Related papers: The effect of undulations on Spontaneous Braid for…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
Some important biomolecules (for instance, bacterial FtsZ and eukaryotic DNA) are known to posses spontaneous (intrinsic) curvature. Using a simple extension of the wormlike chain model, we study the response of a weakly bending filament in…
Dual mechanical braiding experiments provide a useful tool with which investigate the nature of interactions between rod-like molecules, for instance actin and DNA. In conditions close to molecular condensation, one would expect an…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
Here we derive and experimentally test a free energy functional that captures the adhesion of DNA-coated emulsion droplets. Generalizing previous approaches, the theory combines important energetic and entropic effects of microscopic DNA…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Helical ribbons arise in many biological and engineered systems, often driven by anisotropic surface stress, residual strain, and geometric or elastic mismatch between layers of a laminated composite. A full mathematical analysis is…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
In mechanical manipulation experiments, a single DNA molecule overwound at constant force undergoes a discontinuous drop in extension as it buckles and forms a superhelical loop (a plectoneme). Further overwinding the DNA, we observe an…
Entangled knots form spontaneously in flexible filaments, yet the influence of the surrounding environment on this process is poorly understood. Here we demonstrate that free-moving particles act as kinetic catalysts for spontaneous…
Inspired by recent experiments on the dynamics of particles and polymers in artificial cytoskeletons and in cells, we introduce a modified Langevin equation for a particle in an environment that is a viscoelastic medium and that is brought…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
Several recent experiments suggest that sharply bent DNA has a surprisingly high bending flexibility, but the cause of this flexibility is poorly understood. Although excitation of flexible defects can explain these results, whether such…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
Induced by proteins within the cell membrane or by differential growth, heating, or swelling, spontaneous curvatures can drastically affect the morphology of thin bodies and induce mechanical instabilities. Yet, the interaction of…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
The spontaneous formation of double helices for filaments under torsion is common and significant. For example, the research on the supercoiling of DNA is helpful for understanding the replication and transcription of DNA. Similar double…