X-ray and neutron scattering studies on some nanoscale structures in molecular biology

Scattering of X-rays and neutrons has been applied to the study of nanostructures with interesting biological functions. The systems studied were the protein calmodulin and its complexes, bacterial virus bacteriophage phi6, and the photosynthetic antenna complex from green sulfur bacteria, chlorosome. Information gathered using various structure determination methods has been combined to the low resolution information obtained from solution scattering. Conformational changes in calmodulin-ligand complex were studied by combining the directional information obtained from residual dipole couplings in nuclear magnetic resonance to the size information obtained from small-angle X-ray scattering from solution. The locations of non-structural protein components in a model of bacteriophage phi6, based mainly on electron microscopy, were determined by neutron scattering, deuterium labeling and contrast variation. New data are presented on the structure of the photosynthetic antenna complex of green sulfur bacteria and filamentous anoxygenic phototrophs, also known as the chlorosome. The X-ray scattering and electron cryomicroscopy results from this system are interpreted in the context of a new structural model detailed in the third paper of this dissertation. The model is found to be consistent with the results obtained from various chlorosome containing bacteria. The effect of carotenoid synthesis on the chlorosome structure and self-assembly are studied by carotenoid extraction, biosynthesis inhibition and genetic manipulation of the enzymes involved in carotenoid biosynthesis. Carotenoid composition and content are found to have a marked effect on the structural parameters and morphology of chlorosomes.

Proton magnetic resonance spectroscopy of a boron neutron capture therapy 10B-carrier, L-p-boronophenylalanine-fructose complex

Boron neutron capture therapy (BNCT) is a radiotherapy that has mainly been used to treat malignant brain tumours, melanomas, and head and neck cancer. In BNCT, the patient receives an intravenous infusion of a 10B-carrier, which accumulates in the tumour area. The tumour is irradiated with epithermal or thermal neutrons, which result in a boron neutron capture reaction that generates heavy particles to damage tumour cells. In Finland, boronophenylalanine fructose (BPA-F) is used as the 10B-carrier. Currently, the drifting of boron from blood to tumour as well as the spatial and temporal accumulation of boron in the brain, are not precisely known. Proton magnetic resonance spectroscopy (1H MRS) could be used for selective BPA-F detection and quantification as aromatic protons of BPA resonate in the spectrum region, which is clear of brain metabolite signals. This study, which included both phantom and in vivo studies, examined the validity of 1H MRS as a tool for BPA detection. In the phantom study, BPA quantification was studied at 1.5 and 3.0 T with single voxel 1H MRS, and at 1.5 T with magnetic resonance imaging (MRSI). The detection limit of BPA was determined in phantom conditions at 1.5 T and 3.0 T using single voxel 1H MRS, and at 1.5 T using MRSI. In phantom conditions, BPA quantification accuracy of ± 5% and ± 15% were achieved with single voxel MRS using external or internal (internal water signal) concentration references, respectively. For MRSI, a quantification accuracy of <5% was obtained using an internal concentration reference (creatine). The detection limits of BPA in phantom conditions for the PRESS sequence were 0.7 (3.0 T) and 1.4 mM (1.5 T) mM with 20 × 20 × 20 mm3 single voxel MRS, and 1.0 mM with acquisition-weighted MRSI (nominal voxel volume 10(RL) × 10(AP) × 7.5(SI) mm3), respectively. In the in vivo study, an MRSI or single voxel MRS or both was performed for ten patients (patients 1-10) on the day of BNCT. Three patients had glioblastoma multiforme (GBM), and five patients had a recurrent or progressing GBM or anaplastic astrocytoma gradus III, and two patients had head and neck cancer. For nine patients (patients 1-9), MRS/MRSI was performed 70-140 min after the second irradiation field, and for one patient (patient 10), the MRSI study began 11 min before the end of the BPA-F infusion and ended 6 min after the end of the infusion. In comparison, single voxel MRS was performed before BNCT, for two patients (patients 3 and 9), and for one patient (patient 9), MRSI was performed one month after treatment. For one patient (patient 10), MRSI was performed four days before infusion. Signals from the tumour spectrum aromatic region were detected on the day of BNCT in three patients, indicating that in favourable cases, it is possible to detect BPA in vivo in the patient’s brain after BNCT treatment or at the end of BPA-F infusion. However, because the shape and position of the detected signals did not exactly match the BPA spectrum detected in the in vitro conditions, assignment of BPA is difficult. The opportunity to perform MRS immediately after the end of BPA-F infusion for more patients is necessary to evaluate the suitability of 1H MRS for BPA detection or quantification for treatment planning purposes. However, it could be possible to use MRSI as criteria in selecting patients for BNCT.

