Properties of the non-Gaussian fixed point in 4D compact U(1) lattice gauge theory

We examine selected properties of the gauge-ball spectrum and fermionic variables in the vicinity of the recently discussed non-Gaussian fixed point of 4D compact U(1) lattice gauge theory within the quenched approximation. Approaching the critical point from within the confinement phase, our data support scaling of $T1^{+-}$ gauge-ball states in units of the string tension square root. The analysis of the chiral condensate within the framework of a scaling form for the equation of state suggests non mean-field values for the magnetic exponents $\delta$ and $\beta_{exp}$.Comment: 73K postscript fil

Collective chemotactic dynamics in the presence of self-generated fluid flows

In micro-swimmer suspensions locomotion necessarily generates fluid motion, and it is known that such flows can lead to collective behavior from unbiased swimming. We examine the complementary problem of how chemotaxis is affected by self-generated flows. A kinetic theory coupling run-and-tumble chemotaxis to the flows of collective swimming shows separate branches of chemotactic and hydrodynamic instabilities for isotropic suspensions, the first driving aggregation, the second producing increased orientational order in suspensions of "pushers" and maximal disorder in suspensions of "pullers". Nonlinear simulations show that hydrodynamic interactions can limit and modify chemotactically-driven aggregation dynamics. In puller suspensions the dynamics form aggregates that are mutually-repelling due to the non-trivial flows. In pusher suspensions chemotactic aggregation can lead to destabilizing flows that fragment the regions of aggregation.Comment: 4 page

Universality of the gauge-ball spectrum of the four-dimensional pure U(1) gauge theory

We continue numerical studies of the spectrum of the pure U(1) lattice gauge theory in the confinement phase, initiated in our previous work. Using the extended Wilson action $S = -\sum_P [\beta \cos(\Theta_P) + \gamma \cos(2\Theta_P)]$ we address the question of universality of the phase transition line in the ($\beta,\gamma$) plane between the confinement and the Coulomb phases. Our present results at $\gamma= -0.5$ for the gauge-ball spectrum are fully consistent with the previous results obtained at $\gamma= -0.2$. Again, two different correlation length exponents, $\nu_{ng} = 0.35(3)$ and $\nu_{g} = 0.49(7)$, are obtained in different channels. We also confirm the stability of the values of these exponents with respect to the variation of the distance from the critical point at which they are determined. These results further demonstrate universal critical behaviour of the model at least up to correlation lengths of 4 lattice spacings when the phase transition is approached in some interval at $\gamma\leq -0.2$.Comment: 16 page

String Loop Corrections to Kahler Potentials in Orientifolds

We determine one-loop string corrections to Kahler potentials in type IIB orientifold compactifications with either N=1 or N=2 supersymmetry, including D-brane moduli, by evaluating string scattering amplitudes.Comment: 80 pages, 4 figure

Significance analysis and statistical mechanics: an application to clustering

This paper addresses the statistical significance of structures in random data: Given a set of vectors and a measure of mutual similarity, how likely does a subset of these vectors form a cluster with enhanced similarity among its elements? The computation of this cluster p-value for randomly distributed vectors is mapped onto a well-defined problem of statistical mechanics. We solve this problem analytically, establishing a connection between the physics of quenched disorder and multiple testing statistics in clustering and related problems. In an application to gene expression data, we find a remarkable link between the statistical significance of a cluster and the functional relationships between its genes.Comment: to appear in Phys. Rev. Let

Single-molecule real-time sequencing combined with optical mapping yields completely finished fungal genome

Next-generation sequencing (NGS) technologies have increased the scalability, speed, and resolution of genomic sequencing and, thus, have revolutionized genomic studies. However, eukaryotic genome sequencing initiatives typically yield considerably fragmented genome assemblies. Here, we assessed various state-of-the-art sequencing and assembly strategies in order to produce a contiguous and complete eukaryotic genome assembly, focusing on the filamentous fungus Verticillium dahliae. Compared with Illumina-based assemblies of the V. dahliae genome, hybrid assemblies that also include PacBio- generated long reads establish superior contiguity. Intriguingly, provided that sufficient sequence depth is reached, assemblies solely based on PacBio reads outperform hybrid assemblies and even result in fully assembled chromosomes. Furthermore, the addition of optical map data allowed us to produce a gapless and complete V. dahliae genome assembly of the expected eight chromosomes from telomere to telomere. Consequently, we can now study genomic regions that were previously not assembled or poorly assembled, including regions that are populated by repetitive sequences, such as transposons, allowing us to fully appreciate an organism’s biological complexity. Our data show that a combination of PacBio-generated long reads and optical mapping can be used to generate complete and gapless assemblies of fungal genomes. IMPORTANCE Studying whole-genome sequences has become an important aspect of biological research. The advent of nextgeneration sequencing (NGS) technologies has nowadays brought genomic science within reach of most research laboratories, including those that study nonmodel organisms. However, most genome sequencing initiatives typically yield (highly) fragmented genome assemblies. Nevertheless, considerable relevant information related to genome structure and evolution is likely hidden in those nonassembled regions. Here, we investigated a diverse set of strategies to obtain gapless genome assemblies, using the genome of a typical ascomycete fungus as the template. Eventually, we were able to show that a combination of PacBiogenerated long reads and optical mapping yields a gapless telomere-to-telomere genome assembly, allowing in-depth genome sanalyses to facilitate functional studies into an organism’s biology

Indirection and computer security.

The discipline of computer science is built on indirection. David Wheeler famously said, 'All problems in computer science can be solved by another layer of indirection. But that usually will create another problem'. We propose that every computer security vulnerability is yet another problem created by the indirections in system designs and that focusing on the indirections involved is a better way to design, evaluate, and compare security solutions. We are not proposing that indirection be avoided when solving problems, but that understanding the relationships between indirections and vulnerabilities is key to securing computer systems. Using this perspective, we analyze common vulnerabilities that plague our computer systems, consider the effectiveness of currently available security solutions, and propose several new security solutions

Peptide Antigen Concentration Modulates Digital NFAT1 Activation in Primary Mouse Naive CD8(+) T Cells as Measured by Flow Cytometry of Isolated Cell Nuclei

Circulating naive T cells exist in a quiescent state. After TCR contact with the cognate peptide presented by APCs in secondary lymphoid structures, T cells undergo a period of rapid transcriptional changes that set the stage for fate-determining effector or memory programming. We describe a novel method to analyze TCR signaling pathway activation in nuclei isolated from primary mouse naive T cells after stimulation with natural peptide Ags. We prelabeled cells with cell tracking dye to easily distinguish CD8(+) T cell nuclei from APC nuclei by conventional flow cytometry. Using this approach, we observed clear digital activation of NFAT1 transcription factor in OT-I T cells stimulated with OVA peptide presented by bulk splenocytes. OVA concentration had discrete control over the fraction of the cells that translocated NFAT1, indicating that a distinct threshold amount of TCR signaling is required to switch on NFAT1 in naive T cells. This behavior was cell contact dependent and qualitatively more exact than the NFAT1 response in ionomycin-stimulated naive T cells. These data contribute to our understanding of the digital behavior of TCR signaling components documented in other studies and indicate how T cells might discriminate log-fold changes in Ag availability during an actual infection. Overall, these results highlight the potential of this coculture nuclei isolation protocol to address stimulation-dependent translocation of proteins in primary lymphocytes