Recognition of double helical DNA by purine oligonucleotides via triple helix formation

Oligonucleotide-directed triple helix formation is one of the most versatile methods for the sequence specific recognition of double helical DNA. Chapter 2 describes affinity cleaving experiments carried out to assess the recognition potential for purine-rich oligonucleotides via the formation of triple helices. Purine-rich oligodeoxyribonucleotides were shown to bind specifically to purine tracts of double helical DNA in the major groove antiparallel to the purine strand of the duplex. Specificity was derived from the formation of reverse Hoogsteen G•GC, A•AT and T•AT triplets and binding was limited to mostly purine tracts. This triple helical structure was stabilized by multivalent cations, destabilized by high concentrations of monovalent cations and was insensitive to pH. A single mismatched base triplet was shown to destabilize a 15 mer triple helix by 1.0 kcal/mole at 25°C. In addition, stability appeared to be correlated to the number of G•GC triplets formed in the triple helix. This structure provides an additional framework as a basis for the design of new sequence specific DNA binding molecules.

In work described in Chapter 3, the triplet specificities and required strand orientations of two classes of DNA triple helices were combined to target double helical sequences containing all four base pairs by alternate strand triple helix formation. This allowed for the use of oligonucleotides containing only natural 3'-5' phosphodiester linkages to simultaneously bind both strands of double helical DNA in the major groove. The stabilities and structures of these alternate strand triple helices depended on whether the binding site sequence was 5'-(purine)_m (pyrimidine)_n-3' or 5'- (pyrimidine)_m (purine)_n-3'.

In Chapter 4, the ability of oligonucleotide-cerium(III) chelates to direct the transesterfication of RNA was investigated. Procedures were developed for the modification of DNA and RNA oligonucleotides with a hexadentate Schiff-base macrocyclic cerium(III) complex. In addition, oligoribonucleotides modified by covalent attachment of the metal complex through two different linker structures were prepared. The ability of these structures to direct transesterification to specific RNA phosphodiesters was assessed by gel electrophoresis. No reproducible cleavage of the RNA strand consistent with transesterification could be detected in any of these experiments.

Enhancing Kerr nonlinearity in an asymmetric double quantum well via Fano interference

We investigate the enhancement of Kerr nonlinearity in an asymmetric GaAs double quantum well via Fano interference, which is caused by tunneling from the excited subband to the continuum. In our structure, owing to Fano interference, the Kerr nonlinearity can be enhanced by appropriately choosing the values of the detunings and the intensity of the pump field, while cancel the linear and nonlinear absorptions.

Enhanced dispersive wave generation by using chirped pulses in a microstructured fiber

A theoretical investigation on the nonlinear pulse propagation and dispersive wave generation in the anomalous dispersion region of a microstructured fiber is presented. By simulating the dispersive wave generation under different conditions. it is found that the generation mechanism of the dispersive wave is mainly due to the pulse trapping across the zero-dispersion wavelength. By varying the initial pulse chirp, the output spectrum can be broadened and the intensity of the dispersive wave can be obviously enhanced. In particular, there exists an optimal positive chirp which maximizes the intensity of the dispersive wave. This effect can be explained by the energy transfer from the Raman soliton to the dispersive wave due to the effect of the pulse trapping and the effect of the higher-order dispersion. From the phase aspect, the explanation of this effect is also included. (C) 2004 Elsevier B.V. All rights reserved.

High efficiency four-wave mixing induced by double-dark resonances in a five-level tripod system

A five-level tripod scheme is proposed for obtaining a high efficiency four-wave-mixing (FWM) process. The existence of double-dark resonances leads to a strong modification of the absorption and dispersion properties against a pump wave at two transparency windows. We show that both of them can be used to open the four-wave mixing channel and produce efficient mixing waves. In particular, higher FWM efficiency is always produced at the transparent window corresponding to the relatively weak-coupling field. By manipulating the intensity of the two coupling fields, the conversion efficiency of FWM can be controlled.

