Characterization of hydrophobin proteins at interfaces and in solutions using x rays

Hydrophobins are a group of particularly surface active proteins. The surface activity is demonstrated in the ready adsorption of hydrophobins to hydrophobic/hydrophilic interfaces such as the air/water interface. Adsorbed hydrophobins self-assemble into ordered films, lower the surface tension of water, and stabilize air bubbles and foams. Hydrophobin proteins originate from filamentous fungi. In the fungi the adsorbed hydrophobin films enable the growth of fungal aerial structures, form protective coatings and mediate the attachment of fungi to solid surfaces. This thesis focuses on hydrophobins HFBI, HFBII, and HFBIII from a rot fungus Trichoderma reesei. The self-assembled hydrophobin films were studied both at the air/water interface and on a solid substrate. In particular, using grazing-incidence x-ray diffraction and reflectivity, it was possible to characterize the hydrophobin films directly at the air/water interface. The in situ experiments yielded information on the arrangement of the protein molecules in the films. All the T. reesei hydrophobins were shown to self-assemble into highly crystalline, hexagonally ordered rafts. The thicknesses of these two-dimensional protein crystals were below 30 Å. Similar films were also obtained on silicon substrates. The adsorption of the proteins is likely to be driven by the hydrophobic effect, but the self-assembly into ordered films involves also specific protein-protein interactions. The protein-protein interactions lead to differences in the arrangement of the molecules in the HFBI, HFBII, and HFBIII protein films, as seen in the grazing-incidence x-ray diffraction data. The protein-protein interactions were further probed in solution using small-angle x-ray scattering. Both HFBI and HFBII were shown to form mainly tetramers in aqueous solution. By modifying the solution conditions and thereby the interactions, it was shown that the association was due to the hydrophobic effect. The stable tetrameric assemblies could tolerate heating and changes in pH. The stability of the structure facilitates the persistence of these secreted proteins in the soil.

First observation of the decay Bs --> Ds K and measurement of the ratio of branching fractions Br(Bs --> DsK)/Br(Bs --> Ds pi)

A combined mass and particle identification fit is used to make the first observation of the decay Bs --> Ds K and measure the branching fraction of Bs --> Ds K relative to Bs --> Ds pi. This analysis uses 1.2 fb^-1 integrated luminosity of pbar-p collisions at sqrt(s) = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron collider. We observe a Bs --> Ds K signal with a statistical significance of 8.1 sigma and measure Br(Bs --> Ds K)/Br(Bs --> Ds pi) = 0.097 +- 0.018(stat) +- 0.009(sys).

Search for the rare decays B+→μ+μ-K+, B0→μ+μ-K*(892)0, and Bs0→μ+μ-ϕ at CDF

We search for b to s\mu^+\mu^- transitions in B meson (B^+, B^0, or B^0_s) decays with 924pb^{-1} of p pbar collisions at sqrt(s)=1.96 TeV collected with the CDF II detector at the Fermilab Tevatron. We find excesses with significances of 4.5, 2.9, and 2.4 standard deviations in the B^+ to \mu^+\mu^-K^+, B^0 to \mu^+\mu^-K^*(892)^0, and B_s^0 to \mu^+\mu^-\phi decay modes, respectively. Using B to J/psi h (h = K^+, K^*(892)^0, phi) decays as normalization channels, we report branching fractions for the previously observed B^+ and B^0 decays, BR(B^+ to \mu^+\mu^-K^+)=(0.59\pm0.15\pm0.04) x 10^{-6}, and BR(B^0 to \mu^+\mu^-K^*(892)^0)=(0.81\pm0.30\pm0.10) x 10^{-6}, where the first uncertainty is statistical, and the second is systematic. These measurements are consistent with the world average results, and are competitive with the best available measurements. We set an upper limit on the relative branching fraction BR(B_s^0 to \mu^+\mu^-\phi)/BR(B_s^0 to J/\psi\phi)

Coherent quasiparticle approximation cQPA and nonlocal coherence

We show that the dynamical Wigner functions for noninteracting fermions and bosons can have complex singularity structures with a number of new solutions accompanying the usual mass-shell dispersion relations. These new shell solutions are shown to encode the information of the quantum coherence between particles and antiparticles, left and right moving chiral states and/or between different flavour states. Analogously to the usual derivation of the Boltzmann equation, we impose this extended phase space structure on the full interacting theory. This extension of the quasiparticle approximation gives rise to a self-consistent equation of motion for a density matrix that combines the quantum mechanical coherence evolution with a well defined collision integral giving rise to decoherence. Several applications of the method are given, for example to the coherent particle production, electroweak baryogenesis and study of decoherence and thermalization.

Search for the rare decays B+→μ+μ-K+, B0→μ+μ-K*(892)0, and Bs0→μ+μ-ϕ at CDF

We search for b→sμ+μ- transitions in B meson (B+, B0, or Bs0) decays with 924  pb-1 of pp̅ collisions at √s=1.96  TeV collected with the CDF II detector at the Fermilab Tevatron. We find excesses with significances of 4.5, 2.9, and 2.4 standard deviations in the B+→μ+μ-K+, B0→μ+μ-K*(892)0, and Bs0→μ+μ-ϕ decay modes, respectively. Using B→J/ψh (h=K+, K*(892)0, ϕ) decays as normalization channels, we report branching fractions for the previously observed B+ and B0 decays, B(B+→μ+μ-K+)=(0.59±0.15±0.04)×10-6, and B(B0→μ+μ-K*(892)0)=(0.81±0.30±0.10)×10-6, where the first uncertainty is statistical, and the second is systematic. We set an upper limit on the relative branching fraction B(Bs0→μ+μ-ϕ)/B(Bs0→J/ψϕ)<2.6(2.3)×10-3 at the 95(90)% confidence level, which is the most stringent to date.

Kevätviljojen siemenviljelyn jatkuvuus K- maatalouden sopimusviljelytiloilla 2010

Maisterin tutkielman tavoitteena oli kartoittaa kevätviljojen siemenviljelyn edellytyksiä Kmaatalouden sopimusviljelytiloilla. Erityisesti oltiin kiinnostuneita kansallisen siementuotantotuen poistumisen vaikutuksesta viljeltävien lajikkeiden lukumäärään ja viljelyaloihin. Tutkielman teoriaosassa tarkasteltiin viljojen siemenviljelyä, sen erityispiirteitä Suomessa ja siihen liittyvää lainsäädäntöä, asetuksia ja maatalouspolitiikkaa. Siemenviljelyä tarkasteltiin paitsi huoltovarmuuden näkökulmasta myös viljelyn taloudellisuuden näkökulmasta. Lisäksi esitettiin sertifioidun ja tilan oman siemenen käyttöön ja laajuuteen vaikuttavia tekijöitä ja siemenen sertifiointiprosessi. Tutkimuksen aineisto perustui maaliskuussa 2010 tehtyyn lomakekyselyyn, joka lähetettiin 119 K-maatalouden sopimussiemenviljelijälle. Kyselyyn vastasi 71 viljelijää, jolloin vastausprosentiksi muodostui 60. Tutkimusmenetelminä aineiston analysoinnissa käytettiin frekvenssijakaumia, keskiarvotestejä ja Kruskall-Wallisin testiä. Tutkimustulosten mukaan kansallisen siementuotannon tuen poistuminen vuoden 2011 alussa ei näyttänyt vaikuttavan siemenviljelyn jatkuvuuteen tai jatkohalukkuuteen. Siementuotannon tukea pidettiin varsin alhaisena, joten sen vaikutus viljelyyn osoittautui vähäiseksi. Huomattavasti enemmän siemenviljelyyn näytti vaikuttavan yleinen maatalouden ja etenkin viljanviljelyn alhainen kannattavuus. Siemenviljelijät katsoivat, etteivät esimerkiksi siementuotannon tuki tai tuen poistuminen korvaa riittävästi tuotannosta aiheutunutta lisätyötä. Toisaalta harva siemenviljelijä aikoi lopettaa tuotannon, vaikka pitivät viljanviljelyä huonosti kannattavana. Tällaiseen näkemykseen saattoi olla syynä se, että viljelijöillä oli siemententuotantoon soveltuva kalusto, ammattitaito ja rutiini tuotantoon. Tutkimukseen osallistuneet viljelijät katsoivat lisäksi, että oma maatila soveltui erittäin hyvin siemententuotantoon. Suurimpana uhkana siementuotannolle kyselyyn vastanneet viljelijät pitivät hukkakauraa omilla tai naapureidensa pelloilla.

Dark solitons in holographic superfluids

We construct dark soliton solutions in a holographic model of a relativistic superfluid. We study the length scales associated with the condensate and the charge density depletion, and find that the two scales differ by a non-trivial function of the chemical potential. By adjusting the chemical potential, we study the variation of the depletion of charge density at the interface.

