Azumaya Objects in Triangulated Bicategories

We introduce the notion of Azumaya object in general homotopy-theoretic settings. We give a self-contained account of Azumaya objects and Brauer groups in bicategorical contexts, generalizing the Brauer group of a commutative ring. We go on to describe triangulated bicategories and prove a characterization theorem for Azumaya objects therein. This theory applies to give a homotopical Brauer group for derived categories of rings and ring spectra. We show that the homotopical Brauer group of an Eilenberg-Mac Lane spectrum is isomorphic to the homotopical Brauer group of its underlying commutative ring. We also discuss tilting theory as an application of invertibility in triangulated bicategories.Comment: 23 pages; final version; to appear in Journal of Homotopy and Related Structure

Homological Localisation of Model Categories

One of the most useful methods for studying the stable homotopy category is localising at some spectrum E. For an arbitrary stable model category we introduce a candidate for the E–localisation of this model category. We study the properties of this new construction and relate it to some well–known categories

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years

Tuning ultrafast electron thermalization pathways in a van der Waals heterostructure

Ultrafast electron thermalization - the process leading to Auger recombination, carrier multiplication via impact ionization and hot carrier luminescence - occurs when optically excited electrons in a material undergo rapid electron-electron scattering to redistribute excess energy and reach electronic thermal equilibrium. Due to extremely short time and length scales, the measurement and manipulation of electron thermalization in nanoscale devices remains challenging even with the most advanced ultrafast laser techniques. Here, we overcome this challenge by leveraging the atomic thinness of two-dimensional van der Waals (vdW) materials in order to introduce a highly tunable electron transfer pathway that directly competes with electron thermalization. We realize this scheme in a graphene-boron nitride-graphene (G-BN-G) vdW heterostructure, through which optically excited carriers are transported from one graphene layer to the other. By applying an interlayer bias voltage or varying the excitation photon energy, interlayer carrier transport can be controlled to occur faster or slower than the intralayer scattering events, thus effectively tuning the electron thermalization pathways in graphene. Our findings, which demonstrate a novel means to probe and directly modulate electron energy transport in nanoscale materials, represent an important step toward designing and implementing novel optoelectronic and energy-harvesting devices with tailored microscopic properties.Comment: Accepted to Nature Physic

An algorithm for producing F-pure ideals

This paper describes a method for computing all F-pure ideals for a given Cartier map of a polynomial ring over a finite field

Protein kinase A regulatory subunit distribution in medulloblastoma

<p>Abstract</p> <p>Background</p> <p>Previous studies showed a differential distribution of the four regulatory subunits of cAMP-dependent protein kinases inside the brain, that changed in rodent gliomas: therefore, the distribution of these proteins inside the brain can give information on the functional state of the cells. Our goal was to examine human brain tumors to provide evidence for a differential distribution of protein kinase A in different tumors.</p> <p>Methods</p> <p>The distribution of detergent insoluble regulatory (R1 and R2) and catalytic subunits of cAMP dependent kinases was examined in pediatric brain tumors by immunohistochemistry and fluorescent cAMP analogues binding.</p> <p>Results</p> <p>R2 is organized in large single dots in medulloblastomas, while it has a different appearance in other tumors. Fluorescent cAMP labelling was observed only in medulloblastoma.</p> <p>Conclusions</p> <p>A different distribution of cAMP dependent protein kinases has been observed in medulloblastoma.</p

Real-Time PyMOL Visualization for Rosetta and PyRosetta

Computational structure prediction and design of proteins and protein-protein complexes have long been inaccessible to those not directly involved in the field. A key missing component has been the ability to visualize the progress of calculations to better understand them. Rosetta is one simulation suite that would benefit from a robust real-time visualization solution. Several tools exist for the sole purpose of visualizing biomolecules; one of the most popular tools, PyMOL (Schrödinger), is a powerful, highly extensible, user friendly, and attractive package. Integrating Rosetta and PyMOL directly has many technical and logistical obstacles inhibiting usage. To circumvent these issues, we developed a novel solution based on transmitting biomolecular structure and energy information via UDP sockets. Rosetta and PyMOL run as separate processes, thereby avoiding many technical obstacles while visualizing information on-demand in real-time. When Rosetta detects changes in the structure of a protein, new coordinates are sent over a UDP network socket to a PyMOL instance running a UDP socket listener. PyMOL then interprets and displays the molecule. This implementation also allows remote execution of Rosetta. When combined with PyRosetta, this visualization solution provides an interactive environment for protein structure prediction and design

Insights into the molecular determinants involved in cap recognition by the vaccinia virus D10 decapping enzyme

Decapping enzymes are required for the removal of the 5′-end m7GpppN cap of mRNAs to allow their decay in cells. While many cap-binding proteins recognize the cap structure via the stacking of the methylated guanosine ring between two aromatic residues, the precise mechanism of cap recognition by decapping enzymes has yet to be determined. In order to get insights into the interaction of decapping enzymes with the cap structure, we studied the vaccinia virus D10 decapping enzyme as a model to investigate the important features for substrate recognition by the enzyme. We demonstrate that a number of chemically modified purines can competitively inhibit the decapping reaction, highlighting the molecular features of the cap structure that are required for recognition by the enzyme, such as the nature of the moiety at positions 2 and 6 of the guanine base. A 3D structural model of the D10 protein was generated which suggests amino acids implicated in cap binding. Consequently, we expressed 17 mutant proteins with amino acid substitutions in the active site of D10 and found that eight are critical for the decapping activity. These data underscore the functional features involved in the non-canonical cap-recognition by the vaccinia virus D10 decapping enzyme