Diffusion of Pure CH4 and Its Binary Mixture with CO2 in Faujasite NaY: A Combination of Neutron Scattering Experiments and Molecular Dynamics Simulations

The self-diffusion properties of pure CH4 and its binary mixture with CO2 within MY zeolite have been investigated by combining an experimental quasi-elastic neutron scattering (QENS) technique and classical Molecular dynamics simulations. The QENS measurements carried out at 200 K led to an unexpected self-diffusivity profile for Pure CH4 with the presence of a maximum for a loading of 32 CH4/unit cell, which was never observed before for the diffusion of apolar species in azeolite system With large windows. Molecular dynamics simulations were performed using two distinct microscopic models for representing the CH4/NaY interactions. Depending on the model, we are able to fairly reproduce either the magnitude or the profile of the self-diffusivity.Further analysis allowed LIS to provide some molecular insight into the diffusion mechanism in play. The QENS measurements report only a slight decrease of the self-diffusivity of CH4 in the presence of CO2 when the CO2 loading increases. Molecular dynamics simulations successfully capture this experimental trend and suggest a plausible microscopic diffusion mechanism in the case of this binary mixture.

Identification of Hadronically Decaying Tau Leptons in Searches for Heavy MSSM Higgs Bosons with the CMS Detector at the CERN LHC

This thesis describes methods for the reliable identification of hadronically decaying tau leptons in the search for heavy Higgs bosons of the minimal supersymmetric standard model of particle physics (MSSM). The identification of the hadronic tau lepton decays, i.e. tau-jets, is applied to the gg->bbH, H->tautau and gg->tbH+, H+->taunu processes to be searched for in the CMS experiment at the CERN Large Hadron Collider. Of all the event selections applied in these final states, the tau-jet identification is the single most important event selection criterion to separate the tiny Higgs boson signal from a large number of background events. The tau-jet identification is studied with methods based on a signature of a low charged track multiplicity, the containment of the decay products within a narrow cone, an isolated electromagnetic energy deposition, a non-zero tau lepton flight path, the absence of electrons, muons, and neutral hadrons in the decay signature, and a relatively small tau lepton mass compared to the mass of most hadrons. Furthermore, in the H+->taunu channel, helicity correlations are exploited to separate the signal tau jets from those originating from the W->taunu decays. Since many of these identification methods rely on the reconstruction of charged particle tracks, the systematic uncertainties resulting from the mechanical tolerances of the tracking sensor positions are estimated with care. The tau-jet identification and other standard selection methods are applied to the search for the heavy neutral and charged Higgs bosons in the H->tautau and H+->taunu decay channels. For the H+->taunu channel, the tau-jet identification is redone and optimized with a recent and more detailed event simulation than previously in the CMS experiment. Both decay channels are found to be very promising for the discovery of the heavy MSSM Higgs bosons. The Higgs boson(s), whose existence has not yet been experimentally verified, are a part of the standard model and its most popular extensions. They are a manifestation of a mechanism which breaks the electroweak symmetry and generates masses for particles. Since the H->tautau and H+->taunu decay channels are important for the discovery of the Higgs bosons in a large region of the permitted parameter space, the analysis described in this thesis serves as a probe for finding out properties of the microcosm of particles and their interactions in the energy scales beyond the standard model of particle physics.

Levitation effect in zeolites: Quasielastic neutron scattering and molecular dynamics study of pentane isomers in zeolite NaY

We report the quasielastic neutron scattering (QENS) and molecular dynamics (MD) investigations into diffusion of pentane isomers in zeolite NaY. The molecular cross section perpendicular to the long molecular axis varies for the three isomers while the mass and the isomer-zeolite interaction remains essentially unchanged. Both QENS and MD results show that the branched isomers neopentane and isopentane have higher self-diffusivities as compared with n-pentane at 300 K in NaY zeolite. This result provides direct experimental evidence for the existence of nonmonotonic, anomalous dependence of self-diffusivity on molecular diameter known as the levitation effect. The energetic barrier at the bottleneck derived from MD simulations exists for n-pentane which lies in the linear regime while no such barrier is seen for neopentane which is located clearly in the anomalous regime.Activation energy is in the order E-a(n-pentane)>E-a(isopentane)>E-a(neopentane) consistent with the predictions of the levitation effect. In the liquid phase, it is seen thatD(n pentane)>D(isopentane)>D(neopentane) and E-a(n-pentane)< E-a(isopentane)< E-a(neopentane). Intermediate scattering function for small wavenumbers obtained from MD follows a single exponential decay for neopentane and isopentane. For n-pentane, a single exponential fit provides a poor fit especially at short times. Cage residence time is largest for n-pentane and lowest for neopentane. For neopentane, the width of the self-part of the dynamic structure factor shows a near monotonic decrease with wavenumber. For n-pentane a minimum is seen near k=0.5 A degrees(-1) suggesting a slowing down of motion around the 12-ring window, the bottleneck for diffusion. Finally, the result that the branched isomer has a higher diffusivity as compared with the linear analog is at variation from what is normally seen.

