69 research outputs found
Variable line profiles due to non-axisymmetric patterns in an accretion disc around a rotating black hole
We have explored spectral line profiles due to spiral patterns in accretion
discs around black holes. A parametrization was employed for the shape and
emissivity of spiral waves, which can be produced by non-axisymmetric
perturbations affecting the disc density and ionization structure. The effects
of the light-travel time, energy shift, and gravitational focusing near to a
rotating black hole were taken into account. A high-resolution ray-tracing code
was used to follow the time variations of the synthetic line profile. A variety
of expected spectral features were examined and the scheme applied to a broad
iron line observed in MCG-6-30-15.Comment: 11 pages (LaTeX), 7 figures (EPS); PASJ accepte
Star-disc interactions in a galactic centre and oblateness of the inner stellar cluster
Structure of a quasi-stationary stellar cluster is modelled assuming that it
is embedded in the gravitational field of a super-massive black hole. Gradual
orbital decay of stellar trajectories is caused by the dissipative interaction
with an accretion disc. Gravitational field of the disc is constructed and its
effect on the cluster structure is taken into account as an axially symmetric
perturbation. Attention is focused on a circumnuclear region (r<10^4
gravitational radii) where the effects of the central black hole and the disc
dominate over the influence of an outer galaxy. It is shown how the stellar
system becomes gradually flattened towards the disc plane. For certain
combinations of the model parameters, a toroidal structure is formed by a
fraction of stars. Growing anisotropy of stellar velocities as well as their
segregation occur. The mass function of the inner cluster is modified and it
progressively departs from the asymptotic form assumed in the outer cluster. A
new stationary distribution can be characterized in terms of velocity
dispersion of the stellar sample in the central region of the modified cluster.Comment: Accepted for publication in MNRAS; 12 pages, 10 figure
PDBench: Evaluating Computational Methods for Protein Sequence Design
Proteins perform critical processes in all living systems: converting solar
energy into chemical energy, replicating DNA, as the basis of highly performant
materials, sensing and much more. While an incredible range of functionality
has been sampled in nature, it accounts for a tiny fraction of the possible
protein universe. If we could tap into this pool of unexplored protein
structures, we could search for novel proteins with useful properties that we
could apply to tackle the environmental and medical challenges facing humanity.
This is the purpose of protein design.
Sequence design is an important aspect of protein design, and many successful
methods to do this have been developed. Recently, deep-learning methods that
frame it as a classification problem have emerged as a powerful approach.
Beyond their reported improvement in performance, their primary advantage over
physics-based methods is that the computational burden is shifted from the user
to the developers, thereby increasing accessibility to the design method.
Despite this trend, the tools for assessment and comparison of such models
remain quite generic. The goal of this paper is to both address the timely
problem of evaluation and to shine a spotlight, within the Machine Learning
community, on specific assessment criteria that will accelerate impact.
We present a carefully curated benchmark set of proteins and propose a number
of standard tests to assess the performance of deep learning based methods. Our
robust benchmark provides biological insight into the behaviour of design
methods, which is essential for evaluating their performance and utility. We
compare five existing models with two novel models for sequence prediction.
