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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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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 consider a lattice model of a mixture of repulsive, attractive, or neutral monodisperse star (species A) and linear (species B) polymers with a third monomeric species C, which may represent free volume. The mixture is next to a hard, infinite plate whose interactions with A and C can be attractive, repulsive, or neutral. These two interactions are the only parameters necessary to specify the effect of the surface on all three components. We numerically study monomer density profiles using the method of Gujrati and Chhajer that has already been previously applied to study polydisperse and monodisperse linear-linear blends next to surfaces. The resulting density profiles always show an enrichment of linear polymers in the immediate vicinity of the surface, due to entropic repulsion of the star core. However, the integrated surface excess of star monomers is sometimes positive, indicating an overall enrichment of stars. This excess increases with the number of star arms only up to a certain critical number and decreases thereafter. The critical arm number increases with compressibility (bulk concentration of C). The method of Gujrati and Chhajer is computationally ultrafast and can be carried out on a PC, even in the incompressible case, when simulations are unfeasible. Calculations of density profiles usually take less than 20 minutes on PCs.
We present an analysis of the impact of structural disorder on the static scattering function of f-armed star branched polymers in d dimensions. To this end, we consider the model of a star polymer immersed in a good solvent in the presence of structural defects, correlated at large distances r according to a power law sim r^{-a}. In particular, we are interested in the ratio g(f) of the radii of gyration of star and linear polymers of the same molecular weight, which is a universal experimentally measurable quantity. We apply a direct polymer renormalization approach and evaluate the results within the double varepsilon=4-d, delta=4-a-expansion. We find an increase of g(f) with an increasing delta. Therefore, an increase of disorder correlations leads to an increase of the size measure of a star relative to linear polymers of the same molecular weight.
Extensive Monte Carlo results are presented for a lattice model of a bottle-brush polymer under good solvent or Theta solvent conditions. Varying the side chain length, backbone length, and the grafting density for a rigid straight backbone, both radial density profiles of monomers and side chain ends are obtained, as well as structure factors describing the scattering from a single side chain and from the total bottle-brush polymer. To describe the structure in the interior of a very long bottle-brush, a periodic boundary condition in the direction along the backbone is used, and to describe effects due to the finiteness of the backbone length, a second set of simulations with free ends of the backbone is performed. In the latter case, the inhomogeneity of the structure in the direction along the backbone is carefully investigated. We use these results to test various phenomenological models that have been proposed to interpret experimental scattering data for bottle-brush macromolecules. These models aim to extract information on the radial density profile of a bottle-brush from the total scattering via suitable convolution approximations. Possibilities to improve such models, guided by our simulation results, are discussed.
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.
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