Experimental and theoretical developments in extended x-ray absorption fine structure (EXAFS) spectroscopy

To obtain accurate information from a structural tool it is necessary to have an understanding of the physical principles which govern the interaction between the probe and the sample under investigation. In this thesis a detailed study of the physical basis for Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy is presented. A single scattering formalism of EXAFS is introduced which allows a rigorous treatment of the central atom potential. A final state interaction formalism of EXAFS is also discussed. Multiple scattering processes are shown to be significant for systems of certain geometries. The standard single scattering EXAFS analysis produces erroneous results if the data contain a large multiple scattering contribution. The effect of thermal vibrations on such multiple scattering paths is also discussed. From symmetry considerations it is shown that only certain normal modes contribute to the Debye-Waller factor for a particular scattering path. Furthermore, changes in the scattering angles induced by thermal vibrations produces additional EXAFS components called modification factors. These factors are shown to be small for most systems.

A study of the physical basis for the determination of structural information from EXAFS data is also presented. An objective method of determining the background absorption and the threshold energy is discussed and involves Gaussian functions. In addition, a scheme to determine the nature of the scattering atom in EXAFS experiments is introduced. This scheme is based on the fact that the phase intercept is a measure of the type of scattering atom. A method to determine bond distances is also discussed and does not require the use of model compounds or calculated phase shifts. The physical basis for this method is the absence of a linear term in the scattering phases. Therefore, it is possible to separate these phases from the linear term containing the distance information in the total phase.

Wide Field-of-view Microscopes and Endoscopes for Time-lapse Imaging and High-throughput Screening

Wide field-of-view (FOV) microscopy is of high importance to biological research and clinical diagnosis where a high-throughput screening of samples is needed. This thesis presents the development of several novel wide FOV imaging technologies and demonstrates their capabilities in longitudinal imaging of living organisms, on the scale of viral plaques to live cells and tissues.

The ePetri Dish is a wide FOV on-chip bright-field microscope. Here we applied an ePetri platform for plaque analysis of murine norovirus 1 (MNV-1). The ePetri offers the ability to dynamically track plaques at the individual cell death event level over a wide FOV of 6 mm × 4 mm at 30 min intervals. A density-based clustering algorithm is used to analyze the spatial-temporal distribution of cell death events to identify plaques at their earliest stages. We also demonstrate the capabilities of the ePetri in viral titer count and dynamically monitoring plaque formation, growth, and the influence of antiviral drugs.

We developed another wide FOV imaging technique, the Talbot microscope, for the fluorescence imaging of live cells. The Talbot microscope takes advantage of the Talbot effect and can generate a focal spot array to scan the fluorescence samples directly on-chip. It has a resolution of 1.2 μm and a FOV of ~13 mm². We further upgraded the Talbot microscope for the long-term time-lapse fluorescence imaging of live cell cultures, and analyzed the cells’ dynamic response to an anticancer drug.

We present two wide FOV endoscopes for tissue imaging, named the AnCam and the PanCam. The AnCam is based on the contact image sensor (CIS) technology, and can scan the whole anal canal within 10 seconds with a resolution of 89 μm, a maximum FOV of 100 mm × 120 mm, and a depth-of-field (DOF) of 0.65 mm. We also demonstrate the performance of the AnCam in whole anal canal imaging in both animal models and real patients. In addition to this, the PanCam is based on a smartphone platform integrated with a panoramic annular lens (PAL), and can capture a FOV of 18 mm × 120 mm in a single shot with a resolution of 100─140 μm. In this work we demonstrate the PanCam’s performance in imaging a stained tissue sample.

Source characteristics of recent and historic earthquakes in Central and Southern California: results from forward modeling

The long- and short-period body waves of a number of moderate earthquakes occurring in central and southern California recorded at regional (200-1400 km) and teleseismic (> 30°) distances are modeled to obtain the source parameters-focal mechanism, depth, seismic moment, and source time history. The modeling is done in the time domain using a forward modeling technique based on ray summation. A simple layer over a half space velocity model is used with additional layers being added if necessary-for example, in a basin with a low velocity lid.

