Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor

We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.

An efficient design of serial and parallel memory using Quantum dot cellular automata

Quantum cellular automata (QCA) is a new technology in the nanometer scale and has been considered as one of the alternative to CMOS technology. In this paper, we describe the design and layout of a serial memory and parallel memory, showing the layout of individual memory cells. Assuming that we can fabricate cells which are separated by 10nm, memory capacities of over 1.6 Gbit/cm2 can be achieved. Simulations on the proposed memories were carried out using QCADesigner, a layout and simulation tool for QCA. During the design, we have tried to reduce the number of cells as well as to reduce the area which is found to be 86.16sq mm and 0.12 nm2 area with the QCA based memory cell. We have also achieved an increase in efficiency by 40%.These circuits are the building block of nano processors and provide us to understand the nano devices of the future.

Response Dynamics of Recirculation Structures in Coaxial Nonpremixed Swirl-Stabilized Flames Subjected to Acoustic Forcing

This paper reports the time-mean and phase-locked response of nonreacting as well as reacting flow field in a coaxial swirling jet/flame (nonpremixed). Two distinct swirl intensities plus two different central pipe flow rates at each swirl setting are investigated. The maximum response is observed at the 105 Hz mode in the range of excitation frequencies (0-315 Hz). The flow/flame exhibited minimal response beyond 300 Hz. It is seen that the aspect ratio change of inner recirculation zone (IRZ) under nonreacting conditions (at responsive modes) manifests as a corresponding increase in the time-mean flame aspect ratio. This is corroborated by similar to 25% decrease in the IRZ transverse width in both flame and cold flow states. In addition, 105 Hz excited states are found to shed high energy regions (eddies) asymmetrically when compared to dormant 315 Hz pulsing frequency. The kinetic energy (KE) of the flow field is subsequently reduced due to acoustic excitation and a corresponding increase (similar to O (1)) in fluctuation intensity is witnessed. The lower swirl intensity case is found to be more responsive than the high swirl case as in the former flow state the resistance offered by IRZ to incoming acoustic perturbations is lower due to inherently low inertia. Next, the phase-locked analysis of flow and flame structure is employed to further investigate the phase dependence of flow/flame response. It is found that the asymmetric shifting of IRZ mainly results at 270 deg acoustic forcing. The 90 deg phase angle forcing is observed to convect the IRZ farther downstream in both swirl cases as compared to other phase angles. The present work aims primarily at providing a fluid dynamic view point to the observed nonpremixed flame response without considering the confinement effects.

Investigations on the physical origin of lateral photovoltage in PbS-colloidal quantum dot/Si heterojunctions

Restricted area heterojunctions, an array of lead sulfide colloidal quantum dots (PbS-CQDs) and crystalline silicon, are studied with a non-destructive remote contact light beam induced current (RC-LBIC) technique. As well as getting good quality active area images we observed an anomalous unipolar signal response for the PbS-CQD/n-Si devices and a conventionally expected bipolar signal profile for the PbS-CQD/p-Si devices. Interestingly, our simulation results consistently yielded a unipolar and bipolar nature in the signals related to the PbSCQD/n-Si and PbS-CQD/p-Si heterostructures, respectively. In order to explain the physical mechanism involved in the unipolar signal response of the PbS-CQD/n-Si devices, we propose a model based on the band alignment in the heterojunctions, in addition to the distribution of photo-induced excess majority carriers across the junction. Given that the RC-LBIC technique is well suited to this context, the presence of these two distinct mechanisms (the bipolar and unipolar nature of the signals) needs to be considered in order to have a better interpretation of the data in the characterization of an array of homo/heterojunctions.

Low Threshold Quantum Dot Lasers

Semiconductor quantum dots have replaced conventional inorganic phosphors in numerous applications. Despite their overall successes as emitters, their impact as laser materials has been severely limited. Eliciting stimulated emission from quantum dots requires excitation by intense short pulses of light typically generated using other lasers. In this Letter, we develop a new class of quantum dots that exhibit gain under conditions of extremely low levels of continuous wave illumination. We observe thresholds as low as 74 mW/cm(2) in lasers made from these materials. Due to their strong optical absorption as well as low lasing threshold, these materials could possibly convert light from diffuse, polychromatic sources into a laser beam.

