220 research outputs found
Sorting signed circular permutations by super short reversals
We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works.We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version rema9096272283FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2013/08293-72014/04718-6306730/2012-0; 477692/2012-5; 483370/2013-411th International Symposium on Bioinformatics Research and Application
The Effective Particle-Hole Interaction and the Optical Response of Simple Metal Clusters
Following Sham and Rice [L. J. Sham, T. M. Rice, Phys. Rev. 144 (1966) 708]
the correlated motion of particle-hole pairs is studied, starting from the
general two-particle Greens function. In this way we derive a matrix equation
for eigenvalues and wave functions, respectively, of the general type of
collective excitation of a N-particle system. The interplay between excitons
and plasmons is fully described by this new set of equations. As a by-product
we obtain - at least a-posteriori - a justification for the use of the TDLDA
for simple-metal clusters.Comment: RevTeX, 15 pages, 5 figures in uufiles format, 1 figure avaible from
[email protected]
Sorting Signed Circular Permutations by Super Short Reversals
International audienceWe consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works
Light Hadron Masses from Lattice QCD
This article reviews lattice QCD results for the light hadron spectrum. We
give an overview of different formulations of lattice QCD, with discussions on
the fermion doubling problem and improvement programs. We summarize recent
developments in algorithms and analysis techniques, that render calculations
with light, dynamical quarks feasible on present day computer resources.
Finally, we summarize spectrum results for ground state hadrons and resonances
using various actions.Comment: 53 pages, 24 figures, one table; Rev.Mod.Phys. (published version);
v2: corrected typ
Human longevity is characterised by high thyroid stimulating hormone secretion without altered energy metabolism
Neuro Imaging Researc
Structural Instability in Polyacene : A Projector Quantum Monte Carlo Study
We have studied polyacene within the Hubbard model to explore the effect of
electron correlations on the Peierls' instability in a system marginally away
from one-dimension. We employ the projector quantum Monte Carlo method to
obtain ground state estimates of the energy and various correlation functions.
We find strong similarities between polyacene and polyacetylene which can be
rationalized from the real-space valence-bond arguments of Mazumdar and Dixit.
Electron correlations tend to enhance the Peierls' instability in polyacene.
This enhancement appears to attain a maximum at and the maximum
shifts to larger values when the alternation parameter is increased. The system
shows no tendency to destroy the imposed bond-alternation pattern, as evidenced
by the bond-bond correlations. The cis- distortion is seen to be favoured over
the trans- distortion. The spin-spin correlations show that undistorted
polyacene is susceptible to a SDW distortion for large interaction strength.
The charge-charge correlations indicate the absence of a CDW distortion for the
parameters studied.Comment: 13 pages, 10 figures available on reques
QCD equation of state at nonzero chemical potential: continuum results with physical quark masses at order mu^2
We determine the equation of state of QCD for nonzero chemical potentials via
a Taylor expansion of the pressure. The results are obtained for N_f=2+1
flavors of quarks with physical masses, on various lattice spacings. We present
results for the pressure, interaction measure, energy density, entropy density,
and the speed of sound for small chemical potentials. At low temperatures we
compare our results with the Hadron Resonance Gas model. We also express our
observables along trajectories of constant entropy over particle number. A
simple parameterization is given (the Matlab/Octave script parameterization.m,
submitted to the arXiv along with the paper), which can be used to reconstruct
the observables as functions of T and mu, or as functions of T and S/N.Comment: 14 pages, 15 figures, version accepted for publication in JHE
CoVITEST: A Fast and Reliable Method to Monitor Anti-SARS-CoV-2 Specific T Cells From Whole Blood
Cellular and humoral immune responses are essential for COVID-19 recovery and protection against SARS-CoV-2 reinfection. To date, the evaluation of SARS-CoV-2 immune protection has mainly focused on antibody detection, generally disregarding the cellular response, or placing it in a secondary position. This phenomenon may be explained by the complex nature of the assays needed to analyze cellular immunity compared with the technically simple and automated detection of antibodies. Nevertheless, a large body of evidence supports the relevance of the T cell's role in protection against SARS-CoV-2, especially in vulnerable individuals with a weakened immune system (such as the population over 65 and patients with immunodeficiencies). Here we propose to use CoVITEST (Covid19 anti-Viral Immunity based on T cells for Evaluation in a Simple Test), a fast, affordable and accessible in-house assay that, together with a diagnostic matrix, allows us to determine those patients who might be protected with SARS-CoV-2-reactive T cells. The method was established using healthy SARS-CoV-2-naïve donors pre- and post-vaccination (n=30), and further validated with convalescent COVID-19 donors (n=51) in a side-by-side comparison with the gold standard IFN-? ELISpot. We demonstrated that our CoVITEST presented reliable and comparable results to those obtained with the ELISpot technique in a considerably shorter time (less than 8 hours). In conclusion, we present a simple but reliable assay to determine cellular immunity against SARS-CoV-2 that can be used routinely during this pandemic to monitor the immune status in vulnerable patients and thereby adjust their therapeutic approaches. This method might indeed help to optimize and improve decision-making protocols for re-vaccination against SARS-CoV-2, at least for some population subsets.Copyright © 2022 Egri, Olivé, Hernández-Rodríguez, Castro, De Guzman, Heredia, Segura, Fernandez, de Moner, Torradeflot, Ballús, Martinez, Vazquez, Costa, Dobaño, Mazza, Mazzotti, Pascal, Juan, González-Navarro and Calderón
Computational Physics on Graphics Processing Units
The use of graphics processing units for scientific computations is an
emerging strategy that can significantly speed up various different algorithms.
In this review, we discuss advances made in the field of computational physics,
focusing on classical molecular dynamics, and on quantum simulations for
electronic structure calculations using the density functional theory, wave
function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012,
Helsinki, Finland, June 10-13, 201
Improved upper limits on the stochastic gravitational-wave background from 2009-2010 LIGO and Virgo data
Gravitational waves from a variety of sources are predicted to superpose to create a stochastic background. This background is expected to contain unique information from throughout the history of the Universe that is unavailable through standard electromagnetic observations, making its study of fundamental importance to understanding the evolution of the Universe. We carry out a search for the stochastic background with the latest data from the LIGO and Virgo detectors. Consistent with predictions from most stochastic gravitational-wave background models, the data display no evidence of a stochastic gravitational-wave signal. Assuming a gravitational-wave spectrum of ΩGW(f)=Ωα(f/fref)α, we place 95% confidence level upper limits on the energy density of the background in each of four frequency bands spanning 41.5-1726 Hz. In the frequency band of 41.5-169.25 Hz for a spectral index of α=0, we constrain the energy density of the stochastic background to be ΩGW(f)\u3c5.6×10-6. For the 600-1000 Hz band, ΩGW(f)\u3c0.14(f/900Hz)3, a factor of 2.5 lower than the best previously reported upper limits. We find ΩGW(f)\u3c1.8×10-4 using a spectral index of zero for 170-600 Hz and ΩGW(f)\u3c1.0(f/1300Hz)3 for 1000-1726 Hz, bands in which no previous direct limits have been placed. The limits in these four bands are the lowest direct measurements to date on the stochastic background. We discuss the implications of these results in light of the recent claim by the BICEP2 experiment of the possible evidence for inflationary gravitational waves
- …