Dynamic behavior of stochastic gene expression models in the presence of bursting

This paper considers the behavior of discrete and continuous mathematical models for gene expression in the presence of transcriptional/translational bursting. We treat this problem in generality with respect to the distribution of the burst size as well as the frequency of bursting, and our results are applicable to both inducible and repressible expression patterns in prokaryotes and eukaryotes. We have given numerous examples of the applicability of our results, especially in the experimentally observed situation that burst size is geometrically or exponentially distributed.Comment: 22 page

Microscopic theory of glassy dynamics and glass transition for molecular crystals

We derive a microscopic equation of motion for the dynamical orientational correlators of molecular crystals. Our approach is based upon mode coupling theory. Compared to liquids we find four main differences: (i) the memory kernel contains Umklapp processes, (ii) besides the static two-molecule orientational correlators one also needs the static one-molecule orientational density as an input, where the latter is nontrivial, (iii) the static orientational current density correlator does contribute an anisotropic, inertia-independent part to the memory kernel, (iv) if the molecules are assumed to be fixed on a rigid lattice, the tensorial orientational correlators and the memory kernel have vanishing l,l'=0 components. The resulting mode coupling equations are solved for hard ellipsoids of revolution on a rigid sc-lattice. Using the static orientational correlators from Percus-Yevick theory we find an ideal glass transition generated due to precursors of orientational order which depend on X and p, the aspect ratio and packing fraction of the ellipsoids. The glass formation of oblate ellipsoids is enhanced compared to that for prolate ones. For oblate ellipsoids with X <~ 0.7 and prolate ellipsoids with X >~ 4, the critical diagonal nonergodicity parameters in reciprocal space exhibit more or less sharp maxima at the zone center with very small values elsewhere, while for prolate ellipsoids with 2 <~ X <~ 2.5 we have maxima at the zone edge. The off-diagonal nonergodicity parameters are not restricted to positive values and show similar behavior. For 0.7 <~ X <~ 2, no glass transition is found. In the glass phase, the nonergodicity parameters show a pronounced q-dependence.Comment: 17 pages, 12 figures, accepted at Phys. Rev. E. v4 is almost identical to the final paper version. It includes, compared to former versions v2/v3, no new physical content, but only some corrected formulas in the appendices and corrected typos in text. In comparison to version v1, in v2-v4 some new results have been included and text has been change

Variational tetrahedral meshing

In this paper, a novel Delaunay-based variational approach to isotropic tetrahedral meshing is presented. To achieve both robustness and efficiency, we minimize a simple mesh-dependent energy through global updates of both vertex positions and connectivity. As this energy is known to be the ∠1 distance between an isotropic quadratic function and its linear interpolation on the mesh, our minimization procedure generates well-shaped tetrahedra. Mesh design is controlled through a gradation smoothness parameter and selection of the desired number of vertices. We provide the foundations of our approach by explaining both the underlying variational principle and its geometric interpretation. We demonstrate the quality of the resulting meshes through a series of examples

StoBeDo: Simulation of the Stochastic Becker-Döring Equations

Simulation of the Stochastic Becker-Döring Equation

First passage times in homogeneous nucleation and self-assembly

18 pages, 9 FiguresMotivated by nucleation and molecular aggregation in physical, chemical and biological settings, we present a thorough analysis of the general problem of stochastic self-assembly of a fixed number of identical particles in a finite volume. We derive the Backward Kolmogorov equation (BKE) for the cluster probability distribution. From the BKE we study the distribution of times it takes for a single maximal cluster to be completed, starting from any initial particle configuration. In the limits of slow and fast self-assembly, we develop analytical approaches to calculate the mean cluster formation time and to estimate the first assembly time distribution. We find, both analytically and numerically, that faster detachment can lead to a shorter mean time to first completion of a maximum-sized cluster. This unexpected effect arises from a redistribution of trajectory weights such that upon increasing the detachment rate, paths that take a shorter time to complete a cluster become more likely

Nucleation time in stochastic Becker-Doring model

International audienc

Temps de premier passage pour la nucléation

International audienc