Complex surface singularities with integral homology sphere links

While the topological types of {normal} surface singularities with homology sphere link have been classified, forming a rich class, until recently little was known about the possible analytic structures. We proved in [Geom. Topol. 9(2005) 699-755] that many of them can be realized as complete intersection singularities of "splice type", generalizing Brieskorn type. We show that a normal singularity with homology sphere link is of splice type if and only if some naturally occurring knots in the singularity link are themselves links of hypersurface sections of the singular point. The Casson Invariant Conjecture (CIC) asserts that for a complete intersection surface singularity whose link is an integral homology sphere, the Casson invariant of that link is one-eighth the signature of the Milnor fiber. In this paper we prove CIC for a large class of splice type singularities. The CIC suggests (and is motivated by the idea) that the Milnor fiber of a complete intersection singularity with homology sphere link Sigma should be a 4-manifold canonically associated to Sigma. We propose, and verify in a non-trivial case, a stronger conjecture than the CIC for splice type complete intersections: a precise topological description of the Milnor fiber. We also point out recent counterexamples to some overly optimistic earlier conjectures in [Trends in Singularities, Birkhauser (2002) 181--190 and Math. Ann. 326(2003) 75--93].Comment: Published by Geometry and Topology at http://www.maths.warwick.ac.uk/gt/GTVol9/paper18.abs.htm

Alexander representation of tangles

A tangle is an oriented 1-submanifold of the cylinder whose endpoints lie on the two disks in the boundary of the cylinder. Using an algebraic tool developed by Lescop, we extend the Burau representation of braids to a functor from the category of oriented tangles to the category of Z[t,t^{-1}]-modules. For (1,1)-tangles (i.e., tangles with one endpoint on each disk) this invariant coincides with the Alexander polynomial of the link obtained by taking the closure of the tangle. We use the notion of plat position of a tangle to give a constructive proof of invariance in this case.Comment: 13 pages, 5 figure

A Large k Asymptotics of Witten's Invariant of Seifert Manifolds

We calculate a large $k$ asymptotic expansion of the exact surgery formula for Witten's $SU(2)$ invariant of Seifert manifolds. The contributions of all flat connections are identified. An agreement with the 1-loop formula is checked. A contribution of the irreducible connections appears to contain only a finite number of terms in the asymptotic series. A 2-loop correction to the contribution of the trivial connection is found to be proportional to Casson's invariant.Comment: 51 pages (Some changes are made to the Discussion section. A surgery formula for perturbative corrections to the contribution of the trivial connection is suggested.

A Contribution of the Trivial Connection to Jones Polynomial and Witten's Invariant of 3d Manifolds I

We use the Chern-Simons quantum field theory in order to prove a recently conjectured limitation on the 1/K expansion of the Jones polynomial of a knot and its relation to the Alexander polynomial. This limitation allows us to derive a surgery formula for the loop corrections to the contribution of the trivial connection to Witten's invariant. The 2-loop part of this formula coincides with Walker's surgery formula for Casson-Walker invariant. This proves a conjecture that Casson-Walker invariant is a 2-loop correction to the trivial connection contribution to Witten's invariant of a rational homology sphere. A contribution of the trivial connection to Witten's invariant of a manifold with nontrivial rational homology is calculated for the case of Seifert manifolds.Comment: 28 page

A TQFT associated to the LMO invariant of three-dimensional manifolds

We construct a Topological Quantum Field Theory (in the sense of Atiyah) associated to the universal finite-type invariant of 3-dimensional manifolds, as a functor from the category of 3-dimensional manifolds with parametrized boundary, satisfying some additional conditions, to an algebraic-combinatorial category. It is built together with its truncations with respect to a natural grading, and we prove that these TQFTs are non-degenerate and anomaly-free. The TQFT(s) induce(s) a (series of) representation(s) of a subgroup ${\cal L}_g$ of the Mapping Class Group that contains the Torelli group. The N=1 truncation produces a TQFT for the Casson-Walker-Lescop invariant.Comment: 28 pages, 13 postscript figures. Version 2 (Section 1 has been considerably shorten, and section 3 has been slightly shorten, since they will constitute a separate paper. Section 4, which contained only announce of results, has been suprimated; it will appear in detail elsewhere. Consequently some statements have been re-numbered. No mathematical changes have been made.

In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-Synuclein within E. coli cells

α-Synuclein is a small protein strongly implicated in the pathogenesis of Parkinson’s disease and related neurodegenerative disorders. We report here the use of in-cell NMR spectroscopy to observe directly the structure and dynamics of this protein within E. coli cells. To improve the accuracy in the measurement of backbone chemical shifts within crowded in-cell NMR spectra, we have developed a deconvolution method to reduce inhomogeneous line broadening within cellular samples. The resulting chemical shift values were then used to evaluate the distribution of secondary structure populations which, in the absence of stable tertiary contacts, are a most effective way to describe the conformational fluctuations of disordered proteins. The results indicate that, at least within the bacterial cytosol, α-synuclein populates a highly dynamic state that, despite the highly crowded environment, has the same characteristics as the disordered monomeric form observed in aqueous solution

Protein folding on the ribosome studied using NMR spectroscopy

NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome-nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity