Bright-field and fluorescence chip-scale microscopy for biological imaging

Optical microscopy is an essential tool in biological science and one of the gold standards for medical examinations. Miniaturization of microscopes can be a crucial stepping stone towards realizing compact, cost-effective and portable platforms for biomedical research and healthcare. This thesis reports on implementations of bright-field and fluorescence chip-scale microscopes for a variety of biological imaging applications. The term “chip-scale microscopy” refers to lensless imaging techniques realized in the form of mass-producible semiconductor devices, which transforms the fundamental design of optical microscopes.

Our strategy for chip-scale microscopy involves utilization of low-cost Complementary metal Oxide Semiconductor (CMOS) image sensors, computational image processing and micro-fabricated structural components. First, the sub-pixel resolving optofluidic microscope (SROFM), will be presented, which combines microfluidics and pixel super-resolution image reconstruction to perform high-throughput imaging of fluidic samples, such as blood cells. We discuss design parameters and construction of the device, as well as the resulting images and the resolution of the device, which was 0.66 µm at the highest acuity. The potential applications of SROFM for clinical diagnosis of malaria in the resource-limited settings is discussed.

Next, the implementations of ePetri, a self-imaging Petri dish platform with microscopy resolution, are presented. Here, we simply place the sample of interest on the surface of the image sensor and capture the direct shadow images under the illumination. By taking advantage of the inherent motion of the microorganisms, we achieve high resolution (~1 µm) imaging and long term culture of motile microorganisms over ultra large field-of-view (5.7 mm × 4.4 mm) in a specialized ePetri platform. We apply the pixel super-resolution reconstruction to a set of low-resolution shadow images of the microorganisms as they move across the sensing area of an image sensor chip and render an improved resolution image. We perform longitudinal study of Euglena gracilis cultured in an ePetri platform and image based analysis on the motion and morphology of the cells. The ePetri device for imaging non-motile cells are also demonstrated, by using the sweeping illumination of a light emitting diode (LED) matrix for pixel super-resolution reconstruction of sub-pixel shifted shadow images. Using this prototype device, we demonstrate the detection of waterborne parasites for the effective diagnosis of enteric parasite infection in resource-limited settings.

Then, we demonstrate the adaptation of a smartphone’s camera to function as a compact lensless microscope, which uses ambient illumination as its light source and does not require the incorporation of a dedicated light source. The method is also based on the image reconstruction with sweeping illumination technique, where the sequence of images are captured while the user is manually tilting the device around any ambient light source, such as the sun or a lamp. Image acquisition and reconstruction is performed on the device using a custom-built android application, constructing a stand-alone imaging device for field applications. We discuss the construction of the device using a commercial smartphone and demonstrate the imaging capabilities of our system.

Finally, we report on the implementation of fluorescence chip-scale microscope, based on a silo-filter structure fabricated on the pixel array of a CMOS image sensor. The extruded pixel design with metal walls between neighboring pixels successfully guides fluorescence emission through the thick absorptive filter to the photodiode layer of a pixel. Our silo-filter CMOS image sensor prototype achieves 13-µm resolution for fluorescence imaging over a wide field-of-view (4.8 mm × 4.4 mm). Here, we demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.

New applications that come from extending seismic networks into buildings

This thesis describes engineering applications that come from extending seismic networks into building structures. The proposed applications will benefit the data from the newly developed crowd-sourced seismic networks which are composed of low-cost accelerometers. An overview of the Community Seismic Network and the earthquake detection method are addressed. In the structural array components of crowd-sourced seismic networks, there may be instances in which a single seismometer is the only data source that is available from a building. A simple prismatic Timoshenko beam model with soil-structure interaction (SSI) is developed to approximate mode shapes of buildings using natural frequency ratios. A closed form solution with complete vibration modes is derived. In addition, a new method to rapidly estimate total displacement response of a building based on limited observational data, in some cases from a single seismometer, is presented. The total response of a building is modeled by the combination of the initial vibrating motion due to an upward traveling wave, and the subsequent motion as the low-frequency resonant mode response. Furthermore, the expected shaking intensities in tall buildings will be significantly different from that on the ground during earthquakes. Examples are included to estimate the characteristics of shaking that can be expected in mid-rise to high-rise buildings. Development of engineering applications (e.g., human comfort prediction and automated elevator control) for earthquake early warning system using probabilistic framework and statistical learning technique is addressed.