Finite Element Analysis of Deformed Legs of Offshore Platform Structures

The element stiffness matrix of the equivalent beam or pipe element of the deformed leg of the platform is derived by the finite element method. The stresses and displacements of some damaged components are calculated, and the numeri-cal solutions agree well with those obtained by the fine mesh finite element method. Finally, as an application of this method, the stresses of some platform structures are calculated and analyzed.

Symmetry of chaotic attractors and kink-antikink structures in CMLs

In this paper the symmetries of coupled map lattices (CMLs) and their attractors are investigated by group and dynamical system theory, as well as numerical simulation, by means of which the kink-antikink patterns of CMLs in space-amplitude plots are discussed.

Numerical study of bluff body flow structures

Our recent progress in numerical studies of bluff body flow structures and a new method for the numerical analysis of near wake flow field for high Reynolds number flow are introduced. The paper consists of three parts. In part one, the evolution of wake vortex structure and variation of forces on a flat plate in harmonic oscillatory flows and in in-line steady-harmonic combined flows are presented by an improved discrete vortex method, as the Keulegan-Carpenter number (KC) varies from 2 to 40 and ratios of U-m to U-0 are of O(10(-1)), O(10) and O(10), respectively. In part 2, a domain decomposition hybrid method, combining the finite-difference and vortex methods for numerical simulation of unsteady viscous separated flow around a bluff body, is introduced. By the new method, some high resolution numerical visualization on near wake evolution behind a circular cylinder at Re = 10(2), 10(3) and 3 x 10(3) are shown. In part 3, the mechanism and the dynamic process for the three-dimensional evolution of the Karman vortex and vortex filaments in braid regions as well as the early features of turbulent structure in the wake behind a circular cylinder are presented numerically by the vortex dynamics method.

Design and synthesis of biofunctional magnetic/fluorescent glyco-nanoparticles and quantum dots and their application as specific molecular imaging probes

206 p.

Photographic investigations in molecular spectroscopy

The determination of the energy levels and the probabilities of transition between them, by the formal analysis of observed electronic, vibrational, and rotational band structures, forms the direct goal of all investigations of molecular spectra, but the significance of such data lies in the possibility of relating them theoretically to more concrete properties of molecules and the radiation field. From the well developed electronic spectra of diatomic molecules, it has been possible, with the aid of the non-relativistic quantum mechanics, to obtain accurate moments of inertia, molecular potential functions, electronic structures, and detailed information concerning the coupling of spin and orbital angular monenta with the angular momentum of nuclear rotation. The silicon fluori1e molecule has been investigated in this laboratory, and is found to emit bands whose vibrational and rotational structures can be analyzed in this detailed fashion.

Like silicon fluoride, however, the great majority of diatomic molecules are formed only under the unusual conditions of electrical discharge, or in high temperature furnaces, so that although their spectra are of great theoretical interest, the chemist is eager to proceed to a study of polyatomic molecules, in the hope that their more practically interesting structures might also be determined with the accuracy and assurance which characterize the spectroscopic determinations of the constants of diatomic molecules. Some progress has been made in the determination of molecule potential functions from the vibrational term values deduced from Raman and infrared spectra, but in no case can the calculations be carried out with great generality, since the number of known term values is always small compared with the total number of potential constants in even so restricted a potential function as the simple quadratic type. For the determination of nuclear configurations and bond distances, however, a knowledge of the rotational terms is required. The spectra of about twelve of the simpler polyatomic molecules have been subjected to rotational analyses, and a number of bond distances are known with considerable accuracy, yet the number of molecules whose rotational fine structure has been resolved even with the most powerful instruments is small. Consequently, it was felt desirable to investigate the spectra of a number of other promising polyatomic molecules, with the purpose of carrying out complete rotational analyses of all resolvable bands, and ascertaining the value of the unresolved band envelopes in determining the structures of such molecules, in the cases in which resolution is no longer possible. Although many of the compounds investigated absorbed too feebly to be photographed under high dispersion with the present infrared sensitizations, the location and relative intensities of their bands, determined by low dispersion measurements, will be reported in the hope that these compounds may be reinvestigated in the future with improved techniques.

Conditional independence in quantum many-body systems

In this thesis, I will discuss how information-theoretic arguments can be used to produce sharp bounds in the studies of quantum many-body systems. The main advantage of this approach, as opposed to the conventional field-theoretic argument, is that it depends very little on the precise form of the Hamiltonian. The main idea behind this thesis lies on a number of results concerning the structure of quantum states that are conditionally independent. Depending on the application, some of these statements are generalized to quantum states that are approximately conditionally independent. These structures can be readily used in the studies of gapped quantum many-body systems, especially for the ones in two spatial dimensions. A number of rigorous results are derived, including (i) a universal upper bound for a maximal number of topologically protected states that is expressed in terms of the topological entanglement entropy, (ii) a first-order perturbation bound for the topological entanglement entropy that decays superpolynomially with the size of the subsystem, and (iii) a correlation bound between an arbitrary local operator and a topological operator constructed from a set of local reduced density matrices. I also introduce exactly solvable models supported on a three-dimensional lattice that can be used as a reliable quantum memory.

Polaronic correction to the first excited electronic energy level in an anisotropic semiconductor quantum dot

Within the framework of second-order Rayleigh-Schrodinger perturbation theory, the polaronic correction to the first excited state energy of an electron in an quantum dot with anisotropic parabolic confinements is presented. Compared with isotropic confinements, anisotropic confinements will make the degeneracy of the excited states to be totally or partly lifted. On the basis of a three-dimensional Frohlich's Hamiltonian with anisotropic confinements, the first excited state properties in two-dimensional quantum dots as well as quantum wells and wires can also be easily obtained by taking special limits. Calculations show that the first excited polaronic effect can be considerable in small quantum dots.

Topics in gravitational-wave science : macroscopic quantum mechanics and black hole physics

The theories of relativity and quantum mechanics, the two most important physics discoveries of the 20th century, not only revolutionized our understanding of the nature of space-time and the way matter exists and interacts, but also became the building blocks of what we currently know as modern physics. My thesis studies both subjects in great depths --- this intersection takes place in gravitational-wave physics.

Gravitational waves are "ripples of space-time", long predicted by general relativity. Although indirect evidence of gravitational waves has been discovered from observations of binary pulsars, direct detection of these waves is still actively being pursued. An international array of laser interferometer gravitational-wave detectors has been constructed in the past decade, and a first generation of these detectors has taken several years of data without a discovery. At this moment, these detectors are being upgraded into second-generation configurations, which will have ten times better sensitivity. Kilogram-scale test masses of these detectors, highly isolated from the environment, are probed continuously by photons. The sensitivity of such a quantum measurement can often be limited by the Heisenberg Uncertainty Principle, and during such a measurement, the test masses can be viewed as evolving through a sequence of nearly pure quantum states.

The first part of this thesis (Chapter 2) concerns how to minimize the adverse effect of thermal fluctuations on the sensitivity of advanced gravitational detectors, thereby making them closer to being quantum-limited. My colleagues and I present a detailed analysis of coating thermal noise in advanced gravitational-wave detectors, which is the dominant noise source of Advanced LIGO in the middle of the detection frequency band. We identified the two elastic loss angles, clarified the different components of the coating Brownian noise, and obtained their cross spectral densities.

The second part of this thesis (Chapters 3-7) concerns formulating experimental concepts and analyzing experimental results that demonstrate the quantum mechanical behavior of macroscopic objects - as well as developing theoretical tools for analyzing quantum measurement processes. In Chapter 3, we study the open quantum dynamics of optomechanical experiments in which a single photon strongly influences the quantum state of a mechanical object. We also explain how to engineer the mechanical oscillator's quantum state by modifying the single photon's wave function.

In Chapters 4-5, we build theoretical tools for analyzing the so-called "non-Markovian" quantum measurement processes. Chapter 4 establishes a mathematical formalism that describes the evolution of a quantum system (the plant), which is coupled to a non-Markovian bath (i.e., one with a memory) while at the same time being under continuous quantum measurement (by the probe field). This aims at providing a general framework for analyzing a large class of non-Markovian measurement processes. Chapter 5 develops a way of characterizing the non-Markovianity of a bath (i.e.,whether and to what extent the bath remembers information about the plant) by perturbing the plant and watching for changes in the its subsequent evolution. Chapter 6 re-analyzes a recent measurement of a mechanical oscillator's zero-point fluctuations, revealing nontrivial correlation between the measurement device's sensing noise and the quantum rack-action noise.

Chapter 7 describes a model in which gravity is classical and matter motions are quantized, elaborating how the quantum motions of matter are affected by the fact that gravity is classical. It offers an experimentally plausible way to test this model (hence the nature of gravity) by measuring the center-of-mass motion of a macroscopic object.

The most promising gravitational waves for direct detection are those emitted from highly energetic astrophysical processes, sometimes involving black holes - a type of object predicted by general relativity whose properties depend highly on the strong-field regime of the theory. Although black holes have been inferred to exist at centers of galaxies and in certain so-called X-ray binary objects, detecting gravitational waves emitted by systems containing black holes will offer a much more direct way of observing black holes, providing unprecedented details of space-time geometry in the black-holes' strong-field region.

The third part of this thesis (Chapters 8-11) studies black-hole physics in connection with gravitational-wave detection.

Chapter 8 applies black hole perturbation theory to model the dynamics of a light compact object orbiting around a massive central Schwarzschild black hole. In this chapter, we present a Hamiltonian formalism in which the low-mass object and the metric perturbations of the background spacetime are jointly evolved. Chapter 9 uses WKB techniques to analyze oscillation modes (quasi-normal modes or QNMs) of spinning black holes. We obtain analytical approximations to the spectrum of the weakly-damped QNMs, with relative error O(1/L^2), and connect these frequencies to geometrical features of spherical photon orbits in Kerr spacetime. Chapter 11 focuses mainly on near-extremal Kerr black holes, we discuss a bifurcation in their QNM spectra for certain ranges of (l,m) (the angular quantum numbers) as a/M → 1. With tools prepared in Chapter 9 and 10, in Chapter 11 we obtain an analytical approximate for the scalar Green function in Kerr spacetime.

Lattice quantum codes and exotic topological phases of matter

This thesis addresses whether it is possible to build a robust memory device for quantum information. Many schemes for fault-tolerant quantum information processing have been developed so far, one of which, called topological quantum computation, makes use of degrees of freedom that are inherently insensitive to local errors. However, this scheme is not so reliable against thermal errors. Other fault-tolerant schemes achieve better reliability through active error correction, but incur a substantial overhead cost. Thus, it is of practical importance and theoretical interest to design and assess fault-tolerant schemes that work well at finite temperature without active error correction.

In this thesis, a three-dimensional gapped lattice spin model is found which demonstrates for the first time that a reliable quantum memory at finite temperature is possible, at least to some extent. When quantum information is encoded into a highly entangled ground state of this model and subjected to thermal errors, the errors remain easily correctable for a long time without any active intervention, because a macroscopic energy barrier keeps the errors well localized. As a result, stored quantum information can be retrieved faithfully for a memory time which grows exponentially with the square of the inverse temperature. In contrast, for previously known types of topological quantum storage in three or fewer spatial dimensions the memory time scales exponentially with the inverse temperature, rather than its square.

This spin model exhibits a previously unexpected topological quantum order, in which ground states are locally indistinguishable, pointlike excitations are immobile, and the immobility is not affected by small perturbations of the Hamiltonian. The degeneracy of the ground state, though also insensitive to perturbations, is a complicated number-theoretic function of the system size, and the system bifurcates into multiple noninteracting copies of itself under real-space renormalization group transformations. The degeneracy, the excitations, and the renormalization group flow can be analyzed using a framework that exploits the spin model's symmetry and some associated free resolutions of modules over polynomial algebras.

Interacting single atoms with nanophotonics for chip-integrated quantum networks

Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N >> 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N >> 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ~100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high controllability, with which we experimentally demonstrate a state-insensitive atom trap. We present initial investigations on nanophotonic crystal based structures as a platform for strong atom-photon interactions. The experimental advances and theoretical investigations carried out in this thesis provide a framework for and open the door to strong single atom-photon interactions using nanophotonics for chip-integrated quantum networks.