arXiv subjects

Alex J. Levine

Publications and source records attributed to Alex J. Levine.

At least 37 records · Page 2Linked to original sources

arXiv2008

Buckling and force propagation along intracellular microtubules

Motivated by recent experiments showing the buckling of microtubules in cells, we study theoretically the mechanical response of, and force propagation along elastic filaments embedded in a non-linear elastic medium. We find that, although embedded microtubules still buckle when their compressive load exceeds the critical value $f_c$ found earlier, the resulting deformation is restricted to a penetration depth that depends on both the non-linear material properties of the surrounding cytoskeleton, as well as the direct coupling of the microtubule to the cytoskeleton. The deformation amplitude depends on the applied load $f$ as $(f- f_c)^{1/2}$. This work shows how the range of compressive force transmission by microtubules can be as large as tens of microns and is governed by the mechanical coupling to the surrounding cytoskeleton.

cond-mat.soft↗

arXiv2007

Corrections to the Saffman-Delbruck mobility for membrane bound proteins

Recent experiments by Y. Gambin et al. [PNAS 103, 2098 (2006)] have called into question the applicability of the Saffman-Delbruck diffusivity for proteins embedded in the lipid bilayers. We present a simple argument to account for this observation that should be generically valid for a large class of transmembrane and membrane bound proteins. Whenever the protein-lipid interactions locally deform the membrane, that deformation generates new hydrodynamic stresses on the protein-membrane complex leading to a suppression of its mobility. We show that this suppression depends on the protein size in a manner consistent with the work of Y. Gambin et al.

cond-mat.soft↗

arXiv2007

Non-equilibrium mechanics and dynamics of motor activated gels

The mechanics of cells is strongly affected by molecular motors that generate forces in the cellular cytoskeleton. We develop a model for cytoskeletal networks driven out of equilibrium by molecular motors exerting transient contractile stresses. Using this model we show how motor activity can dramatically increase the network's bulk elastic moduli. We also show how motor binding kinetics naturally leads to enhanced low-frequency stress fluctuations that result in non-equilibrium diffusive motion within an elastic network, as seen in recent \emph{in vitro} and \emph{in vivo} experiments.

cond-mat.soft↗

arXiv2007

The effect of curvature and topology on membrane hydrodynamics

We study the mobility of extended objects (rods) on a spherical liquid-liquid interface to show how this quantity is modified in a striking manner by both the curvature and the topology of the interface. We present theoretical calculations and experimental measurements of the interfacial fluid velocity field around a moving rod bound to the crowded interface of a water-in-oil droplet. By using different droplet sizes, membrane viscosities, and rod lengths, we show that the viscosity mismatch between the interior and exterior fluids leads to a suppression of the fluid flow on small droplets that cannot be captured by the flat interface predictions.

cond-mat.soft↗

arXiv2007

Rheology and Contact Lifetime Distribution in Dense Granular Flows

We study the rheology and distribution of interparticle contact lifetimes for gravity-driven, dense granular flows of non-cohesive particles down an inclined plane using large-scale, three dimensional, granular dynamics simulations. Rather than observing a large number of long-lived contacts as might be expected for dense flows, brief binary collisions predominate. In the hard particle limit, the rheology conforms to Bagnold scaling, where the shear stress is quadratic in the strain rate. As the particles are made softer, however, we find significant deviations from Bagnold rheology; the material flows more like a viscous fluid. We attribute this change in the collective rheology of the material to subtle changes in the contact lifetime distribution involving the increasing lifetime and number of the long-lived contacts in the softer particle systems.

cond-mat.soft↗

arXiv2007

Unfolding cross-linkers as rheology regulators in F-actin networks

We report on the nonlinear mechanical properties of a statistically homogeneous, isotropic semiflexible network cross-linked by polymers containing numerous small unfolding domains, such as the ubiquitous F-actin cross-linker Filamin. We show that the inclusion of such proteins has a dramatic effect on the large strain behavior of the network. Beyond a strain threshold, which depends on network density, the unfolding of protein domains leads to bulk shear softening. Past this critical strain, the network spontaneously organizes itself so that an appreciable fraction of the Filamin cross-linkers are at the threshold of domain unfolding. We discuss via a simple mean-field model the cause of this network organization and suggest that it may be the source of power-law relaxation observed in in vitro and in intracellular microrheology experiments. We present data which fully justifies our model for a simplified network architecture.

