59 research outputs found
An ancestral secretory apparatus in the protozoan parasite Giardia intestinalis
The protozoan parasite Giardia intestinalis belongs to one of the earliest diverged eukaryotic lineages. This is also reflected in a simple intracellular organization, as Giardia lacks common subcellular compartments such as mitochondria, peroxisomes, and apparently also a Golgi apparatus. During encystation, developmentally regulated formation of large secretory compartments containing cyst wall material occurs. Despite the lack of any morphological similarities, these encystation-specific vesicles (ESVs) show several biochemical characteristics of maturing Golgi cisternae. Previous studies suggested that Golgi structure and function are induced only during encystation in Giardia, giving rise to the hypothesis that ESVs, as a Giardia Golgi equivalent, are generated de novo. Alternatively, ESV compartments could be built on the template structure of a cryptic Golgi in trophozoites in response to ER export of cyst wall material during encystation. We addressed this question by defining the molecular framework of the Giardia secretory apparatus using a comparative genomic approach. Analysis of the corresponding transcriptome during growth and encystation revealed surprisingly little stage-specific regulation. A panel of antibodies was generated against selected marker proteins to investigate the developmental dynamics of the endomembrane system. We show evidence that Giardia accommodates the export of large amounts of cyst wall material through re-organization of membrane compartment(s) in trophozoites with biochemical similarities to ESVs. This suggests that ESVs are selectively stabilized Golgi-like compartments in a unique and archetypical secretory system, which arise from a structural template in trophozoites rather than being generated de novo
Linear theory and velocity correlations of clusters
Linear theory provides a reasonable description of the velocity correlations
of biased tracers both perpendicular and parallel to the line of separation,
provided one accounts for the fact that the measurement is almost always made
using pair-weighted statistics. This introduces an additional term which, for
sufficiently biased tracers, may be large. Previous work suggesting that linear
theory was grossly in error for the components parallel to the line of
separation ignored this term.Comment: 5 pages, 2 figures, MNRAS accepte
The Inverse Redshift-Space Operator: Reconstructing Cosmological Density and Velocity Fields
We present the linear inverse redshift space operator which maps the galaxy
density field derived from redshift surveys from redshift space to real space.
Expressions are presented for observers in both the CMBR and Local Group rest
frames. We show how these results can be generalised to flux--limited galaxy
redshift surveys. These results allow the straightforward reconstruction of
real space density and velocity fields without resort to iterative or
numerically intensive inverse methods. As a corollary to the inversion of the
density in the Local Group rest frame we present an expression for estimating
the real space velocity dipole from redshift space, allowing one to estimate
the Local Group dipole without full reconstruction of the redshift survey. We
test these results on some simple models and find the reconstruction is very
accurate. A new spherical harmonic representation of the redshift distortion
and its inverse is developed, which simplifies the reconstruction and allows
analytic calculation of the properties of the reconstructed redshift survey. We
use this representation to analyse the uncertainties in the reconstruction of
the density and velocity fields from redshift space, due to only a finite
volume being available. Both sampling and shot-noise variance terms are derived
and we discuss the limits of reconstruction analysis. We compare the
reconstructed velocity field with the true velocity field and show that
reconstruction in the Local Group rest frame is preferable, since this
eliminates the major source of uncertainty from the dipole mode. These results
can be used to transform redshift surveys to real space and may be used as part
of a full likelihood analysis to extract cosmological parameters.Comment: 13 pages (Latex), 6 postscript figures included, accepted for
publication in MNRA
The velocity-density relation in the spherical model
We study the cosmic velocity-density relation using the spherical collapse
model (SCM) as a proxy to non-linear dynamics. Although the dependence of this
relation on cosmological parameters is known to be weak, we retain the density
parameter Omega_m in SCM equations, in order to study the limit Omega_m -> 0.
