27,069 research outputs found
A branch-and-cut approach to physical mapping with end-probes
A fundamental problem in computational biology is the construction of physical maps of chromosomes from hybridization experiments between unique probes and clones of chromosome fragments in the presence of error. Alizadeh, Karp, Weisser and Zweig (Algorithmica 13:1/2, 52-76, 1995) first considered a maximum-likelihood model of the problem that is equivalent to finding an ordering of the probes that minimizes a weighted sum of errors, and developed several effective heuristics. We show that by exploiting information about the end-probes of clones, this model can be formulated as a weighted Betweenness Problem. This affords the significant advantage of allowing the well-developed tools of integer linear-programming and branch-and-cut algorithms to be brought to bear on physical mapping, enabling us for the first time to solve small mapping instances to optimality even in the presence of high error. We also show that by combining the optimal solution of many small overlapping Betweenness Problems, one can effectively screen errors from larger instances, and solve the edited instance to optimality as a Hamming-Distance Traveling Salesman Problem. This suggests a new combined approach to physical map construction
Hidden horizons in non-relativistic AdS/CFT
We study boundary Green's functions for spacetimes with non-relativistic
scaling symmetry. For this class of backgrounds, scalar modes with large
transverse momentum, or equivalently low frequency, have an exponentially
suppressed imprint on the boundary. We investigate the effect of these modes on
holographic two-point functions. We find that the boundary Green's function is
generically insensitive to horizon features on small transverse length scales.
We explicitly demonstrate this insensitivity for Lifshitz z=2, and then use the
WKB approximation to generalize our findings to Lifshitz z>1 and RG flows with
a Lifshitz-like region. We also comment on the analogous situation in
Schroedinger spacetimes. Finally, we exhibit the analytic properties of the
Green's function in these spacetimes.Comment: Abstract and Introduction updated, typos correcte
Projected Constraints on Modified Gravity Cosmologies from 21 cm Intensity Mapping
We present projected constraints on modified gravity models from the
observational technique known as 21 cm intensity mapping, where cosmic
structure is detected without resolving individual galaxies. The resulting map
is sensitive to both BAO and weak lensing, two of the most powerful
cosmological probes. It is found that a 200 m x 200 m cylindrical telescope,
sensitive out to z=2.5, would be able to distinguish DGP from most dark energy
models, and constrain the Hu & Sawicki f(R) model to |f_{R0}| < 9*10^(-6) at
95% confidence. The latter constraint makes extensive use of the lensing
spectrum in the nonlinear regime. These results show that 21 cm intensity
mapping is not only sensitive to modifications of the standard model's
expansion history, but also to structure growth. This makes intensity mapping a
powerful and economical technique, achievable on much shorter time scales than
optical experiments that would probe the same era.Comment: 10 pages, 5 figures, 1 table. Added references and expanded
discussion. As resubmitted to Phys. Rev. D, in response to reviewer comment
Spacelike boundaries from the c=1 Matrix Model
We find classical solutions of two dimensional noncritical string theory
which give rise to geometries with spacelike boundaries, similar to spacetimes
with cosmological event horizons. In the c=1 matrix model, these solutions have
a representation as simple time dependent configurations. We obtain the causal
structure of the resulting spacetimes. Using the macroscopic loop transform, we
probe the form of the tachyon condensate in the asymptotic regions.Comment: 22 pages, 5 figures, v2: reference added, v3: minor correction
Sequence organization of feline leukemis virus DNA in infected cells
A restriction site map has been deduced of unintegrated and integrated FeLV viral DNA found in human RD cells after experimental infection with the Gardner-Arnstein strain of FeLV. Restriction fragments were ordered by single and double enzyme digests followed by Southern transfer (1) and hybridization with 32P-labeled viral cDNA probes. The restriction map was oriented with respect to the 5' and 3' ends of viral RNA by using a 3' specific hybridization probe. The major form of unintegrated viral DNA found was a 8.7 kb linear DNA molecule bearing a 450 bp direct long terminal redundancy (LTR) derived from both 5' and 3' viral RNA sequences. Minor, circular forms, 8.7 kb and 8.2 kb in length were also detected, the larger one probably containing two adjacent copies of the LTR and the smaller one containing one copy of the LTR. Integrated copies of FeLV are colinear with the unintegrated linear form and contain the KpnI and SmaI sites found in each LTR
Computational Molecular Biology
Computational Biology is a fairly new subject that arose in response to the computational problems posed by the analysis and the processing of biomolecular sequence and structure data. The field was initiated in the late 60's and early 70's largely by pioneers working in the life sciences. Physicists and mathematicians entered the field in the 70's and 80's, while Computer Science became involved with the new biological problems in the late 1980's. Computational problems have gained further importance in molecular biology through the various genome projects which produce enormous amounts of data. For this bibliography we focus on those areas of computational molecular biology that involve discrete algorithms or discrete optimization. We thus neglect several other areas of computational molecular biology, like most of the literature on the protein folding problem, as well as databases for molecular and genetic data, and genetic mapping algorithms. Due to the availability of review papers and a bibliography this bibliography
Non-extremal fractional branes
We construct non-extremal fractional D-brane solutions of type-II string
theory at the Z_2 orbifold point of K3. These solutions generalize known
extremal fractional-brane solutions and provide further insights into N=2
supersymmetric gauge theories and dual descriptions thereof. In particular, we
find that for these solutions the horizon radius cannot exceed the non-extremal
enhancon radius. As a consequence, we conclude that a system of non-extremal
fractional branes cannot develop into a black brane. This conclusion is in
agreement with known dual descriptions of the system.Comment: 29 pages, LaTeX. v2: 30 pages; equation (3.4) corrected; typos fixed;
discussion in section 3 streamlined and slightly extended; reference adde
Mutual information and the F-theorem
Mutual information is used as a purely geometrical regularization of
entanglement entropy applicable to any QFT. A coefficient in the mutual
information between concentric circular entangling surfaces gives a precise
universal prescription for the monotonous quantity in the c-theorem for d=3.
This is in principle computable using any regularization for the entropy, and
in particular is a definition suitable for lattice models. We rederive the
proof of the c-theorem for d=3 in terms of mutual information, and check our
arguments with holographic entanglement entropy, a free scalar field, and an
extensive mutual information model.Comment: 80 pages, 16 figure
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