Order preserving pattern matching on trees and DAGs

The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem where a set of text strings is given as a tree or a DAG. We show that the OPPM problem for a single pattern $p$ of length $m$ and a text tree $T$ of size $N$ can be solved in $O(m+N)$ time if the characters of $p$ are drawn from an integer alphabet of polynomial size. The time complexity becomes $O(m \log m + N)$ if the pattern $p$ is over a general ordered alphabet. We then show that the OPPM problem for a single pattern and a text DAG is NP-complete

APCVD of dual layer transparent conductive oxides for photovoltaic applications

We report the atmospheric pressure chemical vapour deposition (APCVD) of a dual layer transparent conductive oxide (TCO). This combines a fluorine doped tin oxide (FTO) base layer with a fluorine doped zinc oxide (FZO) top layer, where we seek to utilise the respective advantages of each material and the differences in their associated industrial deposition process technologies. Deposition of a 250 nm thick FZO layer on FTO was enough to develop features seen with FZO only layers. The crystallographic orientation determined by the FZO dopant concentration. Changes to the deposition parameters of the underlying FTO layer effected stack roughness and carrier concentration, and hence optical scattering and absorption. Photovoltaic cells have been fabricated using this TCO structure showing promising performance, with efficiencies as high as 10.21% compared to reference FTO only values of 9.02%. The bulk of the coating was FTO, providing the majority of conductivity and the large surface features associated with this material, whilst keeping the overall cost low by utilising the very fast growth rates achievable. The FTO was capped with a thinner FZO layer to provide a top surface suitable for wet chemical or plasma etching, allowing the surface morphology to be tuned for specific applications

Evolved star water maser cloud size determined by star size

Cool, evolved stars undergo copious mass loss but the details of how the matter is returned to the ISM are still under debate. We investigated the structure and evolution of the wind at 5 to 50 stellar radii from Asymptotic Giant Branch and Red Supergiant stars. 22-GHz water masers around seven evolved stars were imaged using MERLIN, at sub-AU resolution. Each source was observed at between 2 and 7 epochs (several stellar periods). We compared our results with long-term Pushchino single dish monitoring. The 22-GHz emission is located in ~spherical, thick, unevenly filled shells. The outflow velocity doubles between the inner and outer shell limits. Water maser clumps could be matched at successive epochs separated by <2 years for AGB stars, or at least 5 years for RSG. This is much shorter than the decades taken for the wind to cross the maser shell, and comparison with spectral monitoring shows that some features fade and reappear. In 5 sources, most of the matched features brighten or dim in concert from one epoch to the next. One cloud in W Hya was caught in the act of passing in front of a background cloud leading to 50-fold, transient amplification. The masing clouds are 1-2 orders of magnitude denser than the wind average and contain a substantial fraction of the mass loss in this region, with a filling factor <1%. The RSG clouds are ~10x bigger than those round the AGB stars. Proper motions are dominated by expansion, with no systematic rotation. The maser clouds survive for decades (the shell crossing time) but the masers are not always beamed in our direction. Radiative effects cause changes in flux density throughout the maser shells on short timescales. Cloud size is proportional to parent star size; clouds have a similar radius to the star in the 22-GHz maser shell. Stellar properties such as convection cells must determine the clumping scale.Comment: Accepted by A&A 2012 July 10 Main text 29 pages, 62 figures Appendix 44 pages, 23 figure

A Grand Canonical Ensemble Approach to the Thermodynamic Properties of the Nucleon in the Quark-Gluon Coupling Model

In this paper, we put forward a way to study the nucleon's thermodynamic properties such as its temperature, entropy and so on, without inputting any free parameters by human hand, even the nucleon's mass and radius. First we use the Lagrangian density of the quark gluon coupling fields to deduce the Dirac Equation of the quarks confined in the gluon fields. By boundary conditions we solve the wave functions and energy eigenvalues of the quarks, and thus get energy-momentum tensor, nucleon mass, and density of states. Then we utilize a hybrid grand canonical ensemble, to generate the temperature and chemical potentials of quarks, antiquarks of three flovars by the four conservation laws of the energy and the valence quark numbers, after which, all other thermodynamic properties are known. The only seemed free paremeter, the nucleon radius is finally determined by the grand potential minimal principle.Comment: 5 pages, LaTe

Nonequilibrium Evolution of Correlation Functions: A Canonical Approach

We study nonequilibrium evolution in a self-interacting quantum field theory invariant under space translation only by using a canonical approach based on the recently developed Liouville-von Neumann formalism. The method is first used to obtain the correlation functions both in and beyond the Hartree approximation, for the quantum mechanical analog of the $\phi^{4}$ model. The technique involves representing the Hamiltonian in a Fock basis of annihilation and creation operators. By separating it into a solvable Gaussian part involving quadratic terms and a perturbation of quartic terms, it is possible to find the improved vacuum state to any desired order. The correlation functions for the field theory are then investigated in the Hartree approximation and those beyond the Hartree approximation are obtained by finding the improved vacuum state corrected up to ${\cal O}(\lambda^2)$. These correlation functions take into account next-to-leading and next-to-next-to-leading order effects in the coupling constant. We also use the Heisenberg formalism to obtain the time evolution equations for the equal-time, connected correlation functions beyond the leading order. These equations are derived by including the connected 4-point functions in the hierarchy. The resulting coupled set of equations form a part of infinite hierarchy of coupled equations relating the various connected n-point functions. The connection with other approaches based on the path integral formalism is established and the physical implications of the set of equations are discussed with particular emphasis on thermalization.Comment: Revtex, 32 pages; substantial new material dealing with non-equilibrium evolution beyond Hartree approx. based on the LvN formalism, has been adde

