Nonadiabatic quantum pumping in mesoscopic nanostructures

We consider a nonadiabatic quantum pumping phenomena in a ballistic narrow constriction. The pumping is induced by a potential that has both spatial and temporal periodicity characterized by $K$ and $\Omega$. In the zero frequency ($\Omega=0$) limit, the transmission through narrow constriction exhibits valley structures due to the opening up of energy gaps in the pumping region -- a consequence of the $K$ periodicity. These valley structures remain robust in the regime of finite $\Omega$, while their energies of occurrence are shifted by about $\hbar\Omega/2$. The direction of these energy shifts depend on the directions of both the phase-velocity of the pumping potential and the transmitting electrons. This frequency dependent feature of the valley structures gives rise to both the asymmetry in the transmission coefficients and the pumping current. An experimental setup is suggested for a possible observation of our nonadiabatic quantum pumping findings.Comment: 4 pages, 2 figure

A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Interconnected Self-Propagating Photopolymer Waveguides: An Alternative to Stereolithography for Rapid Formation of Lattice-Based Open-Cellular Materials

Recently, a new technique has been developed to create unique open-cellular materials with micro-scale truss, or lattice features ranging from tens to hundreds of microns. These materials are formed from a three-dimensional, interconnected array of self-propagating photopolymer waveguides. By utilizing this self-propagating effect, three-dimensional open-cellular polymer materials can be formed in seconds. In addition, intrinsic to the process is the ability to control specific micro-lattice parameters which ultimately affect the bulk material properties. Unlike stereolithography, this new fabrication technique is rapid (~ minutes to form an entire part) and relies on a single two-dimensional exposure surface to form three-dimensional structures (thickness > 25 mm possible). This combination of speed and planar scalability opens the possibility for large-scale mass manufacturing. The utility of these new materials range from lightweight energy absorbing structures to thermal management materials to bio-scaffolds.Mechanical Engineerin

CHO genome mining for synthetic promoter design

Synthetic promoters are an attractive alternative for use in mammalian hosts such as CHO cells as they can be designed de novo with user-defined functionalities. In this study, we describe and validate a method for bioprocess-directed design of synthetic promoters utilizing CHO genomic sequence information. We designed promoters with two objective features, (i) constitutive high-level recombinant gene transcription, and (ii) upregulated transcription under mild hypothermia or late-stage culture. CHO genes varying in transcriptional activity were selected based on a comparative analysis of RNA-Seq transcript levels in normal and biphasic cultures in combination with estimates of mRNA half-life from published genome scale datasets. Discrete transcription factor regulatory elements (TFREs) upstream of these genes were informatically identified and functionally screened in vitro to identify a subset of TFREs with the potential to support high activity recombinant gene transcription during biphasic cell culture processes. Two libraries of heterotypic synthetic promoters with varying TFRE combinations were then designed in silico that exhibited a maximal 2.5-fold increase in transcriptional strength over the CMV-IE promoter after transient transfection into host CHO-K1 cells. A subset of synthetic promoters was then used to create stable transfectant pools using CHO-K1 cells under glutamine synthetase selection. Whilst not achieving the maximal 2.5-fold increase in productivity over stable pools harboring the CMV promoter, all stably transfected cells utilizing synthetic promoters exhibited increased reporter production - up to 1.6-fold that of cells employing CMV, both in the presence or absence of intron A immediately downstream of the promoter. The increased productivity of stably transfected cells harboring synthetic promoters was maintained during fed-batch culture, with or without a transition to mild hypothermia at the onset of stationary phase. Our data exemplify that it is important to consider both host cell and intended bioprocess contexts as design criteria in the de novo construction of synthetic genetic parts for mammalian cell engineering

Proton strangeness form factors in (4,1) clustering configurations

We reexamine a recent result within a nonrelativistic constituent quark model (NRCQM) which maintains that the uuds\bar s component in the proton has its uuds subsystem in P state, with its \bar s in S state (configuration I). When the result are corrected, contrary to the previous result, we find that all the empirical signs of the form factors data can be described by the lowest-lying uuds\bar s configuration with \bar s in P state that has its uuds subsystem in $S$ state (configuration II). Further, it is also found that the removal of the center-of-mass (CM) motion of the clusters will enhance the contributions of the transition current considerably. We also show that a reasonable description of the existing form factors data can be obtained with a very small probability P_{s\bar s}=0.025% for the uuds\bar s component. We further see that the agreement of our prediction with the data for G_A^s at low-q^2 region can be markedly improved by a small admixture of configuration I. It is also found that by not removing CM motion, P_{s\bar s} would be overestimated by about a factor of four in the case when transition dominates over direct currents. Then, we also study the consequence of a recent estimate reached from analyzing the existing data on quark distributions that P_{s\bar s} lies between 2.4-2.9% which would lead to a large size for the five-quark (5q) system, as well as a small bump in both G^s_E+\eta G^s_M and G^s_E in the region of q^2 =< 0.1 GeV^2.Comment: Prepared for The Fifth Asia-Pacific Conference on Few-Body Problems in Physics 2011 in Seoul, South Korea, 22-26 August 201

