3,308 research outputs found
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<sub>CTT</sub>). 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<sub>CTT</sub> preferentially samples conformations that are geometrically
well-suited as substrates for processive phosphorylation by the cognate
kinase GSK3. We suggest that DP<sub>CTT</sub> 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<sub>CTT</sub> 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
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
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
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 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
) 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
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