerically the critical behavior of a modified, active Asakura-Oosawa model for colloid-polymer mixtures. The colloids are modeled as self-propelled particles with Vicsek-like interactions. This system undergoes phase separation between a colloid-rich and a polymer-rich phase, whereby the phase diagram depends on the strength of the Vicsek-like interactions. Employing a subsystem-block-density distribution analysis, we determine the critical point and make an attempt to estimate the critical exponents. In contrast to the passive model, we find that the critical point is not located on the rectilinear diameter. A first estimate of the critical exponents $\beta$ and $\nu$ is consistent with the underlying 3d-Ising universality class observed for the passive model., Comment: 9 pages, 8 figures

Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion caused by the monomer-wall repulsion. A coarse-grained bead-spring model with bond bending potential is studied, varying both the contour length and the persistence length of the polymers, as well as the monomer concentration in the solution (good solvent conditions are assumed throughout, and solvent molecules are not included explicitly). The profiles of monomer density and pressure tensor components near the wall are studied, and the surface tension of the solution is obtained. While the surface tension slightly decreases with chain length for flexible polymers, it clearly increases with chain length for stiff polymers. Thus, at fixed density and fixed chain length the surface tension also increases with increasing persistence length. Chain ends always are enriched near the wall, but this effect is much larger for stiff polymers than for flexible ones. Also the profiles of the mean square gyration radius components near the wall and the nematic order parameter are studied to clarify the conditions where wall-induced nematic order occurs., Comment: 17 pages, 24 figures

As a model for a suspension of hard-sphere like colloidal particles where small nonadsorbing dissolved polymers create a depletion attraction, we introduce an effective colloid-colloid potential closely related to the Asakura-Oosawa model but that does not have any discontinuities. In simulations, this model straightforwardly allows the calculation of the pressure from the Virial formula, and the phase transition in the bulk from the liquid to crystalline solid can be accurately located from a study where a stable coexistence of a crystalline slab with a surrounding liquid phase occurs. For this model, crystalline nuclei surrounded by fluid are studied both by identifying the crystal-fluid interface on the particle level (using suitable bond orientational order parameters to distinguish the phases) and by "thermodynamic" means. I.e., the latter method amounts to compute the enhancement of chemical potential and pressure relative to their coexistence values. We show that the chemical potential can be obtained from simulating thick films, where one wall with a rather long range repulsion is present, since near this wall the Widom particle insertion method works, exploiting the fact that the chemical potential in the system is homogeneous. Finally, the surface excess free energy of the nucleus is obtained, for a wide range of nuclei volumes. From this method, it is established that classical nucleation theory works, showing that for the present model the anisotropy of the interface excess free energy of crystals and their resulting nonspherical shape has only a very small effect on the barrier.

Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar (HP) lattice protein model. By employing large scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that, even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.

A fluid in equilibrium in a finite volume $V$ with particle number $N$ at a density $\rho = N/V$ exceeding the onset density $\rho_f $ of freezing may exhibit phase coexistence between a crystalline nucleus and surrounding fluid. Using a method suitable for the estimation of the chemical potential of dense fluids we obtain the excess free energy due to the surface of the crystalline nucleus. There is neither a need to precisely locate the interface nor to compute the (anisotropic) interfacial tension. As a test case, a soft version of the Asakura-Oosawa model for colloid polymer-mixtures is treated. While our analysis is appropriate for crystal nuclei of arbitrary shape, we find the nucleation barrier to be compatible with a spherical shape, and consistent with classical nucleation theory., Comment: printed in Physical Review Letters,2015

Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing $3_1$, $5_1$ knots and catenanes made up of two unknotted rings scale like $N^{1/3}$ in the limit of large ring sizes $N$. This is consistent with the crumpled globule model and similar findings for unknotted rings. For small ring lengths knots occupy a significant fraction of the ring. The scaling of typical ring sizes for small $N$ thus depends on the particular knot type and the exponent is generally larger than 0.4., Comment: 5 pages, 5 figures

As a generic example for crystals where the crystal-fluid interface tension depends on the orientation of the interface relative to the crystal lattice axes, the nearest neighbor Ising model on the simple cubic lattice is studied over a wide temperature range, both above and below the roughening transition temperature. Using a thin film geometry $L_x \times L_y \times L_z$ with periodic boundary conditions along the z-axis and two free $L_x \times L_y$ surfaces at which opposing surface fields $\pm H_{1}$ act, under conditions of partial wetting, a single planar interface inclined under a contact angle $\theta < \pi/2$ relative to the yz-plane is stabilized. In the y-direction, a generalization of the antiperiodic boundary condition is used that maintains the translational invariance in y-direction despite the inhomogeneity of the magnetization distribution in this system. This geometry allows a simultaneous study of the angle-dependent interface tension, the contact angle, and the line tension (which depends on the contact angle, and on temperature). All these quantities are extracted from suitable thermodynamic integration procedures. In order to keep finite size effects as well as statistical errors small enough, rather large lattice sizes (of the order of 46 million sites) are found necessary, availability of very efficient code implementation of graphics processing units (GPUs) was crucial for the feasibility of this study., Comment: 22 pages, 14 figures

