The mechanism of pattern selection in coupled map lattices

The pattern selection of one-dimensional coupled map lattices is studied in this paper. It is shown by spatiotemporal variable separation that there exists a threshold wavelength in pattern selection which possesses wave-like structures in space and periodic chaotic motion in time.

Aperiodic structures in optics and integrated optics and the transverse Bragg reflector laser

The first part of this work describes the uses of aperiodic structures in optics and integrated optics. In particular, devices are designed, fabricated, tested and analyzed which make use of a chirped grating corrugation on the surface of a dielectric waveguide. These structures can be used as input-output couplers, multiplexers and demultiplexers, and broad band filters.

Next, a theoretical analysis is made of the effects of a random statistical variation in the thicknesses of layers in a dielectric mirror on its reflectivity properties. Unlike the intentional aperiodicity introduced in the chirped gratings, the aperiodicity in the Bragg reflector mirrors is unintentional and is present to some extent in all devices made. The analysis involved in studying these problems relies heavily on the coupled mode formalism. The results are compared with computer experiments, as well as tests of actual mirrors.

The second part of this work describes a novel method for confining light in the transverse direction in an injection laser. These so-called transverse Bragg reflector lasers confine light normal to the junction plane in the active region, through reflection from an adjacent layered medium. Thus, in principle, it is possible to guide light in a dielectric layer whose index is lower than that of the surrounding material. The design, theory and testing of these diode lasers are discussed.

Structure Prediction of G-Protein Coupled Receptors

G-protein coupled receptors (GPCRs) form a large family of proteins and are very important drug targets. They are membrane proteins, which makes computational prediction of their structure challenging. Homology modeling is further complicated by low sequence similarly of the GPCR superfamily.

In this dissertation, we analyze the conserved inter-helical contacts of recently solved crystal structures, and we develop a unified sequence-structural alignment of the GPCR superfamily. We use this method to align 817 human GPCRs, 399 of which are nonolfactory. This alignment can be used to generate high quality homology models for the 817 GPCRs.

To refine the provided GPCR homology models we developed the Trihelix sampling method. We use a multi-scale approach to simplify the problem by treating the transmembrane helices as rigid bodies. In contrast to Monte Carlo structure prediction methods, the Trihelix method does a complete local sampling using discretized coordinates for the transmembrane helices. We validate the method on existing structures and apply it to predict the structure of the lactate receptor, HCAR1. For this receptor, we also build extracellular loops by taking into account constraints from three disulfide bonds. Docking of lactate and 3,5-dihydroxybenzoic acid shows likely involvement of three Arg residues on different transmembrane helices in binding a single ligand molecule.

Protein structure prediction relies on accurate force fields. We next present an effort to improve the quality of charge assignment for large atomic models. In particular, we introduce the formalism of the polarizable charge equilibration scheme (PQEQ) and we describe its implementation in the molecular simulation package Lammps. PQEQ allows fast on the fly charge assignment even for reactive force fields.

Finite differences and a coupled analytic technique with applications to explosions and earthquakes

An analytic technique is developed that couples to finite difference calculations to extend the results to arbitrary distance. Finite differences and the analytic result, a boundary integral called two-dimensional Kirchhoff, are applied to simple models and three seismological problems dealing with data. The simple models include a thorough investigation of the seismologic effects of a deep continental basin. The first problem is explosions at Yucca Flat, in the Nevada test site. By modeling both near-field strong-motion records and teleseismic P-waves simultaneously, it is shown that scattered surface waves are responsible for teleseismic complexity. The second problem deals with explosions at Amchitka Island, Alaska. The near-field seismograms are investigated using a variety of complex structures and sources. The third problem involves regional seismograms of Imperial Valley, California earthquakes recorded at Pasadena, California. The data are shown to contain evidence of deterministic structure, but lack of more direct measurements of the structure and possible three-dimensional effects make two-dimensional modeling of these data difficult.

Design of antenna-coupled lumped-element titanium nitride KIDs for long-wavelength multi-band continuum imaging

Many applications in cosmology and astrophysics at millimeter wavelengths including CMB polarization, studies of galaxy clusters using the Sunyaev-Zeldovich effect (SZE), and studies of star formation at high redshift and in our local universe and our galaxy, require large-format arrays of millimeter-wave detectors. Feedhorn and phased-array antenna architectures for receiving mm-wave light present numerous advantages for control of systematics, for simultaneous coverage of both polarizations and/or multiple spectral bands, and for preserving the coherent nature of the incoming light. This enables the application of many traditional "RF" structures such as hybrids, switches, and lumped-element or microstrip band-defining filters.

Simultaneously, kinetic inductance detectors (KIDs) using high-resistivity materials like titanium nitride are an attractive sensor option for large-format arrays because they are highly multiplexable and because they can have sensitivities reaching the condition of background-limited detection. A KID is a LC resonator. Its inductance includes the geometric inductance and kinetic inductance of the inductor in the superconducting phase. A photon absorbed by the superconductor breaks a Cooper pair into normal-state electrons and perturbs its kinetic inductance, rendering it a detector of light. The responsivity of KID is given by the fractional frequency shift of the LC resonator per unit optical power.

However, coupling these types of optical reception elements to KIDs is a challenge because of the impedance mismatch between the microstrip transmission line exiting these architectures and the high resistivity of titanium nitride. Mitigating direct absorption of light through free space coupling to the inductor of KID is another challenge. We present a detailed titanium nitride KID design that addresses these challenges. The KID inductor is capacitively coupled to the microstrip in such a way as to form a lossy termination without creating an impedance mismatch. A parallel plate capacitor design mitigates direct absorption, uses hydrogenated amorphous silicon, and yields acceptable noise. We show that the optimized design can yield expected sensitivities very close to the fundamental limit for a long wavelength imager (LWCam) that covers six spectral bands from 90 to 400 GHz for SZE studies.

Excess phase (frequency) noise has been observed in KID and is very likely caused by two-level systems (TLS) in dielectric materials. The TLS hypothesis is supported by the measured dependence of the noise on resonator internal power and temperature. However, there is still a lack of a unified microscopic theory which can quantitatively model the properties of the TLS noise. In this thesis we derive the noise power spectral density due to the coupling of TLS with phonon bath based on an existing model and compare the theoretical predictions about power and temperature dependences with experimental data. We discuss the limitation of such a model and propose the direction for future study.

The wave transmission coefficients and coupling loss factors of point connected structures

This analysis is concerned with the calculation of the elastic wave transmission coefficients and coupling loss factors between an arbitrary number of structural components that are coupled at a point. A general approach to the problem is presented and it is demonstrated that the resulting coupling loss factors satisfy reciprocity. A key aspect of the method is the consideration of cylindrical waves in two-dimensional components, and this builds upon recent results regarding the energetics of diffuse wavefields when expressed in cylindrical coordinates. Specific details of the method are given for beam and thin plate components, and a number of examples are presented. © 2002 Acoustical Society of America.

Shock transmission and eigenvalue veering within a coupled system.

The operation of dynamical systems in harsh environments requires continuous monitoring. Internal sensors may be used to monitor the conditions in real time. A typical example is the sensor and electronic components used in space structures which, especially during launch, are subject to huge g force. The paper will present an experimental and theoretical study on a simplified model used to analyze the possible cause of high acceleration on the enclosed sensors and equipments due to impulsive loading. The model system consists of two beams coupled using compliant connections. An impulse hammer excites one beam, and vibrations are transmitted to the indirectly driven beam. A theoretical model is developed using a Rayleigh-Ritz approach and validated using experimental results in both the frequency and time domains. Monto Carlo simulation was done with random masses positioned on the indirectly driven beam to determine the worst-case conditions for maximum peak acceleration. Highest acceleration levels were found when mode matching in the two beams led to veering behavior in the coupled modes. The results suggest guidelines for the detailed design of internal components of a structure exposed to shock loading from its environment. [The authors thank Schlumberger Cambridge Research for financial support.].

Hybrid deterministic-statistical modelling of built-up structures

When used correctly, Statistical Energy Analysis (SEA) can provide good predictions of high frequency vibration levels in built-up structures. Unfortunately, the assumptions that underlie SEA break down as the frequency of excitation is reduced, and the method does not yield accurate predictions at "medium" frequencies (and neither does the Finite Element Method, which is limited to low frequencies). A basic problem is that parts of the system have a short wavelength of deformation and meet the requirements of SEA, while other parts of the system do not - this is often referred to as the "mid-frequency" problem, and there is a broad class of mid-frequency vibration problems that are of great concern to industry. In this paper, a coupled deterministic-statistical approach referred to as the Hybrid Method (Shorter & Langley, 2004) is briefly described, and some results that demonstrate how the method overcomes the aforementioned difficulties are presented.

