R. C. Penner

We introduce a new model of proteins that extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be stored and manipulated as triples of permutations, and these methods are therefore amenable to fast computer implementation. Applications include the refinement of structural protein classifications and the prediction of geometric and other properties of proteins from their chemical structures.

We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be stored and manipulated as triples of permutations, and these methods are therefore amenable to fast computer implementation. Applications include the refinement of structural protein classifications and the prediction of geometric and other properties of proteins from their chemical structures.

Infinite presentations are given for all of the higher Torelli groups of once-punctured surfaces. In the case of the classical Torelli group, a finite presentation of the corresponding groupoid is also given, and finite presentations of the classical Torelli groups acting trivially on homology modulo N are derived for all N. Furthermore, the first Johnson homomorphism, which is defined from the classical Torelli group to the third exterior power of the homology of the surface, is shown to lift to an explicit canonical 1-cocycle of the Teichmüller space. The main tool for these results is the known mapping class group invariant ideal cell decomposition of the Teichmüller space.This new 1-cocycle is mapping class group equivariant, so various contractions of its powers yield various combinatorial (co)cycles of the moduli space of curves, which are also new. Our combinatorial construction can be related to former works of Kawazumi and the first-named author with the consequence that the algebra generated by the cohomology classes represented by the new cocycles is precisely the tautological algebra of the moduli space.There is finally a discussion of prospects for similarly finding cocycle lifts of the higher Johnson homomorphisms.

Infinite presentations are given for all of the higher Torelli groups of once-punctured surfaces. In the case of the classical Torelli group, a finite presentation of the corresponding groupoid is also given, and finite presentations of the classical Torelli groups acting trivially on homology modulo N are derived for all N. Furthermore, the first Johnson homomorphism, which is defined from the classical Torelli group to the third exterior power of the homology of the surface, is shown to lift to an explicit canonical 1-cocycle of the Teichmueller space. The main tool for these results is the known mapping class group invariant ideal cell decomposition of the Teichmueller space. This new 1-cocycle is mapping class group equivariant, so various contractions of its powers yield various combinatorial (co)cycles of the moduli space of curves, which are also new. Our combinatorial construction can be related to former works of Kawazumi and the first-named author with the consequence that the algebra generated by the cohomology classes represented by the new cocycles is precisely the tautological algebra of the moduli space. There is finally a discussion of prospects for similarly finding cocycle lifts of the higher Johnson homomorphisms.

Several topological and homological operads based on families of projectively weighted arcs in bounded surfaces are introduced and studied. The spaces underlying the basic operad are identified with open subsets of a compactification due to Penner of a space closely related to Riemann's moduli space. Algebras over these operads are shown to be Batalin-Vilkovisky algebras, where the entire BV structure is realized simplicially. Furthermore, our basic operad contains the cacti operad up to homotopy, and it similarly acts on the loop space of any topological space. New operad structures on the circle are classified and combined with the basic operad to produce geometrically natural extensions of the algebraic structure of BV algebras, which are also computed.Comment: Published by Geometry and Topology at http://www.maths.warwick.ac.uk/gt/GTVol7/paper15.abs.htm

Several new families of wavelets, which are derived from earlier work by the author on Teichmüller theory, are introduced and studied. These wavelets are associated with the modular group rather than the affine group of the real line as for classical wavelets. In further contrast to the usual setting, there are explicit and essentially algebraic formulas relating wavelet and Fourier expansions. Furthermore, rather than relying on equally spaced multiscale sampling methods, the wavelet expansions introduced here rely instead on an explicit, nonuniformly spaced, multiscale sampling method that depends upon the Farey sequence of classical number theory. These ingredients combine to give novel methods for calculating wavelet, Fourier, and Hilbert transforms with potential applications to myriad problems in electrical engineering. By employing a new characteristic length associated to 2 × 2 matrices, finiteness and convergence properties of the wavelet expansions are derived. For functions with more than 5/2 derivatives inL², one of our wavelet families forms a frame and the Hilbert transform is calculable in hyperbolic coordinates.