One-dimensional models for organic magnetic materials

In the preparation of small organic paramagnets, these structures may conceptually be divided into spin-containing units (SCs) and ferromagnetic coupling units (FCs). The synthesis and direct observation of a series of hydrocarbon tetraradicals designed to test the ferromagnetic coupling ability of m-phenylene, 1,3-cyclobutane, 1,3- cyclopentane, and 2,4-adamantane (a chair 1,3-cyclohexane) using Berson TMMs and cyclobutanediyls as SCs are described. While 1,3-cyclobutane and m-phenylene are good ferromagnetic coupling units under these conditions, the ferromagnetic coupling ability of 1,3-cyclopentane is poor, and 1,3-cyclohexane is apparently an antiferromagnetic coupling unit. In addition, this is the first report of ferromagnetic coupling between the spins of localized biradical SCs.

The poor coupling of 1,3-cyclopentane has enabled a study of the variable temperature behavior of a 1,3-cyclopentane FC-based tetraradical in its triplet state. Through fitting the observed data to the usual Boltzman statistics, we have been able to determine the separation of the ground quintet and excited triplet states. From this data, we have inferred the singlet-triplet gap in 1,3-cyclopentanediyl to be 900 cal/mol, in remarkable agreement with theoretical predictions of this number.

The ability to simulate EPR spectra has been crucial to the assignments made here. A powder EPR simulation package is described that uses the Zeeman and dipolar terms to calculate powder EPR spectra for triplet and quintet states.

Methods for characterizing paramagnetic samples by SQUID magnetometry have been developed, including robust routines for data fitting and analysis. A precursor to a potentially magnetic polymer was prepared by ring-opening metathesis polymerization (ROMP), and doped samples of this polymer were studied by magnetometry. While the present results are not positive, calculations have suggested modifications in this structure which should lead to the desired behavior.

Source listings for all computer programs are given in the appendix.

Analysis and optimization of stress wave propagation in two-dimensional granular crystals with defects

Granular crystals are compact periodic assemblies of elastic particles in Hertzian contact whose dynamic response can be tuned from strongly nonlinear to linear by the addition of a static precompression force. This unique feature allows for a wide range of studies that include the investigation of new fundamental nonlinear phenomena in discrete systems such as solitary waves, shock waves, discrete breathers and other defect modes. In the absence of precompression, a particularly interesting property of these systems is their ability to support the formation and propagation of spatially localized soliton-like waves with highly tunable properties. The wealth of parameters one can modify (particle size, geometry and material properties, periodicity of the crystal, presence of a static force, type of excitation, etc.) makes them ideal candidates for the design of new materials for practical applications. This thesis describes several ways to optimally control and tailor the propagation of stress waves in granular crystals through the use of heterogeneities (interstitial defect particles and material heterogeneities) in otherwise perfectly ordered systems. We focus on uncompressed two-dimensional granular crystals with interstitial spherical intruders and composite hexagonal packings and study their dynamic response using a combination of experimental, numerical and analytical techniques. We first investigate the interaction of defect particles with a solitary wave and utilize this fundamental knowledge in the optimal design of novel composite wave guides, shock or vibration absorbers obtained using gradient-based optimization methods.

Three-dimensional models of mantle convection : influence of phase transitions and temperature-dependent viscosity

Two of the most important questions in mantle dynamics are investigated in three separate studies: the influence of phase transitions (studies 1 and 2), and the influence of temperature-dependent viscosity (study 3).

(1) Numerical modeling of mantle convection in a three-dimensional spherical shell incorporating the two major mantle phase transitions reveals an inherently three-dimensional flow pattern characterized by accumulation of cold downwellings above the 670 km discontinuity, and cylindrical 'avalanches' of upper mantle material into the lower mantle. The exothermic phase transition at 400 km depth reduces the degree of layering. A region of strongly-depressed temperature occurs at the base of the mantle. The temperature field is strongly modulated by this partial layering, both locally and in globally-averaged diagnostics. Flow penetration is strongly wavelength-dependent, with easy penetration at long wavelengths but strong inhibition at short wavelengths. The amplitude of the geoid is not significantly affected.

(2) Using a simple criterion for the deflection of an upwelling or downwelling by an endothermic phase transition, the scaling of the critical phase buoyancy parameter with the important lengthscales is obtained. The derived trends match those observed in numerical simulations, i.e., deflection is enhanced by (a) shorter wavelengths, (b) narrower up/downwellings (c) internal heating and (d) narrower phase loops.

