Background Configurations, Confinement and Deconfinement on a Lattice with BPS Monopole Boundary Conditions

Finite temperature SU(2) lattice gauge theory is investigated in a 3D cubic box with fixed boundary conditions provided by a discretized, static BPS monopole solution with varying core scale $\mu$. Using heating and cooling techniques we establish that for discrete $\mu$-values stable classical solutions either of self-dual or of pure magnetic type exist inside the box. Having switched on quantum fluctuations we compute the Polyakov line and other local operators. For different $\mu$ and at varying temperatures near the deconfinement transition we study the influence of the boundary condition on the vacuum inside the box. In contrast to the pure magnetic background field case, for the self-dual one we observe confinement even for temperatures quite far above the critical one.Comment: to appear in EPJ

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

2D/3D Metallic Nano-objects Self-Organized in an Organic Molecular Thin Film

We present the fabrication and investigation of the properties of nanocomposite structures consisting of two-dimensional (2D) and three-dimensional (3D) metallic nano-objects self-organized on the surface and inside of organic molecular thin-film copper tetrafluorophthalocyanine (CuPcF4). Metallic atoms, deposited under ultrahigh vacuum (UHV) conditions onto the organic ultrathin film, diffuse along the surface and self-assemble into a system of 2D metallic overlayers. At the same time, the majority of the metal atoms diffuse into the organic matrix and self-organize into 3D nanoparticles (NPs) in a well-defined manner. The evolution of the morphology and electronic properties of such structures as a function of nominal metal content is studied under UHV conditions using transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HR-TEM), and photoelectron spectroscopy (PES) techniques. Using HR-TEM, we have observed the periodicity of atomic planes of individual silver NPs. The steady formation of agglomerates from individual single nanocrystallites with intercrystallite boundaries is observed as well. PES reveals generally weak chemical interactions between silver and the organic matrix and n-doping of CuPcF4 at the initial stages of silver deposition, which is associated with charge transfer from the 2D wetting layer on the basis of core-level spectra shift analysis. Copyright © 2020 American Chemical Society

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 ($\bar II$) 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 $\Lambda_{QCD}$ 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.

TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes. Using a transgenic screen in zebrafish, thymocyte selection–associated high mobility group box protein (TOX) was uncovered as a collaborating oncogenic driver that accelerated T-ALL onset by expanding the initiating pool of transformed clones and elevating genomic instability. TOX is highly expressed in a majority of human T-ALL and is required for proliferation and continued xenograft growth in mice. Using a wide array of functional analyses, we uncovered that TOX binds directly to KU70/80 and suppresses recruitment of this complex to DNA breaks to inhibit nonhomologous end joining (NHEJ) repair. Impaired NHEJ is well known to cause genomic instability, including development of T-cell malignancies in KU70- and KU80-deficient mice. Collectively, our work has uncovered important roles for TOX in regulating NHEJ by elevating genomic instability during leukemia initiation and sustaining leukemic cell proliferation following transformation

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