29,855 research outputs found
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
- …