Investigating the topology of interacting networks - Theory and application to coupled climate subnetworks

Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems of interest should be treated, more appropriately, as interacting networks or networks of networks. Here we introduce a novel graph-theoretical framework for studying the interaction structure between subnetworks embedded within a complex network of networks. This framework allows us to quantify the structural role of single vertices or whole subnetworks with respect to the interaction of a pair of subnetworks on local, mesoscopic and global topological scales. Climate networks have recently been shown to be a powerful tool for the analysis of climatological data. Applying the general framework for studying interacting networks, we introduce coupled climate subnetworks to represent and investigate the topology of statistical relationships between the fields of distinct climatological variables. Using coupled climate subnetworks to investigate the terrestrial atmosphere's three-dimensional geopotential height field uncovers known as well as interesting novel features of the atmosphere's vertical stratification and general circulation. Specifically, the new measure "cross-betweenness" identifies regions which are particularly important for mediating vertical wind field interactions. The promising results obtained by following the coupled climate subnetwork approach present a first step towards an improved understanding of the Earth system and its complex interacting components from a network perspective

Photoemission Spectroscopy from Inhomogeneous Models of Cuprates

We investigate the electronic dynamics in the underdoped cuprates focusing on the effects of one-dimensional charge stripes. We address recent experimental Angular-Resolved Photoemission Spectra results on (La$_{1.28}$Nd$_{0.6}$Sr$_{0.12}$)CuO$_4$. We find that various inhomogeneous models can account for the distribution of quasiparticle weights close to momentum ${\bf k}=(\pi,0)$ and symmetry related points. The observed flat dispersion region around the same ${\bf k}$ point can only be addressed by certain classes of those inhomogeneous models which locally break spin symmetry. Homogeneous models including hopping elements up to second neighbors cannot reproduce the experimental quasiparticle weight, since most of it is centered around ${\bf k}=(\frac {\pi}{2},\frac {\pi} {2})$.Comment: 5 pages, color figure

Search for Photoproduction of Axionlike Particles at GlueX

We present a search for axionlike particles, a, produced in photon-proton collisions at a center-of-mass energy of approximately 4 GeV, focusing on the scenario where the a-gluon coupling is dominant. The search uses a → γγ and a → π+π−π0 decays, and a data sample corresponding to an integrated luminosity of 168  pb−1 collected with the GlueX detector. The search for a → γγ decays is performed in the mass range of 180 \u3c ma \u3c480  MeV, while the search for a → π+π−π0 decays explores the 600 \u3c ma \u3c 720  MeV region. No evidence for a signal is found, and 90% confidence-level exclusion limits are placed on the a-gluon coupling strength. These constraints are the most stringent to date over much of the mass ranges considered

Measuring Black Hole Spin using X-ray Reflection Spectroscopy

I review the current status of X-ray reflection (a.k.a. broad iron line) based black hole spin measurements. This is a powerful technique that allows us to measure robust black hole spins across the mass range, from the stellar-mass black holes in X-ray binaries to the supermassive black holes in active galactic nuclei. After describing the basic assumptions of this approach, I lay out the detailed methodology focusing on "best practices" that have been found necessary to obtain robust results. Reflecting my own biases, this review is slanted towards a discussion of supermassive black hole (SMBH) spin in active galactic nuclei (AGN). Pulling together all of the available XMM-Newton and Suzaku results from the literature that satisfy objective quality control criteria, it is clear that a large fraction of SMBHs are rapidly-spinning, although there are tentative hints of a more slowly spinning population at high (M>5*10^7Msun) and low (M<2*10^6Msun) mass. I also engage in a brief review of the spins of stellar-mass black holes in X-ray binaries. In general, reflection-based and continuum-fitting based spin measures are in agreement, although there remain two objects (GROJ1655-40 and 4U1543-475) for which that is not true. I end this review by discussing the exciting frontier of relativistic reverberation, particularly the discovery of broad iron line reverberation in XMM-Newton data for the Seyfert galaxies NGC4151, NGC7314 and MCG-5-23-16. As well as confirming the basic paradigm of relativistic disk reflection, this detection of reverberation demonstrates that future large-area X-ray observatories such as LOFT will make tremendous progress in studies of strong gravity using relativistic reverberation in AGN.Comment: 19 pages. To appear in proceedings of the ISSI-Bern workshop on "The Physics of Accretion onto Black Holes" (8-12 Oct 2012). Revised version adds a missing source to Table 1 and Fig.6 (IRAS13224-3809) and corrects the referencing of the discovery of soft lags in 1H0707-495 (which were in fact first reported in Fabian et al. 2009

Genetic and bioinformatic analyses of the expression and function of PI3K regulatory subunit PIK3R3 in an Asian patient gastric cancer library

10.1186/1755-8794-5-34BMC Medical Genomics5