A high pressure xenon time projection chamber for double beta decay

This thesis describes the design, construction and performance of a high-pressure, xenon, gas time projection chamber (TPC) for the study of double beta decay in ^(136) Xe. The TPC when operating at 5 atm can accommodate 28 moles of 60% enriched ^(136) Xe. The TPC has operated as a detector at Caltech since 1986. It is capable of reconstructing a charged particle trajectory and can easily distinguish between different kinds of charged particles. A gas purification and xenon gas recovery system were developed. The electronics for the 338 channels of readout was developed along with a data acquistion system. Currently, the detector is being prepared at the University of Neuchatel for installation in the low background laboratory situated in the St. Gotthard tunnel, Switzerland. In one year of runtime the detector should be sensitive to a 0ν lifetime of the order of 10^(24) y, which corresponds to a neutrino mass in the range 0.3 to 3.3 eV.

Controllable atom localization via double-dark resonances in a tripod system

We propose an atom localization scheme for a tripod-type atom making use of the sharp absorption peak resulting from interacting double-dark resonances. It is demonstrated that the probability of finding the atom at a particular position, as well as the localization precision, can be dramatically enhanced. The probability can be doubled by adjusting the Rabi frequency of the control field to the maximum Rabi frequency of the standing-wave field. Moreover, much better spatial resolution can be achieved for smaller detunings of the control and the standing-wave fields. (c) 2006 Optical Society of America.

Active phase control and frequency chirp effects on supercontinuum generation in high birefringence photonic crystal fiber

An acoustic-optics programmable dispersive filter (AOPDF) was first employed to actively control the linearly polarized femtosecond pump pulse frequency chirp for supercontinuum (SC) generation in a high birefringence photonic crystal fiber (PCF). By accurately controlling the second order phase distortion and polarization direction of incident pulses, the output SC spectrum can be tuned to various spectral energy distributions and bandwidths. The pump pulse energy and bandwidth are preserved in our experiment. It is found that SC with broader bandwidth can be generated with positive chirped pump pulses except when the chirp value is larger than the optimal value, and the same optimal value exists for the pump pulses polarized along the two principal axes. With optimal positive chirp, more than 78% of the pump energy can be transferred to below 750 nm. Otherwise, negative chirp will weaken the blue-shift broadening and the SC bandwidth. (C) 2007 Elsevier B.V. All rights reserved.

Transmission spectrum of a double quantum-dot-nanocavity system in photonic crystals

We investigate the optical transmission properties of a combined system which consists of two quantum-dot-nanocavity subsystems indirectly coupled to a waveguide in a planar photonic crystal. A Mollow-like triplet and the growth of sidebands are found, reflecting intrinsic optical responses in the complex microstructure.

Quantum interference in laser-induced nonsequential double ionization in diatomic molecules: Role of alignment and orbital symmetry

We address the influence of the orbital symmetry and the molecular alignment with respect to the laser-field polarization on laser-induced nonsequential double ionization of diatomic molecules, in the length and velocity gauges. We work within the strong-field approximation and assume that the second electron is dislodged by electron-impact ionization, and also consider the classical limit of this model. We show that the electron-momentum distributions exhibit interference maxima and minima due to electron emission at spatially separated centers. The interference patterns survive integration over the transverse momenta for a small range of alignment angles, and are sharpest for parallel-aligned molecules. Due to the contributions of the transverse-momentum components, these patterns become less defined as the alignment angle increases, until they disappear for perpendicular alignment. This behavior influences the shapes and the peaks of the electron-momentum distributions.

Generation of sub-5 fs pulses through cascade of filamentation and hollow fiber compression

A pulse-compression scheme based on cascade of filamentation and hollow fiber has been demonstrated, Pulses with duration of sub-5 fs and energy of 0.2 mJ near 800 nm have been generated by compressing the similar to 40 fs pulses from a commercial laser system. This method is promising to generate near monocycle high energy pulses. [GRAPHICS] Measured autocorrelation curve of the final compressed pulses with duration of sub-5 fs (black solid) and the simulated autocorrelation curve of 4.6 fs pulse near 800 rim (red dash) (C) 2008 by Astro Ltd. Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA