Related papers: Molecular elasticity and the geometric phase
Bending of worm-like polymers carries an energy penalty which results in the appearance of a persistence length l such that the polymer is straight on length scales smaller than l and bends only on length scales larger than this length.…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
A buckled sheet offers a reservoir of material that can be unfurled at a later time. For sufficiently thin yet stiff materials, this geometric process has a striking mechanical feature: when the slack runs out, the material locks to further…
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…
We present a lattice model for polymer solutions, explicitly incorporating interactions with a bath of solvent and cosolvent molecules. By exploiting the well-known analogy between polymer systems and the $O(n)$-vector spin model in the…
We present a theoretical framework for the linear and nonlinear visco-elastic properties of reversibly crosslinked networks of semiflexible polymers. In contrast to affine models where network strain couples to the polymer end-to-end…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
We develop topological methods for characterizing the relationship between polymer chain entanglement and bulk viscoelastic responses. We introduce generalized Linking Number and Writhe characteristics that are applicable to open linear…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
We suggested a geometric approach to address the external field influence on the DNA molecules, described by the WLC model via geometric coupling. It consists in the introduction of the effective metrics depending on the potential of the…
We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases…
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and…
I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…
We study a model of a semiflexible long chain polymer confined to a two-dimensional slit of width $w$, and interacting with the walls of the slit. The interactions with the walls are controlled by Boltzmann weights $a$ and $b$, and the…
We measure elastomechanical spectra for a family of thin shells. We show that these spectra can be described by a "semiclassical" trace formula comprising periodic orbits on geodesics, with the periods of these orbits consistent with those…
We analyse the elastic energy of an intercalated smectic where orientationally ordered polymers with an average orientation varying from layer to layer are intercalated between smectic planes. The lowest order terms in the coupling between…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…