The earthquakes studied fall into two geographic regions: 1) the western Transverse Ranges, and 2) the western Imperial Valley. Earthquakes in the western Transverse Ranges include the 1987 Whittier Narrows earthquake, several offshore earthquakes that occurred between 1969 and 1981, and aftershocks to the 1983 Coalinga earthquake (these actually occurred north of the Transverse Ranges but share many characteristics with those that occurred there). These earthquakes are predominantly thrust faulting events with the average strike being east-west, but with many variations. Of the six earthquakes which had sufficient short-period data to accurately determine the source time history, five were complex events. That is, they could not be modeled as a simple point source, but consisted of two or more subevents. The subevents of the Whittier Narrows earthquake had different focal mechanisms. In the other cases, the subevents appear to be the same, but small variations could not be ruled out.

The recent Imperial Valley earthquakes modeled include the two 1987 Superstition Hills earthquakes and the 1969 Coyote Mountain earthquake. All are strike-slip events, and the second 1987 earthquake is a complex event With non-identical subevents.

In all the earthquakes studied, and particularly the thrust events, constraining the source parameters required modeling several phases and distance ranges. Teleseismic P waves could provide only approximate solutions. P_(nl) waves were probably the most useful phase in determining the focal mechanism, with additional constraints supplied by the SH waves when available. Contamination of the SH waves by shear-coupled PL waves was a frequent problem. Short-period data were needed to obtain the source time function.

In addition to the earthquakes mentioned above, several historic earthquakes were also studied. Earthquakes that occurred before the existence of dense local and worldwide networks are difficult to model due to the sparse data set. It has been noticed that earthquakes that occur near each other often produce similar waveforms implying similar source parameters. By comparing recent well studied earthquakes to historic earthquakes in the same region, better constraints can be placed on the source parameters of the historic events.

The Lompoc earthquake (M=7) of 1927 is the largest offshore earthquake to occur in California this century. By direct comparison of waveforms and amplitudes with the Coalinga and Santa Lucia Banks earthquakes, the focal mechanism (thrust faulting on a northwest striking fault) and long-period seismic moment (10^(26) dyne cm) can be obtained. The S-P travel times are consistent with an offshore location, rather than one in the Hosgri fault zone.

Historic earthquakes in the western Imperial Valley were also studied. These events include the 1942 and 1954 earthquakes. The earthquakes were relocated by comparing S-P and R-S times to recent earthquakes. It was found that only minor changes in the epicenters were required but that the Coyote Mountain earthquake may have been more severely mislocated. The waveforms as expected indicated that all the events were strike-slip. Moment estimates were obtained by comparing the amplitudes of recent and historic events at stations which recorded both. The 1942 event was smaller than the 1968 Borrego Mountain earthquake although some previous studies suggested the reverse. The 1954 and 1937 earthquakes had moments close to the expected value. An aftershock of the 1942 earthquake appears to be larger than previously thought.

Method for measuring the lateral aberrations of a lithographic projection system with mirror-symmetric FOCAL marks

A novel method for measuring the imaging quality of a projection system with mirror-symmetric FOCAL marks is proposed, and the principle of the method is described. Through experiments, it is demonstrated that not only the axial aberrations but also the lateral aberrations can be measured with high accuracy by the method. The advantages of the method include obtaining more aberrations than the FOCAL technique and making it much simpler to perform a full-scale measurement of the imaging quality of a lithographic projection system. (C) 2006 Society of Photo-Optical Instrumentation Engineers.

图像深度估计的光学微分方法

讨论了光学微分方法在图像深度估计问题中的应用。基于线性成像理论对Farid提出的光学微分模型进行了推广，即用于图像深度估计的两幅图像在成像过程中可以满足任意阶的线性微分关系。此模型拓宽了光学微分的概念，使两次成像之间关系有了更多的光学微分形式。围绕如何选择合适的光学微分关系以使系统的整体性能达到最优，分析了光学成像系统的参量对于图像深度估计的精度以及纵向分辨力的影响，并且对光学微分方法中的关键光学元件—光学掩模板的构建方法及优化问题也作了初步的探讨。

Simulations and mechanisms of subtropical low-cloud response to climate change

This thesis focuses on improving the simulation skills and the theoretical understanding of the subtropical low cloud response to climate change.

First, an energetically consistent forcing framework is designed and implemented for the large eddy simulation (LES) of the low-cloud response to climate change. The three representative current-day subtropical low cloud regimes of cumulus (Cu), cumulus-over-stratocumulus, and stratocumulus (Sc) are all well simulated with this framework, and results are comparable to the conventional fixed-SST approach. However, the cumulus response to climate warming subject to energetic constraints differs significantly from the conventional approach with fixed SST. Under the energetic constraint, the subtropics warm less than the tropics, since longwave (LW) cooling is more efficient with the drier subtropical free troposphere. The surface latent heat flux (LHF) also increases only weakly subject to the surface energetic constraint. Both factors contribute to an increased estimated inversion strength (EIS), and decreased inversion height. The decreased Cu-depth contributes to a decrease of liquid water path (LWP) and weak positive cloud feedback. The conventional fixed-SST approach instead simulates a strong increase in LHF and deepening of the Cu layer, leading to a weakly negative cloud feedback. This illustrates the importance of energetic constraints to the simulation and understanding of the sign and magnitude of low-cloud feedback.

