Related papers: Statistical mechanics of double-helical polymers
Hydrogels have a distinct combination of mechanical and water-transport behaviors. As hydrogels stiffen, they become less permeable. Here, we combine semi-dilute polymer theory with the Kozeny-Carman equation to develop a simple scaling law…
We study cholesteric order in liquid crystal shells with planar degenerate anchoring. We observe that the bipolar and radial configurations intensively reported for bulk droplets have a higher degree of complexity when the liquid crystal is…
Limited-valency colloidal particles can self-assemble into polymeric structures analogous to molecules. While their structural equilibrium properties have attracted wide attention, insight into their dynamics has proven challenging. Here,…
We study a two-dimensional model for interacting colloidal particles which displays spontaneous clustering. Within this model we investigate the competition between the pinning to a periodic corrugation potential, and a sideways constant…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…
This paper examines the effect of cooling on disentanglement forces in polymers and the implications for both single chain pullout and polymer dynamics. I derive the explicit dependence of the distribution of these forces on temperature,…
Using continuum elasticity theory, we describe the elastic behavior of helical coils with an asymmetric double-helix structure and identify conditions, under which they become very rigid. Theoretical insight gained for macro-structures…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Self-avoiding polymers in strictly two-dimensional ($d=2$) melts are investigated by means of molecular dynamics simulation of a standard bead-spring model with chain lengths ranging up to N=2048. % The chains adopt compact configurations…
Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit: from natural polynucleotides and polypeptides to synthetic…
The statistical theory of flow stress, including yield strength, for polycrystalline materials under quasi-static plastic deformation suggested in [arxiv:1803.08247[cond-mat.mtr-sci], arxiv:1805.08623[cond-mat.mtr-sci]] is developed in the…
The dynamics of many glassy systems are known to exhibit string-like hopping motions each consisting of a line of particles displacing one and other. By using molecular dynamics simulations of glassy polymers, we show that these motions…
Single partially confined collapsed polymers are studied in two dimensions. They are described by self-avoiding random walks with nearest-neighbour attractions below the $\Theta$-point, on the surface of an infinitely long cylinder. For the…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
Drawing inspiration from the concept of the "primitive path" of a linear chain in melt conditions, we introduce here a numerical protocol which allows us to detect, in an unambiguous manner, the "primitive shapes" of ring polymers in…
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…
Atomistic (atom-scale) and coarse-grained (meso-scale) simulations of structure and dynamics of poly-isoprene melts are compared. The local structure and chain packing is mainly determined by the atomistic details of the polymer…
The joint statistical properties of two free energies computed at two different temperatures in {\it the same sample} of $(1+1)$ directed polymers is studied in terms of the replica technique. The scaling dependence of the reduced free…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…