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