Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space

We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors approximately local deformations of the chain. The degree of bias is controlled by a parameter b. The method is tested on a reduced model protein with 54 amino acids and the Ramachandran torsion angles as its only degrees of freedom, for different b. Without excessive fine tuning, we find that the effective step size can be increased by a factor of three compared to the unbiased b=0 case. The method may be useful for kinetic studies, too.Comment: 14 pages, 4 figure

Requirements for contractility in disordered cytoskeletal bundles

Actomyosin contractility is essential for biological force generation, and is well understood in highly organized structures such as striated muscle. Additionally, actomyosin bundles devoid of this organization are known to contract both in vivo and in vitro, which cannot be described by standard muscle models. To narrow down the search for possible contraction mechanisms in these systems, we investigate their microscopic symmetries. We show that contractile behavior requires non-identical motors that generate large enough forces to probe the nonlinear elastic behavior of F-actin. This suggests a role for filament buckling in the contraction of these bundles, consistent with recent experimental results on reconstituted actomyosin bundles.Comment: 10 pages, 6 figures; text shortene

Contractile units in disordered actomyosin bundles arise from F-actin buckling

Bundles of filaments and motors are central to contractility in cells. The classic example is striated muscle, where actomyosin contractility is mediated by highly organized sarcomeres which act as fundamental contractile units. However, many contractile bundles in vivo and in vitro lack sarcomeric organization. Here we propose a model for how contractility can arise in actomyosin bundles without sarcomeric organization and validate its predictions with experiments on a reconstituted system. In the model, internal stresses in frustrated arrangements of motors with diverse velocities cause filaments to buckle, leading to overall shortening. We describe the onset of buckling in the presence of stochastic actin-myosin detachment and predict that buckling-induced contraction occurs in an intermediate range of motor densities. We then calculate the size of the "contractile units" associated with this process. Consistent with these results, our reconstituted actomyosin bundles contract at relatively high motor density, and we observe buckling at the predicted length scale.Comment: 5 pages, 4 figures, Supporting text and movies attache

Depairing critical current achieved in superconducting thin films with through-thickness arrays of artificial pinning centers

Large area arrays of through-thickness nanoscale pores have been milled into superconducting Nb thin films via a process utilizing anodized aluminum oxide thin film templates. These pores act as artificial flux pinning centers, increasing the superconducting critical current, Jc, of the Nb films. By optimizing the process conditions including anodization time, pore size and milling time, Jc values approaching and in some cases matching the Ginzburg-Landau depairing current of 30 MA/cm^2 at 5 K have been achieved - a Jc enhancement over as-deposited films of more than 50 times. In the field dependence of Jc, a matching field corresponding to the areal pore density has also been clearly observed. The effect of back-filling the pores with magnetic material has then been investigated. While back-filling with Co has been successfully achieved, the effect of the magnetic material on Jc has been found to be largely detrimental compared to voids, although a distinct influence of the magnetic material in producing a hysteretic Jc versus applied field behavior has been observed. This behavior has been tested for compatibility with currently proposed models of magnetic pinning and found to be most closely explained by a model describing the magnetic attraction between the flux vortices and the magnetic inclusions.Comment: 9 pages, 10 figure

Structural Responses of Quasi-2D Colloid Fluids to Excitations Elicited by Nonequilibrium Perturbations

We investigate the response of a dense monodisperse quasi-two-dimensional (q2D) colloid suspension when a particle is dragged by a constant velocity optical trap. Consistent with microrheological studies of other geometries, the perturbation induces a leading density wave and trailing wake, and we use Stokesian Dynamics (SD) simulations to parse direct colloid-colloid and hydrodynamic interactions. We go on to analyze the underlying individual particle-particle collisions in the experimental images. The displacements of particles form chains reminiscent of stress propagation in sheared granular materials. From these data, we can reconstruct steady-state dipolar flow patterns that were predicted for dilute suspensions and previously observed in granular analogs to our system. The decay of this field differs, however, from point Stokeslet calculations, indicating that the finite size of the colloids is important. Moreover, there is a pronounced angular dependence that corresponds to the surrounding colloid structure, which evolves in response to the perturbation. Put together, our results show that the response of the complex fluid is highly anisotropic owing to the fact that the effects of the perturbation propagate through the structured medium via chains of colloid-colloid collisions

Exact Solution of the Munoz-Eaton Model for Protein Folding

A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for a generic protein, for any choice of the energy and entropy parameters, and in principle allows the model to be used as a first tool to characterize the dynamics of a protein of known native state and equilibrium population. Applications to a $\beta$-hairpin and to protein CI-2, with comparisons to previous results, are also shown.Comment: 4 pages, 5 figures, RevTeX 4. To be published in Phys. Rev. Let