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Jan Kierfeld

Publications and source records attributed to Jan Kierfeld.

At least 37 records · Page 2Linked to original sources
arXiv2017

Event-chain Monte Carlo algorithms for three- and many-particle interactions

We generalize the rejection-free event-chain Monte Carlo algorithm from many particle systems with pairwise interactions to systems with arbitrary three- or many-particle interactions. We introduce generalized lifting probabilities between particles and obtain a general set of equations for lifting probabilities, the solution of which guarantees maximal global balance. We validate the resulting three-particle event-chain Monte Carlo algorithms on three different systems by comparison with conventional local Monte Carlo simulations: (i) a test system of three particles with a three-particle interaction that depends on the enclosed triangle area; (ii) a hard-needle system in two dimensions, where needle interactions constitute three-particle interactions of the needle end points; (iii) a semiflexible polymer chain with a bending energy, which constitutes a three-particle interaction of neighboring chain beads. The examples demonstrate that the generalization to many-particle interactions broadens the applicability of event-chain algorithms considerably.

cond-mat.stat-mech↗
arXiv2015

Shapes of sedimenting soft elastic capsules in a viscous fluid

Soft elastic capsules which are driven through a viscous fluid undergo shape deformation coupled to their motion. We introduce an iterative solution scheme which couples hydrodynamic boundary integral methods and elastic shape equations to find the stationary axisymmetric shape and the velocity of an elastic capsule moving in a viscous fluid at low Reynolds numbers. We use this approach to systematically study dynamical shape transitions of capsules with Hookean stretching and bending energies and spherical rest shape sedimenting under the influence of gravity or centrifugal forces. We find three types of possible axisymmetric stationary shapes for sedimenting capsules with fixed volume: a pseudospherical state, a pear-shaped state, and buckled shapes. Capsule shapes are controlled by two dimensionless parameters, the Föppl-von-Kármán number characterizing the elastic properties and a Bond number characterizing the driving force. For increasing gravitational force the spherical shape transforms into a pear shape. For very large bending rigidity (very small Föppl-von-Kármán number) this transition is discontinuous with shape hysteresis. The corresponding transition line terminates, however, in a critical point, such that the discontinuous transition is not present at typical Föppl-von-Kármán numbers of synthetic capsules. In an additional bifurcation, buckled shapes occur upon increasing the gravitational force. This type of instability should be observable for generic synthetic capsules. All shape bifurcations can be resolved in the force-velocity relation of sedimenting capsules, where up to three capsule shapes with different velocities can occur for the same driving force. All three types of possible axisymmetric stationary shapes are stable with respect to rotation during sedimentation.

cond-mat.soft↗
arXiv2015

Controlling adsorption of semiflexible polymers on planar and curved substrates

We study the adsorption of semiflexible polymers such as polyelectrolytes or DNA on planar and curved substrates, e.g., spheres or washboard substrates via short-range potentials using extensive Monte-Carlo simulations, scaling arguments, and analytical transfer matrix techniques. We show that the adsorption threshold of stiff or semiflexible polymers on a planar substrate can be controlled by polymer stiffness: adsorption requires the highest potential strength if the persistence length of the polymer matches the range of the adsorption potential. On curved substrates, i.e., an adsorbing sphere or an adsorbing washboard surface, the adsorption can be additionally controlled by the curvature of the surface structure. The additional bending energy in the adsorbed state leads to an increase of the critical adsorption strength, which depends on the curvature radii of the substrate structure. For an adsorbing sphere, this gives rise to an optimal polymer stiffness for adsorption, i.e., a local minimum in the critical potential strength for adsorption, which can be controlled by curvature. For two- and three-dimensional washboard substrates, we identify the range of persistence lengths and the mechanisms for an effective control of the adsorption threshold by the substrate curvature.

cond-mat.soft↗
arXiv2015

Monte Carlo Simulation of Dense Polymer Melts Using Event Chain Algorithms

We propose an efficient Monte Carlo algorithm for the off-lattice simulation of dense hard sphere polymer melts using cluster moves, called event chains, which allow for a rejection-free treatment of the excluded volume. Event chains also allow for an efficient preparation of initial configurations in polymer melts. We parallelize the event chain Monte Carlo algorithm to further increase simulation speeds and suggest additional local topology-changing moves ("swap" moves) to accelerate equilibration. By comparison with other Monte Carlo and molecular dynamics simulations, we verify that the event chain algorithm reproduces the correct equilibrium behavior of polymer chains in the melt. By comparing intrapolymer diffusion time scales, we show that event chain Monte Carlo algorithms can achieve simulation speeds comparable to optimized molecular dynamics simulations. The event chain Monte Carlo algorithm exhibits Rouse dynamics on short time scales. In the absence of swap moves, we find reptation dynamics on intermediate time scales for long chains.

