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R. F. Bruinsma

Publications and source records attributed to R. F. Bruinsma.

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Elasticity Theory and Shape Transitions of Viral Shells

Recently, continuum elasticity theory has been applied to explain the shape transition of icosahedral viral capsids - single-protein-thick crystalline shells - from spherical to buckled/faceted as their radius increases through a critical value determined by the competition between stretching and bending energies of a closed 2D elastic network. In the present work we generalize this approach to capsids with non-icosahedral symmetries, e.g., spherocylindrical and conical shells. One key new physical ingredient is the role played by nonzero spontaneous curvature. Another is associated with the special way in which the energy of the twelve topologically-required five-fold sites depends on the background local curvature of the shell in which they are embedded. Systematic evaluation of these contributions leads to a shape phase diagram in which transitions are observed from icosahedral to spherocylindrical capsids as a function of the ratio of stretching to bending energies and of the spontaneous curvature of the 2D protein network. We find that the transition from icosahedral to spherocylindrical symmetry is continuous or weakly first-order near the onset of buckling, leading to extensive shape degeneracy. These results are discussed in the context of experimentally observed variations in the shapes of a variety of viral capsids.

physics.bio-ph

Raft Instability of Biopolymer Gels

Following recent X-ray diffraction experiments by Wong, Li, and Safinya on biopolymer gels, we apply Onsager excluded volume theory to a nematic mixture of rigid rods and strong ``$π/2$'' cross-linkers obtaining a long-ranged, highly anisotropic depletion attraction between the linkers. This attraction leads to breakdown of the percolation theory for this class of gels, to breakdown of Onsager's second-order virial method, and to formation of heterogeneities in the form of raft-like ribbons.

cond-mat.soft

Electrostatic complexation of spheres and chains under elastic stress

We consider the complexation of highly charged semiflexible polyelectrolytes with oppositely charged macroions. On the basis of scaling arguments we discuss how the resulting complexes depend on the persistence length of the polyelectrolyte, the salt concentration, and the sizes and charges of the chain and the macroions. We study first the case of complexation with a single sphere and calculate the wrapping length of the chain. We then extend our considerations to complexes involving many wrapped spheres and study cooperative effects. The mechanical properties of such a complex under an external deformation are evaluated.

cond-mat.soft

Polymer reptation and nucleosome repositioning

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem arises in the case of globular aggregates of proteins (histones) that are wound by DNA in the chromosomes of plants and animals; these beads (nucleosomes) are multiply wrapped and yet are able to reposition themselves over long distances, while remaining bound by the DNA chain.

cond-mat.soft

Elastically-Driven Linker Aggregation between Two Semi-Flexible Polyelectrolytes

The behavior of mobile linkers connecting two semi-flexible charged polymers, such as polyvalent counterions connecting DNA or F-actin chains, is studied theoretically. The chain bending rigidity induces an effective repulsion between linkers at large distances while the inter-chain electrostatic repulsion leads to an effective short range inter-linker attraction. We find a rounded phase transition from a dilute linker gas where the chains form large loops between linkers to a dense disordered linker fluid connecting parallel chains. The onset of chain pairing occurs within the rounded transition.

cond-mat.soft