cond-mat.soft↗

arXiv2006

Intermolecular Adhesion in Conjugated Polymers

Conjugated polymers are observed to aggregate in solution. To account for this observation we propose a inter-chain binding mechanism based on the intermolecular tunneling of the delocalized $π$-electrons occurring at points where the polymers cross. This tunneling mechanism predicts specific bound structures of chain that depend on whether they are semiconducting or metallic. Semiconducting chains should form polyacene-like states exhibiting binding at every other site, while (doped) metallic chains can bind at each site. We also show that solitons co-localize with the intermolecular binding sites thereby strengthening the binding effect and investigate the conformational statistics of the resulting bimolecular aggregates.

cond-mat.soft↗

arXiv2006

Capillary wave dynamics on supported viscoelastic films: Single and double layers

We study the capillary wave dynamics of a single viscoelastic supported film and of a double layer of immiscible viscoelastic supported films. Using both simple scaling arguments and a continuum hydrodynamic theory, we investigate the effects of viscoelasticity and interfacial slip on the relaxation dynamics of these capillary waves. Our results account for the recent observation of a wavelength-independent decay rate for capillary waves in a supported polystyrene/brominated polystyrene double layer [X. Hu {\em et al.}, Phys. Rev. E {\bf 74}, 010602 (R) (2006)].

cond-mat.soft↗

arXiv2006

Filamin cross-linked semiflexible networks: Fragility under strain

The semiflexible F-actin network of the cytoskeleton is cross-linked by a variety of proteins including filamin, which contain Ig-domains that unfold under applied tension. We examine a simple semiflexible network model cross-linked by such unfolding linkers that captures the main mechanical features of F-actin networks cross-linked by filamin proteins and show that under sufficiently high strain the network spontaneously self-organizes so that an appreciable fraction of the filamin cross-linkers are at the threshold of domain unfolding. We propose an explanation of this organization based on a mean-field model and suggest a qualitative experimental signature of this type of network reorganization under applied strain that may be observable in intracellular microrheology experiments of Crocker et al.

cond-mat.soft↗

arXiv2005

Plug flow and the breakdown of Bagnold scaling in cohesive granular flows

Cohesive granular media flowing down an inclined plane are studied by discrete element simulations. Previous work on cohesionless granular media demonstrated that within the steady flow regime where gravitational energy is balanced by dissipation arising from intergrain forces, the velocity profile in the flow direction scales with depth in a manner consistent with the predictions of Bagnold. Here we demonstrate that this Bagnold scaling does not hold for the analogous steady-flows in cohesive granular media. We develop a generalization of the Bagnold constitutive relation to account for our observation and speculate as to the underlying physical mechanisms responsible for the different constitutive laws for cohesive and noncohesive granular media.

cond-mat.soft↗

arXiv2004

The nonlinear elasticity of an $α$-helical polypeptide: Monte Carlo studies

We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local chain bending modulus. We compute numerically the bending and stretching compliances of this molecule as well as the nonlinear interaction between stretching and torque over a wide range of model parameters. The numerical results agree well with previous mean-field and perturbative calculations where they are expected to do so. The Monte Carlo simulations allow us to examine the response of the chain to large forces and torques where the perturbative approaches fail. In addition we extend our mean-field analysis by studying the fluctuation dominated regime at the force-induced denaturation transition.

cond-mat.soft↗

arXiv2004

The nonlinear elasticity of an $α$-helical polypeptide

We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending modulus. Using this model we compute the extensional compliance of an alpha-helix under tensile stress, the bending compliance of the molecule under externally imposed torques, and the nonlinear interaction of such torques and forces on the molecule. We find that, due to coupling of the ``internal'' secondary structure variables to the conformational degrees of freedom of the polymer, the molecule has a highly nonlinear response to applied stress and force couples. In particular we demonstrate a sharp lengthening transition under applied force and a buckling transition under applied torque. Finally, we speculate that the inherent bistability of the molecule may underlie protein conformational change \emph{in vivo}.

