Barrier crossing of semiflexible polymers

We consider the motion of semiflexible polymers in double-well potentials. We calculate shape, energy, and effective diffusion constant of kink excitations, and in particular their dependence on the bending rigidity of the semiflexible polymer. For symmetric potentials, the kink motion is purely diffusive whereas kink motion becomes directed in the presence of a driving force on the polymer. We determine the average velocity of the semiflexible polymer based on the kink dynamics. The Kramers escape over the potential barriers proceeds by nucleation and diffusive motion of kink-antikink pairs, the relaxation to the straight configuration by annihilation of kink-antikink pairs. Our results apply to the activated motion of biopolymers such as DNA and actin filaments or synthetic polyelectrolytes on structured substrates.Comment: 7 pages, 3 figure

Point force manipulation and activated dynamics of polymers adsorbed on structured substrates

We study the activated motion of adsorbed polymers which are driven over a structured substrate by a localized point force.Our theory applies to experiments with single polymers using, for example, tips of scanning force microscopes to drag the polymer.We consider both flexible and semiflexible polymers,and the lateral surface structure is represented by double-well or periodic potentials. The dynamics is governed by kink-like excitations for which we calculate shapes, energies, and critical point forces. Thermally activated motion proceeds by the nucleation of a kink-antikink pair at the point where the force is applied and subsequent diffusive separation of kink and antikink. In the stationary state of the driven polymer, the collective kink dynamics can be described by an one-dimensional symmetric simple exclusion process.Comment: 7 pages, 2 Figure

The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation

There is a body of literature that describes the geometry and the physics of filopodia using either stochastic models or partial differential equations and elasticity and coarse-grained theory. Comparatively, there is a paucity of models focusing on the regulation of the network of proteins that control the formation of different actin structures. Using a combination of in-vivo and in-vitro experiments together with a system of ordinary differential equations, we focused on a small number of well-characterized, interacting molecules involved in actin-dependent filopodia formation: the actin remodeler Eps8, whose capping and bundling activities are a function of its ligands, Abi-1 and IRSp53, respectively; VASP and Capping Protein (CP), which exert antagonistic functions in controlling filament elongation. The model emphasizes the essential role of complexes that contain the membrane deforming protein IRSp53, in the process of filopodia initiation. This model accurately accounted for all observations, including a seemingly paradoxical result whereby genetic removal of Eps8 reduced filopodia in HeLa, but increased them in hippocampal neurons, and generated quantitative predictions, which were experimentally verified. The model further permitted us to explain how filopodia are generated in different cellular contexts, depending on the dynamic interaction established by Eps8, IRSp53 and VASP with actin filaments, thus revealing an unexpected plasticity of the signaling network that governs the multifunctional activities of its components in the formation of filopodia

Activated dynamics of semiflexible polymers on structured substrates

We study the thermally activated motion of semiflexible polymers in double-well potentials using field-theoretic methods. Shape, energy, and effective diffusion constant of kink excitations are calculated, and their dependence on the bending rigidity of the semiflexible polymer is determined. For symmetric potentials, the kink motion is purely diffusive whereas kink motion becomes directed in the presence of a driving force. We determine the average velocity of the semiflexible polymer based on the kink dynamics. The Kramers escape over the potential barriers proceeds by nucleation and diffusive motion of kink-antikink pairs, the relaxation to the straight configuration by annihilation of kink-antikink pairs. We consider both uniform and point-like driving forces. For the case of point-like forces the polymer crosses the potential barrier only if the force exceeds a critical value. Our results apply to the activated motion of biopolymers such as DNA and actin filaments or of synthetic polyelectrolytes on structured substrates