Structure and stability of chiral beta-tapes: a computational coarse-grained approach

We present two coarse-grained models of different levels of detail for the description of beta-sheet tapes obtained from equilibrium self-assembly of short rationally designed oligopeptides in solution. Here we only consider the case of the homopolymer oligopeptides with the identical sidegroups attached, in which the tapes have a helicoid surface with two equivalent sides. The influence of the chirality parameter on the geometrical characteristics, namely the diameter, inter-strand distance and pitch, of the tapes have been investigated. The two models are found to produceequivalent results suggesting a considerable degree of universality in conformations of the tapes.Comment: 24 pages, 5 PS figures. Accepted to J. Chem. Phy

On the conformational structure of a stiff homopolymer

In this paper we complete the study of the phase diagram and conformational states of a stiff homopolymer. It is known that folding of a sufficiently stiff chain results in formation of a torus. We find that the phase diagram obtained from the Gaussian variational treatment actually contains not one, but several distinct toroidal states distinguished by the winding number. Such states are separated by first order transition curves terminating in critical points at low values of the stiffness. These findings are further supported by off-lattice Monte Carlo simulation. Moreover, the simulation shows that the kinetics of folding of a stiff chain passes through various metastable states corresponding to hairpin conformations with abrupt U-turns.Comment: 9 pages, 16 PS figures. Journal of Chemical Physics, in pres

How Stress Can Reduce Dissipation in Glasses

We propose that stress can decrease the internal friction of amorphous solids, either by increasing the potential barriers of defects, thus reducing their tunneling and thermal activation that produce loss, or by decreasing the coupling between defects and phonons. This stress can be from impurities, atomic bonding constraints, or externally applied stress. Externally applied stress also reduces mechanical loss through dissipation dilution. Our results are consistent with the experiments, and predict that stress could substantially reduce dielectric loss and increase the thermal conductivity.Comment: 9 pages, 7 figure

Control of Material Damping in High-Q Membrane Microresonators

We study the mechanical quality factors of bilayer aluminum/silicon-nitride membranes. By coating ultrahigh-Q Si3N4 membranes with a more lossy metal, we can precisely measure the effect of material loss on Q's of tensioned resonator modes over a large range of frequencies. We develop a theoretical model that interprets our results and predicts the damping can be reduced significantly by patterning the metal film. Using such patterning, we fabricate Al-Si3N4 membranes with ultrahigh Q at room temperature. Our work elucidates the role of material loss in the Q of membrane resonators and informs the design of hybrid mechanical oscillators for optical-electrical-mechanical quantum interfaces