107,311 research outputs found
A New Halo Finding Method for N-Body Simulations
We have developed a new halo finding method, Physically Self-Bound (PSB)
group finding algorithm, which can efficiently identify halos located even at
crowded regions. This method combines two physical criteria such as the tidal
radius of a halo and the total energy of each particle to find member
particles. Two hierarchical meshes are used to increase the speed and the power
of halo identification in the parallel computing environments. First, a coarse
mesh with cell size equal to the mean particle separation is
used to obtain the density field over the whole simulation box. Mesh cells
having density contrast higher than a local cutoff threshold
are extracted and linked together for those adjacent to each other. This
produces local-cell groups. Second, a finer mesh is used to obtain density
field within each local-cell group and to identify halos. If a density shell
contains only one density peak, its particles are assigned to the density peak.
But in the case of a density shell surrounding at least two density peaks, we
use both the tidal radii of halo candidates enclosed by the shell and the total
energy criterion to find physically bound particles with respect to each halo.
Similar to DENMAX and HOP, the \hfind method can efficiently identify small
halos embedded in a large halo, while the FoF and the SO do not resolve such
small halos. We apply our new halo finding method to a 1-Giga particle
simulation of the CDM model and compare the resulting mass function
with those of previous studies. The abundance of physically self-bound halos is
larger at the low mass scale and smaller at the high mass scale than proposed
by the Jenkins et al. (2001) who used the FoF and SO methods. (abridged)Comment: 10 pages, 8 figs, submitted to Ap
D1 and D5-Brane Actions in AdS_m x S^n
The kappa-invariant and supersymmetric actions of D1 and D5-branes in AdS_3 x
S^3 are investigated, as well as the action of a D5-brane in an AdS_5 x S^5
background. The action of a D5-brane lying totally in an AdS_3 x S^3 background
is found. Some progress was made towards finding the action for the D5-brane
free to move in the whole AdS_3 x S^3 x T^4 space, however the supersymmetric
action found here is not kappa-invariant and the reasons the method used did
not find a kappa-invariant solution are discussed.Comment: 17pp, Latex, improved explanations, a definition adde
Comment on ``Solution of Classical Stochastic One-Dimensional Many-Body Systems''
In a recent Letter, Bares and Mobilia proposed the method to find solutions
of the stochastic evolution operator with a
non-trivial quartic term . They claim, ``Because of the conservation of
probability, an analog of the Wick theorem applies and all multipoint
correlation functions can be computed.'' Using the Wick theorem, they expressed
the density correlation functions as solutions of a closed set of
integro-differential equations.
In this Comment, however, we show that applicability of Wick theorem is
restricted to the case only.Comment: 1 page, revtex style, comment on paper Phys. Rev. Lett. {\bf 83},
5214 (1999
Clinical exome performance for reporting secondary genetic findings.
BACKGROUND
:
Reporting clinically actionable incidental
genetic findings in the course of clinical exome testing is
recommended by the American College of Medical Genet-
ics and Genomics (ACMG). However, the performance of
clinical exome methods for reporting small subsets of genes
has not been previously reported.
METHODS
:
In this study, 57 exome data sets performed as
clinical (n
!
12) or research (n
!
45) tests were retrospec-
tively analyzed. Exome sequencing data was examined for
adequacy in the detection of potentially pathogenic variant
locations in the 56 genes described in the ACMG incidental
findings recommendation. All exons of the 56 genes were
examined for adequacy of sequencing coverage. In addition,
nucleotide positions annotated in HGMD (Human Gene
Mutation Database) were examined.
RESULTS
:
The 56 ACMG genes have 18336 nucleotide
variants annotated in HGMD. None of the 57 exome
data sets possessed a HGMD variant. The clinical exome
test had inadequate coverage for
"
50% of HGMD vari-
ant locations in 7 genes. Six exons from 6 different genes
had consistent failure across all 3 test methods; these
exons had high GC content (76%–84%).
CONCLUSIONS
:
The use of clinical exome sequencing
for the interpretation and reporting of subsets of genes
requires recognition of the substantial possibility of
inadequate depth and breadth of sequencing coverage
at clinically relevant locations. Inadequate depth of
coverage may contribute to false-negative clinical ex-
ome results
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