cond-mat.soft↗
arXiv2015

Elasticity of Interfacial Rafts of Hard Particles with Soft Shells

We study an elasticity model for compressed protein monolayers or particle rafts at a liquid interface. Based on the microscopic view of hard-core particles with soft shells, a bead-spring model is formulated and analyzed in terms of continuum elasticity theory. The theory can be applied, for example, to hydrophobin-coated air-water interfaces or, more generally, to liquid interfaces coated with an adsorbed monolayer of interacting hard-core particles. We derive constitutive relations for such particle rafts and describe the buckling of compressed planar liquid interfaces as well as their apparent Poisson ratio. We also use the constitutive relations to obtain shape equations for pendant or buoyant capsules attached to a capillary, and to compute deflated shapes of such capsules. A comparison with capsules obeying the usual Hookean elasticity (without hard cores) reveals that the hard cores trigger capsule wrinkling. Furthermore, it is shown that a shape analysis of deflated capsules with hard-core/soft-shell elasticity gives apparent elastic moduli which can be much higher than the original values if Hookean elasticity is assumed.

cond-mat.soft↗
arXiv2014

Feedback Mechanism for Microtubule Length Regulation by Stathmin Gradients

We formulate and analyze a theoretical model for the regulation of microtubule (MT) polymerization dynamics by the signaling proteins Rac1 and stathmin. In cells, the MT growth rate is inhibited by cytosolic stathmin, which, in turn, is inactivated by Rac1. Growing MTs activate Rac1 at the cell edge, which closes a positive feedback loop. We investigate both tubulin sequestering and catastrophe promotion as mechanisms for MT growth inhibition by stathmin. For a homogeneous stathmin concentration in the absence of Rac1, we find a switch-like regulation of the MT mean length by stathmin. For constitutively active Rac1 at the cell edge, stathmin is deactivated locally, which establishes a spatial gradient of active stathmin. In this gradient, we find a stationary bimodal MT length distributions for both mechanisms of MT growth inhibition by stathmin. One subpopulation of the bimodal length distribution can be identified with fast growing and long pioneering MTs in the region near the cell edge, which have been observed experimentally. The feedback loop is closed through Rac1 activation by MTs. For tubulin sequestering by stathmin, this establishes a bistable switch with two stable states: one stable state corresponds to upregulated MT mean length and bimodal MT length distributions, i.e., pioneering MTs; the other stable state corresponds to an interrupted feedback with short MTs. Stochastic effects as well as external perturbations can trigger switching events. For catastrophe promoting stathmin we do not find bistability.

q-bio.SC↗
arXiv2014

Parallelized event chain algorithm for dense hard sphere and polymer systems

We combine parallelization and cluster Monte Carlo for hard sphere systems and present a parallelized event chain algorithm for the hard disk system in two dimensions. For parallelization we use a spatial partitioning approach into simulation cells. We find that it is crucial for correctness to ensure detailed balance on the level of Monte Carlo sweeps by drawing the starting sphere of event chains within each simulation cell with replacement. We analyze the performance gains for the parallelized event chain and find a criterion for an optimal degree of parallelization. Because of the cluster nature of event chain moves massive parallelization will not be optimal. Finally, we discuss first applications of the event chain algorithm to dense polymer systems, i.e., bundle-forming solutions of attractive semiflexible polymers.

cond-mat.stat-mech↗
arXiv2014

Osmotic buckling of spherical capsules

We study the buckling of elastic spherical shells under osmotic pressure with the osmolyte concentration of the exterior solution as control parameter. We compare our results for the bifurcation behavior with results for buckling under mechanical pressure control, that is, with an empty capsule interior. We find striking differences for the buckling states between osmotic and mechanical buckling. Mechanical pressure control always leads to fully collapsed states with opposite sides in contact, whereas uncollapsed states with a single finite dimple are generic for osmotic pressure control. For sufficiently large interior osmolyte concentrations, osmotic pressure control is qualititatively similar to buckling under volume control with the volume prescribed by the osmolyte concentrations inside and outside the shell. We present a quantitative theory which also captures the influence of shell elasticity on the relation between osmotic pressure and volume. These findings are relevant for the control of buckled shapes in applications. We show how the osmolyte concentration can be used to control the volume of buckled shells. An accurate analytic formula is derived for the relation between the osmotic pressure, the elastic moduli and the volume of buckled capsules. This also allows to use elastic capsules as osmotic pressure sensors or to deduce elastic properties and the internal osmolyte concentration from shape changes in response to osmotic pressure changes. We apply our findings to published experimental data on polyelectrolyte capsules.