We show that in this regime the considered relation is strictly linear, for
arbitrary values of the density contrast, on the contrary to some claims in the
literature. On the other hand, we confirm that for realistic values of Omega_m
the exact relation in the SCM is well approximated by the classic formula of
Bernardeau (1992), both for voids (delta<0) and for overdensities up to delta ~
3. Inspired by this fact, we find further analytic approximations to the
relation for the whole range delta from -1 to infinity. Our formula for voids
accounts for the weak Omega_m-dependence of their maximal rate of expansion,
which for Omega_m < 1 is slightly smaller that 3/2. For positive density
contrasts, we find a simple relation div v = 3 H_0 (Omega_m)^(0.6) [
(1+delta)^(1/6) - (1+delta)^(1/2) ], that works very well up to the turn-around
(i.e. up to delta ~ 13.5 for Omega_m = 0.25 and neglected Omega_Lambda). Having
the same second-order expansion as the formula of Bernardeau, it can be
regarded as an extension of the latter for higher density contrasts. Moreover,
it gives a better fit to results of cosmological numerical simulations.Comment: 11 pages, 6 figures. Accepted for publication in MNRA
Mass transfer in eccentric binaries: the new Oil-on-Water SPH technique
To measure the onset of mass transfer in eccentric binaries we have developed
a two-phase SPH technique. Mass transfer is important in the evolution of close
binaries, and a key issue is to determine the separation at which mass transfer
begins. The circular case is well understood and can be treated through the use
of the Roche formalism. To treat the eccentric case we use a newly-developed
two phase system. The body of the donor star is made up from high-mass "water"
particles, whilst the atmosphere is modelled with low-mass "oil" particles.
Both sets of particles take part fully in SPH interactions. To test the
technique we model circular mass-transfer binaries containing a 0.6 Msun donor
star and a 1 Msun white dwarf; such binaries are thought to form cataclysmic
variable (CV) systems. We find that we can reproduce a reasonable CV
mass-transfer rate, and that our extended atmosphere gives a separation that is
too large by aproximately 16%, although its pressure scale height is
considerably exaggerated. We use the technique to measure the semi-major axis
required for the onset of mass transfer in binaries with a mass ratio of q=0.6
and a range of eccentricities. Comparing to the value obtained by considering
the instantaneous Roche lobe at pericentre we find that the radius of the star
required for mass transfer to begin decreases systematically with increasing
eccentricity.Comment: 9 pages, 8 figures, accepted by MNRA
The Dynamics and Stability of Circumbinary Orbits
We numerically investigate the dynamics of orbits in 3D circumbinary
phase-space as a function of binary eccentricity and mass fraction. We find
that inclined circumbinary orbits in the elliptically-restricted three-body
problem display a nodal libration mechanism in the longitude of the ascending
node and in the inclination to the plane of the binary. We (i) analyse and
quantify the behaviour of these orbits with reference to analytical work
performed by Farago & Laskar (2010) and (ii) investigate the stability of these
orbits over time. This work is the first dynamically aware analysis of the
stability of circumbinary orbits across both binary mass fraction and binary
eccentricity. This work also has implications for exoplanetary astronomy in the
existence and determination of stable orbits around binary systems.Comment: Monthly Notices of the Royal Astronomical Society. in pres
Rotation of the cluster of galaxies A2107
We present indications of rotation in the galaxy cluster A2107 by a method
that searches for the maximum gradient in the velocity field in a flat
disk-like model of a cluster. Galaxies from cumulative sub-samples containing
more and more distant members from the cluster centre, are projected onto an
axis passing through the centre and we apply a linear regression model on the
projected distances and the line-of-sight velocities . The axis with the
maximum linear correlation coefficient defines the
direction of the maximum velocity gradient, and consequently it presents the
major axis of the apparently elliptical cluster. Because the effects of
rotation are subtle, we put strong emphasis on the estimation of the
uncertainties of the results by implementing different bootstrap techniques. We
have found the rotational effects are more strongly expressed from distances
Mpc from the cluster centre. The total virial mass of the
cluster is (3.2\pm0.6)\times10^{14} {\cal M}_{\sun}, while the virial mass,
corrected for the rotation, is (2.8\pm0.5) \times 10^{14}{\cal M}_{\sun}.Comment: 7 pages, 9 figures gzipped tar file. to be published in MNRA
Measuring the escape velocity and mass profiles of galaxy clusters beyond their virial radius
The caustic technique uses galaxy redshifts alone to measure the escape
velocity and mass profiles of galaxy clusters to clustrocentric distances well
beyond the virial radius, where dynamical equilibrium does not necessarily
hold. We provide a detailed description of this technique and analyse its
possible systematic errors. We apply the caustic technique to clusters with
mass M_200>=10^{14}h^{-1} M_sun extracted from a cosmological hydrodynamic
