Semiflexible Polymer Rings Research Articles

Topological gelation of reconnecting polymers

DNA recombination is a ubiquitous process that ensures genetic diversity. Contrary to textbook pictures, DNA recombination, as well as generic DNA translocations, occurs in a confined and highly entangled environment. Inspired by this observation, here, we investigate a solution of semiflexible polymer rings undergoing generic cutting and reconnection operations under spherical confinement. Our setup may be realized using engineered DNA in the presence of recombinase proteins or by considering micelle-like components able to form living (or reversibly breakable) polymer rings. We find that in such systems, there is a topological gelation transition, which can be triggered by increasing either the stiffness or the concentration of the rings. Flexible or dilute polymers break into an ensemble of short, unlinked, and segregated rings, whereas sufficiently stiff or dense polymers self-assemble into a network of long, linked, and mixed loops, many of which are knotted. We predict that the two phases should behave qualitatively differently in elution experiments monitoring the escape dynamics from a permeabilized container. Besides shedding some light on the biophysics and topology of genomes undergoing DNA reconnection in vivo, our findings could be leveraged in vitro to design polymeric complex fluids-e.g., DNA-based complex fluids or living polymer networks-with desired topologies.

Energy localization and shape transformations in semiflexible polymer rings.

Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the internal excitations and the bending degrees of freedom of the chain modifies the local bending rigidity of the chain. In the absence of driving the array takes a circular shape. When the energy pumped into the system exceeds some critical value the chain undergoes a nonequilibrium phase transition: The circular shape of the aggregate becomes unstable and the chain takes the shape of an ellipse or, in general, of a polygon. The excitation energy distribution becomes spatially nonuniform: It localizes in such places where the chain is more flat. The weak interaction of the chain with a flat surface restricts the dynamics to a flat manifold.

Gaussian semiflexible rings under angular and dihedral restrictions.

Semiflexible polymer rings whose bonds obey both angular and dihedral restrictions [M. Dolgushev and A. Blumen, J. Chem. Phys. 138, 204902 (2013)], are treated under exact closure constraints. This allows us to obtain semianalytic results for their dynamics, based on sets of Langevin equations. The dihedral restrictions clearly manifest themselves in the behavior of the mean-square monomer displacement. The determination of the equilibrium ring conformations shows that the dihedral constraints influence the ring curvature, leading to compact folded structures. The method for imposing such constraints in Gaussian systems is very general and it allows to account for heterogeneous (site-dependent) restrictions. We show it by considering rings in which one site differs from the others.

Dynamics of a semiflexible polymer or polymer ring in shear flow

Polymers exposed to shear flow exhibit a remarkably rich tumbling dynamics. While rigid rods rotate on Jeffery orbits, a flexible polymer stretches and coils up during tumbling. Theoretical results show that in both of these asymptotic regimes the corresponding tumbling frequency f(c) in a linear shear flow of strength γ scales as a power law Wi(2/3) in the Weissenberg number Wi = γτ, where τ is a characteristic time of the polymer's relaxational dynamics. For a flexible polymer these theoretical results are well confirmed by a large body of experimental single molecule studies. However, for the intermediate semiflexible regime, especially relevant for cytoskeletal filaments like F-actin and microtubules, the situation is less clear. While recent experiments on single F-actin filaments are still interpreted within the classical Wi(2/3) scaling law, theoretical results indicated deviations from it. Here we perform extensive Brownian dynamics simulations to explore the tumbling dynamics of semiflexible polymers over a broad range of shear strength and the polymer's persistence length l(p). We find that the Weissenberg number alone does not suffice to fully characterize the tumbling dynamics, and the classical scaling law breaks down. Instead, both the polymer's stiffness and the shear rate are relevant control parameters. Based on our Brownian dynamics simulations we postulate that in the parameter range most relevant for cytoskeletal filaments there is a distinct scaling behavior with f(c) τ* = Wi(3/4)f(c)(x) with Wi = γτ* and the scaling variable x = (l(p)/L)(Wi)(-1/3); here τ* is the time the polymer's center of mass requires to diffuse its own contour length L. Comparing these results with experimental data on F-actin we find that the Wi(3/4) scaling law agrees quantitatively significantly better with the data than the classical Wi(2/3) law. Finally, we extend our results to single ring polymers in shear flow, and find similar results as for linear polymers with slightly different power laws.

Multiscale Entanglement in Ring Polymers under Spherical Confinement

The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated by using advanced numerical methods. By using stringent and robust algorithms for locating knots, we characterize how the knot length l(k) depends on the ring contour length L(c) and the radius of the confining sphere R(c). In the no- and strong-confinement cases, we observe weak knot localization and complete knot delocalization, respectively. We show that the complex interplay of l(k), L(c), and R(c) that seamlessly bridges these two limits can be encompassed by a simple scaling argument based on deflection theory. The same argument is used to rationalize the multiscale character of the entanglement that emerges with increasing confinement.