cond-mat.soft↗
arXiv2014

The secondary buckling transition: wrinkling of buckled spherical shells

We theoretically explain the complete sequence of shapes of deflated spherical shells. Decreasing the volume, the shell remains spherical initially, then undergoes the classical buckling instability, where an axisymmetric dimple appears, and, finally, loses its axisymmetry by wrinkles developing in the vicinity of the dimple edge in a secondary buckling transition. We describe the first axisymmetric buckling transition by numerical integration of the complete set of shape equations and an approximate analytic model due to Pogorelov. In the buckled shape, both approaches exhibit a locally compressive hoop stress in a region where experiments and simulations show the development of polygonal wrinkles, along the dimple edge. In a simplified model based on the stability equations of shallow shells, a critical value for the compressive hoop stress is derived, for which the compressed circumferential fibres will buckle out of their circular shape in order to release the compression. By applying this wrinkling criterion to the solutions of the axisymmetric models, we can calculate the critical volume for the secondary buckling transition. Using the Pogorelov approach, we also obtain an analytical expression for the critical volume at the secondary buckling transition: The critical volume difference scales linearly with the bending stiffness, whereas the critical volume reduction at the classical axisymmetric buckling transition scales with the square root of the bending stiffness. These results are confirmed by another stability analysis in the framework of Donnel, Mushtari and Vlasov (DMV) shell theory, and by numerical simulations available in the literature.

cond-mat.soft↗
arXiv2014

Depinning of stiff directed lines in random media

Driven elastic manifolds in random media exhibit a depinning transition to a state with non-vanishing velocity at a critical driving force. We study the depinning of stiff directed lines, which are governed by a bending rigidity rather than line tension. Their equation of motion is the (quenched) Herring-Mullins equation, which also describes surface growth governed by surface diffusion. Stiff directed lines are particularly interesting as there is a localization transition in the static problem at a finite temperature and the commonly exploited time ordering of states by means of Middleton's theorems (A. Middleton, Phys. Rev. Lett. 68, 670 (1992)) is not applicable. We employ analytical arguments and numerical simulations to determine the critical exponents and compare our findings with previous works and functional renormalization group results, which we extend to the different line elasticity. We see evidence for two distinct correlation length exponents.

cond-mat.stat-mech↗
arXiv2014

Secondary polygonal instability of buckled spherical shells

When a spherical elastic capsule is deflated, it first buckles axisymmetrically and subsequently loses its axisymmetry in a secondary instability, where the dimple acquires a polygonal shape. We explain this secondary polygonal buckling in terms of wrinkles developing at the inner side of the dimple edge in response to compressive hoop stress. Analyzing the axisymmetric buckled shape, we find a compressive hoop stress with parabolic stress profile at the dimple edge. We further show that there exists a critical value for this hoop stress, where it becomes favorable for the membrane to buckle out of its axisymmetric shape, thus releasing the compression. The instability mechanism is analogous to the formation of wrinkles under compressive stress. A simplified stability analysis allows us to quantify the critical stress for secondary buckling. Applying this secondary buckling criterion to the axisymmetric shapes, we can determine the critical volume for secondary buckling. Our analytical result is in close agreement with existing numerical data.

cond-mat.soft↗
arXiv2014

Effects of microtubule mechanics on hydrolysis and catastrophes

We introduce a model for microtubule mechanics containing lateral bonds between dimers in neighboring protofilaments, bending rigidity of dimers, and repulsive interactions between protofilaments modeling steric constraints to investigate the influence of mechanical forces on hydrolysis and catastrophes. We use the allosteric dimer model, where tubulin dimers are characterized by an equilibrium bending angle, which changes from $0^\circ$ to $22^\circ$ by hydrolysis of a dimer. This also affects the lateral interaction and bending energies and, thus, the mechanical equilibrium state of the microtubule. As hydrolysis gives rise to conformational changes in dimers, mechanical forces also influence the hydrolysis rates by mechanical energy changes modulating the hydrolysis rate. The interaction via the microtubule mechanics then gives rise to correlation effects in the hydrolysis dynamics, which have not been taken into account before. Assuming a dominant influence of mechanical energies on hydrolysis rates, we investigate the most probable hydrolysis pathways both for vectorial and random hydrolysis. Investigating the stability with respect to lateral bond rupture, we identify initiation configurations for catastrophes along the hydrolysis pathways and values for a lateral bond rupture force. If we allow for rupturing of lateral bonds between dimers in neighboring protofilaments above this threshold force, our model exhibits avalanche-like catastrophe events.

