Unfolding dynamics of proteins under applied force

Understanding the mechanisms of protein folding is a major challenge that is being addressed effectively by collaboration between researchers in the physical and life sciences. Recently, it has become possible to mechanically unfold proteins by pulling on their two termini using local force probes such as the atomic force microscope. Here, we present data from experiments in which synthetic protein polymers designed to mimic naturally occurring polyproteins have been mechanically unfolded. For many years protein folding dynamics have been studied using chemical denaturation, and we therefore firstly discuss our mechanical unfolding data in the context of such experiments and show that the two unfolding mechanisms are not the same, at least for the proteins studied here. We also report unexpected observations that indicate a history effect in the observed unfolding forces of polymeric proteins and explain this in terms of the changing number of domains remaining to unfold and the increasing compliance of the lengthening unstructured polypeptide chain produced each time a domain unfolds

Uniaxial and biaxial soft deformations of nematic elastomers

We give a geometric interpretation of the soft elastic deformation modes of nematic elastomers, with explicit examples, for both uniaxial and biaxial nematic order. We show the importance of body rotations in this non-classical elasticity and how the invariance under rotations of the reference and target states gives soft elasticity (the Golubovic and Lubensky theorem). The role of rotations makes the Polar Decomposition Theorem vital for decomposing general deformations into body rotations and symmetric strains. The role of the square roots of tensors is discussed in this context and that of finding explicit forms for soft deformations (the approach of Olmsted).Comment: 10 pages, 10 figures, RevTex, AmsTe

Phase Separation in Binary Fluid Mixtures with Continuously Ramped Temperature

We consider the demixing of a binary fluid mixture, under gravity, which is steadily driven into a two phase region by slowly ramping the temperature. We assume, as a first approximation, that the system remains spatially isothermal, and examine the interplay of two competing nonlinearities. One of these arises because the supersaturation is greatest far from the meniscus, creating inversion of the density which can lead to fluid motion; although isothermal, this is somewhat like the Benard problem (a single-phase fluid heated from below). The other is the intrinsic diffusive instability which results either in nucleation or in spinodal decomposition at large supersaturations. Experimental results on a simple binary mixture show interesting oscillations in heat capacity and optical properties for a wide range of ramp parameters. We argue that these oscillations arise under conditions where both nonlinearities are important

Loss of solutions in shear banding fluids in shear banding fluids driven by second normal stress differences

Edge fracture occurs frequently in non-Newtonian fluids. A similar instability has often been reported at the free surface of fluids undergoing shear banding, and leads to expulsion of the sample. In this paper the distortion of the free surface of such a shear banding fluid is calculated by balancing the surface tension against the second normal stresses induced in the two shear bands, and simultaneously requiring a continuous and smooth meniscus. We show that wormlike micelles typically retain meniscus integrity when shear banding, but in some cases can lose integrity for a range of average applied shear rates during which one expects shear banding. This meniscus fracture would lead to ejection of the sample as the shear banding region is swept through. We further show that entangled polymer solutions are expected to display a propensity for fracture, because of their much larger second normal stresses. These calculations are consistent with available data in the literature. We also estimate the meniscus distortion of a three band configuration, as has been observed in some wormlike micellar solutions in a cone and plate geometry.Comment: 23 pages, to be published in Journal of Rheolog

Lattice Boltzmann Simulations of Liquid Crystal Hydrodynamics

We describe a lattice Boltzmann algorithm to simulate liquid crystal hydrodynamics. The equations of motion are written in terms of a tensor order parameter. This allows both the isotropic and the nematic phases to be considered. Backflow effects and the hydrodynamics of topological defects are naturally included in the simulations, as are viscoelastic properties such as shear-thinning and shear-banding.Comment: 14 pages, 5 figures, Revte

Adams and Olmsted Reply to comment on article "A non-monotonic constitutive model is not necessary to obtain shear banding phenomena in entangled polymer solution" [Phys. Rev. Lett. 102, 067801 (2009), arXiv:0805.0679]

Wang [Phys. Rev. Lett. 103, 219801 (2009)] makes the following points about our Letter [Phys. Rev. Lett. 102, 067801 (2009), arXiv:0805.0679]: (1) He infers that, "contrary to its title, shear banding emerged from monotonic curves only if there was a stress gradient", and he points out that nonquiescent relaxation was found (experimentally) after step strain in geometries without a stress gradient. (2) He disagrees with the values of the parameters we used. (3) In some recent experiments the flow was homogeneous after cessation of step strain, and only subsequently developed nonquiescent macroscopic motion. We only showed step strains that developed an inhomogeneity before cessation of flow. In this reply we address these points.Comment: Reply to Comment of S.-Q. Wang, Phys. Rev. Lett. 103, 219801 (2009

The activation energy for GaAs/AlGaAs interdiffusion

Copyright 1997 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. This article appeared in Journal of Applied Physics 82, 4842 (1997) and may be found at

Lateral phase separation in mixtures of lipids and cholesterol

In an effort to understand "rafts" in biological membranes, we propose phenomenological models for saturated and unsaturated lipid mixtures, and lipid-cholesterol mixtures. We consider simple couplings between the local composition and internal membrane structure, and their influence on transitions between liquid and gel membrane phases. Assuming that the gel transition temperature of the saturated lipid is shifted by the presence of the unsaturated lipid, and that cholesterol acts as an external field on the chain melting transition, a variety of phase diagrams are obtained. The phase diagrams for binary mixtures of saturated/unsaturated lipids and lipid/cholesterol are in semi-quantitative agreement with the experiments. Our results also apply to regions in the ternary phase diagram of lipid/lipid/cholesterol systems

Inhomogeneous High Frequency Expansion-Free Gravitational Waves

We describe a natural inhomogeneous generalization of high frequency plane gravitational waves. The waves are high frequency waves of the Kundt type whose null propagation direction in space-time has vanishing expansion, twist and shear but is not covariantly constant. The introduction of a cosmological constant is discussed in some detail and a comparison is made with high frequency gravity waves having wave fronts homeomorphic to 2-spheres.Comment: 18 pages, Latex file, accepted for publication in Physical Review