Maximum entropy principle applied to semiflexible ring polymers

Based on the success of the maximum entropy principle (MEP) in the study of semiflexible treelike polymers [M. Dolgushev and A. Blumen, J. Chem. Phys. 131, 044905 (2009)], it is of much interest to establish MEP's potential for general semiflexible polymers which contain loops. Here, we embark on this endeavor by considering discrete semiflexible polymer rings in a Rouse-type scheme. Now, for treelike polymers a beads-and-bonds (i.e., a discrete) picture is essential for an easy inclusion of branching points. Moreover, one may envisage (similar to our former work [M. Dolgushev and A. Blumen, J. Chem. Phys. 131, 044905 (2009)]) to impose for each angle between two bonds a distinct stiffness condition. Working in this way leads already for a polymer ring to a complicated problem. Hence, we follow a reduced variational approach as applied earlier to polymer chains, in which a single Lagrange multiplier is used for each set of identical conditions imposed on topologically equivalent bonds and bonds' orientations. In this way, we obtain for the discrete ring an analytically closed form which involves Chebyshev polynomials. This expression turns out to lead to a series of solutions: Apart from the regular solution, several other solutions appear. One may be tempted to discard the other solutions, since for them the potential energy matrix is not positive definite. A more careful analysis based on topological features suggests, however, that such solutions can be assigned to rings displaying knots. Monte Carlo simulations which take excluded volume interactions into account agree with our interpretation.

Buckling of stiff polymer rings in weak spherical confinement

Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nanobiomaterials. We investigate the conformations of a semiflexible polymer ring in weak spherical confinement imposed by an impenetrable shell. We develop an analytic argument for the dominating polymer trajectory depending on polymer flexibility considering elastic and entropic contributions. Monte Carlo simulations are performed to assess polymer ring conformations in probability densities and by the shape measures asphericity and nature of asphericity. Comparison of the analytic argument with the mean asphericity and the mean nature of asphericity confirm our reasoning to explain polymer ring conformations in the stiff regime, where elastic response prevails.

Excluded Volume Effects on Semiflexible Ring Polymers

Two-dimensional semiflexible polymer rings are studied both by imaging circular DNA adsorbed on a mica surface and by Monte Carlo simulations of phantom polymers as well as of polymers with finite thickness. Comparison of size and shape of the different models over the full range of flexibilities shows that excluded volume caused by finite thickness induces an anisotropic increase of the main axes of the conformations, a change of shape, accomplished by an enhanced correlation along the contour.

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.

Confinement induces conformational transition of semiflexible polymer rings to figure eight form

Employing Monte Carlo simulations of semiflexible polymer rings in weak spherical confinement a conformational transition to figure eight shaped, writhed configurations is discovered and quantified.

A semiflexible polymer ring acting as a nano-propeller

The dynamics of a rotating elastic nano-ring driven in a viscous fluid by an externally applied torque about a specific axis is studied using elasto-hydrodynamic simulations. We show that a helical deformation of the ring filament is excited, and that this leads to directed propulsion which is independent of the direction of rotation. It is found that the propulsive force and efficiency initially increase as the torque is increased, and then decrease discontinuously at a buckling transition at a critical torque. This unique propulsive behavior at the shape transition arises due to its specific geometry, i.e., circularity of an elastic filament. The implications of the behavior for artificial microscopic devices are discussed.

Phase transitions in pressurized semiflexible polymer rings

We propose and study a model for the equilibrium statistical mechanics of a pressurized semiflexible polymer ring in two dimensions. The Hamiltonian has a term which couples to the algebraic or signed area of the ring and a term which accounts for bending (semiflexibility). The model allows for self-intersections. Using a combination of Monte Carlo simulations, Flory-type scaling theory, mean-field approximations, and lattice enumeration techniques, we obtain a phase diagram in which collapsed and inflated phases are separated by a continuous transition. The scaling properties of the averaged area as a function of the number of units of the ring are derived. For large pressures, the asymptotic behavior of the area is calculated for both continuum and lattice versions of the model. For small pressures, the area is obtained through a known mapping onto the quantum mechanical problem of an electron moving in a magnetic field. The simulation data agree well with the analytic and mean-field results.

Shapes of Semiflexible Polymer Rings

The shape of semiflexible polymer rings is studied over their whole range of flexibility. Investigating the joint distribution of asphericity and the nature of asphericity as well as their respective averages, we find two distinct shape regimes depending on the flexibility of the polymer. For a small perimeter to persistence length the fluctuating rings exhibit only planar, elliptical configurations. At higher flexibilities three-dimensional, crumpled structures arise. Analytic calculations confirm the qualitative behavior of the averaged shape parameters and the elliptical shape in the stiff regime.

Opening of a weak link in a semiflexible ring polymer

The dynamics of contact formation between different parts of a long chain molecule is of considerable interest in biology. The related processes of opening of a loop or closing to form a loop also are of considerable interest and have attracted the attention of experimentalists/theorists. For closing, results are available in the completely flexible limit. However, this limit is not realized in many cases. Recently, there have been investigations for the semiflexible case too. We develop an approach, which leads to an easy description of the dynamics, incorporating semiflexibility rigorously into account. With this approach, the dynamics of a semiflexible polymer ring formed by a weak bond between the two ends can be modeled as the escape of a particle over a barrier in a multidimensional potential energy surface. We then calculate the rate of opening using a multidimensional transition state theory. Effects of friction on the rate are also taken into account using the standard coupling to a bath of harmonic oscillators. We find that for shorter chains (i.e., semiflexible), the rate of opening is strongly length dependent and is well described by the equation A(L/lp)v exp(Blp/L), with L as the length, and lp as the persistence length, A, B as the constants, and v approximately 1.2.

Adsorption of a ring polymer onto a surface

The problem of a semiflexible polymer ring consisting of N monomers and constrained to walk among M perallel layers is solved in the lattice model approximation for various lattices. The monomer units of the ring can have arbitrary interaction energies with the surface Δe i for layer i, and additionally, it can have an internal stiffness energy which is a function of the angle between contiguous bonds