Arrow ribbon graphs

We introduce an additional structure on ribbon graphs, arrow structure. We extend the Bollob\'as-Riordan polynomial to ribbon graph with this structure. The extended polynomial satisfies the contraction-deletion relations and naturally behaves with respect to the partial duality of ribbon graphs. We construct an arrow ribbon graph from a virtual link whose extended Bollob\'as-Riordan polynomial specializes to the arrow polynomial of the virtual link recently introduced by H.Dye and L.Kauffman. This result generalizes the classical Thistlethwaite theorem to the arrow polynomial of virtual links.Comment: to appear in Journal of Knot Theory and Its Ramification

On the Average Genus of a Graph

Not all rational numbers are possibilities for the average genus of an individual graph. The smallest such numbers are determined, and varied examples are constructed to demonstrate that a single value of average genus can be shared by arbitrarily many different graphs. It is proved that the number one is a limit point of the set of possible values for average genus and that the complete graph K4 is the only 3-connected graph whose average genus is less than one. Several problems for future study are suggested

A Rigorous Derivation of the Gross-Pitaevskii Energy Functional for a Two-Dimensional Bose Gas

We consider the ground state properties of an inhomogeneous two-dimensional Bose gas with a repulsive, short range pair interaction and an external confining potential. In the limit when the particle number $N$ is large but $\bar\rho a^2$ is small, where $\bar\rho$ is the average particle density and $a$ the scattering length, the ground state energy and density are rigorously shown to be given to leading order by a Gross-Pitaevskii (GP) energy functional with a coupling constant $g\sim 1/|\ln(\bar\rho a^2)|$. In contrast to the 3D case the coupling constant depends on $N$ through the mean density. The GP energy per particle depends only on $Ng$. In 2D this parameter is typically so large that the gradient term in the GP energy functional is negligible and the simpler description by a Thomas-Fermi type functional is adequate.Comment: 14 pages, no figures, latex 2e. References, some clarifications and an appendix added. To appear in Commun. Math. Phy

Native Electrospray and Electron-Capture Dissociation in FTICR Mass Spectrometry Provide Top-Down Sequencing of a Protein Component in an Intact Protein Assembly

The intact yeast alcohol dehydrogenase (ADH) tetramer of 147 kDa was introduced into a FTICR mass spectrometer by native electrospray. Electron capture dissociation of the entire 23+ to 27+ charge state distribution produced the expected charge-reduced ions and, more unexpectedly, 39 c-type peptide fragments that identified N-terminus acetylation and the first 55 amino acids. The results are in accord with the crystal structure of yeast ADH, which shows that the C-terminus is buried at the assembly interface, whereas the N-terminus is exposed, allowing ECD to occur. This remarkable observation shows promise that a top-down approach for intact protein assemblies will be effective for characterizing their components, inferring their interfaces, and obtaining both proteomics and structural biology information in one experiment

Levels of self-consistency in the GW approximation

We perform $GW$ calculations on atoms and diatomic molecules at different levels of self-consistency and investigate the effects of self-consistency on total energies, ionization potentials and on particle number conservation. We further propose a partially self-consistent $GW$ scheme in which we keep the correlation part of the self-energy fixed within the self-consistency cycle. This approximation is compared to the fully self-consistent $GW$ results and to the $G W_0$ and the $G_0W_0$ approximations. Total energies, ionization potentials and two-electron removal energies obtained with our partially self-consistent $GW$ approximation are in excellent agreement with fully self-consistent $GW$ results while requiring only a fraction of the computational effort. We also find that self-consistent and partially self-consistent schemes provide ionization energies of similar quality as the $G_0W_0$ values but yield better total energies and energy differences.Comment: 11 pages, 3 figures, 3 table

Precursor Lesions of High-Grade Serous Ovarian Carcinoma: Morphological and Molecular Characteristics

The lack of proven screening tools for early detection and the high mortality of ovarian serous carcinoma (OSC), particularly high grade, have focused attention on identifying putative precursor lesions with distinct morphological and molecular characteristics. The finding of occult invasive and intraepithelial fallopian tube carcinomas in prophylactically removed specimens from asymptomatic high-risk BRCA 1/2-mutation carriers supports the notion of an origin for OSC in the fallopian tube. The intraepithelial carcinomas have been referred to as serous intraepithelial carcinomas (STICs) but our own findings (unpublished data) and recent reports have drawn attention to a spectrum of changes that fall short of STICs that we have designated serous tubal intraepithelial lesions (STILs)

Tetrahydroaminoacridine (THA) reduces voltage-dependent calcium currents in rat sensory neurons

Tetrahydroaminoacridine (THA) is a centrally active anticholinesterase that also interacts with neuronal K+ and Na+ channels and cardiac Ca2+ channels. The effects of THA on neuronal voltage-dependent Ca2+ channels are not known. We tested the effects of THA (25 nM-250 [mu]M) on the Ca2+ current components of acutely dissociated rat nodose ganglion and dorsal root ganglion (DRG) neurons using the whole cell patch clamp recording technique. THA reduced the low-threshold (T) and high-threshold (N/L) Ca2+ current components in a concentration-dependent manner (IC50 [congruent with] 125 [mu]M for T; [congruent with] 80 [mu]M for (N/L). Minimal current reduction was seen below ~ 10 [mu]M. Our results show that THA reduces voltage-dependent Ca2+ currents in rodent sensory neurons suggesting another means by which THA may affect Ca2+-dependent physiologic processes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29032/1/0000064.pd

Classical quasi-particle dynamics in trapped Bose condensates

The dynamics of quasi-particles in repulsive Bose condensates in a harmonic trap is studied in the classical limit. In isotropic traps the classical motion is integrable and separable in spherical coordinates. In anisotropic traps the classical dynamics is found, in general, to be nonintegrable. For quasi-particle energies E much smaller than thechemical potential, besides the conserved quasi-particle energy, we identify two additional nearly conserved phase-space functions. These render the dynamics inside the condensate (collective dynamics) integrable asymptotically for E/chemical potential very small. However, there coexists at the same energy a dynamics confined to the surface of the condensate, which is governed by a classical Hartree-Fock Hamiltonian. We find that also this dynamics becomes integrable for E/chemical potential very small, because of the appearance of an adiabatic invariant. For E/chemical potential of order 1 a large portion of the phase-space supports chaotic motion, both, for the Bogoliubov Hamiltonian and its Hartree-Fock approximant. To exemplify this we exhibit Poincar\'e surface of sections for harmonic traps with the cylindrical symmetry and anisotropy found in TOP traps. For E/chemical potential very large the dynamics is again governed by the Hartree-Fock Hamiltonian. In the case with cylindrical symmetry it becomes quasi-integrable because the remaining small chaotic components in phase space are tightly confined by tori.Comment: 13 pages Latex, 6 eps.gz-figure

Commissioning and Calibrating the CMS Silicon Strip Tracker

The data acquisition system for the CMS Silicon Strip Tracker (SST) is based around a custom analogue front-end ASIC, an analogue optical link system and an off-detector VME board that performs digitization, zero-suppression and data formatting. A complex procedure is required to optimally configure, calibrate and synchronize the 107 channels of the SST readout system. We present an overview of this procedure, which will be used to commission and calibrate the SST during the integration, Start-Up and operational phases of the experiment. Recent experiences from the CMS Magnet Test Cosmic Challenge and system tests at the Tracker Integration Facility are also reported