arXiv subjects

Peter Virnau

Publications and source records attributed to Peter Virnau.

At least 37 records · Page 2Linked to original sources

arXiv2021

Knot formation of dsDNA pushed inside a nanochannel

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.

cond-mat.soft↗

arXiv2021

Circuits and excitations to enable Brownian token-based computing with skyrmions

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.

cond-mat.mes-hall↗

arXiv2021

Shear-thinning in Polymer Melts -- Molecular Origins and Hybrid Multiscale Simulations

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.

cond-mat.soft↗

arXiv2021

Commensurability between element symmetry and the number of skyrmions governing skyrmion diffusion in confined geometries

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.

cond-mat.mtrl-sci↗

arXiv2021

Skyrmion Lattice Phases in Thin Film Multilayer

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.

cond-mat.mtrl-sci↗

arXiv2021

Critical behaviour in active lattice models of motility-induced phase separation

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.

cond-mat.stat-mech↗

arXiv2018

Thermal skyrmion diffusion applied in probabilistic computing

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.

cond-mat.mtrl-sci↗

arXiv2018

Do the contact angle and line tension of surface-attached droplets depend on the radius of curvature?

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 $(Θ)$ 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 $[Θ(R)-Θ_{\infty}] \propto 1/R$, $Θ_{\infty}$ 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.

cond-mat.soft↗

arXiv2017

Critical behavior of active Brownian particles

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 $\text{Pe}_{\text{cr}}=40(2)$, $ϕ_{\text{cr}}=0.597(3)$. Based on this estimate, we study the corresponding critical exponents $β$, $γ/ν$, and $ν$. Our results are incompatible with the 2D-Ising exponents, thus raising the question whether there exists a corresponding non-equilibrium universality class.

cond-mat.soft↗

arXiv2017

Mapping onto ideal chains overestimates self-entanglements in polymer melts

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.

cond-mat.soft↗

arXiv2017

Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

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.

cond-mat.soft↗

arXiv2017

Free Energy Barriers for Crystal Nucleation from Fluid Phases

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 $ΔF^*=(4π/3)^{1/3}\barγ(V^*)^{2/3}+const.$ with the nucleus volume $V^*$, and the effective surface tension $\barγ$ that accounts implicitly for the nonspherical shape can be precisely estimated.

cond-mat.stat-mech↗

arXiv2016

Phase behavior of active Brownian disks, spheres, and dumbbells

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.

cond-mat.soft↗

arXiv2016

Estimation of the critical behavior in an active colloidal system with Vicsek-like interactions

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 $β$ and $ν$ is consistent with the underlying 3d-Ising universality class observed for the passive model.

cond-mat.soft↗

arXiv2016

Semiflexible Polymers Under Good Solvent Conditions Interacting With Repulsive Walls

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.

cond-mat.soft↗

arXiv2015

Crystal nuclei in melts: A Monte Carlo simulation of a model for attractive colloids

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.

cond-mat.soft↗

arXiv2015

Sequence determines degree of knottedness in a coarse-grained protein model

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.

cond-mat.soft↗

arXiv2015

Finite size effects on liquid-solid phase coexistence and the estimation of crystal nucleation barriers

A fluid in equilibrium in a finite volume $V$ with particle number $N$ at a density $ρ= N/V$ exceeding the onset density $ρ_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.

cond-mat.stat-mech↗