Internal protein dynamics shifts the distance to the mechanical transition state

Mechanical unfolding of polyproteins by force spectroscopy provides valuable insight into their free energy landscapes. Most experiments of the unfolding process have been fit to two-state and/or one dimensional models, with the details of the protein and its dynamics often subsumed into a zero-force unfolding rate and a distance x(u)(1D) to the transition state. We consider the entire phase space of a model protein under a constant force, and show that x(u)(1D) contains a sizeable contribution from exploring the full multidimensional energy landscape. This effect is greater for proteins with many degrees of freedom that are affected by force; and surprisingly, we predict that externally attached flexible linkers also contribute to the measured unfolding characteristics

Instability of Myelin Tubes under Dehydration: deswelling of layered cylindrical structures

We report experimental observations of an undulational instability of myelin figures. Motivated by this, we examine theoretically the deformation and possible instability of concentric, cylindrical, multi-lamellar membrane structures. Under conditions of osmotic stress (swelling or dehydration), we find a stable, deformed state in which the layer deformation is given by \delta R ~ r^{\sqrt{B_A/(hB)}}, where B_A is the area compression modulus, B is the inter-layer compression modulus, and h is the repeat distance of layers. Also, above a finite threshold of dehydration (or osmotic stress), we find that the system becomes unstable to undulations, first with a characteristic wavelength of order \sqrt{xi d_0}, where xi is the standard smectic penetration depth and d_0 is the thickness of dehydrated region.Comment: 5 pages + 3 figures [revtex 4

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 of Rigid-Rod Suspensions in Shear Flow

We analyze the behavior of a suspension of rigid rod-like particles in shear flow using a modified version of the Doi model, and construct diagrams for phase coexistence under conditions of constant imposed stress and constant imposed strain rate, among paranematic, flow-aligning nematic, and log-rolling nematic states. We calculate the effective constitutive relations that would be measured through the regime of phase separation into shear bands. We calculate phase coexistence by examining the stability of interfacial steady states and find a wide range of possible ``phase'' behaviors.Comment: 23 pages 19 figures, revised version to be published in Physical Review

Effect of Ordering on Spinodal Decomposition of Liquid-Crystal/Polymer Mixtures

Partially phase-separated liquid-crystal/polymer dispersions display highly fibrillar domain morphologies that are dramatically different from the typical structures found in isotropic mixtures. To explain this, we numerically explore the coupling between phase ordering and phase separation kinetics in model two-dimensional fluid mixtures phase separating into a nematic phase, rich in liquid crystal, coexisting with an isotropic phase, rich in polymer. We find that phase ordering can lead to fibrillar networks of the minority polymer-rich phase

A molecular dynamics simulation of polymer crystallization from oriented amorphous state

Molecular process of crystallization from an oriented amorphous state was reproduced by molecular dynamics simulation for a realistic polyethylene model. Initial oriented amorphous state was obtained by uniaxial drawing an isotropic glassy state at 100 K. By the temperature jump from 100 K to 330 K, there occurred the crystallization into the fiber structure, during the process of which we observed the developments of various order parameters. The real space image and its Fourier transform revealed that a hexagonally ordered domain was initially formed, and then highly ordered crystalline state with stacked lamellae developed after further adjustment of the relative heights of the chains along their axes.Comment: 4 pages, 3 figure

Rheological Chaos in a Scalar Shear-Thickening Model

We study a simple scalar constitutive equation for a shear-thickening material at zero Reynolds number, in which the shear stress \sigma is driven at a constant shear rate \dot\gamma and relaxes by two parallel decay processes: a nonlinear decay at a nonmonotonic rate R(\sigma_1) and a linear decay at rate \lambda\sigma_2. Here \sigma_{1,2}(t) = \tau_{1,2}^{-1}\int_0^t\sigma(t')\exp[-(t-t')/\tau_{1,2}] {\rm d}t' are two retarded stresses. For suitable parameters, the steady state flow curve is monotonic but unstable; this arises when \tau_2>\tau_1 and 0>R'(\sigma)>-\lambda so that monotonicity is restored only through the strongly retarded term (which might model a slow evolution of material structure under stress). Within the unstable region we find a period-doubling sequence leading to chaos. Instability, but not chaos, persists even for the case \tau_1\to 0. A similar generic mechanism might also arise in shear thinning systems and in some banded flows.Comment: Reference added; typos corrected. To appear in PRE Rap. Com

Shear-banding in a lyotropic lamellar phase, Part 1: Time-averaged velocity profiles

Using velocity profile measurements based on dynamic light scattering and coupled to structural and rheological measurements in a Couette cell, we present evidences for a shear-banding scenario in the shear flow of the onion texture of a lyotropic lamellar phase. Time-averaged measurements clearly show the presence of structural shear-banding in the vicinity of a shear-induced transition, associated to the nucleation and growth of a highly sheared band in the flow. Our experiments also reveal the presence of slip at the walls of the Couette cell. Using a simple mechanical approach, we demonstrate that our data confirms the classical assumption of the shear-banding picture, in which the interface between bands lies at a given stress $\sigma^\star$. We also outline the presence of large temporal fluctuations of the flow field, which are the subject of the second part of this paper [Salmon {\it et al.}, submitted to Phys. Rev. E]

Conformational transitions of a semiflexible polymer in nematic solvents

Conformations of a single semiflexible polymer chain dissolved in a low molecular weight liquid crystalline solvents (nematogens) are examined by using a mean field theory. We takes into account a stiffness and partial orientational ordering of the polymer. As a result of an anisotropic coupling between the polymer and nematogen, we predict a discontinuous (or continuous) phase transition from a condensed-rodlike conformation to a swollen-one of the polymer chain, depending on the stiffness of the polymer. We also discuss the effects of the nematic interaction between polymer segments.Comment: 4 pages, 4 figure

Non-local rheology in dense granular flows -- Revisiting the concept of fluidity

Granular materials belong to the class of amorphous athermal systems, like foams, emulsion or suspension they can resist shear like a solid, but flow like a liquid under a sufficiently large applied shear stress. They exhibit a dynamical phase transition between static and flowing states, as for phase transitions of thermodynamic systems, this rigidity transition exhibits a diverging length scales quantifying the degree of cooperatively. Several experiments have shown that the rheology of granular materials and emulsion is non-local, namely that the stress at a given location does not depend only on the shear rate at this location but also on the degree of mobility in the surrounding region. Several constitutive relations have recently been proposed and tested successfully against numerical and experimental results. Here we use discrete elements simulation of 2D shear flows to shed light on the dynamical mechanism underlying non-locality in dense granular flows