Search for new physics in the μμ+e/μ+E̸T channel with a low-pT lepton threshold at the Collider Detector at Fermilab

A search for new physics using three-lepton (trilepton) data collected with the CDF II detector and corresponding to an integrated luminosity of 976 pb-1 is presented. The standard model predicts a low rate of trilepton events, which makes some supersymmetric processes, such as chargino-neutralino production, measurable in this channel. The mu+mu+l signature is investigated, where l is an electron or a muon, with the additional requirement of large missing transverse energy. In this analysis, the lepton transverse momenta with respect to the beam direction (pT) are as low as 5 GeV/c, a selection that improves the sensitivity to particles which are light as well as to ones which result in leptonically decaying tau leptons. At the same time, this low-p_T selection presents additional challenges due to the non-negligible heavy-quark background at low lepton momenta. This background is measured with an innovative technique using experimental data. Several dimuon and trilepton control regions are investigated, and good agreement between experimental results and standard-model predictions is observed. In the signal region, we observe one three-muon event and expect 0.4+/-0.1 mu+mu+l events

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN.

Inclusive Search for Standard Model Higgs Boson Production in the WW Decay Channel using the CDF II Detector

We present a search for standard model (SM) Higgs boson production using ppbar collision data at sqrt(s) = 1.96 TeV, collected with the CDF II detector and corresponding to an integrated luminosity of 4.8 fb-1. We search for Higgs bosons produced in all processes with a significant production rate and decaying to two W bosons. We find no evidence for SM Higgs boson production and place upper limits at the 95% confidence level on the SM production cross section (sigma(H)) for values of the Higgs boson mass (m_H) in the range from 110 to 200 GeV. These limits are the most stringent for m_H > 130 GeV and are 1.29 above the predicted value of sigma(H) for mH = 165 GeV.

Measurement of the top quark mass and pp̅ →tt̅ cross section in the all-hadronic mode with the CDF II detector

We present a measurement of the top quark mass and of the top-antitop pair production cross section using p-pbar data collected with the CDFII detector at the Tevatron Collider at the Fermi National Accelerator Laboratory and corresponding to an integrated luminosity of 2.9 fb-1. We select events with six or more jets satisfying a number of kinematical requirements imposed by means of a neural network algorithm. At least one of these jets must originate from a b quark, as identified by the reconstruction of a secondary vertex inside the jet. The mass measurement is based on a likelihood fit incorporating reconstructed mass distributions representative of signal and background, where the absolute jet energy scale (JES) is measured simultaneously with the top quark mass. The measurement yields a value of 174.8 +- 2.4(stat+JES) ^{+1.2}_{-1.0}(syst) GeV/c^2, where the uncertainty from the absolute jet energy scale is evaluated together with the statistical uncertainty. The procedure measures also the amount of signal from which we derive a cross section, sigma_{ttbar} = 7.2 +- 0.5(stat) +- 1.0 (syst) +- 0.4 (lum) pb, for the measured values of top quark mass and JES.

The International Large Detector: Letter of Intent

The International Large Detector (ILD) is a concept for a detector at the International Linear Collider, ILC. The ILC will collide electrons and positrons at energies of initially 500 GeV, upgradeable to 1 TeV. The ILC has an ambitious physics program, which will extend and complement that of the Large Hadron Collider (LHC). A hallmark of physics at the ILC is precision. The clean initial state and the comparatively benign environment of a lepton collider are ideally suited to high precision measurements. To take full advantage of the physics potential of ILC places great demands on the detector performance. The design of ILD is driven by these requirements. Excellent calorimetry and tracking are combined to obtain the best possible overall event reconstruction, including the capability to reconstruct individual particles within jets for particle ow calorimetry. This requires excellent spatial resolution for all detector systems. A highly granular calorimeter system is combined with a central tracker which stresses redundancy and efficiency. In addition, efficient reconstruction of secondary vertices and excellent momentum resolution for charged particles are essential for an ILC detector. The interaction region of the ILC is designed to host two detectors, which can be moved into the beam position with a push-pull scheme. The mechanical design of ILD and the overall integration of subdetectors takes these operational conditions into account.

Performance analysis of a suprathreshold, stochastic resonance based nonlinear detector

In this paper we introduce a nonlinear detector based on the phenomenon of suprathreshold stochastic resonance (SSR). We first present a model (an array of 1-bit quantizers) that demonstrates the SSR phenomenon. We then use this as a pre-processor to the conventional matched filter. We employ the Neyman-Pearson(NP) detection strategy and compare the performances of the matched filter, the SSR-based detector and the optimal detector. Although the proposed detector is non-optimal, for non-Gaussian noises with heavy tails (leptokurtic) it shows better performance than the matched filter. In situations where the noise is known to be leptokurtic without the availability of the exact knowledge of its distribution, the proposed detector turns out to be a better choice than the matched filter.

Neutron diffraction evidence for oxygen dimers in Bi-Ca-Sr-Cu-O superconductors

A comparative neutron diffraction study of Bi2CaSr2Cu2O8+δ, Bi2Ca2SrCu2O8+δ and Bi2Ca1.5Y0.5SrCu2O8+δ has not only shown the presence of considerable oxygen excess in the Bi layers, but also evidence for oxygen pairing giving rise to O1−2 or O2−2 type species, probably the latter. The proportion of the paired species increases when Y partly replaces Ca. Furthermore, the Tc decreases with an increase in paired species.