Biopolymer Elasticity

In recent years molecular elasticity has emerged as an active area of research: there are experiments that probe mechanical properties of single biomolecules such as DNA and Actin, with a view to understanding the role of elasticity of these polymers in biological processes such as transcription and protein-induced DNA bending. Single molecule elasticity has thus emerged as an area where there is a rich cross-fertilization of ideas between biologists, chemists and theoretical physicists. In this article we present a perspective on this field of research

Onset of Shear Waves In A Bacterial Bath: A Novel Effect

Recent experiments on particle diffusion in bacterial baths indicate the formation of correlated structures in the form of bacterial swirls. Here we predict that such a structural ordering would give rise to the new effect of propagating shear waves in a bacterial bath at length scales of the order of a swirl, which corresponds to time scales of the order of the lifetime of a swirl. Our prediction can be tested against future experiments in bacterial baths.Comment: To appear in Fluctuation and Noise Letter

Jamming dynamics in grain mixtures : An extended hydrodynamic approach

We study jamming in granular mixtures from the novel point of view of extended hydrodynamics. Using a hard sphere binary mixture model we predict that a few large grains are expected to get caged more effectively in a matrix of small grains compared to a few small grains in a matrix of larger ones. A similar effect has been experimentally seen in the context of colloidal mixtures.Comment: To appear in ``Fluctuation and Noise Letters'

The Writhe Distribution Of Stretched Polymers

Motivated by experiments in which single DNA molecules are stretched and twisted we consider a perturbative approach around very high forces, where we determine the writhe distribution in a simple, analytically tractable model. Our results are in agreement with recent simulations and experiments.Comment: updated addres

Inequivalence of Statistical Ensembles in Single Molecule Measurements

We study the role of fluctuations in single molecule experimental measurements of force-extension curves. We use the Worm Like Chain (WLC) model to bring out the connection between the Helmholtz ensemble characterized by the Free Energy and the Gibbs ensemble characterized by the Free Energy . We consider the rigid rod limit of the WLC model as an instructive special case to bring out the issue of ensemble inequivalence. We point out the need for taking into account the free energy of transition when one goes from one ensemble to another. We also comment on the ``phase transition'' noticed in an isometric setup for semiflexible polymers and propose a realization of its thermodynamic limit. We present general arguments which rule out non-monotonic force-extension curves in some ensembles and note that these do not apply to the isometric ensemble.Comment: to appear in Physical Review