Wall-thickness changes predicted in hollow-drawn tubing

Hollow-tube drawing or tube sinking theory is based on the concept of continuous distribution of dislocations. Material composition, parameter influence, and die-angle are determining factors in derivation of the theoretical model

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Claws, Disorder, and Conformational Dynamics of the C Terminal Region of Human Desmoplakin

Multicellular organisms consist of cells that interact via elaborate adhesion complexes. Desmosomes are membrane-associated adhesion complexes that mechanically tether the cytoskeletal intermediate filaments (IFs) between two adjacent cells, creating a network of tough connections in tissues such as skin and heart. Desmoplakin (DP) is the key desmosomal protein that binds IFs, and the DP·IF association poses a quandary: desmoplakin must stably and tightly bind IFs to maintain the structural integrity of the desmosome. Yet, newly synthesized DP must traffic along the cytoskeleton to the site of nascent desmosome assembly without “sticking” to the IF network, implying weak or transient DP···IF contacts. Recent work reveals that these contacts are modulated by post-translational modifications (PTMs) in DP’s C-terminal tail (DP_CTT). Using molecular dynamics simulations, we have elucidated the structural basis of these PTM-induced effects. Our simulations, nearing 2 μs in aggregate, indicate that phosphorylation of S2849 induces an “arginine claw” in desmoplakin’s C-terminal tail. If a key arginine, R2834, is methylated, the DP_CTT preferentially samples conformations that are geometrically well-suited as substrates for processive phosphorylation by the cognate kinase GSK3. We suggest that DP_CTT is a molecular switch that modulates, via its conformational dynamics, DP’s overall efficacy as a substrate for GSK3. Finally, we show that the fluctuating DP_CTT can contact other parts of DP, suggesting a competitive binding mechanism for the modulation of DP···IF interactions

Mesoscale theory of grains and cells: crystal plasticity and coarsening

Solids with spatial variations in the crystalline axes naturally evolve into cells or grains separated by sharp walls. Such variations are mathematically described using the Nye dislocation density tensor. At high temperatures, polycrystalline grains form from the melt and coarsen with time: the dislocations can both climb and glide. At low temperatures under shear the dislocations (which allow only glide) form into cell structures. While both the microscopic laws of dislocation motion and the macroscopic laws of coarsening and plastic deformation are well studied, we hitherto have had no simple, continuum explanation for the evolution of dislocations into sharp walls. We present here a mesoscale theory of dislocation motion. It provides a quantitative description of deformation and rotation, grounded in a microscopic order parameter field exhibiting the topologically conserved quantities. The topological current of the Nye dislocation density tensor is derived from a microscopic theory of glide driven by Peach-Koehler forces between dislocations using a simple closure approximation. The resulting theory is shown to form sharp dislocation walls in finite time, both with and without dislocation climb.Comment: 5 pages, 3 figure

Beyond the fundamental noise limit in coherent optical fiber links

It is well known that temperature variations and acoustic noise affect ultrastable frequency dissemination along optical fiber. Active stabilization techniques are in general adopted to compensate for the fiber-induced phase noise. However, despite this compensation, the ultimate link performances remain limited by the so called delay-unsuppressed fiber noise that is related to the propagation delay of the light in the fiber. In this paper, we demonstrate a data post-processing approach which enables us to overcome this limit. We implement a subtraction algorithm between the optical signal delivered at the remote link end and the round-trip signal. In this way, a 6 dB improvement beyond the fundamental limit imposed by delay-unsuppressed noise is obtained. This result enhances the resolution of possible comparisons between remote optical clocks by a factor of 2. We confirm the theoretical prediction with experimental data obtained on a 47 km metropolitan fiber link, and propose how to extend this method for frequency dissemination purposes as well

Detailed Analysis of Balmer Lines in a Sloan Digital Sky Survey Sample of 90 Broad Line Active Galactic Nuclei

In order to contribute to the general effort aiming at the improvement of our knowledge about the physical conditions within the Broad Line Region (BLR) of Active Galactic Nuclei (AGN), here we present the results achieved by our analysis of the spectral properties of a sample of 90 broad line emitting sources, collected at the Sloan Digital Sky Survey (SDSS) database. By focusing our attention mainly onto the Balmer series of hydrogen emission lines, which is the dominant feature in the optical wavelength range of many BLR spectra, we extracted several flux and profile measurements, which we related to other source properties, such as optical continuum luminosities, inferred black hole masses, and accretion rates. Using the Boltzmann Plot method to investigate the Balmer line flux ratios as a function of the line profiles, we found that broader line emitting AGN typically have larger H_alpha / H_beta and smaller H_gamma / H_beta and H_delta / H_beta line ratios. With the help of some recent investigations, we model the structure of the BLR and we study the influence of the accretion process on the properties of the BLR plasma.Comment: 14 pages, 11 figures, fixes the wrong names of 4 objects; published on Ap

High resolution spectroscopy of the extended narrow-line region of IC 5063 and NGC 7212

We studied the properties of the gas of the extended narrow line region (ENLR) of two Seyfert 2 galaxies: IC 5063 and NGC 7212. We analysed high resolution spectra to investigate how the main properties of this region depend on the gas velocity. We divided the emission lines in velocity bins and we calculated several line ratios. Diagnostic diagrams and SUMA composite models (photo-ionization + shocks), show that in both galaxies there might be evidence of shocks significantly contributing in the gas ionization at high |V|, even though photo-ionization from the active nucleus remains the main ionization mechanism. In IC 5063 the ionization parameter depends on V and its trend might be explained assuming an hollow bi-conical shape for the ENLR, with one of the edges aligned with the galaxy disk. On the other hand, NGC 7212 does not show any kind of dependence. The models show that solar O/H relative abundances reproduce the observed spectra in all the analysed regions. They also revealed an high fragmentation of the gas clouds, suggesting that the complex kinematics observed in these two objects might be caused by interaction between the ISM and high velocity components, such as jets.Comment: 29 pages, 32 figures, accepted for publication in MNRA

Contribution of a Disk Component to Single Peaked Broad Lines of Active Galactic Nuclei

We study the disk emission component hidden in the single-peaked Broad Emission Lines (BELs) of Active Galactic Nuclei (AGN). We compare the observed broad lines from a sample of 90 Seyfert 1 spectra taken from the Sloan Digital Sky Survey with simulated line profiles. We consider a two-component Broad Line Region (BLR) model where an accretion disk and a surrounding non-disk region with isotropic cloud velocities generate the simulated BEL profiles. The analysis is mainly based in measurements of the full widths (at 10%, 20% and 30% of the maximum intensity) and of the asymmetries of the line profiles. Comparing these parameters for the simulated and observed H$\alpha$ broad lines, we {found} that the hidden disk emission {may} be present in BELs even if the characteristic {of two peaked line profiles is} absent. For the available sample of objects (Seyfert 1 galaxies with single-peaked BELs), our study indicates that, {in the case of the hidden disk emission in single peaked broad line profiles}, the disk inclination tends to be small (mostly $i<25^\circ$) and that the contribution of the disk emission to the total flux should be smaller than the contribution of the surrounding region.Comment: 18 Figures, 1 Table, MNRAS-accepted. MNRAS-accepte