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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.
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 gr
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
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 hydr
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
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