simulation of a LambdaCDM universe. With a few tens of redshifts per squared
comoving megaparsec within the cluster, the caustic technique, on average,
recovers the profile of the escape velocity from the cluster with better than
10 percent accuracy up to r~4 r_200. The caustic technique also recovers the
mass profile with better than 10 percent accuracy in the range (0.6-4) r_200,
but it overestimates the mass up to 70 percent at smaller radii. This
overestimate is a consequence of neglecting the radial dependence of the
filling function F_beta(r). The 1-sigma uncertainty on individual escape
velocity profiles increases from ~20 to ~50 percent when the radius increases
from r~0.1 r_200 to ~4 r_200. Individual mass profiles have 1-sigma uncertainty
between 40 and 80 percent within the radial range (0.6-4) r_200. We show that
the amplitude of these uncertainties is completely due to the assumption of
spherical symmetry, which is difficult to drop. Alternatively, we can apply the
technique to synthetic clusters obtained by stacking individual clusters: in
this case, the 1-sigma uncertainty on the escape velocity profile is smaller
than 20 percent out to 4 r_200. The caustic technique thus provides reliable
average profiles which extend to regions difficult or impossible to probe with
other techniques.Comment: MNRAS accepted, 20 page
Redshift space correlations and scale-dependent stochastic biasing of density peaks
We calculate the redshift space correlation function and the power spectrum
of density peaks of a Gaussian random field. In the linear regime k < 0.1
h/Mpc, the redshift space power spectrum is
P^s_{pk}(k,u) = exp(-f^2 s_{vel}^2 k^2 u^2) * [b_{pk}(k) + b_{vel}(k) f
u^2]^2 * P_m(k), where u is the angle with respect to the line of sight,
s_{vel} is the one-dimensional velocity dispersion, f is the growth rate, and
b_{pk}(k) and b_{vel}(k) are k-dependent linear spatial and velocity bias
factors. For peaks, the value of s_{vel} depends upon the functional form of
b_{vel}. The peaks model is remarkable because it has unbiased velocities --
peak motions are driven by dark matter flows -- but, in order to achieve this,
b_{vel} is k-dependent. We speculate that this is true in general: k-dependence
of the spatial bias will lead to k-dependence of b_{vel} even if the biased
tracers flow with the dark matter. Because of the k-dependence of the linear
bias parameters, standard manipulations applied to the peak model will lead to
k-dependent estimates of the growth factor that could erroneously be
interpreted as a signature of modified dark energy or gravity. We use the
Fisher formalism to show that the constraint on the growth rate f is degraded
by a factor of two if one allows for a k-dependent velocity bias of the peak
type. We discuss a simple estimate of nonlinear evolution and illustrate the
effect of the peak bias on the redshift space multipoles. For k < 0.1 h/Mpc,
the peak bias is deterministic but k-dependent, so the configuration space bias
is stochastic and scale dependent, both in real and redshift space. We provide
expressions for this stochasticity and its evolution (abridged).Comment: 24 pages, 7 figures (v3): references added (v4): added
figure+appendix. In press in PR
Modeling scale-dependent bias on the baryonic acoustic scale with the statistics of peaks of Gaussian random fields
Models of galaxy and halo clustering commonly assume that the tracers can be
treated as a continuous field locally biased with respect to the underlying
mass distribution. In the peak model pioneered by BBKS, one considers instead
density maxima of the initial, Gaussian mass density field as an approximation
to the formation site of virialized objects. In this paper, the peak model is
extended in two ways to improve its predictive accuracy. Firstly, we derive the
two-point correlation function of initial density peaks up to second order and
demonstrate that a peak-background split approach can be applied to obtain the
k-independent and k-dependent peak bias factors at all orders. Secondly, we
explore the gravitational evolution of the peak correlation function within the
Zel'dovich approximation. We show that the local (Lagrangian) bias approach
emerges as a special case of the peak model, in which all bias parameters are
scale-independent and there is no statistical velocity bias. We apply our
formulae to study how the Lagrangian peak biasing, the diffusion due to large
scale flows and the mode-coupling due to nonlocal interactions affect the scale
dependence of bias from small separations up to the baryon acoustic oscillation
(BAO) scale. For 2-sigma density peaks collapsing at z=0.3, our model predicts
a ~ 5% residual scale-dependent bias around the acoustic scale that arises
mostly from first-order Lagrangian peak biasing (as opposed to second-order
gravity mode-coupling). We also search for a scale dependence of bias in the
large scale auto-correlation of massive halos extracted from a very large
N-body simulation provided by the MICE collaboration. For halos with mass
M>10^{14}Msun/h, our measurements demonstrate a scale-dependent bias across the
BAO feature which is very well reproduced by a prediction based on the peak
model.Comment: (v1): 23 pages text, 8 figures + appendix (v2): typos fixed,
references added, accepted for publication in PR
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