Absolute Calibration of a 200 MeV Proton Polarimeter for Use with the Brookhaven Linac

This work was supported by the National Science Foundation Grant NSF PHY 81-14339 and by Indiana Universit

Large scale numerical investigation of excited states in poly(phenylene)

A density matrix renormalisation group scheme is developed, allowing for the first time essentially exact numerical solutions for the important excited states of a realistic semi-empirical model for oligo-phenylenes. By monitoring the evolution of the energies with chain length and comparing them to the experimental absorption peaks of oligomers and thin films, we assign the four characteristic absorption peaks of phenyl-based polymers. We also determine the position and nature of the nonlinear optical states in this model.Comment: RevTeX, 10 pages, 4 eps figures included using eps

The low-lying excitations of polydiacetylene

The Pariser-Parr-Pople Hamiltonian is used to calculate and identify the nature of the low-lying vertical transition energies of polydiacetylene. The model is solved using the density matrix renormalisation group method for a fixed acetylenic geometry for chains of up to 102 atoms. The non-linear optical properties of polydiacetylene are considered, which are determined by the third-order susceptibility. The experimental 1Bu data of Giesa and Schultz are used as the geometric model for the calculation. For short chains, the calculated E(1Bu) agrees with the experimental value, within solvation effects (ca. 0.3 eV). The charge gap is used to characterise bound and unbound states. The nBu is above the charge gap and hence a continuum state; the 1Bu, 2Ag and mAg are not and hence are bound excitons. For large chain lengths, the nBu tends towards the charge gap as expected, strongly suggesting that the nBu is the conduction band edge. The conduction band edge for PDA is agreed in the literature to be ca. 3.0 eV. Accounting for the strong polarisation effects of the medium and polaron formation gives our calculated E(nBu) ca. 3.6 eV, with an exciton binding energy of ca. 1.0 eV. The 2Ag state is found to be above the 1Bu, which does not agree with relaxed transition experimental data. However, this could be resolved by including explicit lattice relaxation in the Pariser- Parr-Pople-Peierls model. Particle-hole separation data further suggest that the 1Bu, 2Ag and mAg are bound excitons, and that the nBu is an unbound exciton.Comment: LaTeX, 23 pages, 4 postscript tables and 8 postscript figure

Dynamics of earthquake nucleation process represented by the Burridge-Knopoff model

Dynamics of earthquake nucleation process is studied on the basis of the one-dimensional Burridge-Knopoff (BK) model obeying the rate- and state-dependent friction (RSF) law. We investigate the properties of the model at each stage of the nucleation process, including the quasi-static initial phase, the unstable acceleration phase and the high-speed rupture phase or a mainshock. Two kinds of nucleation lengths L_sc and L_c are identified and investigated. The nucleation length L_sc and the initial phase exist only for a weak frictional instability regime, while the nucleation length L_c and the acceleration phase exist for both weak and strong instability regimes. Both L_sc and L_c are found to be determined by the model parameters, the frictional weakening parameter and the elastic stiffness parameter, hardly dependent on the size of an ensuing mainshock. The sliding velocity is extremely slow in the initial phase up to L_sc, of order the pulling speed of the plate, while it reaches a detectable level at a certain stage of the acceleration phase. The continuum limits of the results are discussed. The continuum limit of the BK model lies in the weak frictional instability regime so that a mature homogeneous fault under the RSF law always accompanies the quasi-static nucleation process. Duration times of each stage of the nucleation process are examined. The relation to the elastic continuum model and implications to real seismicity are discussed.Comment: Title changed. Changes mainly in abstract and in section 1. To appear in European Physical Journal

The influence of nozzle geometry on corner flows in supersonic wind tunnels

In supersonic flows, the separation in streamwise corners is a significant and widely encountered problem which can not be reliably predicted with the numerical methods commonly used in industry. The few previous studies on this topic have suggested conflicting corner flow topologies. Experiments of supersonic flow are typically conducted in wind tunnels with rectangular cross-sections, which use either a symmetric (full) or asymmetric (half-liner) nozzle configuration. However, the effect of the nozzle arrangement on the corner flow itself is not known. This paper examines the influence of nozzle geometry on the corner regions of a Mach 2.5 flow using a joint experimental-computational approach. The full setup and half-liner configuration are shown to produce different corner flow structures. The corner regions of the full setup and top corners of the half-liner exhibit thin sidewall boundary layers and a single primary vortex on the floor or ceiling. Meanwhile, the bottom corners of the half-liner configuration contain thick sidewall boundary layers and a counter-rotating vortex pair. Considerable vertical velocities are measured within the sidewall boundary layers. These are directed towards the tunnel centre-height for the full setup and downwards with the half-liner. The differences in sidewall cross flows between the two nozzle arrangements are likely due to distinct pressure distributions in the nozzle, where the secondary flows are set up. Measurements suggest that these nozzle-dependent transverse flows are responsible for the differences in corner flowfield between the two configurations. The proposed mechanism also explains observed differences in corner flow topology between previous studies in the literature; nozzle geometry therefore appears to be the dominant influence on corner flows in supersonic wind tunnels

Simultaneous alignment and folding of protein sequences

Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically,partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments,partiFold-Align significantly outperforms state-of-the-art pairwise sequence alignment tools in the most difficult low sequence homology case and improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types