q-bio.SC↗
arXiv2014

Wrinkling of Random and Regular Semiflexible Polymer Networks

We investigate wrinkling of two-dimensional random and triangular semiflexible polymer networks under shear. Both types of semiflexible networks exhibit wrinkling above a small critical shear angle, which scales with an exponent of the bending modulus between 1.9 and 2.0. Random networks exhibit hysteresis at the wrinkling threshold. Wrinkling lowers the total elastic energy by up to 20% and strongly affects the elastic properties of all semiflexible networks such as the crossover between bending and stretching dominated behavior. In random networks, we also find evidence for metastable wrinkled configurations. While the disordered microstructure of random networks affects the scaling behavior of wrinkle amplitudes, it has little effect on wrinkle wavelength. Therefore, wrinkles represent a robust, microstructure-independent assay of shear strain or elastic properties.

cond-mat.soft↗
arXiv2014

Semiflexible polymer rings on topographically and chemically structured surfaces

We investigate morphologies of semiflexible polymer rings, such as circular DNA, which are adsorbed onto topographically or chemically structured substrate surfaces. We classify all equilibrium morphologies for two striped surface structures, (i) topographical surface grooves and (ii) chemically structured surface domains. For both types of stripes, we find four equilibrium shapes: a round toroidal and a confined elongated shape as well as two shapes containing bulges. We determine the complete bifurcation diagram of these morphologies as a function of their contour length and the ratio of adhesive strength to bending rigidity. For more complex geometries consisting of several stripes we find a cascade of transitions between elongated shapes. Finally, we compare our findings to ring condensation by attractive interactions.

cond-mat.soft↗
arXiv2013

Elastometry of Deflated Capsules: Elastic Moduli from Shape and Wrinkle Analysis

Elastic capsules, prepared from droplets or bubbles attached to a capillary (as in a pendant drop tensiometer), can be deflated by suction through the capillary. We study this deflation and show that a combined analysis of the shape and wrinkling characteristics enables us to determine the elastic properties in situ. Shape contours are analyzed and fitted using shape equations derived from nonlinear membrane-shell theory to give the elastic modulus, Poisson ratio and stress distribution of the membrane. We include wrinkles, which generically form upon deflation, within the shape analysis. Measuring the wavelength of wrinkles and using the calculated stress distribution gives the bending stiffness of the membrane. We compare this method with previous approaches using the Laplace-Young equation and illustrate the method on two very different capsule materials: polymerized octadecyltrichlorosilane (OTS) capsules and hydrophobin (HFBII) coated bubbles. Our results are in agreement with the available rheological data. For hydrophobin coated bubbles the method reveals an interesting nonlinear behavior consistent with the hydrophobin molecules having a rigid core surrounded by a softer shell.

cond-mat.soft↗
arXiv2013

Stiff directed lines in random media

We investigate the localization of stiff directed lines with bending energy by a short-range random potential. We apply perturbative arguments, Flory scaling arguments, a variational replica calculation, and functional renormalization to show that a stiff directed line in 1+d dimensions undergoes a localization transition with increasing disorder for d > 2=3. We demonstrate that this transition is accessible by numerical transfer matrix calculations in 1+1 dimensions and analyze the properties of the disorder dominated phase in detail. On the basis of the two-replica problem, we propose a relation between the localization of stiff directed lines in 1+d dimensions and of directed lines under tension in 1+3d dimensions, which is strongly supported by identical free energy distributions. This shows that pair interactions in the replicated Hamiltonian determine the nature of directed line localization transitions with consequences for the critical behavior of the Kardar-Parisi-Zhang (KPZ) equation. We support the proposed relation to directed lines via multifractal analysis revealing an analogous Anderson transition-like scenario and a matching correlation length exponent. Furthermore, we quantify how the persistence length of the stiff directed line is reduced by disorder.

cond-mat.stat-mech↗
arXiv2013

Cooperative dynamics of microtubule ensembles: Polymerization forces and rescue-induced oscillations

We investigate the cooperative dynamics of an ensemble of N microtubules growing against an elastic barrier. Microtubules undergo so-called catastrophes, which are abrupt stochastic transitions from a growing to a shrinking state, and rescues, which are transitions back to the growing state. Microtubules can exert pushing or polymerization forces on an obstacle, such as an elastic barrier if the growing end is in contact with the obstacle. We use dynamical mean-field theory and stochastic simulations to analyze a model where each microtubule undergoes catastrophes and rescues and where microtubules interact by force sharing. For zero rescue rate, cooperative growth terminates in a collective catastrophe. The maximal polymerization force before catastrophes grows linearly with N for small N or a stiff elastic barrier, in agreement with available experimental results, whereas it crosses over to a logarithmic dependence for larger N or a soft elastic barrier. For a nonzero rescue rate and a soft elastic barrier, the dynamics becomes oscillatory with both collective catastrophe and rescue events, which are part of a robust limit cycle. Both the average and maximal polymerization forces then grow linearly with N, and we investigate their dependence on tubulin on-rates and rescue rates, which can be involved in cellular regulation mechanisms. We further investigate the robustness of the collective catastrophe and rescue oscillations with respect to different catastrophe models.

q-bio.SC↗