Statistical distributions in the folding of elastic structures

The behaviour of elastic structures undergoing large deformations is the result of the competition between confining conditions, self-avoidance and elasticity. This combination of multiple phenomena creates a geometrical frustration that leads to complex fold patterns. By studying the case of a rod confined isotropically into a disk, we show that the emergence of the complexity is associated with a well defined underlying statistical measure that determines the energy distribution of sub-elements,``branches'', of the rod. This result suggests that branches act as the ``microscopic'' degrees of freedom laying the foundations for a statistical mechanical theory of this athermal and amorphous system

Digraphs and cycle polynomials for free-by-cyclic groups

Let \phi \in \mbox{Out}(F_n) be a free group outer automorphism that can be represented by an expanding, irreducible train-track map. The automorphism $\phi$ determines a free-by-cyclic group $\Gamma=F_n \rtimes_\phi \mathbb Z,$ and a homomorphism $\alpha \in H^1(\Gamma; \mathbb Z)$. By work of Neumann, Bieri-Neumann-Strebel and Dowdall-Kapovich-Leininger, $\alpha$ has an open cone neighborhood $\mathcal A$ in $H^1(\Gamma;\mathbb R)$ whose integral points correspond to other fibrations of $\Gamma$ whose associated outer automorphisms are themselves representable by expanding irreducible train-track maps. In this paper, we define an analog of McMullen's Teichm\"uller polynomial that computes the dilatations of all outer automorphism in $\mathcal A$.Comment: 41 pages, 20 figure

Effects of inherited structures on inversion tectonics: Examples from the Asturian Basin (NW Iberian Peninsula) interpreted in a Computer Assisted Virtual Environment (CAVE)

Map shows mid-nineteenth century Texas counties, major cities, towns, roads, railroads, and areas of Native American habitation. Includes detailed notes on map. Insets: "Plan of Sabine Lake," "Plan of the Northern Part of Texas," and "Plan of Galveston Bay." Relief shown by hachures. Depths shown by soundings on inset. Scales [ca. 1:2,350,000], [ca. 1: 529,000], [ca. 1:3,800,000], and [ca. 1:887,000]

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page