Active control of high frequency vibration in uncertain structures

The active suppression of structural vibration is normally achieved by either feedforward or feedback control. In the absence of a suitable reference signal feedforward control cannot be employed and feedback control is the only viable approach. Conventional feedback control algorithms (e.g. LQR and LQG) are designed on the basis of a mathematical model of the system and ideally the performance of the system should be robust against uncertainties in this model. The aim of this paper is to numerically investigate the robustness of LQR and LQG algorithms by designing the controller for a nominal system, and then assessing (via Monte Carlo simulation) the effects of uncertainties in the system. The ultimate concern is with the control of high frequency vibrations, where the short wavelength of the structural deformation induces a high sensitivity to imperfection. It is found that standard algorithms such as LQR and LQG are generally unfeasible for this case. This leads to a consideration of design strategies for the robust active control of high frequency vibrations. The system chosen for the numerical simulation concerns two coupled plates, which are randomized by the addition of point masses at random locations.

Coupling model uncertainty for coupled rainfall/runoff and surface water quality models in river problems

Coupled hydrology and water quality models are an important tool today, used in the understanding and management of surface water and watershed areas. Such problems are generally subject to substantial uncertainty in parameters, process understanding, and data. Component models, drawing on different data, concepts, and structures, are affected differently by each of these uncertain elements. This paper proposes a framework wherein the response of component models to their respective uncertain elements can be quantified and assessed, using a hydrological model and water quality model as two exemplars. The resulting assessments can be used to identify model coupling strategies that permit more appropriate use and calibration of individual models, and a better overall coupled model response. One key finding was that an approximate balance of water quality and hydrological model responses can be obtained using both the QUAL2E and Mike11 water quality models. The balance point, however, does not support a particularly narrow surface response (or stringent calibration criteria) with respect to the water quality calibration data, at least in the case examined here. Additionally, it is clear from the results presented that the structural source of uncertainty is at least as significant as parameter-based uncertainties in areal models. © 2012 John Wiley & Sons, Ltd.

Efficient hole transport in asymmetric coupled InGaN multiple quantum wells

InGaN based light emitting devices (LEDs) with asymmetric coupled quantum wells (AS-QWs) and conventional symmetric coupled quantum wells (CS-QWs) active structures were grown by metal-organic chemical vapor deposition technique. The LEDs with AS-QWs active region show improved light emission intensity and reduced forward voltage compared with LEDs with CS-QWs active region. Based on the electroluminescence measurements and the devices structure analysis, it can be concluded that these improvements are mainly attributed to the efficient hole tunneling through barriers and consequently the uniform distribution of carriers in the AS-QWs. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3254232]

Plasmons in vertically coupled InAs/GaAs quantum dots

We investigate plasmon excitations in a quantum wire that consists of an infinite one-dimensional array of vertically coupled InAs/GaAs strained quantum dots (QDs). The research is carried out in the framework of random-phase approximation using effective-mass theory. Our formalism is capable of studying plasmons with strong tunneling among QDs, which frustrate the conventionally adopted tight-binding approximation. Based on this formalism, a systematic study on the intraminiband or intrasubband plasmon in vertically coupled InAs/GaAs strained QDs is presented. It is found that an increase of the dot spacing will inevitably reduce the plasmon energy. In contrast, the role of dot height is relatively complex and depends on the dot spacing. The results demonstrate the possibility to engineer collective excitations in low dimensional systems by simply changing their geometric configuration.

Effective-mass theory for coupled quantum dots grown on (11N)-oriented substrates

The electronic structures of coupled quantum dots grown on (11N)-oriented substrates are studied in the framework of effective-mass envelope-function theory. The results show that the all-hole subbands have the smallest widths and the optical properties are best for the (113), (114), and (115) growth directions. Our theoretical results agree with the available experimental data. Our calculated results are useful for the application of coupled quantum dots in photoelectric devices.

Collective and single-particle excitations in coupled quantum wires in magnetic fields

The full spectra of magnetoplasmons and single-particle excitations are obtained of coupled one-dimensional electron gases in parallel semiconductor quantum wires with tunneling. We show the effects of the interwire Coulomb interaction and the tunneling, as well as the magnetic-field-induced localization on the elementary excitations in symmetric and asymmetric coulped quantum wire structures. The interacton and resonance between the plasmon and the intersubband single-particle excitations are found in magnetic fields.