Related papers: Molecular elasticity and the geometric phase
Exact solutions for the elastic and thermodynamic properties for the wormlike chain model are elaborated in terms of Mathieu functions. The smearing of the classical Euler buckling instability for clamped polymers is analyzed for the…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
We review the physical properties of macromolecular networks, consisting of semiflexible polymers such as actin. We start by giving a theoretical analysis of the conformational statistics and mechanical response of single filaments.…
The analytical solution of the recently proposed ideal chain polymer mean-spherical approximation (Yu.Kalyuzhnyi, Mol.Phys., 94, 735(1998)) is presented for the multicomponent mixture of charged hard-sphere linear chain flexible molecules.…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
We introduce a simple geometric model for a double-stranded and double-helical polymer. We study the statistical mechanics of such polymers using both analytical techniques and simulation. Our model has a single energy-scale which…
We study energy relaxation in a phenomenological model for polymer built from rheological considerations: a one dimensional nonlinear lattice with dissipative couplings. These couplings are well known in polymer's community to be possibly…
We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from…
We use the lattice model of directed walks to investigate the conformational as well as the adsorption properties of a semiflexible homopolymer chain immersed in a good solvent in two and three dimensions. To account for the stiffness in…
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
The buckling instabilities of core-shell systems, comprising an interior elastic sphere, attached to an exterior shell, have been proposed to underlie myriad biological morphologies. To fully discuss such systems, however, it is important…
We connect the theories of the deformation of elastic surfaces and phase surfaces arising in the description of almost periodic patterns. In particular, we show parallels between asymptotic expansions for the energy of elastic surfaces in…
The linear viscoelastic response of flexible polymer solutions in the dilute and semidilute unentangled regimes is investigated using Brownian dynamics simulations. The relaxation modulus and dynamic moduli are computed over a wide range of…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
We propose a novel phase-field model to predict elastic microphase separation in polymer gels. To this end, we extend the Cahn-Hilliard free-energy functional to incorporate an elastic strain energy and a coupling term. These contributions…
Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influence the…