Chance and Necessity in Evolution: Lessons from RNA

The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are realized much more frequently than others), (2) the notion of shape space covering (that all typical shapes are realized in a small neighborhood of any random sequence), and (3) the notion of a neutral network (that sequences folding into the same typical shape form networks that percolate through sequence space). Neutral networks loosen the requirements on the mutation rate for selection to remain effective. The original (genotypic) error threshold has to be reformulated in terms of a phenotypic error threshold. With regard to adaptation, neutrality has two seemingly contradictory effects: It acts as a buffer against mutations ensuring that a phenotype is preserved. Yet it is deeply enabling, because it permits evolutionary change to occur by allowing the sequence context to vary silently until a single point mutation can become phenotypically consequential. Neutrality also influences predictability of adaptive trajectories in seemingly contradictory ways. On the one hand it increases the uncertainty of their genotypic trace. At the same time neutrality structures the access from one shape to another, thereby inducing a topology among RNA shapes which permits a distinction between continuous and discontinuous shape transformations. To the extent that adaptive trajectories must undergo such transformations, their phenotypic trace becomes more predictable.Comment: 37 pages, 14 figures; 1998 CNLS conference; high quality figures at http://www.santafe.edu/~walte

Multi-party entanglement in graph states

Graph states are multi-particle entangled states that correspond to mathematical graphs, where the vertices of the graph take the role of quantum spin systems and edges represent Ising interactions. They are many-body spin states of distributed quantum systems that play a significant role in quantum error correction, multi-party quantum communication, and quantum computation within the framework of the one-way quantum computer. We characterize and quantify the genuine multi-particle entanglement of such graph states in terms of the Schmidt measure, to which we provide upper and lower bounds in graph theoretical terms. Several examples and classes of graphs will be discussed, where these bounds coincide. These examples include trees, cluster states of different dimension, graphs that occur in quantum error correction, such as the concatenated [7,1,3]-CSS code, and a graph associated with the quantum Fourier transform in the one-way computer. We also present general transformation rules for graphs when local Pauli measurements are applied, and give criteria for the equivalence of two graphs up to local unitary transformations, employing the stabilizer formalism. For graphs of up to seven vertices we provide complete characterization modulo local unitary transformations and graph isomorphies.Comment: 22 pages, 15 figures, 2 tables, typos corrected (e.g. in measurement rules), references added/update

The effect of compression on the global optimization of atomic clusters

Recently, Locatelli and Schoen proposed a transformation of the potential energy that aids the global optimization of Lennard-Jones clusters with non-icosahedral global minima. These cases are particularly difficult to optimize because the potential energy surface has a double funnel topography with the global minimum at the bottom of the narrower funnel. Here we analyse the effect of this type of transformation on the topography of the potential energy surface. The transformation, which physically corresponds to a compression of the cluster, firstly reduces the number of stationary points on the potential energy surface. Secondly, we show that for a 38-atom cluster with a face-centred-cubic global minimum the transformation causes the potential energy surface to become increasingly dominated by the funnel associated with the global minimum. The transformation has been incorporated in the basin-hopping algorithm using a two-phase approach.Comment: 9 pages, 6 figures, revte

Term-Specific Eigenvector-Centrality in Multi-Relation Networks

Fuzzy matching and ranking are two information retrieval techniques widely used in web search. Their application to structured data, however, remains an open problem. This article investigates how eigenvector-centrality can be used for approximate matching in multi-relation graphs, that is, graphs where connections of many different types may exist. Based on an extension of the PageRank matrix, eigenvectors representing the distribution of a term after propagating term weights between related data items are computed. The result is an index which takes the document structure into account and can be used with standard document retrieval techniques. As the scheme takes the shape of an index transformation, all necessary calculations are performed during index tim

The Tensor Track, III

We provide an informal up-to-date review of the tensor track approach to quantum gravity. In a long introduction we describe in simple terms the motivations for this approach. Then the many recent advances are summarized, with emphasis on some points (Gromov-Hausdorff limit, Loop vertex expansion, Osterwalder-Schrader positivity...) which, while important for the tensor track program, are not detailed in the usual quantum gravity literature. We list open questions in the conclusion and provide a rather extended bibliography.Comment: 53 pages, 6 figure

Nuclear structure calculations with a separable approximation for Skyrme interactions

A finite rank separable approximation for the quasiparticle RPA calculations with Skyrme interactions that was proposed in our previous work is extended to take into account the coupling between one- and two-phonon terms in the wave functions of excited states. It is shown that characteristics calculated within the suggested approach are in a good agreement with available experimental data.Comment: 6 pages, proceedings of the International Symposium on Physics of Unstable Nuclei (ISPUN02), Halong Bay, Vietnam, November 20-25, 200