Density functional theory and demixing of binary hard rod-polymer mixtures

A density functional theory for a mixture of hard rods and polymers modeled as chains built of hard tangent spheres is proposed by combining the functional due to Yu and Wu for the polymer mixtures [J. Chem. Phys. {\bf 117}, 2368 (2002)] with the Schmidt's functional [Phys. Rev. E {\bf 63}, 50201 (2001)] for rod-sphere mixtures. As a simple application of the functional, the demixing transition into polymer-rich and rod-rich phases is examined. When the chain length increases, the phase boundary broadens and the critical packing fraction decreases. The shift of the critical point of a demixing transition is most noticeable for short chains.Comment: 4 pages,2 figures, in press, PR

Interplay between Folding and Assembly of Fibril-Forming Polypeptides.

Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this self-assembly as a function of temperature and hydrophobicity of the residues on the outside of the building block. We find the self-assembly can occur via two different pathways - a random aggregation-folding route, and a templated-folding process - thus indicating a strong coupling between folding and assembly. The simulation results can explain experimental evidence that assembly through stacking of folded building blocks is rarely observed, at the experimental concentrations. The model thus provides a generic picture of hierarchical fibril formation.Comment: Accepted in Physical Review Letter

The Asakura-Oosawa model in the protein limit: the role of many-body interactions

We study the Asakura-Oosawa model in the "protein limit", where the penetrable sphere radius $R_{AO}$ is much greater than the hard sphere radius $R_c$. The phase behaviour and structure calculated with a full many-body treatment show important qualitative differences when compared to a description based on pair potentials alone. The overall effect of the many-body interactions is repulsive.Comment: 9 pages and 11 figures, submitted to J. Phys.: Condensed Matter, special issue "Effective many-body interactions and correlations in soft matter

An integral equation approach to effective interactions between polymers in solution

We use the thread model for linear chains of interacting monomers, and the ``polymer reference interaction site model'' (PRISM) formalism to determine the monomer-monomer pair correlation function $h_{mm}(r)$ for dilute and semi-dilute polymer solutions, over a range of temperatures from very high (where the chains behave as self-avoiding walks) to below the $\theta$ temperature, where phase separation sets in. An inversion procedure, based on the HNC integral equation, is used to extract the effective pair potential between ``average'' monomers on different chains. An accurate relation between $h_{mm}(r)$, $h_{cc}(r)$ [the pair correlation function between the polymer centers of mass (c.m.)], and the intramolecular form factors is then used to determine $h_{cc}(r)$, and subsequently extract the effective c.m.-c.m. pair potential $v_{cc}(r)$ by a similar inversion procedure. $v_{cc}(r)$ depends on temperature and polymer concentration, and the predicted variations are in reasonable agreement with recent simulation data, except at very high temperatures, and below the $\theta$ temperature.Comment: 13 pages, 13 figures, revtex ; revised versio

Enhanced stability of layered phases in parallel hard-spherocylinders due to the addition of hard spheres

There is increasing evidence that entropy can induce microphase separation in binary fluid mixtures interacting through hard particle potentials. One such phase consists of alternating two dimensional liquid-like layers of rods and spheres. We study the transition from a uniform miscible state to this ordered state using computer simulations and compare results to experiments and theory. We conclude that (1) there is stable entropy driven microphase separation in mixtures of parallel rods and spheres, (2) adding spheres smaller then the rod length decreases the total volume fraction needed for the formation of a layered phase, therefore small spheres effectively stabilize the layered phase; the opposite is true for large spheres and (3) the degree of this stabilization increases with increasing rod length.Comment: 11 pages, 9 figures. Submitted to Phys. Rev. E. See related website http://www.elsie.brandeis.ed

Fluorescence microscopy visualization of halomucin, a secreted 927 kDa protein surrounding Haloquadratum walsbyi cells

At the time of its first publication, halomucin from Haloquadratum walsbyi strain HBSQ001 was the largest archaeal protein known (9159 aa). It has a predicted signal sequence, making it likely to be an extracellular or secreted protein. Best BLAST matches were found to be mammalian mucins that protect tissues to dehydration and chemical stress. It was hypothesized that halomucin participates in protection against desiccation by retaining water in a hull around the halophilic organisms that live at the limits of water activity. We visualized Halo quadratum cells by staining their intracellular polyhydroxybutyrate granules using Nile Blue. Halomucin was stained by immunofluorescence with antibodies generated against synthetic peptides derived from the halomucin amino acid sequence. Polyhydroxybutyrate stained cells were reconstructed in 3D which highlights not only the highly regular square shape but also the extreme flatness of Haloquadratum. Double-staining proves halomucin to be extracellular but to be only loosely associated to cells in agreement with its hypothesized function