Evidence for a Narrow Near-Threshold Structure in the J/ψϕ Mass Spectrum in B+→J/ψϕK+ Decays

Evidence is reported for a narrow structure near the $J/\psi\phi$ threshold in exclusive $B^+\to J/\psi\phi K^+$ decays produced in $\bar{p} p $ collisions at $\sqrt{s}=1.96 \TeV$. A signal of $14\pm5$ events, with statistical significance in excess of 3.8 standard deviations, is observed in a data sample corresponding to an integrated luminosity of $2.7 \ifb$, collected by the CDF II detector. The mass and natural width of the structure are measured to be $4143.0\pm2.9(\mathrm{stat})\pm1.2(\mathrm{syst}) \MeVcc$ and $11.7^{+8.3}_{-5.0}(\mathrm{stat})\pm3.7(\mathrm{syst}) \MeVcc$.

Measurement of the top quark mass at CDF using the “neutrino ϕ weighting” template method on a lepton plus isolated track sample

We present a measurement of the top quark mass with t-tbar dilepton events produced in p-pbar collisions at the Fermilab Tevatron $\sqrt{s}$=1.96 TeV and collected by the CDF II detector. A sample of 328 events with a charged electron or muon and an isolated track, corresponding to an integrated luminosity of 2.9 fb$^{-1}$, are selected as t-tbar candidates. To account for the unconstrained event kinematics, we scan over the phase space of the azimuthal angles ($\phi_{\nu_1},\phi_{\nu_2}$) of neutrinos and reconstruct the top quark mass for each $\phi_{\nu_1},\phi_{\nu_2}$ pair by minimizing a $\chi^2$ function in the t-tbar dilepton hypothesis. We assign $\chi^2$-dependent weights to the solutions in order to build a preferred mass for each event. Preferred mass distributions (templates) are built from simulated t-tbar and background events, and parameterized in order to provide continuous probability density functions. A likelihood fit to the mass distribution in data as a weighted sum of signal and background probability density functions gives a top quark mass of $165.5^{+{3.4}}_{-{3.3}}$(stat.)$\pm 3.1$(syst.) GeV/$c^2$.

Coherent quantum Boltzmann equations from cQPA

We reformulate and extend our recently introduced quantum kinetic theory for interacting fermion and scalar fields. Our formalism is based on the coherent quasiparticle approximation (cQPA) where nonlocal coherence information is encoded in new spectral solutions at off-shell momenta. We derive explicit forms for the cQPA propagators in the homogeneous background and show that the collision integrals involving the new coherence propagators need to be resummed to all orders in gradient expansion. We perform this resummation and derive generalized momentum space Feynman rules including coherent propagators and modified vertex rules for a Yukawa interaction. As a result we are able to set up self-consistent quantum Boltzmann equations for both fermion and scalar fields. We present several examples of diagrammatic calculations and numerical applications including a simple toy model for coherent baryogenesis.

Practical Proposals for Specifying k-Nearest Neighbours Weights Matrices

In this article we introduce and evaluate testing procedures for specifying the number k of nearest neighbours in the weights matrix of spatial econometric models. The spatial J-test is used for specification search. Two testing procedures are suggested: an increasing neighbours testing procedure and a decreasing neighbours testing procedure. Simulations show that the increasing neighbours testing procedures can be used in large samples to determine k. The decreasing neighbours testing procedure is found to have low power, and is not recommended for use in practice. An empirical example involving house price data is provided to show how to use the testing procedures with real data.

K -shell diagram and hypersatellite spectra of 4d transition elements

The K-shell diagram (K alpha(1,2) and K beta(1,3)) and hypersatellite (HS) (K-h alpha(1,2)) spectra of Y, Zr, Mo, and Pd have been measured with high energy-resolution using photoexcitation by 90 keV synchrotron radiation. Comparison of the measured and ab initio calculated HS spectra demonstrates the importance of quantum electrodynamical (QED) effects for the HS spectra. Phenomenological fits of the measured spectra by Voigt functions yield accurate values for the shift of the HS from the diagram lines, the splitting of the HS lines, and their intensity ratio. Good agreement with theory was found for all quantities except for the intensity ratio, which is dominated by the intermediacy of the coupling of the angular momenta. The observed deviations imply that our current understanding of the variation of the coupling scheme from LS to jj across the periodic table may require some revision.