Asymptotic Search for Ground States of SU(2) Matrix Theory

We introduce a complete set of gauge-invariant variables and a generalized Born-Oppenheimer formulation to search for normalizable zero-energy asymptotic solutions of the Schrodinger equation of SU(2) matrix theory. The asymptotic method gives only ground state candidates, which must be further tested for global stability. Our results include a set of such ground state candidates, including one state which is a singlet under spin(9).Comment: 51 page

Accurate Noise Projection for Reduced Stochastic Epidemic Models

We consider a stochastic Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological model. Through the use of a normal form coordinate transform, we are able to analytically derive the stochastic center manifold along with the associated, reduced set of stochastic evolution equations. The transformation correctly projects both the dynamics and the noise onto the center manifold. Therefore, the solution of this reduced stochastic dynamical system yields excellent agreement, both in amplitude and phase, with the solution of the original stochastic system for a temporal scale that is orders of magnitude longer than the typical relaxation time. This new method allows for improved time series prediction of the number of infectious cases when modeling the spread of disease in a population. Numerical solutions of the fluctuations of the SEIR model are considered in the infinite population limit using a Langevin equation approach, as well as in a finite population simulated as a Markov process.Comment: 38 pages, 10 figures, new title, Final revision to appear in Chao

The Algebras of Large N Matrix Mechanics

Extending early work, we formulate the large N matrix mechanics of general bosonic, fermionic and supersymmetric matrix models, including Matrix theory: The Hamiltonian framework of large N matrix mechanics provides a natural setting in which to study the algebras of the large N limit, including (reduced) Lie algebras, (reduced) supersymmetry algebras and free algebras. We find in particular a broad array of new free algebras which we call symmetric Cuntz algebras, interacting symmetric Cuntz algebras, symmetric Bose/Fermi/Cuntz algebras and symmetric Cuntz superalgebras, and we discuss the role of these algebras in solving the large N theory. Most important, the interacting Cuntz algebras are associated to a set of new (hidden) local quantities which are generically conserved only at large N. A number of other new large N phenomena are also observed, including the intrinsic nonlocality of the (reduced) trace class operators of the theory and a closely related large N field identification phenomenon which is associated to another set (this time nonlocal) of new conserved quantities at large N.Comment: 70 pages, expanded historical remark

Sashimi plots: Quantitative visualization of RNA sequencing read alignments

We introduce Sashimi plots, a quantitative multi-sample visualization of mRNA sequencing reads aligned to gene annotations. Sashimi plots are made using alignments (stored in the SAM/BAM format) and gene model annotations (in GFF format), which can be custom-made by the user or obtained from databases such as Ensembl or UCSC. We describe two implementations of Sashimi plots: (1) a stand-alone command line implementation aimed at making customizable publication quality figures, and (2) an implementation built into the Integrated Genome Viewer (IGV) browser, which enables rapid and dynamic creation of Sashimi plots for any genomic region of interest, suitable for exploratory analysis of alternatively spliced regions of the transcriptome. Isoform expression estimates outputted by the MISO program can be optionally plotted along with Sashimi plots. Sashimi plots can be used to quickly screen differentially spliced exons along genomic regions of interest and can be used in publication quality figures. The Sashimi plot software and documentation is available from: http://genes.mit.edu/burgelab/miso/docs/sashimi.htmlComment: 2 figure

Analyzing Powers and Spin Correlation Coefficients for p+d Elastic Scattering at 135 and 200 MeV

The proton and deuteron analyzing powers and 10 of the possible 12 spin correlation coefficients have been measured for p+d elastic scattering at proton bombarding energies of 135 and 200 MeV. The results are compared with Faddeev calculations using two different NN potentials. The qualitative features of the extensive data set on the spin dependence in p+d elastic scattering over a wide range of angles presented here are remarkably well explained by two-nucleon force predictions without inclusion of a three-nucleon force. The remaining discrepancies are, in general, not alleviated when theoretical three-nucleon forces are included in the calculations.Comment: 43 pages, 12 figures, accepted for publication by Phys. Rev.

Discovery of a Jet-Like Structure at the High Redshift QSO CXOMP J084128.3+131107

The Chandra Multiwavelength Project (ChaMP) has discovered a jet-like structure associated with a newly recognized QSO at redshift z=1.866. The system was 9.4 arcmin off-axis during an observation of 3C 207. Although significantly distorted by the mirror PSF, we use both a raytrace and a nearby bright point source to show that the X-ray image must arise from some combination of point and extended sources, or else from a minimum of three distinct point sources. We favor the former situation, as three unrelated sources would have a small probability of occurring by chance in such a close alignment. We show that interpretation as a jet emitting X-rays via inverse Compton (IC) scattering on the cosmic microwave background (CMB) is plausible. This would be a surprising and unique discovery of a radio-quiet QSO with an X-ray jet, since we have obtained upper limits of 100 microJy on the QSO emission at 8.46 GHz, and limits of 200 microJy for emission from the putative jet.Comment: 12 pages including 4 figures. Accepted for publication by ApJ Letter