144 research outputs found
Entropy-driven cutoff phenomena
In this paper we present, in the context of Diaconis' paradigm, a general
method to detect the cutoff phenomenon. We use this method to prove cutoff in a
variety of models, some already known and others not yet appeared in
literature, including a chain which is non-reversible w.r.t. its stationary
measure. All the given examples clearly indicate that a drift towards the
opportune quantiles of the stationary measure could be held responsible for
this phenomenon. In the case of birth- and-death chains this mechanism is
fairly well understood; our work is an effort to generalize this picture to
more general systems, such as systems having stationary measure spread over the
whole state space or systems in which the study of the cutoff may not be
reduced to a one-dimensional problem. In those situations the drift may be
looked for by means of a suitable partitioning of the state space into classes;
using a statistical mechanics language it is then possible to set up a kind of
energy-entropy competition between the weight and the size of the classes.
Under the lens of this partitioning one can focus the mentioned drift and prove
cutoff with relative ease.Comment: 40 pages, 1 figur
Spin-based all-optical quantum computation with quantum dots: understanding and suppressing decoherence
We present an all-optical implementation of quantum computation using
semiconductor quantum dots. Quantum memory is represented by the spin of an
excess electron stored in each dot. Two-qubit gates are realized by switching
on trion-trion interactions between different dots. State selectivity is
achieved via conditional laser excitation exploiting Pauli exclusion principle.
Read-out is performed via a quantum-jump technique. We analyze the effect on
our scheme's performance of the main imperfections present in real quantum
dots: exciton decay, hole mixing and phonon decoherence. We introduce an
adiabatic gate procedure that allows one to circumvent these effects, and
evaluate quantitatively its fidelity
On a Generalization of Zaslavsky's Theorem for Hyperplane Arrangements
We define arrangements of codimension-1 submanifolds in a smooth manifold
which generalize arrangements of hyperplanes. When these submanifolds are
removed the manifold breaks up into regions, each of which is homeomorphic to
an open disc. The aim of this paper is to derive formulas that count the number
of regions formed by such an arrangement. We achieve this aim by generalizing
Zaslavsky's theorem to this setting. We show that this number is determined by
the combinatorics of the intersections of these submanifolds.Comment: version 3: The title had a typo in v2 which is now fixed. Will appear
in Annals of Combinatorics. Version. 2: 19 pages, major revision in terms of
style and language, some results improved, contact information updated, final
versio
Hopf algebras and Markov chains: Two examples and a theory
The operation of squaring (coproduct followed by product) in a combinatorial
Hopf algebra is shown to induce a Markov chain in natural bases. Chains
constructed in this way include widely studied methods of card shuffling, a
natural "rock-breaking" process, and Markov chains on simplicial complexes.
Many of these chains can be explictly diagonalized using the primitive elements
of the algebra and the combinatorics of the free Lie algebra. For card
shuffling, this gives an explicit description of the eigenvectors. For
rock-breaking, an explicit description of the quasi-stationary distribution and
sharp rates to absorption follow.Comment: 51 pages, 17 figures. (Typographical errors corrected. Further fixes
will only appear on the version on Amy Pang's website, the arXiv version will
not be updated.
Detector Description and Performance for the First Coincidence Observations between LIGO and GEO
For 17 days in August and September 2002, the LIGO and GEO interferometer
gravitational wave detectors were operated in coincidence to produce their
first data for scientific analysis. Although the detectors were still far from
their design sensitivity levels, the data can be used to place better upper
limits on the flux of gravitational waves incident on the earth than previous
direct measurements. This paper describes the instruments and the data in some
detail, as a companion to analysis papers based on the first data.Comment: 41 pages, 9 figures 17 Sept 03: author list amended, minor editorial
change
Large-Scale Neighbor-Joining with NINJA
Abstract Neighbor-joining is a well-established hierarchical clustering algorithm for inferring phylogenies. It begins with observed distances between pairs of sequences, and clustering order depends on a metric related to those distances. The canonical algorithm requires O(n3) time and O(n2) space for n sequences, which precludes application to very large sequence families, e.g. those containing 100,000 sequences. Datasets of this size are available today, and such phylogenies will play an increasingly important role in comparative genomics studies. Recent algorithmic advances have greatly sped up neighbor-joining for inputs of thousands of sequences, but are limited to fewer than 13,000 sequences on a system with 4GB RAM. In this paper, I describe an algorithm that speeds up neighbor-joining by dramatically reducing the number of distance values that are viewed in each iteration of the clustering procedure, while still computing a correct neighbor-joining tree. This algorithm can scale to inputs larger than 100,000 sequences because of external-memory-efficient data structures. A free implementation may by obtained fro
New insights into the genetic etiology of Alzheimer's disease and related dementias
Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele
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