113 research outputs found
Bogolyubov-Hartree-Fock approach to studying the QCD ground state
The quark's behaviour while influenced by a strong stochastic gluon field is
analyzed. An approximate procedure for calculating the effective Hamiltonian is
developed and the corresponding ground state within the Hartree-Fock-Bogolyubov
approach is found. The comparative analysis of various Hamiltonian models is
given and transition to the chiral limit in the Keldysh model is discussed in
detail.Comment: 18 pages, 4 figures, new version of the manuscrip
Direct detection of a single photon by humans
Despite investigations for over 70 years, the absolute limits of human vision have remained unclear. Rod cells respond to individual photons, yet whether a single-photon incident on the eye can be perceived by a human subject has remained a fundamental open question. Here we report that humans can detect a single-photon incident on the cornea with a probability significantly above chance. This was achieved by implementing a combination of a psychophysics procedure with a quantum light source that can generate single-photon states of light. We further discover that the probability of reporting a single photon is modulated by the presence of an earlier photon, suggesting a priming process that temporarily enhances the effective gain of the visual system on the timescale of seconds
Alignathon: A competitive assessment of whole-genome alignment methods
© 2014 Earl et al. Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments
Phonon-Like Excitations of the Instanton Liquid
The phonon-like excitations of (anti)-instanton liquid () due to
adiabatic variations of vacuum wave functions are studied in this paper. The
kinetic energy term is found and proper effective Lagrangian for such
excitations is evaluated.The properties of their spectrum, while the
corresponding masses are defined by with prevailing
chromoelectric component, are investigated based on the phenomenology of QCD
vacuum already developed.Comment: 7 page
Semiclassical Approximation for Non-Abelian Field Strength Correlators in the Instanton Dilute Gas Model
Field strength correlators are semi-classically evaluated in the dilute gas
model of non-Abelian sources (instantons) and compared with lattice data for
QCD at zero temperature. We show that one of the Euclidean invariant, tensorial
structures vanishes for configurations being purely selfdual or anti-selfdual.
We compute the invariant functions contributing to the correlators within the
two lowest orders in an instanton density expansion. Fitting instanton size and
density for quenched and full QCD, we obtain a reasonable description.Comment: 29 pages (revtex) including 3 figures, revised for publication in
Phys. Rev.
Megahertz pulse trains enable multi-hit serial femtosecond crystallography experiments at X-ray free electron lasers
The European X-ray Free Electron Laser (XFEL) and Linac Coherent Light Source (LCLS) II are extremely intense sources of X-rays capable of generating Serial Femtosecond Crystallography (SFX) data at megahertz (MHz) repetition rates. Previous work has shown that it is possible to use consecutive X-ray pulses to collect diffraction patterns from individual crystals. Here, we exploit the MHz pulse structure of the European XFEL to obtain two complete datasets from the same lysozyme crystal, first hit and the second hit, before it exits the beam. The two datasets, separated by <1 µs, yield up to 2.1 Å resolution structures. Comparisons between the two structures reveal no indications of radiation damage or significant changes within the active site, consistent with the calculated dose estimates. This demonstrates MHz SFX can be used as a tool for tracking sub-microsecond structural changes in individual single crystals, a technique we refer to as multi-hit SFX
Mechanochemical modeling of dynamic microtubule growth involving sheet-to-tube transition
Microtubule dynamics is largely influenced by nucleotide hydrolysis and the
resultant tubulin configuration changes. The GTP cap model has been proposed to
interpret the stabilizing mechanism of microtubule growth from the view of
hydrolysis effects. Besides, the microtubule growth involves the closure of a
curved sheet at its growing end. The curvature conversion also helps to
stabilize the successive growth, and the curved sheet is referred to as the
conformational cap. However, there still lacks theoretical investigation on the
mechanical-chemical coupling growth process of microtubules. In this paper, we
study the growth mechanisms of microtubules by using a coarse-grained molecular
method. Firstly, the closure process involving a sheet-to-tube transition is
simulated. The results verify the stabilizing effect of the sheet structure,
and the minimum conformational cap length that can stabilize the growth is
demonstrated to be two dimers. Then, we show that the conformational cap can
function independently of the GTP cap, signifying the pivotal role of
mechanical factors. Furthermore, based on our theoretical results, we describe
a Tetris-like growth style of microtubules: the stochastic tubulin assembly is
regulated by energy and harmonized with the seam zipping such that the sheet
keeps a practically constant length during growth.Comment: 23 pages, 7 figures. 2 supporting movies have not been uploaded due
to the file type restriction
Angle-resolved photoemission spectroscopy of the cuprate superconductors
This paper reviews the most recent ARPES results on the cuprate
superconductors and their insulating parent and sister compounds, with the
purpose of providing an updated summary of the extensive literature in this
field. The low energy excitations are discussed with emphasis on some of the
most relevant issues, such as the Fermi surface and remnant Fermi surface, the
superconducting gap, the pseudogap and d-wave-like dispersion, evidence of
electronic inhomogeneity and nano-scale phase separation, the emergence of
coherent quasiparticles through the superconducting transition, and many-body
effects in the one-particle spectral function due to the interaction of the
charge with magnetic and/or lattice degrees of freedom. The first part of the
paper introduces photoemission spectroscopy in the context of strongly
interacting systems, along with an update on the state-of-the-art
instrumentation. The second part provides a brief overview of the scientific
issues relevant to the investigation of the low energy electronic structure by
ARPES. The rest of the paper is devoted to the review of experimental results
from the cuprates and the discussion is organized along conceptual lines:
normal-state electronic structure, interlayer interaction, superconducting gap,
coherent superconducting peak, pseudogap, electron self energy and collective
modes. Within each topic, ARPES data from the various copper oxides are
presented.Comment: Reviews of Modern Physics, in press. A HIGH-QUALITY pdf file is
available at http://www.physics.ubc.ca/~damascel/RMP_ARPES.pd
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