Універсітэт. - № 11 (2114)

PERMON makes use of theoretical results in quadratic programming algorithms and domain decomposition methods. It is built on top of the PETSc framework for numerical computations. This paper describes its fundamental packages and shows their applications. We focus here on contact problems of mechanics decomposed by means of a FETI-type non-overlapping domain decomposition method. These problems lead to inequality constrained quadratic programming problems that can be solved by our PermonQP package.11510

Tubulin is actively exported from the nucleus through the Exportin1/CRM1 pathway

Microtubules of all eukaryotic cells are formed by α- and β-tubulin heterodimers. In addition to the well known cytoplasmic tubulins, a subpopulation of tubulin can occur in the nucleus. So far, the potential function of nuclear tubulin has remained elusive. In this work, we show that α- and β-tubulins of various organisms contain multiple conserved nuclear export sequences, which are potential targets of the Exportin 1/CRM1 pathway. We demonstrate exemplarily that these NES motifs are sufficient to mediate export of GFP as model cargo and that this export can be inhibited by leptomycin B, an inhibitor of the Exportin 1/CRM1 pathway. Likewise, leptomycin B causes accumulation of GFP-tagged tubulin in interphase nuclei, in both plant and animal model cells. Our analysis of nuclear tubulin content supports the hypothesis that an important function of nuclear tubulin export is the exclusion of tubulin from interphase nuclei, after being trapped by nuclear envelope reassembly during telophase

Raman spectroscopy of regulatory protein Omega from Streptococcus pyogenes plasmid pSM19035 and complexes with operator DNA

Abstract. pSM19035-encoded homodimeric ω protein (ω2) regulates transcription of genes required for control of plasmid copy number and stable inheritance. ω2 belongs to the MetJ/Arc structural superfamily of repressors forming a ribbon-helixhelix (RHH) DNA binding motif, and binds specifically to operator regions containing at least two consecutive copies of heptad sequences 5 -A /TATCAC A /T-3 in direct or inverted orientation. Solution properties of a double stranded 19 base-pairs oligonucleotide designed to model an operator DNA binding site of ω2 (top strand 5 -GCG AATCACA TGTGATT GG-3 ), ω2, and the ω2:19-bp DNA complex were analysed by Raman spectroscopy. The Raman data indicate a sequence specific induced fit of both interacting macromolecules with ω2 binding to the major groove of the DNA, large perturbations of the DNA attributable to base unstacking, changes in vibrational modes of deoxyribose moieties, and protein-induced DNA bending. Protein marker bands indicate that α-helices are preserved, whereas amino acid side chains are largely perturbed, and unordered structures and turns become extensively restructured. Raman difference bands are consistent with interactions of thymine, adenine and cytosine with ω2 side chains. The results suggest that the central TCA/TGA stretch of the heptads might be the main target site for ω2 binding to operator DNA

Genotyping a second growth coast redwood forest : a high throughput methodology

The idea that excitonic (electronic) coherences are of fundamental importance to natural photosynthesis gained popularity when slowly dephasing quantum beats (QBs) were observed in the two-dimensional electronic spectra of the Fenna–Matthews–Olson (FMO) complex at 77 K. These were assigned to superpositions of excitonic states, a controversial interpretation, as the strong chromophore–environment interactions in the complex suggest fast dephasing. Although it has been pointed out that vibrational motion produces similar spectral signatures, a concrete assignment of these oscillatory signals to distinct physical processes is still lacking. Here we revisit the coherence dynamics of the FMO complex using polarization-controlled two-dimensional electronic spectroscopy, supported by theoretical modelling. We show that the long-lived QBs are exclusively vibrational in origin, whereas the dephasing of the electronic coherences is completed within 240 fs even at 77 K. We further find that specific vibrational coherences are produced via vibronically coupled excited states. The presence of such states suggests that vibronic coupling is relevant for photosynthetic energy transfer

A three-scale domain decomposition method for the 3D analysis of debonding in laminates

The prediction of the quasi-static response of industrial laminate structures requires to use fine descriptions of the material, especially when debonding is involved. Even when modeled at the mesoscale, the computation of these structures results in very large numerical problems. In this paper, the exact mesoscale solution is sought using parallel iterative solvers. The LaTIn-based mixed domain decomposition method makes it very easy to handle the complex description of the structure; moreover the provided multiscale features enable us to deal with numerical difficulties at their natural scale; we present the various enhancements we developed to ensure the scalability of the method. An extension of the method designed to handle instabilities is also presented

Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers

In a companion paper by Cohen-Adad et al. we introduce the spine generic quantitative MRI protocol that provides valuable metrics for assessing spinal cord macrostructural and microstructural integrity. This protocol was used to acquire a single subject dataset across 19 centers and a multi-subject dataset across 42 centers (for a total of 260 participants), spanning the three main MRI manufacturers: GE, Philips and Siemens. Both datasets are publicly available via git-annex. Data were analysed using the Spinal Cord Toolbox to produce normative values as well as inter/intra-site and inter/intra-manufacturer statistics. Reproducibility for the spine generic protocol was high across sites and manufacturers, with an average inter-site coefficient of variation of less than 5% for all the metrics. Full documentation and results can be found at https://spine-generic.rtfd.io/. The datasets and analysis pipeline will help pave the way towards accessible and reproducible quantitative MRI in the spinal cord