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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 a special three body interaction and impacts on the behaviour both locally and non-locally. When thick polymers undergo compaction due to an attractive self-interaction, we find a new type of phase transition between a compact phase and a swollen phase at zero temperature on increasing the thickness. In the vicinity of this transition, short tubes form space filling helices and sheets as observed in protein native state structures. Upon increasing the chain length, or the number of chains, we numerically find a crossover from secondary structure motifs to a quite distinct class of structures akin to the semi-crystalline phase of polymers or amyloid fibers in polypeptides.
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We explore the effect of an attractive interaction between parallel-aligned polymers, which are perpendicularly grafted on a substrate. Such an attractive interaction could be due to, e.g., reversible cross-links. The competition between permanent grafting favoring a homogeneous state of the polymer brush and the attraction, which tends to induce in-plane collapse of the aligned polymers, gives rise to an instability of the homogeneous phase to a bundled state. In this latter state the in-plane translational symmetry is spontaneously broken and the density is modulated with a finite wavelength, which is set by the length scale of transverse fluctuations of the grafted polymers. We analyze the instability for two models of aligned polymers: directed polymers with a line tension and weakly bending chains with a bending stiffness.
In this chapter we review concepts and theories of polymer dynamics. We think of it as an introduction to the topic for scientists specializing in other subfields of statistical mechanics and condensed matter theory, so, for the readers reference, we start with a short review of the equilibrium static properties of polymer systems. Most attention is paid to the dynamics of unentangled polymer systems, where apart from classical Rouse and Zimm models we review some recent scaling and analytical generalizations. The dynamics of systems with entanglements is also briefly reviewed. Special attention is paid to the discussion of comparatively weakly understood topological states of polymer systems and possible approaches to the description of their dynamics.
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the absence of hydrodynamic interactions. The dsDNA is modelled with one bead-spring element per basepair, and the polymer dynamics is described by the Langevin equation. The key to efficiency is that we describe the equations of motion for the polymer in terms of the amplitudes of the polymers fluctuation modes, as opposed to the use of the physical positions of the beads. We show that, within an accuracy tolerance level of $5%$ of several key observables, the model allows for single Langevin time steps of $approx1.6$, 8, 16 and 16 ps for a dsDNA model-chain consisting of 64, 128, 256 and 512 basepairs (i.e., chains of 0.55, 1.11, 2.24 and 4.48 persistence lengths) respectively. Correspondingly, in one hour, a standard desktop computer can simulate 0.23, 0.56, 0.56 and 0.26 ms of these dsDNA chains respectively. We compare our results to those obtained from other methods, in particular, the (inextensible discretised) WLC model. Importantly, we demonstrate that at the same level of discretisation, i.e., when each discretisation element is one basepair long, our algorithm gains about 5-6 orders of magnitude in the size of time steps over the inextensible WLC model. Further, we show that our model can be mapped one-on-one to a discretised version of the extensible WLC model; implying that the speed-up we achieve in our model must hold equally well for the latter. We also demonstrate the use of the method by simulating efficiently the tumbling behaviour of a dsDNA segment in a shear flow.
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the helix-coil transition. Since the formation of helices implies a dramatic shortening of the polymer dimensions, an externally imposed end-to-end distance R affects the equilibrium helical fraction of the polymer and the resulting force- extension curves show anomalous plateau regimes. In this article, we investigate the behaviour of a cross-linked network of such helicogenic molecules, particularly, focusing on the coupling of the (average) helical content present in a network to the externally imposed strain. We show that both an elongation and compression can lead to an increase in helical domains under appropriate conditions.
We calculate the scattering intensity of dilute and semi-dilute solutions of star polymers. The star conformation is described by a model introduced by Daoud and Cotton. In this model, a single star is regarded as a spherical region of a semi-dilute polymer solution with a local, position dependent screening length. For high enough concentrations, the outer sections of the arms overlap and build a semi-dilute solution (a sea of blobs) where the inner parts of the actual stars are embedded. The scattering function is evaluated following a method introduced by Auvray and de Gennes. In the dilute regime there are three regions in the scattering function: the Guinier region (low wave vectors, q R << 1) from where the radius of the star can be extracted; the intermediate region (1 << q R << f^(2/5)) that carries the signature of the form factor of a star with f arms: I(q) ~ q^(-10/3); and a high wavevector zone (q R >> f^(2/5)) where the local swollen structure of the polymers gives rise to the usual q^(-5/3) decay. In the semi-dilute regime the different stars interact strongly, and the scattered intensity acquires two new features: a liquid peak that develops at a reciprocal position corresponding to the star-star distances; and a new large wavevector contribution of the form q^(-5/3) originating from the sea of blobs.
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