Second, an extended eddy-diffusivity mass-flux (EDMF) closure for the unified representation of sub-grid scale (SGS) turbulence and convection processes in general circulation models (GCM) is presented. The inclusion of prognostic terms and the elimination of the infinitesimal updraft fraction assumption makes it more flexible for implementation in models across different scales. This framework can be consistently extended to formulate multiple updrafts and downdrafts, as well as variances and covariances. It has been verified with LES in different boundary layer regimes in the current climate, and further development and implementation of this closure may help to improve our simulation skills and understanding of low-cloud feedback through GCMs.

Method for measuring the lateral aberrations of a lithographic projection system with mirror-symmetric FOCAL marks

A novel method for measuring the imaging quality of a projection system with mirror-symmetric FOCAL marks is proposed, and the principle of the method is described. Through experiments, it is demonstrated that not only the axial aberrations but also the lateral aberrations can be measured with high accuracy by the method. The advantages of the method include obtaining more aberrations than the FOCAL technique and making it much simpler to perform a full-scale measurement of the imaging quality of a lithographic projection system. (C) 2006 Society of Photo-Optical Instrumentation Engineers.

Longitudinal dispersion in laboratory and natural streams

This study concerns the longitudinal dispersion of fluid particles which are initially distributed uninformly over one cross section of a uniform, steady, turbulent open channel flow. The primary focus is on developing a method to predict the rate of dispersion in a natural stream.

Taylor's method of determining a dispersion coefficient, previously applied to flow in pipes and two-dimensional open channels, is extended to a class of three-dimensional flows which have large width-to-depth ratios, and in which the velocity varies continuously with lateral cross-sectional position. Most natural streams are included. The dispersion coefficient for a natural stream may be predicted from measurements of the channel cross-sectional geometry, the cross-sectional distribution of velocity, and the overall channel shear velocity. Tracer experiments are not required.

Large values of the dimensionless dispersion coefficient D/rU* are explained by lateral variations in downstream velocity. In effect, the characteristic length of the cross section is shown to be proportional to the width, rather than the hydraulic radius. The dimensionless dispersion coefficient depends approximately on the square of the width to depth ratio.

A numerical program is given which is capable of generating the entire dispersion pattern downstream from an instantaneous point or plane source of pollutant. The program is verified by the theory for two-dimensional flow, and gives results in good agreement with laboratory and field experiments.

Both laboratory and field experiments are described. Twenty-one laboratory experiments were conducted: thirteen in two-dimensional flows, over both smooth and roughened bottoms; and eight in three-dimensional flows, formed by adding extreme side roughness to produce lateral velocity variations. Four field experiments were conducted in the Green-Duwamish River, Washington.

Both laboratory and flume experiments prove that in three-dimensional flow the dominant mechanism for dispersion is lateral velocity variation. For instance, in one laboratory experiment the dimensionless dispersion coefficient D/rU* (where r is the hydraulic radius and U* the shear velocity) was increased by a factory of ten by roughening the channel banks. In three-dimensional laboratory flow, D/rU* varied from 190 to 640, a typical range for natural streams. For each experiment, the measured dispersion coefficient agreed with that predicted by the extension of Taylor's analysis within a maximum error of 15%. For the Green-Duwamish River, the average experimentally measured dispersion coefficient was within 5% of the prediction.