Finally, we test the designs produced by these models with AlphaFold2, a
state-of-the-art structure-prediction algorithm, to determine if they are
likely to fold into the intended 3D shapes.Comment: 9 pages, 5 figure
Intracerebral Implantation of Hydrogel-Coupled Adhesion Peptides: Tissue Reaction
Arg-Gly-Asp peptides (RGD) were synthesized
and chemically coupled to the bulk of N-(2-hydroxypropyl) methacrylamide-based polymer
hydrogels. Fourier Transform Infrared Spectroscopy
(FFIR) and amino acid analysis confirmed
the peptide coupling to the polymer. Activated
and control (unmodified) polymer matrices were
stereotaxically implanted in the striata of rat
brains, and two months later the brains were
processed for immunohistochemistry using antibodies
for glial acidic fibrillary protein (GFAP),
laminin and neurofilaments. RGD-containing
polymer matrices promoted stronger adhesion to
the host tissue than the unmodified polymer
matrices. In addition, the RGD-grafted polymer
implants promoted and supported the growth
and spread of GFAP-positive glial tissue onto
and into the hydrogels. Neurofilament-positive
fibers were also seen running along the surface
of the polymer and, in some instances, penetrating
the matrix. These findings are discussed
in the context of using bioactive polymers as a
new approach for promoting tissue repair and
axonal regeneration of damaged structures of
the central nervous system
Enhanced activity of massive black holes by stellar capture assisted by a self-gravitating accretion disc
We study the probability of close encounters between stars from a nuclear
cluster and a massive black hole. The gravitational field of the system is
dominated by the black hole in its sphere of influence. It is further modified
by the cluster mean field (a spherical term) and a gaseous disc/torus (an
axially symmetric term) causing a secular evolution of stellar orbits via Kozai
oscillations. Intermittent phases of large eccentricity increase the chance
that stars become damaged inside the tidal radius of the central hole. Such
events can produce debris and lead to recurring episodes of enhanced accretion
activity. We introduce an effective loss cone and associate it with tidal
disruptions during the high-eccentricity phases of the Kozai cycle. By
numerical integration of the trajectories forming the boundary of the loss cone
we determine its shape and volume. We also include the effect of relativistic
advance of pericentre. The potential of the disc has the efffect of enlarging
the loss cone and, therefore, the predicted number of tidally disrupted stars
should grow by factor of ~10^2. On the other hand, the effect of the cluster
mean potential together with the relativistic pericentre advance act against
the eccentricity oscillations. In the end we expect the tidal disruption events
to be approximately ten times more frequent in comparison with the model in
which the three effects -- the cluster mean field, the relativistic pericentre
advance, and the Kozai mechanism -- are all ignored. The competition of
different influences suppresses the predicted star disruption rate as the black
hole mass increases. Hence, the process under consideration is more important
for intermediate-mass black holes, M_bh~10^4M_s.Comment: 10 pages, 5 figures; Astronomy & Astrophysics accepte
Numerical simulation of small perturbation on an accretion disk due to the collision of a star with the disk near the black hole
In this paper, perturbations of an accretion disk by a star orbiting around a
black hole are studied. We report on a numerical experiment, which has been
carried out by using a parallel-machine code originally developed by D\"{o}nmez
(2004). An initially steady state accretion disk near a non-rotating
(Schwarzschild) black hole interacts with a "star", modeled as an initially
circular region of increased density. Part of the disk is affected by the
interaction. In some cases, a gap develops and shock wave propagates through
the disk. We follow the evolution for order of one dynamical period and we show
how the non-axisymetric density perturbation further evolves and moves
downwards where the material of the disk and the star become eventually
accreted onto the central body.
When the star perturbs the steady state accretion disk, the disk around the
black hole is destroyed by the effect of perturbation. The perturbed accretion
disk creates a shock wave during the evolution and it loses angular momentum
when the gas hits on the shock waves. Colliding gas with the shock wave is the
one of the basic mechanism of emitting the rays in the accretion disk. The
series of supernovae occurring in the inner disk could entirely destroy the
disk in that region which leaves a more massive black hole behind, at the
center of galaxies.Comment: 20pages, 8 figures, accepted for publication in Astrophysics and
Space Scienc
On highly eccentric stellar trajectories interacting with a self-gravitating disc in Sgr A*
We propose that Kozai's phenomenon is responsible for the long-term evolution
of stellar orbits near a supermassive black hole. We pursue the idea that this
process may be driven by a fossil accretion disc in the centre of our Galaxy,
causing the gradual orbital decay of stellar trajectories, while setting some
stars on highly elliptic orbits. We evolve model orbits that undergo repetitive
transitions across the disc over the period of ~10^7 years. We assume that the
disc mass is small compared to the central black hole, and its gravitational
field comparatively weak, yet non-zero, and we set the present values of
orbital parameters of the model star consistent with those reported for the S2
star in Sagittarius A*. We show how a model trajectory decays and circularizes,
but at some point the mean eccentricity is substantially increased by Kozai's
resonance. In consequence the orbital decay of highly eccentric orbits is
accelerated. A combination of an axially symmetric gravitational field and
dissipative environment can provide a mechanism explaining the origin of stars
on highly eccentric orbits tightly bound to the central black hole. In the
context of other S-stars, we can conclude that an acceptable mass of the disc
(i.e., M_d<=1 percent of the black hole mass) is compatible with their
surprisingly young age and small pericentre distances, provided these stars
were formed at r<=10^5 gravitational radii.Comment: Accepted for publication in A&A; 9 pages, 6 figures. Revised version
with minor language corrections (no change in content
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