Biomedical subjects

Alex J Levine

Publications and source records attributed to Alex J Levine.

11 recordsLinked to original sources

PubMed2006

Nonlinear elasticity of an alpha-helical polypeptide: Monte Carlo studies.

We report on Monte Carlo studies of the elastic properties of the helix-coil wormlike 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 characterize the nonlinear elastic properties of these molecules including their response to applied tensile forces and bending torques both individually and in combination. We find a pronounced effect of applied torque on the extensional compliance of the molecule and a similar effect of tension on the bending compliance. Finally we speculate that the strongly nonlinear response of alpha-helical polypeptides to combinations of torque and force plays a role in allosteric transitions in proteins.

Elasticity↗

PubMed2006

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 contains Ig domains that unfold under applied tension. We examine a simple filament 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 sufficient 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 and test a mean-field model to account for this effect. We also 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.

Actins↗

PubMed2005

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.

Journal Article↗

PubMed2005

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, braidlike structures, or tightly bound in a parallel configuration.

Journal Article↗

PubMed2005

Nonlinear elasticity of an alpha -helical polypeptide.

We study a minimal extension of the wormlike chain model to describe polypeptides having alpha-helical secondary structure. In this model the presence or 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 in vivo.

Computer Simulation↗

PubMed2004

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

We study the dynamics of extended rodlike 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 exhibit purely local drag, in which the drag coefficient is algebraic in the rod dimensions. We also study the dynamics of the internal modes of a semiflexible inclusion and find two dynamical regimes in the relaxation spectrum.

Elasticity↗

PubMed2004

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 rodlike 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. These methods can also be simply extended to treat viscoelastic systems.

Cell Membrane↗

PubMed2003

Deformation of cross-linked semiflexible polymer networks.

Networks of filamentous proteins play a crucial role in cell mechanics. These cytoskeletal networks, together with various cross-linking and other associated proteins largely determine the (visco)elastic response of cells. In this Letter we study a model system of cross-linked, stiff filaments in order to explore the connection between the microstructure under strain and the macroscopic response of cytoskeletal networks. We find two distinct regimes as a function primarily of cross-link density and filament rigidity: one characterized by affine deformation and one by nonaffine deformation. We characterize the crossover between these two.

Biopolymers↗

PubMed2002

Dynamics of viscoelastic membranes.

We determine both the in-plane and out-of-plane dynamics of viscoelastic membranes separating two viscous fluids in order to understand microrheological studies of such membranes. We demonstrate the general viscoelastic signatures in the dynamics of shear, bending, and compression modes. We show that these modes remain independent in the presence of hydrodynamic interactions. The full response functions for motion both in-plane and out-of-plane are derived for the general case of viscoelastic films in contact with arbitrary viscous fluids. Specifically, we derive closed-form expressions for the in-plane longitudinal and transverse response functions for viscous membranes embedded in fluid media. We also find a screening of the otherwise two-dimensional character of the response to point forces due to the presence of the solvent.

Journal Article↗

PubMed2002

Stability of monomer-dimer piles.

We present an experimental and theoretical study of piles consisting of monodisperse spherical grains mixed with a weight fraction nu(d) of dimer grains made by the rigid bonding of two such spherical grains. The maximum static angle of stability tantheta(c) of the pile increases from 0.45 to 1.1 and the grain packing fraction Phi decreases from 0.58 to 0.52 as nu(d) is increased from 0 to 1. The stability of these piles appears to be controlled by the grains sitting on the surface, which roll out of their local "traps" as the tilt angle is increased. We attribute the increase in tan theta(c)(nu(d)) to the enhanced stability of dimers on the surface, such that at higher tilt angles, there are sufficiently many stable surface traps available to accommodate the reduced density of monomers on the surface. A full characterization of the grain-scale roughness of the surface is required to quantitatively account for the changes in theta(c) with nu(d).

Journal Article↗

PubMed2001

Two-point microrheology and the electrostatic analogy.

The recent experiments of Crocker et al. [Phys. Rev. Lett. 85, 888 (2000)] suggest that microrheological measurements obtained from the correlated fluctuations of widely-separated probe particles determine the rheological properties of soft, complex materials more accurately than do the more traditional particle autocorrelations. This presents an interesting problem in viscoelastic dynamics. We develop an important, simplifying analogy between the present viscoelastic problem and classical electrostatics. Using this analogy and direct calculation we analyze both the one- and two-particle correlations in a viscoelastic medium in order to explain this observation.

Journal Article↗