Metrologia de instrumentos endodônticos por microscopia eletrônica de varredura e análise digital de imagens: uma proposta metodológica

A padronização para a fabricação de instrumentos endodônticos em aço inoxidável contribuiu para o desenvolvimento de novos aspectos geométricos. Surgiram propostas de alterações no desenho da haste helicoidal, da seção reta transversal, da ponta, da conicidade e do diâmetro na extremidade (D0). Concomitantemente, o emprego de ligas em Níquel-Titânio possibilitou a produção de instrumentos acionados a motor, largamente empregados hoje. A cada ano a indústria lança instrumentos com diversas modificações, sem, contudo, disponibilizar informações suficientes quanto às implicações clínicas destas modificações. Existe um crescente interesse no estudo dos diferentes aspectos geométricos e sua precisa metrologia. Tradicionalmente, a aferição de aspectos geométricos de instrumentos endodônticos é realizada visualmente através de microscopia ótica. Entretanto, esse procedimento visual é lento e subjetivo. Este trabalho propõe um novo método para a metrologia de instrumentos endodônticos baseado no microscópio eletrônico de varredura e na análise digital das imagens. A profundidade de campo do MEV permite obter a imagem de todo o relevo do instrumento endodôntico a uma distância de trabalho constante. Além disso, as imagens obtidas pelo detector de elétrons retro-espalhados possuem menos artefatos e sombras, tornando a obtenção e análise das imagens mais fáceis. Adicionalmente a análise das imagens permite formas de mensuração mais eficientes, com maior velocidade e qualidade. Um porta-amostras específico foi adaptado para obtenção das imagens dos instrumentos endodônticos. Ele é composto de um conector elétrico múltiplo com terminais parafusados de 12 pólos com 4 mm de diâmetro, numa base de alumínio coberta por discos de ouro. Os nichos do conector (terminais fêmeas) têm diâmetro apropriado (2,5 mm) para o encaixe dos instrumentos endodônticos. Outrossim, o posicionamento ordenado dos referidos instrumentos no conector elétrico permite a aquisição automatizada das imagens no MEV. Os alvos de ouro produzem, nas imagens de elétrons retro-espalhados, melhor contraste de número atômico entre o fundo em ouro e os instrumentos. No porta-amostras desenvolvido, os discos que compõem o fundo em ouro são na verdade, alvos do aparelho metalizador, comumente encontrados em laboratórios de MEV. Para cada instrumento, imagens de quatro a seis campos adjacentes de 100X de aumento são automaticamente obtidas para cobrir todo o comprimento do instrumento com a magnificação e resolução requeridas (3,12 m/pixel). As imagens obtidas são processadas e analisadas pelos programas Axiovision e KS400. Primeiro elas são dispostas num campo único estendido de cada instrumento por um procedimento de alinhamento semi-automático baseado na inter-relação com o Axiovision. Então a imagem de cada instrumento passa por uma rotina automatizada de análise de imagens no KS400. A rotina segue uma sequência padrão: pré-processamento, segmentação, pós-processamento e mensuração dos aspectos geométricos.

A novel FOCAL technique based on BP-ANN

In this paper, the feed-forward back-propagation artificial neural network (BP-ANN) algorithm is introduced in the traditional Focus Calibration using Alignment procedure (FOCAL) technique, and a novel FOCAL technique based on BP-ANN is proposed. The effects of the parameters, such as the number of neurons on the hidden-layer and the number of training epochs, on the measurement accuracy are analyzed in detail. It is proved that the novel FOCAL technique based on BP-ANN is more reliable and it is a better choice for measurement of the image quality parameters. (c) 2005 Elsevier GmbH. All rights reserved.

Depth-sensitive analysis of fluorine on lunar sample surfaces and in carbonaceous chondrites by a nuclear resonant reaction technique

The nuclear resonant reaction ¹⁹F(ρ,αγ)¹⁶O has been used to perform depth-sensitive analyses of fluorine in lunar samples and carbonaceous chondrites. The resonance at 0.83 MeV (center-of-mass) in this reaction is utilized to study fluorine surface films, with particular interest paid to the outer micron of Apollo 15 green glass, Apollo 17 orange glass, and lunar vesicular basalts. These results are distinguished from terrestrial contamination, and are discussed in terms of a volcanic origin for the samples of interest. Measurements of fluorine in carbonaceous chondrites are used to better define the solar system fluorine abundance. A technique for measurement of carbon on solid surfaces with applications to direct quantitative analysis of implanted solar wind carbon in lunar samples is described.

The design and development of the Windermere Profiler. An instrument for measuring how various environmental parameters vary with depth in lakes, reservoirs and rivers

A review article detailing the background, development and functionality of the Windermere Profiler, a multi parameter environmental monitoring instrument for use in lakes, reservoirs and rivers. The article explains the requirement for regular data collection by the Freshwater Biological Association at Windermere. The article covers the requirements of a profiling instrument, the design considerations, the electronic circuitry, the computer program, the operation of the computer software, the profiler in use and further developments to the design. A number of figures and images accompany the article.