Design and analysis of nucleic acid reaction pathways

Nucleic acids are a useful substrate for engineering at the molecular level. Designing the detailed energetics and kinetics of interactions between nucleic acid strands remains a challenge. Building on previous algorithms to characterize the ensemble of dilute solutions of nucleic acids, we present a design algorithm that allows optimization of structural features and binding energetics of a test tube of interacting nucleic acid strands. We extend this formulation to handle multiple thermodynamic states and combinatorial constraints to allow optimization of pathways of interacting nucleic acids. In both design strategies, low-cost estimates to thermodynamic properties are calculated using hierarchical ensemble decomposition and test tube ensemble focusing. These algorithms are tested on randomized test sets and on example pathways drawn from the molecular programming literature. To analyze the kinetic properties of designed sequences, we describe algorithms to identify dominant species and kinetic rates using coarse-graining at the scale of a small box containing several strands or a large box containing a dilute solution of strands.

Selective data gathering in community sensor networks

Smartphones and other powerful sensor-equipped consumer devices make it possible to sense the physical world at an unprecedented scale. Nearly 2 million Android and iOS devices are activated every day, each carrying numerous sensors and a high-speed internet connection. Whereas traditional sensor networks have typically deployed a fixed number of devices to sense a particular phenomena, community networks can grow as additional participants choose to install apps and join the network. In principle, this allows networks of thousands or millions of sensors to be created quickly and at low cost. However, making reliable inferences about the world using so many community sensors involves several challenges, including scalability, data quality, mobility, and user privacy.

This thesis focuses on how learning at both the sensor- and network-level can provide scalable techniques for data collection and event detection. First, this thesis considers the abstract problem of distributed algorithms for data collection, and proposes a distributed, online approach to selecting which set of sensors should be queried. In addition to providing theoretical guarantees for submodular objective functions, the approach is also compatible with local rules or heuristics for detecting and transmitting potentially valuable observations. Next, the thesis presents a decentralized algorithm for spatial event detection, and describes its use detecting strong earthquakes within the Caltech Community Seismic Network. Despite the fact that strong earthquakes are rare and complex events, and that community sensors can be very noisy, our decentralized anomaly detection approach obtains theoretical guarantees for event detection performance while simultaneously limiting the rate of false alarms.

Mechanistic studies of reactions at the single-molecule level using microfluidics with applications in molecular diagnostics

Motivated by needs in molecular diagnostics and advances in microfabrication, researchers started to seek help from microfluidic technology, as it provides approaches to achieve high throughput, high sensitivity, and high resolution. One strategy applied in microfluidics to fulfill such requirements is to convert continuous analog signal into digitalized signal. One most commonly used example for this conversion is digital PCR, where by counting the number of reacted compartments (triggered by the presence of the target entity) out of the total number of compartments, one could use Poisson statistics to calculate the amount of input target.

However, there are still problems to be solved and assumptions to be validated before the technology is widely employed. In this dissertation, the digital quantification strategy has been examined from two angles: efficiency and robustness. The former is a critical factor for ensuring the accuracy of absolute quantification methods, and the latter is the premise for such technology to be practically implemented in diagnosis beyond the laboratory. The two angles are further framed into a “fate” and “rate” determination scheme, where the influence of different parameters is attributed to fate determination step or rate determination step. In this discussion, microfluidic platforms have been used to understand reaction mechanism at single molecule level. Although the discussion raises more challenges for digital assay development, it brings the problem to the attention of the scientific community for the first time.

This dissertation also contributes towards developing POC test in limited resource settings. On one hand, it adds ease of access to the tests by incorporating massively producible, low cost plastic material and by integrating new features that allow instant result acquisition and result feedback. On the other hand, it explores new isothermal chemistry and new strategies to address important global health concerns such as cyctatin C quantification, HIV/HCV detection and treatment monitoring as well as HCV genotyping.

Biossorção de tório e urânio pela macroalga marinha sargassum filipendula

Por ser um material de baixo custo e apresentar propriedades ligantes, a macroalga marinha Sargassum filipendula vem sendo utilizada como material biossorvente no processo de biossorção de metais. No presente trabalho a alga marrom foi utilizada no estudo cinético e de equilíbrio dos íons de tório e urânio individuais e os resultados comparados à biossorção desses metais em sistema binário. Os testes foram realizados nas concentrações 1 e 10 mg/L e pH= 1,0 e 4,0 na temperatura de 25 1C. A melhor condição para biossorção de tório foi encontrada para 1 mg/L e pH= 1,0, enquanto que para urânio foi em 1 mg/L e pH= 4,0. O estudo cinético de biossorção de tório mostrou que o modelo de segunda ordem descreve melhor os dados experimentais em 1 mg/L (R2= 0,9987) e 10 mg/L (R2= 0,9919) em pH= 1,0 e 1 mg/L (R2= 0,9976) em pH= 4,0, enquanto em 10 mg/L (R2= 0,9787) pH= 4,0 a curva encontrada representou uma cinética de primeira ordem. Para a cinética de urânio os dois modelos se adequaram bem aos dados em ambas as condições experimentais. O estudo de equilíbrio mostrou um perfil crescente de captação de tório, com uma remoção de 96% e 54% do metal em pH= 1,0 e 4,0, respectivamente, a partir da Co= 1 mg/L. A melhor eficiência de captação dos íons de urânio foi de 33% para Co= 100 mg/L em pH= 1,0 e 71% para Co= 1 mg/L em pH= 4,0. Os dados experimentais da isoterma de tório mostraram-se mais adequados ao modelo de Freundlich para pH= 1,0, enquanto que para o pH= 4,0 esses foram melhor representados pelo modelo de Langmuir, com valores de coeficiente de determinação superiores. Em relação à isoterma do urânio, o modelo de Freundlich representou bem os dados experimentais. Os parâmetros de equilíbrio calculados a partir do modelo de Langmuir (kL, qmax ) e Freundlich (kF, n) indicaram uma maior afinidade da biomassa pelos íons de tório em ambas as condições experimentais. O estudo de equilíbrio do sistema binário mostrou que a biossorção dos íons de tório não é afetada pela presença do urânio em solução. Por outro lado, a sorção do urânio foi fortemente afetada pela coexistência com os íons de tório.