(3) A systematic investigation into the effects of temperature-dependent viscosity on mantle convection has been performed in three-dimensional Cartesian geometry, with a factor of 1000-2500 viscosity variation, and Rayleigh numbers of 10^5-10^7. Enormous differences in model behavior are found, depending on the details of rheology, heating mode, compressibility and boundary conditions. Stress-free boundaries, compressibility, and temperature-dependent viscosity all favor long-wavelength flows, even in internally heated cases. However, small cells are obtained with some parameter combinations. Downwelling plumes and upwelling sheets are possible when viscosity is dependent solely on temperature. Viscous dissipation becomes important with temperature-dependent viscosity.

The sensitivity of mantle flow and structure to these various complexities illustrates the importance of performing mantle convection calculations with rheological and thermodynamic properties matching as closely as possible those of the Earth.

A short training program improves the accuracy of portion-size estimates in future dietitians

[EN] The objective of this study was to determine whether a short training program, using real foods, would decreased their portion-size estimation errors after training. 90 student volunteers (20.18±0.44 y old) of the University of the Basque Country (Spain) were trained in observational techniques and tested in food-weight estimation during and after a 3-hour training period. The program included 57 commonly consumed foods that represent a variety of forms (125 different shapes). Estimates of food weight were compared with actual weights. Effectiveness of training was determined by examining change in the absolute percentage error for all observers and over all foods over time. Data were analyzed using SPSS vs. 13.0. The portion-size errors decreased after training for most of the foods. Additionally, the accuracy of their estimates clearly varies by food group and forms. Amorphous was the food type estimated least accurately both before and after training. Our findings suggest that future dietitians can be trained to estimate quantities by direct observation across a wide range of foods. However this training may have been too brief for participants to fully assimilate the application.

The optoelectronic swept-frequency laser and its applications in ranging, three-dimensional imaging, and coherent beam combining of chirped-seed amplifiers

This thesis explores the design, construction, and applications of the optoelectronic swept-frequency laser (SFL). The optoelectronic SFL is a feedback loop designed around a swept-frequency (chirped) semiconductor laser (SCL) to control its instantaneous optical frequency, such that the chirp characteristics are determined solely by a reference electronic oscillator. The resultant system generates precisely controlled optical frequency sweeps. In particular, we focus on linear chirps because of their numerous applications. We demonstrate optoelectronic SFLs based on vertical-cavity surface-emitting lasers (VCSELs) and distributed-feedback lasers (DFBs) at wavelengths of 1550 nm and 1060 nm. We develop an iterative bias current predistortion procedure that enables SFL operation at very high chirp rates, up to 10^16 Hz/sec. We describe commercialization efforts and implementation of the predistortion algorithm in a stand-alone embedded environment, undertaken as part of our collaboration with Telaris, Inc. We demonstrate frequency-modulated continuous-wave (FMCW) ranging and three-dimensional (3-D) imaging using a 1550 nm optoelectronic SFL.

We develop the technique of multiple source FMCW (MS-FMCW) reflectometry, in which the frequency sweeps of multiple SFLs are "stitched" together in order to increase the optical bandwidth, and hence improve the axial resolution, of an FMCW ranging measurement. We demonstrate computer-aided stitching of DFB and VCSEL sweeps at 1550 nm. We also develop and demonstrate hardware stitching, which enables MS-FMCW ranging without additional signal processing. The culmination of this work is the hardware stitching of four VCSELs at 1550 nm for a total optical bandwidth of 2 THz, and a free-space axial resolution of 75 microns.

We describe our work on the tomographic imaging camera (TomICam), a 3-D imaging system based on FMCW ranging that features non-mechanical acquisition of transverse pixels. Our approach uses a combination of electronically tuned optical sources and low-cost full-field detector arrays, completely eliminating the need for moving parts traditionally employed in 3-D imaging. We describe the basic TomICam principle, and demonstrate single-pixel TomICam ranging in a proof-of-concept experiment. We also discuss the application of compressive sensing (CS) to the TomICam platform, and perform a series of numerical simulations. These simulations show that tenfold compression is feasible in CS TomICam, which effectively improves the volume acquisition speed by a factor ten.