cond-mat.stat-mech↗

arXiv2004

Intermolecular adhesion in conducting polymers

We analyze the interaction of two conducting, charged polymer chains in solution using a minimal model for their electronic degrees of freedom. We show that a crossing of the two chains in which the polymers pass within Angstroms of each other leads to a decrease of the electronic energy of the combined system that is significantly larger than the thermal energy and thus promotes interchain aggregation. We consider the competition of this attractive interaction with the screened electrostatic repulsion and thereby propose a phase diagram for such polymers in solution; depending on the charge density and persistence length of the chains, the polymers may be unbound, bound in loose, braid-like structures, or tightly bound in a parallel configuration.

cond-mat.soft↗

arXiv2004

The helix--coil transition on the worm--like chain

I propose a variation of the standard worm--like chain model to account for internal order parameter (helix/coil) fields on the polymer chain. This internal order parameter field influences polymer conformational statistics by locally modifying the persistence length of the chain. Using this model, I make predictions for the bending and stretching response of an alpha-helical domain of a protein. In particular, I show that alpha-helical protein domains will buckle under applied torque. This highly nonlinear elastic behavior may be important in the understanding of allosteric control of biochemical pathways.

cond-mat.soft↗

arXiv2003

Dynamics of rigid and flexible extended bodies in viscous films and membranes

We study the dynamics of extended rod-like bodies in (or associated with) membranes and films. We demonstrate a striking difference between the mobilities in films and bulk fluids, even when the dissipation is dominated by the fluid stress: for large inclusions we find that rotation and motion perpendicular to the rod axis exhibits purely local drag, in which the drag coefficient is algebraic in the rod dimensions. We also study the dynamics of the {\em internal} modes of a semiflexible inclusion and find two dynamical regimes in the relaxation spectrum.

cond-mat.soft↗

arXiv2003

On the mobility of extended bodies in viscous films and membranes

We develop general methods to calculate the mobilities of extended bodies in (or associated with) membranes and films. We demonstrate a striking difference between in-plane motion of rod-like inclusions and the corresponding case of bulk (three-dimensional) fluids: for rotations and motion perpendicular to the rod axis, we find purely local drag, in which the drag coefficient is purely algebraic in the rod dimensions. These results, as well as the calculational methods are applicable to such problems as the diffusion of objects in or associated with Langmuir films and lipid membranes. The methods can also be simply extended to treat viscoelastic systems.

cond-mat.soft↗

arXiv2001

Stability of Monomer-Dimer Piles

We measure how strong, localized contact adhesion between grains affects the maximum static critical angle, theta_c, of a dry sand pile. By mixing dimer grains, each consisting of two spheres that have been rigidly bonded together, with simple spherical monomer grains, we create sandpiles that contain strong localized adhesion between a given particle and at most one of its neighbors. We find that tan(theta_c) increases from 0.45 to 1.1 and the grain packing fraction, Phi, decreases from 0.58 to 0.52 as we increase the relative number fraction of dimer particles in the pile, nu_d, from 0 to 1. We attribute the increase in tan(theta_c(nu_d)) to the enhanced stability of dimers on the surface, which reduces the density of monomers that need to be accomodated in the most stable surface traps. A full characterization and geometrical stability analysis of surface traps provides a good quantitative agreement between experiment and theory over a wide range of nu_d, without any fitting parameters.

cond-mat.soft↗

arXiv2001

Shear-induced Diffusion in Dilute Suspensions of Charged Colloids

We propose a model for the nonequilibrium enhancement of colloidal self-diffusion in an externally imposed shear flow in charged systems. The enhancement of diffusion is calculated in terms of the electrostatic, two--body interactions between the particles in the shear flow. In the high shear rate, low volume fraction limit in which our model is valid, we compare these calculations to the experiments of Qiu et al. [Phys. Rev. Lett. 61, 2554 (1988)].

cond-mat.soft↗