http://hdl.handle.net/1721.1/7865 Thu, 20 Jun 2013 01:57:34 GMT 2013-06-20T01:57:34Z http://hdl.handle.net/1721.1/79262 Computational tools for modeling and measuring chromosome structure Ross, Brian Christopher DNA conformation within cells has many important biological implications, but there are challenges both in modeling DNA due to the need for specialized techniques, and experimentally since tracing out in vivo conformations is currently impossible. This thesis contributes two computational projects to these efforts. The first project is a set of online and offline calculators of conformational statistics using a variety of published and unpublished methods, addressing the current lack of DNA model-building tools intended for general use. The second project is a reconstructive analysis that could enable in vivo mapping of DNA conformation at high resolution with current experimental technology. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2012.; Cataloged from PDF version of thesis.; Includes bibliographical references (p. 99-112). Sun, 01 Jan 2012 00:00:00 GMT http://hdl.handle.net/1721.1/79262 2012-01-01T00:00:00Z http://hdl.handle.net/1721.1/79261 Study of density fluctuations and particle transport at the edge of I-mode plasmas Dominguez, Arturo, Ph. D. Massachusetts Institute of Technology The wide range of plasma parameters available on Alcator C-Mod has led to the accessibility of many regimes of operation. Since its commissioning, C-Mod has accessed the Linear ohmic confinement, Saturated ohmic confinement, L-Mode and ELM-free, ELMy and Enhanced D[alpha] H-Mode regimes. Recently, another novel regime, the IMode, has been identified[1][2][3][4]. I-modes feature the presence of steep H-Mode-like electron and ion temperature gradients at the edge of the plasma with L-Mode-like density profiles. The I-Mode, in contrast to the Hl-mode, shows very weak degradation of energy confinement with increased input power, and routinely reaches H98 > 1 while operating at low edge collisionalities ... making it a good candidate for reactor relevant tokamaks. Also relevant for reactors, this regime can be sustained in steady state for more than -15 energy confinement times without the need for ELMs to regulate particle and impurity confinement. Changes in edge density, temperature and magnetic field fluctuations accompany the L-mode to I-mode transition, with reduction of fluctuations in the 50-150kHz range as well as the appearance of a Weakly Coherent Mode (WCM) in the 200-300kHz range, analogous to the Quasi-Coherent Mode (QCM) characteristic of the Enhanced D[alpha] H-mode. Previous work[4] has established a connection between the midrange fluctuation suppression and reduction in the effective thermal diffusivity, Xye, in the pedestal region. The mechanism in I-mode for maintaining sufficient particle transport to avoid impurity accumulation and instabilities has been unclear. The O-mode reflectometry system has been extensively used for the characterization and detection of the I-mode and the WCM, in part, enhanced by upgrades to the system which enabled the baseband detection of density fluctuations at an array of cutoff locations at the edge of the plasma[5] [6] [7]. Using a novel model, the autopower signals of reflectometry channels detecting the density fluctuations have been decomposed into a broadband component and a WCM component. The latter is then used to estimate the intensity of the WCM. In parallel, the particle transport across the LCFS in I-mode plasmas has been estimated using a volume integrated particle transport model, where ionization source measurements are acquired using D[alpha] profiles measured near the outboard midplane. This model takes into account the anisotropic ionization source density around the periphery of the plasma by introducing an asymmetry factor, [sigma], which is then estimated using a study of I-Mode to H-Mode transitions. The results imply that measurements at the outboard midplane overestimate the surface-averaged influx. Finally, a comparison has been made between the particle flux across the LCFS of the I-mode and the intensity of the WCM, which shows a generally positive correlation between the two. This is supporting evidence that the WCM is, in fact, responsible for maintaining particle and impurity transport across the edge of the I-mode energy transport barrier. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, September 2012.; Cataloged from PDF version of thesis.; Includes bibliographical references (p. 201-208). Sun, 01 Jan 2012 00:00:00 GMT http://hdl.handle.net/1721.1/79261 2012-01-01T00:00:00Z http://hdl.handle.net/1721.1/79259 Studies of ICRF mode conversion with phase contrast imaging and full-wave simulations in Alcator C-Mod Tsujii, Naoto Radio frequency (rf) waves in the ion cyclotron range of frequencies (ICRF) are widely used for heating fusion plasmas. In a multi-ion-species plasma, the launched fast waves convert to ion cyclotron waves and ion Bernstein waves in the vicinity of the two-ion hybrid resonance between the cyclotron resonances. The mode converted waves are of interest as actuators to optimize plasma performance through current drive and flow drive. Numerical simulations are essential to describe these processes accurately in a realistic tokamak geometry, and it is important that these simulation codes be validated against experiment. The phase contrast imaging (PCI) technique has been used on Alcator C-Mod to measure directly the rf waves. The measurements were compared to predictions of full-wave simulations using a synthetic diagnostic method. The measured mode converted wave intensity was found to be a factor of ~50 weaker than what was expected from the linear wave theory in a strong mode conversion regime. The agreement improved when the wave intensity was weaker, which is a possible indication of nonlinear wave physics being involved. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2012.; Cataloged from PDF version of thesis.; Includes bibliographical references (p. 199-211). Sun, 01 Jan 2012 00:00:00 GMT http://hdl.handle.net/1721.1/79259 2012-01-01T00:00:00Z http://hdl.handle.net/1721.1/79258 W boson cross sections and single spin asymmetries in polarized proton-proton collisions at [square root of] s =500 GeV at STAR Corliss, Ross (Ross Cameron) Understanding the structure of the proton is an ongoing effort in the particle physics community. Existing in the region of nonperturbative QCD, the various models for proton structure must be informed and constrained by experimental data. In 2009, the STAR experiment at Brookhaven National Lab recorded over 12 pb-1 of data from polarized p+p collisions at 500 GeV center-of-mass energy provided by the RHIC accelerator. This has offered a first look at the spin-dependent production of W+(-) bosons, and hence at the spin-flavor structure of the proton, where the main production mode is through d+u (u+d) annihilation. Using STAR's large Time Projection Chamber and its wide-acceptance electromagnetic calorimeters, it is possible to identify the e+ + v (e- + v) decay mode of the W bosons produced. This thesis presents the first STAR measurement of charge-separated W production, both the pseudorapidity-dependent ratio and the longitudinal single-spin asymmetry. These results show good agreement with theoretical expectations, validating the methods used and paving the way for the analysis of larger datasets that will be available soon. In the near future the range of this measurement will be augmented with the Forward GEM Tracker. A discussion of the design and implementation of this upgrade is also included, along with projections for its impact. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Physics, 2012.; In title on title page, "[square root of]" appears as the mathematical symbol. Title as it appears in MIT Degrees Awarded booklet, September 2012: W production in polarized proton-proton collisions at 500 GeV at STAR. Cataloged from PDF version of thesis.; Includes bibliographical references (p. 167-169). Sun, 01 Jan 2012 00:00:00 GMT http://hdl.handle.net/1721.1/79258 2012-01-01T00:00:00Z