On Conway-Gordon type theorems for graphs in the Petersen family

For every spatial embedding of each graph in the Petersen family, it is known that the sum of the linking numbers over all of the constituent 2-component links is congruent to 1 modulo 2. In this paper, we give an integral lift of this formula in terms of the square of the linking number and the second coefficient of the Conway polynomial.Comment: 13 pages, 5 figures. arXiv admin note: text overlap with arXiv:1104.082

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize the solutions to the corresponding tangle equations by certain knotted graphs. By investigating planarity conditions on these graphs we show that there is a unique biologically relevant solution. That is, we show there is a unique rational tangle solution, which is also the unique solution with small crossing number.Comment: 60 pages, 74 figure

The quantum phases of matter

I present a selective survey of the phases of quantum matter with varieties of many-particle quantum entanglement. I classify the phases as gapped, conformal, or compressible quantum matter. Gapped quantum matter is illustrated by a simple discussion of the Z_2 spin liquid, and connections are made to topological field theories. I discuss how conformal matter is realized at quantum critical points of realistic lattice models, and make connections to a number of experimental systems. Recent progress in our understanding of compressible quantum phases which are not Fermi liquids is summarized. Finally, I discuss how the strongly-coupled phases of quantum matter may be described by gauge-gravity duality. The structure of the large N limit of SU(N) gauge theory, coupled to adjoint fermion matter at non-zero density, suggests aspects of gravitational duals of compressible quantum matter.Comment: 35 pages, 21 figures; Rapporteur presentation at the 25th Solvay Conference on Physics, "The Theory of the Quantum World", Brussels, Oct 2011; (v2+v3+v4) expanded holographic discussion and referencin

Navigating in a sea of repeats in RNA-seq without drowning

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which transposable elements are one of the main examples. Most transcriptome assemblers are based on de Bruijn graphs and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. The results of this work are twofold. First, we introduce a formal model for repre- senting high copy number repeats in RNA-seq data and exploit its properties for inferring a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying in a de Bruijn graph a subgraph with this charac- teristic is NP-complete. In a second step, we show that in the specific case of a local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs. In particular, we designed and implemented an algorithm to efficiently identify AS events that are not included in repeated regions. Finally, we validate our results using synthetic data. We also give an indication of the usefulness of our method on real data

Analysis of the shearing instability in nonlinear convection and magnetoconvection

Numerical experiments on two-dimensional convection with or without a vertical magnetic field reveal a bewildering variety of periodic and aperiodic oscillations. Steady rolls can develop a shearing instability, in which rolls turning over in one direction grow at the expense of rolls turning over in the other, resulting in a net shear across the layer. As the temperature difference across the fluid is increased, two-dimensional pulsating waves occur, in which the direction of shear alternates. We analyse the nonlinear dynamics of this behaviour by first constructing appropriate low-order sets of ordinary differential equations, which show the same behaviour, and then analysing the global bifurcations that lead to these oscillations by constructing one-dimensional return maps. We compare the behaviour of the partial differential equations, the models and the maps in systematic two-parameter studies of both the magnetic and the non-magnetic cases, emphasising how the symmetries of periodic solutions change as a result of global bifurcations. Much of the interesting behaviour is associated with a discontinuous change in the leading direction of a fixed point at a global bifurcation; this change occurs when the magnetic field is introduced