We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of knots on a single DNA strand., Comment: 6 pages, 7 figures

The computation of interfacial free energies between coexisting phases (e.g.~saturated vapor and liquid) by computer simulation methods is still a challenging problem due to the difficulty of an atomistic identification of an interface, and due to interfacial fluctuations on all length scales. The approach to estimate the interfacial tension from the free energy excess of a system with interfaces relative to corresponding single-phase systems does not suffer from the first problem but still suffers from the latter. Considering $d$-dimensional systems with interfacial area $L^{d-1}$ and linear dimension $L_z$ in the direction perpendicular to the interface, it is argued that the interfacial fluctuations cause logarithmic finite-size effects of order $\ln (L) / L^{d-1}$ and order $\ln (L_z)/L ^{d-1}$, in addition to regular corrections (with leading order $\text{const}/L^{d-1}$). A phenomenological theory predicts that the prefactors of the logarithmic terms are universal (but depend on the applied boundary conditions and the considered statistical ensemble). The physical origin of these corrections are the translational entropy of the interface as a whole, "domain breathing" (coupling of interfacial fluctuations to the bulk order parameter fluctuations of the coexisting domains), and capillary waves. Using a new variant of the ensemble switch method, interfacial tensions are found from Monte Carlo simulations of $d=2$ and $d=3$ Ising models and a Lennard Jones fluid. The simulation results are fully consistent with the theoretical predictions., Comment: 27 pages, 16 figures

The ensemble-switch method for computing wall excess free energies of condensed matter is extended to estimate the interface free energies between coexisting phases very accurately. By this method, system geometries with linear dimensions $L$ parallel and $L_z$ perpendicular to the interface with various boundary conditions in the canonical or grandcanonical ensemble can be studied. Using two- and three-dimensional Ising models, the nature of the occurring logarithmic finite size corrections is studied. It is found crucial to include interfacial fluctuations due to "domain breathing"., Comment: 5 pages, 4 figures

We study the structure and phase behavior of a binary mixture where one of the components is self-propelling in nature. The inter-particle interactions in the system were taken from the Asakura-Oosawa model, for colloid-polymer mixtures, for which the phase diagram is known. In the current model version the colloid particles were made active using the Vicsek model for self-propelling particles. The resultant active system was studied by molecular dynamics methods and integral equation theory. Both methods produce results consistent with each other and demonstrate that the Vicsek model based activity facilitates phase separation, thus broadening the coexistence region., Comment: 5 figures, 5 pages

The conventional theory of homogeneous and heterogeneous nucleation in a supersaturated vapor is tested by Monte Carlo simulations of the lattice gas (Ising) model with nearest-neighbor attractive interactions on the simple cubic lattice. The theory considers the nucleation process as a slow (quasi-static) cluster (droplet) growth over a free energy barrier $\Delta F^*$, constructed in terms of a balance of surface and bulk term of a "critical droplet" of radius $R^*$, implying that the rates of droplet growth and shrinking essentially balance each other for droplet radius $R=R^*$. For heterogeneous nucleation at surfaces, the barrier is reduced by a factor depending on the contact angle. Using the definition of "physical" clusters based on the Fortuin-Kasteleyn mapping, the time-dependence of the cluster size distribution is studied for "quenching experiments" in the kinetic Ising model, and the cluster size $\ell ^*$ where the cluster growth rate changes sign is estimated. These studies of nucleation kinetics are compared to studies where the relation between cluster size and supersaturation is estimated from equilibrium simulations of phase coexistence between droplet and vapor in the canonical ensemble. The chemical potential is estimated from a lattice version of the Widom particle insertion method. For large droplets it is shown that the "physical clusters" have a volume consistent with the estimates from the lever rule. "Geometrical clusters" (defined such that each site belonging to the cluster is occupied and has at least one occupied neighbor site) yield valid results only for temperatures less than 60% of the critical temperature, where the cluster shape is non-spherical. We show how the chemical potential can be used to numerically estimate $\Delta F^*$ also for non-spherical cluster shapes., Comment: accepted for Physical Review E, 2013

The Asakura-Oosawa model for colloid-polymer mixtures is studied by Monte Carlo simulations at densities inside the two-phase coexistence region of fluid and solid. Choosing a geometry where the system is confined between two flat walls, and a wall-colloid potential that leads to incomplete wetting of the crystal at the wall, conditions can be created where a single nanoscopic wall-attached crystalline cluster coexists with fluid in the remainder of the simulation box. Following related ideas that have been useful to study heterogeneous nucleation of liquid droplets at the vapor-liquid coexistence, we estimate the contact angles from observations of the crystalline clusters in thermal equilibrium. We find fair agreement with a prediction based on Young's equation, using estimates of interface and wall tension from the study of flat surfaces. It is shown that the pressure versus density curve of the finite system exhibits a loop, but the pressure maximum signifies the "droplet evaporation-condensation" transition and thus has nothing in common with a van der Waals-like loop. Preparing systems where the packing fraction is deep inside the two-phase coexistence region, the system spontaneously forms a "slab state", with two wall-attached crystalline domains separated by (flat) interfaces from liquid in full equilibrium with the crystal in between; analysis of such states allows a precise estimation of the bulk equilibrium properties at phase coexistence.

Langevin Dynamics simulations are used to study the effect of shear on a two-dimensional colloidal crystal confined by structured parallel walls. When walls are sheared very slowly, only two or three crystalline layers next to the walls move along with them, while the inner layers of the crystal are only slightly tilted. At higher shear velocities, this inner part of the crystal breaks into several pieces with different orientations. The velocity profile across the slit is reminiscent of shear-banding in flowing soft materials, where liquid and solid regions coexist; the difference, however, is that in the latter case the solid regions are glassy while here they are crystalline. At even higher shear velocities, the effect of the shearing becomes smaller again. Also the effective temperature near the walls (deduced from the velocity distributions of the particles) decreases again when the wall velocity gets very large. When the walls are placed closer together, thereby introducing a misfit, a structure containing a soliton staircase arises in simulations without shear. Introducing shear increases the disorder in these systems until no solitons are visible any more. Instead, similar structures like in the case without misfit result. At high shear rates, configurations where the incommensurability of the crystalline structure is compensated by the creation of holes become relevant.

Colloidal systems are often modelled as fluids of hard particles (possibly with an additional soft attraction, e.g. caused by polymers also contained in the suspension). in simulations of such systems, the virial theorem cannot be straightforwardly applied to obtain the components of the pressure tensor. In systems confined by walls, it is hence also not straightforward to extract the excess energy due to the wall (the "wall tension") from the pressure tensor anisotropy. A comparative evaluation of several methods to circumvent this problem is presented, using as examples fluids of hard spheres and the Asakura-Oosawa model of colloid-polymer mixtures with a size ratio $q=0.15$ (for which the effect of the polymers can be integrated out to yield an effective attractive potential between the colloids). Factors limiting the accuracy of the various methods are carefully discussed, and controlling these factors very good mutual agreement between the various methods is found., Comment: 15 pages, 6 figures

A comparative simulation study of polymer brushes formed by grafting at a planar surface either flexible linear polymers (chain length $N_L$) or (non-catenated) ring polymers (chain length $N_R=2 N_L$) is presented. Two distinct off-lattice models are studied, one by Monte Carlo methods, the other by Molecular Dynamics, using a fast implementation on graphics processing units (GPUs). It is shown that the monomer density profiles $\rho(z)$ in the $z$-direction perpendicular to the surface for rings and linear chains are practically identical, $\rho_R(2 N_L, z)=\rho_L(N_L, z)$. The same applies to the pressure, exerted on a piston at hight z, as well. While the gyration radii components of rings and chains in $z$-direction coincide, too, and increase linearly with $N_L$, the transverse components differ, even with respect to their scaling properties: $R_{gxy}^{(L)} \propto N_L^{1/2}$, $R_{gxy}^{(R)} \propto N_L^{0.4}$. These properties are interpreted in terms of the statistical properties known for ring polymers in dense melts., Comment: 13 pages, 4 figures

Hard-sphere fluids confined between parallel plates a distance $D$ apart are studied for a wide range of packing fractions, including also the onset of crystallization, applying Monte Carlo simulation techniques and density functional theory. The walls repel the hard spheres (of diameter $\sigma$) with a Weeks-Chandler-Andersen (WCA) potential $V_{WCA}(z) = 4 \epsilon [(\sigma_w/z)^{12}-(\sigma_w/z)^6 + 1/4]$, with range $\sigma_w = \sigma/2$. We vary the strength $\epsilon$ over a wide range and the case of simple hard walls is also treated for comparison. By the variation of $\epsilon$ one can change both the surface excess packing fraction and the wall-fluid $(\gamma_{wf})$ and wall-crystal $(\gamma_{wc})$ surface free energies. Several different methods to extract $\gamma_{wf}$ and $\gamma_{wc}$ from Monte Carlo (MC) simulations are implemented, and their accuracy and efficiency is comparatively discussed. The density functional theory (DFT) using Fundamental Measure functionals is found to be quantitatively accurate over a wide range of packing fractions; small deviations between DFT and MC near the fluid to crystal transition need to be studied further. Our results on density profiles near soft walls could be useful to interpret corresponding experiments with suitable colloidal dispersions., Comment: 23 pages, 7 ps, eps figures

Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal growth, etc.). This article reviews two methods to estimate both interfacial free energies and line tensions by Monte Carlo simulations of simple models, (e.g. the Ising model, a symmetrical binary Lennard-Jones fluid exhibiting a miscibility gap, and a simple Lennard-Jones fluid). One method is based on thermodynamic integration. This method is useful to study flat and inclined interfaces for Ising lattices, allowing also the estimation of line tensions of three-phase contact lines, when the interfaces meet walls (where "surface fields" may act). A generalization to off-lattice systems is described as well. The second method is based on the sampling of the order parameter distribution of the system throughout the two-phase coexistence region of the model. Both the interface free energies of flat interfaces and of (spherical or cylindrical) droplets (or bubbles) can be estimated, including also systems with walls, where sphere-cap shaped wall-attached droplets occur. The curvature-dependence of the interfacial free energy is discussed, and estimates for the line tensions are compared to results from the thermodynamic integration method. Basic limitations of all these methods are critically discussed, and an outlook on other approaches is given.

Employing Molecular Dynamics simulations of a chemically realistic model of 1,4-polybutadiene between graphite walls we show that the mass exchange between layers close to the walls is a slow process already in the melt state. For the glass transition of confined polymers this process competes with the slowing down due to packing effects and intramolecular rotation barriers.

We study the excess free energy due to phase coexistence of fluids by Monte Carlo simulations using successive umbrella sampling in finite LxLxL boxes with periodic boundary conditions. Both the vapor-liquid phase coexistence of a simple Lennard-Jones fluid and the coexistence between A-rich and B-rich phases of a symmetric binary (AB) Lennard-Jones mixture are studied, varying the density rho in the simple fluid or the relative concentration x_A of A in the binary mixture, respectively. The character of phase coexistence changes from a spherical droplet (or bubble) of the minority phase (near the coexistence curve) to a cylindrical droplet (or bubble) and finally (in the center of the miscibility gap) to a slab-like configuration of two parallel flat interfaces. Extending the analysis of M. Schrader, P. Virnau, and K. Binder [Phys. Rev. E 79, 061104 (2009)], we extract the surface free energy gamma (R) of both spherical and cylindrical droplets and bubbles in the vapor-liquid case, and present evidence that for R -> Infinity the leading order (Tolman) correction for droplets has sign opposite to the case of bubbles, consistent with the Tolman length being independent on the sign of curvature. For the symmetric binary mixture the expected non-existence of the Tolman length is confirmed. In all cases {and for a range of radii} R relevant for nucleation theory, gamma(R) deviates strongly from gamma (Infinity) which can be accounted for by a term of order gamma(Infinity)/gamma(R)-1 ~ 1/R^2. Our results for the simple Lennard-Jones fluid are also compared to results from density functional theory and we find qualitative agreement in the behavior of gamma(R) as well as in the sign and magnitude of the Tolman length., Comment: 25 pages, submitted to J. Chem. Phys

A modern graphics processing unit (GPU) is able to perform massively parallel scientific computations at low cost. We extend our implementation of the checkerboard algorithm for the two dimensional Ising model [T. Preis et al., J. Comp. Phys. 228, 4468 (2009)] in order to overcome the memory limitations of a single GPU which enables us to simulate significantly larger systems. Using multi-spin coding techniques, we are able to accelerate simulations on a single GPU by factors up to 35 compared to an optimized single Central Processor Unit (CPU) core implementation which employs multi-spin coding. By combining the Compute Unified Device Architecture (CUDA) with the Message Parsing Interface (MPI) on the CPU level, a single Ising lattice can be updated by a cluster of GPUs in parallel. For large systems, the computation time scales nearly linearly with the number of GPUs used. As proof of concept we reproduce the critical temperature of the 2D Ising model using finite size scaling techniques.

Phase transitions of systems confined in long cylindrical pores (capillary condensation, wetting, crystallization, etc.) are intrinsically not sharply defined but rounded. The finite size of the cross section causes destruction of long range order along the pore axis by spontaneous nucleation of domain walls. This rounding is analyzed for two models (Ising/lattice gas and Asakura-Oosawa model for colloid-polymer mixtures) by Monte Carlo simulations and interpreted by a phenomenological theory. We show that characteristic differences between the behavior of pores of finite length and infinitely long pores occur. In pores of finite length a rounded transition occurs first, from phase coexistence between two states towards a multi-domain configuration. A second transition to the axially homogeneous phase follows near pore criticality., Comment: PRL, accepted