4,841 research outputs found
Center vortex model for the infrared sector of SU(3) Yang-Mills theory: Topological susceptibility
The topological susceptibility of the SU(3) random vortex world-surface
ensemble, an effective model of infrared Yang-Mills dynamics, is investigated.
The model is implemented by composing vortex world-surfaces of elementary
squares on a hypercubic lattice, supplemented by an appropriate specification
of vortex color structure on the world-surfaces. Topological charge is
generated in this picture by writhe and self-intersection of the vortex
world-surfaces. Systematic uncertainties in the evaluation of the topological
charge, engendered by the hypercubic construction, are discussed. Results for
the topological susceptibility are reported as a function of temperature and
compared to corresponding measurements in SU(3) lattice Yang-Mills theory. In
the confined phase, the topological susceptibility of the random vortex
world-surface ensemble appears quantitatively consistent with Yang-Mills
theory. As the temperature is raised into the deconfined regime, the
topological susceptibility falls off rapidly, but significantly less so than in
SU(3) lattice Yang-Mills theory. Possible causes of this deviation, ranging
from artefacts of the hypercubic description to more physical sources, such as
the adopted vortex dynamics, are discussed.Comment: 30 pages, 6 figure
Energy Density of Vortices in the Schroedinger Picture
The one-loop energy density of an infinitely thin static magnetic vortex in
SU(2) Yang-Mills theory is evaluated using the Schroedinger picture. Both the
gluonic fluctuations as well as the quarks in the vortex background are
included. The energy density of the magnetic vortex is discussed as a function
of the magnetic flux. The center vortices correspond to local minima in the
effective potential. These minima are degenerated with the perturbative vacuum
if the fermions are ignored. Inclusion of fermions lifts this degeneracy,
raising the vortex energy above the energy of the perturbative vacuum.Comment: 25 pages, 2 figure
Lattice QCD study of the Boer-Mulders effect in a pion
The three-dimensional momenta of quarks inside a hadron are encoded in
transverse momentum-dependent parton distribution functions (TMDs). This work
presents an exploratory lattice QCD study of a TMD observable in the pion
describing the Boer-Mulders effect, which is related to polarized quark
transverse momentum in an unpolarized hadron. Particular emphasis is placed on
the behavior as a function of a Collins-Soper evolution parameter quantifying
the relative rapidity of the struck quark and the initial hadron, e.g., in a
semi-inclusive deep inelastic scattering (SIDIS) process. The lattice
calculation, performed at the pion mass m_pi = 518 MeV, utilizes a definition
of TMDs via hadronic matrix elements of a quark bilocal operator with a
staple-shaped gauge connection; in this context, the evolution parameter is
related to the staple direction. By parametrizing the aforementioned matrix
elements in terms of invariant amplitudes, the problem can be cast in a Lorentz
frame suited for the lattice calculation. In contrast to an earlier nucleon
study, due to the lower mass of the pion, the calculated data enable
quantitative statements about the physically interesting limit of large
relative rapidity. In passing, the similarity between the Boer-Mulders effects
extracted in the pion and the nucleon is noted.Comment: 16 pages, 9 figures, 3 table
Writhe of center vortices and topological charge -- an explicit example
The manner in which continuum center vortices generate topological charge
density is elucidated using an explicit example. The example vortex
world-surface contains one lone self-intersection point, which contributes a
quantum 1/2 to the topological charge. On the other hand, the surface in
question is orientable and thus must carry global topological charge zero due
to general arguments. Therefore, there must be another contribution, coming
from vortex writhe. The latter is known for the lattice analogue of the example
vortex considered, where it is quite intuitive. For the vortex in the
continuum, including the limit of an infinitely thin vortex, a careful analysis
is performed and it is shown how the contribution to the topological charge
induced by writhe is distributed over the vortex surface.Comment: 33 latex pages, 10 figures incorporating 14 ps files. Furthermore,
the time evolution of the vortex line discussed in this work can be viewed as
a gif movie, available for download by following the PostScript link below --
watch for the cute feature at the self-intersection poin
Topological Susceptibility of Yang-Mills Center Projection Vortices
The topological susceptibility induced by center projection vortices
extracted from SU(2) lattice Yang-Mills configurations via the maximal center
gauge is measured. Two different smoothing procedures, designed to eliminate
spurious ultraviolet fluctuations of these vortices before evaluating the
topological charge, are explored. They result in consistent estimates of the
topological susceptibility carried by the physical thick vortices
characterizing the Yang-Mills vacuum in the vortex picture. This susceptibility
is comparable to the one obtained from the full lattice Yang-Mills
configurations. The topological properties of the SU(2) Yang-Mills vacuum can
thus be accounted for in terms of its vortex content.Comment: 12 revtex pages, 6 ps figures included using eps
A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions
The sheer amounts of biological data that are generated in recent years have
driven the development of network analysis tools to facilitate the
interpretation and representation of these data. A fundamental challenge in
this domain is the reconstruction of a protein-protein subnetwork that
underlies a process of interest from a genome-wide screen of associated genes.
Despite intense work in this area, current algorithmic approaches are largely
limited to analyzing a single screen and are, thus, unable to account for
information on condition-specific genes, or reveal the dynamics (over time or
condition) of the process in question. Here we propose a novel formulation for
network reconstruction from multiple-condition data and devise an efficient
integer program solution for it. We apply our algorithm to analyze the response
to influenza infection in humans over time as well as to analyze a pair of ER
export related screens in humans. By comparing to an extant, single-condition
tool we demonstrate the power of our new approach in integrating data from
multiple conditions in a compact and coherent manner, capturing the dynamics of
the underlying processes.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Dissection of the amyloid formation pathway in AL amyloidosis
In antibody light chain (AL) amyloidosis, overproduced light chain (LC) fragments accumulate as fibrils in organs and tissues of patients. In vitro, AL fibril formation is a slow process, characterized by a pronounced lag phase. The events occurring during this lag phase are largely unknown. We have dissected the lag phase of a patient-derived LC truncation and identified structural transitions that precede fibril formation. The process starts with partial unfolding of the V-L domain and the formation of small amounts of dimers. This is a prerequisite for the formation of an ensemble of oligomers, which are the precursors of fibrils. During oligomerization, the hydrophobic core of the LC domain rearranges which leads to changes in solvent accessibility and rigidity. Structural transitions from an anti-parallel to a parallel beta-sheet secondary structure occur in the oligomers prior to amyloid formation. Together, our results reveal a rate-limiting multi-step mechanism of structural transitions prior to fibril formation in AL amyloidosis, which offers, in the long run, opportunities for therapeutic intervention. AL amyloidosis is caused by the accumulation of overproduced light chain (LC) fragments as fibrils in patient organs and it is the most prevalent systemic amyloidosis. Here, the authors combine biochemical and biophysical experiments to characterise the lag phase of a patient-derived truncated LC and they identify structural transitions that precede fibril formation
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