Polilaktida oinarri duten inplante polimeriko biodegradagarrien diseinu, fabrikazio eta propietateak

[EU]3D inprimaketa gaur egun, biomedikuntzaren garapenerako aukera ezberdinak ematen dituen teknologia iraultzaile gisa aurkezten da; bai medikuntza arloan formazio eta ikerkuntzarako erreminta gisa, baita dispositibo berrien diseinu eta fabrikaziorako. Bere abantailarik aipagarriena prototipaketa azkarra da. Gainera, teknologia honek barne egitura eta forma ezberdineko objektuak fabrikatzea ahalbidetzen du koste lehiakor batean. Lan honen helburua 3D inprimagailuen bidezko prototipoen fabrikazioan zentratzen da, horretarako lehengai bezala polimero biodegradagarri eta biobateragarria erabiliz. Horrez gain, metodo tradizionalarekin konparatuz teknologia honek izan ditzakeen abantailak ere aztertu nahi dira, ez bakarrik alde ekonomikoari edo denborari begira, baita fabrikatutako objektuen propietateei begira ere. Dena dela, horrekin hasi aurretik ezaugarritze fisiko eta termikoa burutu beharko zaie lehengaiei, 3D inprimagailuaren parametroen aukeraketa egokia egiteko eta parametro horien eta amaierako produktuaren kalitate, egitura eta propietateen artean erlazio egokia ezartzeko. Lan hau aurrera eramateko poli(L-laktida)-rekin (PLLA) egingo da lan, bai ehun ingeniaritzan baita hezurren apurketen finkapenerako dispositiboetan oso erabilia izan den polimeroa.

Reloj basado en señales GPS con corrección digital para PTP-Master

[ES]este proyecto trata sobre el desarrollo de un core en una FPGA para conseguir, gracias a un módulo GPS, una referencia temporal precisa, necesaria para un equipo PTP master (IEEE-1588), a bajo coste y con calidad Grand Master.

Reloj basado en señales GPS con corrección por tensión para PTP-Master

[ES]El proyecto presentado a continuación muestra la elaboración de un core para ser embebido dentro de las denominadas FPGAs (Field Programmable Gate Array), cuya finalidad es la creación de una referencia temporal, en arquitectura de 64bits, gracias a un módulo GPS (Global Positioning System), lo más cercana posible al orden de las decenas de nano-segundos, para poder ser insertado en un equipo PTP-Master (Precision Time Protocol - Master) (IEEE (Institute of Electrical and Electronics Engineers) - 1588), a bajo coste y con calidad comparable a la de los dispositivos Grand Master.

Avaliação da sorção de Cu (II) e Hg (II) pela Sargassum sp modificado com epicloridrina

É crescente o aumento da preocupação do homem com a contaminação de ambientes aquáticos uma vez que da subsistência dos mesmos depende o bem estar de todos. Ao mesmo tempo em que cresce a preocupação tem aumentado a quantidade de pesquisas em busca de tecnologias alternativas ao tratamento e remediação de efluentes aquosos contaminados pelas mais diversas substâncias incluindo os metais pesados. Nas últimas décadas, tem crescido o número de trabalhos avaliando a capacidade de sorção e a viabilidade da utilização de biossorventes de baixo custo na captação de íons metálicos e um desses materiais são as biomassas de algas pardas. Dentre os vários gêneros existentes no planeta o território brasileiro é rico na macroalga do gênero Sargassum. Muito embora a composição dessas biomassas varie o principal constituinte das mesmas é o ácido algínico e seus sais alcalinos na forma de um copolímero linear, homopolimérico, com unidades do ácido manurônico, (M), (1-4)-β-D- ligado e seu epímero em C-5 nos resíduos α-L-gulurônicos, (G), respectivamente, covalentemente ligados entre si em sequencias diferenciadas ou em blocos. Os monômeros podem aparecer em blocos homopoliméricos consecutivos, resíduos G (unidades G), resíduos consecutivos M (unidades M), pequenas unidades alternadas M e G (blocos MG), ou em blocos aleatoriamente organizados. A proposta dessa dissertação é realizar a modificação do copolímero existente na biomassa com epicloridrina, avaliar e comparar a captação de íons Cu (II) e Hg (II) pela biomassa da alga Sargassum sp., com a biomassa não modificada e resultados publicados na literatura

