Viscoelastic response of contractile filament bundles

The actin cytoskeleton of adherent tissue cells often condenses into filament bundles contracted by myosin motors, so-called stress fibers, which play a crucial role in the mechanical interaction of cells with their environment. Stress fibers are usually attached to their environment at the endpoints, but possibly also along their whole length. We introduce a theoretical model for such contractile filament bundles which combines passive viscoelasticity with active contractility. The model equations are solved analytically for two different types of boundary conditions. A free boundary corresponds to stress fiber contraction dynamics after laser surgery and results in good agreement with experimental data. Imposing cyclic varying boundary forces allows us to calculate the complex modulus of a single stress fiber.Comment: Revtex with 24 pages, 7 Postscript figures included, accepted for publication in Phys. Rev.

An asymptotic form of the reciprocity theorem with applications in x-ray scattering

The emission of electromagnetic waves from a source within or near a non-trivial medium (with or without boundaries, crystalline or amorphous, with inhomogeneities, absorption and so on) is sometimes studied using the reciprocity principle. This is a variation of the method of Green's functions. If one is only interested in the asymptotic radiation fields the generality of these methods may actually be a shortcoming: obtaining expressions valid for the uninteresting near fields is not just a wasted effort but may be prohibitively difficult. In this work we obtain a modified form the reciprocity principle which gives the asymptotic radiation field directly. The method may be used to obtain the radiation from a prescribed source, and also to study scattering problems. To illustrate the power of the method we study a few pedagogical examples and then, as a more challenging application we tackle two related problems. We calculate the specular reflection of x rays by a rough surface and by a smoothly graded surface taking polarization effects into account. In conventional treatments of reflection x rays are treated as scalar waves, polarization effects are neglected. This is a good approximation at grazing incidence but becomes increasingly questionable for soft x rays and UV at higher incidence angles. PACs: 61.10.Dp, 61.10.Kw, 03.50.DeComment: 19 pages, 4 figure

The graded Jacobi algebras and (co)homology

Jacobi algebroids (i.e. `Jacobi versions' of Lie algebroids) are studied in the context of graded Jacobi brackets on graded commutative algebras. This unifies varios concepts of graded Lie structures in geometry and physics. A method of describing such structures by classical Lie algebroids via certain gauging (in the spirit of E.Witten's gauging of exterior derivative) is developed. One constructs a corresponding Cartan differential calculus (graded commutative one) in a natural manner. This, in turn, gives canonical generating operators for triangular Jacobi algebroids. One gets, in particular, the Lichnerowicz-Jacobi homology operators associated with classical Jacobi structures. Courant-Jacobi brackets are obtained in a similar way and use to define an abstract notion of a Courant-Jacobi algebroid and Dirac-Jacobi structure. All this offers a new flavour in understanding the Batalin-Vilkovisky formalism.Comment: 20 pages, a few typos corrected; final version to be published in J. Phys. A: Math. Ge

Gauge transformations and symmetries of integrable systems

We analyze several integrable systems in zero-curvature form within the framework of $SL(2,\R)$ invariant gauge theory. In the Drienfeld-Sokolov gauge we derive a two-parameter family of nonlinear evolution equations which as special cases include the Kortweg-de Vries (KdV) and Harry Dym equations. We find residual gauge transformations which lead to infinintesimal symmetries of this family of equations. For KdV and Harry Dym equations we find an infinite hierarchy of such symmetry transformations, and we investigate their relation with local conservation laws, constants of the motion and the bi-Hamiltonian structure of the equations. Applying successive gauge transformatinos of Miura type we obtain a sequence of gauge equivalent integrable systems, among them the modified KdV and Calogero KdV equations.Comment: 18pages, no figure Journal versio

Near-optimal mean value estimates for multidimensional Weyl sums

We obtain sharp estimates for multidimensional generalisations of Vinogradov's mean value theorem for arbitrary translation-dilation invariant systems, achieving constraints on the number of variables approaching those conjectured to be the best possible. Several applications of our bounds are discussed

Local and nonlocal solvable structures in ODEs reduction

Solvable structures, likewise solvable algebras of local symmetries, can be used to integrate scalar ODEs by quadratures. Solvable structures, however, are particularly suitable for the integration of ODEs with a lack of local symmetries. In fact, under regularity assumptions, any given ODE always admits solvable structures even though finding them in general could be a very difficult task. In practice a noteworthy simplification may come by computing solvable structures which are adapted to some admitted symmetry algebra. In this paper we consider solvable structures adapted to local and nonlocal symmetry algebras of any order (i.e., classical and higher). In particular we introduce the notion of nonlocal solvable structure

Interferometry of Direct Photons in Central 280Pb+208Pb Collisions at 158A GeV

Two-particle correlations of direct photons were measured in central 208Pb+208Pb collisions at 158 AGeV. The invariant interferometric radii were extracted for 100<K_T<300 MeV/c and compared to radii extracted from charged pion correlations. The yield of soft direct photons, K_T<300 MeV/c, was extracted from the correlation strength and compared to theoretical calculations.Comment: 5 pages, 4 figure

Mutational Biases and Selective Forces Shaping the Structure of Arabidopsis Genes

Recently features of gene expression profiles have been associated with structural parameters of gene sequences in organisms representing a diverse set of taxa. The emerging picture indicates that natural selection, mediated by gene expression profiles, has a significant role in determining genic structures. However the current situation is less clear in plants as the available data indicates that the effect of natural selection mediated by gene expression is very weak. Moreover, the direction of the patterns in plants appears to contradict those observed in animal genomes. In the present work we analized expression data for >18000 Arabidopsis genes retrieved from public datasets obtained with different technologies (MPSS and high density chip arrays) and compared them with gene parameters. Our results show that the impact of natural selection mediated by expression on genes sequences is significant and distinguishable from the effects of regional mutational biases. In addition, we provide evidence that the level and the breadth of gene expression are related in opposite ways to many structural parameters of gene sequences. Higher levels of expression abundance are associated with smaller transcripts, consistent with the need to reduce costs of both transcription and translation. Expression breadth, however, shows a contrasting pattern, i.e. longer genes have higher breadth of expression, possibly to ensure those structural features associated with gene plasticity. Based on these results, we propose that the specific balance between these two selective forces play a significant role in shaping the structure of Arabidopsis genes

Structure and mechanism of acetolactate decarboxylase

Acetolactate decarboxylase catalyzes the conversion of both enantiomers of acetolactate to the (R)-enantiomer of acetoin, via a mechanism that has been shown to involve a prior rearrangement of the non-natural (R)-enantiomer substrate to the natural (S)-enantiomer. In this paper, a series of crystal structures of ALDC complex with designed transition state mimics are reported. These structures, coupled with inhibition studies and site-directed mutagenesis provide an improved understanding of the molecular processes involved in the stereoselective decarboxylation/protonation events. A mechanism for the transformation of each enantiomer of acetolactate is proposed