Influence of fluctuations in actin structure on myosin V step size

We study the influence of disorder in the helical actin structure on the myosin V step size, predicted from the elastic lever arm model. We show that fluctuations of +-5 degrees per actin subunit, as proposed by Egelman et al., significantly alter the distribution of step sizes and improve the agreement with experimental data.Comment: 5 pages, 4 figures, to appear in J. Chem. Inf. Mode

The binding dynamics of tropomyosin on actin

We discuss a theoretical model for the cooperative binding dynamics of tropomyosin to actin filaments. Tropomyosin binds to actin by occupying seven consecutive monomers. The model includes a strong attraction between attached tropomyosin molecules. We start with an empty lattice and show that the binding goes through several stages. The first stage represents fast initial binding and leaves many small vacancies between blocks of bound molecules. In the second stage the vacancies annihilate slowly as tropomyosin molecules detach and re-attach. Finally the system approaches equilibrium. Using a grain-growth model and a diffusion-coagulation model we give analytical approximations for the vacancy density in all regimes.Comment: REVTeX, 10 pages, 9 figures; to appear in Biophysical Journal; minor correction

Charge-carrier transport properties of ultrathin Pb films

The charge-carrier transport properties of ultrathin metallic films are analysed with ab-initio methods using the density functional theory (DFT) on free-standing single crystalline slabs in the thickness range between 1 and 8 monolayers and compared with experiments for Pb films on Si(111). A strong interplay between bandstructure, quantised in the direction normal to the ultrathin film, charge-carrier scattering mechanisms and magnetoconduction was found. Based on the bandstructure obtained from the DFT, we used standard Boltzmann transport theory in two dimensions to obtain results for the electronic transport properties of 2 to 8 monolayers thick Pb(111) slabs with and without magnetic field. Comparison of calculations and experiment for the thickness dependence of the dc conductivity shows that the dominant scattering mechanism of electrons is diffuse elastic interface scattering for which the assumption of identical scattering times for all subbands and directions, used in this paper, is a good approximation. Within this model we can explain the thickness dependences of the electric conductivity and of the Hall coefficient as well as the anomalous behaviour of the first Pb layer.Comment: 7 pages incl. 9 figures, submitted to the European Physical Journal

Nonlinear elastic and electronic properties of Mo_6S_3I_6 nanowires

The properties of Mo_6S_3I_6 nanowires were investigated with ab initio calculations based on the density-functional theory. The molecules build weakly coupled one-dimensional chains with three sulfur atoms in the bridging planes between the Mo octahedra, each dressed with six iodines. Upon uniaxial strain along the wires, each bridging plane shows two energy minima, one in the ground state with the calculated Young modulus Y=82 GPa, and one in the stretched state with Y=94 GPa. Both values are at least four times smaller than the experimental values and the origin of the discrepancy remains a puzzle. The ideal tensile strength is about 8.4 GPa, the chains break in the Mo-Mo bonds within the octahedra and not in the S bridges. The charge-carrier conductivity is strongly anisotropic and the Mo_6S_3I_6 nanowires behave as quasi-one-dimensional conductors in the whole range of investigated strains. The conductivity is extremely sensitive to strain, making this material very suitable for stain gauges. Very clean nanowires with good contacts may be expected to behave as ballistic quantum wires over lengths of several $\mu$m. On the other hand, with high-impedance contacts they are good candidates for the observation of Luttinger liquid behaviour. The pronounced 1D nature of the Mo_6S_3I_6 nanowires makes them a uniquely versatile and user-friendly system for the investigation of 1D physics.Comment: 7 pages, 8 figures include

Efficiency limits of the three-sphere swimmer

We consider a swimmer consisting of a collinear assembly of three spheres connected by two slender rods. This swimmer can propel itself forward by varying the lengths of the rods in a way that is not invariant under time reversal. Although any non-reciprocal strokes of the arms can lead to a net displacement, the energetic efficiency of the swimmer is strongly dependent on the details and sequences of these strokes, and also the sizes of the spheres. We define the efficiency of the swimmer using Lighthill's criterion, i.e., the power that is needed to pull the swimmer by an external force at a certain speed, divided by the power needed for active swimming with the same average speed. Here, we determine numerically the optimal stroke sequences and the optimal size ratio of the spheres, while limiting the maximum extension of the rods. Our calculation takes into account both far-field and near-field hydrodynamic interactions. We show that, surprisingly, the three-sphere swimmer with unequal spheres can be more efficient than the equally-sized case. We also show that the variations of efficiency with size ratio is not monotonic and there exists a specific size ratio at which the swimmer has the highest efficiency. We find that the swimming efficiency initially rises by increasing the maximum allowable extension of the rods, and then converges to a maximum value. We calculate this upper limit analytically and report the highest value of efficiency that the three-sphere swimmer can reach.Comment: 7 pages, 3 figure

Step Patterns on Vicinal Reconstructed Surfaces

Step patterns on vicinal $(2\times1)$ reconstructed surfaces of noble metals Au(110) and Pt(110), miscut towards the (100) orientation, are investigated. The free energy of the reconstructed surface with a network of crossing opposite steps is calculated in the strong chirality regime when the steps cannot make overhangs. It is explained why the steps are not perpendicular to the direction of the miscut but form in equilibrium a network of crossing steps which make the surface to look like a fish skin. The network formation is the consequence of competition between the -- predominantly elastic -- energy loss and entropy gain. It is in agreement with recent scanning-tunnelling-microscopy observations on vicinal Au(110) and Pt(110) surfaces.Comment: 11 pages with 5 eps figures in text. Uses psfig and elsart.sty (ELSEVIER Science). To be published in Surf. Sc

Elastically coupled molecular motors

We study the influence of filament elasticity on the motion of collective molecular motors. It is found that for a backbone flexibility exceeding a characteristic value (motor stiffness divided through the mean displacement between attached motors), the ability of motors to produce force reduces as compared to rigidly coupled motors, while the maximum velocity remains unchanged. The force-velocity-relation in two different analytic approximations is calculated and compared with Monte-Carlo simulations. Finally, we extend our model by introducing motors with a strain-dependent detachment rate. A remarkable crossover from the nearly hyperbolic shape of the Hill curve for stiff backbones to a linear force-velocity relation for very elastic backbones is found. With realistic model parameters we show that the backbone flexibility plays no role under physiological conditions in muscles, but it should be observable in certain in vitro assays.Comment: REVTeX, 13 pages, 11 figures; presentation improved; to appear in European Physical Journal B; a Java applet showing the simulation is accessible at http://www.physik.tu-muenchen.de/~avilfan/ecmm