高分辨率光纤光栅温度传感器的研究

报道了一种具有高分辨率和高效且价廉的解调系统的光纤布拉格光栅(FBG)温度传感器。提出了光纤光栅的金属槽封装技术，以提高传感光栅的温度灵敏性。研究了金属槽封装光栅的温度灵敏性，理论分析和实验结果表明，封装光栅的温度灵敏系数比普通裸光栅提高了3．6倍。系统利用一长周期光栅(LPG)作为线性滤波器，宽带光源经此长周期光栅调制后入射到传感光栅，可解调布拉格传感光栅的波长位移。理论分析与实验结果一致，系统可达到的温度分辨率为0．02℃。

光纤光栅高温传感器的研究

提出了一种能够测量高温的光纤布拉格光栅（FBG）传感器结构。利用线膨胀系数和长度均不同的两种金属细杆和光纤布拉格光栅设计而成的传感头，能够将被测温度转化为光栅的应变，解调由应变引起的光栅波长漂移，即可得知待测的温度。目前在实验室实现了500℃的动态范围和1℃的温度分辨率，实验结果与理论分析一致。

Zn-VI/Cu2O Heterojunctions for Earth-Abundant Photovoltaics

The need for sustainable energy production motivates the study of photovoltaic materials, which convert energy from sunlight directly into electricity. This work has focused on the development of Cu₂O as an earth-abundant solar absorber due to the abundance of its constituent elements in the earth's crust, its suitable band gap, and its potential for low cost processing. Crystalline wafers of Cu₂O with minority carrier diffusion lengths on the order of microns can be manufactured in a uniquely simple fashion — directly from copper foils by thermal oxidation. Furthermore, Cu₂O has an optical band gap of 1.9 eV, which gives it a detailed balance energy conversion efficiency of 24.7% and the possibility for an independently connected Si/Cu₂O dual junction with a detailed balance efficiency of 44.3%.

However, the highest energy conversion efficiency achieved in a photovoltaic device with a Cu₂O absorber layer is currently only 5.38% despite the favorable optical and electronic properties listed above. There are several challenges to making a Cu₂O photovoltaic device, including an inability to dope the material, its relatively low chemical stability compared to other oxides, and a lack of suitable heterojunction partners due to an unusually small electron affinity. We have addressed the low chemical stability, namely the fact that Cu₂O is an especially reactive oxide due to its low enthalpy of formation (ΔH_f⁰ = -168.7 kJ/mol), by developing a novel surface preparation technique. We have addressed the lack of suitable heterojunction partners by investigating the heterojunction band alignment of several Zn-VI materials with Cu₂O. Finally, We have addressed the typically high series resistance of Cu₂O wafers by developing methods to make very thin, bulk Cu₂O, including devices on Cu₂O wafers as thin as 20 microns. Using these methods we have been able to achieve photovoltages over 1 V, and have demonstrated the potential of a new heterojunction material, Zn(O,S).

二次光栅在波前测量中的应用

采用一种特殊的二次光栅用于激光波前测量, 它对非零级衍射光束具有不同的聚焦效应, 其光栅线为圆弧型而非直线。导出了在会聚光束情况下的两平面成像在单一像平面上的距离关系, 实验上实现了二次光栅用于会聚光束的波前测量, 测量得到会聚光束具有较大的散焦(-2.93λ)和球差(1.34λ), 与该透镜引起波前的离焦像差理论理想值(-2.695λ)基本符合。该技术可以实现波前的高空间分辨力和高精度实时测量, 大大减少光学元件数量, 降低装置成本。由于大功率激光束的不稳定性, 其波前变化非常快, 所以该方法的实时性非

高精度微结构聚合物光栅的复制技术

光栅复制是降低光栅制造成本,提高产量的一条有效途径。研究了利用紫外压印技术复制微结构光栅的方法。使用玻璃基底矩形浮雕结构的微结构光栅作为母光栅,给出了利用聚二甲基硅氧烷(PDMS)制作光栅模具和在光敏聚合物材料上复制微结构光栅的详细过程。经过优化工艺条件,成功地复制了一系列不同周期和开口比的微结构光栅,测试了复制光栅和母光栅的衍射图像和0级与±1级的衍射强度,结果表明,复制光栅和母光栅的衍射图像与光强分布基本一致。