We develop chirped-wave phase-locking techniques, and apply them to coherent beam combining (CBC) of chirped-seed amplifiers (CSAs) in a master oscillator power amplifier configuration. The precise chirp linearity of the optoelectronic SFL enables non-mechanical compensation of optical delays using acousto-optic frequency shifters, and its high chirp rate simultaneously increases the stimulated Brillouin scattering (SBS) threshold of the active fiber. We characterize a 1550 nm chirped-seed amplifier coherent-combining system. We use a chirp rate of 5*10^14 Hz/sec to increase the amplifier SBS threshold threefold, when compared to a single-frequency seed. We demonstrate efficient phase-locking and electronic beam steering of two 3 W erbium-doped fiber amplifier channels, achieving temporal phase noise levels corresponding to interferometric fringe visibilities exceeding 98%.

Fabrication of two-dimensional periodic nanostructures by two-beam interference of femtosecond pulses

Two-dimensional periodic nanostructures on ZnO crystal surface were fabricated by two-beam interference of 790 nm femtosecond laser. The long period is, as usually reported, determined by the interference pattern of two laser beams. Surprisingly, there is another short periodic nanostructures with periods of 220-270 nm embedding in the long periodic structures. We studied the periods, orientation, and the evolution of the short periodic nanostructures, and found them analogous to the self-organized nanostructures induced by single fs laser beam. (C) 2008 Optical Society of America.

Three-dimensional self-assembly of brush block copolymers to photonic crystals

The development of Ring Opening Metathesis Polymerization has allowed the world of block copolymers to expand into brush block copolymers. Brush block copolymers consist of a polymer backbone with polymeric side chains, forcing the backbone to hold a stretched conformation and giving it a worm-like shape. These brush block copolymers have a number of advantages over tradition block copolymers, including faster self-assembly behavior, larger domain sizes, and much less entanglement. This makes them an ideal candidate in the development of a bottom-up approach to forming photonic crystals. Photonic crystals are periodic nanostructures that transmit and reflect only certain wavelengths of light, forming a band gap. These are used in a number of coatings and other optical uses. One and two dimensional photonic crystals are commercially available, though are often expensive and difficult to manufacture. Previous work has focused on the creation of one dimensional photonic crystals from brush block copolymers. In this thesis, I will focus on the synthesis and characterization of asymmetric brush block copolymers for self-assembly into two and three dimensional photonic crystals. Three series of brush block copolymers were made and characterized by Gel Permeation Chromatography and Nuclear Magnetic Resonance spectroscopy. They were then made into films through compressive thermal annealing and characterized by UV-Vis Spectroscopy and Scanning Electron Microscopy. Evidence of non-lamellar structures were seen, indicating the first reported creation of two or three dimensional photonic crystals from brush block copolymers.

Reduced deep-tissue image degradation in three-dimensional multiphoton microscopy with concentric two-color two-photon fluorescence excitation

We theoretically demonstrate that enhanced penetration depth in three-dimensional multiphoton microscopy can be achieved using concentric two-color two-photon (C2C2P) fluorescence excitation in which the two excitation beams are separated in space before reaching their common focal spot. Monte Carlo simulation shows that, in comparison with the one-color two-photon excitation scheme, the C2C2P fluorescence microscopy provides a significantly greater penetration depth for imaging into a highly scattering medium. (C) 2008 Optical Society of America.

Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

A new high-order Fourier continuation-based elasticity solver for complex three-dimensional geometries

This thesis presents a new approach for the numerical solution of three-dimensional problems in elastodynamics. The new methodology, which is based on a recently introduced Fourier continuation (FC) algorithm for the solution of Partial Differential Equations on the basis of accurate Fourier expansions of possibly non-periodic functions, enables fast, high-order solutions of the time-dependent elastic wave equation in a nearly dispersionless manner, and it requires use of CFL constraints that scale only linearly with spatial discretizations. A new FC operator is introduced to treat Neumann and traction boundary conditions, and a block-decomposed (sub-patch) overset strategy is presented for implementation of general, complex geometries in distributed-memory parallel computing environments. Our treatment of the elastic wave equation, which is formulated as a complex system of variable-coefficient PDEs that includes possibly heterogeneous and spatially varying material constants, represents the first fully-realized three-dimensional extension of FC-based solvers to date. Challenges for three-dimensional elastodynamics simulations such as treatment of corners and edges in three-dimensional geometries, the existence of variable coefficients arising from physical configurations and/or use of curvilinear coordinate systems and treatment of boundary conditions, are all addressed. The broad applicability of our new FC elasticity solver is demonstrated through application to realistic problems concerning seismic wave motion on three-dimensional topographies as well as applications to non-destructive evaluation where, for the first time, we present three-dimensional simulations for comparison to experimental studies of guided-wave scattering by through-thickness holes in thin plates.