Swimming in circles: Motion of bacteria near solid boundaries

Near a solid boundary, E. coli swims in clockwise circular motion. We provide a hydrodynamic model for this behavior. We show that circular trajectories are natural consequences of force-free and torque-free swimming, and the hydrodynamic interactions with the boundary, which also leads to a hydrodynamic trapping of the cells close to the surface. We compare the results of the model with experimental data and obtain reasonable agreement. In particular, we show that the radius of curvature of the trajectory increases with the length of the bacterium body.Comment: Also available at http://people.deas.harvard.edu/~lauga

Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows

We describe a computational protocol to aid the design of small molecule and peptide drugs that target protein-protein interactions, particularly for anti-cancer therapy. To achieve this goal, we explore multiple strategies, including finding binding hot spots, incorporating chemical similarity and bioactivity data, and sampling similar binding sites from homologous protein complexes. We demonstrate how to combine existing interdisciplinary resources with examples of semi-automated workflows. Finally, we discuss several major problems, including the occurrence of drug-resistant mutations, drug promiscuity, and the design of dual-effect inhibitors.Fil: Goncearenco, Alexander. National Institutes of Health; Estados UnidosFil: Li, Minghui. Soochow University; China. National Institutes of Health; Estados UnidosFil: Simonetti, Franco Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Shoemaker, Benjamin A. National Institutes of Health; Estados UnidosFil: Panchenko, Anna R. National Institutes of Health; Estados Unido

How Phase Transitions induce classical behaviour

We continue the analysis of the onset of classical behaviour in a scalar field after a continuous phase transition, in which the system-field, the long wavelength order parameter of the model, interacts with an environment, of its own short-wavelength modes and other fields, neutral and charged, with which it is expected to interact. We compute the decoherence time for the system-field modes from the master equation and directly from the decoherence functional (with identical results). In simple circumstances the order parameter field is classical by the time the transition is complete.Comment: 10 pages, 1 figure: To be published in the International Journal of Theoretical Physics (2005) as part of the Proceedings of the "Peyresq Physics 9" meeting (2004) on "Micro and Macro structures of spacetime",ed. E. Verdague

Saliva from nymph and adult females of Haemaphysalis longicornis: a proteomic study

BACKGROUND: Haemaphysalis longicornis is a major vector of Theileria spp., Anaplasma phagocytophilum, Babesia spp. and Coxiella burnetti in East Asian countries. All life stages of ixodid ticks have a destructive pool-feeding style in which they create a pool-feeding site by lacerating host tissue and secreting a variety of biologically active compounds that allows the tick to evade host responses, enabling the uptake of a blood meal. The identification and functional characterization of tick saliva proteins can be useful to elucidate the molecular mechanisms involved in tick development and to conceive new anti-tick control methods. METHODS: H. longicornis tick saliva was collected from fully engorged nymphs and fully engorged adults induced by dopamine or pilocarpine, respectively. Saliva was digested with trypsin for LC-MS/MS sequencing and peptides were searched against tick and rabbit sequences. RESULTS: A total of 275 proteins were identified, of which 135 were tick and 100 were rabbit proteins. Of the tick proteins, 30 proteins were identified exclusively in fully engorged nymph saliva, 74 in fully engorged adult females, and 31 were detected in both stages. The identified tick proteins include heme/iron metabolism-related proteins, oxidation/detoxification proteins, enzymes, proteinase inhibitors, tick-specific protein families, and cytoskeletal proteins. Proteins involved in signal transduction, transport and metabolism of carbohydrate, energy, nucleotide, amino acids and lipids were also detected. Of the rabbit proteins, 13 were present in nymph saliva, 48 in adult saliva, and 30 were present in both. The host proteins include immunoglobulins, complement system proteins, antimicrobial proteins, serum albumin, peroxiredoxin, serotransferrin, apolipoprotein, hemopexin, proteinase inhibitors, and hemoglobin/red blood cells-related products. CONCLUSIONS: This study allows the identification of H. longicornis saliva proteins. In spontaneously detached tick saliva various proteins were identified, although results obtained with saliva of fully engorged ticks need to be carefully interpreted. However, it is interesting to note that proteins identified in this study were also described in other tick saliva proteomes using partially engorged tick saliva, including hemelipoprotein, proteases, protease inhibitors, proteins related to structural functions, transporter activity, metabolic processes, and others. In conclusion, these data can provide a deeper understanding to the biology of H. longicornis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-015-0918-y) contains supplementary material, which is available to authorized users